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10.1101/2024.11.06.622333 | Interplay between autophagy, the unfolded protein response and the cytoplasmic heat stress response during heat stress in maize | Tang, J.; Li, Z.; Bassham, D. C. | Diane C Bassham | Iowa State University | 2024-11-08 | 1 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622333.source.xml | High temperatures can substantially reduce plant survival and reproduction, and therefore decrease crop productivity. Plants activate several pathways in response to high temperatures, including the endoplasmic reticulum (ER) unfolded protein response (UPR), the cytoplasmic heat stress response, and autophagy, which together aid in stress tolerance by refolding or degrading misfolded and unfolded proteins. The relationship between the UPR and autophagy is known, as ER stress activates the UPR, and a key activator of the UPR, Inositol-requiring enzyme type 1 (IRE1B), upregulates autophagy. To assess the relationship between the distinct responses to heat stress in maize, we analyzed the effect of disruption of the UPR, via a bzip60 mutant, on autophagy. We found that genes related to autophagy are upregulated in the bzip60 mutant, and that autophagy is activated in this mutant even in the absence of stress. We in turn analyzed the effect of loss of autophagy on the UPR. The bZIP60 mRNA spliced form, a marker for the UPR, was increased in mutants in ATG10, a core component of the autophagy machinery, during ER stress. By contrast, bZIP60 splicing was unaffected in atg10 mutants in response to heat, whereas cytoplasmic heat stress components were increased. Loss of autophagy therefore differentially affects other heat stress response pathways, depending on the specific stress conditions leading to the activation of the pathways. | null | biorxiv |
10.1101/2024.11.05.622021 | Natural Bacteriocins as Potential Drug Candidates Targeting Core Proteins in Mastitis Pathogens of Dairy Cattle | Hasnat, S.; Rahman, M. M.; Yeasmin, F.; Jubair, M.; Helmy, Y. A.; Islam, T.; Hoque, M. N. | M. Nazmul Hoque | Bangabandhu Sheikh Mujibur Rahman Agricultural University | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622021.source.xml | Mastitis poses a major challenge in the dairy industry, with rising antibiotic-resistant strains underscoring the urgent need for alternative antimicrobial strategies. This study aimed to (i) identify essential core proteins in clinical mastitis (CM)-causing pathogens using genomic approach, and (ii) assess the efficacy of natural antimicrobial peptides as novel therapeutic agents targeting the selected core proteins for the rational management of mastitis in dairy cows. Through a core genomic analysis of 16 CM-causing pathogens, including strains of Staphylococcus aureus, S. warneri, Streptococcus agalactiae, S. uberis, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, P. putida, and P. asiatica, we identified 65 core proteins shared among these pathogens. Among them, ten proteins including PhoH, TrpB, FtsZ, HslV, HupB, RibH, InfA, MurA, GlxK, and Rho were found to be essential for the survival and virulence of these pathogens. Importantly, further novelty, resistance, and virulence assessments identified Rho and HupB as potential therapeutic targets. A comprehensive screening of 70 bacteriocin peptides (BPs) revealed 14 BPs that effectively interacted with both Rho and HupB proteins. Further analysis showed that BP8 and BP32 disrupt Rho protein function by blocking transcription termination process, while BP8, BP39, and BP40 prevent HupB from binding to DNA. These findings confirm the promising stability and efficacy of BP8 against both target proteins in CM-pathogens, highlighting it as a promising broad-spectrum therapeutic agent. Our computational study identified Rho and HupB as key proteins in CM-causing pathogens, which can be targeted by natural bacteriocins like BP8, suggesting its potential for developing effective and sustainable therapeutics against mastitis in dairy cattle. | null | biorxiv |
10.1101/2024.11.05.622022 | Single-Cell Analysis of Gene Regulatory Networks in the Mammary Glands of P4HA1-knockout mice | Gupta, A.; Huang, L.; Liu, J.; Xu, R.; Wu, W. | Wei Wu | Carnegie Mellon University | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622022.source.xml | Prolyl hydroxylation, catalyzed by collagen prolyl-4 hydroxylase (P4H), is a crucial post-translational modification involved in collagen biosynthesis. P4HA1, an isoform of P4H, plays a prominent role in stabilizing hypoxia-inducible factor-1alpha (HIF-1alpha). P4HA1 is frequently upregulated in highly aggressive triple-negative breast cancer and has been implicated in tumor progression, metastasis, and chemoresistance. In this study, we investigated the role of P4HA1 in mouse mammary glands by analyzing gene regulatory networks (GRNs) in basal epithelial cells across two mouse groups: control (5Ht) and P4HA1-knockout (6Ho) mice. Specifically, we employed a single-cell network inference approach, integrating single-cell RNA sequencing with the SCENIC pipeline, and incorporated multiple validation strategies to construct gene regulatory networks (GRNs) specific to basal epithelial cells from each mouse group. Despite the inherent challenges of single-cell data, our approach identified robust and reproducible GRN patterns across both mouse groups. Based on these patterns, we identified subclusters of basal epithelial cells with similar regulatory profiles across the two mouse groups and a unique subcluster in the control mice with a distinct regulatory pattern absent in the P4HA1-deficient 6Ho mice. This unique subcluster exhibited concurrent activation and potential crosstalks between stem cell development and inflammatory response pathways, underscoring the crucial role of P4HA1 in regulating these biological processes linked to cancer progression. We validated these findings through multiple approaches, including experimental validation. Given that the loss of P4HA1 disrupts the interplay between stem cells and inflammation, our results suggest that targeting P4HA1 may offer a promising therapeutic strategy for breast cancer treatment. | null | biorxiv |
10.1101/2024.11.05.622072 | Examining Changes in Gramicidin Current Induced by Endocannabinoids | Mayar, S.; Cyr-Athis, A.; D'Avanzo, N. | Nazzareno D\'Avanzo | Universite de Montreal | 2024-11-08 | 1 | new results | cc_by | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622072.source.xml | Endocannabinoids are a diverse family of lipid molecules, which circulate in the human body, impacting the cardiovascular and the nervous systems. Endocannabinoids can influence pain perception, appetite, stress responses, mood, memory and learning. Regulation of these lipids present a promising therapeutic avenue for numerous neurological disorders. In addition to acting as agonists to cannabinoid receptors (CBRs), endocannabinoids can also modulate the function of various ion channels and receptors independently of CBRs. This modulation of function can arise from direct binding to the channel proteins, or via changes to the lipid properties such as membrane elasticity/stiffness, curvature, or hydrophobic thickness. Here, we assess the effects of endocannabinoids on membrane properties by examining changes in gramicidin (gA) currents in Xenopus oocytes. Endocannabinoids from both classes (Fatty acid ethanolamides (FAEs) and 2-monoacylglycerols (2-MGs)) are studied and current-voltage relationships are assessed. Employing gramicidin channels as molecular force probes can enable both predictive and quantitative studies on the impact of bilayer-mediated regulation on membrane protein function by endocannabinoids. | null | biorxiv |
10.1101/2024.11.05.622073 | Neratinib, a clinical drug against breast cancer, protects against atherosclerosis via ASK1 inhibition | Zhang, F.; Yin, Y.; Wang, Z.; Wu, X.; Kamato, D.; Weng, J.; Xu, S. | Suowen Xu | Anhui Provincial Key Laboratory of Metabolic Health and Panvascular Diseases | 2024-11-08 | 1 | new results | cc_no | pharmacology and toxicology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622073.source.xml | Atherosclerosis commences with endothelial dysfunction and the retention of cholesterol within the vessel wall, followed by a chronic inflammatory response. Cholesterol-lowering strategies (such as statins and PCSK9 inhibitors) are primarily used for treating patients with atherosclerotic cardiovascular diseases, but leaving the therapeutic dilemma of residual inflammatory risk. To address this challenge, we employed Connectivity Map (CMap) screening for inflammation mechanism-based anti-atherosclerotic compounds using perturbational datasets obtained from TNFalpha and IL-1beta-stimulated human endothelial cells. This screening process allow us to identify Neratinib, a clinical drug against breast cancer, as the hit compound with potential anti-inflammatory actions in endothelial cells. Further studies reveal that Neratinib inhibited endothelial cell inflammation elicited by three different pro-inflammatory stimuli (TNFalpha, IL-1beta and LPS). Intriguingly, the anti-inflammatory effect of Neratinib was independent of its classical target HER2/ERBB2 inhibition. Mechanistically, Neratinib directly binds ASK1 and suppresses ASK1 activation. In both male and female Ldlr-/- mice, treatment with Neratinib decreased the plaque area, reduced the necrotic core size and mitigated macrophage infiltration to stabilize plaques. Lastly, we observed that Neratinib, in conjunction with the use of Rosuvastatin (a standard lipid-lowering drug), led to a reduction in serum lipids, and produced synergistic anti-atherosclerotic effects. Olink proteomics study suggested that combination treatment alleviated inflammation-related cytokines/chemokines in the serum from Ldlr-/- mice. Taken together, these findings support the concept that Neratinib could be tested for its potential as a "repurposed" drug for vascular inflammation and atherosclerosis, thereby streamlining efforts to translate preclinical discoveries to clinical testing in humans. | null | biorxiv |
10.1101/2024.11.07.622452 | From aerial drone to QTL: Leveraging next-generation phenotyping to reveal the genetics of color and height in field-grown Lactuca sativa | Dijkhuizen, R. F.; van Eijnatten, A. L.; Mehrem, S. L.; van den Bergh, E. S.; van Lieshout, J.; Spaninks, K.; Kaandorp, S.; Offringa, R.; Proveniers, M.; Van den Ackerveken, G.; Snoek, B. L. | Basten L. Snoek | Utrecht University | 2024-11-08 | 1 | new results | cc_by_nc | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622452.source.xml | In recent years, the automation of genotyping has significantly enhanced the efficiency of genome-wide association studies. Due to this development, phenotyping is now usually the rate-limiting step, especially in the field. Efforts are now focused on further automating in-field phenotyping. Here we present a GWAS study on 194 field-grown accessions of lettuce (Lactuca sativa). These accessions were non-destructively phenotyped at two time points 15 days apart using an unmanned aerial vehicle. Our high throughput phenotyping approach integrates an RGB camera, a multispectral camera to measure the reflectance at 5 wavelengths (blue, green, red, red edge, near-infrared), and precise height estimation. We used the mean and other descriptives such as median, quantiles, minimum and maximum to quantify different aspects of color and height variation in lettuce from the drone images. Using this approach, we confirm several previously described QTLs, now in populations grown under field conditions and identify several new QTLs for plant-height and color. | null | biorxiv |
10.1101/2024.11.07.622415 | The paternally derived genome opposes seed dormancy induction by the mother plant in Arabidopsis | Barros-Galvao, T.; Chen, X.; Penfield, S. | Steven Penfield | John Innes Centre | 2024-11-08 | 1 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622415.source.xml | Seed dormancy in Arabidopsis is known to be mediated by the interaction of maternal and zygotic genomes during seed maturation. While studies have revealed the extensive influence of maternal processes on dormancy and germination, less is known about the influence of the father. Here we exploit differences in ploidy to explore the role of the paternal genome on progeny seed dormancy. We show that paternal genome acts to reduce seed dormancy regardless of maternal genome dose, resulting in lower dormancy in tetraploid Arabidopsis versus genetically identical diploids. We show that this paternal effect requires synthesis of RNA Polymerase IV-dependent RNAs in the male gametophyte which oppose the dormancy-inducing effects of maternal siRNAs on seed coat and endosperm development. We conclude that the paternal genome has evolved to subvert the dormancy-inducing role of the mother plant in progeny seeds. | null | biorxiv |
10.1101/2024.11.06.622292 | Efficient and Versatile Rapeseed Transformation for New Breeding Technologies | Ille, K.; Melzer, S. | Siegbert Melzer | Kiel University | 2024-11-08 | 1 | new results | cc_no | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622292.source.xml | Many gene functions are widely studied and understood in Arabidopsis; however, the lack of efficient transformation systems often limits the application and verification of this knowledge in crop plants. Brassica napus L., a member of the Brassicaceae family, is usually transformed by Agrobacterium-mediated hypocotyl transformation, but not all growth types are equally amenable to transformation. In particular, winter-type rapeseed, which requires vernalization to initiate flowering, is recalcitrant to in vitro regeneration and transformation. The analysis of gene functions in rapeseed is further complicated by the allotetraploid nature of its genome and the genome triplication within the Brassica genus, which has led to the presence of a large number of gene homologs for each Arabidopsis ortholog. We have established a transformation method that facilitates the regeneration of winter-type rapeseed by using the WUSCHEL gene from Beta vulgaris. This allowed us to efficiently transform winter-type and spring-type rapeseed in small-scale experiments. As proof of principle, we targeted Bna.CLV3 and Bna.SPL9/15 with CRISPR/Cas9 and showed that entire gene families are effectively edited using this transformation protocol. This allowed us to simultaneously study many redundantly acting homologous genes in rapeseed. We observed mutant phenotypes for Bna.CLV3 and Bna.SPL9/15 in primary transformants, indicating that biallelic knockouts were obtained for up to eight genes. This allowed an initial phenotypic characterization to be performed already a few months after starting the experiment. | null | biorxiv |
10.1101/2024.11.07.622539 | From Quantitative Trait Loci towards Mechanisms: Linkage Integration Hypothesis Testing (LIgHT) Sheds Light on the Mechanisms of Genetically Modulated Stress Tolerance | Hoh, D.; Osei-Bonsu, I.; Kanazawa, A.; Fisher, N.; Cruz, J.; Roberts, P. A.; Huynh, B.-L.; Kramer, D. M. | Donghee Hoh | Michigan State University | 2024-11-08 | 1 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622539.source.xml | The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTL) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea (Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of photosystems I (PSI) and II (PSII), photoprotective nonphotochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLM). The patterns of QTL linkages indicated chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLM. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation is modulated by thylakoid fatty acid composition, as suggested in Hoh et al., 2022. We propose the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations. | null | biorxiv |
10.1101/2024.11.08.622588 | OsMORF protein selectively promotes the dual-localized RNA editing factor OsPGL1 binding to its target RNA | Xiao, H.; Wang, Q.; Lin, Y.; Zhong, Y.; Ma, C.; Lin, H. | Haijun Xiao | Sichuan University | 2024-11-08 | 1 | new results | cc_no | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622588.source.xml | Post-transcriptional RNA editing plays a key regulatory role and serves as a genetic information proofreading mechanism. In flowering plants, RNA editing typically involves the removal of amino groups from cytidine to produce uridine in both plastids and mitochondria. In our previous work, we identified OsPGL1 as a rare organelle editing factor that regulates both mitochondrial and chloroplast RNA in rice. This protein mediates RNA editing and is associated with several OsMORFs. We speculated that they may form editing complex to regulate editing events, but we are still unclear about the detailed mechanism between OsMORF proteins and OsPGL1, as well as their roles in target RNA recognition and binding. In this study, we found that three OsMORFs can significantly promote the binding of OsPGL1 to target RNA in vitro. Notably, OsMORF8 can promote OsPGL1 to form a homologous dimer, thereby enhancing RNA binding to a greater extent. The E and DYW motifs do not affect the role of MORF proteins in RNA editing events, ruling out the potential influence of these two special motifs. In addition, we predicted a series of supercomplex structures of OsPGL1, the OsPGL1-RNA ligand complex, the OsPGL1-OsMORF2-OsMORF8-OsMORF9 complex, and the OsPGL1-OsMORF2-OsMORF8-OsMORF9-RNA complex. We determined that the conformational changes and newly added positively charged surface caused by OsMORF on OsPGL1 are the main reasons for MORF to promote the binding of OsPGL1 to RNA. Based on some new discoveries, we have expanded the RNA editing complex model, which greatly enhances our understanding of plant RNA editing complexes. | null | biorxiv |
10.1101/2024.11.08.622588 | OsMORF protein selectively promotes the dual-localized RNA editing factor OsPGL1 binding to its target RNA | Xiao, H.; Wang, Q.; Lin, Y.; Zhong, Y.; Ma, C.; Lin, H. | Haijun Xiao | Sichuan University | 2024-11-09 | 2 | new results | cc_no | plant biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622588.source.xml | Post-transcriptional RNA editing plays a key regulatory role and serves as a genetic information proofreading mechanism. In flowering plants, RNA editing typically involves the removal of amino groups from cytidine to produce uridine in both plastids and mitochondria. In our previous work, we identified OsPGL1 as a rare organelle editing factor that regulates both mitochondrial and chloroplast RNA in rice. This protein mediates RNA editing and is associated with several OsMORFs. We speculated that they may form editing complex to regulate editing events, but we are still unclear about the detailed mechanism between OsMORF proteins and OsPGL1, as well as their roles in target RNA recognition and binding. In this study, we found that three OsMORFs can significantly promote the binding of OsPGL1 to target RNA in vitro. Notably, OsMORF8 can promote OsPGL1 to form a homologous dimer, thereby enhancing RNA binding to a greater extent. The E and DYW motifs do not affect the role of MORF proteins in RNA editing events, ruling out the potential influence of these two special motifs. In addition, we predicted a series of supercomplex structures of OsPGL1, the OsPGL1-RNA ligand complex, the OsPGL1-OsMORF2-OsMORF8-OsMORF9 complex, and the OsPGL1-OsMORF2-OsMORF8-OsMORF9-RNA complex. We determined that the conformational changes and newly added positively charged surface caused by OsMORF on OsPGL1 are the main reasons for MORF to promote the binding of OsPGL1 to RNA. Based on some new discoveries, we have expanded the RNA editing complex model, which greatly enhances our understanding of plant RNA editing complexes. | null | biorxiv |
10.1101/2024.11.07.622526 | Jasmonate Primes Plant Responses to Extracellular ATP through Purinoceptor P2K1 | Jewell, J. B.; Carlton, A.; Bartley, L. E.; Tanaka, K. | Kiwamu Tanaka | Department of Plant Pathology, Washington State University | 2024-11-08 | 1 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622526.source.xml | Extracellular ATP (eATP) signaling in Arabidopsis thaliana is mediated by the purinoceptor P2K1. Previous studies have clarified that the downstream transcriptional responses to eATP involve jasmonate (JA)-based signaling components such as the JA receptor (COI1) and JA-responsive bHLH transcription factors (MYCs). However, the specific contributions of JA signaling itself on eATP signaling are unexplored. Here, we report that JA primes plant responses to eATP through P2K1. Our findings show that JA treatment significantly upregulates P2K1 transcription, corroborating our observation that JA facilitates eATP-induced cytosolic calcium elevation and transcriptional reprogramming in a JA signaling-dependent manner. Additionally, we find that salicylic acid represses eATP-induced plant response. These results suggest that JA accumulation during biotic or abiotic stresses may potentiate eATP signaling, enabling plants to better cope with subsequent stress events. | null | biorxiv |
10.1101/2024.11.08.622591 | Dual NBT Approach: Gene Editing and Intragenesis to promote Fire Blight Resistance in Apple using MdAGG defense lectins. | Bodelot, A.; Dousset, N.; Ravon, E.; Heintz, C.; Brisset, M.-N.; Degrave, A.; VERGNE, E. | Emilie VERGNE | Univ. Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, 49000, Angers, France | 2024-11-08 | 1 | new results | cc_by_nc | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622591.source.xml | Fire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of effective sources of resistance to E. amylovora have been identified. To diversify these sources, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as M. domestica agglutinins (MdAGG). When loss-of-function editions were introduced into MdAGG genes, the plant's ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora. | null | biorxiv |
10.1101/2024.11.07.622501 | An algal nutrient-replete, optimized medium for fast growth and high triacylglycerol accumulation | Jeffers, T. L.; McCombs, R.; Schmollinger, S.; Merchant, S. S.; Niyogi, K. K.; Roth, M. S. | Melissa S Roth | University of California, Berkeley | 2024-11-08 | 1 | new results | cc_by | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622501.source.xml | Microalgae are promising sources to sustainably meet the global needs for energy and products. Algae grow under different trophic conditions, where nutritional status regulates biosynthetic pathways, energy production, and growth. The green alga <em>Chromochloris zofingiensis</em> has strong economic potential because it co-produces biofuel precursors and the high-value antioxidant astaxanthin while accumulating biomass when grown mixotrophically. As an emerging reference alga for photosynthesis, metabolism, and bioproduction, <em>C. zofingiensis</em> needs a defined, optimized medium to standardize experiments during fast growth. Because the interplay of glucose consumption (+Glc) and mineral deficiency influences photosynthesis, growth, and the production of lipids and astaxanthin, we designed a replete nutrient medium tailored to the <em>C. zofingiensis</em> cellular ionome. We combined inductively coupled plasma mass spectrometry (ICP-MS) and +Glc growth curves to determine a medium that is nutrient replete for at least 5 days of +Glc logarithmic growth. We found that there are high nutritional needs for phosphorus and sulfur during mixotrophy. Iron was the only element measured for which the cellular concentration correlated with exogenous concentration and was iteratively adjusted until the internal <em>ionome</em> was consistent through the logarithmic growth phase. This <em>Chromochloris</em>-Optimized Ratio of Elements (CORE) medium supports fast growth and high biomass without causing excess nutrient toxicity. This defined, nutrient-replete standard is important for future <em>C. zofingiensis</em> investigations and can be adapted for other species to support high biomass. The method used to develop CORE medium shows how ionomics informs replicable media design and may be applied in industrial settings to inform cost-effective biofuel production. | null | biorxiv |
10.1101/2024.11.08.622454 | Time and temperature-resolved transcriptomic analysis of Arabidopsis splicing-related mutants | Nardeli, S. M.; El Arbi, N.; Dikaya, V.; Rojas-Murcia, N.; Goretti, D.; Schmid, M. | Markus Schmid | Department of Plant Biology, Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden | 2024-11-08 | 1 | new results | cc_by_nc_nd | plant biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622454.source.xml | Temperature plays a crucial role in plant growth and development, influencing numerous physiological processes throughout the plant life cycle. Ambient temperature fluctuations can significantly affect transcriptomic adjustments, which are essential for plants to adapt to ever-changing environmental conditions. Despite the known impacts of extreme temperatures on plant physiology, there remains a knowledge gap regarding the specific effects of moderate changes in ambient temperatures on transcriptomic responses. This study employs strand-specific mRNA sequencing (RNA-seq) to assess how different splicing-related mutants respond to varying ambient temperatures, providing a valuable resource to the research community. Analysis of our time-resolved temperature-regulated alternative RNA splicing data reveals that common and exclusive use of the splicing machinery plays pivotal roles in thermoresponsive growth. Furthermore, our analyses demonstrate that moderate temperature changes are translated into widespread transcriptomic responses, including adjustments of the circadian clock and significant splicing changes in light and temperature genes. These results highlight the importance of these particular signaling pathways in adapting to new temperature regimes and suggest future experiments to study the role of alternative RNA splicing in temperature adaptation. Taken together, our results provide insights regarding the role of RNA splicing in plant responses to ambient temperature changes, highlighting the biological relevance of transcriptomic adjustments in enhancing plant resilience and adaptation to climate variability. | null | biorxiv |
10.1101/2024.11.05.622080 | CCR2-driven monocyte recruitment is protective against radiotherapy-induced intestinal toxicity | Pun, N.; Cytlak, U. M.; Lee, D.; Domingues, R. G.; Cheadle, E. J.; Forster, D.; Williams, K. J.; Graham, G.; Hepworth, M. R.; Travis, M. A.; Illidge, T. M.; Dyer, D. P. | Douglas Philip Dyer | University of Manchester | 2024-11-08 | 1 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622080.source.xml | Radiotherapy (RT) is essential in treating abdominal and pelvic cancers but often damages the healthy tissues, particularly the intestines, leading to radiation-induced toxicities with limited treatment options. While the immune system is known to regulate tissue damage, immune mechanisms involved in RT-induced intestinal toxicity are not fully understood. CT-guided localised intestinal irradiation, single-cell RNA sequencing (scRNA-seq) and flow cytometry revealed RT-induced chemokine-dependent recruitment of immune cells. Deletion of C-C chemokine receptor (Ccr)1, Ccr2, Ccr3 and Ccr5, blocked recruitment and worsened radiation induced toxicities. Furthermore, CCR2-deficient mice showed exacerbated weight loss and intestinal permeability, while the transfer of Ly6C+ monocytes alleviated symptoms. Mechanistically, IL-17 cytokine production by group 3 innate lymphoid cells (ILC3s), a critical factor in maintaining intestinal barrier integrity, was reduced in irradiated CCR2-/-, however the transfer of Ly6C+ monocytes resulted in increased IL-17 levels. These findings demonstrate the critical importance of CCR2-mediated monocyte recruitment in mitigating RT-induced toxicities. | null | biorxiv |
10.1101/2024.11.07.622487 | Arbuscular mycorrhizal fungal genotype and nuclear organization as driving factors in host plant nutrient acquisition and stable carbon capture | Ferguson, R.; Mugambi, K. M.; Villeneuve-Laroche, M.; Kallenbach, C. M.; Antunes, P.; Corradi, N. | Nicolas Corradi | University of Ottawa | 2024-11-08 | 1 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622487.source.xml | Arbuscular mycorrhizal fungi (AMF) are obligate root symbionts of most plants that improve plant growth by transferring nutrients into plant roots through networks of soil hyphae. These hyphal networks represent a carbon sink in soil, thus it has been suggested that these fungi can also boost atmospheric carbon sequestration, highlighting their potential role in managing greenhouse emissions. In this study, we aimed to determine whether certain AMF genotypes and nuclear organizations (homokaryons vs heterokaryons) are associated with higher rates of host plant yield and carbon storage. To assess this, we compared Sudan-grass (Sorghum x drummondii) AMF inoculation across 8 strains of Rhizophagus irregularis: 4 homokaryotic and 4 heterokaryotic strains. Sudan-grass was grown in a growth chamber, which included 13C-CO2 pulse labeling to track plant carbon into AMF. AMF inoculation increased total and root biomass, as well as phosphorous, magnesium and manganese uptake in the host. Heterokaryons led to greater root biomass, as well as less variable increases in shoot phosphorous. Host biomass had a significant positive effect on mycorrhizal carbon inputs to the soil. Mycorrhizal inputs to the mineral associated organic carbon - a more persistent carbon pool with slow turnover - were overall greater in heterokaryons than in homokaryons but varied significantly among strains. This indicates that the potential for carbon storage by mycorrhizal carbon inputs varies based on both fungal genomic identity and nuclear organization. Overall, inoculation improved the yield of Sudan-grass and resulted in significant inter-strain variation in persistent carbon contributions to the soil. This work highlights the importance of considering genotype and nuclear identity in assessments of AMF as bio-stimulants and drivers of carbon sequestration. | null | biorxiv |
10.1101/2024.11.05.622061 | Defensive symbionts provide high protection against natural enemies at low cost to hosts: a meta-analysis | Cesar, C. S.; Santos, E. S. A.; Cogni, R. | Rodrigo Cogni | University of Sao Paulo | 2024-11-08 | 1 | new results | cc_no | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622061.source.xml | Defensive symbionts (i.e., symbionts that protect hosts against natural enemies) are common in nature, infecting many arthropod species. Defensive symbioses likely arose from host-symbiont interactions that are costly for hosts and evolved over time to a facultative mutualism. Hence, the role symbionts play in protecting hosts against natural enemies might be one of the reasons for their successful spread in nature. Here, we conducted a meta-analysis to investigate the costs and benefits of hosting symbionts in arthropods. We gathered approximately 3,000 effect sizes from 226 studies. Our results show that in the presence of natural enemies (i.e., hosts infected with pathogens or parasites), symbionts provide protection, positively affecting the fitness of their hosts. In the absence of natural enemies, symbionts caused little reduction in host fitness. Overall, protection was six times higher than the cost to hosts, indicating that symbionts provide high protection at low cost to hosts. We also found that natural enemies attacking hosts infected with symbionts have a significant reduction in their fitness. Moreover, the level of protection and cost for both hosts and natural enemies varies between host families, fitness components, and between natural and introduced symbionts (i.e., if the symbiont is natural of that species or if it was transinfected into a new species). Our results reveal a broad generality of protection at little cost for hosts, which may explain the successful spread of symbionts in wild arthropod populations. | null | biorxiv |
10.1101/2024.11.05.621908 | The Condensin II Complex Regulates the Expression of Essential Gene Expression Programs During Erythropoiesis | Abid, D.; Murphy, K.; Murphy, Z.; Rahman, N.; Getman, M.; Steiner, L. | Laurie Steiner | University of Rochester Department of Pediatrics | 2024-11-08 | 1 | new results | cc_no | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.621908.source.xml | Erythropoiesis is characterized by dramatic changes in gene expression in the context of a cell that is rapidly proliferating while simultaneously condensing its nucleus in anticipation of enucleation. The mechanisms that maintain high level expression of erythroid genes and promote nuclear condensation remain poorly understood. Condensin II is a ring-like complex that promotes mitotic chromatin condensation and has roles in regulating interphase chromatin architecture and gene expression. We interrogated the role of Condensin II in erythropoiesis using an erythroid-specific deletion of the Condensin II subunit, Ncaph2. Ncaph2 loss resulted in severe embryonic anemia with lethality at embryonic day 13.5. Ncaph2 mutant erythroid cells had dysregulated maturation and disrupted cell cycle progression, but surprisingly Ncaph2 was dispensable for nuclear condensation. Genomic studies revealed that Ncaph2 occupied the promoter of key erythroid and cell cycle genes that were downregulated following Ncaph2 loss. Together, our results demonstrate an essential role for Ncaph2 in the gene expression programs that regulate cell cycle progression and erythroid differentiation, and identify a key role for the Condensin II complex in the regulation of a lineage-specific differentiation program. | null | biorxiv |
10.1101/2024.11.05.622020 | Multi-omic latent variable data integration reveals multicellular structure pathways associated with resistance to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion in Uganda | Cox, M. S.; Dill-McFarland, K. A.; Simmons, J. D.; Benchek, P.; Mayanja-Kizza, H.; Boom, W. H.; Stein, C. M.; Hawn, T. R. | Madison Shay Cox | University of Washington School of Medicine | 2024-11-08 | 1 | new results | cc_by | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622020.source.xml | Understanding the mechanisms of early clearance of Mycobacterium tuberculosis (Mtb) may illuminate new therapeutic strategies for tuberculosis (TB). We previously found genetic, epigenetic, and transcriptomic signatures associated with resistance (resister, RSTR) to tuberculin skin test (TST)/interferon gamma release assay (IGRA) conversion among highly exposed TB contacts. We hypothesized that integration of these datasets with multi-omic latent factor methods would detect pathways differentiating RSTR patients from those with latent infection (LTBI) which were not differentiated by individual dataset analyses. We pre-filtered and scaled features with the largest change between LTBI and RSTR groups for 126 patients with data in at least two of five data modalities: single nucleotide polymorphisms (SNP), monocyte RNAseq (baseline and Mtb-stimulated conditions), and monocyte epigenetics (methylation and ATAC-seq). Using multiomic latent factor analysis (MOFA), we generated ten latent factors on the subset of 33 patients with all five datasets available, four of which were different between LTBI and RSTR (FDR < 0.1). Factor 4, which was the most integrated of the significant factors, showed the greatest difference between RSTR and LTBI groups (FDR < 0.001). Three additional latent factor data integration methods also distinguished the RSTR and LTBI groups and identified overlapping features with MOFA. Using pathway analysis and a cluster-based enrichment method, we identified biologic functions associated with latent factors and found that MOFA Factors 2-4 include functions related to cell-cell adhesion, cell shape, and development of multicellular structures. In summary, latent variable integration methods uncovered signatures associated with resistance to TST/IGRA conversion that were not detected within individual dataset analyses and included pathways associated with cellular interactions and multicellular structures. | null | biorxiv |
10.1101/2024.11.05.622056 | Machine learning reveals novel targets for both glioblastoma and osteosarcoma | Li, N.; Ward, M.; Bashir, M.; Cao, Y.; Datta, A.; Li, Z.; Zhang, S. | Zhaoyu Li | University of Western Australia | 2024-11-08 | 1 | new results | cc_no | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622056.source.xml | Glioblastoma and osteosarcoma originate from the same lineage, yet patients with these two tumour types show significant differences in survival outcomes. Transcriptomic analysis comparing these tumours reveals that over 65% genes show similar expression patterns. Principal component analysis further demonstrates substantial similarities between these two tumour types, albeit with discernible differences. Deep learning analysis employing an autoencoder unveils nuanced distinctions and similarities of these two tumours at a high resolution. A classification model, leveraging gradient boosting with eXtreme Gradient Boosting (XGBoost), achieves high accuracy in distinguishing between these two tumour types. Identification of key contributors to the model performance is facilitated by SHapley Additive exPlanations (SHAP), yielding two lists of top target genes with and without considering gender. Notably, these SHAP targets tend to cluster within one or two networks of signalling pathways. Remarkably, gene expression levels of many of these SHAP targets alone can recapitulate survival differences solely based on clinical data between glioblastoma and osteosarcoma patients. Of particular interest, C2ORF72 emerges as a common target from both lists, representing an uncharacterised protein with promising potential as a novel target for diagnostic, prognostic, and therapeutic target for both glioblastoma and osteosarcoma. | null | biorxiv |
10.1101/2024.11.05.622062 | Classifying Irritable Bowel Syndrome Using Spatio-Temporal Graph Convolution Networks on Brain fMRI Data | Wu, J.; Zhuang, S.; Zhuang, Z.; Xie, L.; Liu, M. | Mengting Liu | School of Biomedical Engineering, Sun Yat-sen University | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622062.source.xml | Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder marked by abdominal pain and changes in stool consistency or frequency. Recent studies have explored the link between IBS and various cognitive deficits using functional MRI. Despite these efforts, an effective diagnostic or predictive model for IBS remains elusive. This shortfall is twofold: firstly, the sample sizes in these studies are typically small, and secondly, the machine learning or deep learning models currently in use fail to adequately detect the subtle and dynamic pathological changes present in fMRI data for IBS. In this study, we extracted rs-fMRI of 79 subjects with IBS and 79 healthy controls, then put them into spatio-temporal graph convolution network (ST-GCN) for classification. We also incorporated a novel interpretability module into this model to identify potential regions of interest (ROI) associated with IBS. Our model outperformed other state-of-the-art ML and DL methods with the highest average accuracy of 83.51% on our dataset. Furthermore, based on the results of our interpretability module, the Inferior Parietal Lobule (IPL.R), Inferior Frontal Orbital part (ORBinf.R), Postcentral Gyrus (PCG.R), Middle Frontal Orbital part (ORBmid.R), and Superior Medial Frontal Orbital part (ORBsupmed.L) were identified as top 5 important brain regions for distinguishing IBS patients from the control group, which are consistent with the brain regions identified in previous literature reviews. We also conducted an external data-driven experiment to further validate the effectiveness of the interpretability module. The results indicate that the selected regions significantly impact IBS. | null | biorxiv |
10.1101/2024.11.05.622045 | DrugProtAI: A guide to the future research of investigational target proteins | Halder, A.; Samantaray, S.; Barbade, S.; Gupta, A.; Srivastava, S. | Sanjeeva Srivastava | Indian Institute of Technology Bombay | 2024-11-08 | 1 | new results | cc_no | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622045.source.xml | Drug design and development are central to clinical research, yet ninety percent of drugs fail to reach the clinic, often due to inappropriate selection of drug targets. Conventional methods for target identification lack precision and sensitivity. While various computational tools have been developed to predict the druggability of proteins, they often focus on limited subsets of the human proteome or rely solely on amino acid properties. To address the challenge of class imbalance between proteins with and without approved drugs, we propose a novel Partitioning Method. We evaluated the druggability potential of 20,273 reviewed human proteins, of which 2,636 have approved drugs. Our comprehensive analysis of 183 features, encompassing biophysical and sequence-derived properties, achieved a median AUC of 0.86 in target predictions. We utilize SHAP (Shapley Additive Explanations) scores to identify key predictors and interpret their contribution to druggability. We have reviewed and evaluated 688 investigational proteins from DrugBank (https://go.drugbank.com/) using our tool, DrugProtAI (https://drugprotai.pythonanywhere.com/). Our tool offers druggability predictions and access to 2M+ publications on drug targets and their effects, aiding in the selection of target proteins for drug development. We believe that insights into key predictors will significantly advance drug development and propel the field forward. | null | biorxiv |
10.1101/2024.11.05.622043 | NovumRNA: accurate prediction of non-canonical tumor antigens from RNA sequencing data | Ausserhofer, M.; Rieder, D.; Facciolla, M.; Lamberti, G.; Lisandrelli, R.; Pellegatta, S.; Trajanoski, Z.; Finotello, F. | Francesca Finotello | University of Innsbruck | 2024-11-08 | 1 | new results | cc_by_nc | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622043.source.xml | Non-canonical tumor-specific antigens (ncTSAs) can expand the pool of targets for cancer immunotherapy, but require robust and comprehensive computational pipelines for their prediction. Here, we present NovumRNA, a fully-automated Nextflow pipeline for predicting different classes of ncTSAs from patients' RNA sequencing data. We extensively validated NovumRNA using publicly-available and newly-generated datasets, demonstrating the robustness of its analytical modules and predictions. NovumRNA analysis of colorectal cancer organoid data revealed comparable ncTSA potential for microsatellite stable and unstable tumors and candidate therapeutic targets for patients with low tumor mutational burden. Finally, our investigation of glioblastoma cell lines demonstrated increased ncTSAs burden upon indisulam treatment, and detection by NovumRNA of therapy-induced ncTSAs, which we could validate experimentally. These findings underscore the potential of NovumRNA for identifying synergistic drugs and novel therapeutic targets for immunotherapy, which could ultimately extend its benefit to a broader patient population. | null | biorxiv |
10.1101/2024.11.05.622044 | PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank | Choudhary, P.; Kunnakkattu, I. R.; Nair, S.; Lawal, D. K.; Pidruchna, I.; Afonso, M. Q. L.; Fleming, J. R.; Velankar, S. | Sameer Velankar | EMBL-European Bioinformatics Institute | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622044.source.xml | The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules. Despite the extensive data available, the complexity of small molecule data in the PDB necessitates specialised tools for effective analysis and visualisation. PDBe has developed a number of tools, including PDBe CCDUtils (https://github.com/PDBeurope/ccdutils) for accessing and enriching ligand data, PDBe Arpeggio (https://github.com/PDBeurope/arpeggio) for analysing interactions between ligands and macromolecules, and PDBe RelLig (https://github.com/PDBeurope/rellig) for identifying the functional roles of ligands (such as reactants, cofactors, or drug-like molecules) within protein-ligand complexes. Furthermore, the enhanced ligand annotations and data generated by these tools are presented in a comprehensive view on the novel PDBe-KB ligand pages, providing a holistic view of small molecules that enables the establishment of their biological contexts (Example page for Imatinib: https://wwwdev.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/STI). By improving the standardisation of ligand identification, adding various annotations, and offering advanced visualisation capabilities, these tools help researchers navigate the complexities of small molecules and their roles in biological systems, facilitating mechanistic understanding of biological functions. The ongoing enhancements to these resources are designed to support the scientific community in gaining valuable insights into ligands and their applications across various fields, including drug discovery, molecular biology, systems biology, structural biology, and pharmacology. | null | biorxiv |
10.1101/2024.11.05.622117 | Stick of Sticks: Structural Features of the Amyloidogenic Peptide-DNA Complex | Arzamastsev, G.; Zabrodskaya, Y.; Garmay, Y.; Vinogradova, D.; Ivanova, N.; Arutyunyan, A.; Verlov, N.; Burdakov, V.; Baymukhametov, T.; Konevega, A. L.; Ivankov, O.; Gorshkova, Y.; Egorov, V. V. | Vladimir V Egorov | Smorodintsev Research Institute of Influenza, Russian Ministry of Health | 2024-11-08 | 1 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622117.source.xml | The search for peptides that can specifically bind to regulatory regions in DNA is a necessary step for creating drugs that can regulate gene expression. The work studies the peculiarities of binding of a model peptide, which carries an ionic self-complementary motif and is capable of forming amyloid-like fibrils, with model double-stranded DNA. The stoichiometric ratios of the components of the complex were found using the retardation method in agarose gel. Using microscale thermophoresis, it was shown that the peptide in the oligomeric amyloid-like state is capable of binding to model 45-bp double-stranded DNA, with a micromolar equilibrium dissociation constant. Using electron and atomic force microscopy, the morphology of peptide-DNA complexes was studied; using dynamic light scattering and nanoparticle tracking analysis, as well as small-angle neutron scattering, the spatial parameters of the resulting DNA-peptide complexes were characterized. Molecular dynamics simulations showed that the arginine side chains of the peptide are prone to interact with guanine nitrogenous bases. It was shown that the formation of peptide-dsDNA complexes interferes with the operation of restriction endonucleases that have guanine-cytosine pairs in the recognition center, which is consistent with the results of prediction of interaction sites obtained using computer modeling. The results of the work can be used in the development of peptides capable of interacting with functional regions of DNA, as well as in the development of new carriers for transfection of DNA constructs. | null | biorxiv |
10.1101/2024.11.05.622090 | Critical Spacing in Cell-Matrix Mechanical Feedback Controls Tissue Condensation | Peng, X.; Huang, Y.; Elson, E. L.; Genin, G. M.; Feng, X.-Q. | Xiangjun Peng | Tsinghua University | 2024-11-08 | 1 | new results | cc_no | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622090.source.xml | The mechanical interplay between cells and their extracellular matrix (ECM) presents a fundamental paradox in mechanobiology: while individual cells respond monotonically to increasing mechanical stimulus, collective cellular behaviors exhibit sharp transitions at critical cell densities. This is particularly evident in tissue condensation, where cell-seeded collagen matrices either dramatically contract or remain unchanged depending on whether the initial cell spacing falls below or above a critical threshold. Here we resolve this apparent contradiction through bio-chemo-mechanical modeling of cell-ECM interactions. We show that while increasing ECM stiffness enhances individual cell activation, it simultaneously weakens the mechanical cross-talk between cells, creating a non-monotonic relationship that governs collective behavior. This competition between local activation and neighbor communication establishes a critical spacing threshold below which cells can mechanically polarize their neighbors through ECM remodeling. The predicted critical spacing aligns with experimental observations of the cell density required for tissue condensation, reconciling single-cell and collective responses. Our model reveals how recursive interactions between cellular contractility and ECM mechanics give rise to emergent spatial ordering, demonstrating how complex multicellular behaviors can emerge from simple mechanical principles. These findings provide a physical basis for understanding mechanobiological signaling, with implications for tissue development and disease progression. | null | biorxiv |
10.1101/2024.11.05.621879 | Spatial multi-omics defines a shared infiltrative signature in glioblastoma at the resection margin | Pai, B.; Ramos, S. I.; Cheng, W. S.; Joshi, T.; Price, G.; Tome-Garcia, J.; Nudelman, G.; Shroff, S.; Beaumont, K.; Raymund, Y.; Sebra, R.; Zaslavsky, E.; Tsankova, N. M. | Nadejda Mincheva Tsankova | Department of Neuroscience and Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA | 2024-11-08 | 1 | new results | cc_no | cancer biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.621879.source.xml | Glioblastoma (GBM) remains an untreatable disease. Understanding GBM's infiltrative biology at the resection margin is limited, despite causing disease recurrence and progression. To address this, we generated a high-throughput single-nucleus (sn)RNA-seq and snATAC-seq multi-omic dataset from six tumors with distinct genomic drivers and combined it with spatial transcriptomics to characterize the unique molecular phenotype of GBM near the margin. By contrasting GBM-specific biology in matching "Core" vs. "Margin" dissections, we define a unique, shared "GBM infiltration" signature, epigenetically co-opted at the margin. We prioritize EGFR as a top differentially expressed and accessible "Margin" marker across GBM subtypes, show its dynamic expression along a core-to-margin infiltration trajectory, and validate its role in migration through CRISPR/Cas9 deletion in two patient-derived models. ChIP-seq occupancy studies furthermore corroborate preferential TEAD1 binding at EGFR"s accessible regulatory elements. This validated multi-omic dataset enables further studies into tumor and microenvironment biology in the context of residual GBM disease. | null | biorxiv |
10.1101/2024.11.05.622136 | An SH3-binding allosteric modulator stabilizes the global conformation of the AML-associated Src-family kinase, Hck | Selzer, A. M.; Gerlach, G.; Gonzalez-Areizaga, G.; Wales, T. E.; Cui, S. Y.; Iyer, P.; Engen, J. R.; Camacho, C.; Ishima, R.; Smithgall, T. E. | Thomas E. Smithgall | University of Pittsburgh | 2024-11-08 | 1 | new results | cc_by_nc_nd | pharmacology and toxicology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622136.source.xml | While ATP-site inhibitors for protein-tyrosine kinases are often effective drugs, their clinical utility can be limited by off-target activity and acquired resistance mutations due to the conserved nature of the ATP-binding site. However, combining ATP-site and allosteric kinase inhibitors can overcome these shortcomings in a double-drugging framework. Here we explored the allosteric effects of two pyrimidine diamines, PDA1 and PDA2, on the conformational dynamics and activity of the Src-family tyrosine kinase Hck, a promising drug target for acute myeloid leukemia. Using 1H-15N HSQC NMR, we mapped the binding site for both analogs to the SH3 domain. Despite the shared binding site, PDA1 and PDA2 had opposing effects on near-full-length Hck dynamics by hydrogen-deuterium exchange mass spectrometry, with PDA1 stabilizing and PDA2 disrupting the overall kinase conformation. Kinase activity assays were consistent with these observations, with PDA2 enhancing kinase activity while PDA1 was without effect. Molecular dynamics simulations predicted selective bridging of the kinase domain N-lobe and SH3 domain by PDA1, a mechanism of allosteric stabilization supported by site-directed mutagenesis of N-lobe contact sites. Cellular thermal shift assays confirmed SH3 domain-dependent interaction of PDA1 with wild-type Hck in myeloid leukemia cells and with a kinase domain gatekeeper mutant (T338M). These results identify PDA1 as a starting point for Src-family kinase allosteric inhibitor development that may work in concert with ATP-site inhibitors to suppress the evolution of resistance. | null | biorxiv |
10.1101/2024.11.05.622109 | SysQuan: repurposing SILAC mice for the affordable absolute quantitation of the human proteome | Mohammed, Y.; Richard, V. R.; Madlangsakay, I. R.; Lao, Y.; Spicer, V.; Popp, R.; Gaither, C.; Hennecken, L.; Kleinekofort, W.; Zahedi, R. P.; Borchers, C. H. | Christoph H Borchers | Segal Cancer Proteomics Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada Gerald Bronfman Department of Oncology, | 2024-11-08 | 1 | new results | cc_no | systems biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622109.source.xml | Relative quantitation, used by most MS-based proteomics laboratories to determine protein fold-changes, requires samples being processed and analyzed together for best comparability through minimizing batch differences. This limits the adoption of MS-based proteomics in population-wide studies, and the detection of subtle but relevant changes in heterogeneous samples. Absolute quantitation circumvents these limitations and enables comparison of results across laboratories, studies, and longitudinally. However, high costs of the essential stable isotope labeled (SIL) standards prevents widespread access and limits the number of quantifiable proteins. Our new approach, called SysQuan, repurposes SILAC mouse tissues/biofluids as system-wide internal standards for matched human samples to enable absolute quantitation of, theoretically, two-thirds of the human proteome using 157,086 shared tryptic peptides. We demonstrate that SysQuan enables quantification of 70% and 31% of the liver and plasma proteomes, respectively. We demonstrate for 14 metabolic proteins that abundant SIL mouse tissues enable cost-effective reverse absolute quantitation in, theoretically, 1000s of human samples. Moreover, 10,000s of light/heavy doublets in untargeted SysQuan datasets enable unique post-acquisition absolute quantitation. SysQuan empowers researchers to replace relative quantitation with affordable absolute quantitation at scale, making data comparable across laboratories, diseases and tissues, enabling completely novel study designs and increasing reusability of data in repositories. | null | biorxiv |
10.1101/2024.11.08.622679 | Field EPSPs of dentate gyrus granule cells studied by selective optogenetic activation of hilar mossy cells in hippocampal slices. | Bernstein, H. L.; Lu, Y.-L.; Botterill, J. J.; Duffy, A. M.; LaFrancois, J. J.; Scharfman, H. E. | Helen E Scharfman | New York University and The Nathan Kline Institute | 2024-11-08 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622679.source.xml | Glutamatergic dentate gyrus (DG) mossy cells (MCs) innervate the primary DG cell type, granule cells (GCs). Numerous MC synapses are on GC proximal dendrites in the inner molecular layer (IML). However, field recordings of the GC excitatory postsynaptic potential (fEPSPs) have not been used to study this pathway selectively. Here we describe methods to selectively activate MC axons in the IML using mice with Cre recombinase expressed in MCs. Slices were made after injecting adeno-associated virus (AAV) encoding channelrhodopsin (ChR2) in the DG. In these slices, we show that fEPSPs could be recorded reliably in the IML in response to optogenetic stimulation of MC axons. Furthermore, fEPSPs were widespread across the septotemporal axis. However, fEPSPs were relatively weak because they were small in amplitude and did not elicit a significant population spike in GCs. They also showed little paired pulse facilitation. We confirmed the extracellular findings with patch clamp recordings of GCs despite different recording chambers and other differences in methods. Together the results provide a simple method for studying MC activation of GCs and add to the evidence that this input is normally weak but widespread across the GC population. | null | biorxiv |
10.1101/2024.11.08.622661 | Investigating the Impact of Habitual Sleep Quality on Episodic Memory Performance: An EEG-Based Representational Similarity Analysis | Seraji, M.; Mirjalili, S.; Duarte, A.; Calhoun, V. D. | Masoud Seraji | Tri-Institutional Georgia State University/Georgia Institute of Technology/Emory University Center for Translational Research in Neuroimaging and Data Science, | 2024-11-08 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622661.source.xml | Sleep is crucial for episodic memory consolidation, yet the impact of habitual sleep quality on memory performance remains underexplored. This study investigates the relationship between sleep quality and episodic memory retrieval using EEG-based representational similarity analysis (RSA). Thirty-six participants wore wrist accelerometers for one week to capture habitual sleep patterns, including total sleep time and restlessness. Memory performance was assessed through a paired associate learning task, with EEG data recorded during encoding and retrieval phases. RSA was applied to EEG oscillatory power across time-frequency windows to examine the neural similarity between encoding and retrieval. The results showed both positive and negative correlations between sleep metric and memory performance, with sleep restlessness being linked to both increases and decreases in neural similarity across specific clusters. These findings emphasize the important role of sleep quality in shaping the neural processes underlying episodic memory retrieval, indicating a strong connection between sleep patterns and memory function. | null | biorxiv |
10.1101/2024.11.05.622086 | Integrated, high-dimensional analysis of CD4 T cell epitope specificities and phenotypes reveals unexpected diversity in the response to Mycobacterium tuberculosis | Mead, H. L.; Kirschman, J. H.; Harms, C. E.; Kelley, E. J.; Soria-Bustos, J.; Nelson, G. A.; Ogongo, P.; Ouma, G.; Ouma, S. G.; Ernst, J. D.; Altin, J. A. | John A Altin | Translational Genomics Research Institute | 2024-11-08 | 1 | new results | cc_no | immunology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622086.source.xml | Immunity to Mycobacterium tuberculosis (Mtb), like many pathogens, is encoded jointly by the antigen specificities and functions of responding CD4 T cells. However, these features span a large two-dimensional possibility space - defined on one axis by the Mtb proteome, and on the other by the T cell transcriptome - that exceeds the dimensionality of existing technologies. Here we present an approach ("CRESTA") that combines highly-multiplexed DNA-barcoded epitope probes, single cell sequencing, and clonal analysis of T Cell Receptors (TCRs) to robustly detect rare antigen-specific CD4 T cells across hundreds of epitopes simultaneously and reveal their transcriptome-wide phenotypes. By comprehensively assaying known epitopes in Mtb-infected participants, we reveal polyclonal and multi-epitope responses across a spectrum of differentiation states, uncover previously-unobserved phenotypic diversity within and between epitopes, and increase the total number of known Mtb epitope-mapped TCRabs by ~8-fold. We expect CRESTA to enable high-dimensional analyses of CD4 T cell responses in various settings, including infection, cancer, autoimmunity and allergy. | null | biorxiv |
10.1101/2024.11.08.622676 | Polyhydroxybutyrate production in freshwater SAR11 (LD12) | Bennett, B. D.; Meier, D. A.; Lanclos, V. C.; Asrari, H.; Coates, J. D.; Thrash, J. C. | J. Cameron Thrash | University of Southern California | 2024-11-08 | 1 | new results | cc_by_nc | microbiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622676.source.xml | SAR11 bacteria (order Pelagibacterales) are oligotrophs and often the most abundant bacterioplankton in aquatic environments. A subset of sequenced SAR11 genomes, predominantly in the brackish and freshwater SAR11 subclades, contain homologs of pha genes, which in other organisms confer the ability to store carbon and energy via polyhydroxyalkanoate (PHA) polymers. Here, we investigated the relevance of PHA production to SAR11 biology. Phylogenetics showed that Pha proteins occurred on a long branch and provided evidence for origin at the common ancestor of the brackish IIIa and freshwater LD12 subclades, followed by horizontal transfer within SAR11. Using the LD12 representative "Candidatus Fonsibacter ubiquis" strain LSUCC0530, we found that a large minority of LSUCC0530 cells contained a single Nile red-staining granule, confirmed that the cells produced polyhydroxybutyrate (PHB), and estimated the total PHB content in the cells. We heterologously expressed the LSUCC0530 phaCAB locus in Escherichia coli, finding it to be functional and the likely origin of the PHB. We also determined that, irrespective of changes to carbon, nitrogen, and phosphorus concentrations, a similar fraction of LSUCC0530 cells generated PHB granules and expression of the phaCAB locus remained constant. We suggest that PHB synthesis in LSUCC0530 may be constitutively active due to the slow growth dynamics and minimal regulation that characterize SAR11 bacteria. This is the first characterization of polymer storage in SAR11, providing new insights into the likely fitness advantage for cells harboring this metabolism. | null | biorxiv |
10.1101/2024.11.08.622663 | p53 engagement is a hallmark of an unfolded protein response in the nucleus of mammalian cells | Park, J. H.; Wandless, T. J. | Thomas J Wandless | Stanford University | 2024-11-08 | 1 | new results | cc_by | cell biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622663.source.xml | Exposure to exogenous and endogenous stress is associated with the intracellular accumulation of aberrant unfolded and misfolded proteins. In eukaryotic cells, protein homeostasis within membrane-bound organelles is regulated by specialized signaling pathways, with the unfolded protein response in the endoplasmic reticulum serving as a foundational example. Yet, it is unclear if a similar surveillance mechanism exists in the nucleus. Here we leveraged engineered proteins called destabilizing domains to acutely expose mammalian cells to nuclear- or cytosolic- localized unfolded protein. We show that the appearance of unfolded protein in either compartment engages a common transcriptional response associated with the transcription factors Nrf1 and Nrf2. Uniquely, only in the nucleus does unfolded protein activate a robust p53-driven transcriptional response and a transient p53-independent cell cycle defect. These studies highlight the distinct effects of localized protein folding stress and the unique protein quality control environment of the nucleus. | null | biorxiv |
10.1101/2024.11.05.622130 | Passing the quadrat: inferring biodiversity change over time and across investigators | Elahi, R.; Micheli, F.; Watanabe, J. M. | Robin Elahi | Stanford University | 2024-11-08 | 1 | new results | cc_by | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622130.source.xml | Long-term ecological monitoring inevitably requires a "passing of the quadrat" from one investigator to another. Here we present the challenge and opportunity of inferring biodiversity change over time and across investigators using a rocky intertidal case study. The intertidal transect was surveyed initially by Willis Hewatt in 1931-1933, then resurveyed in detail by Rafe Sagarin, Sarah Gilman, and their mentors in 1993. In total, the transect has been resurveyed 17 times over the past three decades, with annual surveys nested within five distinct investigator eras. We addressed two goals with our dataset. First, we asked whether temporal change in several biodiversity metrics (species richness, Hill-Shannon and Hill-Simpson diversity, spatial beta diversity) was sensitive to investigator era. Second, we identified recent ecological "winners" and "losers", relative to the historical baseline, and asked whether such designations can change over time (1993-2023). We show that investigators contributed to variable trends in species richness over time, and we hypothesize that sampling effort contributed to this effect. In contrast, we highlight declines in the biodiversity of common species (Hill-Shannon) and dominant species (Hill-Simpson) over time, in the absence of investigator effects. These declines were associated with the rise of a few numerically dominant species and a trend of increasing spatial similarity. Relative to the historical baseline, ecological winners included certain barnacles, anemones, and turban snails, while losers included mussels, urchins, limpets and a host of more cryptic taxa. However, we show that such designations can be complicated by non-linear population trajectories and discuss mechanisms related to climate change versus potential artifacts related to investigator effort. We finish with recommendations and emphasize the value of marine stations in providing a venue for sustained periodic ecological monitoring at small spatial scales, long duration, and fine taxonomic resolution. | null | biorxiv |
10.1101/2024.11.06.621913 | Too hot for the weeds? Exploring the impact of climate change in herbaceous Convolvulaceae in Cerrado and Mata Atlantica biomes (SE Brazil) | Barbosa, J. C. J.; Alves, F. V. S.; Moreira, A. L. C.; Loeuille, B.; Chatrou, L. W.; Simao-Bianchini, R.; Simoes, A. R. G. | Juliana Cruz Jardim Barbosa | Nucleo de Conservacao da Biodiversidade, Centro de Pesquisa, Instituto de Pesquisas Ambientais, Sao Paulo, SP, Brazil | 2024-11-08 | 1 | new results | cc_no | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.621913.source.xml | Aim: We investigated the potential resilience to climatic change of nine species of weeds in Convolvulaceae, using predictive spatial modeling across two contrasting biomes in Southeastern Brazil: Cerrado (=Savanna) and Mata Atlantica (=Atlantic Forest). We inferred future changes in distribution area, the climatic variables that will be most impactful, and the potential occurrence of future climatic refuges. Location: Southeastern Brazil (Sao Paulo, Brazil). Methods: A total of 195, taxonomically vetted, distribution records were compiled for nine species of Convolvulaceae. Potential distribution areas were modelled in RStudio 1.3.1056 with R 3.6.3 using modleR; environmental layers used were the 19 bioclimatic variables with 30 seconds resolution. After a correlation analysis, four bioclimatic variables were selected for distribution modelling: Temperature Seasonality (BIO4), Mean Temperature of Wettest Quarter (BIO8), Precipitation of Wettest Month (BIO13) and Precipitation of Driest Quarter (BIO17). The species distribution modelling was performed using the Maxent algorithm for the present time (1960-1990) and for future projections (2050 and 2070), under two different scenarios of projections, moderate and pessimistic. The final distribution models were generated through the selection of primary models with a minimum level of TSS (True Skills Statistics) equal to 0.7. Results: The analysed species demonstrated different levels of response to climatic change: Distimake aegyptius, D. dissectus, and Evolvulus pteurocaulon exhibited a gain in the climatic suitability range, regardless of the future scenarios. Other species, such as E. glomeratus, Ipomoea bonariensis, and I. alba showed a decline in climatic suitability range, more accentuated in the pessimistic scenario . Three species showed a positive response in a moderate future scenario, but a decline in the most extreme projection. Areas that may act, in the future, as climatic refuges for the displaced species are also highlighted, in view of being prioritised for conservation. | null | biorxiv |
10.1101/2024.11.05.622112 | How do body size and habitat fragmentation influence extinction in lizards? A long-term case study on artificial islands in the Brazilian Cerrado | Miranda, R. B.; Abbott, K. C.; Martin, R. A.; Brandao, R. A. | Rogerio B. Miranda | Case Western Reserve University | 2024-11-08 | 1 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622112.source.xml | Habitat fragmentation is known to cause extinctions and species turnover, but the factors that allow some species to persist while others become locally extinct are not well understood. Landscape flooding following the construction of hydroelectric dams causes a particularly dramatic form of fragmentation disturbance, where former terrestrial habitats become aquatic and former hilltops become land-bridge islands. As such, reservoir land-bridge islands have become a successful model for accessing the impacts of fragmentation on biodiversity. We used the lizard community, to assess species sensitivity to habitat structural change during land-bridge island formation. We monitored the lizard community for 23 years before, during, and after the flooding of the Serra da Mesa Dam reservoir. Over the course of our study, the diversity of the lizard community on land-bridge islands and mainland sites along the shores of the newly formed reservoir declined from 19 to six species. We found that in Serra da Mesa islands, lizards with large body sizes (e.g., Teiidae and Tropiduridae) decreased in abundance along the flooding process, thereby increasing their extinction risk. In contrast, we found a high abundance of small-bodied lizards (Gekkonidae, Gymnophthalmidae, Scincidae, and Sphaerodactylidae) on Serra da Mesa islands. Richness on the islands declined dramatically, resulting in communities currently with one highly abundant species, Gymnodactylus amarali. For the sake of biodiversity conservation, island or fragment sizes must be considered for maintaining a reasonable number of species and our characterization of the local extinction patterns may provide relevant information to mitigate wildlife depletion due to habitat fragmentation. | null | biorxiv |
10.1101/2024.11.05.622102 | Broad thermal tolerance and high mitochondrial genetic connectivity in the pinfish (Lagodon rhomboides) | Eaton, K. M.; Samenuk, J. E.; Thaxton, L.; Chaves, V.; Bernal, M. A. | Katherine M Eaton | Auburn University | 2024-11-08 | 1 | new results | cc_by_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622102.source.xml | Pinfish (Lagodon rhomboides) are highly abundant in coastal ecosystems of the Gulf of Mexico and western Atlantic Ocean and serve as a crucial link in marine food webs. Despite their ecological relevance, little is known about this species' susceptibility to anthropogenic climate change. Here, we characterized patterns of mitochondrial genetic divergence and examined the upper thermal tolerance of pinfish across a large portion of the species' range. We found little evidence of population genetic differentiation among distant localities with divergent temperature regimes (e.g., Mexico and North Carolina), using two mitochondrial markers (CytB and COI). This suggests high genetic connectivity, which implies low potential for local adaptation of populations to different thermal conditions along a latitudinal gradient. To further examine population-scale differences in thermal tolerance, we assessed the critical thermal maxima (CTmax) of pinfish from four localities: North Carolina, Florida Keys, Alabama, and Texas. We found that CTmax was similar across sites, with all localities showing an average CTmax within a 1{degrees}C temperature range (34.5-35.5{degrees}C). This suggests that southern populations of pinfish may be more susceptible to the detrimental effects of ocean warming, as individuals in lower latitudes regularly experience temperatures within a few degrees of their CTmax. Finally, we examined the influence of varying salinity on the upper thermal limit of the pinfish and found that pinfish show no variation in CTmax under salinity conditions ranging from hypo- to hyper-saline (15-35 ppt). These results show that pinfish can tolerate a wide range of environmental parameters, but may rely on phenotypic plasticity rather than local adaptation to distinct conditions to cope with different environmental regimes. | null | biorxiv |
10.1101/2024.11.05.622099 | Parallel in-depth analysis of repeat expansions: an updated Clin-CATS workflow for nanopore R10 flow cells | Scholz, V.; Schoenrock, V.; Erdmann, H.; Prokosch, V.; Schoedel, M.; Almus, M.; Sauer, M.; Mayer, V.; Breithausen, E.; van Buren, I.; Dineiger, C.; Heintz, C.; Hallermayr, A.; Neuhann, T.; Holinski-Feder, E.; Abicht, A.; Benet-Pages, A.; Lucas, M. C. | Morghan C Lucas | MGZ - Medical Genetics Center, Munich, Germany | 2024-11-08 | 1 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622099.source.xml | Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. We present an updated Clinical Nanopore Cas9-Targeted Sequencing (Clin-CATS) workflow for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the ONT wf-human-variation Epi2Me workflow, including the Straglr tool to analyze basecalled reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 within the ataxia panel and introduces new gene panels for myopathy, neurodegeneration, and ALS/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. | null | biorxiv |
10.1101/2024.11.05.622084 | Characterizing gene expression profiles of various tissue states in stony coral tissue loss disease using a feature selection algorithm | Beavers, K. M.; Gutierrez-Andrade, D.; Van Buren, E. W.; Emery, M. A.; Brandt, M. E.; Apprill, A.; Mydlarz, L. D. | Kelsey M Beavers | Texas Advanced Computing Center | 2024-11-08 | 1 | new results | cc_by_nc_nd | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622084.source.xml | Stony coral tissue loss disease (SCTLD) remains a substantial threat to coral reef diversity already threatened by global climate change. Restoration efforts and effective treatment of SCTLD requires an in-depth understanding of its pathogenesis in the coral holobiont as well as mechanisms of disease resistance. Here, we present a supervised machine learning framework to describe SCTLD progression in a major reef-building coral, Montastraea cavernosa, and its dominant algal endosymbiont, Cladocopium goreaui. Utilizing support vector machine recursive feature elimination (SVM-RFE) in conjunction with differential expression analysis, we identify a subset of biologically relevant genes that exhibit the highest classification performance across three types of coral tissues collected from a natural reef environment: apparently healthy tissue on an apparently healthy colony, apparently healthy tissue on a SCTLD-affected colony, and lesion tissue on a SCTLD-affected colony. By analyzing gene expression signatures associated with these tissue health states in both the coral host and its algal endosymbiont (family Symbiodiniaceae), we describe key processes involved in SCTLD resistance and disease progression within the coral holobiont. Our findings further support evidence that SCTLD causes dysbiosis between the coral host and its Symbiodinaiceae and additionally describes the metabolic and immune shifts that occur as the holobiont transitions from a healthy to a diseased state. This supervised machine learning framework offers a novel approach to accurately assess the health states of endangered coral species and brings us closer to developing effective solutions for disease monitoring and intervention. | null | biorxiv |
10.1101/2024.11.05.622195 | Optimizing Angiopep-2 Density on Polymeric Nanoparticles for Enhanced Blood-Brain Barrier Penetration and Glioblastoma Targeting: Insights from In Vitro and In Vivo Experiments | Zhang, W.; Refaat, A.; Li, H.; Zhu, D.; Tong, Z.; Nicolazzo, J. A.; Peng, B.; Bai, H.; Esser, L.; Voelcker, N. H. | Nicolas H. Voelcker | Monash Institute of Pharmaceutical Sciences, Monash University; Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Faci | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622195.source.xml | The blood-brain barrier (BBB) poses a formidable challenge to efficient drug delivery into the brain. One promising approach involves leveraging receptor-mediated transcytosis facilitated by Angiopep-2 peptide (Ang-2)-conjugated nanoparticles. However, the precise impact of Ang-2 density on BBB penetration remains poorly understood. In this study, we developed a versatile polymeric nanoparticle system with tuneable Ang-2 surface density and systemically examined its influence on BBB penetration through various in vitro assays and an in vivo study. Our findings revealed a nuanced relationship between Ang-2 surface density and BBB penetration across the different experimental setups. In 2D cell culture, we observed a positive correlation between Ang-2 surface density and cellular association in hCMEC/D3 cells, characterized by a distinctive inflection point. Conversely, in the Transwell model, higher Ang-2 density correlated negatively with BBB penetration, whereas the BBB-GBM-on-a-chip showed the opposite trend. These disparities may arise from differences in avidity under static versus dynamic conditions, potentially modulating nanoparticle interactions due to fluidic forces. In vivo studies revealed that higher Ang-2 densities facilitated nanoparticle transport across the BBB, consistent with the findings of the BBB-GBM-on-a-chip model. Furthermore, loading doxorubicin into nanoparticles with optimal Ang-2 density resulted in controlled pH-responsive release and enhanced anticancer effect against U87 GBM cells in both 2D cell cultures and a 3D BBB-GBM-on-a-chip model. These results underscore the critical importance of optimizing Ang-2 surface density for efficient BBB penetration and emphasize the utility of dynamic models in preclinical in vitro assessment of novel nanoparticle formulations for targeted delivery to the brain. | null | biorxiv |
10.1101/2024.11.06.621821 | In vivo engineered quadrivalent CAR-macrophages break tumor barrier,remodel TME and overcome tumor heterogeneity through antigen spreading | Zhang, S.; Lu, H.; Zhang, H.; Ding, X.; Wu, Q.; Lei, A.; Kong, N.; Zhang, J. | Jin Zhang | Center for Stem Cell and Regenerative Medicine, Department of Basic Medical Sciences, and Bone Marrow Transplantation Center of the First Affiliated Hospital, Z | 2024-11-08 | 1 | new results | cc_no | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.621821.source.xml | CAR-macrophages have shown promising prospect in treating solid tumors. Ex vivo engineered CAR-macrophages face the challenge of low transfection efficiency, long preparation cycle, and limited cell number. Here, we designed two novel CAR molecules, GPC3-CAR-Super IL-2 and FAP-CAR-{bigtriangleup}TGF{beta}RII from the perspective of targeting tumor cells and improving tumor microenvironment, and generated quadrivalent CAR-macrophages in vivo for treating solid tumors by the LNP-mRNA system. We found that in vivo engineered quadrivalent CAR-macrophages can strongly activate tumor immunity and achieve complete tumor regression without significant side effects. Mechanically, in vivo engineered quadrivalent CAR-macrophages broke down physical barriers around the tumor constructed by CAFs and significantly promoted infiltration and expansion of CD8+ T cells. Moreover, the transiently formed CAR-macrophages in vivo are sufficient to form long-lasting T cell memory which can effectively prevent tumor recurrence. Most importantly, in vivo engineered CAR-macrophages also stimulated T cell memory against antigen-negative tumor cells through antigen spreading, which might effectively prevent the immune escape of heterogeneous tumor cells. Overall, we developed a platform of in vivo CAR-macrophages with dual roles as a tumor-killing effector cell and a recurrence-preventing vaccine. | null | biorxiv |
10.1101/2024.11.05.621838 | devider: long-read reconstruction of many diverse haplotypes | Shaw, J.; Boucher, C.; Yu, Y. W.; Noyes, N.; Li, H. | Jim Shaw | Dana-Farber Cancer Institute and Harvard University | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.621838.source.xml | Reconstructing haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized techniques. We present devider, an algorithm for haplotyping small sequences--such as viruses or genes--from long-read sequencing. devider uses a positional de Bruijn graph with sequence-to-graph alignment on an alphabet of informative alleles to provide a fast assembly-inspired approach compatible with various long-read sequencing technologies. On a synthetic Nanopore dataset containing seven HIV strains, devider recovered 97% of the haplotype content compared to 86% for the next best method while taking < 4 minutes and 1 GB of memory for > 8,000x coverage. Benchmarking on synthetic mixtures of antimicrobial resistance (AMR) genes showed that devider recovered 83% of haplotypes, 23 percentage points higher than the next best method. On real PacBio and Nanopore datasets, devider recapitulates previously known results in seconds, disentangling a bacterial community with > 10 strains and an HIV-1 co-infection dataset. We used devider to investigate the within-host diversity of a long-read bovine gut metagenome enriched for AMR genes, discovering 13 distinct haplotypes for a tet(Q) tetracycline resistance gene with > 18,000x coverage and 6 haplotypes for a CfxA2 beta-lactamase gene. We found clear recombination blocks for these AMR gene haplotypes, showcasing devider's ability to unveil ecological signals for heterogeneous mixtures. | null | biorxiv |
10.1101/2024.11.06.622212 | An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain | Piluso, S.; Veraszto, C.; Carey, H.; Delattre, E.; L'Yvonnet, T.; Colnot, E.; Romani, A.; Bjaalie, J. G.; Markram, H.; Keller, D. | Sebastien Piluso | Blue Brain Project, Ecole Polytechnique Federale de Lausanne (EPFL), Campus Biotech, 1202 Geneva, Switzerland | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622212.source.xml | Brain atlases are essential for quantifying cellular composition in mouse brain regions. The Allen Institute's Common Coordinate Framework version 3 (CCFv3) is widely used, delineating over 600 anatomical regions, but it lacks coverage for the most rostral and caudal brain parts, including the main olfactory bulb, cerebellum, and medulla. Additionally, the CCFv3 omits key cerebellar layers, and its corresponding Nissl-stained reference volume is not precisely aligned, limiting its utilisability. To address these issues, we developed an extended atlas, the Blue Brain Project CCFv3 augmented (CCFv3aBBP), which includes a fully annotated mouse brain and an improved Nissl reference aligned in the CCFv3. This enhanced atlas also features the central nervous system annotation (CCFv3cBBP). Using this resource, we aligned 734 Nissl-stained brains to produce an average Nissl template, enabling an updated distribution of neuronal soma positions. These data are available as an open-source resource, broadening applications such as improved alignment precision, cell type mapping, and multimodal data integration. | null | biorxiv |
10.1101/2024.11.06.622202 | Prediction of context-specific regulatory programs and pathways using interpretable deep learning | Doncevic, D.; Ramirez Alvarez, C.; Li, A.; Zhang, Y.; von Bachmann, A.; Noack, K.; Herrmann, C. | Daria Doncevic | Heidelberg University | 2024-11-08 | 1 | new results | cc_by_nc | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622202.source.xml | Variational autoencoders (VAEs) are being widely adopted for the analysis of single-cell RNA sequencing (scRNA-seq) data. As with any non-linear models, however, they lack interpretability, which is a crucial aspect in the biomedical field where researchers want to be able to trust their model predictions. Our previously developed OntoVAE model addressed this issue by integrating biological ontologies in the decoder, which made the neuronal activations correspond to pathway activities. However, when multiple covariates are present, disentangling their relative contributions is challenging. To address this limitation, we developed COBRA, a VAE tool that combines the interpretable decoder part of OntoVAE with an adversarial approach that separates covariate effects in the latent space. In this work, we demonstrate the use of COBRA on two different scRNA-seq datasets in different contexts. We applied the tool to an interferon stimulated mouse dataset to separate the effects of celltype and treatment on transcription factors and biological pathways. We furthermore showed how COBRA can be used to predict the state of unseen celltypes. | null | biorxiv |
10.1101/2024.11.06.622203 | Mapping the Molecular Landscape of Thyroid Neoplasms: A Comprehensive Proteomic and Phosphoproteomic Analysis Across Tumors of Follicular Origin | Bossart, J.; Tajbakhsh, K.; Stanowska, O.; Weber, A.; Zboray, R.; Perren, A.; Buljan, M. | Marija Buljan | Swiss Federal Laboratories for Materials Science and Technology | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622203.source.xml | Thyroid nodules are a widespread phenomenon, with follicular cell-derived thyroid tumors being the most prevalent type of endocrine tumor, spanning from benign through low grade malignant to aggressive neoplasms with dismal prognosis. In clinical practice, histopathological criteria are primarily used to determine malignancy and aggressiveness. Therefore, accurate classification may result in surgical procedures for diagnostic reasons, associated with an imbalanced risk/benefit ratio. In recent years, the use of integrated proteomic approaches has proven valuable in expanding the molecular understanding of thyroid neoplasms, with implications in classification, yet remains understudied in divergent thyroid nodules. Here we show the delineation of subtype-specific and malignancy-dependent molecular characteristics through integrative proteomic and phosphoproteomic analysis of 53 human thyroid tissues, encompassing five frequent benign and malignant tumors. We found that the (phospho)-proteomic profiles enable a clear stratification of malignant and benign thyroid tissues. The method also performs well in delineating follicular adenoma (FA) and follicular thyroid carcinoma (FTC) samples. Beside the dysregulation of cell cycle control, apoptosis, and metabolic reprogramming associated with tumor development and malignancy, we further report increased alterations within the well-established oncogenic RAS/BRAF/MAPK and AKT/MTOR signaling pathways, which, contrary to the prevailing paradigm, did not clearly differentiate between FTC and papillary thyroid carcinoma (PTC). In addition, activities of ATM, PLK2-3, and GRK5-6 kinases were predicted to be strongly upregulated in malignant subtypes. Together, this study provides an in-depth insight into molecular changes in different thyroid tumor subtypes. These findings highlight the potential of integrated proteomic approaches to refine our understanding of complex diseases like cancer. As such, they offer a pathway to more precise diagnostic and personalized treatment strategies. | null | biorxiv |
10.1101/2024.11.05.622005 | Interpretable PROTAC degradation prediction with structure-informed deep ternary attention framework | Chen, Z.; Gu, C.; Tan, S.; Wang, X.; Li, Y.; He, M.; Lu, R.; Sun, S.; Hsieh, C.-Y.; Yao, X.; Liu, H.; Heng, P.-A. | Huanxiang Liu | Macao Polytechnic University | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622005.source.xml | Proteolysis Targeting Chimeras (PROTACs) are heterobifunctional ligands that form ternary complexes with Protein Of Interests (POIs) and E3 ligases, exploiting the ubiquitin-proteasome system to degrade disease-causing proteins, promising to drug the undruggable. While PROTAC research primarily relies on costly and time-consuming wet experimental approaches, deep learning offers a promising avenue to accelerate development and reduce expenses. However, existing deep learning methods for PROTAC degradation prediction often overlook the significance of hierarchical molecular representation and protein structural information, hindering effective data modeling. Moreover, their black-box nature limits the interpretability of computational outcomes, failing to provide intuitive insights into substructure interactions within the PROTAC system. This study introduces PROTAC-STAN, a structure-informed deep ternary attention network (STAN) framework for interpretable PROTAC degradation prediction. PROTAC-STAN represents PROTAC molecules across atom, molecule, and property hierarchies and incorporates structure information for POIs and E3 ligases using a protein language model infused with structural data. Furthermore, it simulates interactions among three entities at the atom and amino acid levels via a novel ternary attention network tailored for the PROTAC system, enhancing interpretability. By integrating hierarchical PROTAC molecule representation, structural embedding of POI and E3 ligase, and ternary attention network modeling interactions, our approach substantially improves prediction accuracy by 10.95% while enabling significant model interpretability via atomic and residue level visualization of molecule and complex. Experiments on the refined public PROTAC dataset demonstrate that PROTAC-STAN outperforms state-of-the-art baselines in overall performance. The excellent performance of PROTAC-STAN is anticipated to establish it as a foundational tool in future research on PROTAC-related drugs, thereby accelerating the development of this field. | null | biorxiv |
10.1101/2024.11.05.622153 | An Exact and Fast SAT Formulation for the DCJ Distance | Sarnaik, A. M.; Chen, K.; Diaz, A.; Shao, M. | Mingfu Shao | Pennsylvania State University | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622153.source.xml | Reducing into a satisfiability (SAT) formulation has been proven effective in solving certain NP-hard problems. In this work, we extend this research by presenting a novel SAT formulation for computing the double-cut-and-join~(DCJ) distance between two genomes with duplicate genes. The DCJ distance serves as a crucial metric in studying genome rearrangement. Previous work achieved an exact solution by transforming it into a maximum cycle decomposition (MCD) problem on the corresponding adjacency graph of two genomes, followed by reducing this problem into an integer linear programming (ILP) formulation. Using both simulated datasets and real genomic datasets, we firmly conclude that the SAT-based method scales much better and runs faster than using ILP, being able to solve a whole new range of instances which the ILP-based method cannot solve in a reasonable amount of time. This underscores the SAT-based approach as a versatile and more powerful alternative to ILP, with promising implications for broader applications in computational biology. | null | biorxiv |
10.1101/2024.11.05.622089 | Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis | MOULICK, A. G.; Patel, R.; Onyema, A. C.; Loverde, S. | Sharon Loverde | CUNY College of Staten Island | 2024-11-08 | 1 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622089.source.xml | This study investigates nucleosome dynamics using both all-atom and coarse-grained (CG) molecular dynamics simulations, focusing on the SIRAH force field. Simulations are performed for two nucleosomal DNA sequences, ASP and Widom-601, over six microseconds at physiological salt concentrations. Comparative analysis of structural parameters, such as groove widths and base pair geometries, reveals good agreement between atomistic and CG models, though CG simulations exhibit broader conformational sampling and greater breathing motion of DNA ends. Principal component analysis (PCA) is applied to DNA structural parameters, revealing multiple free energy minima, especially in CG simulations. These findings highlight the potential of the SIRAH CG force field for studying large-scale nucleosome dynamics, offering insights into DNA repositioning and sequence-dependent behavior. | null | biorxiv |
10.1101/2024.11.08.622658 | Engineered acetylation patterns drive large-scale chromatin organization in vitro | Fukai, Y.; Kujirai, T.; Wakamori, M.; Kanamura, S.; Yamauchi, L.; Zeraati, S.; Tanegashima, C.; Kadota, M.; Kurumizaka, H.; Umehara, T.; Kawaguchi, K. | Kyogo Kawaguchi | RIKEN | 2024-11-08 | 1 | new results | cc_by_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622658.source.xml | Cells exhibit distinct patterns of gene expression that intrinsically depend on chromatin structure and dynamics, where chromatin is a complex polymer composed of the genome and proteins such as the histone octamer. Three-dimensional chromatin structures inside cells have been investigated using conformation capture experiments and high-resolution imaging, revealing correlations between large-scale structural changes and gene expression patterns during cellular processes such as differentiation. Chemical modifications of histones, including acetylation and methylation of histone tail regions, serve as key molecular mechanisms behind these distinct conformations by altering nucleosome interactions and recruiting other factors. While in vitro reconstituted chromatin enables controlled studies of histone modifications, current methods are either limited to short arrays or lack control over histone density and modification patterns. Reconstituting gene-scale level chromatin remains technically challenging, particularly for long arrays containing heterogeneous modification patterns. Here we establish a protocol for stitching together independently reconstituted smaller nucleosome arrays to construct a 96-mer array with controlled histone modification patterns at 12-mer resolution. Through single-molecule microscopy, we find that H4-tail-acetylated nucleosome density significantly affects the fluctuation amplitude and time scale, whose relation can be explained by a model of polymer dynamics. We further characterize the structure of the reconstituted arrays by in vitro conformation capture experiments and find how distal contact patterns and features resembling in vivo higher-order chromatin organization can emerge depending on the heterogeneous modification patterns. This platform enables the investigation of gene-scale chromatin's physical properties in relation to modification patterns and solution environments, providing insights into the links between chromatin modifications, structure, and function. | null | biorxiv |
10.1101/2024.11.05.622105 | Sticky enzymes: increased metabolic efficiency via substrate-dependent enzyme clustering | Martinez-Calvo, A.; Zhou, J.; Zhang, Y.; Wingreen, N. S. | Alejandro Martinez-Calvo | Princeton University | 2024-11-08 | 1 | new results | cc_no | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622105.source.xml | Coclustering of subsequent enzymes in a pathway can accelerate the processing of metabolic intermediates, with benefits including increased pathway fluxes, reduced toxicity, and sensitive branch-point regulation. While the optimal organization of such clusters has been explored theoretically, little is known about how to achieve such organization inside cells. Here we propose that phase-separating enzymes can self-organize into nearly-optimally sized and spaced clusters, provided that their "stickines" is regulated by local substrate availability. In a nutshell, enzyme clusters only form when and where they are needed to process substrate. We study a mathematical model that implements this scheme for simple metabolic pathways, including all thermodynamic constraints. We find that pathway fluxes can be increased by 50 to 1000-fold and toxic metabolites can be decreased by 10 to 100-fold, at realistic enzyme densities. Finally, we discuss how enzyme "stickiness" could be allosterically regulated. This study presents a self-organization strategy that goes beyond current paradigms for natural and engineered enzyme clusters, and thus represents a motivating challenge to the fields of synthetic biology and metabolic engineering. | null | biorxiv |
10.1101/2024.11.06.622193 | A Multi-Modal Deep Learning Framework with Both Sequence and Structure for Tumor Antigens Prediction | Jin, R.; Ge, J.; Zhang, G.; Deng, Z.; Hsieh, K.; Hou, T.; Zhou, R. | Ruhong Zhou | Zhejiang University | 2024-11-08 | 1 | new results | cc_no | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622193.source.xml | Tumor antigens are key targets in cancer immunotherapies that can be recognized by T cell receptor and induce immune responses. However, precision screening of immunogenic tumor antigens remains a great challenge due to human leukocyte antigen (HLA) restriction and tumor antigen escape. Here, we introduce MultiTAP (Multi-modal Tumor Antigen Predictor), a pioneering multi-modal framework with TCR-peptide-HLA sequence and structure features incorporating an attention mechanism designed to accurately identify tumor antigens with immunogenic properties. By constructing the multi-modal TCR-peptide-HLA Dataset (TPHD) and integrating its sequence and structure, we perform antigen feature enhancement using peptide-HLA (pHLA) structural features at the residue level, achieving interpretable prediction of immunogenicity for tumor antigens. Relative to existing baseline models, the MultiTAP framework has exhibited superior efficacy in predicting the immunogenicity of tumor antigens. Through comprehensive out-of-distribution (OOD) assessments, MultiTAP has maintained predictive robustness across diverse HLA phenotypes and the continuously evolving landscape of epitope distributions. Overall, MultiTAP presents a brand-new and promising approach for cancer immunotherapies that target tumor antigens. | null | biorxiv |
10.1101/2024.11.06.622206 | Fractional Calculus in Epigenetics | Nasrolahpour, H.; Pellegrini, M.; Skovranek, T. | Hosein Nasrolahpour | University of Tehran | 2024-11-08 | 1 | new results | cc_no | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622206.source.xml | DNA methylation, a pivotal epigenetic modification, plays a critical role in regulating gene expression. Understanding its dynamics with age is essential for elucidating ageing processes and developing biomarkers. This short note presents a theoretical framework for modelling DNA methylation dynamics using a fractional calculus approach, extending standard exponential models to accommodate the complex, heterogeneous nature of methylation changes over time. The fractional-calculus representation of the methylation process, described by the fractional-order differential equation and its solution based on the Mittag-Leffler function, not only provides better results in the sense of R2, RMSE, and MSE criteria but also offers a more general model, where the standard exponential model is only one special case. | null | biorxiv |
10.1101/2024.11.06.622216 | Endurance Exercise Elevates Plasma Mature Brain-Derived Neurotrophic Factor through Child- and Adulthood, with Amplified Effects in Adults | Edman, S.; Starck, J.; Corell, L.; Hangasjarvi, W.; von Finckenstein, A.; Reimeringer, M.; Reitzner, S. M.; Norrbom, J.; Moberg, M.; von Walden, F. | Sebastian Edman | Karolinska Institute | 2024-11-08 | 1 | new results | cc_by_nc_nd | physiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622216.source.xml | Background: Brain-derived neurotrophic factor (BDNF) is a neurotrophin that plays a central role in neuronal health. BDNF exists in two primary isoforms, the mature form (mBDNF) and its precursor (proBDNF), with opposing downstream effects on neuronal function. The positive effect of exercise on plasma levels of the BDNF-isoforms has been extensively studied in adults. However, equivalent investigations are lacking in children and youth. Methods: Twenty healthy children (9-12 years old), 19 adolescents (13-17 years old), and 39 adults (23-49 years old) donated venous blood before and after a 45-minute run. Platelet-poor plasma was analyzed for pro- and mBDNF using enzyme-linked immunosorbent assay. Maximal oxygen uptake and anthropometric data were assessed in all participants, while Tanner stage, circulating sex hormones, and accelerometry-based activity level were assessed in children and adolescents. Results: We found that children, adolescents, and adults have similar basal levels of pro- (337-543 pg ml-1) and mBDNF (650-1111 pg . ml-1). For children and adolescents, basal levels of mBDNF correlated with average time spent in vigorous activity (r=0.5794, p=0.0015). In response to acute endurance exercise, mBDNF increased by 701 +/- 946, 1232 +/- 1105, and 1557 +/- 1168 pg +/- ml-1 in children, adolescents, and adults, respectively. The acute endurance exercise did not affect proBDNF levels (p>0.05). Conclusion: Our results demonstrate that basal plasma pro- and mBDNF levels do not depend on age and maturity. Plasma mBDNF levels increase following endurance exercise in all age groups, but to a greater extent in adults. | null | biorxiv |
10.1101/2024.11.08.622668 | RTF1 mediates epigenetic control of Th17 cell differentiation via H2B monoubiquitination | Galan, C.; Lu, G.; Gill, R.; Li, D.; Liu, Y.; Huh, J. R.; Hang, S. | Saiyu Hang | Genentech | 2024-11-08 | 1 | new results | cc_no | immunology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.08.622668.source.xml | A gene encoding the transcription factor RTF1 has been associated with an increased risk of ulcerative colitis (UC). In this study, we investigated its function in modulating T cells expressing interleukin-17A (Th17 cells), a cardinal cell type promoting intestinal inflammation. Our results indicate that Rtf1 deficiency disrupts the differentiation of Th17 cells, while leaving regulatory T cells (Treg) unaffected. Mechanistically, RTF1 facilitates histone H2B monoubiquitination (H2Bub1), which requires its histone modification domain (HMD), for supporting Th17 cell function. Impaired Th17 differentiation was also observed in cells lacking the H2Bub1 E3 ligase subunit RNF40, an enzyme known to physically interact with RTF1. Thus, our study underscores the essential role of RTF1 in H2Bub1-mediated epigenetic regulation of Th17 cell differentiation. Understanding this process will likely provide valuable insights into addressing Th17-associated inflammatory disorders. | null | biorxiv |
10.1101/2024.11.05.621954 | Enemy release of introduced parasitoids does not affect their establishment or success | Kishinevsky, M.; Ferrer-Suay, M.; Ives, A. R. | Miriam Kishinevsky | Department of Integrative Biology, University of Wisconsin-Madison | 2024-11-08 | 1 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.621954.source.xml | The enemy release hypothesis, that the success of invading species is due to release from natural enemies that occur in their home range but not in the new range, can be an important explanation for successful invasions. Testing this hypothesis is difficult, however, because testing requires documented cases of not only successful, but also unsuccessful invasions. Therefore, observational data on after-the-fact establishment following unintentional introductions is insufficient, because they only include successful invasions. Here, we investigate the role of enemy release for parasitoid biological control agents and their hyperparasitoid natural enemies. We created a dataset of all aphid parasitoid wasp species introduced into North America, including data on their hyperparasitoid species in the native and new range. In total, information on 29 species of primary parasitoids and 54 species of hyperparasitoids was obtained, combining to create 259 parasitoid-hyperparasitoid species associations. Results show that introduced parasitoids experience partial enemy release, but the degree of enemy release does not affect the chance of successful establishment or successful control. This lack of effect of enemy release might be due to the broad geographical range of the hyperparasitoids (perhaps from unintentional introductions) which reduces the degree of enemy release. In addition, the life-history traits of the hyperparasitoid communities in the new range were different from the native range, with relatively more generalist hyperparasitoid species in the new range. These results show that introduced natural enemies can experience enemy release, but that this does not necessarily help to predict their successful establishment. | null | biorxiv |
10.1101/2024.11.05.622154 | Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays | Nguyen, T. N.; Cosgrove, E. J.; Chen, N.; Lehr, N.; Lokey, M.; Beaudry, F. E. G.; Fitzpatrick, S. W.; Miller, K. E.; Fitzpatrick, J. W.; Clark, A. G. | Tram N Nguyen | Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY | 2024-11-08 | 1 | new results | cc_no | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.05.622154.source.xml | Whole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) had been widespread across Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater magnitude of loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay. | null | biorxiv |
10.1101/2024.11.06.622323 | JOnTADS: a unified caller for TADs and stripes in Hi-C data | Zeng, Q.; Xiang, G.; Zhang, Y.; Hardison, R. C.; Li, Q. | Qunhua Li | Pennsylvannia State University | 2024-11-08 | 1 | new results | cc_by_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622323.source.xml | Topologically associating domains (TADs) and stripes are important architectural structures on Hi-C data that are important for gene regulation. We present Joint Optimized nested TADs and Stripes (JOnTADS), a unified caller for TADs and stripes in Hi-C data. JOnTADS effectively identifies hierarchical TADs and stripes in population Hi-C and micro-C datasets, and hierarchical TADs in single-cell Hi-C data. It provides robust identifications aligned with known biology and effectively captures interaction frequency variations in contact maps across diverse contexts. When multiple samples are available, JOnTADS leverages shared information across samples in TAD identification, reducing unwanted variation in TAD boundary identification while preserving biological differences. This approach enables robust identifications in single-cell Hi-C data, effectively addressing challenges posed by data sparsity. JOnTADS is computationally efficient and requires minimal user tuning. | null | biorxiv |
10.1101/2024.11.06.622293 | AI-Augmented Physics-Based Docking for Antibody-Antigen Complex Prediction | Gaudreault, F.; Sulea, T.; Corbeil, C. | Christopher Corbeil | National Research Council Canada | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622293.source.xml | Predicting the structure of antibody-antigen complexes is a challenging task with significant implications for the design of better antibody therapeutics. However, the levels of success have remained dauntingly low, particularly when high standards for model quality are required, a necessity for efficient antibody design. Artificial intelligence (AI) has significantly impacted the landscape of structure prediction for antibodies, both alone and in complex with their antigens. We utilized AI-guided antibody modeling tools to generate ensembles displaying diversity in the complementarity-determining region (CDR) and integrated those into our previously published AlphaFold2-rescored docking pipeline, a strategy called AI-augmented physics-based docking. We highlight that the quality of the ensemble is crucial for docking performance, that including too many models can be detrimental and that prioritization of models is essential for achieving good performance. In this study, we also compare docking performance with AlphaFold, the new benchmark in the field. We distinguish between two types of success tailored to specific downstream applications: 1) criteria sufficient for epitope mapping, where gross quality is adequate and can complement experimental techniques, and 2) criteria for producing higher-quality models suitable for engineering purposes. Our results robustly demonstrate the advantages of AI-augmented docking over AlphaFold2, further accentuated when higher standards in quality are imposed. Docking performance is noticeably lower than the one of AlphaFold3 in both epitope mapping and antibody design. While we observe a strong dependence on CDR-H3 length for physics-based tools on their ability to successfully predict, this helps define an applicability range where physics-based docking can be competitive to AlphaFold3. | null | biorxiv |
10.1101/2024.11.06.622245 | Molecular Simulations Meet Personalized Medicine. The Mechanism of Action of ClC-5 Antiporter and the Origin of Dent's Disease | Macaluso, V.; Perez, C.; Soliva, R.; Westermaier, Y.; Diaz, L.; Wieczor, M.; Orozco, M. | Modesto Orozco | IRB Barcelona | 2024-11-08 | 1 | new results | cc_by_nc | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622245.source.xml | ClC-5 is a Cl-/H+ antiporter crucial for the homeostasis of the entire organism, and whose functional deficiencies cause pathologies such as Dent's disease, a rare genetic disorder that can have lethal consequences. While the clinical aspects of the pathology are known, its molecular basis is elusive, which hampers the development of potential therapies. We present here a systematic study, where we explore the mechanism of transport of ClC-5, deciphering the choreography of structural changes required for the transport of chloride ions and protons in opposing directions. Once the mechanism is determined, we explore how the 523deltaVal deletion linked to Dent's disease hampers the correct functioning of the transporter, despite having a very minor structural impact. Our study highlights how state-of-the-art simulation methods can provide information on the origin of rare diseases and serve as a tool in personalized medicine. | null | biorxiv |
10.1101/2024.11.06.622270 | Disentangling folding from energetic traps in simulations of disordered proteins | Lotthammer, J. M.; Holehouse, A. S. | Alex S Holehouse | Washington University in St. Louis | 2024-11-08 | 1 | new results | cc_by_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622270.source.xml | Protein conformational heterogeneity plays an essential role in a myriad of different biological processes. Extensive conformational heterogeneity is especially characteristic of intrinsically disordered proteins and protein regions (collectively IDRs), which lack a well-defined three-dimensional structure and instead rapidly exchange between a diverse ensemble of configurations. An emerging paradigm recognizes that the conformational biases encoded in IDR ensembles can play a central role in their biological function, necessitating understanding these sequence-ensemble relations. All-atom simulations have provided critical insight into our modern understanding of the solution behavior of IDRs. However, effectively exploring the accessible conformational space associated with large, heterogeneous ensembles is challenging. In particular, identifying poorly sampled or energetically trapped regions of disordered proteins in simulations often relies on qualitative assessment based on visual inspection of simulations and/or analysis data. These approaches, while convenient, run the risk of masking poorly-sampled simulations. In this work, we present an algorithm for quantifying per-residue local conformational heterogeneity in protein simulations. Our work builds on prior work and compares the similarity between backbone dihedral angle distributions generated from molecular simulations in a limiting polymer model and across independent all-atom simulations. In this regime, the polymer model serves as a statistical reference model for extensive conformational heterogeneity in a real chain. Quantitative comparisons of probability vectors generated from these simulations reveal the extent of conformational sampling in a simulation, enabling us to distinguish between situations in which protein regions are well-sampled, poorly-sampled, or folded. To demonstrate the effectiveness of this approach, we apply our algorithm to several toy, synthetic, and biological systems. Accurately assessing local conformational sampling in simulations of IDRs will help better quantify new enhanced sampling methods, ensure force field comparisons are equivalent, and provide confidence that conclusions drawn from simulations are robust. | null | biorxiv |
10.1101/2024.11.06.622354 | Tear secretion via a paracellular pathway in lacrimal gland is regulated by myosin-mediated modulation of tight junction permeability | Ohno, Y.; Hu, G.; Robak, D.; Zheng, W. S.; Ebrahim, S. | Yuta Ohno | University of Virginia/Asahi University | 2024-11-08 | 1 | new results | cc_by_nc_nd | physiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622354.source.xml | Dry eye, characterized by symptoms of ocular discomfort and visual disturbances due to decreased tear secretion, affects 16 million Americans. Yet, there is currently no cure for dry eye as the mechanistic details of water secretion in the tear-producing lacrimal gland have not been fully elucidated. While a transcellular water secretion pathway via water channels like AQP5 has been reported, the existence and function of a paracellular pathway via tight junctions between epithelial cells remains controversial. The actomyosin cytoskeleton localizes to the apical junctions of epithelial cells across organs and regulates tight junction integrity. Here, we report that non-muscle myosin IIC (NMIIC) is enriched at apical junctions of ductal epithelial cells in the lacrimal gland, leading us to hypothesize that NMIIC regulates tear secretion through modulation of tight junction permeability. Consistent with this hypothesis, we found that tear volume after carbachol stimulation was significantly increased in mice lacking NMIIC, and levels of the tight junction protein ZO-1 were significantly reduced. Furthermore, pharmacological activation of NMIIC by 4-Hydroxyacetophenone in wildtype mice significantly inhibited tear secretion. In summary, our findings reveal a paracellular water secretion pathway in the lacrimal gland, which is regulated by NMIIC-mediated modulation of ductal cell tight junctional permeability, and can be targeted by small molecules. | null | biorxiv |
10.1101/2024.11.06.622250 | Metaproteomic profiling of the secretome of a granule-forming Ca. Accumulibacter enrichment | van Olst, B.; Eerden, S. A.; Estok, N. A.; Roy, S.; Abbas, B.; Lin, Y.; van Loosdrecht, M.; Pabst, M. | Martin Pabst | Delft University of Technology, TUD. | 2024-11-08 | 1 | new results | cc_by | systems biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622250.source.xml | Extracellular proteins are supposed to play crucial roles in the formation and structure of biofilms and aggregates. However, often little is known about these proteins, in particular for microbial communities. Here, we use two advanced metaproteomic approaches to study the extracellular proteome in a granular Candidatus Accumulibacter enrichment as a proxy for microbial communities that form solid microbial granules, such as used in biological wastewater treatment. Limited proteolysis of whole granules and metaproteome isolation from the culture's supernatant successfully identified over 50% of the protein biomass to be secreted. Moreover, structural and sequence-based classification identified 387 proteins, corresponding to over 50% of the secreted biomass, with characteristics that could aid the formation of aggregates, including filamentous, beta-barrel containing, and cell surface proteins. However, while most filamentous proteins originated from Ca. Accumulibacter, among others cell surface proteins did not. This suggests that not only a range of different proteins, but also multiple organisms contribute to granular biofilm formation. Therefore, the obtained extracellular metaproteome data from the granular Ca. Accumulibacter enrichment provides a resource for exploring proteins that potentially support the formation and stability of granular biofilms, whereas the demonstrated approaches can be applied to explore biofilms of microbial communities in general. | null | biorxiv |
10.1101/2024.11.06.622326 | Multi-dimensional social relationships shape social attention in monkeys | Liu, S.; Huang, J.; Chen, S.; Platt, M. L.; Yang, Y. | Yan Yang | Institute of Biophysics, Chinese Academy of Sciences | 2024-11-08 | 1 | new results | cc_by | neuroscience | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622326.source.xml | Social relationships guide individual behavior and ultimately shape the fabric of society. Primates exhibit particularly complex, differentiated, and multidimensional social relationships, which form interwoven social networks, reflecting both individual social tendencies and specific dyadic interactions. How the patterns of behavior that underlie these social relationships emerge from moment-to-moment patterns of social information processing remains unclear. Here, we assess social relationships among a group of four monkeys, focusing on aggression, grooming, and proximity. We show that individual differences in social attention vary with individual differences in patterns of general social tendencies and patterns of individual engagement with specific partners. Oxytocin administration altered social attention and its relationship to both social tendencies and dyadic relationships, particularly grooming and aggression. Our findings link the dynamics of visual information sampling to the dynamics of primate social networks. | null | biorxiv |
10.1101/2024.11.06.622031 | Behavioral and neural evidence for perceptual predictions in social interactions | Lu, J.; Riecke, L.; de Gelder, B. | Beatrice de Gelder | Maastricht University | 2024-11-08 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622031.source.xml | The ability to predict others' behavior is crucial for social interactions. The goal of the present study was to test whether predictions are derived during observation of social interactions and whether these predictions influence how the whole-body emotional expressions of the agents are perceived. Using a novel paradigm, we induced social predictions in participants by presenting them with a short video of a social interaction in which a person approached another person and greeted him by touching the shoulder in either a neutral or an aggressive fashion. The video was followed by a still image showing a later stage in the interaction and we measured participants' behavioral and neural responses to the still image, which was either congruent or incongruent with the emotional valence of the touching. We varied the strength of the induced predictions by parametrically reducing the saliency of emotional cues in the video. Behaviorally, we found that reducing the emotional cues in the video led to a significant decrease in participants' ability to correctly judge the appropriateness of the emotional reaction in the image. At the neural level, EEG recordings revealed that observing an angry reaction elicited significantly larger N170 amplitudes than observing a neutral reaction. This emotion effect was only found in the high prediction condition (where the context in the preceding video was intact and clear), not in the mid and low prediction conditions. We further found that incongruent conditions elicited larger N300 amplitudes than congruent conditions only for the neutral images. Our findings provide evidence that viewing the initial stages of social interactions triggers predictions about their outcome in early cortical processing stages. | null | biorxiv |
10.1101/2024.11.06.622146 | Sex-specific attenuation of photoreceptor degeneration by reserpine in a rhodopsin P23H rat model of autosomal dominant retinitis pigmentosa | Song, H. B.; Campello, L.; Mondal, A.; Chen, H. Y.; English, M. A.; Glen, M.; Vanlandingham, P.; Farjo, R.; Swaroop, A. | Anand Swaroop | National Eye Institute | 2024-11-08 | 1 | new results | cc0 | neuroscience | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622146.source.xml | Inherited retinal degenerations (IRDs) constitute a group of clinically and genetically diverse vision-impairing disorders. Retinitis pigmentosa (RP), the most common form of IRD, is characterized by gradual dysfunction and degeneration of rod photoreceptors, followed by the loss of cone photoreceptors. Recently, we identified reserpine as a lead molecule for maintaining rod survival in mouse and human retinal organoids as well as in the rd16 mouse, which phenocopy Leber congenital amaurosis caused by mutations in the cilia-centrosomal gene CEP290 (Chen et al. eLife 2023;12:e83205. DOI: https://doi.org/10.7554/eLife.83205). Here, we show the therapeutic potential of reserpine in a rhodopsin P23H rat model of autosomal dominant RP. At postnatal day (P) 68, when males and females are analyzed together, the reserpine-treated rats exhibit higher rod-derived scotopic b-wave amplitudes compared to the controls with little or no change in scotopic a-wave or cone-derived photopic b-wave. Interestingly, the reserpine-treated female rats display enhanced scotopic a- and b-waves and photopic b-wave responses at P68, along with a better contrast threshold and increased outer nuclear layer thickness. The female rats demonstrate better preservation of both rod and cone photoreceptors following reserpine treatment. Retinal transcriptome analysis reveals sex-specific responses to reserpine, with significant upregulation of phototransduction genes and proteostasis-related pathways, and notably, genes associated with stress response. This study builds upon our previously reported results reaffirming the potential of reserpine for gene-agnostic treatment of IRDs and emphasizes the importance of biological sex in retinal disease research and therapy development. | null | biorxiv |
10.1101/2024.11.06.622340 | ENaC contributes to macrophage dysfunction in cystic fibrosis | Moran, J.; Pugh, C.; Brown, N.; Thomas, A.; Zhang, S.; McCauley, E.; Cephas, A.; Shrestha, C.; Partida-Sanchez, S.; Bai, S.; Bruscia, E. M.; Kopp, B. | Benjamin Kopp | Emory University | 2024-11-08 | 1 | new results | cc_no | immunology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622340.source.xml | Background: Cystic fibrosis (CF) is a chronic systemic disease caused by dysfunctional or absent cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is expressed in human immune cells and plays a role in regulating innate immunity both directly and indirectly. Besides CFTR, research indicates that the epithelial sodium channel (ENaC) also contributes to dysfunction in CF airway epithelial cells. However, the impact of non-CFTR ion channel dysfunction on CF immune responses is not yet fully understood. A precise understanding of how CF immune function is regulated by ion channels may allow antibiotic-and mutation-agnostic treatment approaches to chronic bacterial infection and inflammation. Therefore, we hypothesized that ENaC is aberrantly expressed in CF macrophages and directly contributes to impaired phagocytic and inflammatory functions. Methods: ENaC expression was characterized in human immune cells isolated from CF and non-CF blood donors. Monocyte-derived macrophage (MDM) function and bacterial killing was tested in the setting of ENaC modulation. Results: Baseline expression of ENaC in human CF MDMs, lymphocytes, and granulocytes was increased at both the transcript and protein level relative to non-CF controls and persisted after exposure to bacteria. Inhibition of CFTR in non-CF MDMs resulted in ENaC overexpression. CFTR modulator treatment reduced but did not eliminate ENaC overexpression in CF MDMs. Interestingly, ENaC inhibition with Amiloride increased CFTR expression. Amiloride-treated CF MDMs also showed normalized ROS production, improved autophagy, and decreased pro-inflammatory cytokine production. Finally, results from an ion channel microarray indicated that sodium channel expression in CF MDMs normalized after Amiloride treatment with minimal effect on other ion channels. Discussion: ENaC is overexpressed in CF immune cells and is associated with abnormal macrophage function. ENaC modulation in immune cells is a novel potential therapeutic target for infection control in CF, either in combination with CFTR modulators, or as a sole agent for patients not currently eligible for CFTR modulators. | null | biorxiv |
10.1101/2024.11.07.622457 | Epstein-Barr Virus Latent Membrane Protein 1 Subverts IMPDH pathways to drive B-cell oncometabolism | Burton, E.; Liang, J. H.; Mitra, B.; Asara, J. M.; Gewurz, B. E. | Benjamin E Gewurz | Brigham and Women\\\'s Hospital, Harvard Medical School, Broad Institute of Harvard and MIT | 2024-11-08 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622457.source.xml | Epstein-Barr virus (EBV) is associated with multiple types of cancers, many of which express the key viral oncoprotein Latent Membrane Protein 1 (LMP1). LMP1 is the only EBV-encoded protein whose expression is sufficient to transform both epithelial and B-cells. Although metabolism reprogramming is a cancer hallmark, much remains to be learned about how LMP1 alters lymphocyte oncometabolism. To gain insights into key B-cell metabolic pathways subverted by LMP1, we performed systematic metabolomic analyses on B cells with conditional LMP1 expression. This approach highlighted that LMP highly induces de novo purine biosynthesis, with xanthosine-5-P (XMP) as one of the most highly LMP1-upregulated metabolites. Consequently, IMPDH inhibition by mycophenolic acid (MPA) triggered apoptosis of LMP1-expressing EBV-transformed lymphoblastoid cell lines (LCL), a key model for EBV-driven immunoblastic lymphomas. Whereas MPA instead caused growth arrest of Burkitt lymphoma cells with the EBV latency I program, conditional LMP1 expression triggered their apoptosis. Although both IMPDH isozymes are expressed in LCLs, only IMPDH2 was critical for LCL survival, whereas both contributed to proliferation of Burkitt cells with the EBV latency I program. Both LMP1 C-terminal cytoplasmic tail domains critical for primary human B-cell transformation were important for XMP production, and each contributed to LMP1-driven Burkitt cell sensitivity to MPA. MPA also de-repressed EBV lytic antigens including LMP1 in latency I Burkitt cells, highlighting crosstalk between the purine biosynthesis pathway and the EBV epigenome. These results suggest novel oncometabolism-based therapeutic approaches to LMP1-driven lymphomas. | null | biorxiv |
10.1101/2024.11.07.622435 | The biotoxin BMAA promotes mesenchymal transition in neuroblastoma cells | Moore, E.; Renner, A.; Dowden, T.; Messer, D.; Hansen, H.; Mull, M.; Goebel, A.; Mawawa, G.; Burton, B.; Pawlus, M. R. | Matthew Ryan Pawlus | Black Hills State University | 2024-11-08 | 1 | new results | cc_by | molecular biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622435.source.xml | Mesenchymal-like cancer cells are an indicator of malignant tumors as they exhibit tumorigenic properties including downregulation of differentiation markers, and increased colony-forming potential, motility, and chemoresistance. We have previously demonstrated that the cyanobacterial biotoxin beta-methylamino-L-alanine (BMAA) is capable of influencing neural cell differentiation state through mechanisms involving the Wnt signaling pathway, suggesting the possibility that BMAA may play a role in influencing other Wnt related differentiation processes including mesenchymal transition. In this study we present evidence characterizing the effects of BMAA on mesenchymal transition in a human neuroblastoma cell line and provide support for the hypothesis that the biotoxin can promote this process in these cells by altering differentiation state, inducing changes in gene expression, and changing cellular function in manners consistent with cellular mesenchymal transition. Results of this study indicate that BMAA exposure may promote carcinogenesis through its effects on cell differentiation state in certain contexts. These results suggest that exposure to the biotoxin BMAA may be an influencing factor in chemotherapy resistance and cancer relapse in neuroblastoma. | null | biorxiv |
10.1101/2024.11.06.622339 | LUMIC: Latent diffUsion for Multiplexed Images of Cells | Hung, A. Z.; Zhang, C. J.; Sexton, J. Z.; O'Meara, M. J.; Welch, J. D. | Joshua D Welch | University of Michigan | 2024-11-08 | 1 | new results | cc_by_nc_nd | molecular biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622339.source.xml | The rapid advancement of high-content, single-cell technologies like robotic confocal microscopy with multiplexed dyes (morphological profiling) can be leveraged to reveal fundamental biology, ranging from microbial and abiotic stress to organ development. Specifically, heterogeneous cell systems can be perturbed genetically or with chemical treatments to allow for inference of causal mechanisms. An exciting strategy to navigate the high-dimensional space of possible perturbation and cell type combinations is to use generative models as priors to anticipate high-content outcomes in order to design informative experiments. Towards this goal, we present the Latent diffUsion for Multiplexed Images of Cells (LUMIC) framework that can generate high quality and high fidelity images of cells. LUMIC combines diffusion models with DINO (self-Distillation with NO labels), a vision-transformer based, self-supervised method that can be trained on images to learn feature embeddings, and HGraph2Graph, a hierarchical graph encoder-decoder to represent chemicals. To demonstrate the ability of LUMIC to generalize across cell lines and treatments, we apply it to a dataset of [~]27,000 images of two cell lines treated with 306 chemicals and stained with three dyes from the JUMP Pilot dataset and a newly-generated dataset of [~]3,000 images of five cell lines treated with 61 chemicals and stained with three dyes. To quantify prediction quality, we evaluate the DINO embeddings, Kernel Inception Distance (KID) score, and recovery of morphological feature distributions. LUMIC significantly outperforms previous methods and generates realistic out-of-sample images of cells across unseen compounds and cell types. | null | biorxiv |
10.1101/2024.11.07.622444 | Dystrophin interacts with Msp300 to Regulate Myonuclear Positioning and Microtubule Organization | Padilla, J. R.; Qiu, Y.; Aleck, G.; Ferreria, L.; Wu, S.; Gibbons, W.; Mandigo, T. R.; Folker, E. S. | Eric S Folker | Boston College | 2024-11-08 | 1 | new results | cc_no | cell biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622444.source.xml | During Drosophila myognesis, myonuclei are actively moved during embryogenesis, and their spacing is maintained through an anchoring mechanism in the fully differentiated myofiber. While we have identified microtubule associated proteins, motors, and nuclear envelope proteins that regulate myonuclear spacing, the developmental time during which each gene functions has not been tested. Here we have identified a Dystrophin as required only for the maintenance of myonuclear spacing. Furthermore, we demonstrate that Dystrophin genetically interacts with the KASH-domain protein Msp300 to maintain myonuclear spacing. Mechanistically, both Dystrophin and Msp300 regulate microtubule organization. Specifically, in animals with disrupted expression of both Dystrophin and Msp300, microtubule colocalization with sarcomeres is reduced. Taken altogether, these data indicate that the peripheral membrane protein Dystrophin, and the outer nuclear membrane protein Msp300, together regulate the organization of the microtubule network which then acts as an anchor to restrict myonuclear movement in contractile myofibers. These data are consistent with growing evidence that myonuclear movement and myonuclear spacing are critical to muscle development, muscle function, and muscle repair and provide a mechanism to connect disparate muscle diseases. | null | biorxiv |
10.1101/2024.11.07.622227 | Greening rates are sensitive to methodology and biology; comment to Sustained greening of the Antarctic Peninsula observed from satellites | Bokhorst, S.; Huisman, S.; de Jonge, I.; Janssen, T.; Cornelissen, H.; Hughes, K.; Convey, P. | Stef Bokhorst | Amsterdam Institute for Life and Environment, VU Amsterdam | 2024-11-08 | 1 | contradictory results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622227.source.xml | Roland et al. claim to provide evidence for a greening trend throughout the Antarctic Peninsula region over the last four decades, based on satellite remote sensing data. However, the early period vegetation cover estimates do not match with the likely extent of vegetated areas in this region at that time, raising doubts about the magnitude of any greening trend. Furthermore, growth rates of mosses and higher plants in Antarctica are insufficient to explain the 14-fold green cover expansion claimed, and neither have such changes been observed at long-term monitoring sites or from field warming studies. The reported satellite time series analyses of the presented trend seems biased by satellite image availability, lack of consistency in the areas covered by imagery and processing pitfalls. Antarctic terrestrial ecosystems are indeed predicted to become greener with climate change, but at much slower rates than reported by Roland et al. | null | biorxiv |
10.1101/2024.11.07.622405 | Epigenetic potential and dispersal propensity in a free-living songbird: a spatial and temporal approach | Jimeno, B.; Tangili, M.; Dominguez, J. C.; Canal, D.; Camacho, C.; Potti, J.; Garcia, J. T.; Martinez-Padilla, J.; Ravinet, M. | Blanca Jimeno | Instituto Pirenaico de Ecologia (Jaca, Spain) | 2024-11-08 | 1 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622405.source.xml | Natal dispersal is a key life-history trait determining fitness and driving population dynamics, genetic structure and species distributions. Despite existing evidence that not all phenotypes are equally likely to successfully establish in new areas, the mechanistic underpinnings of natal dispersal remain poorly understood. The propensity to disperse into a new environment can be favored by a high degree of phenotypic plasticity which facilitates local adaptation and may be achieved via epigenetic mechanisms, which modify gene expression and enable rapid phenotypic changes. Epigenetic processes occur in particular genomic regions (e.g. DNA methylation on CpG sites in vertebrates), and thus individual genomes may differ in their capacity to be modified epigenetically. This 'Epigenetic potential' (EP) may represent the range of phenotypic plasticity attainable by an individual, and be a key determinant of successful settlement in novel areas. We investigated the association between EP, quantified as the number of genome-wide CpG variants, and natal dispersal propensity in a long-term study population of Pied flycatchers (Ficedula hypoleuca) monitored since colonization of a new habitat 35 years ago. We tested this association at three levels, comparing EP between: i) individuals dispersing between and within habitat patches; ii) immigrants to the population and locally-born individuals; and iii) individuals from first (comprising colonizers or their direct descendants) and latter generations of the population (consisting of locally-born individuals, which did not show natal dispersal). Results show a significant, positive association between EP and dispersal propensity in comparisons i) and iii), but not ii). Furthermore, CpG variants were non-randomly distributed across the genome, suggesting species- and/or population-specific CpGs being more frequent in promoters and exons. Our findings point to EP playing a role in dispersal propensity at spatial and temporal scales, supporting the idea that epigenetically-driven phenotypic plasticity facilitates dispersal and environmental coping in free-living birds. | null | biorxiv |
10.1101/2024.11.06.622224 | Relative Effects of Habitat Amount and Fragmentation Per Se on the Genetic Diversity of The Glanville Fritillary Butterfly | Fernandez Multigner, L.; Bras, A.; DiLeo, M.; Saastamoinen, M. | Lola Fernandez Multigner | University of Helsinki, Finland | 2024-11-08 | 1 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622224.source.xml | Habitat loss and fragmentation are considered the key drivers of biodiversity loss. Understanding their relative roles is difficult as habitat loss and fragmentation tend to co-occur. It has been proposed that the total habitat amount available in the local landscape mainly drives species richness while fragmentation per se, the breaking apart of habitat independent of habitat amount, has negligible or even a positive effect on biodiversity. Several studies support this at the species richness level. Yet, the potential effects of fragmentation per se on genetic diversity at the landscape scale are understudied. Using the Glanville fritillary butterfly metapopulation in the Aland islands, we tested the effects of fragmentation per se on genetic diversity using a landscape-based approach and 2,610 individuals genotyped at 40 neutral SNP markers. We assessed the independent effect of habitat amount and fragmentation (i.e. number of patches) within the local landscape on the focal patch genetic diversity. The amount of habitat in the local landscape had a positive effect on genetic diversity, while fragmentation per se had a more negligible impact on the genetic diversity. Our results thus highlight that all fragments, even the small ones, likely contribute to the maintenance of genetic diversity of the focal population. | null | biorxiv |
10.1101/2024.11.06.622201 | Identifying parsimonious pathways of accumulation and convergent evolution from binary data | Giannakis, K.; Aga, O. N. L.; Moen, M. T.; Drange, P. G.; Johnston, I. | Iain Johnston | University of Bergen | 2024-11-08 | 1 | new results | cc_by | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622201.source.xml | How stereotypical, and hence predictable, are evolutionary and accumulation dynamics? Here we consider processes -- from genome evolution to cancer progression -- involving the irreversible accumulation of binary features (characters), which can be modelled as Markov processes on a hypercubic transition network. We seek subgraphs of such networks that can generate a given set of paired before-after observations and minimize a topological cost function, involving criteria on out-branching which are interpretable in terms of biological parsimony. A transition network supporting a single, deterministic dynamic pathway is maximally simple and lowest cost, and branches (corresponding to possibly different next steps) increase cost, particularly if these branches are "deep", occurring at early stages in the dynamics. In this sense, the lowest-cost subgraph measures how stereotypical the evolutionary or accumulation process is, and also identifies good start points for likelihood-based inference. The problem is solvable in polynomial time for cross-sectional observations by building on an existing method due to Gutin, and we provide a polynomial-time estimate in the more general case of pairs of observed states. We use this approach to define a "stereotypy index" reflecting the extent of evolutionary predictability. We demonstrate use cases in the evolution of antimicrobial resistance, organelle genomes, and cancer progression, and provide a software implementation at https://github.com/StochasticBiology/hyperDAGs . | null | biorxiv |
10.1101/2024.11.06.622341 | Backward collateral sensitivity can restore antibiotic susceptibility | Chowdhury, F. R.; Findlay, B. | Brandon Findlay | Concordia University | 2024-11-08 | 1 | new results | cc_no | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622341.source.xml | The prevalence of antibiotic resistance continues to rise, rendering many valuable drugs ineffective. Antibiotic cycling regimens that incorporate collateral sensitivity (CS), the phenomenon where resistance to one antibiotic leads to hypersensitivity to another, are hypothesized to slow the evolution of antibiotic resistance. However, the repeatability of CS interactions and their ability to drive bacterial extinction and resensitizations remain unclear. In this study, we thoroughly investigate four drug pairs proposed for cycling regimens with experimental evolution. We find that reported pairwise CS interactions are not always robust, and even when they are, forward CS (where resistance to drug A leads to hypersensitivity to drug B) does not reliably reduce resistance or promote bacterial extinction. Instead, we find that if evolution of resistance to drug B in naive cells is associated with CS to drug A, a phenomenon we term backward CS, drug A-resistant cells can be rendered more sensitive to A again when resistance to B develops. We describe the mechanism of resistance disruption via backward CS in an aminoglycoside-{beta}-lactam pair, where perturbation of the electron transport chain to inhibit aminoglycoside entry impairs {beta}-lactam efflux. Overall, we highlight the importance of applying antibiotics in the correct order in cycling regimens and identify robust CS interactions that may be used to design treatment regimens less likely to lead to resistance evolution. | null | biorxiv |
10.1101/2024.11.06.622284 | SelNeTime: a python package inferring effective population size and selection intensity from genomic time series data | Uhl, M.; de Navascues, M.; boitard, s.; Servin, B. | simon boitard | INRAE | 2024-11-08 | 1 | new results | cc_by_nc | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622284.source.xml | Genomic samples collected from a single population over several generations provide direct access to the genetic diversity changes occurring within a specific time period. This provides information about both demographic and adaptive processes acting on the population during that period. A common approach to analyze such data is to model observed allele counts in finite samples using a Hidden Markov model (HMM) where hidden states are true allele frequencies over time (i.e. a trajectory). The HMM framework allows to compute the full likelihood of the data, while accounting both for the stochastic evolution of population allele frequencies along time and for the noise arising from sampling a limited number of individuals at possibly spread out generations. Several such HMM methods have been proposed so far, differing mainly in the way they model the transition probabilities of the Markov chain. Following @par2019, we consider here the Beta with Spikes approximation, which avoids the computational issues associated to the Wright-Fisher model while still including fixation probabilities, in contrast to other standard approximations of this model like the Gaussian or Beta distributions. To facilitate the analysis and exploitation of genomic time series data, we present an improved version of Paris et al (2019)'s approach, denoted SelNeTime, whose computation time is drastically reduced and which accurately estimates effective population size in addition to the selection intensity at each locus. This method is implemented in a user friendly python package, which also allows to easily simulate genomic time series data under a user-defined evolutionary model and sampling design. | null | biorxiv |
10.1101/2024.11.07.622434 | Integrative cell bin segmentation on spatial transcriptomics by Voronoi | Lin, M. | Ming Lin | University of Nottingham | 2024-11-08 | 1 | new results | cc_by | genetics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622434.source.xml | Spatial transcriptomics is undergoing rapid advancements and iterations. It is a beneficial tool to significantly enhance our understanding of tissue organization and relationships between cells. Recent technological advancements have achieved subcellular resolution, providing much denser spot placement for downstream analysis. A key challenge for this following analysis is accurate cell segmentation and the assignment of spots to individual cells. The primary objective of this study was to evaluate the effectiveness of a new cell segmentation approach based on subcellular level spatial transcriptomic data by confirming nuclei positions and using Voronoi diagrams, compared to direct clustering with cellbin data. Our findings demonstrate that the Voronoi method not only outperforms traditional methods in providing clearer boundaries and better separation of cell types but also excels in preserving the most transcripts, addressing the issue of low capture efficiency. This integrative methodology presents a substantial advancement in spatial transcriptomics, offering improved cell type classification and spatial pattern recognition. All codes in the paper are available at the GitHub repository: https://github.com/Charlottttttte/Cell_Segmentation_Voronoi | null | biorxiv |
10.1101/2024.11.07.622475 | Metabolic and neuroactivity imbalances in plasma from aniridia patients with PAX6 haploinsufficiency | Cunha, D. L.; Kit, V.; Skinner, J.; Welch, A. A.; Moosajee, M. | Mariya Moosajee | UCL Institute of Ophthalmology, Department Brain Sciences, London, UK; Moorfields Eye Hospital NHS Foundation Trust, London, UK; The Francis Crick Institute, Lo | 2024-11-08 | 1 | new results | cc_by_nc_nd | genetics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622475.source.xml | PAX6 is a transcription factor crucial for the development of the eye, pancreas, and brain. Heterozygous variants resulting in PAX6 haploinsufficiency are the main genetic cause of congenital aniridia, characterized by both anterior and posterior ocular defects and sight loss. The extra-ocular features of PAX6 haploinsufficiency are becoming more widely recognised, with systemic manifestations like obesity, diabetes, and neurological/behavioural disorders being reported. In this study, we uncovered the metabolomic profile of the blood plasma from 25 PAX6-related aniridia patients compared to gender and age-matched controls. We found significant disruptions in lipid and energy metabolism, increased oxidative stress and neurotransmitters imbalances, as well as alterations linked to the gut microbiome. This study identified novel metabolic changes associated with PAX6 haploinsufficiency, providing evidence for the systemic aetiology of congenital aniridia and emphasizing the need for multidisciplinary management and further exploration into ocular and systemic therapeutic approaches. | null | biorxiv |
10.1101/2024.11.06.622344 | Evolutionarily guided transcription factor design programs novel T cell states | Takacsi-Nagy, O.; Hartman, A.; Chen, A. Y.; Yin, Y.; Reeder, G. C.; Kernick, C.; Lu, J.; McClellan, A. K.; Raposo, C. J.; Theberath, N. E.; Yan, P. K.; Eyquem, J.; Roth, T. L.; Satpathy, A. T. | Ansuman T Satpathy | Stanford University School of Medicine | 2024-11-08 | 1 | new results | cc_by_nc_nd | genetics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622344.source.xml | Protein-coding genes in the human genome evolved via modular rearrangement of domains from ancestral genes. Here, we develop a scalable, evolutionarily guided method to assemble novel protein-coding genes from constituent domains within a protein family, termed DESynR (Domain Engineered via Synthesis and Recombination) genes. Using primary human chimeric antigen receptor T cells as a model system, we find that the expression of DESynR Activator Protein-1 (AP-1) transcription factors (TFs) significantly outperforms the overexpression of natural AP-1 TFs in multiple functional assays in vitro and in vivo. Top DESynR AP-1 TFs exhibit non-intuitive architectures of constituent domains, including from TFs that are not canonically expressed in T cells. DESynR AP-1 TFs induce broad transcriptional and epigenetic reprogramming of T cells and, in some cases, lead to the development of non-natural T cell states, engaging gene expression modules from disparate human cell types. Taken together, we demonstrate that novel configurations of existing protein domains may uncover non-evolved genes that program cell states with therapeutically relevant functions. | null | biorxiv |
10.1101/2024.11.07.622399 | GCfix: A Fast and Accurate Fragment Length-SpecificMethod for Correcting GC Bias in Cell-Free DNA | Rafeed, C.; Poh, Z. W.; Jacobsen Skanderup, A.; Wong, L. | Chowdhury Rafeed | National University of Singapore | 2024-11-08 | 1 | new results | cc_by_nc_nd | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622399.source.xml | Motivation: Cell-free DNA (cfDNA) analysis has wide-ranging clinical applications due to its non-invasive nature. However, cfDNA fragmentomics and copy number analysis can be complicated by GC bias. There is a lack of GC correction software based on rigorous cfDNA GC bias analysis. Furthermore, there is no standardized metric for comparing GC bias correction methods across large sample sets, nor a rigorous experiment setup to demonstrate their effectiveness on cfDNA data at various coverage levels. Results: We present GCfix, a method for robust GC bias correction in cfDNA data across diverse coverages. Developed following an in-depth analysis of cfDNA GC bias at the region and fragment length levels, GCfix is both fast and accurate. It works on all reference genomes and generates correction factors, tagged BAM files, and corrected coverage tracks. We also introduce two orthogonal performance metrics for (1) comparing the fragment count density distribution of GC content between expected and corrected samples, and (2) evaluating coverage profile improvement post-correction. GCfix outperforms existing cfDNA GC bias correction methods on these metrics. Availability: GCfix software and code for reproducing the figures are publicly accessible on GitHub. | null | biorxiv |
10.1101/2024.11.07.619809 | Image-based DNA Sequencing Encoding for Detecting Low-Mosaicism Somatic Mobile Element Insertions | Tan, M.; Lin, Z.; Chen, Z.; Park, J.; He, Z.; Zhou, H.; Lee, E. A.; Gao, Z.; Zhu, X. | Xiaowei Zhu | City University of Hong Kong | 2024-11-08 | 1 | new results | cc_by_nc_nd | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.619809.source.xml | Active LINE-1 (L1), Alu, and SVA mobile elements in the human genome are capable of retrotransposition, resulting in novel mobile element insertions (MEIs) in both germline and somatic tissues. Detecting MEIs through DNA sequencing relies on supporting reads overlapping MEI junctions; however, artifacts from DNA amplification, sequencing, and alignment errors produce numerous false positives. Systematic detection of somatic MEIs, particularly those with low mosaicism, remains a significant challenge. Previous methods had required a high number of supporting reads which limits the detection sensitivity, or human inspections that are susceptible to biases. Here, we developed RetroNet, an algorithm that encodes MEI-supporting sequencing reads into images, and employs a deep neural network to identify somatic MEIs with as few as two reads. Trained on extensive and diverse datasets and benchmarked across various conditions, RetroNet surpasses previous methods and eliminates the need for extensive manual examinations. When applied to bulk whole genome sequencing of a cancer cell line, RetroNet achieved an average precision of 0.885 and recall of 0.845 for detecting somatic L1 insertions, including four true mutations with only two supporting reads. RetroNet is applicable to the rapidly generated short-read sequencing data and has the potential to provide further insights into the functional and pathological implications of somatic retrotranspositions. | null | biorxiv |
10.1101/2024.11.06.622371 | The genome of the sapphire damselfish Chrysiptera cyanea: a new resource to support further investigation of the evolution of Pomacentrids | Gairin, E.; Miura, S.; Takamiyagi, H.; Herrera, M.; Laudet, V. | Emma Gairin | Okinawa Institute of Science and Technology | 2024-11-08 | 1 | new results | cc_by | genomics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622371.source.xml | The number of high-quality genomes is rapidly growing across taxa. However, it remains limited for coral reef fish of the Pomacentrid family, with most research focused on anemonefish. Here, we present the first assembly for a Pomacentrid of the genus Chrysiptera. Using PacBio long-read sequencing with a coverage of 94.5x, the genome of the Sapphire Devil, Chrysiptera cyanea was assembled and annotated. The final assembly consisted of 896 Mb pairs across 91 contigs, with a BUSCO completeness of 97.6%. 28,173 genes were identified. Comparative analyses with available chromosome-scale assemblies for related species identified contig-chromosome correspondences. This genome will be useful to use as a comparison to study the specific adaptations linked to symbiosis life of the closely related anemonefish. Furthermore, this species is present in most tropical coastal areas in the Indo-West Pacific and could become a model for environmental monitoring. This work will allow to expand coral reef research efforts and highlights the power of long-read assemblies to retrieve high quality genomes. | null | biorxiv |
10.1101/2024.11.06.621276 | Development of a Multifunctional Extracorporeal Life Support (ECLS) System for Lung and Kidney Support: The Pneuma-K ECLS System | Kwon, J.; Weiss, D. J.; Lee, P. C.; Lee, J. K. | Jake K. Lee | Exorenal Inc. | 2024-11-08 | 1 | new results | cc_no | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.621276.source.xml | Multi-organ failure (MOF), particularly in the coexistence of acute kidney injury (AKI) and acute lung injury (ALI), presents a significant challenge in intensive care units (ICU) and is associated with exceedingly high mortality rates. Respiratory and renal failures are frequently managed by extracorporeal membrane oxygenation (ECMO) and continuous renal replacement therapy (CRRT), respectively. However, employing these therapies using separate devices requires specialized facilities, adds to complexity, and increases the risks of clotting due to the extensive artificial surface areas involved. Therefore, an integrated device capable of providing simultaneous respiratory and renal support is essential. This paper introduces the Pneuma-K ECLS system, which incorporates a multifunctional detoxifying filter (MDF) capable of performing gas exchange and renal replacement in a single cartridge. Ex-vivo blood tests confirmed the ability of the MDF to oxygenate blood, remove carbon dioxide, and eliminate uremic toxins. In addition, animal experiments demonstrated the considerable clinical potential of this novel integrated extracorporeal life support approach. Integrating respiratory and renal support into a singular device could mitigate risks, conserve resources, and enhance the survival rates of critically ill patients suffering from concurrent lung and kidney failure. | null | biorxiv |
10.1101/2024.11.06.622338 | Impact of Paraben on Uterine Collagen: An Integrated and Targeted Correlative Approach Using Second Harmonic Generation Microscopy, Nanoindentation, and Atomic Force Microscopy | Arshee, M. R.; Shukla, R.; Li, J.; BAGCHI, I. C.; Ziv-Gal, A.; Johnson, A. J. W. | Amy J Wagoner Johnson | University of Illinois at Urbana-Champaign | 2024-11-08 | 1 | new results | cc_by | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622338.source.xml | This study investigates the structural and mechanical changes in uterine collagen following exposure to propylparaben (PP), using a combined methodology of Second Harmonic Generation (SHG) microscopy, Nanoindentation (NI), and Atomic Force Microscopy (AFM). SHG analysis identified significant disorganization in collagen fibril orientation in the circumferential layer and heterogeneous distribution of regions with elevated forward to backward ratios (F/B) across all uterine layers due to PP exposure. High F/B can indicate multiple potential fibril-level changes like thickened fibrils, higher crosslinking, fibril disorganization - changes not fully decipherable by SHG alone. Recognizing this limitation, the study employs NI and AFM to provide complementary mechanical and nanoscale insights. NI revealed increased indentation modulus in the exposed uteri, suggesting increased stiffness. Co-registration of the indentation response with SHG parameters uncovered that elevated F/B regions show enhanced mechanical stiffness, suggesting a fibrotic transformation following PP exposure. AFM was specifically performed on regions identified by SHG as having low or high F/B, providing the necessary nanoscale resolution to elucidate the structural changes in fibrils that are likely responsible for the observed alterations. This approach confirmed the presence of disordered and entangled collagen fibrils in the circumferential layer in all regions and an increase in fibril diameter in the high F/B regions in the exposed uteri. Together, these findings demonstrate significant alterations in collagen architecture due to PP exposure, revealing disruptions at both the fiber and fibril levels and highlighting the potential for broader applications of the multi-scale, multi-modal approach in collagenous tissue studies. | null | biorxiv |
10.1101/2024.11.06.621942 | Harnessing micrometer-scale tPA beads for high plasmin flux and accelerated fibrinolysis | Osmond, M. J.; Dabertrand, F.; Quillinan, N.; Su, E. J.; Lawrence, D. A.; Marr, D. W. M.; Neeves, K. B. | Keith B Neeves | University of Colorado, Denver | Anschutz Medical Campus | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioengineering | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.621942.source.xml | Rapid restoration of blood flow is critical in treating acute ischemic stroke. Current fibrinolytic therapies using tissue plasminogen activator (tPA) are limited by low recanalization rates and risks of off-target bleeding. Here, we present a strategy using tPA immobilized on micrometer-scale beads to enhance local plasmin generation. We synthesized tPA-functionalized beads of varying sizes (0.1 m and 1.0 m) and evaluated their efficacy. In vitro assays demonstrated that 1.0 m tPA-beads generated higher plasmin flux compared to free tPA and 0.1 m beads, overcoming antiplasmin inhibition and promoting a self-propagating wave of fibrinolysis. In a murine model of acute ischemic stroke, intravenous administration of 1.0 m tPA-beads at doses nearly two orders of magnitude lower than the standard free tPA dose led to rapid and near-complete thrombus removal within minutes. This approach addresses kinetic and transport limitations of current therapies and may reduce the risk of hemorrhagic complications. | null | biorxiv |
10.1101/2024.11.06.622369 | scHiCcompare: an R package for differential analysis of single-cell Hi-C data | Nguyen, M.; Wall, B. P. G.; Harrell, J. C.; Dozmorov, M. G. | Mikhail G Dozmorov | Virginia Commonwealth University | 2024-11-08 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622369.source.xml | Changes in the three-dimensional (3D) structure of the human genome are key indicators of cancer and developmental disorders. Techniques like chromatin conformation capture (Hi-C) have been developed to study these global 3D structures, typically requiring millions of cells and an extremely high sequencing depth (around 1 billion reads per sample) for bulk Hi-C. In contrast, single-cell Hi-C (scHi-C) captures 3D structures at the individual cell level but faces significant data sparsity, marked by a high proportion of zeros. While differential analysis methods exist for bulk Hi-C data, they are limited for scHi-C data. To address this, we developed a method for differential scHi-C analysis, building on existing techniques in the HiCcompare R package. Our approach imputes sparse scHi-C data by considering genomic distances and creates pseudo-bulk Hi-C matrices by summing condition-specific data. The data are normalized using LOESS regression, and differential chromatin interactions are detected via Gaussian Mixture Model (GMM) clustering. Our workflow outperforms existing methods in identifying differential chromatin interactions across various genomic distances, fold changes, resolutions, and sample sizes in both simulated and experimental contexts. This allows for effective detection of cell type-specific differences in chromatin structure, which has meaningful associations with biological and epigenetic features. Our method is implemented in the scHiCcompare R package, available at https://github.com/dozmorovlab/scHiCcompare. | null | biorxiv |
10.1101/2024.11.06.622318 | BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories | Mukhaleva, E.; Manookian, B.; Chen, H.; Ma, N.; Wei, W.; Urbaniak, K.; Gogoshin, G.; Bhattacharya, S.; Vaidehi, N.; RODIN, A. S.; Branciamore, S. | Sergio Branciamore | Beckman Research Institute of the City of Hope | 2024-11-08 | 1 | new results | cc_by_nc | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622318.source.xml | Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical datasets. Concurrently, our ability to perform long-timescale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially. However, the analysis of MD simulation trajectories has not been data-driven but rather dependent on the user's prior knowledge of the systems, thus limiting the scope and utility of the MD simulations. Recently, we pioneered using BNM for analyzing the MD trajectories of protein complexes. The resulting BN models yield novel fully data-driven insights into the functional importance of the amino acid residues that modulate proteins' function. In this report, we describe the BaNDyT software package that implements the BNM specifically attuned to the MD simulation trajectories data. We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software's uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. This provides a powerful and versatile mechanism for users to control the workflow. As an application example, we have utilized this methodology and associated software to study how membrane proteins, specifically the G protein-coupled receptors, selectively couple to G proteins. The software can be used for analyzing MD trajectories of any protein as well as polymeric materials. | null | biorxiv |
10.1101/2024.11.06.622096 | Single-cell atlas of the human immune system reveals sex-specific dynamics of immunosenescence | Rios, M. S.; Ripoll-Cladellas, A.; Omidi, F.; Ballouz, S.; Alquicira-Hernandez, J.; Oelen, R.; Franke, L.; van der Wijst, M. G. P.; Powell, J. E.; Mele, M. | Marta Mele | Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona, Spain | 2024-11-08 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622096.source.xml | Immunosenescence, the gradual deterioration of the immune system with age, leads to an increased susceptibility to a range of diseases associated with immune dysfunction. Notably, sex is an important variable underlying how immune aging unfolds, as, for instance, autoimmunity develops with aging differently between males and females. Even though some clinical and molecular differences have been identified between male and female immunosenescence, it is not known to what extent sex affects the dynamic composition of immune cells over time. Here, we analyze a large single-cell RNA-sequencing dataset of peripheral blood mononuclear cells from a sex-balanced cohort of 982 human donors providing novel transcriptional and cellular insights into immune aging at an unprecedented resolution. We uncover that aging induces cell type-dependent and sex-specific transcriptional shifts that translate into a differential abundance of distinct immune cell subpopulations. These shifts predominantly involve translation-related genes, indicating a strong link between transcriptional and translational throughput with cell function and consequent immune cell composition. This sexual dimorphism overlaps known autoimmune disease-related genetic variants and results in the differential enrichment of functionally distinct immune populations. Specifically, we uncover that a cytotoxic CD8+ T effector memory subpopulation with an NK-like phenotype accumulates with age only in females and identify a distinct B cell subpopulation that expands with age exclusively in males, representing novel sex-specific hallmarks of immune aging. Our findings underscore the hidden complexity of immune aging and demonstrate the value of high-resolution, single-cell analyses in large population cohorts. This research paves the way for future sex-specific interventions targeting immunosenescence to ultimately promote a personalized approach to foster healthy aging. | null | biorxiv |
10.1101/2024.11.06.622393 | Tardigrade Dsup: Interactions with DNA and protection of cells from oxidative stress | Ni, G. S.; Su, H.; Zhu, Y.; Dhiman, A.; Zhou, H.-X.; Lin, W.; Hao, N. | Nan Hao | University of California San Diego | 2024-11-08 | 1 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622393.source.xml | The remarkable capability of Tardigrade to survive under extreme conditions has been partially attributed to Dsup, an intrinsically disordered, highly positively charged protein. Dsup has been shown to bind to DNA in vitro, a property that has been associated with the capability of Dsup to exhibit stress-protective effects when expressed in mammalian cells. However, DNA binding of Dsup has not been visualized in living cells and expression of Dsup in different cell types was associated with either protective or detrimental effects. In addition, the effect of Dsup expression has not been clearly demonstrated at the organism level. Here we combined molecular dynamics (MD) simulations and fluorescence lifetime imaging microscopy (FLIM)-Forster resonance energy transfer (FRET) to interrogate Dsup-DNA interactions and demonstrated Dsup binding to DNA in living mammalian cells. Furthermore, Dsup expression in both HEK293T cells and yeast enhanced cell survival in the presence of hydrogen peroxide, suggesting that the presence of Dsup allows both mammalian and yeast cells to better cope with oxidative stress conditions. This study provides a better understanding of the property and functional role of Dsup and lays a foundation to explore new approaches to enhance stress resistance. | null | biorxiv |
10.1101/2024.11.06.622276 | Denoising Reveals Low-Occupancy Populations in Protein Crystals | Fadini, A.; Apostolopoulou, V.; Lane, T. J.; van Thor, J. J. | Alisia Fadini | Cambridge Institute for Medical Research | 2024-11-08 | 1 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622276.source.xml | Advances in structural biology increasingly focus on uncovering protein dynamics and transient or weak macromolecular complexes. Such studies require modeling of low-occupancy species, for instance time-evolving intermediates and bound ligands. In protein crystallography, difference maps that compare paired perturbed and reference datasets are a powerful way to identify and aid modeling of low-occupancy species. Current methods to generate difference maps, however, rely on manually tuned parameters and, in cases of weak signal due to low occupancy, can fail to extract clear, chemically interpretable signals. We address these issues, first by showing negentropy is an effective metric to assess difference map quality and can therefore be used to automatically determine parameters needed during difference map calculation. Leveraging this, we apply total variation denoising, an image restoration technique that requires a choice of regularization parameter, to crystallographic difference maps. We show that total variation denoising improves map signal-to-noise and enables us to estimate the latent phase contribution of low-occupancy states. This technology opens new possibilities for time-resolved and ligand-screening crystallography in particular, allowing the detection of states that previously could not be resolved due to their inherently low occupancy. | null | biorxiv |
10.1101/2024.11.07.622398 | Elucidating the Mechanism Underlying UBA7-UBE2L6 Disulfide Complex Formation | Chen, P.-T.; Yeh, J.-Y.; Weng, J.-H.; Wu, K.-P. | Kuen-Phon Wu | Academia Sinica | 2024-11-08 | 1 | new results | cc_by_nc_nd | biophysics | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622398.source.xml | We elucidate cryo-EM structure and formation of the ubiquitin-associated bovine UBA7-UBE2L6 disulfide complex, shedding light on a highly specific and evolutionarily conserved mechanism governing ISG15 conjugation, a pivotal process in the immune response. UBA7 displays a unique capacity to recognize UBE2L6, distinct from this latter homolog UBE2L3, highlighting the intricacies of cellular regulation. Inter-species interactions of the resulting complex further underscore its significance. We characterize three crucial factors that influence UBA7-UBE2L6 disulfide complex formation: (1) strong binding affinity and specificity; (2) conformational differences in the catalytic cysteine capping loop (CCL); and (3) increased thiolate/thiol ratios at catalytic cysteines. Modification of any of these factors profoundly impacts complex activation and the ISG15 transfer cascade. This redox-sensitive complex implies a link between oxidative stress and regulation of the immune response, highlighting a potential therapeutic target for modulating immune reactions arising from infections and inflammatory conditions. | null | biorxiv |
10.1101/2024.11.07.622423 | Copper induces p53 unfolding in cancer cells, resulting in invasion and chemoresistance | Muller, P. A. J.; Bell, S. J.; Richards, H. L.; Massey, E. J.; Newson, Z.; Tarrant, E.; Morrison, M.; Galvin, M.; Simpson, K.; Le Quesne, J.; Aschauer, L.; von Grabowiecki, Y. | Patricia A. J. Muller | Durham University | 2024-11-08 | 1 | new results | cc_no | cancer biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622423.source.xml | Copper has been shown to play an important role in cancers, enhancing cell proliferation, remodelling the microenvironment and enhancing the function of oncogenes. Here we show that copper turns the tumour suppressor p53 protein into a pro-oncogenic protein. Mutations in the TP53 gene often lead to expression of various mutant p53 proteins. Mutant proteins often lose some or all wild type function and gain novel pro-tumourigenic functions, which can be partially attributed to protein unfolding. Here we show that copper accumulates in tumours, unfolds WTp53 and promotes chemoresistance. Unfolding of WT p53 results in interaction with mutant p53-specific interacting proteins TAp63 and Ago2 and promotes invasion. Interestingly, partially-functional p53 mutants that are frequently observed in lung cancers, are more affected by copper than WTp53. Our results suggest that small increases in copper impair WT p53 function and augment mutant p53 function, which could partially be restored by the chelator Trien. | null | biorxiv |
10.1101/2024.11.07.622424 | YY1 Enhances the Stability of HIF-1α Protein by Interacting with NUSAP1 in Macrophages within the Prostate Cancer Microenvironment | Li, W.; Chen, S.; Lu, J.; Mao, W.; Zheng, S.; Zhang, M.; Wu, T.; Chen, Y.; Lu, K.; Chu, C.; Shu, C.; Hou, Y.; Yang, X.; Shi, N.; Chen, Z.; Zhang, L.; Zhang, L.; Na, R.; Chen, M.; Ju, S.; Zhang, D.; Ma, Y.; Xu, B. | Bin Xu | Southeast University | 2024-11-08 | 1 | new results | cc_by | cancer biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622424.source.xml | Immune checkpoint therapy for prostate cancer (PCa) has failed in clinical trials; however, the precise underlying mechanisms involved remain elusive. PCa, a classic "immune-cold" tumor, is characterized by an immunosuppressive tumor microenvironment. Within this milieu, macrophages, the predominant immune cell population, have a propensity to infiltrate the hypoxic zones of tumors. In a previous study, we showed that Yin Yang 1 (YY1) is highly expressed in macrophages in PCa tissues. Here, through multiplexed imaging mass cytometry (IMC) of a PCa tissue microarray, we further demonstrate that YY1+ macrophages aggregate in hypoxic areas of tumors and that hypoxia promotes the phase separation of YY1 in the nucleus by increasing YY1 tyrosine phosphorylation in macrophages. Furthermore, YY1 binds to NUSAP1 and promotes the SUMOylation of HIF-1, which promotes phase separation and stabilization of the HIF-1 protein. We also demonstrated that either treatment with a small molecule inhibitor (tenapanor) to decrease the YY1-NUSAP1-HIF-1 interaction or myeloid-specific YY1 gene knockout impairs subcutaneous PCa tumor formation. Furthermore, we present a first-generation tetrahedral DNA nanostructure (TDN) based on the proteolysis targeting chimera (PROTAC) technique, named YY1-DcTAC, which targets and degrades YY1 in tumor-associated macrophages. In a PCa mouse model, YY1-DcTAC exhibited prolonged drug efficacy, robust macrophage-specific responsiveness, potent antitumor effects, and increased CD8+ T cell tumor infiltration. In summary, our findings underscore the pivotal role of YY1 within the hypoxia/HIF-1 pathway in tumor-associated macrophages and affirm the therapeutic potential of targeting YY1 for treating PCa. | null | biorxiv |
10.1101/2024.11.06.622394 | Uttroside B, a US-FDA-Designated Orphan Drug Against Hepatocellular Carcinoma (HCC), Impedes Non-alcoholic Steatohepatitis (NASH) and NASH -Induced HCC | Rayginia, T. P.; Keerthana, C. K.; Aiswarya, S. U.; Sadiq, S. C.; S, J.; Varma, S. S.; P, M. J.; Swetha, M.; Retnakumary, A. P.; Nath, L. R.; Kalimuthu, K.; Jaikumar, V. S.; Sundaram, S.; Anto, N. P.; Isakov, N.; Harikumar, K. B.; Lankalapalli, R. S. B.; Anto, R. J. | Ruby John Anto | Centre of Excellence in Nutraceuticals, Bio360 LifeScience Park, Thiruvananthapuram | 2024-11-08 | 1 | new results | cc_no | cancer biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622394.source.xml | Introduction: Non-alcoholic steatohepatitis (NASH) is characterized by excessive accumulation of fat, accompanied by inflammation and liver injury. NASH can lead to chronic conditions like fibrosis and cirrhosis, and has an elevated risk of progressing to hepatocellular carcinoma (HCC). Currently there are no FDA-approved drugs for the treatment of NASH. Objectives: Our discovery of Uttroside B (Utt-B), a phytosaponin isolated from Solanum nigrum Linn., which exhibits remarkable anti-HCC potential, has gained global recognition and is currently a US-FDA-designated orphan drug against HCC. The present study highlights Utt-B as an anti-NASH molecule, by utilizing a High-Fat-Diet murine model, and as an inhibitor to the progression of NASH to HCC, using a streptozotocin-induced steatohepatitis-derived HCC animal model, thereby warranting its further validation as a propitious candidate drug molecule against NASH and NASH-induced HCC. Methods: High fat diet-induced NASH and streptozotocin-induced steatohepatitis-derived HCC were developed in C57BL/6 mice. Utt-B was administered intraperitoneally. q-PCR, immunoblotting and staining techniques such as Haematoxylin and eosin, Oil Red O, Sirius Red and Massons Trichrome, were performed to assess the therapeutic potency of Utt-B against NASH. Nanostring n-Counter analysis was conducted to verify the anti-fibrotic potential of Utt-B in NASH-induced HCC mouse model. Results: Utt-B ameliorates the pathological features such as, steatosis, hepatocyte ballooning and inflammation associated with NASH. Utt-B up-regulates the expression of autophagy markers ATG7, Beclin-1 and LC-III and down-regulates the expression of -SMA, the indicator protein for the activation of hepatic stellate cells. Utt-B hinders the development of fibrosis and halts the progression of NASH to HCC in NASH-induced HCC mouse model. Conclusion: Our investigation reveals that Utt-B effectively alleviates NASH and abrogates its progression to HCC. As no treatment options are currently available against NASH, our findings are very relevant and strengthen the prospect of developing Utt-B as a potent drug for the treatment of NASH and NASH-induced HCC. Keywords: Uttroside B; NASH; HCC; NAFLD; Lipogenesis; Fibrogenesis | null | biorxiv |
10.1101/2024.11.06.622320 | Topoisomerase IIb binding underlies frequently mutated elements in cancer genomes | Uusküla-Reimand, L.; Lee, C. A.; Oh, R. H.; Klein, Z. P.; Adler, N.; Alvi, S. A.; Langille, E.; Pasini, E.; Cheng, K. C.; Abd-Rabbo, D.; Hou, H.; Tsai, R.; Bhat, M.; Schramek, D.; Wilson, M. D.; Reimand, J. | Jüri Reimand | University of Toronto | 2024-11-08 | 1 | new results | cc_by_nc | cancer biology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.622320.source.xml | Type-II topoisomerases resolve topological stress in DNA through controlled double-strand breaks. While TOP2A is a chemotherapy target in proliferating cells, the ubiquitously expressed TOP2B is a potential off-target. Here we explore roles of TOP2B in mutagenesis by generating DNA-binding maps of TOP2B, CTCF, and RAD21 in human cancer samples and analysing these maps for driver mutations and mutational processes in 6500 whole cancer genomes. TOP2B-CTCF-RAD21 and TOP2B-RAD21 sites are enriched in somatic mutations and structural variants (SVs), especially at evolutionary conserved sites displaying high transcription and long-range chromatin interactions. TOP2B binding underlies SVs and hotspot mutations in cancer-driving genes such as TP53, MYC, FOXA1, and VHL, and many cis-regulatory elements. We show that the TOP2B-bound mutational hotspot at RMRP drives tumor initiation and growth in vivo. These data highlight TOP2B as a protector of the genome from topological challenges whose aberrant activity promotes driver and passenger mutations in cancer genomes. | null | biorxiv |
10.1101/2024.11.07.622127 | Human adipose-derived mesenchymal stromal cells improved wound healing in enterocutaneous fistulizing disease mouse model | Marsiano, N.; Levi, Y.; Schneider, P.; Schouten, I.; Nisim-Eliraz, E.; Yagel, S.; Kong, K.-F.; Lombardo, E.; Shpigel, N. Y. | Nahum Y Shpigel | The Koret School of Veterinary Medicine, Hebrew University of Jerusalem, Israel | 2024-11-08 | 1 | new results | cc_by_nd | pathology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622127.source.xml | A significant complication of Crohn disease is the formation of perianal fistulas. While local application of human adipose tissue-derived mesenchymal stromal cells (AT-MSC INN Darvadstrocel, Takeda) is an approved therapy for this condition, challenges in studying human clinical tissue and the absence of a robust experimental model have hindered deeper understanding of the preclinical efficacy and mechanisms behind the therapy. We have developed a model that closely mimics the clinical scenario, using human gut tissue transplanted subcutaneously into SCID mice. In this model, enterocutaneous fistulas are reliably induced by combining imiquimod-induced psoriatic dermatitis above the transplant with systemic lipopolysaccharide (LPS), a major component of the bacterial cell wall. Similar to clinical observations, local application of AT-MSC significantly improved fistula wound healing and re-epithelialization. This model system enabled comprehensive tissue harvesting for histopathological analysis, spatial transcriptomics, and protein profiling. Our findings demonstrate that AT-MSC applied around the fistula wound survive for up to three weeks, migrating into the fistula tract and further into the inflamed human gut tissue. Within the fistula tract, AT-MSCs acquired immune-active properties, with increased expression of SOD2 and CCL2, and were associated with a substantial population of M2 macrophages. In contrast, AT-MSC located in healthy tissue near the fistula remained stationary, adopting a fibroblast-like phenotype within a collagen-rich extracellular matrix. These preclinical results support the safety and efficacy of AT-MSC for treating fistulizing gut disease. Furthermore, our data suggest that the inflamed fistula tract acts as a scaffold promoting AT-MSC activity and migration. Enhancing SOD2 and CCL2 expression through pre-activation or genetic modification may further improve the therapeutic potential of these cells. | null | biorxiv |
10.1101/2024.11.06.616796 | The Trade-Off Between Torque and Power with Speed: A Study of Shoulder Performance During an Isokinetic and Multiplanar Task | Lee, K. D. L.; Rainbow, M. J.; Lee, E. C. S. | Michael J Rainbow | Queen\\\'s University | 2024-11-08 | 1 | new results | cc_by_nc | physiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.06.616796.source.xml | The human shoulder likely evolved under selective pressures favouring diverse tasks that require high mobility, speed, and torque. For example, humans are uniquely adept at high-speed and accurate throwing. Prior work has aimed to quantify the kinematics and kinetics of upper limb movements in isometric or uniplanar motions. However, we still do not fully understand the trade-offs of shoulder torque and power with angular velocity during functional tasks that are reflective of demands that may be relevant to the shoulder's evolution. We developed a novel approach for upper limb 3D inverse dynamic calculations by integrating motion capture with an instrumented cable machine. Twenty-five participants performed a crossbody, isokinetic upper limb motion at various cable speeds in a rigid and free torso condition (self-imposed). Shoulder torque decreased significantly (p < 0.05) with increasing angular velocity in 19 and 16 participants for the constrained and unconstrained conditions, respectively. Shoulder power increased significantly (p < 0.05) with angular velocity for 6 and 11 participants for constrained and unconstrained, respectively. T-tests revealed no statistical difference between the torso conditions for torque and power against angular velocity. Our findings suggest that despite having a trade-off in torque and velocity, the shoulder may be tuned to produce power over a wide range of velocities independent of energy transfer from the lower extremities. | null | biorxiv |
10.1101/2024.11.07.622441 | Unlocking the power of gene banks: diversity in base growth temperature provides opportunities for climate-smart agriculture | Gambart, C.; van Wesemael, J.; Swennen, R.; Tardieu, F.; Carpentier, S. | Sebastien Carpentier | Alliance of Bioversity International and CIAT | 2024-11-08 | 1 | new results | cc_by_nc_nd | physiology | https://www.biorxiv.org/content/early/2024/11/08/2024.11.07.622441.source.xml | Implementation of context-specific solutions, including cultivation of varieties adapted to current and future climatic conditions, were found to be effective in establishing resilient, climate-smart agricultural systems. Gene banks play a pivotal role in this. However, a large fraction of the collections remains neither genotyped nor phenotyped. Hypothesising that significant genotypic diversity in Musa temperature responses exists, this study aimed to assess the diversity in the worlds largest banana gene bank in terms of base temperature (Tbase) and to evaluate its impact on plant performance in the East African highlands during a projected climate scenario. 116 gene bank accessions were evaluated in the BananaTainer, a tailor-made high throughput phenotyping installation. Plant growth was quantified in response to temperature and genotype-specific Tbase were modelled. Growth response of two genotypes was validated under greenhouse conditions, and gas exchange capacity measurements were made. The model revealed genotype-specific Tbase, with 30 % of the accessions showing a Tbase below the reference of 14 C. The Mutika/Lujugira subgroup, endemic to the East African highlands, appeared to display a low Tbase, although within subgroup diversity was revealed. Greenhouse validation further showed low T sensitivity/tolerance to be related to the photosynthetic capacity. This study, therefore, significantly advances the debate of within species diversity in temperature growth responses, while at the same time unlocking the power of gene banks. Moreover, we provide a high throughput method to reveal the existing genotypic diversity in temperature responses, paving the way for future research to establish climate-smart varieties. | null | biorxiv |