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10.1101/2024.11.08.622131 | Cell fate determination is associated with changes in competing transcriptional units in the human GATA1 and GATA2 lineage-determining transcription factors | Anderson, E. M.; Li, H.; Ruesch, M.; Wright, P. W.; Freud, A. G.; Anderson, S. K. | Stephen K Anderson | National Cancer Institute | 2024-11-09 | 1 | new results | cc_no | developmental biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622131.source.xml | The GATA1 and GATA2 transcription factors play a central role in early cell fate decisions in hematopoietic progenitor cells. Although the switch from GATA2 to GATA1 occupancy at GATA-binding sites in erythroblast-specific genes has been extensively studied, the underlying molecular mechanisms controlling this switch are not fully elucidated. An antisense promoter in the 5' region of the GATA2 gene produces a long non-coding RNA that has been shown to affect GATA2 transcription and erythroblast differentiation. The recent identification of an antisense promoter in the first intron of the GATA1 gene indicates that similar promoter competition mechanisms operate in these genes, potentially controlling GATA1/GATA2 levels in a probabilistic manner. In the current study we perform a comprehensive evaluation of GATA1 and GATA2 transcripts in human CD34 progenitors either freshly isolated or differentiated in vitro and the human leukemia cell lines K562 and HL60. The ratio of competing sense and antisense transcripts varied significantly with differentiation status, suggesting that promoter competition controls cell fate decisions. Treatment of HL60 cells with differentiating agents resulted in significant changes in the ratio of GATA2 sense to antisense promoter activity, in agreement with previous results showing that sense and antisense transcription are associated with distinct cellular phenotypes. | null | biorxiv |
10.1101/2024.11.08.622587 | A comprehensive representation of selection at loci with multiple alleles that allows complex forms of genotypic fitness | Vellnow, N.; Gossmann, T. I.; Waxman, D. | Toni Ingolf Gossmann | TU Dortmund University | 2024-11-09 | 1 | new results | cc_by_nc_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622587.source.xml | Genetic diversity is central to the process of evolution. Both natural selection and random genetic drift are influenced by the level of genetic diversity of a population; selection acts on diversity while drift samples from it. At a given locus in a diploid population, each individual carries only two alleles, but the population as a whole can possess a much larger number of alleles, with the upper limit constrained by twice the population size. This allows for many possible types of homozygotes and heterozygotes. Moreover, there are biologically important loci, for example those related to the MHC complex, the ABO blood types, and cystic fibrosis, that exhibit a large number of alleles. Despite this, much of population genetic theory, and data analysis, are limited to considering biallelic loci. However, to the present, what is lacking is a flexible expression for the force of selection that allows an arbitrary number of alleles (and hence an arbitrary number of heterozygotes), along with a variety of forms of fitness. In this work, we remedy this absence by giving an analytical representation of the force of selection that emphasises the very different roles played by the diversity of the population, and the fitnesses of different genotypes. The result presented facilitates our understanding and applies in a variety of different situations involving multiple alleles. This includes situations where fitnesses are: additive, multiplicative, randomly fluctuating, frequency-dependent, and it allows fitnesses which involve explicit gene interactions, such as heterozygote advantage. | null | biorxiv |
10.1101/2024.11.08.622694 | Small molecule oxybutynin rescues proliferative capacity of complex III-defective MPCs | Qu, Y.; Edwards, K.; Li, M.; Liu, Y.; Tsai, P.-Y.; Cheng, C.; Blum, J.; Acor, N.; Oshoe, T.; Rooney, K.; Walter, C.; Thirumlaikumar, V. P.; Thalacker-Mercer, A.; Skirycz, A.; Barrow, J. | Joeva Barrow | Cornell University | 2024-11-09 | 1 | new results | cc_no | cell biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622694.source.xml | Mitochondrial disease encompasses a group of genetically inherited disorders hallmarked by an inability of the respiratory chain to produce sufficient ATP. These disorders present with multisystemic pathologies that predominantly impact highly energetic tissues such as skeletal muscle. There is no cure or effective treatment for mitochondrial disease. We have discovered a small molecule known as oxybutynin that can bypass Complex III mitochondrial dysfunction in primary murine and human skeletal muscle progenitor cells (MPCs). Oxybutynin administration improves MPC proliferative capacity, enhances cellular glycolytic function, and improves myotube formation. Mechanistically, results from our isothermal shift assay indicates that oxybutynin interacts with a suite of proteins involved in mRNA processing which then trigger the upregulation biological pathways to circumvent CIII mitochondrial dysfunction. Taken together, we provide evidence for the small molecule oxybutynin as a potential therapeutic candidate for the future treatment of CIII mitochondrial dysfunction. | null | biorxiv |
10.1101/2024.11.08.622727 | Challenges in inferring breathing rhythms from olfactory bulb local field potentials | Rafilson, S. E.; Hess, N.; Findley, T. M.; Smear, M. | Matt Smear | University of Oregon | 2024-11-09 | 1 | new results | cc_by_nc | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622727.source.xml | Odors convey useful navigational and episodic information, yet much of the chemical world remains inaccessible without active sampling through sniffing. To effectively interpret olfactory cues, the brain must unify odor-driven activity with respiratory cycles, making accurate respiratory measurements critical in understanding olfactory bulb (OB) dynamics. Previous studies have shown that behavioral signals are often present in primary sensory areas, and OB local field potentials (LFPs) have long been known to couple with respiration. Here we investigated whether OB LFPs can reliably recover the precise timing and frequency of respiration. Our results indicate that OB LFPs across multiple frequency bands align with respiratory cycles. Using time and frequency domain methods, we show that 2-12 Hz LFP oscillations effectively track respiratory frequency. However, a monotonic relationship between LFP-respiratory delay and sniffing frequency, which varies across animals, renders the recovery of precise respiratory events challenging. This work demonstrates the complex and individualized relationship between rodent respiration and OB LFPs, contributing to our understanding of how respiratory signals are represented in the OB. | null | biorxiv |
10.1101/2024.11.08.622735 | Targeting Corticotropin-Releasing Hormone Receptor Type 1 (CRHR1) Neurons: Validating the Specificity of a Novel Transgenic Crhr1-FlpO Mouse | Hardy, M.; Chen, Y.; Baram, T. Z.; Justice, N. J. | Tallie Z Baram | University of California Irvine | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622735.source.xml | Introduction: Corticotropin-releasing hormone (CRH) signaling through its cognate receptors, CRHR1 and CRHR2, contributes to diverse stress-related functions in the mammalian brain. Whereas CRHR2 is predominantly expressed in choroid plexus and blood vessels, CRHR1 is abundantly expressed in neurons in discrete brain regions, including the neocortex, hippocampus and nucleus accumbens. Activation of CRHR1 influences motivated behaviors, emotional states, and learning and memory. However, it is unknown whether alterations in CRHR1 signaling contribute to aberrant motivated behaviors observed, for example, in stressful contexts. These questions require tools to manipulate CRHR1 selectively. Here we describe and validate a novel Crhr1-FlpO mouse. Methods: Using bacterial artificial chromosome (BAC) transgenesis, we engineered a transgenic mouse that expresses FlpO recombinase in CRHR1-expressing cells. We used two independent methods to assess the specificity of FlpO to CRHR1-expressing cells. First, we injected Crhr1-FlpO mice with Flp-dependent viruses expressing fluorescent reporter molecules. Additionally, we crossed the Crhr1-FlpO mouse with a transgenic Flp-dependent reporter mouse. CRHR1 and reporter molecules were identified using immunocytochemistry and visualized via confocal microscopy in several brain regions in which CRHR1 expression and function is established. Results: Expression of Flp-dependent viral constructs was highly specific to CRHR1-expressing cells in all regions examined (over 90% co-localization). In accord, robust and specific expression of the Flp-dependent transgenic reporter was observed in a reporter mouse, recapitulating endogenous CRHR1 expression. Conclusions: The Crhr1-FlpO mouse enables selective genetic access to CRHR1-expressing cells within the mouse brain. When combined with Cre-lox or site-specific recombinases, the mouse facilitates intersectional manipulations of CRHR1-expressing neurons. | null | biorxiv |
10.1101/2024.11.08.622712 | Projections between the globus pallidus externa and cortex span motor and non-motor regions | Ferenczi, E. A.; Wang, W.; Biswas, A.; Pottala, T.; Dong, Y.; Chan, A. K.; Albanese, M. A.; Sohur, R. S.; Jia, T.; Mastro, K. J.; Sabatini, B. L. | Bernardo L Sabatini | Howard Hughes Medical Institute, Harvard Medical School | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622712.source.xml | The globus pallidus externa (GPe) is a heterogenous nucleus of the basal ganglia, with intricate connections to other basal ganglia nuclei, as well as direct connections to the cortex. The anatomic, molecular and electrophysiologic properties of cortex-projecting pallidocortical neurons are not well characterized. Here we show that pallidocortical neurons project to diverse motor and non-motor cortical regions, are organized topographically in the GPe, and segregate into two distinct electrophysiological and molecular phenotypes. In addition, we find that the GPe receives direct synaptic input back from deep layers of diverse motor and non-motor cortical regions, some of which form reciprocal connections onto pallidocortical neurons. These results demonstrate the existence of a fast, closed-loop circuit between the GPe and the cortex which is ideally positioned to integrate information about behavioral goals, internal states, and environmental cues to rapidly modulate behavior. | null | biorxiv |
10.1101/2024.11.09.622790 | Encoding opposing valences through frequency-dependent transmitter switching in single peptidergic neurons | Kim, D.-I.; Kang, S. J.; Jhang, J.; Jo, Y. S.; Park, S.; Ye, M.; Pyeon, G. H.; Im, G.-H.; Kim, S.-G.; Han, S. | Sung Han | The Salk Institute for Biological Studies | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622790.source.xml | Peptidergic neurons often co-express fast transmitters and neuropeptides in separate vesicles with distinct release properties. However, the release dynamics of each transmitter in various contexts have not been fully understood in behaving animals. Here, we demonstrate that calcitonin gene-related peptide (CGRP) neurons in the external lateral subdivision of the parabrachial nucleus (CGRPPBel) encode opposing valence via differential release, rather than co-release, of glutamate and neuropeptides, according to firing rate. Glutamate is released preferentially at lower firing rates with minimal release at higher firing rates, whereas neuropeptides are released at higher firing rates, resulting in frequency-dependent switching of transmitters. Aversive stimuli evoke high frequency responses with accompanying neuropeptide release to encode negative valence, whereas appetitive stimuli evoke low frequency responses with glutamate release to encode positive valence. Our study reveals a previously unknown capability of single CGRPPBel neurons to bidirectionally encode valence via frequency-dependent differential release of transmitters in vivo. | null | biorxiv |
10.1101/2024.11.08.622738 | Bichromatic exon-reporters reveal voltage-gated Ca2+-channel splice-isoform diversity across Drosophila neurons in vivo | Macleod, G. T.; Feghhi, T.; Hernandez, R.; Oliva, C. D.; Mahneva, O. | Gregory T Macleod | Tulane University | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622738.source.xml | Every neuron contains the same genomic information but its complement of proteins is the product of countless neuron-specific steps including pre-mRNA splicing. Despite advances in RNA sequencing techniques, pre-mRNA splicing biases that favor one isoform over another are largely inscrutable in live neurons in situ. Here, in Drosophila, we developed bichromatic fluorescent reporters to investigate alternate splicing of cacophony - a gene that codes the pore-forming 1-subunit of the primary neuronal voltage-gated Ca2+ channel (VGCC). These reporters reveal a neuron-specific pattern of exon biases, including stereotypical differences between neurons of the same neurotransmitter type and ostensibly the same function. Information about exon splicing biases of individual neurons in vivo provides clues to the role of VGCC motifs and the role of those neurons in the context of local circuits. The application of this technology to a large gene such as cacophony provides a precedence for effective exon-reporter design for other Drosophila genes. | null | biorxiv |
10.1101/2024.11.08.622698 | Alternative EEG pre-processing pipelines can lead to conflicting conclusions regarding cortical excitation/inhibition ratio | Racz, F. S.; Mac-Auliffe, D.; Mukli, P.; Milton, J.; Cabrera, J. L.; Millan, J. d. R. | Frigyes Samuel Racz | The University of Texas at Austin | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622698.source.xml | Confluent recent evidence indicates that the spectral slope of 1/f neurophysiological recordings is correspondent to cortical excitation/inhibition (E/I) ratio. In this framework, a steeper power spectrum (i.e., one with a larger spectral exponent {beta}) is indicative of stronger inhibitory tone and thus lower E/I ratio, and vice versa. While the tools commonly utilized for estimating {beta} are mostly consistent, there appears to be a lack of standardization among data processing protocols for slope analysis. In this work our goal is to draw attention to a fundamental consequence of this issue, namely that even in a confined, comparative research environment, applying different pre-processing steps to electroencephalography (EEG) data can lead to conflicting conclusions in terms of the E/I ratio. To this end, we analyzed resting-state EEG recordings in two independent datasets, containing data collected with eyes open (EO) and eyes closed (EC), with the latter considered as a physiological state with stronger inhibitory tone. Our analysis confirmed consistently in both cohorts that applying different spatial filtering schemes in an otherwise identical analytical pipeline indicated a decrease in E/I ratio over the prefrontal cortex in one case, but not the other when transitioning from EO to EC. In contrast, this same pattern was apparent over the occipital cortex regardless of the pre-processing scheme. This empirical evidence calls for the development of a standardized data processing protocol for EEG-based analyses of the E/I ratio. | null | biorxiv |
10.1101/2024.11.08.622714 | The development of aperiodic neural activity in the human brain | Cross, Z. R.; Gray, S. M.; Dede, A. J. O.; Rivera, Y. M.; Yin, Q.; Vahidi, P.; Rau, E. M. B.; Cyr, C.; Holubecki, A. M.; Asano, E.; Lin, J. J.; McManus, O. K.; Sattar, S.; Saez, I.; Girgis, F.; King-Stephens, D.; Weber, P. B.; Laxer, K. D.; Schuele, S. U.; Rosenow, J. M.; Wu, J. Y.; Kam, S. K.; Raskin, J. S.; Chang, E. F.; Shaikhouni, A.; Brunner, P.; Roland, J. L.; Braga, R. M.; Knight, R. T.; Ofen, N.; Johnson, E. L. | Zachariah Reuben Cross | Northwestern Feinberg School of Medicine, Northwestern University | 2024-11-09 | 1 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622714.source.xml | The neurophysiological mechanisms supporting brain maturation are fundamental to attention and memory capacity across the lifespan. Human brain regions develop at different rates, with many regions developing into the third and fourth decades of life. Here, in this preregistered study (https://osf.io/gsru7), we analyzed intracranial EEG (iEEG) recordings from widespread brain regions in a large developmental cohort. Using task-based (i.e., attention to-be-remembered visual stimuli) and task-free (resting-state) data from 101 children and adults (5.93 - 54.00 years, 63 males; n electrodes = 5691), we mapped aperiodic (1/f-like) activity, a proxy of excitation:inhibition (E:I) balance with steeper slopes indexing inhibition and flatter slopes indexing excitation. We reveal that aperiodic slopes flatten with age into young adulthood in both association and sensorimotor cortices, challenging models of early sensorimotor development based on brain structure. In prefrontal cortex (PFC), attentional state modulated age effects, revealing steeper task-based than task-free slopes in adults and the opposite in children, consistent with the development of cognitive control. Age-related differences in task-based slopes also explained age-related gains in memory performance, linking the development of PFC cognitive control to the development of memory. Last, with additional structural imaging measures, we reveal that age-related differences in gray matter volume are differentially associated with aperiodic slopes in association and sensorimotor cortices. Our findings establish developmental trajectories of aperiodic activity in localized brain regions and illuminate the development of PFC inhibitory control during adolescence in the development of attention and memory. | null | biorxiv |
10.1101/2024.11.09.622780 | Can ERPs and neural oscillations be used to differentiate skilled and unskilled player performance in an ecologically valid sporting model? | Winstanley, M.; Drust, B. | Mike Winstanley | University of Birmingham, Centre for Human Brain Health | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622780.source.xml | The present study seeks to identify neural correlates of high performance in ecological valid, sporting tasks and quantify the differences between high skilled and low skilled players. To do this, Esports is chosen to be the sporting model to facilitate clean brain activity recordings whilst playing sport, something that is considerably more challenging with traditional sports. Participants are first separated into a skilled or unskilled group based on their Esports performance using objective classification measures to identify the presence of a higher and lower performing groups. Their brain activity is then recorded as they complete a visuomotor psychophysics task and Esports aim-training tasks. The first task requires discrete movements, the second sequential movements. Results indicate that there are several key differences in the brain activity of skilled players that facilitate a higher level of performance. Firstly, skilled players display enhanced response in time-domain activity of occipital parietal electrodes, displaying significantly higher p100 amplitude (sensor-space) and higher p300 amplitude (source-space). Peak decoding using MVPA, classifying brain activity between skilled or unskilled players, is achieved during the first 300ms of the response. Furthermore, skilled players modulate visual attention, gated by alpha oscillations, to release the visual system before target onset. As a result, visual information is consciously accessed more readily to be utilized for a motor response. Skilled players show an increase in frontal-midline theta during Esports performance facilitating management of cognitive load and repeated execution of precise movements. Due to the nature of the model, applied implications are suggested for both coaches and athletes of all sports to utilize this research. Specifically, performance improvement of players could be facilitated by identifying deficits in their brain activity and talent identification, by observing the neural correlates reported in developing players. Future research should focus on adapting evoked, rather than induced brain activity recording during Esports competition. | null | biorxiv |
10.1101/2024.11.09.622778 | Anterior cingulate neurons display subregion-specific interaction with frontal eye fields as revealed by combined antidromic stimulation and resting state imaging | Babapoor-Farrokhran, S.; Major, A. J.; Johnston, K. D.; Miller, E. K.; Camprodon, J. A.; Everling, S. | Alex J. Major | The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA | 2024-11-09 | 1 | new results | cc_by_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622778.source.xml | The anterior cingulate cortex (ACC) is thought to exert cognitive control over saccade generation in the frontal eye fields (FEF), but the nature of this interaction remains unclear. Although prior imaging studies have suggested ACC interacts with FEF, few studies have confirmed this by electrophysiological recordings. This study aimed to characterize the functional connectivity between ACC and medial and lateral FEF during cognitive saccade tasks. We combined resting-state functional MRI (rs-fMRI) with single-unit electrophysiology in two macaque monkeys performing memory-guided saccade and pro-/anti-saccade tasks. Anti- and ortho-dromic stimulation was used to electrophysiologically identify ACC neurons mono- and polysynaptically connected to FEF. We analyzed ACC neuronal selectivity for different task aspects and correlated these properties with both positive and negative rs-fMRI functional connectivity between ACC and FEF subregions. Anti- and ortho-dromically identified ACC neurons were predominantly connected to medial FEF, which showed stronger positive functional connectivity with ACC compared to lateral FEF. Sites with higher proportions of task-selective neurons yielded stronger functional connectivity with FEF. This stronger functional connectivity was particularly related to the delay and saccadic periods of different cognitive saccade tasks. Using combined imaging and electrophysiology, our findings provide converging evidence for functional interactions between ACC and FEF, predominantly medial FEF regions which encode large amplitude saccades. The correlation between functional connectivity and task-related neuronal selectivity supports ACC's interaction with FEF in the modulation of saccade generation and cognitive control. Additionally, we report suggestive evidence that mono- and poly-synaptic connections may be related to positive functional connectivity, but we found no such relationship for negative functional connectivity (anticorrelations). These results advance our understanding of prefrontal cortical interactions in oculomotor control and the electrophysiological mechanisms of positive and negative resting-state functional connectivity. | null | biorxiv |
10.1101/2024.11.09.622728 | Sex differences in central amygdala glutamate responses to calcitonin gene-related peptide | Lorsung, R.; Cramer, N.; Alipio, J. B.; Ji, Y.; Han, S.; Masri, R.; Keller, A. | Rebecca Lorsung | University of Maryland Baltimore | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622728.source.xml | Women are disproportionately affected by chronic pain compared to men. While societal and environmental factors contribute to this disparity, sex-based biological differences in the processing of pain are also believed to play significant roles. The central lateral nucleus of the amygdala (CeLC) is a key region for the emotional-affective dimension of pain, and a prime target for exploring sex differences in pain processing since a recent study demonstrated sex differences in CGRP actions in this region. Inputs to CeLC from the parabrachial nucleus (PB) play a causal role in aversive processing, and release both glutamate and calcitonin gene-related peptide (CGRP). CGRP is thought to play a crucial role in chronic pain by potentiating glutamatergic signaling in CeLC. However, it is not known if this CGRP-mediated synaptic plasticity occurs similarly in males and females. Here, we tested the hypothesis that female CeLC neurons experience greater potentiation of glutamatergic signaling than males following endogenous CGRP exposure. Using trains of optical stimuli to evoke transient CGRP release from PB terminals in CeLC, we find that subsequent glutamatergic responses are preferentially potentiated in CeLC neurons from female mice. This potentiation was CGRP-dependent and involved a postsynaptic mechanism. This sex difference in CGRP sensitivity may explain sex differences in affective pain processing. | null | biorxiv |
10.1101/2024.11.09.622275 | Retrospective Attention Can Trigger Visual Perception Without Dependence on Either Cue Awareness or Target Reporting | Li, Y.; Wan, X.; Mao, M.; Jin, L.; Zhang, X. | Ye Li | South China Normal University | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622275.source.xml | Retrospective attention, guided by cues after stimulus offset, enhances perception of threshold-level Gabor patches. The neural mechanisms underlying this effect, and its dependence on cue awareness and target reporting, remain unclear. Using EEG in report and no-report paradigms with visible and invisible post-cues, we found that orientation discrimination improved with retro-cues regardless of cue visibility. Compared to visible conditions, under invisible conditions, retro-cueing effects were weaker, limited to stimulus onset asynchronies (SOAs) of 66.67 ms, and linked to N2pc component. Visible retro-cueing effects persisted at SOAs of 100 ms, evoking strong P3b in report condition and weak VAN in no-report condition. Multivariate pattern analysis showed that in report conditions, neural processing of cued targets was earlier, stronger, and more generalized in the frontoparietal region; in no-report conditions, only cued targets were decoded in the parieto-occipital region. Our findings indicate that retrospective attention can trigger visual perception independently of cue awareness and the target reporting, thus contributing to current discussions on theories of consciousness. | null | biorxiv |
10.1101/2024.11.08.622733 | Medial prefrontal cortical neurotransmitters reactive to relapse-promoting and relapse-suppressing cues in rats trained to self-administer cocaine or alcohol | Nedelescu, H.; Miliano, C.; Wagner, G.; Kerr, T.; Gregus, A.; Weiss, F.; Buczynski, M.; Suto, N. | Nobuyoshi Suto | Mayo Clinic | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622733.source.xml | Environmental cues conditioned to signal drug availability (S+) or omission (S-) activate specific neurons (neuronal ensembles/engram cells) within the medial prefrontal cortex (mPFC) to promote and suppress drug relapse in rats. However, the neurochemical source of such cue-specific activation remains unknown. In this study, we determined extracellular neurotransmitter fluctuations reactive to S+ vs. S- in the infralimbic (IL) and prelimbic (PL) cortices of male rats trained to lever-press for cocaine or alcohol self-administration. In cocaine- or alcohol-trained rats exposed to S+, no significant neurotransmitter fluctuations were observed in IL or PL. In cocaine-trained rats exposed to S-, glutamate, serotonin, taurine and adenosine were increased in PL but not in IL. In alcohol-trained rats exposed to S-, glutamate was increased, while dopamine and GABA were decreased, in IL but not in PL. Although S+ reactive neurotransmitters driving neuronal activation in mPFC remains to be elucidated, glutamate is likely the source of such activation by S- in rats trained to self-administer cocaine or alcohol. While drugs used for self-administration and cue-conditioning appear to dictate the type and anatomical specificity of S- evoked neurotransmission within mPFC, glutamate may serve as a common therapeutic target to mimic relapse-suppression by S- across cocaine and alcohol use disorders (CUD and AUD). In contrast, serotonin, taurine and adenosine may serve as the targets in CUD, while dopamine and GABA may serve as the targets in AUD. | null | biorxiv |
10.1101/2024.11.07.622553 | Neural Context Reinstatement of Recurring Events | Broitman, A. W.; Kahana, M. J. | Adam W. Broitman | University of Pennsylvania | 2024-11-09 | 1 | new results | cc_by_nc_nd | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622553.source.xml | Episodic recollection involves retrieving context information bound to specific events. However, autobiographical memory largely comprises recurrent, similar experiences that become integrated into joint representations. In the current study, we extracted a neural signature of temporal context from scalp electroencephalography (EEG) to investigate whether recalling a recurring event accompanies the reinstatement of one or multiple instances of its occurrence. We asked 52 young adults to study and recall lists of words that included both once-presented and repeated items. Participants recalled repeated items in association with neighboring list items from each occurrence, but with stronger clustering around the repetition's initial occurrence. Furthermore, multivariate spectral EEG analyses revealed that neural activity from just prior to the recall of these words resembled patterns of activity observed near the item's first occurrence, but not its second. Together, these results suggest that the initial occurrence of an event carries stronger temporal context associations than later repetitions. | null | biorxiv |
10.1101/2024.11.09.622721 | A Neural Network Model of Visual Attention Integrating Biased Competition and Reinforcement Learning | Morgan, J. M.; Albanna, B.; Herman, J. P. | James P Herman | University of Pittsburgh | 2024-11-09 | 1 | new results | cc_no | neuroscience | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622721.source.xml | We present a neural network model of visual attention (NNMVA) that integrates biased competition and reinforcement learning to capture key aspects of attentional behavior. The model combines self-attention mechanisms from Vision Transformers (ViTs), Long Short-Term Memory (LSTM) networks for working memory, and an actor critic reinforcement learning framework to map visual inputs to behavioral outputs. The self-attention mechanism simulates biased competition among artificial neural representations, determining their influence on working memory, which in turn provides top-down feedback to guide attention. Trained end-to-end with reinforcement learning using reward feedback paralleling learning processes in non-human primates the NNMVA replicates key behavioral signatures of attention, such as improved performance and faster reaction times for cued stimuli. Manipulating the model's attention mechanisms affects performance in ways analogous to experimental manipulations in primate frontal eye fields and superior colliculus. Additionally, artificially inducing attentional biases alters value estimates and temporal difference (TD) errors, offering predictions about how attention may interact with dopamine related learning signals in the brain. Our findings suggest that reward-driven behavior alone can account for several key correlates of attention, providing a computational framework to explore the interplay between attention and reinforcement learning in both biological and artificial systems. | null | biorxiv |
10.1101/2024.11.08.622602 | Pathogenesis and immune response to respiratory coronaviruses in their natural porcine host | Sedaghat-Rostami, E.; Carr, B. V.; Yang, L.; Keep, S.; Lean, F. Z. X.; Atkinson, I.; Fones, A.; Paudyal, B.; Kirk, J.; Vatzia, E.; Gubbins, S.; Bickerton, E.; Briggs, E.; Nunez, A. Z. X.; MacNee, A.; Moffat, K.; Freimanis, G.; Rollier, C.; Muir, A.; Richard, A. C.; Angelopoulos, N.; Gerner, W.; Tchilian, E. | Elma Tchilian | Pirbright Institute | 2024-11-09 | 1 | new results | cc_by | immunology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622602.source.xml | Porcine respiratory coronavirus (PRCV) is a naturally occurring pneumotropic coronavirus in the pig, providing a valuable large animal model to study acute respiratory disease. PRCV pathogenesis and the resulting immune response was investigated in pigs, the natural large animal host. We compared two strains, ISU-1 and 135, which induced differing levels of pathology in the respiratory tract to elucidate the mechanisms leading to mild or severe disease. The 135 strain induced greater pathology which was associated with higher viral load and stronger spike-specific antibody and T cell responses. In contrast, the ISU-1 strain triggered mild pathology with a more balanced immune response and greater abundance of T regulatory cells. A higher frequency of putative T follicular helper cells was observed in animals infected with strain 135 at 11 days post-infection. Single-cell RNA-sequencing of bronchoalveolar lavage revealed differential gene expression in B and T cells between animals infected with 135 and ISU-1 at 1 day post infection. These genes were associated with cell adhesion, migration, and immune regulation. Along with increased IL-6 and IL-12 production, these data suggest that heightened inflammatory responses to the 135 strain may contribute to pronounced pneumonia. Among BAL immune cell populations, B cells and plasma cells exhibited the most gene expression divergence between pigs infected with different PRCV strains, highlighting their potential role in maintaining immune homeostasis in the respiratory tract. These findings indicate the potential of the PRCV model for studying coronavirus induced respiratory disease and identifying mechanisms that determine infection outcomes. | null | biorxiv |
10.1101/2024.11.09.622705 | Drugs Commonly Used in Fungal Infection Risk Conditions Promote Drug Tolerance or Resistance in Candida albicans | Obermeier, M.; Esparza Mora, M. A.; Heese, O.; Cohen, N.; Varma, S. J.; Tober-Lau, P.; Hartl, J.; Kurth, F.; Berman, J.; Ralser, M. | Markus Ralser | Charité - Universitätsmedizin Berlin, Department of Biochemistry, Berlin, Germany | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622705.source.xml | Background Fungal infections are an increasing concern, particularly among immunocompromised patients and those with comorbidities who require multiple medications. However, the effects of drugs targeting human pathways on fungal cells, and whether they influence antifungal drug responses, are poorly understood. Methods We systematically analyzed clinical guidelines to shortlist non-antifungal drugs commonly used in conditions that increase the likelihood of fungal infections. Focusing on the most prevalent fungal pathogen, we then tested how these drugs affected the antifungal response of Candida albicans to two commonly used antifungals, fluconazole and anidulafungin. Drug interactions identified were further assessed using checkerboard and disk diffusion assays. Finally, antifungal treatment efficacy of fluconazole in combination with negatively interaction drugs was evaluated in an in vivo Galleria mellonella model of disseminated C. albicans infection. Findings Out of 119 drugs frequently co-administered with antifungals in 40 conditions associated with a high risk of fungal infections, 34 compounds affected the antifungal drug response in C. albicans, with most drugs reducing or antagonising antifungal efficacy, several through increasing resistance or tolerance. Notably, fluconazole combinations with carvedilol and loperamide promoted antifungal resistance in both fungal cultures and in Galleria mellonella. Interpretation Our findings suggest that medications frequently taken by patients at risk of fungal infections regularly act on the fungal pathogens and can affect the effectiveness of antifungals. We propose that human drugs acting on fungal pathogens may be an underestimated factor contributing to the evolution of antifungal tolerance and resistance. | null | biorxiv |
10.1101/2024.11.08.622737 | Drospondin, a novel glial-secreted glycoprotein, controls the development and function of the Drosophila nervous system | Rojo-Cortes, F.; Roa-Siegfried, C.; Fuenzalida-Uribe, N.; Amado-Hinojosa, P.; Gonzalez-Ramirez, M.-C.; Almonacid-Torres, I.; Birman, S.; Goodman, L. D.; Kanka, O.; Oliva, C.; Marzolo, M.-P.; Campusano, J. M. | Jorge M Campusano | Pontificia Universidad Católica de Chile | 2024-11-09 | 1 | new results | cc_no | developmental biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622737.source.xml | Reelin is a secreted glycoprotein with roles in the development of the mammalian hippocampus and cerebral cortex. This vertebrate signaling molecule also contributes to adult brain function. Mammalian Reelin increases the complexity of Drosophila Mushroom Body (MB) neurites, an effect mediated by LpR1 and LpR2, the orthologs of mammalian Reelin receptors. Paradoxically, to date, no Reelin ortholog has been described in Drosophila. Here, we report that the protein product of the uncharacterized Drosophila CG17739 gene, named Drospondin, shares sequence homology with vertebrate F-spondin and Reelin. We show that Drospondin is expressed in glial cells and is crucial for MB development. Our results also show that Drospondin interacts genetically with LpRs and that human Reelin rescues structural defects in Drospondin-deficient flies. Furthermore, Drospondin-deficient flies exhibit altered sleep homeostasis, locomotion, and social behaviors. Our results reveal that flies express a functional homolog of mammalian Reelin that controls the development and function of the Drosophila nervous system. | null | biorxiv |
10.1101/2024.11.07.622474 | Genetic Basis, Quantitative Nature, and Functional Relevance of Evolutionarily Conserved DNA Methylation | Dong, Z.; Schaffner, S.; Fu, M.; Whitehead, J.; MacIsaac, J. L.; Rehkopf, D. H.; Boyce, W. T.; Rosero-Bixby, L.; Quintana-Murci, L.; Patin, E.; Miller, G. E.; Korthauer, K.; Kobor, M. S. | Michael S. Kobor | University of British Columbia | 2024-11-09 | 1 | new results | cc_by_nc | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622474.source.xml | DNA methylation (DNAm) is a key epigenetic mark that modulates regulatory elements and gene expression, playing a crucial role in mammalian development and physiological function. Despite extensive characterization of DNAm profiles across species, little is known about its evolutionary conservation. Here, we conducted a comparative epigenome-wide analysis of great apes to identify and characterize sequence- and methylation-conserved CpGs (MCCs). Using 202 DNAm arrays, alongside 6 matched genotype and 13 matched transcriptomic datasets, we identified 11,500 MCCs for which methylation was evolutionarily related to sequences of CpGs and methylation quantitative trait loci. MCCs were the most stable across healthy human tissues and exhibited weaker genetic associations than other CpGs. Moreover, MCCs showed minimal associations with demographic, environmental factors, and noncancer diseases, yet demonstrated stronger associations with certain cancers than other CpGs, particularly gastrointestinal cancers. Functional enrichment analysis revealed that genes associated with MCC methylation in cancer were enriched for cancer driver genes and canonical cancer pathways, highlighting a significant regulatory role for MCCs in tumorigenesis. Collectively, our findings reveal the extent of DNAm conservation in great ape evolution, its association with genetic conservation, and its relevance to human diseases. These integrative analyses offer evolutionary insights into epigenetic variation and its functional implications in human populations. | null | biorxiv |
10.1101/2024.11.09.622763 | Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation | Kulkarni, O.; Mathew, R. J.; Zaveri, L.; Jana, R.; Singh, N. K.; Ara, S.; Tallapaka, K. B.; Sowpati, D. T. | Divya Tej Sowpati | CSIR Centre for Cellular and Molecular Biology | 2024-11-09 | 1 | new results | cc_by_nd | genomics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622763.source.xml | Long read sequencing technologies such as Oxford Nanopore (ONT) offer direct detection of DNA base modifications. While several tools and models have been developed to identify DNA methylation from nanopore data, they are often restricted to 5-methylcytosine (5mC) and older flowcell (FC) chemistry. The performance and accuracy of newer models, including those developed by ONT, remain unknown, particularly for their new FC chemistry (R10.4.1) and sampling rate (5kHz). Here, using a variety of bacterial and human datasets, we systematically evaluate the performance of existing methylation models for 5mC (both CpG and non-CpG contexts), 6-methyladenine, and 4-methylcytosine. We also demonstrate the effect of other parameters such as sequencing depth, read quality, basecalling mode, and more importantly, the presence of neighboring DNA modifications. Our work thus provides important information to researchers utilizing nanopore sequencing to study DNA modifications, and highlights the lacunae in current generation methylation detection models. | null | biorxiv |
10.1101/2024.11.08.622731 | Structural landscape of AAA+ ATPase motor states in the substrate-degrading human 26S proteasome reveals conformation-specific binding of TXNL1 | Martin, A.; Arkinson, C.; Gee, C. L.; Zhang, Z.; Dong, K. | Andreas Martin | HHMI, UC Berkeley | 2024-11-09 | 1 | new results | cc_by_nc_nd | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622731.source.xml | The 26S proteasome targets many cellular proteins for degradation during general homeostasis, protein quality control, and the regulation of vital processes. A broad range of proteasome-interacting cofactors thereby modulates these functions and aids in substrate degradation. Here, we solved several high-resolution structures of the redox active cofactor TXNL1 bound to the human 26S proteasome at saturating and sub-stoichiometric concentrations by time resolved cryo-EM. We identified distinct binding modes of TXNL1 that depend on the proteasome conformational and ATPase motor states. Together with biophysical and biochemical experiments, our structural studies reveal that the resting-state proteasome prior to substrate engagement with the ATPase motor binds TXNL1 with low affinity and in variable positions on top of the Rpn11 deubiquitinase. In contrast, the actively degrading proteasome shows additional interactions leading to high-affinity TXNL1 binding, whereby the C-terminal tail of TXNL1 covers the catalytic groove of the Rpn11 deubiquitinase and coordinates the active-site Zn2+. Furthermore, these cryo-EM structures of the degrading proteasome capture the ATPase hexamer in all registers of spiral-staircase arrangements and thus visualize the complete ATP-hydrolysis cycle of the AAA+ motor, indicating temporally asymmetric hydrolysis and conformational changes in bursts during mechanical substrate unfolding and translocation. Remarkably, we catch the proteasome in the act of unfolding the beta-barrel mEos3.2 substrate while the ATPase hexamer is in a particular spiral staircase register. Our findings challenge current models for protein translocation through hexameric AAA+ motors and reveal how the proteasome uses its distinct but broad range of conformational states to coordinate cofactor binding and substrate processing. | null | biorxiv |
10.1101/2024.11.09.622779 | DnaB and DciA: Mechanisms of Helicase Loading and Translocation on ssDNA | Gao, N.; Mazzoletti, D.; Peng, A.; Olinares, P. D. B.; Morrone, C.; Garavaglia, A.; Gouda, N.; Tsoy, S.; Mendoza, A.; Chowdhury, A.; Cerullo, A. R.; Bhavsar, H.; Rossi, F.; Rizzi, M.; Chait, B.; Miggiano, R.; Jeruzalmi, D. | David Jeruzalmi | Department of Chemistry and Biochemistry, City College of New York, New York, NY 10031, USA. Ph.D. Programs in Biochemistry, Biology, and Chemistry, The Graduat | 2024-11-09 | 1 | new results | cc_no | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622779.source.xml | Replicative helicases are assembled on chromosomes by helicase loaders before initiation of DNA replication. Here, we investigate mechanisms used by the bacterial DnaB replicative helicase and the DciA helicase loader. In the present structure of the DnaB-ssDNA-ATP-gamma-S complex, the amino-terminal (NTD) tier, previously found as an open spiral in a GDP-AlF4 complex, was observed to adopt a closed planar arrangement. Further, the DnaB subunit at the top of the carboxy-terminal spiral (CTD) tier is displaced by ~25 A between the two forms. We suggest that remodeling the NTD layer between closed planar and open spiral configurations and migration of two distinct CTDs to the top of the DnaB spiral, which is repeated three times, mediates hand-over-hand translocation. Although DciA loaders from Vibrio cholerae and Mycobacterium tuberculosis feature an inverted domain arrangement, they use Lasso domains to contact DnaB near the Docking-Linker-Helix interface. Up to three copies of Vc-DciA bind to Vc-DnaB and suppress its ATPase activity during loading onto physiological DNA substrates. Our data suggest that DciA loads DnaB onto DNA using the ring-opening mechanism. | null | biorxiv |
10.1101/2024.11.09.622773 | Crystal structure of plant γ-glutamyl peptidase 1 with dual roles in sulfur metabolism and implications for oxidative stress regulation | Sone, K.; Ito, T.; Yamada, C.; Kashima, T.; Miyanaga, A.; Ohkama-Ohtsu, N.; Fushinobu, S. | Shinya Fushinobu | Department of Biotechnology, The University of Tokyo | 2024-11-09 | 1 | new results | cc_no | biochemistry | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622773.source.xml | {gamma}-Glutamyl peptidase 1 (GGP1) plays a dual role in primary and secondary sulfur metabolism in Arabidopsis thaliana. During glutathione (GSH) turnover, GGP1 hydrolyzes the isopeptide bond of GSH to degrade the tripeptide into Glu and Cys-Gly. During glucosinolate and camalexin biosynthesis, GGP1 processes GSH conjugates, which have a large substituent at the thiol side chain, by hydrolyzing the same isopeptide bond of {gamma}-Glu. In the present study, we determined the crystal structures of the following GGP1 forms: ligand-free, Glu complex, covalent {gamma}-Glu intermediate, and disulfide-linked S-S inactive forms. The intermediate structure, in which {gamma}-Glu is covalently linked to the nucleophile C100, was trapped by mutating the catalytic His to Asn (H192N). In the Glu complex and {gamma}-Glu intermediate structures, Glu bound to the S1 subsite is extensively recognized by several hydrogen bonds. The substrate recognition of the Cys-Gly moiety at the S1' and S2' subsites was revealed by modeling GSH in the active site. Mutational analysis indicated that R206 plays an important role in substrate binding by forming a salt bridge with Gly at the S2' subsite. An open pocket is present beyond the thiol side chain of Cys in the S1' subsite, which contributed to the dual activity of GGP1 toward GSH and GSH conjugates. The S-S inactive structure was obtained by soaking GGP1 crystals in Cys-Gly, and the catalytic cysteine (C100) partially formed a disulfide bond with a neighboring C154 residue. The partial inactivation of GGP1 in the presence of a pro-oxidant (Cys-Gly) has revealed its possible role in oxidative stress regulation in Arabidopsis. | null | biorxiv |
10.1101/2024.11.07.622410 | Language model generates cis-regulatory elements across prokaryotes | Xia, Y.; Sun, J.; Du, X.; Liang, Z.; Shi, W.; Guo, S.; Huo, Y.-X. | Yi-Xin Huo | Beijing Institute of Technology | 2024-11-09 | 1 | new results | cc_by_nc_nd | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622410.source.xml | Deep learning had succeeded in designing Cis-regulatory elements (CREs) for certain species, but necessitated training data derived from experiments. Here, we present Promoter-Factory, a protocol that leverages language models (LM) to design CREs for prokaryotes without experimental prior. Millions of sequences were drawn from thousands of prokaryotic genomes to train a suite of language models, named PromoGen2, and achieved the highest zero-shot promoter strength prediction accuracy among tested LMs. Artificial CREs designed with Promoter-Factory achieved a 100% success rate to express gene in Escherichia coli, Bacillus subtilis, and Bacillus licheniformis. Furthermore, most of the promoters designed targeting Jejubacter sp. L23, a halophilic bacterium without available CREs, were active and successfully drove lycopene overproduction. The generation of 2 million putative promoters across 1,757 prokaryotic genera, along with the Promoter-Factory protocol, will significantly expand the sequence space and facilitate the development of an extensive repertoire of prokaryotic CREs. | null | biorxiv |
10.1101/2024.11.07.622529 | RIBOSS detects novel translational events by combining long- and short-read transcriptome and translatome profiling | Lim, C. S.; Brown, C. | Chun Shen Lim | University of Otago | 2024-11-09 | 1 | new results | cc_by | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622529.source.xml | Ribosome profiling is a high-throughput sequencing technique that captures the positions of translating ribosomes on RNAs. Recent advancements in ribosome profiling include achieving highly-phased ribosome footprints for plant translatomes and more recently for bacterial translatomes. This substantially increases the specificity of detecting open reading frames (ORFs) that can be translated, such as small ORFs located upstream and downstream of the annotated ORFs. However, most genomes (e.g. bacterial genomes) lack the annotations for the transcription start and termination sites. This hinders the systematic discovery of novel ORFs in the 'untranslated' regions in ribosome profiling data. Here we develop a new computational pipeline called RIBOSS. We use RIBOSS to leverage long-read and short-read data for de novo transcriptome assembly, and highly-phased ribosome profiling data for detecting novel translational events in the newly assembled transcriptome. We demonstrate the capability of RIBOSS using recently published metatranscriptome and translatome data for Salmonella enterica serovar Typhimurium. The RIBOSS Python modules are versatile and can be used to analyse prokaryotic or eukaryotic data. In sum, RIBOSS is the first computational pipeline to integrate long- and short-read sequencing technologies to investigate translation. RIBOSS is freely available at https://github.com/lcscs12345/riboss. | null | biorxiv |
10.1101/2024.11.07.622480 | Computational Modeling and Analysis of the TGF-β-induced ERK and SMAD Pathways | Chung, S.; Cooper, C. R.; Farach-Carson, M. C.; Ogunnaike, B. A. | Mary C. Farach-Carson | University of Texas Health Science Center at Houston School of Dentistry | 2024-11-09 | 1 | new results | cc_by_nc_nd | systems biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622480.source.xml | Transforming growth factor-{beta} (TGF-{beta}), an important cytokine that plays a key role in many diseases regulates a wide array of cellular and physiologic processes via several TGF-{beta}-driven signaling cascades, including the SMAD and non-SMAD-driven pathways. However, the detailed mechanisms by which TGF-{beta} induces such diverse responses remain poorly understood. In particular, compared to the SMAD-dependent pathway, SMAD-independent pathways such as the ERK/MAPK pathway, which is critical in cancer progression, are less characterized. Here, we develop an integrated mechanistic model of the TGF-{beta}-triggered ERK activation pathway and its crosstalk with the SMAD pathway, an analysis of which demonstrates how SMAD dynamics can be significantly modulated and regulated by the ERK pathway. In particular, SMAD-mediated transcription can be altered and delayed due to expedited phosphorylation of the linker of SMAD by TGF-{beta}-activated ERK; and enhanced ERK activity, but attenuated SMAD activity, can be achieved simultaneously by fast turnover of TGF-{beta} receptors via lipid-rafts. Also, in silico mutations of the TGF-{beta} pathways reveal that the dynamic characteristics of both SMAD and ERK signaling may change significantly during cancer development. Specifically, normal cells may exhibit enhanced and sustained SMAD signaling with transient ERK activation, whereas cancerous cells may produce elevated and prolonged ERK signaling with enervated SMAD activation. These distinctive differences between normal and cancerous signaling behavior provide clues concerning, and potential explanations for, the seemingly contradictory roles played by TGF-{beta} during cancer progression. We demonstrate how crosstalk among various branch pathways of TGF-{beta} can influence overall cellular behavior. Based on model analysis, we hypothesize that aberrant molecular alterations drive changes in the intensity and duration of SMAD and ERK signaling during cancer progression and ultimately lead to an imbalance between the SMAD and ERK pathways in favor of tumor promotion. Thus, to treat cancer patients with a genetic signature of oncogenic Ras effectively may require at least a combination therapy to restore both the expression of TGF-{beta} receptors and the GTPase activity of Ras. | null | biorxiv |
10.1101/2024.11.07.622236 | Translocation of gut Enterococcus faecalis trains myeloid bone marrow progenitors via the C-type lectin receptor Mincle | Robles-Vera, I.; Sancho, D. | David Sancho | Centro Nacional de Investigaciones Cardiovasculares | 2024-11-09 | 1 | new results | cc_by_nc_nd | immunology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622236.source.xml | Impairment of the intestinal barrier allows the systemic translocation of commensal bacteria, inducing a pro-inflammatory state in the host. To address potential mechanisms underlying this link, we explored innate immune responses following increased gut permeability upon administration of dextran sulfate sodium (DSS) to mice. Microbiota translocation induced trained immunity (TI) in mouse myeloid bone marrow progenitors (BMPs). Enterococcus faecalis was the predominant bacteria detected in the bone marrow (BM) following DSS treatment. Notably, live or heat-killed E. faecalis induced reprogramming of mouse BMPs in vitro and in vivo and enhanced macrophage inflammatory activity, also training human monocytes. E. faecalis sensing by the C-type lectin receptor Mincle (Clec4e-/-) is essential for TI induction in BMPs. Consequently, Clec4e-/- mice showed impaired TI upon E. faecalis or reduced pathology following DSS treatment. Our results identify E. faecalis as inducer of TI-related inflammation that may contribute to pathologies associated with increased gut permeability. | null | biorxiv |
10.1101/2024.11.08.621386 | Phenotypic high-throughput screening identifies modulators of gut microbial choline metabolism | Woo, A. Y. M.; Sandoval-Espinola, W. J.; Bollenbach, M.; Wong, A.; Sakanaka-Yokoyama, M.; Zhang, Q.; Nieto, V.; Rey, F. E.; Balskus, E. P. | Emily P. Balskus | Harvard University | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.621386.source.xml | Anaerobic metabolism of dietary choline to trimethylamine (TMA) by the human gut microbiome is a disease-associated pathway. The host's impaired ability to oxidize TMA to trimethylamine-N-oxide (TMAO) results in trimethylaminuria (TMAU), while elevated serum TMAO levels have been positively correlated with cardiometabolic disease. Small molecule inhibition of gut bacterial choline metabolism attenuates the development of disease in mice, highlighting the therapeutic potential of modulating this metabolism. Inhibitors previously developed to target this pathway are often designed to mimic choline, the substrate of the key TMA-generating enzyme choline-trimethylamine lyase (CutC). Here, we use a growth-based phenotypic high-throughput screen and medicinal chemistry to identify distinct chemical scaffolds that can modulate anaerobic microbial choline metabolism and lower TMAO levels in vivo. These results illustrate the potential of using phenotypic screening to rapidly discover new inhibitors of gut microbial metabolic activities. | null | biorxiv |
10.1101/2024.11.08.622732 | Commonalities and differences in the Cryptococcus neoformans response to ingestion by protozoal and mammalian phagocytic cells suggests host cell metabolism as a target for intracellular survival | Dragotakes, Q.; Jacobs, E.; Gerbig, G.; Greengo, S.; Jedlicka, A.; Dziedzic, A.; Casadevall, A. | Quigly Dragotakes | Johns Hopkins | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622732.source.xml | The outcome of the interaction between Cryptococcus neoformans and infected hosts can be determined by whether the fungal cell survives ingestion by phagocytic cells. This applies to both unicellular and multicellular hosts such as amoeba and animals, respectively. Ingestion by phagocytic cells results in the formation of the cryptococcal phagosome but this structure has proved difficult to isolate. In this study, we report the successful isolation of cryptococcal phagosomes from murine and human phagocytes, followed by their characterization using proteomic and transcriptional analysis. Comparison of cryptococcal proteins from Acanthamoeba castellanii, Mus musculus, and Homo sapiens phagocytes revealed the existence of a shared set suggesting a conserved fungal response to ingestion by phagocytic cells. Given that the cryptococcal intracellular pathogenic strategy is ancient, dating to at least to the cretaceous epoch, these results are consistent with the notion that the fungal response to ingestion reflects the result of selection pressures by environmental ameboid predators over eons of evolutionary time. We propose the existence of a conserved cryptococcal toolkit for intracellular survival that includes metabolic enzymes. We propose that host cell metabolic disruption provides a common strategy for the cryptococcal survival after ingestion by phylogenetically distant phagocytic hosts. | null | biorxiv |
10.1101/2024.11.08.622711 | Microbial Differences Accurately Identifies Global SERT KO Phenotype in Mice | Leitman, M.; Katza, W.; Zhang, D.; Pawar, S.; Shera, S.; Hernandez, L.; Dong, T. | Tien Dong | University of California, Los Angeles | 2024-11-09 | 1 | new results | cc_by_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622711.source.xml | Altered serotonin signaling is a well-established contributor to depression, with the serotonin transporter gene (SERT) playing a critical role in regulating serotonin reuptake. Mice lacking SERT (SERT -/-) serve as a robust model for depression, exhibiting significant depressive-like behaviors compared to littermate wild-type (SERT +/+) controls. In this study, we aimed to determine the relationship between gut microbiota composition and depressive behaviors in SERT -/- mice. Behavioral assays, including the Forced Swim Test (FST) and Tail Suspension Test (TST), confirmed that SERT -/- mice exhibited significantly increased immobility times compared to SERT +/+ mice (FST: p = 0.004; TST: p = 0.080), consistent with a depressive phenotype. Utilizing littermate controls, shotgun metagenomic sequencing of fecal samples revealed significant differences in alpha diversity between the two groups of mice, as measured by the Shannon entropy index (p = 0.05). Additionally, our bacterial co-occurrence network analysis uncovered distinct structural differences in microbial interactions between SERT -/- and SERT +/+ mice (p = 0.001), suggesting shifts in microbiome stability and functionality between the groups. We created a microbial depression score utilizing the top five bacteria taxa that were differentially abundant between SERT -/- and SERT +/+ mice: Clostridium sp. MD294, Acetatifactor MGBC165152, Desulfovibrio MGBC129232, Oscillibacter MGBC161747, and Schaedlerella MGBC000001. This microbial depression score correlated strongly with immobility times in the FST (r = 0.705, p < 0.0006) and TST (r = 0.401, p < 0.09). A random forest classifier based on these taxa accurately distinguished SERT -/- from SERT +/+ mice (accuracy = 0.82). These findings suggest that gut microbial species composition is highly associated with depressive-like behaviors in SERT -/- mice, likely via alterations in serotonin signaling pathways, and may offer potential targets for microbiome-based interventions in depression. | null | biorxiv |
10.1101/2024.11.08.622677 | Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter? | Nickols, W. A.; McIver, L. J.; Walsh, A.; Zhang, Y.; Nearing, J.; Asnicar, F.; Nguyen, L.; Hartmann, E. M.; Franzosa, E. A.; Huttenhower, C.; Thompson, K. N. | Kelsey N. Thompson | Harvard University | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622677.source.xml | Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles. | null | biorxiv |
10.1101/2024.11.09.622791 | Isolation, Characterization, and Identification of Nitrogen Fixing Bacteria from Rhizosphere of Sonneratia apetala Collected from Sundarbans | Rimi, A. A.; Roshnee, F. I.; Shuvro, K.; Tasin, M. H. R.; Akter, R.; Islam, M. E.; Islam, K. M. D.; Rahman, S. M. M.; Billah, M. M. | Md Morsaline Billah | Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna-9208, Bangladesh | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622791.source.xml | Nitrogen is a crucial element for plant growth, driving vibrant greenery, photosynthesis, and overall vitality. This research focused on isolating, characterizing, and identifying nitrogen-fixing bacteria from the rhizosphere of Sonneratia apetala in the Sundarbans, Khulna, Bangladesh, with the goal of assessing their potential as biofertilizers. Despite the Sundarbans rich microbial diversity, less than 5 to 10% of species have been identified due to challenges in culturing, which has limited exploration of their applications. In this study, nitrogen-fixing bacteria were isolated using nitrogen-free media, including yeast extract mannitol agar(YEMA) and Burks media, followed by an ammonification test to select ammonia-producing bacteria. This process yielded ten nitrogen-fixing bacterial isolates capable of producing indole-3-acetic acid (IAA). Various biochemical tests, including oxidase, catalase, methyl red, indole, urease, citrate, triple sugar iron, and starch hydrolysis, were conducted. The isolates, designated AK1 to AK10, were identified as Rossellomorea sp., Clostridium sp., Achromobacter sp., Pseudomonas sp., Gluconacetobacter sp., Scytonema sp., Pseudomonas sp., Nesterenkonia sp., Gluconacetobacter sp., and Bacillus sp., respectively. Additionally, isolates AK1, AK3, AK4, and AK10 were confirmed through 16S rRNA sequencing. A pot test further revealed that isolate AK-1 significantly stimulated the growth and development of maize seedlings. Future studies are needed to examine the impact of these bacterial isolates on crop yield and seed quality, to better determine their suitability as biofertilizers. | null | biorxiv |
10.1101/2024.11.08.622696 | Assessing reliability and accuracy of qPCR, dPCR and ddPCR for estimating mtDNA copy number in songbird blood and sperm cells | Bagdonaite, L.; Leder, E. H.; Lifjeld, J. T.; Johnsen, A.; Mauvisseau, Q. | Laima Bagdonaite | Natural History Museum, University of Oslo | 2024-11-09 | 1 | new results | cc_by_nc_nd | molecular biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622696.source.xml | Mitochondrial DNA copy number varies across species, individuals and cell types. Two avian cell types carrying a relatively low number of mitochondria are the red blood cells and spermatozoa. While previous studies investigating variation of mitochondrial abundance in animal sperm have generally used quantitative PCR (qPCR), this method shows potential limitations when quantifying low abundant targets. To mitigate such issues, we investigated and compared the reliability and accuracy of qPCR, digital PCR (dPCR) and droplet digital PCR (ddPCR) to quantify high and low concentration DNA. Using synthetic DNA, we found that both dPCR and ddPCR displayed lower Limit of Detection and Limit of Quantification than qPCR. Using DNA extracted from blood and sperm cells of Eurasian Siskin, we found that qPCR, dPCR and ddPCR reliably quantified mitochondrial DNA in sperm samples, but showed significant differences when analyzing typically lower levels of mtDNA in blood. We found that ddPCR consistently showed lower variation among replicates. These analyses provide critical insights and recommendations for future studies aiming to quantify target mtDNA. Our study indicates that dPCR and ddPCR are the preferred methods when working with samples with low abundance of mtDNA. | null | biorxiv |
10.1101/2024.11.09.622792 | Perilipin 5 Phosphorylation is Dispensable for Upregulation of Hepatic Lipid Metabolism Genes upon Fasting but Required for Insulin Receptor Substrate 2 Expression in Male Mice | Bovee, C.; Grandgenett, R.; Trevino, M.; Dutta, S.; Peachee, S.; Kopriva, S.; Haider, F.; Liu, S.; Bhardwaj, G.; Penniman, C.; O'Neill, B.; Imai, Y. | Yumi Imai | University of Iowa | 2024-11-09 | 1 | new results | cc_no | molecular biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622792.source.xml | Objective Perilipin 5 (PLIN5) is a lipid droplet protein highly expressed in cells that actively oxidize fatty acids. Previous in vitro studies have revealed that PLIN5 phosphorylation (p-PLIN5) at serine 155 by PKA is critical for transcriptional regulation of PPARa target genes by which PLIN5 adapt cells for fatty acid oxidation. We aim to determine the extent of p-PLIN5 in vivo and the consequence of impaired PLIN5 phosphorylation in the liver by using a whole-body knock-in of phosphorylation resistant PLIN5 (SA/SA) in mice. Methods We measured PLIN5 and p-PLIN5 with mass spectrometry and Phos-tag gels. We assessed serum chemistry in WT and SA/SA mice upon fasting. RNA sequencing and qPCR compared the gene expression in the liver of SA/SA and WT mice after overnight fast. Results Plin5 phosphorylation at S155 was increased in the liver LD fraction of fasted mice compared with that of fed mice by mass spectrometry (p<0.05). qPCR of key lipid metabolism genes did not differ between WT and SA/SA liver upon fasting. Male SA/SA mice had a higher fasting blood glucose (p<0.05) without a difference in body weight, serum insulin, or serum lipids. IRS2 was reduced in the liver of fasted male SA/SA mice (p<0.05). Conclusion: PLIN5 S155 phosphorylation is dispensable for the upregulation of lipid metabolism genes important for fasting response in vivo. Impaired phosphorylation also had little effect on serum lipids or liver TG. However, SA/SA mice showed decreased IRS2 expression in the liver, which may contribute to glucose intolerance in SA/SA male mice. | null | biorxiv |
10.1101/2024.11.07.622440 | Unpacking fitness differences between two invaders in a multispecies context | Freire, T. F. A.; Madec, S.; Gjini, E. | Erida Gjini | Center for Computational and Stochastic Mathematics, Instituto Superior Tecnico, University of Lisbon, Lisbon, Portugal | 2024-11-09 | 1 | new results | cc_by_nc_nd | ecology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622440.source.xml | Ecosystems are constantly exposed to new strains of a given species. Which strain will be able to invade a resident multi-species community depends on the strain's relative fitness. Here we develop an approach to quantify fitness differences between two co-invading strains based on the replicator equation. By assuming that the resident species' frequencies remain constant during the initial phase of invasion, we are able to determine the invasion fitness differential between the two strains, which drives growth rate differences post-invasion. We then apply our approach to a critical current global problem: invasion of the gut microbiota by antibiotic resistant strains of the pathobiont Escherichia coli. Our results underscore the context-dependent nature of fitness and demonstrate how species frequencies in a host environment can explicitly modulate the selection coefficient between two strains. This framework can predict relative fitness in new environments and may contribute to design strategies to lower resistance levels in microbiomes. | null | biorxiv |
10.1101/2024.11.08.622685 | Precise Lineage Tracking Using Molecular Barcodes Demonstrates Fitness Trade-offs for Ivermectin Resistance in Nematodes | Stevenson, Z. C.; Laufer, E.; Estevez, A. O.; Robinson, K.; Phillips, P. C. | Patrick C. Phillips | University of Oregon | 2024-11-09 | 1 | new results | cc_by_nd | evolutionary biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622685.source.xml | A fundamental tenet of evolutionary genetics is that the direction and strength of selection on individual loci varies with the environment. Barcoded evolutionary lineage tracking is a powerful approach for high-throughput measurement of selection within experimental evolution that to date has largely been restricted to studies within microbial systems, largely because the random integration of barcodes within animals is limited by physical and molecular protection of the germline. Here, we use the recently developed TARDIS barcoding system in Caenorhabditis elegans (Stevenson et al., 2023) to implement the first randomly inserted genomic-barcode experimental evolution animal model and use this system to precisely measure the influence of the concentration of the anthelmintic compound ivermectin on the strength of selection on an ivermectin resistance cassette. The combination of the trio of knockouts in neuronally expressed GluCl channels, avr-14, avr-15, and glc-1, has been previously demonstrated to provide resistance to ivermectin at high concentrations. Varying the concentration of ivermectin in liquid culture allows the strength of selection on these genes to be precisely controlled within populations of millions of individuals, yielding the largest animal experimental evolution study to date. The frequency of each barcode was determined at multiple time points via sequencing at deep coverage and then used to estimate the fitness of the individual lineages in the population. The mutations display a high cost to resistance at low concentrations, rapidly losing out to wildtype genotypes, but the balance tips in their favor when the ivermectin concentration exceeds 2nM. This trade-off in resistance is likely generated by a hindered rate of development in resistant individuals. Our results demonstrate that C. elegans can be used to generate high precision estimates of fitness using a high-throughput barcoding approach to yield novel insights into evolutionarily and economically important traits. | null | biorxiv |
10.1101/2024.11.07.622307 | A consensus variant-to-function score to functionally prioritize variants for disease | Fabiha, T.; Raine, I.; Kundu, S.; Pampari, A.; Abramov, S.; Boytsov, A.; Strouse, K.; Dura, K.; Fang, W.; Kerner, G.; Butts, J.; Ali, T.; Gschwind, A.; Mualim, K. S.; Moore, J. E.; Weng, Z.; Ulirsch, J.; Ji, H. E.; Vierstra, J.; Reddy, T. E.; Montgomery, S. B.; Engreitz, J.; Kundaje, A.; Tewhey, R.; Price, A.; Dey, K. | Kushal Dey | Memorial Sloan Kettering Cancer Center; Weill Cornell Medicine | 2024-11-09 | 1 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622307.source.xml | Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score that assigns a single value to each common single-nucleotide variant in the genome, and helps to predict and characterize causal disease variants. The cV2F score leverages features reflecting variant-level experimentally and computationally predicted function (e.g. allelic imbalance and sequence-based deep learning models) and element-level function (e.g. predicted enhancers), and learns optimal combinations of features by training a gradient boosting model on GWAS fine-mapping results. The cV2F-annotated variants attained an AUPRC of 0.822 at identifying held-out fine-mapped variants. Variants with high cV2F scores are highly enriched for heritability (14.2x, s.e. 0.5) across 66 diseases/traits, are uniquely informative for disease heritability, and are highly predictive of variants implicated by reporter assays; cV2F substantially outperforms previous variant-to-function scores using all of these metrics. GWAS fine-mapping of 110 diseases/traits informed by cV2F identified 14.3% more confidently fine-mapped (PIP > 0.95) variants than non-functionally informed fine-mapping. We further constructed tissue/cell line-specific cV2F scores that prioritize variants based on regulatory potential in specific tissues/cell lines, attaining high heritability enrichment for tissue-related diseases/traits (15.6x, s.e. 2.3) while providing independent information (average correlation of 0.27 with the primary cV2F score). We highlight examples of GWAS loci for which cV2F pinpoints causal variants with high confidence and elucidates their functional role. | null | biorxiv |
10.1101/2024.11.07.622307 | A consensus variant-to-function score to functionally prioritize variants for disease | Fabiha, T.; Evergreen, I.; Kundu, S.; Pampari, A.; Abramov, S.; Boytsov, A.; Strouse, K.; Dura, K.; Fang, W.; Kerner, G.; Butts, J.; Ali, T.; Gschwind, A.; Mualim, K. S.; Moore, J. E.; Weng, Z.; Ulirsch, J.; Ji, H. E.; Vierstra, J.; Reddy, T. E.; Montgomery, S. B.; Engreitz, J.; Kundaje, A.; Tewhey, R.; Price, A.; Dey, K. | Kushal Dey | Memorial Sloan Kettering Cancer Center; Weill Cornell Medicine | 2024-11-10 | 2 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/10/2024.11.07.622307.source.xml | Identifying and functionally characterizing causal disease variants in genome-wide association studies remains a pressing challenge. Here, we construct a consensus variant-to-function (cV2F) score that assigns a single value to each common single-nucleotide variant in the genome, and helps to predict and characterize causal disease variants. The cV2F score leverages features reflecting variant-level experimentally and computationally predicted function (e.g. allelic imbalance and sequence-based deep learning models) and element-level function (e.g. predicted enhancers), and learns optimal combinations of features by training a gradient boosting model on GWAS fine-mapping results. The cV2F-annotated variants attained an AUPRC of 0.822 at identifying held-out fine-mapped variants. Variants with high cV2F scores are highly enriched for heritability (14.2x, s.e. 0.5) across 66 diseases/traits, are uniquely informative for disease heritability, and are highly predictive of variants implicated by reporter assays; cV2F substantially outperforms previous variant-to-function scores using all of these metrics. GWAS fine-mapping of 110 diseases/traits informed by cV2F identified 14.3% more confidently fine-mapped (PIP > 0.95) variants than non-functionally informed fine-mapping. We further constructed tissue/cell line-specific cV2F scores that prioritize variants based on regulatory potential in specific tissues/cell lines, attaining high heritability enrichment for tissue-related diseases/traits (15.6x, s.e. 2.3) while providing independent information (average correlation of 0.27 with the primary cV2F score). We highlight examples of GWAS loci for which cV2F pinpoints causal variants with high confidence and elucidates their functional role. | null | biorxiv |
10.1101/2024.11.08.622724 | Generation of a novel constitutive smooth muscle cell-specific Myh11-driven Cre mouse model | Dong, K.; Bai, Z.; He, X.; Zhang, L.; Hu, G.; Yao, Y.; Cai, C.-L.; Zhou, J. | Jiliang Zhou | https://www.augusta.edu/ | 2024-11-09 | 1 | new results | cc_no | genetics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622724.source.xml | Dysfunction in either embryonic or postnatal vascular smooth muscle cells (SMCs) significantly contributes to the progression of various cardiovascular diseases. Therefore, elucidating the molecular mechanisms governing VSMC development and homeostasis is crucial. MYH11 is the most reliable lineage gene for SMCs and has been utilized to develop tamoxifen-inducible Cre driver lines for achieving SMC-specific gene manipulation by crossing with mice carrying the loxP-flanked gene, particularly in adult mice. For studies involving SMCs during embryogenesis, the commonly used constitutive Cre driver is controlled by the Tagln (SM22a) promoter. However, this Cre driver exhibits activity in multiple non-SMC populations, including cardiomyocytes and skeletal muscle precursors, introducing confounding effects. Additionally, most existing SMC-specific Cre drivers are generated using a transgenic approach, raising concerns about random site integration and variable gene copy numbers. To address these limitations, we report a novel Cre mouse model generated by knock-in (KI) of a nuclear-localized Cre recombinase into the Myh11 gene locus using homologous recombination. We confirmed that the Cre activity precisely recapitulates endogenous Myh11 expression by crossing with Rosa26 mTmG or tdTomato reporter mice. Moreover, Myh11-driven Cre can efficiently delete the floxed allele of the transcription factor Tead1 specifically in SMCs. The Tead1 SMC-specific knockout mice did not exhibit an overt phenotype, thereby circumventing the embryonic lethal phenotype mediated by Tagln-driven Cre, as we previously reported. These findings establish this novel Cre driver line as a robust tool for tracing the Myh11-positive SMC lineage and manipulating gene function specifically in SMCs during embryonic development in mice. | null | biorxiv |
10.1101/2024.11.07.622479 | TissueMosaic enables cross-sample differential analysis of spatial transcriptomics datasets through self-supervised representation learning | Kambhampati, S.; D'Alessio, L.; Grab, F.; Fleming, S. J.; Chen, F.; Babadi, M. | Sandeep Kambhampati | Harvard University | 2024-11-09 | 1 | new results | cc_no | bioinformatics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622479.source.xml | Spatial transcriptomics allows for the measurement of gene expression within native tissue context, thereby improving our understanding of how cell states are modulated by their microenvironment. Despite technological advancements, computational methods to link cell states with their microenvironment and perform comparative analysis across different samples and conditions are still underdeveloped. To address this, we introduce TissueMosaic (Tissue MOtif-based SpAtial Inference across Conditions), a self-supervised convolutional neural network designed to discover and represent tissue architectural motifs from multi-sample spatial transcriptomic datasets (https://github.com/broadinstitute/TissueMosaic). TissueMosaic effectively maps structurally similar tissue motifs close together in a learned latent space. TissueMosaic further links these motifs to gene expression, enabling the study of how changes in tissue structure impact function. TissueMosaic increases the signal-to-noise ratio of differential expression analysis through a motif enrichment strategy, resulting in more reliable detection of genes that covary with tissue structure. Here, we demonstrate TissueMosaic on high resolution spatial transcriptomics datasets across tissues, learning representations that outperform neighborhood cell-type composition baselines and existing methods on downstream tasks. We highlight genes and pathways in these tissues that are associated with changes in tissue structure across external conditions. These findings underscore the potential of self-supervised learning to significantly advance spatial transcriptomics research. | null | biorxiv |
10.1101/2024.11.06.622264 | Phenylacetic acid metabolism in land plants: novel pathways and metabolites | Hladik, P.; Brunoni, F.; Zukauskaite, A.; Zatloukal, M.; Belicek, J.; Kopecny, D.; Briozzo, P.; Ferchaud, N.; Novak, O.; Pencik, A. | Ales Pencik | Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences & Faculty of Science, Palacky University, Olomouc, Czech Republ | 2024-11-09 | 1 | new results | cc_by | plant biology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.06.622264.source.xml | In recent years, substantial progress has been made in exploring auxin conjugation and metabolism, primarily aiming at indole-3-acetic acid (IAA). However, the metabolic regulation of another key auxin, phenylacetic acid (PAA), remains largely uncharacterized. Here, we provide a comprehensive exploration of PAA metabolism in land plants. Through LC-MS screening across multiple plant species and their organs, we identified four previously unreported endogenous PAA metabolites: phenylacetyl-leucine (PAA-Leu), phenylacetyl-phenylalanine (PAA-Phe), phenylacetyl-valine (PAA-Val), and phenylacetyl-glucose (PAA-glc). Enzyme assays, genetic evidence, crystal structures, and docking studies demonstrate that PAA and IAA share core metabolic machinery, revealing a complex regulatory network that maintains auxin homeostasis. Furthermore, our study of PAA conjugation with amino acids and glucose suggests limited compensatory mechanisms within known conjugation pathways, pointing to the existence of alternative metabolic routes in land plants. These insights advance our knowledge of auxin-specific metabolic networks and highlight the unique complexity within plant hormone regulation. | null | biorxiv |
10.1101/2024.11.08.622749 | Identification of Covalent Cyclic Peptide Inhibitors Targeting Protein-Protein Interactions Using Phage Display | Wang, S.; Faucher, F. F.; Bertolini, M.; Kim, H.; Yu, B.; Cao, L.; Roeltgen, K.; Lovell, S.; Shanker, V.; Boyd, S. D.; Wang, L.; Bartenschlager, R.; Bogyo, M. | Matthew Bogyo | Stanford University | 2024-11-09 | 1 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622749.source.xml | Peptide macrocycles are promising therapeutics for a variety of disease indications due to their overall metabolic stability and potential to make highly selective binding interactions with targets. Recent advances in covalent macrocycle peptide discovery, driven by phage and mRNA display methods, have enabled the rapid identification of highly potent and selective molecules from large libraires of diverse macrocycles. However, there are currently limited examples of macrocycles that can be used to disrupt protein-protein interactions and even fewer examples that function by formation of a covalent bond to a target protein. In this work, we describe a directed counter-selection method that enables identification of covalent macrocyclic ligands targeting a protein-protein interaction using a phage display screening platform. This method utilizes binary and ternary screenings of a chemically modified phage display library, employing the stable and weakly reactive aryl fluorosulfate electrophile. We demonstrate the utility of this approach using the SARS-CoV-2 Spike-ACE2 protein-protein interaction and identify multiple covalent macrocyclic inhibitors that disrupt this interaction. The resulting compounds displayed antiviral activity against live virus that was irreversible after washout due to the covalent binding mechanism. These results highlight the potential of this screening platform for developing covalent macrocyclic drugs that disrupt protein-protein interactions with long lasting effects. | null | biorxiv |
10.1101/2024.11.08.622755 | Carotenoid pigments enhance rhodopsin-mediated phototrophy by light-harvesting and photocycle-accelerating | Fujiwara, T.; Hosaka, T.; Hasegawa-Takano, M.; Nishimura, Y.; Tominaga, K.; Mori, K.; Nishino, S.; Takahashi, Y.; Uchikubo-Kamo, T.; Hanada, K.; Maoka, T.; Takaichi, S.; Inoue, K.; Shirouzu, M.; Yoshizawa, S. | Susumu Yoshizawa | The University of Tokyo | 2024-11-09 | 1 | new results | cc_by_nc_nd | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622755.source.xml | Microbial rhodopsins, photoreceptor proteins widely distributed in marine microorganisms, receive large amount of light energy that sustains marine ecosystems. Although rhodopsins generally harbor retinal as their only chromophore, a recent study reported that carotenoid antennae transfer light energy to the retinal in proteorhodopsins, proton pump rhodopsins abundant in marine environments. Here, using marine bacterial isolates, we detected energy transfer from a carotenoid (myxol) to retinal not only in proteorhodopsin but also in the chloride ion-pumping rhodopsin. Carotenoid binding improved the light utilization efficiency of the proteorhodopsin by accelerating the photocycle, together with facilitating light-harvesting. The carotenoid-binding ability is conserved in rhodopsins of the phylum Bacteroidota, which are widely transcribed in the photic zone. These findings suggest that the distribution of carotenoid-binding rhodopsins is more taxon-specific than previously thought, thus underscoring the importance of carotenoid-binding rhodopsins that provide an extended light utilization strategy in the environmental adaptation of marine bacteria. | null | biorxiv |
10.1101/2024.11.08.622053 | A bacterial cell wall repair and modification system to resist host antibacterial factors | Burnier, J.; Gallay, C.; Bruce, K.; Bjanes, E.; Martin, L.; Jim, K. K.; Tsui, T.; Cremers, A.; Mignolet, J.; Vollmer, D.; Biboy, J.; Nizet, V.; Vollmer, W.; Winkler, M. E.; Veening, J.-W. | Jan-Willem Veening | University of Lausanne | 2024-11-09 | 1 | new results | cc_by | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.08.622053.source.xml | Pathogenic bacteria have acquired the ability to resist antibacterial defense mechanisms of the host. Streptococci are common in animal microbiota and include opportunistic pathogens like Group A Streptococcus (GAS) and Streptococcus pneumoniae (pneumococcus). While the conserved streptococcal S protein has been identified as a key factor in GAS virulence, its exact function is unclear. Here, we show that the pneumococcal S protein is crucial for resisting against host-derived antimicrobials by coordinating cell wall modification and repair. Specifically, we show that S proteins are septally localized through their transmembrane domain and contain an extracellular peptidoglycan (PG) binding LysM domain which is required for its function. Protein-protein and genetic interaction studies demonstrate that the pneumococcal S protein directly interacts with a PG synthase, class A penicillin binding protein PBP1a, and the PG deacetylase PgdA. Single-molecule experiments reveal that the fraction of circumferentially moving PBP1a molecules is reduced in the absence of S protein. Consistent with an impaired PBP1a function, streptococci lacking S protein exhibit increased susceptibility to cell wall targeting antibiotics and altered cell morphologies. PG analysis showed reduced N-deacetylation of glycans in the S. pneumoniae S protein mutant, indicating reduced PgdA activity. We show that pneumococci lacking the S protein cannot persist transient penicillin treatment, are more susceptible to the human antimicrobial peptide LL-37 and to lysozyme, and show decreased virulence in zebrafish and mice. Our data support a model in which S proteins regulate PBP1a activity and play a key role in coordinating PG repair and modification. This cell wall sentinel control system provides defense against host-derived and environmental antimicrobial attack. | null | biorxiv |
10.1101/2024.11.09.622756 | Characterization of a GpsB-associated regulator of PBP1a reveals the organization of the cell wall remodeling complex of Streptococcus pneumoniae | Millat, H.; Lenoir, C.; Falcou, C.; Cluzel, C.; Zapun, A.; Roper, D.; Morlot, C.; Ducret, A.; Grangeasse, C. | Christophe Grangeasse | Universite de Lyon/CNRS | 2024-11-09 | 1 | new results | cc_no | microbiology | https://www.biorxiv.org/content/early/2024/11/09/2024.11.09.622756.source.xml | Class A PBPs (aPBPs) play a key role in the biosynthesis and remodeling of peptidoglycan, the main component of the bacterial cell wall. The human bacterial pathogen Streptococcus pneumoniae produces three aPBPs, which are regulated to maintain the bacterium ovoid shape. Although their exact functions remain unclear, evidence suggests that PBP1a and PBP2a activities are closely coordinated. In this study, we elucidated the function of an unknown function protein named GarP (GpsB-associated regulator of PBP1a), in the regulation of PBP1a activity. We showed that GarP localizes to the division septum and its absence leads to morphological defects. We further identified a GpsB-binding motif in GarP as well as in PBP2a, the PG deacetylase PgdA and the muramidase MpgA. Our analysis of genetic and protein interactions, combined with cell imaging, supports a model of a molecular complex that coordinates PG remodeling during S. pneumoniae cell division. | null | biorxiv |
10.1101/2024.11.07.622502 | Bayesian nonparametric analysis of residence times for protein-lipid interactions in Molecular Dynamics simulations | Sexton, R. C.; Fazel, M.; Schweiger, M. C.; Presse, S.; Beckstein, O. | Oliver Beckstein | Arizona State University | 2024-11-09 | 1 | new results | cc_by | biophysics | https://www.biorxiv.org/content/early/2024/11/09/2024.11.07.622502.source.xml | Molecular Dynamics (MD) simulations are a versatile tool to investigate the interactions of proteins within their environments, in particular of membrane proteins with the surrounding lipids. However, quantitative analysis of lipid-protein binding kinetics has remained challenging due to considerable noise and low frequency of long binding events, even in hundreds of microseconds of simulation data. Here we apply Bayesian nonparametrics to compute residue-resolved residence time distributions from MD trajectories. Such an analysis characterizes binding processes at different timescales (quantified by their kinetic off-rate) and assigns to each trajectory frame a probability of belonging to a specific process. In this way, we classify trajectory frames in an unsupervised manner and obtain, for example, different binding poses or molecular densities based on the timescale of the process. We demonstrate our approach by characterizing interactions of cholesterol with six different G-protein coupled receptors (A2AAR, {beta}2AR, CB1R, CB2R, CCK1R, CCK2R) simulated with coarse-grained MD simulations with the MARTINI model. The nonparametric Bayesian analysis allows us to connect the coarse binding time series data to the underlying molecular picture and, thus, not only infers accurate binding kinetics with error distributions from MD simulations but also describes molecular events responsible for the broad range of kinetic rates. | null | biorxiv |