title: Copy-scAT: Deconvoluting single-cell chromatin accessibility of genetic subclones in cancer

abstract: Single-cell epigenomic assays have tremendous potential to illuminate mechanisms of transcriptional control in functionally diverse cancer cell populations. However, application of these techniques to clinical tumor specimens has been hampered by the current inability to distinguish malignant from non-malignant cells, which potently confounds data analysis and interpretation. Here we describe Copy-scAT, an R package that uses single-cell epigenomic data to infer copy number variants (CNVs) that define cancer cells. Copy-scAT enables studies of subclonal chromatin dynamics in complex tumors like glioblastoma. By deploying Copy-scAT, we uncovered potent influences of genetics on chromatin accessibility profiles in individual subclones. Consequently, some genetic subclones were predisposed to acquire stem-like or more differentiated molecular phenotypes, reminiscent of developmental paradigms. Copy-scAT is ideal for studies of the relationships between genetics and epigenetics in malignancies with high levels of intratumoral heterogeneity and to investigate how cancer cells interface with their microenvironment.


title: Single-molecule FRET dynamics of molecular motors in an ABEL Trap

abstract: Single-molecule Forster resonance energy transfer (smFRET) of molecular motors provides transformative insights into their dynamics and conformational changes both at high temporal and spatial resolution simultaneously. However, a key challenge of such FRET investigations is to observe a molecule in action for long enough without restricting its natural function. The Anti-Brownian ELectrokinetic Trap (ABEL trap) sets out to combine smFRET with molecular confinement to enable observation times of up to several seconds while removing any requirement of tethered surface attachment of the molecule in question. In addition, the ABEL traps inherent ability to selectively capture FRET active molecules accelerates the data acquisition process. In this work we exemplify the capabilities of the ABEL trap in performing extended timescale smFRET measurements on the molecular motor Rep, which is crucial for removing protein blocks ahead of the advancing DNA replication machinery and for restarting stalled DNA replication. We are able to monitor single Rep molecules up to 6 s with sub-millisecond time resolution capturing multiple conformational switching events during the observation time. Here we provide a step-by-step guide for the rational design, construction and implementation of the ABEL trap for smFRET detection of Rep in vitro. We include details of how to model the electric potential at the trap site and use Hidden Markov analysis of the smFRET trajectories.

category: biophysics


title: Mouse Single Islet β Cell Transcriptomics Reveal Sexually Dimorphic Transcriptomes and Type 2 Diabetes Genes

abstract: Type 2 diabetes (T2D), characterized by malfunction of pancreatic {beta} cells, is affected by multiple cues including sex differences. Nevertheless, mechanisms of sex differences in type 2 diabetes susceptibility and pathogenesis remain unclear. Using single-cell RNA sequencing (scRNA-seq) technology, we showed that sexual dimorphism of transcriptome exists in mouse {beta} cells. Our analysis further revealed the existence of sex-dependent type 2 diabetes altered genes in high fat diet induced T2D model, suggesting divergences in pathological mechanisms of type 2 diabetes between sexes. Our results indicated that sex should be taken into consideration when treating diabetes, which was further validated by the sex-matched and sex-mismatched islet transplantation in mice. Compared to sex-matched transplants, sex-mismatched transplants showed downregulation of genes involved in the longevity regulating pathway in {beta} cells and led to impaired glucose tolerance in diabetic mice. Taken together, our findings could advance current understanding of type 2 diabetes pathogenesis with sexually dimorphic perspectives and provide new insights to the development of precision medicine.

category: bioinformatics


title: Autonomic/Central Coupling during Daytime Sleep Differs between Older and Younger People

abstract: Age-dependent functional changes are mirrored by declines in both the central the autonomic nervous systems and have been related to pathological aging. Prior studies in our group have identified a temporal coupling of Autonomic and Central Events (ACEs) during sleep using electrocardiogram to measure heart rate and electroencephalography to measure brain rhythms, with heart rate bursts (HRBs) temporally coincided with increased slow-wave-activity (SWA, 0.5-1Hz) and sigma activity (12-15Hz), followed by parasympathetic surge (RRHF) during non-rapid eye movement (NREM) sleep. ACEs predicted working memory (WM) improvement in young adults. Given that there are paralleling age-related declines in both the ANS and CNS, the current study investigated differences in ACE activity during daytime sleep in older and younger adults and their functional impact on working memory. Compared to youngers, older adults showed lower amplitude of ACEs during NREM sleep, but no age-related difference during Wake. Furthermore, while younger adults demonstrated a parasympathetic surge after HRBs, older adults showed a different pattern, with a earlier rise and maintenance of the RRHF. Finally, we examined whether ACE predicted WM in older adults. We found that older adults with good WM show stronger coupling, whereas low WM performers had less robust ACE activity. Taken together, our results demonstrated that autonomic-central coupling declines with age, with possible links to deterioration in WM function. Given that age-related deterioration in autonomic and central nervous system activity is implicated in pathological decline, the current findings may facilitate novel insights to the cognitive neuroscience of aging.

category: neuroscience


title: Spatial population genetics in heavily managed species: Separating patterns of historical translocation from contemporary gene flow in white-tailed deer

abstract: Approximately 100 years ago, unregulated harvest nearly eliminated white-tailed deer (Odocoileus virginianus) from eastern North America, which subsequently served to catalyze wildlife management as a national priority. An extensive stock-replenishment effort soon followed, with deer broadly translocated among states as a means of re-establishment. However, an unintended consequence was that natural patterns of gene flow became obscured and pre-translocation signatures of population structure were replaced. We applied cutting-edge molecular and biogeographic tools to disentangle genetic signatures of historical management from those reflecting spatially heterogeneous dispersal by evaluating 35,099 single nucleotide polymorphisms (SNPs) derived via reduced-representation genomic sequencing from 1,143 deer sampled state-wide in Arkansas. We then employed Simpsons diversity index to summarize ancestry assignments and visualize spatial genetic transitions. Using sub-sampled transects across these transitions, we tested clinal patterns across loci against theoretical expectations of their response under scenarios of recolonization and restricted dispersal. Two salient results emerged: (A) Genetic signatures from historic translocations are demonstrably apparent; and (B) Geographic filters (major rivers; urban centers; highways) now act as inflection points for the distribution of this contemporary ancestry. These results yielded a state-wide assessment of contemporary population structure in deer as driven by historic translocations as well as ongoing processes. In addition, the analytical framework employed herein to effectively decipher extant/historic drivers of deer distribution in Arkansas are also applicable for other biodiversity elements with similarly complex demographic histories.

category: evolutionary biology


title: Dorsal raphe nucleus to anterior cingulate cortex 5-HTergic neural circuit modulates consolation and sociability

abstract: Consolation is a common response to the distress of others in humans and some social animals, but the neural mechanisms underlying this behavior are not well characterized. By using socially monogamous mandarin voles, we found that optogenetic or chemogenetic inhibition of 5-HTergic neurons in the dorsal raphe nucleus (DR) or optogenetic inhibition of 5-HT terminals in the anterior cingulate cortex (ACC) significantly decreased allogrooming time in the consolation test and reduced sociability in the three-chamber test. The release of 5-HT within the ACC and the activity of DR neurons were significantly increased during allogrooming, sniffing and social approaching. Finally, we found that the activation of 5-HT1A receptors in the ACC was sufficient to reverse consolation and sociability deficits induced by the chemogenetic inhibition of 5-HTergic neurons in the DR. Our study provided first direct evidence that DR-ACC 5-HTergic neural circuit is implicated in consolation-like behaviors and sociability.


title: Influence of sensory modality and control dynamics on human path integration

abstract: Path integration is a sensorimotor computation that can be used to infer latent dynamical states by integrating self-motion cues. We studied the influence of sensory observation (visual/vestibular) and latent control dynamics (velocity/acceleration) on human path integration using a novel motion-cueing algorithm. Sensory modality and control dynamics were both varied randomly across trials, as participants controlled a joystick to steer to a memorized target location in virtual reality. Visual and vestibular steering cues allowed comparable accuracies only when participants controlled their acceleration, suggesting that vestibular signals, on their own, fail to support accurate path integration in the absence of sustained acceleration. Nevertheless, performance in all conditions reflected a failure to fully adapt to changes in the underlying control dynamics, a result that was well explained by a bias in the dynamics estimation. This work demonstrates how an incorrect internal model of control dynamics affects navigation in volatile environments in spite of continuous sensory feedback.


title: EEG Cross-Frequency Phase Synchronization as an Index of Memory Matching in Visual Search

abstract: Visual perception is influenced by our expectancies about incoming sensory information. It is assumed that mental templates of expected sensory input are created and compared to actual input, which can be matching or not. When such mental templates are held in working memory, cross-frequency phase synchronization (CFS) between theta and gamma band activity has been proposed to serve matching processes between prediction and sensation. We investigated how this is affected by the number of activated templates that could be matched by comparing conditions where participants had to keep either one or multiple templates in mind for successful visual search. We found a transient CFS between EEG theta and gamma activity in an early time window around 150ms after search display presentation, in right hemispheric parietal cortex. Our results suggest that for single template conditions, stronger transient theta-gamma CFS at posterior sites contralateral to target presentation can be observed than for multiple templates. This can be interpreted as evidence to the idea of sequential attentional templates. But mainly, it is understood in line with previous theoretical accounts strongly arguing for transient synchronization between posterior theta and gamma phase as a neural correlate of matching incoming sensory information with contents from working memory and as evidence for limitations in memory matching during multiple template search.


title: Cone Opponent Functional Domains in Primary Visual Cortex Combine Signals for Color Appearance Mechanisms

abstract: Studies of color perception have led to mechanistic models of how cone-opponent signals from retinal ganglion cells are integrated to generate color appearance. But it is unknown how this hypothesized integration occurs in the brain. Here we show that cone-opponent signals transmitted from retina to primary visual cortex (V1) are integrated through highly organized circuits within V1 to implement the color opponent interactions required for color appearance. Combining intrinsic signal optical imaging (ISI) and 2-photon calcium imaging (2PCI) at single cell resolution, we demonstrate cone-opponent functional domains (COFDs) that combine L/M cone-opponent and S/L+M cone-opponent signals following the rules predicted from psychophysical studies of color perception. These give rise to an orderly organization of hue preferences of the neurons within the COFDs and the generation of hue "pinwheels". Thus, spatially organized neural circuits mediate an orderly transition from cone-opponency to color appearance that begins in V1.


title: RNA-sequencing manifests the intrinsic role of MAPKAPK2 in facilitating molecular crosstalk during HNSCC pathogenesis

abstract:
BackgroundTranscriptome profiling has been pivotal in better comprehending the convoluted biology of tumors including head and neck squamous cell carcinoma (HNSCC). Recently, growing evidence has implicated the role of mitogen-activated protein kinase-activated protein kinase-2 (MAPKAPK2 or MK2) in many human diseases including tumors. MK2 has been recently reported as a critical regulator of HNSCC that functions via modulating the transcript turnover of crucial genes involved in its pathogenesis. Comprehensive MK2-centric transcriptomic analyses could help the scientific community to delve deeper into MK2-pathway driven mechanisms of tumor progression, but such studies have not yet been reported. Consequently, to delineate the biological relevance of MK2 and its intricate crosstalk in the tumor milieu, an extensive transcriptome analysis of HNSCC was conceptualized and effectuated with MK2 at the nexus.

MethodsIn the current study, comprehensive next-generation sequencing-based transcriptome profiling was accomplished to ascertain global patterns of mRNA expression profiles in both in vitro and in vivo models of the HNSCC microenvironment. The findings of the RNA-sequencing analysis were cross-validated via robust validation using nCounter gene expression assays, immunohistochemistry, and real-time quantitative polymerase chain reaction (RT-qPCR).

ResultsTranscriptomic characterization followed by annotation and differential gene expression analyses identified certain MK2-regulated candidate genes constitutively involved in regulating HNSCC pathogenesis, and the biological significance of these genes was established by pathway enrichment analysis. Additionally, advanced gene expression assays through the nCounter system in conjunction with immunohistochemical analysis validated the transcriptome profiling outcomes quite robustly. Furthermore, the results obtained from immunohistochemistry and transcript stability analysis indicated the crucial role of MK2 in the modulation of the expression pattern of these genes in HNSCC tumors and cells.

ConclusionsConclusively, the findings have paved the way toward the identification of new effective tumor markers and potential molecular targets for HNSCC management. The results have accentuated the importance of certain differentially expressed MK2-regulated genes that are constitutively involved in HNSCC pathogenesis to potentially serve as putative candidates for future endeavors pertaining to diagnosis and therapeutic interventions for HNSCC.

category: cancer biology


title: Identification of a Proteomic Signature of Senescence in Primary Human Mammary Epithelial Cells

abstract: Senescence is a permanent cell cycle arrest that occurs in response to cellular stress. Because senescent cells promote age-related disease, there has been considerable interest in defining the proteomic alterations in senescent cells. Because senescence differs greatly depending on cell type and senescence inducer, continued progress in the characterization of senescent cells is needed. Here, we analyzed primary human mammary epithelial cells (HMECs), a model system for aging, using mass spectrometry-based proteomics. By integrating data from replicative senescence, immortalization by telomerase reactivation, and drug-induced senescence, we identified a robust proteomic signature of HMEC senescence consisting of 77 upregulated and 36 downregulated proteins. This approach identified known biomarkers, such as downregulation of the nuclear lamina protein lamin-B1 (LMNB1), and novel upregulated proteins including the {beta}-galactoside-binding protein galectin-7 (LGALS7). Gene ontology enrichment analysis demonstrated that senescent HMECs upregulated lysosomal proteins and downregulated RNA metabolic processes. We additionally integrated our proteomic signature of senescence with transcriptomic data from senescent HMECs to demonstrate that our proteomic signature can discriminate proliferating and senescent HMECs even at the transcriptional level. Taken together, our results demonstrate the power of proteomics to identify cell type-specific signatures of senescence and advance the understanding of senescence in primary HMECs.

category: systems biology


title: Lytic bacteriophages facilitate antibiotic sensitization of Enterococcus faecium

abstract: Enterococcus faecium, a commensal of the human intestine, has emerged as a hospital-adapted, multi-drug resistant (MDR) pathogen. Bacteriophages (phages), natural predators of bacteria, have regained attention as therapeutics to stem the rise of MDR bacteria. Despite their potential to curtail MDR E. faecium infections, the molecular events governing E. faecium-phage interactions remain largely unknown. Such interactions are important to delineate because phage selective pressure imposed on E. faecium will undoubtedly result in phage resistance phenotypes that could threaten the efficacy of phage therapy. In an effort to understand the emergence of phage resistance in E. faecium, three newly isolated lytic phages were used to demonstrate that E. faecium phage resistance is conferred through an array of cell wall-associated molecules, including secreted antigen A (SagA), enterococcal polysaccharide antigen (Epa), wall teichoic acids, capsule, and an arginine-aspartate-aspartate (RDD) protein of unknown function. We find that capsule and Epa are important for robust phage adsorption and that phage resistance mutations in sagA, epaR, and epaX enhance E. faecium susceptibility to ceftriaxone, an antibiotic normally ineffective due to its low affinity for enterococcal penicillin binding proteins. Consistent with these findings, we provide evidence that phages potently synergize with cell wall (ceftriaxone and ampicillin) and membrane-acting (daptomycin) antimicrobials to slow or completely inhibit the growth of E. faecium. Our work demonstrates that the evolution of phage resistance comes with fitness defects resulting in drug sensitization and that lytic phages could potentially serve as antimicrobial adjuvants in treating E. faecium infections.

category: microbiology


title: The COVID-19 PHARMACOME: A method for the rational selection of drug repurposing candidates from multimodal knowledge harmonization

abstract: The SARS-CoV-2 pandemic has challenged researchers at a global scale. The scientific communitys massive response has resulted in a flood of experiments, analyses, hypotheses, and publications, especially in the field of drug repurposing. However, many of the proposed therapeutic compounds obtained from SARS-CoV-2 specific assays are not in agreement and thus demonstrate the need for a singular source of COVID-19 related information from which a rational selection of drug repurposing candidates can be made. In this paper, we present the COVID-19 PHARMACOME, a comprehensive drug-target-mechanism graph generated from a compilation of 10 separate disease maps and sources of experimental data focused on SARS-CoV-2 / COVID-19 pathophysiology. By applying our systematic approach, we were able to predict the synergistic effect of specific drug pairs, such as Remdesivir and Thioguanosine or Nelfinavir and Raloxifene, on SARS-CoV-2 infection. Experimental validation of our results demonstrate that our graph can be used to not only explore the involved mechanistic pathways, but also to identify novel combinations of drug repurposing candidates.


title: PspA adopts an ESCRT-III-like fold and remodels bacterial membranes

abstract: PspA is the main effector of the phage shock protein (Psp) system and preserves the bacterial inner membrane integrity and function. Here, we present the 3.6 [A] resolution cryo-EM structure of PspA assembled in helical rods. PspA monomers adopt a canonical ESCRT-III fold in an extended open conformation. PspA rods are capable of enclosing lipids and generate positive membrane curvature. Using cryo-EM we visualized how PspA remodels membrane vesicles into m-sized structures and how it mediates the formation of internalized vesicular structures. Hot spots of these activities are zones derived from PspA assemblies, serving as lipid transfer platforms and linking previously separated lipid structures. These membrane fusion and fission activities are in line with the described functional properties of bacterial PspA/IM30/LiaH proteins. Our structural and functional analyses reveal that bacterial PspA belongs to the evolutionary ancestry of ESCRT-III proteins involved in membrane remodeling.


title: A phospho-regulated ensemble signal motif of α-TAT1 drives dynamic microtubule acetylation

abstract: Spatiotemporally dynamic microtubule acetylation underlies diverse physiological events ranging from cell migration to intracellular trafficking, autophagy and viral infections. Despite its ubiquity, the molecular mechanisms that regulate the sole microtubule acetylating agent, -tubulin N-acetyltransferase 1 (-TAT1) remain obscure. Here we report that dynamic intracellular localization of -TAT1 unexpectedly determines the efficiency of microtubule acetylation. Specifically, we newly identified a conserved signal motif in the intrinsically disordered C-terminus of -TAT1, consisting of three competing regulatory elements - nuclear export, nuclear import and cytosolic retention. Their balance is tuned via phosphorylation by serine-threonine kinases including CDK1 and CK2. While the un-phosphorylated form resides both in the cytosol and nucleus, the phosphorylated form binds to specific 14-3-3 adapters and accumulates in the cytosol for maximal substrate access. Cytosolic localization of -TAT1 predominantly mediates microtubule acetylation, cell proliferation and DNA damage response. In contrast to other molecules with a similar phospho-regulated signal motif including transcription factors, -TAT1 uniquely uses the nucleus as a hideout. As amino acid mutations to the motif have been reported in cancer patients, the present mechanism of subcellular -TAT1 localization may help uncover a spatiotemporal code of microtubule acetylation in normal and aberrant cell functions.

category: cell biology


title: Virus-host interactions shape viral dispersal giving rise to distinct classes of travelling waves in spatial expansions

abstract:
Reaction-diffusion waves have long been used to describe the growth and spread of populations undergoing a spatial range expansion. Such waves are generally classed as either pulled, where the dynamics are driven by the very tip of the front and stochastic fluctuations are high, or pushed, where cooperation in growth or dispersal results in a bulk-driven wave in which fluctuations are suppressed. These concepts have been well studied experimentally in populations where the cooperation leads to a density-dependent growth rate. By contrast, relatively little is known about experimental populations that exhibit density-dependent dispersal.

Using bacteriophage T7 as a test organism, we present novel experimental measurements that demonstrate that the diffusion of phage T7, in a lawn of host E. coli, is hindered by steric interactions with host bacteria cells. The coupling between host density, phage dispersal and cell lysis caused by viral infection results in an effective density-dependent diffusion coefficient akin to cooperative behavior. Using a system of reaction-diffusion equations, we show that this effect can result in a transition from a pulled to pushed expansion. Moreover, we find that a second, independent density-dependent effect on phage dispersal spontaneously emerges as a result of the viral incubation period, during which phage is trapped inside the host unable to disperse. Additional stochastic agent-based simulations reveal that lysis time dramatically affects the rate of diversity loss in viral expansions. Taken together, our results indicate both that bacteriophage can be used as a controllable laboratory population to investigate the impact of density-dependent dispersal on evolution, and that the genetic diversity and adaptability of expanding viral populations could be much greater than is currently assumed.


title: Hybrid dedicated and distributed coding in PMd/M1 provides separation and interaction of bilateral arm signals

abstract: Pronounced activity is observed in both hemispheres of the motor cortex during preparation and execution of unimanual movements. The organizational principles of bi-hemispheric signals and the functions they serve throughout motor planning remain unclear. Using an instructed-delay reaching task in monkeys, we identified two components in population responses spanning PMd and M1. A "dedicated" component, which segregated activity at the level of individual units, emerged in PMd during preparation. It was most prominent following movement when M1 became strongly engaged, and principally involved the contralateral hemisphere. In contrast to recent reports, these dedicated signals solely accounted for divergence of arm-specific neural subspaces. The other "distributed" component mixed signals for each arm within units, and the subspace containing it did not discriminate between arms at any stage. The statistics of the population response suggest two functional layers of the cortical network: one that spans both hemispheres for supporting preparatory and ongoing processes, and another that is predominantly housed in the contralateral hemisphere and specifies unilateral output.


title: A graph neural network model to estimate cell-wise metabolic flux using single cell RNA-seq data

abstract: The metabolic heterogeneity, and metabolic interplay between cells and their microenvironment have been known as significant contributors to disease treatment resistance. However, with the lack of a mature high-throughput single cell metabolomics technology, we are yet to establish systematic understanding of intra-tissue metabolic heterogeneity and cooperation phenomena among cell populations. To mitigate this knowledge gap, we developed a novel computational method, namely scFEA (single cell Flux Estimation Analysis), to infer single cell fluxome from single cell RNA-sequencing (scRNA-seq) data. scFEA is empowered by a comprehensively reconstructed human metabolic map into a factor graph, a novel probabilistic model to leverage the flux balance constraints on scRNA-seq data, and a novel graph neural network based optimization solver. The intricate information cascade from transcriptome to metabolome was captured using multi-layer neural networks to fully capitulate the non-linear dependency between enzymatic gene expressions and reaction rates. We experimentally validated scFEA by generating an scRNA-seq dataset with matched metabolomics data on cells of perturbed oxygen and genetic conditions. Application of scFEA on this dataset demonstrated the consistency between predicted flux and metabolic imbalance with the observed variation of metabolite abundance in the matched metabolomics data. We also applied scFEA on five publicly available scRNA-seq and spatial transcriptomics datasets and identified context and cell group specific metabolic variations. The cell-wise fluxome predicted by scFEA empowers a series of downstream analysis including identification of metabolic modules or cell groups that share common metabolic variations, sensitivity evaluation of enzymes with regards to their impact on the whole metabolic flux, and inference of cell-tissue and cell-cell metabolic communications.


title: Ancestry Inference Using Reference Labeled Clusters of Haplotypes

abstract:
We present ARCHes, a fast and accurate haplotype-based approach for inferring an individuals ancestry composition. Our approach works by modeling haplotype diversity from a large, admixed cohort of hundreds of thousands, then annotating those models with population information from reference panels of known ancestry. The running time of ARCHes does not depend on the size of a reference panel because training and testing are separate processes, and the inferred population-annotated haplotype models can be written to disk and reused to label large test sets in parallel (in our experiments, it averages less than one minute to assign ancestry from 32 populations to 1,001 sections of a genotype using 10 CPU). We test ARCHes on public data from the 1,000 Genomes Project and HGDP as well as simulated examples of known admixture. Our results demonstrate that ARCHes outperforms RFMix at correctly assigning both global and local ancestry at finer population scales regardless of the amount of population admixture.

Author SummaryHuman DNA is inherited from ancestors that come from different populations across the globe and across time. Being able to identify which of those populations make up an individuals DNA, how much they contribute, and on which chromosomes, is currently an important open research problem with many applications in the study of human diversity and history. As DNA sequencing and genotyping technology has developed, we have greater and greater amounts of data, which allows for the development of new sophisticated machine learning methods to approach this problem, and presents a need to process large amounts of data efficiently. These methods learn from examples of DNA data from known populations, and must be robust to differences in size and diversity among those reference populations. We present a new approach to this problem called ARCHes (Ancestry inference using Reference labeled Clusters of Haplotypes), that models the global diversity of small segments of human DNA sequence ("haplotypes"), and the extent to which these haplotypes are associated with each of a set of population reference panels. It then computes the most likely population assignments and the points along the genome where the populations change. Our experiments show that ARCHes has superior accuracy compared to a state-of-the-art method in identifying source populations and their locations on the genome, regardless of the number of different populations present in the genome, how closely related those populations are. ARCHes is also able to model populations despite having a small amount of population reference DNA data.

category: genomics


title: Topological Tuning of DNA Mobility in Entangled Solutions of Supercoiled Plasmids

abstract: Understanding the behaviour of ring polymers in dense solutions is one of the most intriguing problems in polymer physics with far-reaching implications from material science to genome biology. Thanks to its natural occurrence in circular form, DNA has been intensively employed as a proxy to study the fundamental physics of ring polymers in different topological states. Yet, torsionally constrained - such as supercoiled - topologies have been largely neglected so far. Extreme entanglement and high supercoiling levels are commonly found in the genetic material of both pro- and eukaryotes and, at the same time, the applicability of existing theoretical models to dense supercoiled DNA is unknown. To address this gap, here we couple large scale Molecular Dynamics (MD) simulations of twistable chains together with Differential Dynamic Microscopy (DDM) of entangled supercoiled DNA plasmids. We discover that, strikingly, and contrarily to what is generally assumed in the literature, a higher degree of supercoiling increases the average size of plasmids in entangled solutions. At the same time, we discover that this is accompanied by an unexpected enhancement in DNA mobility. We reconcile these apparently contradicting findings as due to the fact that supercoiling drives highly asymmetric plasmid conformations, decreases inter-plasmids entanglements and, in particular, reduces the number of threadings between DNA rings. Our numerical and experimental results also suggest a way to topologically tune DNA mobility via supercoiling, thus enabling the orthogonal control over the (micro)rheology of DNA-based complex fluids with respect to other traditional methods such as DNA length or concentration.


title: A high-throughput method for measuring critical thermal limits of leaves by chlorophyll imaging fluorescence

abstract: Plant thermal tolerance is a crucial research area as the climate warms and extreme weather events become more frequent. Leaves exposed to temperature extremes have inhibited photosynthesis and will accumulate damage to photosystem II (PSII) if tolerance thresholds are exceeded. Temperature-dependent changes in basal chlorophyll fluorescence (T-F0) can be used to identify the critical temperature at which PSII is inhibited. We developed and tested a high-throughput method for measuring the critical temperatures for PSII at low (CTMIN) and high (CTMAX) temperatures using a Maxi-Imaging fluorimeter and a thermoelectric Peltier plate heating/cooling system. We examined how experimental conditions: wet vs dry surfaces for leaves and heating/cooling rate, affect CTMIN and CTMAX across four species. CTMAX estimates were not different whether measured on wet or dry surfaces, but leaves were apparently less cold tolerant when on wet surfaces. Heating/cooling rate had a strong effect on both CTMAX and CTMIN that was species-specific. We discuss potential mechanisms for these results and recommend settings for researchers to use when measuring T-F0. The approach that we demonstrated here allows the high-throughput measurement of a valuable ecophysiological parameter that estimates the critical temperature thresholds of leaf photosynthetic performance in response to thermal extremes.

category: plant biology


title: Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil

abstract:
Viruses play an essential role in shaping microbial community structures and serve as reservoirs for genetic diversity in many ecosystems. In hyperarid desert environments, where life itself becomes scarce and loses diversity, the interactions between viruses and host populations have remained elusive. Here, we resolved host-virus interactions in the soil metagenomes of the Atacama Desert hyperarid core, one of the harshest terrestrial environments on Earth. We show evidence of diverse viruses infecting a wide range of hosts found in sites up to 205 km apart. Viral genomes carried putative extremotolerance features (i.e. DNA repair proteins, enzymes against oxidative damage, spore formation proteins) and auxiliary metabolic genes, indicating that viruses could mediate the spread of microbial resilience against environmental stress across the desert. We propose a mutualistic model of host-virus interactions in the hyperarid core where viruses seek protection in microbial cells as lysogens or pseudolysogens, while viral extremotolerance genes aid survival of their hosts. Our results suggest that the host-virus interactions in the Atacama Desert soils are dynamic and complex, shaping uniquely adapted microbiomes in this highly selective and hostile environment.

ImportanceDeserts are one of the largest and rapidly expanding terrestrial ecosystems characterized by low biodiversity and biomass. The hyperarid core of the Atacama Desert, previously thought to be devoid of life, is one of the harshest environments supporting only scant biomass of highly adapted microbes. While there is growing evidence that viruses play essential roles in shaping the diversity and structure of nearly every ecosystem, very little is known about the role of viruses in desert soils, especially where viral contact with viable hosts is significantly reduced. Our results indicate that diverse viruses are widely dispersed across the desert, potentially spreading key stress resilience and metabolic genes to ensure host survival. The desertification accelerated by climate change expands both the ecosystem cover and the ecological significance of the desert virome. This study sheds light on the complex virus-host interplay that shapes the unique microbiome in desert soils.


title: High-Resolution, Large Imaging Volume, and Multi-View Single Objective Light-Sheet Microscopy

abstract: Recent developments in Oblique Plane Microscopy (OPM) have shown that it can achieve high spatio-temporal resolution. Here we describe a single objective light-sheet microscope based on oblique plane illumination that achieves: (i) large field of view and high-resolution imaging via a custom remote focusing objective; (ii) fast volumetric imaging by means of light-sheet stabilised stage scanning - a novel scanning modality that extends the imaging volume without compromising imaging speed nor quality; (iii) multi-view imaging by alternating the orientation of light-sheet illumination and detection to improve the image quality on large samples; (iv) simpler design and ergonomics by remote placement of coverslips to allow inverted imaging, enabling imaging across scales in a high-throughput format. Overall, we achieved a resolution of 450 nm laterally and 2 m axially and a field of view of 3000 m x 800 m x 300 m. We demonstrate the speed, field of view, resolution and versatility of our novel instrument by imaging various systems, including zebrafish whole brain activity, Drosophila egg chamber development, and zebrafish development - up to nine embryos simultaneously.

category: developmental biology


title: Differential dopaminergic modulation of spontaneous cortico-subthalamic activity in Parkinson's disease

abstract: Pathological oscillations including elevated beta activity in the subthalamic nucleus (STN) and between STN and cortical areas are a hallmark of neural activity in Parkinsons disease (PD). Oscillations also play an important role in normal physiological processes and serve distinct functional roles at different points in time. We characterised the effect of dopaminergic medication on oscillatory whole-brain networks in PD in a time-resolved manner by employing a hidden Markov model on combined STN local field potentials and magnetoencephalography (MEG) recordings from 17 PD patients. Dopaminergic medication led to coherence within the medial and orbitofrontal cortex in the delta/theta frequency range. This is in line with known side effects of dopamine treatment such as deteriorated executive functions in Parkinsons disease. In addition, dopamine caused the beta band activity to switch from an STN-mediated motor network to a frontoparietal-mediated one. In contrast, dopamine did not modify local STN-STN coherence in PD. STN-STN synchrony emerged both on and off medication. By providing electrophysiological evidence for the differential effects of dopaminergic medication on the discovered networks, our findings open further avenues for electrical and pharmacological interventions in PD.


title: Resveratrol And Pterostilbene Potently Inhibit SARS-CoV-2 Replication In Vitro

abstract: The current COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an enormous impact on human health and economy. In search for therapeutic options, researchers have proposed resveratrol, a food supplement with known antiviral, anti-inflammatory and anti-oxidant properties as an advantageous antiviral therapy for SARS-CoV-2 infection. Here, we provide evidence that both resveratrol and its metabolically more stable structural analog, pterostilbene, exhibit potent antiviral properties against SARS-CoV-2 in vitro. Resveratrol and pterostilbene showed antiviral activity in African green monkey kidney cells and in human primary bronchial epithelial cells cultured in an air-liquid interface system. Both compounds actively inhibit virus replication within infected cells as reduced virus progeny production was observed when the compound was added at post-inoculation conditions. Without replenishment of the compound, antiviral activity was observed up to roughly 5 rounds of replication, demonstrating the long-lasting effect of these compounds. Collectively, our data indicate that resveratrol and pterostilbene are promising antiviral compounds to treat SARS-CoV-2 infection. Because these results represent laboratory findings in cells, we advocate evaluation of these compounds in clinical trials before statements are made whether or not these drugs are advantageous for COVID-19 treatment.


title: An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic

abstract: We report the likely most recent common ancestor of SARS-CoV-2 - the coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide as soon as weeks after the first reported cases of COVID-19. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic. There have been multiple replacements of predominant coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We provide a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/).


title: Nature-inspired Circular-economy Recycling (NaCRe) for Proteins: Proof of Concept

abstract: The billion tons of synthetic polymer-based materials (i.e. plastics) produced every year are one of the greatest challenges that humanity has to face. Nature produces even more natural polymers, yet they are sustainable. For example, proteins are sequence-defined natural polymers, that are constantly recycled when living systems feed. Indeed, digestion is the protein depolymerization into amino acids (i.e. the monomers) followed by their re-assembly into new proteins of arbitrarily different sequence and function. This process breaks a common recycling paradigm where a material is recycled into itself. Organisms feed of random protein mixtures that are  recycled into new proteins whose identity depends on the cells needs at the time of protein synthesis. Currently, advanced materials are increasingly made of proteins, but the abovementioned ideal recyclability of such materials has yet to be recognized and established. In this study mixtures of several (up to >30) peptides and/or proteins were depolymerized into their amino acid constituents, and these amino acids were used to synthesize new fluorescent, and bio-active proteins extra-cellularly by using an amino acid-free cell-free transcription-translation system. Proteins with high relevance in materials engineering ({beta}-lactoglobulin films, used for water filtration, or silk fibroin solutions) were successfully recycled into biotechnologically relevant proteins (green, and red fluorescent proteins, catechol 2,3-dioxygenase). The potential long-term impact of this approach to recycling lies in its compatibility with circular-economy models where raw materials remain in use as long as possible, thus reducing the burden on the planet.

category: biochemistry


title: Unsupervised tensor decomposition-based method to extract candidate transcription factors as histone modification bookmarks in post-mitotic transcriptional reactivation

abstract: The histone group added to a gene sequence must be removed during mitosis to halt transcription during the DNA replication stage of the cell cycle. However, the detailed mechanism of this transcription regulation remains unclear. In particular, it is not realistic to reconstruct all appropriate histone modifications throughout the genome from scratch after mitosis. Thus, it is reasonable to assume that there might be a type of "bookmark" that retains the positions of histone modifications, which can be readily restored after mitosis. We developed a novel computational approach comprising tensor decomposition (TD)-based unsupervised feature extraction (FE) to identify transcription factors (TFs) that bind to genes associated with reactivated histone modifications as candidate histone bookmarks. To the best of our knowledge, this is the first application of TD-based unsupervised FE to the cell division context and phases pertaining to the cell cycle in general. The candidate TFs identified with this approach were functionally related to cell division, suggesting the suitability of this method and the potential of the identified TFs as bookmarks for histone modification during mitosis.


title: TopoStats - a program for automated tracing of biomolecules from AFM images

abstract: We present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, 90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub (https://github.com/afm-spm/TopoStats) and is intended to be modified and adapted for use if required.


title: The Kappa Opioid Receptor is required for some intermittent alcohol drinking induced changes in stress and threat responding in male C57BL/6J mice

abstract:
The dynorphin/kappa opioid receptor (KOR) system in the brain regulates both stressful experiences and negative, aversive states during withdrawal from drugs of abuse. We explored the role of this system during acute withdrawal from long-term alcohol drinking. Male C57BL/6J mice were subjected to repeated forced swim tests, home cage exposure to a predator odor, and a visual threat after intermittent access to alcohol or water. Systemic injection of KOR antagonist norBNI reversed alcohol-related differences in immobility time during the second swim test and reduced burying behavior in response to predator odor, but did not affect behavioral response to visual threat.

HighlightsO_LIIntermittent alcohol drinking changed stress reactions in mice.
C_LIO_LIKOR antagonist norBNI altered some, but not all, stress responses in alcohol drinkers
C_LI


title: Evolutionary ecology of natural comammox Nitrospira populations

abstract: Microbes commonly exists in diverse and complex communities where species interact, and their genomic repertoires evolve over time. Our understanding of species interactions and evolution has increased in the last decades, but most studies of evolutionary dynamics are based on single species in isolation or in experimental systems composed of few interacting species. Here, we use the microbial ecosystem found in groundwater-fed sand filters as a model to avoid this limitation. In these open systems, diverse microbial communities experience relatively stable conditions, and the coupling between chemical and biological processes is generally well defined. Metagenomic analysis of 12 sand filters revealed systematic co-occurrence of at least five comammox Nitrospira species, likely promoted by low ammonium concentrations. These Nitrospira species showed intra-population sequence diversity, although possible clonal expansion was detected in few abundant local comammox populations. They showed low homologous recombination and strong purifying selection, the latter process being especially strong in genes essential in energy metabolism. Positive selection was detected on genes related to resistance to foreign DNA and phages. We found that, compared to other habitats, groundwater-fed sand filters impose strong purifying selection and low recombination on comammox Nitrospira populations. These results suggest that evolutionary processes are more affected by habitat type than by species identity. Together, this study improves our understanding of species interactions and evolution in complex microbial communities, and sheds light on the environmental dependency of evolutionary processes.


title: Host phylogeny and host ecology structure the mammalian gut microbiota at different taxonomic scales

abstract: The gut microbiota is critical for host function. Among mammals, host phylogenetic relatedness and diet are strong drivers of gut microbiota structure, but one factor may be more influential than the other. Here, we used 16S rRNA gene sequencing to determine the relative contributions of host phylogeny and host dietary guild in structuring the gut microbiotas of 11 herbivore species from 5 families living sympatrically in southwest Kenya. Herbivore species were classified as grazers, browsers, or mixed-feeders. We found that gut microbiotas were highly species-specific, and that host taxonomy accounted for more variation in the gut microbiota (30%) than did host dietary guild (10%) or sample month (8%). Overall, similarity among gut microbiotas increased with host phylogenetic relatedness (r=0.73), yet this relationship was not consistent among seven closely related Bovid host species (r=0.21 NS). Within bovids, host dietary guild explained more of the variation in the gut microbiota than did host species. Lastly, while we found that the gut microbiotas of herbivores residing in southwest Kenya converge with those of distinct populations of conspecifics from central Kenya, fine-scale differences in the abundances of bacterial amplicon sequence variants (ASVs) between individuals from the two regions were also observed. Overall, our findings suggest that host phylogeny and taxonomy strongly structure the gut microbiota, but these gut microbial communities could be furthered modified by host ecology, especially among closely related host species.

category: ecology


title: Extraintestinal pathogenic Escherichia coli (ExPEC) are associated with prolonged carriage of extended-spectrum β-lactamase-producing E. coli acquired during travel

abstract:
ObjectivesExtended-spectrum {beta}-lactamase-producing Escherichia coli (ESBL-Ec) are frequently acquired during international travel, contributing to the global spread of antimicrobial resistance. Human-adapted ESBL-Ec are predicted to exhibit increased intestinal carriage duration, resulting in a higher likelihood of onward human-to-human transmission. Yet, bacterial determinants of increased carriage duration are unknown. Previous studies analysed small traveler cohorts, with short follow-up times, or did not employ high-resolution molecular typing, and were thus unable to identify bacterial traits associated with long-term carriage.

MethodsIn a prospective cohort study of 2001 international travelers, we analysed 160 faecal ESBL-Ec isolates from all 38 travelers who acquired ESBL-Ec during travel and subsequently carried ESBL-Ec for at least 12 months after return, by whole-genome sequencing. For 17 travelers, we confirmed the persistence of ESBL-Ec strains through single nucleotide variant typing. To identify determinants of increased carriage duration, we compared the 17 long-term carriers ([≥]12 months carriage) with 33 age-, sex- and destination-matched short-term carriers (<1 month carriage). Long-read sequencing was employed to investigate ESBL plasmid persistence.

ResultsWe show that in healthy travelers with very low antibiotic usage, extraintestinal pathogenic lineages of E. coli (ExPEC) are significantly more likely to persist than other E. coli lineages. The long-term carriage of E. coli from ExPEC lineages is mainly driven by sequence type 131 and phylogroup D E. coli.

ConclusionsAlthough ExPEC frequently cause extra-intestinal infections such as bloodstream infections, our results imply that ExPEC are also efficient intestinal colonizers, which potentially contributes to their onward transmission.


title: A single-mode associates global patterns of brain network structure and behavior across the human lifespan

abstract:
Multiple human behaviors improve early in life, peaking in young adulthood, and declining thereafter. Several properties of brain structure and function progress similarly across the lifespan. Cognitive and neuroscience research has approached aging primarily using associations between a few behaviors, brain functions, and structures. Because of this, the multivariate, global factors relating brain and behavior across the lifespan are not well understood. We investigated the global patterns of associations between 334 behavioral and clinical measures and 376 brain structural connections in 594 individuals across the lifespan. A single-axis associated changes in multiple behavioral domains and brain structural connections (r=0.5808). Individual variability within the single association axis well predicted the age of the subject (r=0.6275). Representational similarity analysis evidenced global patterns of interactions across multiple brain network systems and behavioral domains. Results show that global processes of human aging can be well captured by a multivariate data fusion approach. [147]

Data availabilityThe source data are provided by the Cambridge Aging Neuroscience Project https://camcan-archive.mrc-cbu.cam.ac.uk/. Brain data derived as part of this project and used as features for all the analyses are available on brainlife.io/pubs:

Code availabilityCode is available on github at https://github.com/bcmcpher/cca_aging and as web services reproducing the analyes at


title: Interpretable network-guided epistasis detection

abstract: Detecting epistatic interactions at the gene level is essential to understanding the biological mechanisms of complex diseases. Unfortunately, genome-wide interaction association studies (GWAIS) involve many statistical challenges that make such detection hard. We propose a multi-step protocol for epistasis detection along the edges of a gene-gene co-function network. Such an approach reduces the number of tests performed and provides interpretable interactions, while keeping type I error controlled. Yet, mapping gene-interactions into testable SNP-interaction hypotheses, as well as computing gene pair association scores from SNP pair ones, is not trivial. Here we compare three SNP-gene mappings (positional overlap, eQTL and proximity in 3D structure) and use the adaptive truncated product method to compute gene pair scores. This method is non-parametric, does not require a known null distribution, and is fast to compute. We apply multiple variants of this protocol to a GWAS inflammatory bowel disease (IBD) dataset. Different configurations produced different results, highlighting that various mechanisms are implicated in IBD, while at the same time, results overlapped with known disease biology. Importantly, the proposed pipeline also differs from a conventional approach were no network is used, showing the potential for additional discoveries when prior biological knowledge is incorporated into epistasis detection.

category: genetics


title: ZETA: a parameter-free statistical test for neuronal responsiveness

abstract: Neurophysiological studies depend on a reliable quantification of whether and when a neuron responds to stimulation. Simple methods to determine responsiveness require arbitrary parameter choices, such as binning size, while more advanced model-based methods require fitting and hyperparameter tuning. These parameter choices can change the results, which invites bad statistical practice and reduces the replicability. New recording techniques that yield increasingly large numbers of cells would benefit from a test for cell-inclusion that requires no manual curation. Here, we present the parameter-free ZETA-test, which outperforms t-tests, ANOVAs, and renewal-process-based methods by including more cells at a similar false-positive rate. We show that our procedure works across brain regions and recording techniques, including calcium imaging and Neuropixels data. Furthermore, in illustration of the method, we show in mouse visual cortex that 1) visuomotor-mismatch and spatial location are encoded by different neuronal subpopulations; and 2) optogenetic stimulation of VIP cells leads to early inhibition and subsequent disinhibition.


title: Macrophage-derived insulin/IGF antagonist ImpL2 regulates systemic metabolism for mounting an effective acute immune response in Drosophila

abstract: In response to invading pathogens, macrophages metabolically polarize towards Hif1-induced aerobic glycolysis, requiring increased supply of nutrients. Here, we show that in order to obtain sufficient resources, Drosophila macrophages release the insulin/IGF antagonist ImpL2, whose expression is regulated by Hif1. ImpL2 remotely induces the release of lipids and carbohydrates from adipose tissue by reducing insulin signaling, followed by increased nutrient accumulation in activated immune cells. ImpL2 thus translates the metabolic requirements of immune cells into a systemic metabolic switch. Although these ImpL2 effects are essential during the acute immune response to streptococcal infection, they become maladaptive upon chronic infection by an intracellular pathogen. The relevance of our model to mammalian immunometabolism is demonstrated by the increased expression of the ImpL2 homolog IGFBP7 in human macrophages exposed to Streptococcus.

category: immunology


title: The intrinsically disordered N-terminus of the voltage-dependent anion channel

abstract:
The voltage-dependent anion channel (VDAC) is a critical {beta}-barrel membrane protein of the mitochondrial outer membrane, which regulates the transport of ions and ATP between mitochondria and the cytoplasm. In addition, VDAC plays a central role in the control of apoptosis and is therefore of great interest in both cancer and neurodegenerative diseases. Although not fully understood, it is presumed that the gating mechanism of VDAC is governed by its N-terminal region which, in the open state of the channel, exhibits an -helical structure positioned midway inside the pore and strongly interacting with the {beta}-barrel wall.

In the present work, we performed molecular simulations with a recently developed force field for disordered systems to shed new light on known experimental results, showing that the N-terminus of VDAC is an intrinsically disordered region (IDR). First, simulation of the N-terminal segment as a free peptide highlighted its disordered nature and the importance of using an IDR-specific force field to properly sample its conformational landscape. Secondly, accelerated dynamics simulation of a double cysteine VDAC mutant under applied voltage revealed metastable low conducting states of the channel representative of closed states observed experimentally. Related structures were characterized by partial unfolding and rearrangement of the N-terminal tail, that led to steric hindrance of the pore. Our results indicate that the disordered properties of the N-terminus are crucial to properly account for the gating mechanism of VDAC.

Author summaryThe voltage-dependent anion channel (VDAC) is a membrane protein playing a pivotal role in the transport of ions or ATP across the mitochondrial outer membrane as well as in the induction of apoptosis. At high enough membrane potential, VDAC is known to transition from an open state to multiple closed states, reducing the flow of ions through the channel and blocking the passage of large metabolites. While the structure of the open state was resolved more than a decade ago, a molecular description of the gating mechanism of the channel is still missing. Here we show that the N-terminus of VDAC is an intrinsically disordered region and that such a property has a profound impact on its dynamics either as a free peptide or as part of the channel. By taking disordered properties of the N-terminus into account, we managed to generate long-lived closed conformations of the channel at experimental values of the membrane potential. Our results provide new insights into the molecular mechanism driving the gating of VDAC.

category: molecular biology


title: TAEL 2.0: An Improved Optogenetic Expression System for Zebrafish

abstract: Inducible gene expression systems are valuable tools for studying biological processes. We previously developed an optogenetic gene expression system called TAEL that is optimized for use in zebrafish. When illuminated with blue light, TAEL transcription factors dimerize and activate gene expression downstream of the TAEL-responsive C120 promoter. By using light as the inducing agent, the TAEL/C120 system overcomes limitations of traditional inducible expression systems by enabling fine spatial and temporal regulation of gene expression. Here, we describe ongoing efforts to improve the TAEL/C120 system. We made modifications to both the TAEL transcriptional activator and the C120 regulatory element, collectively referred to as TAEL 2.0. We demonstrate that TAEL 2.0 consistently induces higher levels of reporter gene expression and at a faster rate, but with comparable background and toxicity as the original TAEL system. With these improvements, we were able to create functional stable transgenic lines to express the TAEL 2.0 transcription factor either ubiquitously or with a tissue-specific promoter. We demonstrate that the ubiquitous line in particular can be used to induce expression at late embryonic and larval stages, addressing a major deficiency of the original TAEL system. This improved optogenetic expression system will be a broadly useful resource for the zebrafish community.


title: Rcn3 is Involved in Postnatal Tendon Development by Regulating Collagen Modification and Fibrillogenesis

abstract: Tendon plays a critical role in the joint movement by transmitting force from muscle to bone. This transmission of force is facilitated by its specialized structure, which consists of highly aligned extracellular matrix consisting predominantly of type I collagen. Tenocytes, fibroblast-like tendon cells residing between the parallel collagen fibers, regulate this specialized tendon matrix. Despite the importance of collagen structure and tenocyte function, the biological mechanisms regulating fibrillogenesis and tenocyte maturation are not well understood. Here we examine the function of Reticulocalbin 3 (Rcn3) in collagen fibrillogenesis and tenocyte maturation during postnatal tendon development using a genetic mouse model. Loss of Rcn3 in tendon caused decreased tendon thickness, abnormal tendon cell maturation, and decreased mechanical properties. Interestingly, Rcn3 deficient mice exhibited a smaller collagen fibril distribution and over-hydroxylation in C-telopeptide cross-linking lysine from 1(1) chain. Additionally, the proline 3-hydroxylation sites in type I collagen were also over-hydroxylated in Rcn3 deficient mice. Our data collectively suggest that Rcn3 is a pivotal regulator of collagen fibrillogenesis and tenocyte maturation during postnatal tendon development.


title: Douglas fir and Norway spruce admixtures to beech forests along a site gradient in Northern Germany - Are soil nutrient conditions affected?

abstract: The establishment of mixed forest stands can be seen as an option to improve soil nutrient conditions and to protect forest ecosystems from various impacts of climate change. Our study analyzed groups of pure mature European beech (Fagus sylvatica; B), Douglas fir (Pseudotsuga menziesii; D) and Norway spruce (Picea abies; S) stands as well as mixtures of beech with either Douglas fir (DB) or spruce (SB), i.e. 5 forest stands per site along Northern Germany with two regionally clearly differing sites conditions (i.e., 3 loess-influenced, loamy sites in the Solling region, southern Lower Saxony and 4 sandy lowland sites further north). In order to determine possible influences of the tree species and their mixtures on soil properties, the organic layer and the mineral topsoil were first chemically characterized for all 35 plots down to a depth of 30 cm (pH, C, N, P, CEC, exchangeable nutrient cation contents and stocks, base saturation-BS). Our results indicated, independent of sites condition, that pure S stands showed the lowest pH and BS, meanwhile B the highest BS. The impact of D varied depending on site condition. On sandy soils, pure D showed higher pH and BS than under pure S, while on loamy soils the pH under D and B was lower than under S. Regarding cations stocks under sandy soils conditions, S stands and its admixture SB depleted soil Ca and Mg stocks more than pure D and B. In contrast, under loamy soil conditions B showed depleted (lowest) soil exchangeable Ca and Mg stocks more than under S stands. Soil exchangeable K under mixed stands were among the highest compared to pure stands, independent of the site condition. Thus, mixed species stands generally decreased soil base cation depletion compared to pure conifer stands. Admixtures of Douglas-fir (DB) seem to lead to smaller changes in pH, CEC and BS than those of Norway spruce, this effect become more important at sandy soil sites. Therefore, forest management may consider mixtures of European beech and Douglas fir as a reasonable management option without apprehending negative effects on soil chemistry.


title: The Phage-shock-protein (PSP) Envelope Stress Response: Discovery of Novel Partners and Evolutionary History

abstract: The phage shock protein (PSP) systems orchestrate a conserved stress response function by stabilizing the cell membrane and protecting bacteria from envelope stress. The full repertoire of PSP components remains poorly characterized. We combined comparative genomics and protein sequence-structure-function analyses to systematically identify homologs, phyletic patterns, domain architectures, and gene neighborhoods to trace the evolution of PSP components across the tree of life. This approach showed that the core component PspA/Snf7 (Psp/ESCRT systems) was present in the Last Universal Common Ancestor and that different clades co-opted a diverse range of partners to constitute distinct PSP systems. We identified several novel partners of the PSP system: (i) the Toastrack domain, which likely facilitates assembling diverse sub-membrane stress-sensing and signaling complexes, (ii) the newly-defined HAAS-PadR-like transcription regulator pair system, and (iii) multiple independent associations with ATPase or CesT/Tir-like chaperones, and Band-7 domain proteins that likely mediate sub-membrane dynamics. Our work also uncovered links between the PSP components and diverse SHOCT-like domains, suggesting a role in assembling membrane-associated complexes of proteins with disparate biochemical functions. Tracing the evolution of Psp cognate proteins provides new insights into the functions of the system and helps predict previously uncharacterized, often lineage-specific, membrane-dynamics and stress-response systems. The conservation of PSP systems across bacterial phyla emphasizes the importance of this stress response system in prokaryotes, while its modular diversity in various lineages indicates the emergence of lineage-specific cell-envelope structures, lifestyles, and adaptation mechanisms. The results can be accessed at https://jravilab.shinyapps.io/psp-evolution.


title: The Phage-shock-protein Envelope Stress Response: Discovery of Novel Partners & Evolutionary History


title: Unique features of stimulus-based probabilistic reversal learning

abstract: Reversal learning paradigms are widely-used assays of behavioral flexibility with their probabilistic versions being more amenable to studying integration of reward outcomes over time. Prior research suggests differences between initial and reversal learning, including higher learning rates, a greater need for inhibitory control, and more perseveration after reversals. However, it is not well-understood what aspects of stimulus-based reversal learning are unique to reversals, and whether and how observed differences depend on reward probability. Here, we used a visual probabilistic discrimination and reversal learning paradigm where male and female rats selected between a pair of stimuli associated with different reward probabilities. We compared accuracy, rewards collected, omissions, latencies, win-stay/lose-shift strategies, and indices of perseveration across two different reward probability schedules. We found that discrimination and reversal learning are behaviorally more unique than similar: latencies to select the better option, win-stay strategies, and perseveration were of a different pattern in reversal learning compared to discrimination learning. Additionally, fit of choice behavior using reinforcement learning models revealed a lower sensitivity to the difference in subjective reward values (greater exploration) and higher learning rates for the reversal phase. Interestingly, a consistent reward probability group difference emerged with a richer environment associated with longer reward collection latencies than a leaner environment. We also replicated previous reports on sex differences in reversal learning. Future studies should systematically compare the neural correlates of fine-grained behavioral measures to reveal possible dissociations in how the circuitry is recruited in each phase.

category: animal behavior and cognition


title: Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

abstract: Tomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by an order of magnitude and significantly improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300kDa) at 3.6 [A] resolution where density for individual side chains is clearly resolved.


title: NIAGADS Alzheimer's GenomicsDB: A resource for exploring Alzheimer's Disease genetic and genomic knowledge

abstract:
INTRODUCTIONThe NIAGADS Alzheimers Genomics Database (GenomicsDB) is an interactive knowledgebase for Alzheimers disease (AD) genetics that provides access to GWAS summary statistics datasets deposited at NIAGADS, a national genetics data repository for AD and related dementia (ADRD).

METHODSThe website makes available >70 genome-wide summary statistics datasets from GWAS and genome sequencing analysis for AD/ADRD. Variants identified from these datasets are mapped to up-to-date variant and gene annotations from a variety of resources and linked to functional genomics data.

The database is powered by a big data optimized relational database and ontologies to consistently annotate study designs and phenotypes, facilitating data harmonization and efficient real-time data analysis and variant or gene report generation.

RESULTSDetailed variant reports provide tabular and interactive graphical summaries of known ADRD associations, as well as highlight variants flagged by the Alzheimers Disease Sequencing Project (ADSP). Gene reports provide summaries of co-located ADRD risk-associated variants and have been expanded to include meta-analysis results from aggregate association tests performed by the ADSP allowing us to flag genes with genetic evidence for AD.

DISCUSSIONThe GenomicsDB makes available >150 million variant annotations, including ~30 million (5 million novel) variants identified as AD-relevant by ADSP, for browsing and real-time mining via the website. With a newly redesigned, efficient, search interface and comprehensive record pages linking summary statistics to variant and gene annotations, this resource makes these data both accessible and interpretable, establishing itself as valuable tool for AD research.


title: Action imitation via trajectory-based or posture-based planning

abstract: Imitation is a significant daily activity involved in social interaction and motor learning. Imitation has been theorized to be performed in at least two ways. In posture-based imitation, individuals reproduce how the body should look and feel, and are sensitive to the relative positioning of body parts. In trajectory imitation, individuals mimic the spatiotemporal motion path of the end effector. There are clear anecdotal situations in which one might benefit from imitating postures (when learning ballet) or trajectories (when learning to reach around objects). However, whether these are in fact distinct methods of imitation, and if so, whether they may be applied interchangeably to perform the same task, remain unknown. If these are indeed separate mechanisms that rely on different computational and neural resources, a cost should be incurred when switching from using one mechanism to the other within the context of a single task. Therefore observing a processing cost would both provide evidence that these are indeed two distinct mechanisms, and that they may be used interchangeably when trying to imitate the same stimulus. To test this, twenty-five healthy young adults performed a sequential multitasking imitation task. Participants were first instructed to pay attention to the limb postures or the hand path of a video-recorded model, then performed a neutral, congruent, or incongruent intervening motor task. Finally, participants imitated the modeled movement. Spatiotemporal imitation accuracy was greatest after a neutral intervening task, and worst after posture matching. When the primary task involved imitating trajectories, the data suggested a processing cost: movements following the posture-matching intervening task were less consistent with baseline (neutral) performance, suggesting performance may be disrupted by the incongruence. This effect was not observed when imitating limb postures. In summary, we present initial evidence of a partial dissociation between posture matching and trajectory imitation as a result of instructions and intervening tasks that is consistent with the existence of two computationally distinct imitation mechanisms.


title: Primary saturation of α,β-unsaturated carbonyl containing fatty acids does not abolish electrophilicity

abstract:
Metabolism of polyunsaturated fatty acids results in the formation of hydroxylated fatty acids that can be further oxidized by dehydrogenases, often resulting in the formation of electrophilic, ,{beta}-unsaturated ketone containing fatty acids. As electrophiles are associated with redox signaling, we sought to investigate the metabolism of the oxo-fatty acid products in relation to their double bond architecture. Using an untargeted liquid chromatography mass spectrometry approach, we identified mono- and di-saturated products of the arachidonic acid-derived 11-oxoeicosatetraenoic acid (11-oxoETE) and mono-saturated metabolites of 15-oxoETE and docosahexaenoic acid-derived 17-oxodocosahexaenoinc acid (17-oxoDHA) in both human A549 lung carcinoma and umbilical vein endothelial cells. Notably, mono-saturated oxo-fatty acids maintained their electrophilicity as determined by nucleophilic conjugation to glutathione while a second saturation of 11-oxoETE resulted in a loss of electrophilicity. These results would suggest that prostaglandin reductase (PTGR1), known for its reduction of the ,{beta}-unsaturated double bond, was not responsible for the saturation of oxo-fatty acids. Surprisingly, knockdown of PTGR1 expression by shRNA confirmed its participation in the formation of 15-oxoETE and 17-oxoDHA mono-saturated metabolites. Furthermore, overexpression of PTGR1 in A549 cells increased the rate and total amount of oxo-fatty acid saturation. These findings will further facilitate the study of electrophilic fatty acid metabolism and signaling in the context of inflammatory diseases and cancer where they have been shown to have anti-inflammatory and anti-proliferative signaling properties.

HighlightsO_LIPrimary saturation of electrophilic fatty acids does not abolish biological activity.
C_LIO_LIProstaglandin reductase 1 reduces double bonds in fatty acids that are structurally similar to 15-keto-prostaglandin E2.
C_LIO_LIProstaglandin reductase 1 reduces non-carbonyl adjacent double bonds.
C_LI


title: Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion

abstract:
The precise spatiotemporal control of nanoscale membrane shape and composition is the result of complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phase, temperature, and curvature. Supported lipid bilayers were created over 50-nm radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.

SignificanceNanoscopic membrane organization and dynamics are critical for cellular function but challenging to experimentally measure. This work brings together super-resolution optical methods with multiscale computational approaches to reveal the interplay between curvature, composition, phase, and diffusion in model membranes. We report that curvature can induce phase separation in otherwise homogeneous membranes and that the phase-curvature coupling has a direct implication on lipid mobility. This discovery advances our understanding of the fundamental membrane biophysics that regulate membrane activities such as endocytosis and viral budding.

category: biophysics


title: Novel Competition test for food rewards reveals stable dominance status in rats

abstract: Social hierarchy is a potent modulator of behavior, that is typically established through overt agonistic interactions between individuals in the group. Once established, social ranks are maintained through subtler interactions allowing the redirection of energy away from agonistic interactions towards other needs. The available tasks for assessing social rank in rats allow the study of the mechanisms by which social hierarches are formed in early phases but fail to assess the maintenance of established hierarchies between stable pairs of animals, which might rely on distinct neurobiological mechanisms. Here we present and validate a novel trial-based dominancy assay, the modified Food Competition test, where established social hierarchies can be identified in the home cage of non-food deprived pairs of male rats. In this task, we introduce a small conflict in the home cage, where access to a new feeder containing palatable pellets can only be gained by one animal at a time. We found that this subtle conflict triggered asymmetric social interactions and resulted in higher consumption of food by one of the animals in the pair, which reliably predicted hierarchy in other tests. Our findings reveal stable dominance status in pair-housed rats and provide a novel tool for the evaluation of established social hierarchies, the modified Food Competition test, that is robust and easy to implement.


title: Novel Competition test for food rewards reveals stable dominance status in adult male rats


title: Decoding representations of discriminatory and hedonic information during appetitive and aversive touch

abstract: Emotion is typically understood to be an internal subjective experience originating in the brain. Yet in the somatosensory system hedonic information is coded by mechanoreceptors at the point of sensory contact before it reaches the central nervous system. It remains unknown, however, how these distinct peripheral channels for tactile hedonic information contribute to representations of interoceptive states relative to exteroceptive experience. In this fMRI study we applied representational similarity analyses with pattern component modeling, a technique that deconstructs representational states into a weighted set of distinct predefined constructs, to dissociate how discriminatory vs. hedonic tactile information, carried by A- and C-/CT-fibers respectively, contributes to population code representations in the human brain. Results demonstrated that information about appetitive and aversive tactile sensation is represented separately from non-hedonic tactile information across cortical structures. Specifically, although hedonic touch originates as a peripheral signal, labeled at the point of contact, representations in somatosensory cortices are guided by experiences of non-hedonic touch, By contrast, representations in regions associated with interoception and affect encode signals of hedonic touch. This provides evidence of complex tactile encoding that involves both external-exteroceptive and internal-interoceptive dimensions. Importantly, hedonic touch contributes to representations of internal state as well as those of externally generated stimulation.


title: Associations between ADHD symptom remission and white matter microstructure: a longitudinal analysis

abstract:
BackgroundAttention-deficit hyperactivity disorder (ADHD) is associated with white matter (WM) microstructure. Our objective was to investigate how WM microstructure is longitudinally related to symptom remission in adolescents and young adults with ADHD.

MethodsWe obtained diffusion-weighted imaging (DWI) data from 99 participants at two time points (mean age baseline: 16.91 years, mean age follow-up: 20.57 years). We used voxel-wise Tract-Based Spatial Statistics (TBSS) with permutation-based inference to investigate associations of inattention (IA) and hyperactivity-impulsivity (HI) symptom change with fractional anisotropy (FA) at baseline, follow-up, and change between time points.

ResultsRemission of combined HI and IA symptoms was significantly associated with reduced FA at follow-up in the left superior longitudinal fasciculus and the left corticospinal tract (CST) (PFWE=0.038 and PFWE=0.044, respectively), mainly driven by an association between HI remission and follow-up CST FA (PFWE=0.049). There was no significant association of combined symptom decrease with FA at baseline or with changes in FA between the two assessments.

ConclusionsIn this longitudinal DWI study of ADHD using dimensional symptom scores, we show that greater symptom decrease is associated with lower follow-up FA in specific WM tracts. Altered FA thus may appear to follow, rather than precede, changes in symptom remission. Our findings indicate divergent WM developmental trajectories between individuals with persistent and remittent ADHD, and support the role of prefrontal and sensorimotor tracts in the remission of ADHD.


title: Human cerebral cortex networks use expanding and contracting state dynamic to shape cortical functions

abstract: We lack viable explanations of how brain functions emerge from collective activities of neurons in networks. We recorded field potentials from many local networks in the human cerebral cortex during a wide variety of brain functions. The network dynamics showed that each local cortical network produced fluctuating attractor states. The state trajectories continuously stretched and contracted during all brain functions, leaving no stable patterns. Different local networks all produced this dynamic, despite different architectures. Single trial stimuli and tasks modified the stretching and contractions. These modified fluctuations cross-correlated among particular networks during specific brain functions. Spontaneous states, rest, sensory, motor and cognitive states all emerged from this dynamic. Its mathematical structure provides a general explanation of cortical dynamics that can be tested experimentally. This universal dynamic is a simple functional organizing principle for brain functions at the mm3 scale that is distinct from existing frameworks.


title: Understanding the emergence of contingent and deterministic exclusion in multispecies communities

abstract: Competitive exclusion can be classified as deterministic or as historically contingent. While competitive exclusion is common in nature, it has remained unclear when multispecies communities should be dominated by deterministic or contingent exclusion. Here, we provide a general theoretical approach to explain both the emergence and sources of competitive exclusion in multispecies communities. We illustrate our approach on an empirical competition system between annual and perennial plant species. First, we find that the life-history of perennial species increases the probability of observing contingent exclusion by increasing their effective intrinsic growth rates. Second, we find that the probability of observing contingent exclusion increases with weaker intraspecific competition, and not with the level of hierarchical competition. Third, we find a shift from contingent exclusion to dominance with increasing numbers of competing species. Our work provides a heuristic framework to increase our understanding about the predictability of species persistence within multispecies communities.


title: Hamilton's rule, gradual evolution, and the optimal (feedback) control of phenotypically plastic traits

abstract: Most traits expressed by organisms, such as gene expression profiles, developmental trajectories, behavioural sequences and reaction norms are function-valued traits (colloquially "phenotypically plastic traits"), since they vary across an individuals age and in response to various internal and/or external factors (state variables). Furthermore, most organisms live in populations subject to limited genetic mixing and are thus likely to interact with their relatives. We here formalise selection on genetically determined function-valued traits of individuals interacting in a group-structured population, by deriving the marginal version of Hamiltons rule for function-valued traits. This rule simultaneously gives a condition for the invasion of an initially rare mutant function-valued trait and its ultimate fixation in the population (invasion thus implies substitution). Hamiltons rule thus underlies the gradual evolution of function-valued traits and gives rise to necessary first-order conditions for their uninvadability (evolutionary stability). We develop a novel analysis using optimal control theory and differential game theory, to simultaneously characterise and compare the first-order conditions of (i) open-loop traits - functions of time (or age) only, and (ii) closed-loop (state-feedback) traits - functions of both time and state variables. We show that closed-loop traits can be represented as the simpler open-loop traits when individuals do no interact or when they interact with clonal relatives. Our analysis delineates the role of state-dependence and interdependence between individuals for trait evolution, which has implications to both life-history theory and social evolution.


title: Muilla lordsburgana (Asparagaceae: Brodiaeoideae), a new species found north of Lordsburg, southwestern New Mexico.

abstract: AO_SCPLOWBSTRACTC_SCPLOWMuilla lordsburgana P.J.Alexander sp. nov. is described from eastern Lordsburg Mesa in the northwestern fringe of the Chihuahuan Desert, southwestern New Mexico. It is very similar to Muilla coronata, a species known in the Mojave Desert of California and a small area of adjacent Nevada. Compared to Muilla coronata, the style and stigma combined are longer, the anthers are longer, the fruits are larger, and the seeds are larger. It has a short flowering period in March, and is difficult or impossible to find at other times of the year. It is narrowly distributed, limited to a band of deep, coarse, sandy soils derived primarily from granite. Several species that are otherwise uncommon in the area also occur in this habitat, including Logfia depressa, Pectocarya platycarpa, and Plagiobothrys arizonicus. Invasive species, especially Erodium cicutarium in the winter annual flora, are generally dominant. Muilla lordsburgana has probably been overlooked until now because it is not easy to observe and occurs in habitats that are not attractive to botanists.


title: Disinhibitory circuitry gates associative synaptic plasticity in olfactory cortex

abstract: Inhibitory microcircuits play an essential role in regulating cortical responses to sensory stimuli. Interneurons that inhibit dendritic or somatic integration in pyramidal neurons act as gatekeepers for neural activity, synaptic plasticity and the formation of sensory representations. Conversely, interneurons that specifically inhibit other interneurons can open gates through disinhibition. In the rodent piriform cortex, relief of dendritic inhibition permits long-term potentiation (LTP) of the recurrent synapses between pyramidal neurons (PNs) thought to underlie ensemble odor representations. We used an optogenetic approach to identify the inhibitory interneurons and disinhibitory circuits that regulate LTP. We focused on three prominent inhibitory neuron classes-somatostatin (SST), parvalbumin (PV), and vasoactive intestinal polypeptide (VIP) interneurons. We find that LTP is gated by the inactivation SST or PV interneurons or by activation of VIP interneurons. Further, activation of VIP interneurons strongly inhibits putative SST-cells during LTP induction, but only weakly inhibit PV-interneurons. Taken together, these findings suggest that VIP-interneurons mediate a disinhibitory circuit that can regulate synaptic plasticity during olfactory processing.


title: JIB-04 has broad-spectrum antiviral activity and inhibits SARS-CoV-2 replication and coronavirus pathogenesis

abstract: Pathogenic coronaviruses represent a major threat to global public health. Here, using a recombinant reporter virus-based compound screening approach, we identified several small-molecule inhibitors that potently block the replication of the newly emerged severe acute respiratory syndrome virus 2 (SARS-CoV-2). Among them, JIB-04 inhibited SARS-CoV-2 replication in Vero E6 cells with an EC50 of 695 nM, with a specificity index of greater than 1,000. JIB-04 showed in vitro antiviral activity in multiple cell types against several DNA and RNA viruses, including porcine coronavirus transmissible gastroenteritis virus. In an in vivo porcine model of coronavirus infection, administration of JIB-04 reduced virus infection and associated tissue pathology, which resulted in improved weight gain and survival. These results highlight the potential utility of JIB-04 as an antiviral agent against SARS-CoV-2 and other viral pathogens.


title: Meta-analysis of MERS, SARS and COVID-19 in vitro Infection Datasets Reveals Common Patterns in Gene and Protein Expression

abstract: Three lethal lower respiratory tract coronavirus epidemics have occurred over the past 20 years. This coincided with major developments in genome-wide gene and protein expression analysis, resulting in a wealth of datasets in the public domain. Seven such in vitro studies were selected for comparative bioinformatic analysis through the VirOmics Playground, a visualisation and exploration platform we developed. Despite the heterogeneous nature of the data sets, several commonalities could be observed across studies and species. Differences, on the other hand, reflected not only variations between species, but also other experimental variables, such as cell lines used for the experiments, infection protocols and viral strains. The datasets analysed here are available online through our platform (https://public.bigomics.ch/app/omicsplayground_viromics).


title: Molecular characterization revealed the role of thaumatin-like proteins in stress response in bread wheat

abstract: Thaumatin-like proteins (TLPs) are related to the pathogenesis-related-5 (PR-5) family and involved in stress response. Herein, a total of 93 TLP genes were identified in the genome of Triticum aestivum. Further, we identified 26, 27, 39 and 37 TLP genes in the Brachypodium distachyon, Oryza sativa, Sorghum bicolor and Zea mays genomes for comparative characterization, respectively. They could be grouped into small and long TLPs with conserved thaumatin signature motif. Tightly clustered genes exhibited conserved gene and protein structure. The physicochemical analyses suggested significant differences between small and long TLPs. Evolutionary analyses suggested the role of duplication events and purifying selection in the expansion of the TLP gene family. Expression analyses revealed the possible roles of TLPs in plant development and abiotic and fungal stress response. Recombinant expression of TaTLP2-B in Saccharomyces cerevisiae provided significant tolerance against cold, heat, drought and salt stresses. The results depicted the importance of TLPs in cereal crops that would be highly useful in future crop improvement programs.


title: Degeneracy and stability in neural circuits of neuromodulators

abstract: Degenerate neural circuits perform the same function despite being structurally different. However, it is unclear whether neural circuits with interacting neuromodulator sources can themselves be degenerate while maintaining the same neuromodulatory function. Here, we address this by computationally modelling the neural circuits of neuromodulators serotonin and dopamine, local glutamatergic and GABAergic interneurons, and their possible interactions, under reward/punishment-based conditioning tasks. We show that a single parsimonious, sparsely connected neural circuit model can recapitulate several separate experimental findings, but not all, suggesting potentially multiple circuits acting in parallel. Using computational simulations and dynamical systems analysis, we demonstrate that several different stable circuit architectures can produce the same observed network activity profile. Further, simulating dopamine (D2) receptor agonist can distinguish among sub-groups of these degenerate networks; a testable model prediction. Overall, this theoretical work suggests the plausibility of degeneracy within neuromodulator circuitry and has important implication for the stable and robust maintenance of neuromodulatory functions.


title: Degeneracy and stability in neural circuits of dopamine and serotonin neuromodulators: A theoretical consideration


title: Novelty is not Surprise: Human exploratory and adaptive behavior in sequential decision-making

abstract: Classic reinforcement learning (RL) theories cannot explain human behavior in response to changes in the environment or in the absence of external reward. Here, we design a deep sequential decision-making paradigm with sparse reward and abrupt environmental changes. To explain the behavior of human participants in these environments, we show that RL theories need to include surprise and novelty, each with a distinct role. While novelty drives exploration before the first encounter of a reward, surprise increases the rate of learning of a world-model as well as of model-free action-values. Even though the world-model is available for model-based RL, we find that human decisions are dominated by model-free action choices. The world-model is only marginally used for planning but is important to detect surprising events. Our theory predicts human action choices with high probability and allows us to dissociate surprise, novelty, and reward in EEG signals.