title: High coverage whole genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

abstract: The 1000 Genomes Project (1kGP) is the largest fully open resource of whole genome sequencing (WGS) data consented for public distribution of raw sequence data without access or use restrictions. The final release of the 1kGP included 2,504 unrelated samples from 26 populations and was based primarily on low coverage WGS. Here, we present a new, high coverage 3,202-sample WGS 1kGP resource, sequenced to a targeted depth of 30X using the Illumina NovaSeq 6000 system, which now includes 602 complete trios. We performed SNV/INDEL calling against the GRCh38 reference using GATKs HaplotypeCaller, and generated a comprehensive set of SVs by integrating multiple analytic methods through a sophisticated machine learning model. We make all the data generated as part of this project publicly available and we envision it to become the new de facto public resource for the worldwide genomics and genetics community.


title: The Memory for Latent Representations: An Account of Working Memory that Builds on Visual Knowledge for Efficient and Detailed Visual Representations

abstract: Visual knowledge obtained from our lifelong experience of the world plays a critical role in our ability to build short-term memories. We propose a mechanistic explanation of how working memories are built from the latent representations of visual knowledge and can then be reconstructed. The proposed model, Memory for Latent Representations (MLR), features a variational autoencoder with an architecture that corresponds broadly to the human visual system and an activation-based binding pool of neurons that binds items attributes to tokenized representations. The simulation results revealed that the shapes of familiar items can be encoded and retrieved efficiently from latents in higher levels of the visual hierarchy. On the other hand, novel patterns that are completely outside the training set can be stored from a single exposure using only latents from early layers of the visual system. Moreover, a given stimulus in working memory can have multiple codes, representing specific visual features such as shape or color, in addition to categorical information. Finally, we validated our model by testing a series of predictions against behavioral results obtained from WM tasks. The model provides a compelling demonstration of how visual knowledge yields compact visual representation for efficient memory encoding.

category: neuroscience


title: A model of working memory for latent representations


title: Transcriptomic and genetic analyses identify the Kruppel-like factor dar1 as a master regulator of tube-shaped long tendon development

abstract: To ensure locomotion and body stability, the active role of muscle contractions relies on a stereotyped muscle pattern set in place during development. This muscle patterning requires a precise assembly of the muscle fibers with the skeleton via a specialized connective tissue, the tendon. Despite evident disparities, little is known about the molecular basis of tendon diversity. Like in vertebrate limbs, Drosophila leg muscles make connections with specific long tendons that extend through different segments. During leg disc development, cell precursors of long tendons rearrange and collectively migrate to form a tube-shaped structure. A specific developmental program underlies this unique feature of tendon-like cells in the Drosophila model. We provide for the first time a transcriptomic profile of leg tendon precursors through fluorescence-based cell sorting. From promising candidates, we identified the Kruppel-like factor dar1 as a critical actor of leg tendon development. Specifically expressed in leg tendon precursors, loss of dar1 disrupts actin-rich filopodia formation and tendon elongation. Our findings show that dar1 acts downstream of stripe as a critical regulator of cytoskeleton remodeling and mediates the recruitment of new stripe-positive tendon progenitors in a cell non-autonomous manner.

category: developmental biology


title: Human spinal cord differentiation proceeds rapidly in vitro and only initially maintains differentiation pace in a heterologous environment

abstract: Species-specific differentiation pace in in vitro assays indicates that some aspects of neural differentiation are driven by cell-autonomous processes. Here we describe a novel in vitro human neural rosette assay that recapitulates the temporal sequence of dorsal spinal cord differentiation but proceeds more rapidly than in the human embryonic spinal cord, suggesting that in vitro conditions lack endogenous signalling dynamics. To test the extent to which this in vitro assay represents a cell intrinsic differentiation programme, human iPSC-derived neural rosettes were homo-chronically grafted into the faster differentiating chicken embryonic neural tube. Strikingly, in vitro human differentiation pace was not accelerated, even in single host-integrated cells. Moreover, rosette differentiation eventually stalled in a neural progenitor cell state. These findings demonstrate the requirement for timely extrinsic signalling to accurately recapitulate human neural differentiation tempo, and suggest that while intrinsic properties limit differentiation pace, such signals are also required to maintain differentiation progression.


title: Leaky wiring of the brain: local cluster of coupled synapses and extracellular signal integration

abstract: The wiring scheme of neurons is key to the function of the brain. Neurons are structurally wired by synapses and it is a long-held view that most synapses in the CNS are sufficiently isolated to avoid cross-talk to AMPA receptors of neighboring synapses. Here we report in hippocampal brain slices that quantal glutamate release activated optical reporter proteins >1.5 {micro}m distant to the releasing synapse. 2P-glutamate uncaging was used to quantitatively probe glutamate spread in the neuropil. Releasing [~]35000 molecules of glutamate ([~]5 vesicles) at a distance of 500 nm to a spine generated an uncaging EPSC reaching [~]30% of the quantal amplitude at synaptic AMPA-Rs. The same stimulus activated [~]70% of the quantal amplitude at NMDA-Rs and still generated clear current and calcium responses when applied at >= 2 {micro}m remote to the spine. Extracellular spread of glutamate on the sub-micrometer scale appeared cooperative and caused supra-additive activation of AMPA-Rs in a spine. These observations are not predicted by previously used models of glutamate diffusion in the neuropil. An extracellular glutamate scavenger system weakly reduced field potential responses but not the quantal amplitude, indicating that a cross-talk component regularly contributes to synaptic transmission. Our data suggest that slight synaptic crosstalk responses at AMPA receptors of [~]2-4 adjacent synapses may be common (>70 synapses for NMDA receptors). Such broadcasting of synaptic signals to very local neighborhoods could stabilize network learning performance and allow for integration of synaptic activity within the extracellular space.


title: Optical analysis of the action range of glutamate in the neuropil


title: Neuronal activity promotes nuclear proteasome-mediated degradation of PDCD4 to regulate activity-dependent transcription

abstract: Activity-dependent gene expression is critical for synapse development and plasticity. To elucidate novel mechanisms linking neuronal activity to changes in transcription, we compared the nuclear proteomes of tetrodotoxin-silenced and bicuculline-stimulated cultured rodent neurons using nuclear-localized APEX2 proximity biotinylation and mass spectrometry. The tumor suppressor protein PDCD4 was enriched in the silenced nuclear proteome, and PDCD4 levels rapidly decreased in the nucleus and cytoplasm of stimulated neurons. The activity-dependent decrease of PDCD4 was prevented by inhibitors of both PKC and proteasome activity and by a phospho-incompetent mutation of Ser71 in the {beta}TRCP ubiquitin ligase-binding motif of PDCD4. We compared the activity-dependent transcriptomes of neurons expressing wildtype or degradation-resistant (S71A) PDCD4. We identified 91 genes as PDCD4 targets at the transcriptional level, including genes encoding proteins critical for synapse formation, remodeling, and transmission. Our findings indicate that regulated degradation of nuclear PDCD4 facilitates activity-dependent transcription in neurons.


title: Loss of ClpP Function in Clostridioides difficile 630 Significantly Impacts Sporulation Systems

abstract: The Gram-positive bacterium Clostridioides difficile is a primary cause of hospital-acquired diarrhea, threatening both immunocompromised and healthy individuals. An important aspect of elucidating mechanisms that drive C. difficile persistence and virulence relies on developing a more complete understanding of sporulation. C. difficile sporulation is the single determinant of transmission and complicates treatment and prevention due to the chemical and physical resilience of spores. Hence, the identification of potentially druggable targets that significantly attenuate sporulation is important. In this report, we describe the impact of the loss of caseinolytic protease P (ClpP) isoforms in C. difficile strain 630 on sporulation phenotypes. Using CRISPR-Cas9 nickase mediated genome editing, stop codons were inserted early in the coding sequence for clpP1 and clpP2 to generate C. difficile mutants that no longer produced ClpP1 or ClpP2. The data show that these genetic modifications lead to altered sporulation phenotypes, germination efficiencies, and cytotoxicity. Comparative proteome profiling of C. difficile 630 WT and clpP mutants reveals potential proteolytic targets of ClpP that are involved in sporulation. These analyses further reveal the potential for preferred co-chaperone interactions for each ClpP isoform. Taken together, our results demonstrate that ClpP, a promising target in other Gram-positive pathogens, holds promise as an anti-sporulation target in C. difficile.

category: microbiology


title: The ability of Pseudomonas aeruginosa to adopt a Small Colony Variant (SCV) phenotype is conserved, and not restricted to clinical isolates

abstract:
A subpopulation of Small Colony Variants (SCVs) is a frequently observed feature of Pseudomonas aeruginosa isolated from cystic fibrosis (CF) lungs biofilms. SCVs have almost exclusively been reported from infected hosts, essentially CF individuals or, by extension, from laboratory cultivation of strains originated from infected hosts. We previously reported the identification of P. aeruginosa SCVs emerging from a non-clinical strain and displaying features shared with clinical SCVs. In the present work, we investigated the ability of 22 P. aeruginosa isolates from various environmental origins to, under laboratory culture conditions, spontaneously adopt a SCV-like smaller alternative morphotype distinguishable from the ancestral parent strain. Unexpectedly, we found that all the P. aeruginosa strains tested have the ability to adopt a SCV morphotype, regardless of their origin. Based on the phenotypes already described for SCVs, the SCV-like morphotypes obtained were clustered in two groups displaying various phenotypic profiles, including one characteristic of already described SCVs. We conclude that the ability to switch to a SCV phenotype is a conserved feature in Pseudomonas aeruginosa.

IMPORTANCEP. aeruginosa is an opportunistic pathogen that thrives in many environments. It is significant public health concern, notably because it is the most prevalent pathogen found in the lungs of people with cystic fibrosis (CF). In infected hosts, its persistence is believed to be related to the emergence of an alternative small colony variant (SCV) phenotype. By reporting the distribution of P. aeruginosa SCVs in various non-clinical environments, this work contributes to understanding a conserved adaptation mechanism used by P. aeruginosa to rapidly adapt in all environments. Counteraction of this strategy could prevent P. aeruginosa persistent infection in the future.


title: Impact of cobas PCR Media Freezing on SARS-CoV-2 Viral RNA Integrity and Whole Genome Sequencing Analyses

abstract: SARS-CoV-2 whole genome sequencing is an important molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swab samples and shipment to reference laboratories is usually required since RNA sequencing is rarely available in routine clinical microbiology laboratories where initial diagnosis and support to outbreak investigations occur. The cobas PCR Media transport medium developed by Roche facilitates high throughput analyses on cobas multianalyzer PCR platforms. There is no data on the stability of SARS-CoV-2 RNA after freezing and thawing of clinical samples in this transport medium, but potential denaturing of the molecular template could impair test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral whole genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Genomic coverage and sequencing depth did not significantly differ between fresh and frozen samples (n=10). For samples with lower viral inoculum and PCR cycle threshold above 30, sequencing quality scores and detection of single nucleotide polymorphisms did not differ either. Freezing of cobas PCR Media does not negatively affect the quality of SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories. Those results support secondary use of diagnostic nasopharyngeal swab material for viral sequencing without requirement for additional clinical samples.

category: molecular biology


title: Bidirectional neuronal migration coordinates retinal morphogenesis bypreventing spatial competition

abstract: While the design of industrial products is often optimized for the sequential assembly of single components, organismal development is hallmarked by the concomitant occurrence of tissue growth and organization. Often this means that proliferating and differentiating cells occur at the same time in a shared tissue environment that continuously changes. How cells adapt to architectural changes in order to prevent spatial interference remains unclear. To understand how cell movements important for growth and organization are orchestrated, we here study the emergence of photoreceptor neurons that occur during the peak of retinal growth using zebrafish, human tissue and human organoids. Quantitative imaging reveals that successful retinal morphogenesis depends on active bidirectional photoreceptor translocation. This leads to a transient transfer of the entire cell population away from the apical proliferative zone. This migration pattern is driven by distinct cytoskeletal machineries, depending on direction: microtubules are required for basal translocation, while actomyosin drives apical movement. Blocking photoreceptor translocation leads to apical overcrowding that hampers progenitor movements. Thus, photoreceptor migration is crucial to prevent competition for space and thereby allows concurrent tissue growth and lamination. This shows that neuronal migration, in addition to its canonical role in cell positioning, is involved in coordinating morphogenesis.


title: Social selection is density dependent but makes little contribution to total selection in New Zealand giraffe weevils

abstract: Social selection occurs when traits of interaction partners influence an individuals fitness and can fundamentally alter total selection strength. Unlike for direct selection, however, we have little idea of what factors influence the strength of social selection. Further, social selection only contributes to overall selection when there is phenotypic assortment, but simultaneous estimates of social selection and phenotypic assortment are rare. Here we estimated social selection on body size in a wild population of New Zealand giraffe weevils (Lasiorhynchus barbicornis). We did this in a range of contexts and measured phenotypic assortment for both sexes. Social selection was mostly absent and not affected by sex ratio or the body size of the focal individual. However, at high densities selection was negative for both sexes, consistent with competitive interactions based on size for access to mates. Phenotypic assortment was also density dependent, flipping from positive at low densities to negative at high densities. However, it was always close to zero, indicating negative social selection at high densities will not greatly impede the evolution of larger body sizes. Despite its predicted importance, social selection may only influence evolutionary change in specific contexts, leaving direct selection as the dominant driver of evolutionary change.

category: evolutionary biology


title: Poly(A) binding protein is required for mRNP remodeling to form P-bodies in mammalian cells

abstract:
Compartmentalization of mRNA through formation of RNA granules is involved in many cellular processes, yet it is not well understood. mRNP complexes undergo dramatic changes in protein compositions, reflected by markers of P-bodies and stress granules. Here, we show that PABPC1, albeit absent in P-bodies, plays important role in P-body formation. Depletion of PABPC1 decreases P-body population in unstressed cells. Upon stress in PABPC1 depleted cells, individual P-bodies fail to form and instead P-body proteins assemble on PABPC1-containing stress granules. We hypothesize that mRNP recruit proteins via PABPC1 to assemble P-bodies, before PABPC1 is displaced from mRNP. Further, we demonstrate that GW182 can mediate P-body assembly. These findings help us understand the early stages of mRNP remodeling and P-body formation.

Summary statementA novel role of poly(A) binding protein is reported in P-body formation

category: biochemistry


title: A non-structural pure enzyme protein forms an LCST type of stimuli-responsive and reversible hydrogel with novel structure and catalytic activity

abstract: Hydrogels have a wide range of applications such as in biomedicine, cosmetics and soft electronics. Compared to polymer hydrogels based on covalent bonding, protein hydrogels offer distinct advantages owing to their biocompatibility and better access to molecular engineering. However, pure and natural protein hydrogels have been seldom reported except for structural proteins like collagen and silk fibrin. Here, we report the unusual ability and mechanism of a unique natural enzyme, lipoate-protein ligase A (LplA) of E. coli to self-assemble into a stimuli-responsive and reversible hydrogel of the low critical solution temperature (LCST) type. This is the first globular and catalytic protein found to form a hydrogel in response to temperature, pH and the presence of ions. Protein structure based analysis reveals the key residues responsible for the gel formation and mutational studies confirms the essential roles of hydrogen bonding between the C-terminal domains and electrostatic interactions in the N-terminal domains. Characterization of phase transitions of wild type LplA and its mutants using small angle X-ray scattering (SAXS) yields details of the gelation process from initial dimer formation over a pre-gel-state to full network development. Further electron microscopic analyses and modeling of SAXS data suggest an unusual interlinked ladder-like structure of the macroscopic crosslinking network with dimers as ladder steps. The unique features of this first reported protein hydrogel may open up hitherto inaccessible applications, especially those taking advantage of the inherent catalytic activity of LplA.


title: Paip2 associates with PABPC1 on mRNA, and may facilitate PABPC1 dissociation from mRNA upon deadenylation

abstract: Poly(A) binding protein cytoplasmic 1 (PABPC1) is an essential translational initiation factor. PABPC1 recognizes proteins through conserved PABPC1-interacting motifs 1 and 2 (PAM1 and PAM2). PABPC1-interacting protein-2 (Paip2) interacts with PABPC1 and modulates its activities. Here, we report that the formation of Paip2/PABPC1 complex protects it from proteasome independent degradation. We also show that PAM2 is critical for Paip2/PABPC1 interaction in vivo, in agreement with the observation that Paip2 requires PAM2 to interact with PABPC1 on mRNA. Lastly, we propose a role for Paip2 in displacing PABPC1 at the final stage of mRNA deadenylation when the poly(A) tail is partly degraded.


title: Structural and functional elucidation of NF-κB signaling by the p75 neurotrophin receptor through recruitment of TRADD

abstract: p75 neurotrophin receptor (p75NTR) is a critical mediator of neuronal death and tissue remodeling and has been implicated in various neurodegenerative diseases. The death domain (DD) of p75NTR is an intracellular signaling hub and has been shown to interact with diverse adaptor proteins. However, the structural mechanism and physiological relevance of the adaptor protein TRADD in neuronal p75NTR signaling remain poorly understood. Here we report an NMR structure of the complex between p75NTR-DD and TRADD-DD and elucidate the structural basis of specific DD recognition in the p75NTR/TRADD signaling pathway. Furthermore, we identify spatiotemporal overlap of p75NTR and TRADD expression in developing cerebellar granule neurons (CGNs) at early postnatal stages and reveal the functional role of TRADD recruitment to p75NTR in the regulation of canonical NF-{kappa}B signaling and cell survival in CGNs. Our results provide a new structural framework for understanding how the recruitment of TRADD to p75NTR through DD interactions creates a membrane-proximal platform to propagate downstream signaling in developing neurons.

category: biophysics


title: Bacterium-Enabled Transient Gene Activation by Artificial Transcription Factor for Resolving Gene Regulation in Maize

abstract: Cellular functions are diversified through intricate transcription regulations, and an understanding gene regulation networks is essential to elucidating many developmental processes and environmental responses. Here, we employed the Transcriptional-Activator Like effectors (TALes), which represent a family of transcription factors that are synthesized by members of the {gamma}-proteobacterium genus Xanthomonas and secreted to host cells for activation of targeted host genes. Through delivery by the maize pathogen, Xanthomonas vasicola pv. vasculorum, designer TALes (dTALes), which are synthetic TALes, were used to induce the expression of the maize gene glossy3 (gl3), a MYB transcription factor gene involved in the cuticular wax biosynthesis. RNA-Seq analysis of leaf samples identified 146 gl3 downstream genes. Eight of the nine known genes known to be involved in the cuticular wax biosynthesis were up-regulated by at least one dTALe. A top-down Gaussian graphical model predicted that 68 gl3 downstream genes were directly regulated by GL3. A chemically induced mutant of the gene Zm00001d017418 from the gl3 downstream gene, encoding aldehyde dehydrogenase, exhibited a typical glossy leaf phenotype and reduced epicuticular waxes. The bacterial protein delivery of artificial transcription factors, dTALes, proved to be a straightforward and powerful approach for the revelation of gene regulation in plants.

category: plant biology


title: Modulating the left inferior frontal cortex by task domain, cognitive challenge and tDCS

abstract: The left inferior frontal cortex (LIFC) is a key region for spoken language processing, but its neurocognitive architecture remains controversial. Here we assess the domain-generality vs. domain-specificity of the LIFC from behavioural, functional neuroimaging and neuromodulation data. Using concurrent fMRI and transcranial direct current stimulation (tDCS) delivered to the LIFC, we investigated how brain activity and behavioural performance are modulated by task domain (naming vs. non-naming), cognitive challenge (low vs. high), and tDCS (anodal vs. sham). The data revealed: (1) co-existence of neural signatures both common and distinct across tasks within the LIFC; (2) domain-preferential effects of task (naming); (3) significant tDCS modulations of activity in a LIFC sub-region selectively during high-challenge naming. The presence of both domain-specific and domain-general signals, and the existence of a gradient of activation where naming relied more on sub-regions within the LIFC, may help reconcile both perspectives on spoken language processing.


title: Mechanism of dopamine binding and allosteric modulation of the human D1 dopamine receptor

abstract: Dopamine is an essential neurotransmitter, which functions are mediated by five G protein-coupled receptors, dopamine D1 to D5 receptors (D1R-D5R) in mammals. Among them, D1R is the most abundantly expressed dopamine receptor in the CNS and is the central receptor mediating excitatory dopamine signaling in multiple dopaminergic pathways. Dysregulation of D1R signaling has been directly linked to Parkinsons disease (PD), schizophrenia, and drug abuse. Due to its fundamental functions in human diseases, D1R has long been the subject of intensive drug development effort toward the treatment of neuropsychiatric diseases. Here, we report the structures of D1R-Gs complex bound to endogenous agonist dopamine and synthetic agonist SKF81297, both with positive allosteric modulator LY3154207. These structures reveal the basis of dopamine recognition, the binding and potential allosteric regulation of DRD1 PAM LY3154207, and provide structural templates for design of subtype-selective D1R ligand for drug discovery targeting DRD1 for treating various CNS diseases.


title: An Incrementally Updatable and Scalable System for Large-Scale Sequence Search using LSM Trees

abstract:
MotivationIn the past few years, researchers have proposed numerous indexing schemes for searching large databases of raw sequencing experiments. Most of these proposed indexes are approximate (i.e. with one-sided errors) in order to save space. Recently, researchers have published exact indexes--Mantis, VariMerge, and Bifrost--that can serve as colored de Bruijn graph representations in addition to serving as k-mer indexes. This new type of index is promising because it has the potential to support more complex analyses than simple searches. However, in order to be useful as indexes for large and growing repositories of raw sequencing data, they must scale to thousands of experiments and support efficient insertion of new data.

ResultsIn this paper, we show how to build a scalable and updatable exact sequence-search index. Specifically, we extend Mantis using the Bentley-Saxe transformation to support efficient updates. We demonstrate Mantiss scalability by constructing an index of{approx} 40K samples from SRA by adding samples one at a time to an initial index of 10K samples.

Compared to VariMerge and Bifrost, Mantis is more efficient in terms of index-construction time and memory, query time and memory, and index size. In our benchmarks, VariMerge and Bifrost scaled to only 5K and 80 samples, respectively, while Mantis scaled to more than 39K samples. Queries were over 24x faster in Mantis than in Bifrost (VariMerge does not immediately support general search queries we require). Mantis indexes were about 2.5x smaller than Bifrosts indexes and about half as big as VariMerges indexes.

AvailabilityThe updatable Mantis implementation is available at https://github.com/splatlab/mantis/tree/mergeMSTs.

Contactrob@cs.umd.edu

Supplementary informationSupplementary data are available online.

category: bioinformatics


title: Large-scale tandem mass spectrum clustering using fast nearest neighbor searching

abstract:
RationaleAdvanced algorithmic solutions are necessary to process the ever increasing amounts of mass spectrometry data that is being generated. Here we describe the falcon spectrum clustering tool for efficient clustering of millions of MS/MS spectra.

Methodsfalcon succeeds in efficiently clustering large amounts of mass spectral data using advanced techniques for fast spectrum similarity searching. First, high-resolution spectra are binned and converted to low-dimensional vectors using feature hashing. Next, the spectrum vectors are used to construct nearest neighbor indexes for fast similarity searching. The nearest neighbor indexes are used to efficiently compute a sparse pairwise distance matrix without having to exhaustively perform all pairwise spectrum comparisons within the relevant precursor mass tolerance. Finally, density-based clustering is performed to group similar spectra into clusters.

ResultsSeveral state-of-the-art spectrum clustering tools were evaluated using a large draft human proteome dataset consisting of 25 million spectra, indicating that alternative tools produce clustering results with different characteristics. Notably, falcon generates larger highly pure clusters than alternative tools, leading to a larger reduction in data volume without the loss of relevant information for more efficient downstream processing.

Conclusionsfalcon is a highly efficient spectrum clustering tool. It is publicly available as open source under the permissive BSD license at https://github.com/bittremieux/falcon.


title: ORFhunteR: an accurate approach for the automatic identification and annotation of open reading frames in human mRNA molecules

abstract:
MotivationModern methods of whole transcriptome sequencing accurately recover nucleotide sequences of RNA molecules present in cells and allow for determining their quantitative abundances. The coding potential of such molecules can be estimated using open reading frames (ORF) finding algorithms, implemented in a number of software packages. However, these algorithms show somewhat limited accuracy, are intended for single-molecule analysis and do not allow selecting proper ORFs in the case of long mRNAs containing multiple ORF candidates.

ResultsWe developed a computational approach, corresponding machine learning model and a package, dedicated to automatic identification of the ORFs in large sets of human mRNA molecules. It is based on vectorization of nucleotide sequences into features, followed by classification using a random forest. The predictive model was validated on sets of human mRNA molecules from the NCBI RefSeq and Ensembl databases and demonstrated almost 95% accuracy in detecting true ORFs. The developed methods and pre-trained classification model were implemented in a powerful ORFhunteR computational tool that performs an automatic identification of true ORFs among large set of human mRNA molecules.

Availability and implementationThe developed open-source R package ORFhunteR is available for the community at GitHub repository (https://github.com/rfctbio-bsu/ORFhunteR), from Bioconductor (https://bioconductor.org/packages/devel/bioc/html/ORFhunteR.html) and as a web application (http://orfhunter.bsu.by).


title: A Network Propagation Approach to Prioritize Long Tail Genes in Cancer

abstract:
IntroductionThe diversity of genomic alterations in cancer pose challenges to fully understanding the etiologies of the disease. Recent interest in infrequent mutations, in genes that reside in the "long tail" of the mutational distribution, uncovered new genes with significant implication in cancer development. The study of these genes often requires integrative approaches with multiple types of biological data. Network propagation methods have demonstrated high efficacy in uncovering genomic patterns underlying cancer using biological interaction networks. Yet, the majority of these analyses have focused their assessment on detecting known cancer genes or identifying altered subnetworks. In this paper, we introduce a network propagation approach that entirely focuses on long tail genes with potential functional impact on cancer development.

ResultsWe identify sets of often overlooked, rarely to moderately mutated genes whose biological interactions significantly propel their mutation-frequency-based rank upwards during propagation in 17 cancer types. We call these sets "upward mobility genes" (UMGs, 28-83 genes per cancer type) and hypothesize that their significant rank improvement indicates functional importance. We report new cancer-pathway associations based on UMGs that were not previously identified using driver genes alone, validate UMGs role in cancer cell survival in vitro--alone and compared to other network methods--using extensive genome-wide RNAi and CRISPR data repositories, and further conduct in vitro functional screenings resulting the validation of 8 previously unreported genes.

ConclusionOur analysis extends the spectrum of cancer relevant genes and identifies novel potential therapeutic targets.


title: Network Propagation-based Prioritization of Long Tail Genes in 17 Cancer Types


title: Derived loss of signal complexity and plasticity in a genus of weakly electric fish

abstract: Signal plasticity can maximize the usefulness of costly animal signals such as the electric organ discharges (EODs) of weakly electric fishes. Some species of the order Gymnotiformes rapidly alter their EOD amplitude and duration in response to circadian cues and social stimuli. How this plasticity is maintained across related species with different degrees of signal complexity is poorly understood. In one genus of weakly electric gymnotiform fish (Brachyhypopomus) only one species, B. bennetti, produces a monophasic signal while all other species emit complex biphasic or multiphasic EOD waveforms produced by two overlapping but asynchronous action potentials in each electric organ cell (electrocyte). One consequence of this signal complexity is the suppression of low-frequency signal content that is detectable by electroreceptive predators. In complex EODs, reduction of the EOD amplitude and duration during daytime inactivity can decrease both predation risk and the metabolic cost of EOD generation. We compared EOD plasticity and its underlying physiology in Brachyhypopomus focusing on B. bennetti. We found that B. bennetti exhibits minimal EOD plasticity, but that its electrocytes retained vestigial mechanisms of biphasic signaling and vestigial mechanisms for modulating the EOD amplitude. These results suggest that this species represents a transitional phenotypic state within a clade where signal complexity and plasticity were initially gained and then lost. We discuss potential the roles of signal mimicry, species recognition, and sexual selection in maintaining the monophasic EOD phenotype in the face of detection by electroreceptive predators.

category: physiology


title: Neuronal modulation in the mouse superior colliculus during covert visual selective attention

abstract: Covert visual attention is accomplished by a cascade of mechanisms distributed across multiple brain regions. Recent studies in primates suggest a parcellation in which visual cortex is associated with enhanced representations of relevant stimuli, whereas subcortical circuits are associated with selection of visual targets and suppression of distractors. Here we identified how neuronal activity in the superior colliculus (SC) of head-fixed mice is modulated during covert visual attention. We found that spatial cues modulated both firing rate and spike-count correlations, and that the cue-related modulation in firing rate was due to enhancement of activity at the cued spatial location rather than suppression at the uncued location. This modulation improved the neuronal discriminability of visual-change-evoked activity between contralateral and ipsilateral SC neurons. Together, our findings indicate that neurons in the mouse SC contribute to covert visual selective attention by biasing processing in favor of locations expected to contain relevant information.


title: Emergence of Probabilistic Representation in the Neural Network of Primary Visual Cortex

abstract: During the early development of mammalian visual system, the distribution of neuronal preferred orientations in the primary visual cortex (V1) gradually shifts to match the major orientation features of an environment, achieving optimal representation of the environment. By combining the computational modeling and experimental electrophysiological recording, we provide a circuitry plasticity mechanism that underlies the developmental emergence of such matched representation in the visual cortical network. Specifically, in a canonical circuit of densely interconnected pyramidal cells and inhibitory parvalbumin-expressing (PV+) fast-spiking interneurons in the V1 layer 2/3, our model successfully simulates the experimental observations and further reveals that the non-uniform inhibition, mediated by local interneurons, exerts a key role in shaping the network representation through spike timing-dependent synaptic modifications. The experimental results confirm that PV+ interneurons in the V1 are capable of providing such non-uniform inhibition during a short period after the vision onset. Thus, our study elucidates a circuitry mechanism for acquisition of the prior knowledge of environment for optimal inference in sensory neural system.


title: The effect of pulse width on the dynamics of pulse-coupled oscillators

abstract: The idealisation of neuronal pulses as{delta} -spikes is a convenient approach in neuroscience but can sometimes lead to erroneous conclusions. We investigate the effect of a finite pulse-width on the dynamics of balanced neuronal networks. In particular, we study two populations of identical excitatory and inhibitory neurons in a random network of phase oscillators coupled through exponential pulses with different widths. We consider three coupling functions, inspired by leaky integrate-and-fire neurons with delay and type-I phase-response curves. By exploring the role of the pulse-widths for different coupling strengths we find a robust collective irregular dynamics, which collapses onto a fully synchronous regime if the inhibitory pulses are sufficiently wider than the excitatory ones. The transition to synchrony is accompanied by hysteretic phenomena (i.e. the co-existence of collective irregular and synchronous dynamics). Our numerical results are supported by a detailed scaling and stability analysis of the fully synchronous solution. A conjectured first-order phase transition emerging for{delta} -spikes is smoothed out for finite-width pulses.


title: Collective dynamics in the presence of finite-width pulses


title: A recurrent cortical model can parsimoniously explain the effect of expectations on sensory processes

abstract: The effect of prior knowledge and expectations on perceptual and decision-making processes have been extensively studied. Yet, the computational mechanisms underlying those effects have been a controversial issue. Recently, using a recursive Bayesian updating scheme, unmet expectations have been shown to entail further computations, and consequently delay perceptual processes. Here we take a step further and model these empirical findings with a recurrent cortical model, which was previously suggested to approximate Bayesian inference (Heeger, 2017). Our model fitting results show that the cortical model can successfully predict the behavioral effects of expectation. That is, when the actual sensory input does not match with the expectations, the sensory process needs to be completed with additional, and consequently longer, computations. We suggest that this process underlies the delay in perceptual thresholds in unmet expectations. Overall our findings demonstrate that a parsimonious recurrent cortical model can explain the effects of expectation on sensory processes.


title: The human visual system preserves the hierarchy of 2-dimensional pattern regularity

abstract: Symmetries are present at many scales in images of natural scenes. A large body of literature has demonstrated contributions of symmetry to numerous domains of visual perception. The four fundamental symmetries, reflection, rotation, translation and glide reflection, can be combined in exactly 17 distinct ways. These wallpaper groups represent the complete set of symmetries in 2D images and have recently found use in the vision science community as an ideal stimulus set for studying the perception of symmetries in textures. The goal of the current study is to provide a more comprehensive description of responses to symmetry in the human visual system, by collecting both brain imaging (Steady-State Visual Evoked Potentials measured using high-density EEG) and behavioral (symmetry detection thresholds) data using the entire set of wallpaper groups. This allows us to probe the hierarchy of complexity among wallpaper groups, in which simpler groups are subgroups of more complex ones. We find that this hierarchy is preserved almost perfectly in both behavior and brain activity: A multi-level Bayesian GLM indicates that for most of the 63 subgroup relationships, subgroups produce lower amplitude responses in visual cortex (posterior probability: > 0.95 for 56 of 63) and require longer presentation durations to be reliably detected (posterior probability: > 0.95 for 49 of 63). This systematic pattern is seen only in visual cortex and only in components of the brain response known to be symmetric-specific. Our results show that representations of symmetries in the human brain are precise and rich in detail, and that this precision is reflected in behavior. These findings expand our understanding of symmetry perception, and open up new avenues for research on how fine-grained representations of regular textures contribute to natural vision.


title: Objective pupillometry shows that perceptual styles covary with autistic-like personality traits

abstract: We measured the modulation of pupil-size (in constant lighting) elicited by observing transparent surfaces of black and white moving dots, perceived as a cylinder rotating about its vertical axis. The direction of rotation was swapped periodically by flipping stereo-depth of the two surfaces. Pupil size modulated in synchrony with the changes in front-surface color (dilating when black). The magnitude of pupillary modulation was larger for participants with higher Autism-Spectrum Quotient (AQ), consistent with a local style of perception, with attention focused on the front surface. The modulation with surface color, and its correlation with AQ, was equally strong when participants passively viewed the stimulus. No other indicator, including involuntary pursuit eye-movements, covaried with AQ. These results reinforce our previous report with a similar bistable stimulus (Turi, Burr, & Binda, 2018), and go on to show that bistable illusory motion is not necessary for the effect, or its dependence on AQ.


title: Exploring the dynamic mechanisms of steady-state visual evoked potentials at the whole-brain level: evidence from a computational study

abstract: Periodic visual stimulation can induce stable steady-state visual evoked potentials (SSVEPs) distributed in multiple brain regions and has potential applications in both neural engineering and cognitive neuroscience. However, the underlying dynamic mechanisms of SSVEPs at the whole-brain level are still not completely understood. Here, we addressed this issue by simulating the rich dynamics of SSVEPs with a large-scale brain model designed with constraints of neuroimaging data acquired from the human brain. By eliciting activity of the occipital areas using an external periodic stimulus, our model was capable of replicating both the spatial distributions and response features of SSVEPs that were observed in experiments. In particular, we confirmed that alpha-band (8-12 Hz) stimulation could evoke stronger SSVEP responses; this frequency sensitivity was due to nonlinear entrainment and resonance, and could be modulated by endogenous factors in the brain. Interestingly, the stimulus-evoked brain networks also exhibited significant superiority in topological properties near this frequency-sensitivity range, and stronger SSVEP responses were demonstrated to be supported by more efficient functional connectivity at the neural activity level. These findings not only provide insights into the mechanistic understanding of SSVEPs at the whole-brain level but also indicate a bright future for large-scale brain modeling in characterizing the complicated dynamics and functions of the brain.


title: Computational exploration of dynamic mechanisms of steady state visual evoked potentials at the whole brain level


title: Memory destabilization during reconsolidation - A consequence of homeostatic plasticity?

abstract: Remembering is not a static process: when retrieved, a memory can be destabilized and become prone to modifications. This phenomenon has been demonstrated in a number of brain regions, but the neuronal mechanisms that rule memory destabilization and its boundary conditions remain elusive. Using two distinct computational models that combine Hebbian plasticity and synaptic downscaling, we show that homeostatic plasticity can function as a destabilization mechanism, accounting for behavioral results of protein synthesis inhibition upon reactivation with different reexposure times. Furthermore, by performing systematic reviews, we identify a series of overlapping molecular mechanisms between memory destabilization and synaptic downscaling, although direct experimental links between both phenomena remain scarce. In light of these results, we propose a theoretical framework where memory destabilization can emerge as an epiphenomenon of homeostatic adaptations prompted by memory retrieval.


title: Pupil Size Reflects Exploration and Exploitation in Visual Search (and It's Like Object-Based Attention)

abstract:
The adaptive gain theory (AGT) posits that activity in the locus coeruleus (LC) is linked to two behavioral modes: exploitation, characterized by focused attention on a single task; and exploration, characterized by a lack of focused attention and frequent switching between tasks. Furthermore, pupil size correlates with LC activity, such that large pupils indicate increased LC firing, and by extension also exploration behavior. Most evidence for this correlation in humans comes from complex behavior in game-like tasks. However, predictions of the AGT naturally extend to a very basic form of behavior: eye movements. To test this, we used a visual-search task. Participants searched for a target among many distractors, while we measured their pupil diameter and eye movements. The display was divided into four randomly generated regions of different colors. Although these regions were irrelevant to the task, participants were sensitive to their boundaries, and dwelled within regions for longer than expected by chance. Crucially, pupil size increased before eye movements that carried gaze from one region to another. We propose that eye movements that stay within regions (or objects) correspond to exploitation behavior, whereas eye movements that switch between regions (or objects) correspond to exploration behavior.

Public Significance StatementWhen people experience increased arousal, their pupils dilate. The adaptive-gain theory proposes that pupil size reflects neural activity in the locus coeruleus (LC), which in turn is associated with two behavioral modes: a vigilant, distractible mode ("exploration"), and a calm, focused mode ("exploitation"). During exploration, pupils are larger and LC activity is higher than during exploitation. Here we show that the predictions of this theory generalize to eye movements: smaller pupils coincide with eye movements indicative of exploitation, while pupils slightly dilate just before make eye movements that are indicative of exploration.


title: Innovations to expand drone data collection and analysis for rangeland monitoring

abstract: In adaptive management of rangelands, monitoring is the vital link that connects management actions with on-the-ground changes. Traditional field monitoring methods can provide detailed information for assessing the health of rangelands, but cost often limits monitoring locations to a few key areas or random plots. Remotely sensed imagery, and drone-based imagery in particular, can observe larger areas than field methods while retaining high enough spatial resolution to estimate many rangeland indicators of interest. However, the geographic extent of drone imagery products is often limited to a few hectares (for resolution [≤] 1 cm) due to image collection and processing constraints. Overcoming these limitations would allow for more extensive observations and more frequent monitoring. We developed a workflow to increase the extent and speed of acquiring, processing, and analyzing drone imagery for repeated monitoring of two common indicators of interest to rangeland managers: vegetation cover and vegetation heights. By incorporating a suite of existing technologies in drones (real-time kinematic GPS), data processing (automation with Python scripts, high performance computing), and cloud-based analysis (Google Earth Engine), we greatly increased the efficiency of collecting, analyzing, and interpreting high volumes of drone imagery for rangeland monitoring. End-to-end, our workflow took 30 days, while a workflow without these innovations was estimated to require 141 days to complete. The technology around drones and image analysis is rapidly advancing which is making high volume workflows easier to implement. Larger quantities of monitoring data will significantly improve our understanding of the impact management actions have on land processes and ecosystem traits.

category: ecology


title: Disentangling the effects of climate change, landscape heterogeneity, and scale on phenological metrics

abstract: Phenology, the study of the timing of cyclical life history events and seasonal changes, is a fundamental aspect of how individual species, communities, and ecosystems will respond to climate change. Both biotic and abiotic phenological patterns are changing rapidly in response to changing seasonal temperatures and other climate-related drivers, and the consequences of these shifts for individual species and entire ecosystems are largely unknown. Landscape-scale simulations can address some of these needs for better predictions by demonstrating how phenology measures can vary with spatial and temporal grain of observations, and how phenological responses can vary with landscape heterogeneity and climate drivers. To explicitly examine the spatial and temporal scale-dependence of multiple phenology measures, we constructed simulated landscapes populated by virtual plant species with realistic phenologies and environmental sensitivities. This enabled us to examine phenology measures and environmental sensitivities along a continuum of spatial and temporal grains, while also controlling other aspects of sampling design. By relating measures of phenology calculated at a given spatiotemporal grain to average environmental conditions at that same grain size, we are able to determine observed environmental sensitivities for multiple phenological metrics at that spatial and temporal scale. We demonstrate that different phenological events change distinctly and predictably with spatial and temporal measurement scale, opening the way to incorporating scaling laws into predictions. Using plant flowering as our example, we identify that the timing of the beginnings or ends of an event (e.g., First Flower date, Last Flower date), can be especially sensitive to the spatial and temporal grain (or resolution) of observations. Our work provides an initial assessment of the role of observation scale in landscape phenology, and a general approach for incorporating scale-dependence into predictions of a variety of phenological time series.


title: Speciation across the Earth driven by global cooling in orchidoid orchids

abstract:
Since Charles Darwin termed it his "abominable mystery", rapid speciation in angiosperms has eluded simple explanation. Climate has been implicated as a major catalyst of diversification, but its effects are thought to be inconsistent over time, between clades and across regions of the globe. Here we test the influence of climate change and geography-related climate factors on the diversification of the orchidoid orchids, a diverse subfamily of enduring fascination since Darwins time. We show that global cooling spurred speciation in assemblages of orchidoids throughout the earth. Employing a phylogenetic framework, we demonstrate that speciation rate is correlated with historic changes in global temperature, but not atmospheric CO2 or sea-level. Cooling-driven diversification is consistent in all tribes, and in Disa, a large genus with well-supported signatures of adaptive evolution. We find no evidence for influences of geography-related climate factors, such as latitudinal and elevation gradients, or for "cradles" of diversity, in analyses of tip rates in the context of 1.5 million georeferenced records. Rather than being an abominable mystery, our results support a simple hypothesis that climate change can rapidly accelerate adaptive radiation in assemblages throughout the globe. Our findings raise the possibility that there are undiagnosed roles for climate change in other major radiations and indicate how contemporary climate change will influence long-term evolutionary processes.

Significance StatementThe staggering biodiversity of angiosperms has been difficult to reconcile with the gradual Darwinian process thought to create it. Changes in climate through the Earths history could have instigated this diversification, but perceived variability across clades and geography has restrained generalization. In this paper, we reconstruct the evolutionary history of a rich orchid subfamily favoured by Darwin (Orchidoideae, 5,000 sps), and use 1.5 million georeferenced records to test when and where those orchid species arose. We find that global cooling between the Oligocene and present day spurred an avalanche of speciation in orchidoid assemblages across the Earth. This work resolves the orchidoid phylogeny and provides a clear example of widespread speciation driven by climate change.


title: Comparison analysis on transcriptomic of different human trophoblast development model

abstract:
AimsMultiple models of trophoblastic cell development were developed. However, systematic comparisons of these cell models are lacking.

Methods and ResultsIn this study, first-trimester chorionic villus and decidua tissues were collected. Transcriptome data was acquired by RNA-seq and the expression levels of trophoblast specific transcription factors were identified by immunofluorescence and RNA-seq data analysis.

Differentially expressed genes between chorionic villus and decidua tissues and its related biological functions were identified. We identified genes that were relatively highly expressed and enriched transcription factors in trophoblast cells of different trophoblast cell models.

ConclusionsThis analysis is of certain significance for further exploration of the development of placenta and the occurrence of pregnancy-related diseases in the future. The datasets and analysis provide a useful source for the researchers in the field of the maternal-fetal interface and the establishment of pregnancy.

category: cell biology


title: Cell Type Hierarchy Reconstruction via Reconciliation of Multi-resolution Cluster Tree

abstract: A wealth of clustering algorithms are available for Single-cell RNA sequencing (scRNA-seq), but it remains challenging to compare and characterize the features across different scales of resolution. To resolve this challenge Multi-resolution Reconciled Tree (MRtree), builds a hierarchical tree structure based on multi-resolution partitions that is highly flexible and can be coupled with most scRNA-seq clustering algorithms. MRtree out-performs bottom-up or divisive hierarchical clustering approaches because it inherits the robustness and versatility of a flat clustering approach, while maintaining the hierarchical structure of cells. Application to fetal brain cells yields insight into subtypes of cells that can be reliably estimated.


title: Trophic resources of the edaphic mesofauna: a worldwide review of the empirical evidence

abstract: Ecosystem sustainable use requires reliable information about its biotic and abiotic structure and functioning. Accurate knowledge of trophic relations is central for the understanding of ecosystem dynamics, which in turn, is essential for food web stability analyzes and the development of sustainable practices. There is a rapid growth in the knowledge on how belowground biodiversity regulates the structure and functioning of terrestrial ecosystems. Although, the available information about trophic relationships is hard to find and fragmented. This gathering the information available worldwide about the food resources of soil mesofauna. From the 3105 hits of the initial search on food resources of soil microarthropods, only a total of 196 published works related particular species, genera, and families to particular trophic resources, the majority of them dealing with soils of the Palearctic region. From the 196 publications we extracted 3009 records relating specific taxonomic groups to their trophic resources, 20% mention saprophytic fungi as a food resource, 16% cite microfauna, 11% mention bacteria, 10% litter and 5% cite Mycorrhizal fungi. The available information was highly skewed, the 73.71% comes from Acari, and within these, 50.62% correspond just to Sarcoptiformes. For Collembola, the literature is scarce, the majority coming from Arthropleona. This review highlights the general lack of information relating species, genera, and families of the soil mesofauna to specific trophic resources. It also highlights that available research mostly comes from European sites, with the use of trophic resources by the mesofauna of the majority of the soils in other parts of the world still largely unknown.


title: Trophic resources of the edaphic microarthropods: a worldwide review of the empirical evidence


title: Comparative reproductive biology of deep-sea ophiuroids inhabiting polymetallic-nodule fields in the Clarion-Clipperton Fracture Zone

abstract: Deep-sea mining in the Pacific Clarion-Clipperton Fracture Zone (CCZ), a low-energy sedimentary habitat with polymetallic nodules, is expected to have considerable and long-lasting environmental impact. The CCZ hosts extraordinarily high species diversity across representatives from all Domains of Life. Data on species biology and ecology remain scarce, however. The current study describes the reproductive biology of Ophiosphalma glabrum (Lutken & Mortensen, 1899) (Ophiosphalmidae) and Ophiacantha cosmica (Lyman, 1878) (Ophiacanthidae), two ophiuroids frequently found in the CCZ. Specimens collected in Spring 2015 and 2019 in four contract areas were examined morphologically and histologically. Size-class frequencies (disc diameter and oocytes feret diameters), sex ratios, gametogenic status, putative reproductive mode and a simple proxy for fecundity are presented. Habitat use differs in each. While Ophiosphalma glabrum is epibenthic, occurring as single individuals, Ophiacantha cosmica often form size-stratified groups living on stalked sponges, suggesting gregarious settlement or retention of offspring (though no brooding individuals were found). Further molecular analyses are needed to establish whether O. cosmica groups are familial. In Ophiosphalma glabrum, for which sample sizes were larger, sex ratios approximated a 1:1 ratio with no size-structuring. In both species, individuals were at various stages of gametogenic maturity but no ripe females were identified. Based on this, O. glabrum is most probably gonochoric. Reproductive mode remains inconclusive for Ophiacantha cosmica. Both species are presumptively lecithotrophic, with vitellogenic-oocyte feret diameters exceeding 250 {micro}m. Oocyte feret diameters at times exceeded 400 {micro}m in Ophiosphalma glabrum, indicating substantial yolk reserves. Estimates of instantaneous fecundity (vitellogenic specimens of O. glabrum only) were confounded by interindividual variability in gonad characteristics. The well-furnished lecithotrophic larvae of O. glabrum would be capable of dispersing even under food-impoverished conditions. The current study examines ophiuroid reproductive biology over multiple localities in the CCZ concurrently for the first time, at sites characterised by differing productivity regimes. The reproductive biology of each species is thus discussed with reference to past evolutionary (habitat stability), contemporary (food supply) and future environmental drivers (potential impacts of deep-sea mining).


title: The role of claw colouration in fiddler crabs' mate choice: Private communication channel or handicap?

abstract:
Colour cues play an important role in sexual selection and conspecific recognition. Literature shows that conspecifics might enjoy their everyday chat, without ever worrying about occasional eavesdroppers (e.g., predators), when information interchange evolves into a private communication channel. Yet, when signalling is converted into foraging cues by predators, their prey must pay the due cost for sustaining conversation. For that matter, fiddler crabs draw attention for having flashy enlarged claws that could potentially attract the attention of many predators. Surprisingly, the costs associated with claw colouration in fiddler crabs are still poorly understood and have never been studied in American species. Here, we initially examine whether hypertrophied claws of American thin-fingered fiddler crabs (Leptuca leptodactyla) reflect UV-light and how conspecific females react to these cues. Then we test two alternative hypotheses concerning the role of claw colouration in fiddler crabs mate choice: a) that claw colouration evolved into a private communication channel, which could have significantly lowered signalling costs for males; b) that claw colouration is conspicuous to potential reproductive partners, as well as to predators, making colour signalling by males very costly (i.e., a handicap). Thereafter, we measured the reflectance spectra from several enlarged claws and modelled their chromatic contrast against the background spectrum, considering the visual systems of conspecific fiddler crabs and two kinds of predators (terns and plovers). We also tested female conspecifics preference towards enlarged claws that reflected UV-light or other colour cues, by artificially altering claw colouration. Our results show a clear female preference for UV reflecting males. We also found that natural enlarged claws should be highly detectable by avian predators, refuting the private communication channel hypothesis. Furthermore, since female fiddler crabs select the most flamboyant claws from the sandy background, claw colouration in fiddler crabs can be understood as an honest signal.

HIGHLIGHTSO_LIThe hypertrophied claws of male Leptuca leptodactyla reflect UV light.
C_LIO_LIFemale fiddler crabs display a natural preference for UV light cues.
C_LIO_LIConspicuous claws function as handicaps and may honestly signal individual quality.
C_LIO_LIMale enlarged claws are more conspicuous to birds than to crabs.
C_LIO_LIOur data refute the presence of a private communication channel in L. leptodactyla.
C_LI

category: animal behavior and cognition


title: A water-reward task assay for evaluating mouse mutualistic cooperative behavior

abstract: Social cooperation is fundamentally important for group animals but rarely studied with mice because of their natural aggressiveness. In the present work, we induced pairs of mice to develop a mutualistic cooperative behavior in a non-divided chamber. Each mouse was first trained to learn to use a water dispenser by occupying a particular zone served as a switch to the dispenser. Two trained mice were then put into a chamber containing two separate zones jointly controlling two dispensers. We recorded the latency before each co-drinking, the number and cumulated time of co-drinking each day during the test. These parameters served as quantitative measurements of cooperative behavior in mice. The whole procedure includes preparation, training and testing phases, which take 15 days in total. This assay provides detailed procedures and analytical methods for investigators to characterize and quantify the mutualistic cooperative behavior. The use of mice as subjects allows convenient coupling to other behavior assays and is amiable to genetic manipulations for mechanistic study.


title: Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Monosaccharide-Modifications with pGlyco3

abstract: We present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A novel glycan ion-indexing algorithm developed in this work for glycan-first search makes pGlyco3 5-40 times faster than other glycoproteomic search engines without decreasing the accuracies and sensitivities. By combining electron-based dissociation spectra, pGlyco3 integrates a fast, dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization (SSGL). Our evaluation based on synthetic and natural glycopeptides showed that the SSGL probabilities estimated by pGlycoSite were proved to be appropriate to localize site-specific glycans. With pGlyco3, we found that N-glycopeptides and O-mannose glycopeptides in yeast samples were extensively modified by ammonia adducts on Hex (aH) and verified the aH-glycopeptide identifications based on released N-glycans and 15N/13C-labeled data. Thus pGlyco3, which is freely available on https://github.com/pFindStudio/pGlyco3/releases, is an accurate and flexible tool to identify glycopeptides and modified saccharide units.


title: Precise, Fast and Comprehensive Analysis of Intact Glycopeptides and Modified Saccharide Units with pGlyco3


title: An MILP Model for Corn Planting and Harvest Scheduling Considering Storage Capacity and Growing Degree Units

abstract: AO_SCPLOWBSTRACTC_SCPLOWCorn planting and harvest scheduling is an important problem due to having a significant impact on corn yield, balancing the capacities for harvest, transport, and storage operations. Different corn hybrids also have different planting window and poor planting and harvest schedules may cause erratic weekly harvest quantities and logistical and productivity issues. In the 2021 Syngenta Crop Challenge, Syngenta released several large datasets that recorded the historical daily growing degree units (GDU) of two sites and provided planting window, required GDUs, and harvest quantity of corn hybrids planted in these two sites. Then, participants of this challenge were asked to schedule planting and harvesting dates of corn hybrids under two storage capacity scenarios so that facilities are not over capacity in harvesting weeks and have consistent weekly harvest quantities. The two storage capacity scenarios include: (1) planting and harvest scheduling given the maximum storage capacity, and (2) planting and harvest scheduling without maximum storage capacity to determine the lowest possible capacity for each site. In this paper, we propose two mixed integer linear programming (MILP) models for solving this problem considering both the storage capacity and the uncertainty in GDUs. Our results indicate that our proposed models can provide optimal planting and harvest scheduling under different GDU possibilities which ensures consistent weekly harvest quantities that are below the maximum capacity.


title: Biophysical and proteomic analyses suggest functions of Pseudomonas syringae pv tomato DC3000 extracellular vesicles in bacterial growth during plant infection

abstract: Vesiculation is a process employed by Gram-negative bacteria to release extracellular vesicles (EVs) into the environment. Bacterial EVs contain molecular cargo from the donor bacterium and play important roles in bacterial survival and growth. Here, we describe EV production in plant-pathogenic Pseudomonas syringae pv. tomato DC3000 (Pto DC3000), the causal agent of bacterial speck disease. Cultured Pto DC3000 exhibited EV structures both on the cell surface and in the vicinity of bacterial cells, observed as outer membrane vesicle (OMV) release. We used in-solution trypsin digestion coupled to mass spectrometry to identify 369 proteins enriched in EVs recovered from cultured Pto DC3000. The predicted localization profile of EV proteins supports the production of EVs also in the form of outer-inner-membrane vesicles (OIMVs). EV production varied slightly between bacterial lifestyles and also occurred in planta. The potential contribution of EVs to Pto DC3000 plant infection was assessed using plant treatments and bioinformatic analysis of the EV-enriched proteins. While these results identify immunogenic activities of the EVs, they also point at roles for EVs in bacterial defences and nutrient acquisition by Pto DC3000.


title: A systematic approach for finding herbicide synergies

abstract: Combining herbicides into a double dose is a common approach to overcome the potential for herbicide resistance by weeds. Many herbicide mixtures can be antagonistic and they are rarely synergistic. Here, 24 commercial herbicides, each representing a mode of action were used to create a matrix of all 276 unique combinations to search for new synergies in agar with Arabidopsis thaliana. Herbicides were used at an appropriate sub-lethal dose such that any synergies gave visible growth inhibition. We found five synergies including three new ones, namely mesotrione-norflurazon, mesotrione-clethodim and paraquat-clomazone. All three new synergies were reproducible in soil-grown conditions. Interestingly, all three new combinations included a bleaching herbicide, suggesting synergy might be a class specific phenomenon. We also found that mesotrione-norflurazon and mesotrione-clethodim combinations remained synergistic against lettuce (Lactuca sativa), but not tef (Eragrostis tef). Our study shows that screening herbicide mixtures against A. thaliana is an efficient approach for finding rare herbicide synergies.


title: Enhanced MATE transporter DTX6/PQT15 confers paraquat resistance

abstract: Paraquat is one of the most widely used non-selective herbicides and has elicited the emergence of paraquat resistant weeds. However, the molecular mechanisms of paraquat resistance are not completely understood. Here we report an Arabidopsis gain-of-function mutant pqt15-D with significantly enhanced resistance to paraquat and the corresponding PQT15 encoding the MATE transporter DTX6. A point mutation at +932 bp in DTX6 causing the G311E amino acid residue change brings about the enhanced paraquat resistance of pqt15-D. Overexpression of DTX6/PQT15 in the wild type also confers strong paraquat resistance, whereas the DTX6/PQT15 knockout mutants exhibits hypersensitive phenotype to paraquat. Moreover, heterologous expression of DTX6 and DTX6-D in E. coli significantly enhances bacterial resistance to paraquat. DTX6/PQT15 mainly localizes in the plasma membrane as shown by DTX6-GFP and functions as a paraquat efflux transporter as demonstrated by paraquat efflux assays with isolated protoplasts and bacterial cells. Taken together, our results demonstrate that DTX6/PQT15 is an efflux transporter and confers paraquat resistance by exporting paraquat out of cytosol, therefore unraveling a molecular mechanism of paraquat resistance in higher plants and providing a promising candidate of generating paraquat resistance crops.


title: Dynamic Gene-Based Ecophysiological Models to Predict Phenotype from Genotype and Environment Data

abstract: Predicting the phenotype from the genotype is one of the major contemporary challenges in biology. This challenge is greater in plants because their development occurs mostly post-embryonically under diurnal and seasonal environmental fluctuations. Current phenotype prediction models do not adequately capture all of these fluctuations or effectively use genotype information. Instead, we have developed a dynamic modular approach that captures the genotype, environment, and Genotype-by-Environment effects to express the time-to-flowering phenotype in real time in Phaseolus vulgaris. The module we describe can be applied to different plant processes and can gradually replace processes in existing crop models. Our model can enable accelerated progress in diverse breeding programs, particularly with the prospects of climate change. Finally, a gene-based simulation model can assist policy decision makers in matters pertaining to prediction of food supplies.


title: Efficient gradient-based parameter estimation for dynamic models using qualitative data

abstract:
MotivationUnknown parameters of dynamical models are commonly estimated from experimental data. However, while various efficient optimization and uncertainty analysis methods have been proposed for quantitative data, methods for qualitative data are rare and suffer from bad scaling and convergence.

ResultsHere, we propose an efficient and reliable framework for estimating the parameters of ordinary differential equation models from qualitative data. In this framework, we derive a semi-analytical algorithm for gradient calculation of the optimal scaling method developed for qualitative data. This enables the use of efficient gradient-based optimization algorithms. We demonstrate that the use of gradient information improves performance of optimization and uncertainty quantification on several application examples. On average, we achieve a speedup of more than one order of magnitude compared to gradient-free optimization. Additionally, in some examples, the gradient-based approach yields substantially improved objective function values and quality of the fits. Accordingly, the proposed framework substantially improves the parameterization of models from qualitative data.

AvailabilityThe proposed approach is implemented in the open-source Python Parameter EStimation TOolbox (pyPESTO). All application examples and code to reproduce this study are available at https://doi.org/10.5281/zenodo.4507613.

category: systems biology


title: CASTLE: A database of synthetic lethal sets predicted from genome-scale metabolic networks

abstract:
SummaryGenome-scale metabolic networks have been reconstructed for hundreds of organisms over the last two decades, with wide-ranging applications, including the identification of drug targets. Constraint-based approaches such as flux balance analysis have been effectively used to predict single and combinatorial drug targets in a variety of metabolic networks. We have previously developed Fast-SL, an efficient algorithm to rapidly enumerate all possible synthetic lethals from metabolic networks. Here, we introduce CASTLE, an online standalone database, which contains synthetic lethals predicted from the metabolic networks of over 130 organisms. These targets include single, double or triple lethal set of genes and reactions, and have been predicted using the Fast-SL algorithm. The workflow used for building CASTLE can be easily applied to other pathogenic models and used to identify novel therapeutic targets.

AvailabilityCASTLE is available at https://ramanlab.github.io/CASTLE/

Contactkraman@iitm.ac.in


title: Spatial transcriptomics reveals unique molecular fingerprints of human nociceptors

abstract:
Nociceptors are specialized sensory neurons that detect damaging or potentially damaging stimuli and are found in the dorsal root (DRG) and trigeminal ganglia. These neurons are critical for the generation of neuronal signals that ultimately create the perception of pain. These neurons are also primary targets for acute and chronic pain therapeutics. Single-cell transcriptomics on mouse nociceptors has transformed our understanding of pain mechanisms. We sought to generate equivalent information for human nociceptors with the goal of identifying transcriptomic signatures of nociceptors, identifying species differences and elucidating new drug targets. We used spatial transcriptomics to molecularly characterize transcriptomes of single dorsal root ganglion (DRG) neurons from 8 organ donors. We identified 12 clusters of human sensory neurons, 5 of which are C nociceptors; as well as 1 A{beta} nociceptor, 2 A{delta}, 2 A{beta} and 1 proprioceptor subtypes. By focusing on expression profiles for ion channels, G-protein coupled receptors (GPCRs) and other pharmacological targets, we provide a rich map of drug targets in the human DRG with direct comparison to mouse sensory neuron transcriptomes. We also compare human DRG neuronal subtypes to non-human primates showing conserved patterns of gene expression among many cell types, but divergence among specific nociceptor subsets. Finally, we identify sex differences in human DRG subpopulation transcriptomes, including a marked increase in CALCA expression in female pruritogen receptor enriched nociceptors. Our data open the door to development of drug discovery programs for new pain targets and unparalleled molecular characterization of clinical sensory disorders.

One Sentence SummaryWe used spatial transcriptomics to molecularly characterize human sensory neurons, comparing them to mouse and non-human primate finding similarities but also divergence, in particular among drug targets.


title: Strain dynamics of specific contaminant bacteria modulate the performance of ethanol biorefineries

abstract: Bioethanol is a viable alternative for fossil fuels, and its use has lowered CO2 emissions by over 500 million tonnes in Brazil alone by replacing more than 40% of the national gasoline consumption. However, contaminant bacteria reduce yields during fermentation. Our understanding of these contaminants is limited to targeted studies, and the interplay of the microbial community and its impact on fermentation efficiency remains poorly understood. Comprehensive surveying and longitudinal analysis using shotgun metagenomics of two major biorefineries over a production season revealed similar patterns in microbial community structure and dynamics throughout the entire fermentation system. Strain resolution metagenomics identified specific Lactobacillus fermentum strains as strongly associated with poor industrial performance and laboratory-scale fermentations revealed yield reductions of up to 4.63{+/-}1.35% depending on the specific contaminating strains. Selective removal of these strains could reduce emissions from the bioethanol industry by more than 2x106 tonnes per year. Using the large-scale Brazilian ethanol fermentations as a model system for studying microbiome-phenotype relationships this study further demonstrates how high-resolution metagenomics can identify culprits of large scale industrial biomanufacturing.


title: Human RNA Nm-MTase FTSJ1: new tRNA targets and role in the regulation of brain-specific genes.

abstract: FTSJ1 is a conserved human 2-O-methyltransferase (Nm-MTase) that modifies several transfer RNAs (tRNAs) at position 32 and the wobble position 34 in the AntiCodon Loop (ACL). Its loss of function has been linked to Non-Syndromic X-Linked Intellectual Disability (NSXLID), and more recently to cancers. However, the molecular mechanisms underlying these pathologies are currently unclear. Here we report a novel FTSJ1 pathogenic variant from a NSXLID patient. Using blood cells derived from this patient and other affected individuals carrying FTSJ1 mutations, we performed an unbiased and comprehensive RiboMethSeq analysis to map the ribose methylation (Nm) on all tRNAs and identify novel targets. In addition, we performed a transcriptome analysis in these cells and found that several genes previously associated with intellectual disability and cancers were deregulated. We also found changes in the miRNA population that suggest potential cross-regulation of some miRNAs with these key mRNA targets. Finally, we show that differentiation of FTSJ1-depleted human neuronal progenitor cells (NPC) into neurons displays long and thin spine neurites compared to control cells. These defects are also observed in Drosophila and are associated with long term memory deficit in this organism. Altogether, our study adds insight into FTSJ1 pathologies in human by the identification of novel FTSJ1 targets and the defect in neuron morphology.

category: genetics


title: The ribose methylation enzyme FTSJ1 has a conserved role in neuron morphology and learning performance


title: Genomic analyses of 10,376 individuals provides comprehensive map of genetic variations, structure and reference haplotypes for Chinese population

abstract: Here, we initiated the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing individuals and 5,481 high-density genotyping individuals. We identified 80.99 million SNPs and INDELs, of which 38.6% are novel. The genetic evidence of Chinese population structure supported the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains. The genetic architecture within North Han was more homogeneous than South Han, and the history of effective population size of Lingnan began to deviate from the other three regions from 6 thousand years ago. In addition, we identified a novel locus (SNX29) under selection pressure and confirmed several loci associated with alcohol metabolism and histocompatibility systems. We observed significant selection of genes on epidermal cell differentiation and skin development only in southern Chinese. Finally, we provided an online imputation server (https://wbbc.westlake.edu.cn/) which could result in higher imputation accuracy compared to the existing panels, especially for lower frequency variants.


title: Chronic paternal morphine exposure increases sensitivity to morphine-derived antinociception

abstract: Parental exposure to drugs of abuse such as opioids can have profound and long-lasting effects on reward processing and drug sensitivity across generations. However, little is known about the impact of long-term paternal exposure to morphine on offspring sensitivity to morphine-derived antinociception during painful experiences. To address this question, we constructed a rat pain scale at millisecond timescales to measure mechanical nociception in a multigenerational morphine exposure paradigm. Surprisingly, while developing the pain scale, we found that von Frey hair filaments (VFHs), the most common stimuli used in pain research, are not painful to rats and morphine did not change the touch-like responses elicited by VFHs. We next deployed this novel pain scale to determine whether chronic morphine exposure in sires impacted pain sensitivity in the next generation. Offspring produced from a cross of morphine-treated sires and drug-naive dams, did not show any baseline changes in sensitivity to mechanical nociception. However, morphine-sired male progeny displayed a higher sensitivity to the antinociceptive properties of morphine, as measured by our pain scale. These findings demonstrate that long-term paternal exposure to morphine increases sensitivity to morphine-derived analgesia in the subsequent generation.


title: Impact of Propionic Acidemia on Brain Astrocytes

abstract:
Propionic acidemia (PA) is an inborn error of metabolism (IEM) caused by mutations in the enzyme propionyl CoA carboxylase (PCC). It is characterized by the inability to break down branched chain amino acids and odd chain fatty acids, causing a buildup of toxic organic acids in blood. PA affects every organ in the body with particularly severe manifestations in the brain, like hyperammonemia, hypomyelination, seizures, cognitive impairments, optic nerve atrophy and autism spectrum disorders. Dietary management and liver transplantation have helped to ameliorate the acute expression of the disorder, but do not prevent the chronic toxicity that builds up in brain. Despite the severe brain manifestation of the disease, little is known about the mechanisms by which PA affects the nervous system.

PCCA and PCCB, the two subunits required for a functional PCC enzyme, are both expressed not only in neurons but also in astrocytes. Using the two rodent genetic models of PA currently available, with mutations in PCCA, we have evaluated the involvement of astrocytes in the neuropathology of propionic acidemia. These mice exhibit cardiac pathology and hyperammonemia, similar to what is observed in patients with PA.

We found that wild type (wt) astrocytes positively respond to treatment with L-Carnitine, a therapeutic approach commonly used in patients with PA, by improved survival and more efficient mitochondrial morphology. Transcriptome analysis from astrocytes derived from the wt or the mutant mice confirm that these astrocytes lack exons 3 and 4 like in the human mutations of PA. However, no other genes/exons were statistically significant with regards to differential expression between astrocytes derived from KO or from WT animals, suggesting that astrocytes in culture may be able to compensate the PCC deficiency.

Histological analysis of neuronal and glial markers during brain development (TUJ1, MAP2 for neurons; nestin and Iba1 for glia) do not show significant alterations neither in distribution nor numbers of cells in the developing brain of the PCCA-/- mice. Analysis in the adult brain of mutant mice shows some variable degree of microgliosis but no indication of reactive astrocytes. No gross abnormalities were observed in cortex, hippocampus, striatum or cerebellum of adult brains of PCCA-/- mice, either.

In summary, astrocytes from PCCA deficient mice show surprisingly little alterations both in vitro and in vivo. Our results evidence the need to further understand the effects of PA in brain cells to help develop potential new therapies that can preserve brain function in children affected by this devastating disease.

HIGHLIGHTSO_LIAstrocytes detoxify ammonia in brain and may be affected by propionic acidemia, a disorder that causes hyperammonemia in brain.
C_LIO_LIRNA seq of astrocytes in culture derived from PCCA mutant mice does not show effect in these cells.
C_LIO_LIIn vivo analysis of glial and neuronal cells also shows no difference in development or adult mutant mice
C_LIO_LIAstrocytes may not be an adequate target of clinical therapies in this disorder
C_LI


title: c-MAF dependent perivascular macrophages regulate diet induced metabolic syndrome

abstract: Macrophages are an essential part of tissue development and physiology. Perivascular macrophages have been described in tissues and appear to play a role in development and disease processes, although it remains unclear what are the key features of these cells. Here, we identify a subpopulation of perivascular macrophages in several organs, characterized by their dependence on the transcription factor c-MAF, displaying non-conventional macrophage markers including LYVE1, Folate receptor 2 and CD38. Conditional deletion of c-MAF in macrophage lineages caused ablation of perivascular macrophages in the brain and altered muscularis macrophages program in the intestine. In the white adipose tissue (WAT), c-MAF deficient perivascular macrophages displayed an altered gene expression profile, which was linked to an increased vascular branching into the tissue. Upon feeding on high fat diet (HFD), mice with c-MAF deficient macrophages showed improved metabolic parameters compared to wild-type mice, including less weight gain, greater glucose tolerance and reduced inflammatory cell profile in WAT. These results define c-MAF as a central regulator of perivascular macrophages cell identity and transcriptional program in vivo and reveal a novel role for this tissue resident macrophage population in the regulation of metabolic syndrome.

category: immunology


title: Nucleosomal Asymmetry Shapes Histone Mark Binding and Promotes Poising at Bivalent Domains

abstract: Promoters of developmental genes in embryonic stem cells (ESCs) are marked by histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in an asymmetric nucleosomal conformation, with each sister histone H3 carrying only one mark. These bivalent domains are thought to poise genes for timely activation upon differentiation. Here we show that asymmetric bivalent nucleosomes recruit repressive H3K27me3 binders but fail to enrich activating H3K4me3 binders, despite presence of H3K4me3, thereby promoting a poised state. Strikingly, the bivalent mark combination further attracts chromatin proteins that are not recruited by each mark individually, including the histone acetyltransferase complex KAT6B (MORF). Knockout of KAT6B blocks neuronal differentiation, demonstrating that bivalency-specific readers are critical for proper ESC differentiation. These findings reveal how histone mark bivalency directly promotes establishment of a poised state at developmental genes, while highlighting how nucleosomal asymmetry is critical for histone mark readout and function.


title: Selection and structural characterisation of anti-TREM2 scFvs that reduce levels of shed ectodomain

abstract: Single point mutations in TREM2, a receptor expressed by microglia in the brain, are associated with an increased risk of neurodegeneration including Alzheimers disease. Numerous studies support a role for TREM2 in sensing damaging stimuli and triggering signalling cascades necessary for neuroprotection. Despite its significant role, ligands and regulators of TREM2 activation, and the mechanisms governing TREM2-dependent responses and its cleavage from the membrane, remain poorly characterised. Here, we present phage display generated scFv antibody binders to human TREM2 ectodomain. Cocrystal structures revealed the binding of two scFvs to an epitope on the globular TREM2 domain distal to the putative ligand-binding site. Enhanced functional activity was observed for oligomeric scFv species which inhibited the production of soluble TREM2 in a HEK293 cell model. We hope that detailed characterisation of their epitopes and properties will facilitate the use of these renewable binders as structural and functional biology tools for TREM2 research.


title: Leaf economics explained by optimality principles

abstract: The worldwide leaf economics spectrum relates leaf lifespan (LL) to leaf dry mass per unit area (LMA)1. By combining three well-supported principles2-4, we show that an isometric relationship between these two quantities maximizes the leafs net carbon gain. This theory predicts a spectrum of equally competent LMA-LL combinations in any given environment, and how their optimal ratio varies across environments. By analysing two large, independent leaf-trait datasets for woody species1,5, we provide quantitative empirical support for the predicted dependencies of LL on LMA and environment in evergreen plants, and for the distinct predicted dependencies of LMA on light, temperature, growing-season length and aridity in evergreen and deciduous plants. We thereby resolve the long-standing question of why deciduous LMA tends to increase (with increasing LL) towards the equator, while evergreen LMA and LL decrease6. We also show how the statistical distribution of LMA within communities can be modelled as an outcome of environmental selection on the global pool of species with diverse values of LMA and LL.


title: A theory of evolutionary dynamics on any complex spatial structure

abstract: Understanding how the spatial arrangement of a population shapes its evolutionary dynamics has been of long-standing interest in population genetics. Most previous studies assume a small number of demes connected by migration corridors, symmetrical structures that most often act as well-mixed populations. Other studies use networks to model the more complex topologies of natural populations and to study the structures that suppress or amplify selection. However, they usually assume very small, regular networks, with strong constraints on the strength of selection considered. Here we build network generation algorithms, evolutionary simulations and derive general analytic approximations for probabilities of fixation in populations with complex spatial structure. By tuning network parameters and properties independent of each other, we systematically span across network families and show that both a networks degree distribution, as well as its node mixing pattern shape the evolutionary dynamics of new mutations. We analytically write the relevant selective parameter, predictive of evolutionary dynamics, as a combination of network statistics. As one application, we use recent imaging datasets and build the cellular spatial networks of the stem cell niches of the bone marrow. Across a wide variety of parameters and regardless of the birth-death process used, we find these networks to be strong suppressors of selection, delaying mutation accumulation in this tissue. We also find that decreases in stem cell population size decrease the suppression strength of the tissue spatial structure, hinting at a potential diminishing spatial suppression in the bone marrow tissue as individuals age.


title: Phylogeny of the damselfishes (Pomacentridae) and patterns of asymmetrical diversification in body size and feeding ecology

abstract: The damselfishes (family Pomacentridae) inhabit near-shore communities in tropical and temperature oceans as one of the major lineages in coral reef fish assemblages. Our understanding of their evolutionary ecology, morphology and function has often been advanced by increasingly detailed and accurate molecular phylogenies. Here we present the next stage of multi-locus, molecular phylogenetics for the group based on analysis of 12 nuclear and mitochondrial gene sequences from 345 of the 422 damselfishes. The resulting well-resolved phylogeny helps to address several important questions about higher-level damselfish relationships, their evolutionary history and patterns of divergence. A time-calibrated phylogenetic tree yields a root age for the family of 55.5 mya, refines the age of origin for a number of diverse genera, and shows that ecological changes during the Eocene-Oligocene transition provided opportunities for damselfish diversification. We explored the idea that body size extremes have evolved repeatedly among the Pomacentridae, and demonstrate that large and small body sizes have evolved independently at least 40 times and with asymmetric rates of transition among size classes. We tested the hypothesis that transitions among dietary ecotypes (benthic herbivory, pelagic planktivory and intermediate omnivory) are asymmetric, with higher transition rates from intermediate omnivory to either planktivory or herbivory. Using multistate hidden-state speciation and extinction models, we found that both body size and dietary ecotype are significantly associated with patterns of diversification across the damselfishes, and that the highest rates of net diversification are associated with medium body size and pelagic planktivory. We also conclude that the pattern of evolutionary diversification in feeding ecology, with frequent and asymmetrical transitions between feeding ecotypes, is largely restricted to the subfamily Pomacentrinae in the Indo-West Pacific. Trait diversification patterns for damselfishes across a fully resolved phylogeny challenge many recent general conclusions about the evolution of reef fishes.


title: Genome wide mapping of DNA lesions by Repair Assisted Damage Detection sequencing - RADD-Seq

abstract: Mapping DNA damage and its repair has immense potential in understanding environmental exposures, their genotoxicity, and their impact on human health. Monitoring changes in genomic stability also aids in the diagnosis of numerous DNA-related diseases, like cancer, and assists in monitoring their progression and prognosis. However, genome-wide maps of DNA damage distribution are challenging to produce. Here we describe the localization of DNA damage and repair loci by Repair Assisted Damage Detection sequencing - RADD-Seq. Based on the enrichment of damage lesions coupled with a pull-down assay and followed by next generation sequencing, this method is easy to perform and can produce compelling results with minimal coverage. RADD-seq enables the localization of both DNA damage and repair sites for a wide range of single-strand damage types. Using this technique, we created a genome-wide map of oxidative DNA damage loci before and after repair. Oxidative lesions were heterogeneously distributed along the human genome, with less damage occurring in tight chromatin regions. Furthermore, we showed repair is prioritized for highly expressed, essential genes and in open chromatin regions. RADD-seq sheds light on cellular repair mechanisms and capable of identifying genomic hotspots prone to mutation.

category: genomics


title: Epstein-Barr virus long non-coding RNA RPMS1 full-length spliceome in transformed epithelial tissue

abstract: Epstein-Barr virus is associated with two types of epithelial neoplasms, nasopharyngeal carcinoma and gastric adenocarcinoma. The viral long non-coding RNA RPMS1 is the most abundantly expressed poly-adenylated viral RNA in these malignant tissues. The RPMS1 gene is known to contain two cassette exons, exon Ia and Ib, and several alternative splicing variants have been described in low-throughput studies. To characterize the entire RPMS1 spliceome we combined long-read sequencing data from the nasopharyngeal cell line C666-1 and a primary gastric adenocarcinoma, with complementary short-read sequencing datasets. We developed FLAME, a Python-based bioinformatics package that can generate complete high resolution characterization of RNA splicing at full-length. Using FLAME, we identified 32 novel exons in the RPMS1 gene, primarily within the large constitutive exons III, V and VII. Two of the novel exons contained retention of the intron between exon III and exon IV, and a novel cassette exon was identified between VI and exon VII. All previously described transcript variants of RPMS1 containing putative ORFs were identified at various levels. Similarly, native transcripts with the potential to form previously reported circular RNA elements were detected. Our work illuminates the multifaceted nature of viral transcriptional repertoires. FLAME provides a comprehensive overview of the relative abundance of alternative splice variants and allows for a wealth of previously unknown splicing events to be unveiled.