title: Secondary metabolites produced during Aspergillus fumigatus and Pseudomonas aeruginosa biofilm formation

abstract:
In Cystic Fibrosis (CF), mucus plaques are formed in the patients lung, creating a hypoxic condition and a propitious environment for colonization and persistence of many microorganisms. There is clinical evidence showing that Aspergillus fumigatus can co-colonize CF patients with Pseudomonas aeruginosa, which has been associated with lung function decline. P. aeruginosa produces several compounds with inhibitory and anti-biofilm effects against A. fumigatus in vitro; however, little is known about the fungal compounds produced in counterattack. Here, we annotated fungal and bacterial secondary metabolites (SM) produced in mixed biofilms in normoxia and hypoxia conditions. We detected nine SMs produced by P. aeruginosa. Phenazines and different analogs of pyoverdin were the main compounds produced by P. aeruginosa, and their secretion were increased by the fungal presence. The roles of the two operons responsible for phenazines production (phzA1 and phzA2) were also investigated showing both mutants are able to produce partial sets of phenazines. We detected a total of 20 SMs secreted by A. fumigatus either in monoculture or in co-culture with P. aeruginosa. All these compounds are secreted during biofilm formation either in normoxia or hypoxia. However, only eight compounds (demethoxyfumitremorgin C, fumitremorgin, ferrichrome, ferricrocin, tricetylfusigen, gliotoxin, gliotoxin E, and pyripyropene A) were detected during the biofilm formation by the co-culture of A. fumigatus and P. aeruginosa upon both normoxia and hypoxia conditions. Overall, we showed how diverse is SM secretion during A. fumigatus and P. aeruginosa mixed culture and how this can affect biofilm formation both in normoxia and hypoxia.

Author SummaryThe interaction between Pseudomonas aeruginosa and Aspergillus fumigatus has been well-characterized in vitro. In this scenario, the bacterium exerts a strong inhibitory effect against the fungus. However, little is known about the metabolites produced by the fungus to counterattack the bacteria. Our work aimed to annotate secondary metabolites (SM) secreted during co-culture between P. aeruginosa and A. fumigatus during biofilm formation in both normoxia and hypoxia. The bacterium produces several different types of phenazines and pyoverdins, in response to the fungus presence. In contrast, we were able to annotate 29 metabolites produced during A. fumigatus biofilm formation but only eight compounds were detected during biofilm formation by the co-culture of A. fumigatus and P. aeruginosa upon both normoxia and hypoxia. In conclusion, we have detected many SMs secreted during A. fumigatus and P. aeruginosa biofilm formation. This analysis can provide several opportunities to understand the interaction between these two species.


title: Lola-I is a developmentally regulated promoter pioneer factor

abstract: While enhancers are often regulated at the level of accessibility by pioneer factors, promoters tend to be constitutively accessible and poised for activation by paused Pol II -- thus are often not considered as sites of developmental regulation. Here we show that the accessibility of promoters and the acquisition of paused Pol II can be subject to developmental regulation by pioneer factors. We show that Lola-I, a Drosophila zinc finger transcription factor, is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene expression. Lola-I mediates this function by binding to the edges of the promoter nucleosomes, which leads to their depletion, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers, providing further evidence that promoters and enhancers display unexpectedly similar characteristics.

category: genomics


title: Proteomics identifies substrates and a novel component in hSnd2-dependent ER protein targeting

abstract: Protein import into the endoplasmic reticulum (ER) is essential for about 30% of the human proteome. It involves targeting of precursor proteins to the ER and insertion into or translocation across the ER membrane. Furthermore, it relies on signals in the precursor polypeptides and components, which read the signals and facilitate their targeting to a protein-conducting channel in the ER membrane, the Sec61 complex. Compared to the SRP- and TRC-dependent pathways, little is known about the SRP-independent/SND pathway. Our aim was to identify additional components and characterize the client spectrum of the human SND pathway. The established strategy of combining depletion of the central hSnd2-component from HeLa cells with proteomic- and differential protein abundance-analysis was used. The SRP and TRC targeting pathways were analyzed in comparison. TMEM109 was characterized as hSnd3. Unlike SRP but similar to TRC, the SND clients are predominantly membrane proteins with N-terminal, central, or C-terminal targeting signals.

category: cell biology


title: Chromosome-level draft assemblies of the snow leopard, African leopard, and tiger (Panthera uncia, Panthera pardus pardus, and Panthera tigris)

abstract: The big cats (genus Panthera) represent some of the most popular and charismatic species on the planet. Although some reference genomes are available for this clade, few are at the chromosome level, inhibiting high-resolution genomic studies. Here, we assemble genomes from three members of the genus, the tiger (Panthera tigris), the snow leopard (Panthera uncia), and the African leopard (Panthera pardus pardus), at chromosome or near-chromosome level. We used a combination of short- and long-read technologies, as well as proximity ligation data from Hi-C technology, to achieve high continuity and contiguity for each individual. We hope these genomes will aid in further evolutionary and conservation research of this iconic group of mammals.


title: Bacterial lipopolysaccharide modulates immune response in the colorectal tumor microenvironment

abstract: Immune responses can have opposing effects in colorectal cancer (CRC), the balance of which may determine whether a cancer regresses, progresses, or potentially metastasizes. These effects are evident in CRC consensus molecular subtypes (CMS) where both CMS1 and CMS4 contain immune infiltrates yet have opposing prognoses. The microbiome has previously been associated with CRC and immune response in CRC but has largely been ignored in the CRC subtype discussion. Using CMS subtyping, we aimed to determine the contributions of the microbiome to the pleiotropic effects evident in immune-infiltrated subtypes. We integrated host gene-expression and meta-transcriptomic data to determine the link between immune characteristics and microbiome contributions in these subtypes and identified lipopolysaccharide (LPS) binding as a potential functional mechanism. We identified candidate bacteria with LPS properties that could affect immune response, focusing on Fusobacterium periodonticum and Bacteroides fragilis in CMS1, and Porphyromonas asaccharolytica in CMS4. Treatment of peripheral blood mononuclear cells (PBMCs) with LPS isolated from these bacteria showed that F. periodonticum stimulates cytokine production in PBMCs while both B. fragilis and P. asaccharolytica had an inhibitory effect. Furthermore, LPS from the latter two species can inhibit the immunogenic properties of F. periodonticum LPS when co-incubated with PBMCs. We propose that different microbes in the CRC tumor microenvironment can alter the local immune activity, with important implications for prognosis and treatment response.

category: cancer biology


title: Elongated Hypocotyl 5 (HY5) regulates BRUTUS (BTS) to maintain Iron homeostasis in Arabidopsis thaliana.

abstract: Iron (Fe) is an essential micronutrient for both plants and animals. Fe limitation significantly reduces crop yield and therefore has adverse impacts on human nutrition. Owing to limited bioavailability of Fe, plants have adapted different strategies that regulate Fe uptake and homeostasis. Particularly, modifications of root growth traits are a key for the survival of plants on Fe-deficient soils. Understanding the molecular basis for these root growth responses will have critical implications for plant breeding. Fe uptake is regulated by a cascade of basic helix-loop-helix (bHLH) transcription factors. In our study, we show that HY5 (Elongated Hypocotyl 5), a member of the basic leucine zipper (bZIP) family of transcription factors plays an important role in the Fe deficiency signalling pathway in Arabidopsis thaliana. The hy5 mutant plants failed to mount an optimum Fe deficiency response and showed severe root growth defects under Fe limitation that could be partially reverted by complementation of hy5 mutant. qRT-PCR analysis revealed that the induction of the genes involved in Fe uptake pathway [FER-like iron deficiency-induced transcription factor (FIT), Ferric Reduction Oxidase 2 (FRO2) and Iron-Regulated Transporter1 (IRT1)] is significantly reduced in the hy5 mutants as compared to the wild-type plants under Fe deficiency. Moreover, we also found that HY5 function is critical for activating the expression of coumarin biosynthesis genes (F6H1, S8H, PDR9 and BGLU42) under Fe deficiency. Interestingly, our results showed that HY5 acts as a negative regulator of BRUTUS (BTS) which is known to negatively regulate Fe deficiency response. Chromatin Immunoprecipitation followed by qPCR revealed direct binding of HY5 to the promoter of BTS. Altogether, our results showed that HY5 plays an important role in regulation of Fe deficiency responses in Arabidopsis.

category: plant biology


title: Survivin prevents the Polycomb Repressor Complex 2 from methylating Histone 3 lysine 27

abstract: Survivin is a small protein that belongs to the inhibitor of apoptosis protein family and participates in cell division and apoptosis. It was actively studied in human cancers, inflammatory diseases and in autoimmune diseases. Here, we reveal that survivin takes part in epigenetic gene silencing by interaction with the polycomb repressive complex 2 (PRC2). PRC2 silences gene expression through tri-methylation of lysine 27 on histone 3 (H3K27). We detected differential expression of PRC2 core subunits in CD4+T cells with different survivin expression. ChIP-seq experiments indicated that survivin binds chromatin that overlap with the regions occupied by PRC2. ChIP-seq of H3K27 in CD4+T cells indicate that inhibition of survivin leads to a substantial increase in H3K27 tri-methylation by PRC2 in contrast to other histone modifications, which lends support to that survivin prevents PRC2 from functioning. Survivin binds peptides derived from PRC2 subunits Ezh2, EED, Suz12 and Jarid2 in a peptide microarray that cover intersubunit interfaces, catalytic residues, and present binding sites for substrates, DNA, and regulatory proteins. Amino acid composition of the peptides has substantial predictive power for survivin interaction in the peptide microarray as determined by multilayer perceptron classification analysis. NMR experiments with 15N labelled survivin indicate that peptide colocalization does not entirely depend on binding mediated by short range interactions. These results indicate that survivin interacts with PRC2, preventing the methylation of H3K27 and specific gene silencing.

category: molecular biology


title: Single cell RNA-seq identifies inflammation-induced loss of CFTR-expressing airway ionocytes in non-eosinophilic asthma

abstract: Asthma is the most common chronic airways disease worldwide and the severe treatment resistant subtype of asthma is responsible for the majority of disease burden. Asthma is heterogeneous in nature and can be classified according to airway infiltrates as eosinophilic or non-eosinophilic (sometimes referred to as Type 2 low), which is further divided into paucigranulocytic (low levels of granulocytes), or neutrophilic asthma characterized by elevated neutrophils, and mixed Type 1 and Type 17 cytokines in airway tissue, sputum, and bronchoalveolar lavage. Severe non-eosinophilic asthma currently has fewer effective treatment options and many of these patients fail to qualify for newer biologic monoclonal therapies. The cystic fibrosis transmembrane conductance regulator (CFTR) is a key protein whose function is dysregulated in multiple respiratory diseases including cystic fibrosis and chronic obstructive pulmonary disease (COPD) and has proven a valuable therapeutic target. Using human bronchial epithelial cells (hBECs) isolated differentiated at air-liquid interface we demonstrated a reduced function of the CFTR in non-eosinophilic asthma. Characterization of the cell and molecular differences in airway epithelial cells between severe asthma subtypes using single cell RNA-sequencing (scRNAseq) revealed that airway epithelial cells from non-eosinophilic asthma, and in particular neutrophilic asthma patients, fail to differentiate into CFTR-expressing ionocytes compared with eosinophilic asthma or healthy donors. We identified a novel ionocyte transcriptional signature, which was present in both bronchial and tracheal airway epithelial samples indicating conserved anatomical gene regulation. Using protein markers and immunofluorescent quantification loss of ionocytes was confirmed in non-eosinophilic asthma hBECs. Similarly, ioncytes were also diminished in the airways of a murine model of neutrophilic-dominant but not eosinophilic allergen asthma models. Furthermore, treatment of hBECs from healthy donors with a neutrophilic asthma-like inflammatory cytokine mixture, but not IL-13, led to loss of ionocytes primarily due to IFN-{gamma}. Inflammation-induced loss of CFTR-expressing ionocytes in airway cells from non-eosinophilic asthma may represent a key feature of disease pathogenesis and a novel drug target for this difficult-to-treat disease.


title: Hydrothermal sulphur bacteria enhance mercury availability for coastal marine organisms

abstract: The hydrothermal compounds massively released into the sea by the geothermal power plant of Bouillante (Guadeloupe, Lesser Antilles) support the growth of sulphur-oxidising bacteria like around black smokers. Opportunistic animals of the bay were previously shown to actively seek and consume the bacterial biofilm. To investigate the role of these bacterial mats in enhancing the transfer of Hg, a highly toxic heavy metal, its concentrations were assessed in sediments, bacteria, and 6 low trophic levels animals from the Bouillante Bay and a Control Site nearby containing only natural sources of Hg. Concentrations of Hg in all samples from Bouillante were greater than those from the Control Site (2 to 627 times higher). A comparison with the Hg concentrations reported in the literature for similar samples types reveals that they are abnormally high in most Bouillante samples. Although bacterial biofilm contained high levels of Hg, the link between bacteria contribution to diet and Hg concentration was more complex than expected, which might be due to interspecific differences in Hg uptake and elimination rates. Species not consuming bacteria (i.e. filter feeders) still presented higher levels of Hg, suggesting that significant amounts of Hg are released along with discharge waters from the Bouillante geothermal plant, and are integrated through diffusion. Differences in Hg concentrations between tissues do not indicate that Hg contained in samples from animals was under the form of MeHg, lowering the biomagnification potential of Hg in the Bouillante Bay trophic food web. Overall, the Bouillante case study emphasises for the first time an important role played by sulphur bacteria mats as a vector of hydrothermal inorganic Hg, and potentially other trace metals emitted in vents area, through dietary pathways.

category: ecology


title: Widespread allele-specific topological domains in the human genome are not confined to imprinted gene clusters.

abstract:
BackgroundThere is widespread interest in the three-dimensional chromatin conformation of the genome and its impact on gene expression. However, these studies frequently do not consider parent-of-origin differences, such as genomic imprinting, which result in monoallelic expression. In addition, genome-wide allele-specific chromatin conformation associations have not been extensively explored. There are few accessible bioinformatic workflows for investigating allelic conformation differences and these require pre-phased haplotypes which are not widely available.

ResultsWe assembled a bioinformatic pipeline, "HiCFlow", which performs haplotype assembly and visualisation of parental chromatin architecture. We benchmarked the pipeline using prototype haplotype phased Hi-C data from GM12878 cells at three disease associated imprinted gene clusters. Using RC-HiC (Region Capture Hi-C) and Hi-C data from further human cell lines (1-7HB2, IMR-90, and H1-hESCs) we were able to robustly identify the known stable allele-specific interactions at the H19/IGF2 locus. Other imprinted loci (DLK1 and SNRPN) were more variable and there was no "canonical imprinted 3D structure", but we could detect allele-specific differences in A/B compartmentalisation. Genome-wide, when TADs were unbiasedly ranked according to their allele-specific contact frequencies, a set of "allele-specific TADs" (ASTADs) could be defined. These occurred in genomic regions of high sequence variation. In addition to imprinted genes, ASTADs were also enriched for allele-specific expressed (ASE) genes. We found loci that have not previously been identified as ASE such as the bitter taste receptors (TAS2Rs).

ConclusionsThis study highlights the widespread differences in chromatin conformation between heterozygous loci and provides a new framework for understanding ASE.


title: Canine lineages reveal genetic drivers of dog behavioral diversification

abstract: Selective breeding of domestic dogs has generated diverse breeds often optimized for performing specialized tasks. Despite the heritability of breed-typical behavioral traits, identification of causal loci has proven challenging due to the complexity of canine population structure. We overcome longstanding difficulties in identifying genetic drivers of canine behavior by developing an innovative framework for understanding relationships between breeds and the behaviors that define them utilizing a dataset of over 4,000 domestic, semi-feral and wild canids and behavioral survey data for over 46,000 dogs. We identify ten major canine genetic lineages and their behavioral correlates, and show that breed diversification is predominantly driven by non-coding regulatory variation. We determine that lineage-associated genes converge in neurodevelopmental co-expression networks, identifying a sheepdog-associated enrichment for interrelated axon guidance functions. This work presents a scaffold for canine diversification that positions the domestic dog as an unparalleled system for revealing the genetic origins of behavioral diversity.


title: Infection signaling and antimicrobial wound care in an ant society

abstract:
Infected wounds pose a major mortality risk in animals. Injuries are common in the ant Megaponera analis which raids pugnacious prey. Here we show that M. analis can determine when wounds are infected and treat them specifically. By applying a variety of antimicrobial compounds and proteins secreted from the metapleural gland to infected wounds, workers reduce the mortality of infected individuals by 90%. Chemical analyses showed that wound infection is associated with specific changes in the cuticular hydrocarbon profile thereby likely allowing nestmates to diagnose the infection state of injured individuals and apply the appropriate antimicrobial treatment. This study demonstrates that the targeted use of antimicrobials to treat infected wounds, previously thought to be a uniquely human behavior, has evolved in insect societies as well.

One-Sentence SummaryAnts use antimicrobial compounds and proteins to successfully treat the infected wounds of nestmates.

category: animal behavior and cognition


title: Integrated molecular analysis reveals two distinct subtypes of pure seminoma of the testis

abstract: Testicular germ cell tumors (TGCT) are the most common solid malignancy in adolescent and young men, with a rising incidence over the past 20 years. Overall, TGCTs are second in terms of the average life years lost per person dying of cancer, and clinical therapeutics without adverse long-term side effects are lacking. Platinum-based regimens for TGCTs have heterogeneous outcomes even within the same histotype that frequently leads to under- and over-treatment. Understanding of molecular differences that lead to diverse outcomes of TGCT patients may improve current treatment approaches. Seminoma is the most common subtype of TGCTs, which can either be pure or present in combination with other histotypes. Here we conducted a computational study of 64 pure seminoma samples from The Cancer Genome Atlas, applied consensus clustering approach to their transcriptomic data and revealed two clinically relevant seminoma subtypes: seminoma subtype 1 and 2. Our analysis identified significant differences in pluripotency stage, activity of double stranded DNA breaks repair mechanisms, rates of loss of heterozygosity, DNA methylation, and expression of lncRNA responsible for cisplatin resistance between the subtypes. Seminoma subtype 1 is characterized by higher pluripotency state, while subtype 2 showed attributes of reprogramming into non-seminomatous TGCT. The seminoma subtypes we identified may provide a molecular underpinning for variable responses to chemotherapy and radiation. Translating these findings into clinical care may help improve risk stratification of seminoma, decrease overtreatment rates, and increase long-term quality of life for TGCT survivors.


title: Systems analysis of metabolic responses to a mixed meal test in an obese cohort reveals links between tissue metabolism and the gut microbiota

abstract: Individuals with prediabetes and type 2 diabetes mellitus (T2DM) have poor ability to adapt to diet-triggered perturbations. We investigated global metabolic responses to a mixed meal test (MMT) in morbidly obese individuals with different diabetic status by performing plasma metabolomic profiling. Abnormal metabolism of carbohydrates, (branched-chain) amino acids, fatty acids and acylcholines in individuals with (pre)diabetes was observed. Moreover, differences in metabolic responses were associated with altered fecal metagenomics and transcriptomes of liver, jejunum and adipose tissues, which revealed a modified gut microbiome and multi-tissue metabolism in individuals having insulin resistance. Finally, using integrative machine learning models, we built a predictive model based on metabolomics data after 2h MMT, and identified possible new biomarkers for glycemic control including N-acetylaspartate and phenylalanine-derived metabolites that may be useful for diagnosis, intervention and prevention of T2DM.

category: systems biology


title: Optimized Repli-seq: Improved DNA Replication Timing Analysis by Next-Generation Sequencing

abstract: The human genome is divided into functional units that replicate at specific times during S-phase. This temporal program is known as replication timing (RT) and is coordinated with the spatial organization of the genome and transcriptional activity. RT is also cell type-specific, dynamically regulated during development, and alterations in RT are observed in multiple diseases. Thus, precise measure of RT is critical to understand the role of RT in gene function regulation. Distinct methods for assaying the RT program exist; however, conventional methods require thousands of cells as input, prohibiting its applicability to samples with limited cell numbers such as those from disease patients or from early developing embryos. Although single-cell analysis of RT has been developed as an alternative, these methods are low throughput and produce low resolution data. Here, we developed an improved method to measure RT genome-wide that enables high resolution analysis of low input samples. This method incorporates direct cell sorting into lysis buffer, as well as DNA fragmentation and library preparation in a single tube, resulting in higher yields, increased quality, and reproducibility with decreased costs. We also performed a systematic data processing analysis to provide standardized parameters for RT measurement. This optimized method facilitates RT analysis and will enable its application to a broad range of studies investigating the role of RT in gene expression, nuclear architecture, and disease.


title: Bimodal regulation of axonal transport by the GDNF-RET signalling axis in healthy and diseased motor neurons

abstract: Deficits in axonal transport are one of the earliest pathological outcomes in several models of amyotrophic lateral sclerosis (ALS), including SOD1G93A mice. Evidence suggests that rescuing these deficits prevents disease progression, stops denervation, and extends survival. Kinase inhibitors have been previously identified as transport enhancers, and are being investigated as potential therapies for ALS. For example, inhibitors of p38 mitogen-activated protein kinase and insulin growth factor receptor 1 have been shown to rescue axonal transport deficits in vivo in symptomatic SOD1G93A mice. In this work, we investigated the impact of RET, the tyrosine kinase receptor for glial cell-line-derived neurotrophic factor (GDNF), as a modifier of axonal transport. We identified fundamental interplay between RET signalling and axonal transport in both wild type and SOD1G93A motor neurons in vitro. We demonstrated that blockade of RET signalling using pharmacological inhibitors and genetic knockdown enhances signalling endosome transport in wild type motor neurons and uncovered a divergence in the response of primary motor neurons to GDNF compared with cell lines. Finally, we demonstrated that inhibition of the GDNF-RET signalling axis rescues in vivo transport deficits in early symptomatic SOD1G93A mice, promoting RET as a potential therapeutic target in the treatment of ALS.

category: neuroscience


title: Osteoclast-mediated resorption primes the skeleton for successful integration during axolotl limb regeneration

abstract: Early events during axolotl limb regeneration include an immune response and the formation of a wound epithelium. These events are linked to a clearance of damaged tissue prior to blastema formation and regeneration of the missing structures. Here, we report the resorption of calcified skeletal tissue as an active, cell-driven and highly regulated event. This process, carried out by osteoclasts, is essential for a successful integration of the newly formed skeleton. Indeed, the extent of resorption is directly correlated with the integration efficiency. Moreover, we identified the wound epithelium as a major regulator of skeletal resorption, likely creating a zone of influence in which signals involved in recruitment/differentiation of osteoclasts are released. Finally, we reported a correlation between resorption and blastema formation, particularly, a coordination of resorption with cartilage condensation. In sum, our results identify resorption as a major event upon amputation, playing a critical role in the overall process of skeletal regeneration.

category: developmental biology


title: Real-time monitoring of endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation

abstract: Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitored Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging platforms with single-molecule Fluorescence Correlation Spectroscopy (FCS), we demonstrate that Fgf8a, produced at the embryonic margin, propagates by free diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a mediated patterning. Manipulation of the Fgf8a input alters the signaling outcome, thereby establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, using diffusion-hindered versions of Fgf8a, we demonstrate that extracellular diffusion of the protein from the source is critical for it to achieve its morphogenic potential.


title: The molecular architecture of cell cycle arrest

abstract: The cellular decision governing the transition between proliferative and arrested states is crucial to the development and function of every tissue. While the molecular mechanisms that regulate the proliferative cell cycle are well established, we know comparatively little about what happens to cells as they diverge into cell cycle arrest. We performed hyperplexed imaging of 49 cell cycle effectors to obtain a map of the molecular architecture that governs cell cycle exit and progression into reversible ("quiescent") and irreversible ("senescent") arrest states. Using this map, we found multiple points of divergence from the proliferative cell cycle; identified stress-specific states of arrest; and resolved the molecular mechanisms governing these fate decisions, which we validated by single-cell, time-lapse imaging. Notably, we found that cells can exit into senescence from either G1 or G2; however, both subpopulations converge onto a single senescent state with a G1-like molecular signature. Cells can escape from this "irreversible" arrest state through the upregulation of G1 cyclins. This comprehensive map provides a first glimpse of the overall organization of cell proliferation and arrest.


title: Targeting Neutrophils Extracellular Traps (NETs) reduces multiple organ injury in a COVID-19 mouse model

abstract: COVID-19 is characterized by severe acute lung injury, which is associated with neutrophils infiltration and release of neutrophil extracellular traps (NETs). COVID-19 treatment options are scarce. Previous work has shown an increase in NETs release in the lung and plasma of COVID-19 patients suggesting that drugs that prevent NETs formation or release could be potential therapeutic approaches for COVID-19 treatment. Here, we report the efficacy of NET-degrading DNase I treatment in a murine model of COVID-19. DNase I decreased detectable levels of NETs, improved clinical disease, and reduced lung, heart, and kidney injuries in SARS-CoV-2-infected K18-hACE2 mice. Furthermore, our findings indicate a potential deleterious role for NETs lung tissue in vivo and lung epithelial (A549) cells in vitro, which might explain part of the pathophysiology of severe COVID-19. This deleterious effect was diminished by the treatment with DNase I. Together, our results support the role of NETs in COVID-19 immunopathology and highlight NETs disruption pharmacological approaches as a potential strategy to ameliorate COVID-19 clinical outcomes.

category: pharmacology and toxicology


title: Weak seed banks influence the signature and detectability of selective sweeps

abstract: Seed banking (or dormancy) is a widespread bet-hedging strategy, generating a form of population overlap, which decreases the magnitude of genetic drift. The methodological complexity of integrating this trait means it is ignored when developing tools to detect selective sweeps. But, as dormancy lengthens the ancestral recombination graph, increasing times to fixation, it can radically change the genomic signals of selection. To detect genes under positive selection in seed banking species it is important to 1) determine whether the efficacy of selection is affected, and 2) predict the patterns of nucleotide diversity at and around positively selected alleles. We present the first tree sequence-based simulation program integrating a weak seed bank to examine the dynamics and genomic footprints of beneficial alleles in a finite population. We find that seed banking generally decreases the probability of fixation and magnifies (respectively decreases) the efficacy of selection for alleles under strong (respectively weak) selection. As seed banking increases the effective recombination rate, footprints of sweeps appear more narrow around the selected sites and are detectable for longer periods of time. The developed simulation tool can be used to predict the footprints of selection and draw statistical inference of past evolutionary events in plants, invertebrates, or fungi with seed banks.

category: evolutionary biology


title: Utilising hippocampal neuronal calcium activity in mouse CA1 for a multimodal optical brain-computer interface

abstract: The hippocampus has been proposed to integrate information from multiple sensory modalities, supporting a comprehensive "cognitive map" for both spatial and non-spatial information. Previous studies have demonstrated decoding of hippocampal spatial information in real time by recording neuronal action potentials with electrodes. However, decoding of hippocampal non-spatial information robustly in real-time has not been previously shown. Here, we utilise the advantages of widefield optical calcium imaging to construct an optical brain-computer interface (BCI) driven by calcium activity of large neuronal ensembles ([~]600 neurons) to decode spatial, visual and auditory information effectively in real time. We developed a high speed end-to-end analysis workflow with advanced machine learning techniques for decoding. This methodology achieves high decoding accuracy and provides a "cognitive translation" approach that may be applied to both research and clinical applications to allow direct neural communication with animals and patients with impairment of function.

category: bioengineering


title: Chemotherapy Signatures Map Evolution of Therapy-Related Myeloid Neoplasms

abstract: Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms1, 2. Pre-leukemic clones (i.e., clonal hematopoiesis) are detectable years before the development of these aggressive malignancies3-5, though the genomic events leading to transformation and expansion are not well-defined. Here, leveraging distinctive chemotherapy-associated mutational signatures6-12 from whole-genome sequencing data and targeted sequencing of pre-chemotherapy samples, we reconstruct the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy is revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan are relatively hypermutated and enriched for complex structural variants (i.e., chromothripsis), while neoplasms with alternative exposures bear a similar profile to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as a temporal barcode in each patients life, we estimate that several complex events and genomic drivers are acquired after chemotherapy exposure. In the case of treatment with high-dose melphalan and autologous stem cell transplantation, we demonstrate that the procedure allows clonal hematopoiesis to escape chemotherapy exposure entirely, and to be reinfused to expand to malignancy. This information reveals a novel mode of malignant progression for therapy-related malignancies that is not reliant on direct mutagenesis or even exposure to chemotherapy, itself, and prompts further investigation into leukemia-permissive effects of cytotoxic drugs.


title: Genomic And Molecular Characterization Of The Wheat Streak Mosaic Virus Resistance Locus 2 (Wsm2) In Common Wheat (Triticum Aestivum. L)

abstract:
Wheat streak mosaic virus is an economically important viral pathogen that threatens global wheat production, particularly in the Great Plains region of the United States. The Wsm2 locus confers resistance to WSMV and has been widely deployed in common wheat varieties adapted to this region. Characterizing the underlying causative genetic variant would contribute to our understanding of viral resistance mechanisms in crops and aid the development of perfect markers for breeding.

In this study, Wsm2 flanking markers were mapped to a 4.0 Mbp region of the wheat reference genome containing 142 candidate genes. Haplotype analysis in seventeen wheat genotypes collected from different agroecological zones indicated that Wsm2 lies in a dynamic region of the genome with extensive structural variation, and that it is likely absent from available genome assemblies of common wheat varieties.

Exome sequencing of the variety  Snowmass, which carries Wsm2, revealed several loss-of-function mutations and copy number variants in the 142 candidate genes within the Wsm2 interval. Six of these genes are differentially expressed in  Snowmass compared to  Antero, a variety lacking Wsm2, including a gene that encodes a nucleotide-binding site leucine-rich repeat (NBS-LRR) type protein with homology to RPM1. A de novo assembly of unmapped RNA-seq reads identified nine transcripts expressed only in  Snowmass, three of which are also induced in response to WSMV inoculation. This study sheds light on the variation underlying Wsm2 and provides a list of candidate genes for subsequent validation.

category: pathology


title: Assessment of Culicidae collection methods for xenomonitoring lymphatic filariasis in malaria co-infection context in Burkina Faso

abstract:
BackgroundEntomological surveillance of lymphatic filariasis (LF) and malaria infections play an important role in the decision-making of national programs, to control or eliminate these both diseases. In order to corroborate infections in the human population, sampling large numbers of mosquitoes is necessary. To overcome this challenge, this study was design to assess the efficiency of four mosquito collection methods for monitoring LF and malaria infections in mosquito population.

Methodology/Principle FindingsMosquito collections were performed between August and September 2018 in four villages (Koulpissy, Seiga, and Peribgan, Saptan), distributed in East and South-West health regions of Burkina Faso. Different collection methods were used: Human Landing Catches (HLC) executed indoor and outdoor, Window Exit-Trap, Double Net Trap (DNT) and Pyrethrum Spray Catches (PSC). Molecular analyses were performed to identify Anopheles gambiae s.l. sibling species and to detect Wuchereria bancrofti and Plasmodium falciparum infection in mosquitoes. A total of 3,322 mosquitoes were collected among this, Anopheles gambiaes.l. was the vector caught in largest proportion (63.82%). An. gambiae s.l. sibling species molecular characterization showed that Anopheles gambiae was the dominant specie in all health regions. The Human Landing Catches (indoor and outdoor) collected the highest proportion of mosquitoes (between 61.5%and 82.79%). For sampling vectors infected to W. bancrofti and P. falciparum, PSC, HLC and Window Exit-Trap were been find as the most effective collection methods.

Conclusions/SignificanceThis study revealed that HLC indoor and outdoor remained the most effective collection methods. Likewise, the results showed the probability to use Window Exit-Trap and PSC collection methods to sample Anopheles infected and can be useful for xenomonitoring for both LF and malaria.

Author summaryIn Burkina Faso the monitoring and evaluation scheme to assess the impact of LF and malaria interventions is only focusing on parasitological tests. While nowadays, the most simple and direct measure of vector borne diseases is xenomonitoring. Thus, in order to confirm both diseases infection rate in the human population, sampling large numbers of mosquitoes is necessary. This study was undertaken in this context to assess the efficiency of four mosquito collection methods for xenomonitoring LF and malaria. Mosquito collections were performed between August and September 2018 in four villages, distributed in East and South-West health regions of Burkina Faso. Human Landing Catches (HLC), Window Exit-Trap, Double Net Trap (DNT) and Pyrethrum Spray Catches (PSC) were evaluated. The results showed that HLC remained the most effective collection method by collecting the highest number of Anopheles (2,388; 71.88% of total). Across the study, mosquito infection rate for Wuchereria bancrofti and Plasmodium falciparum were 0.004 and 0.13 respectively. To collect vectors infected it was found that Window Exit-Trap and PSC were efficiencies. In conclusion, HLC has shown to be appropriate for collect large number of mosquitoes. Likewise, Window Exit-Trap and PSC can be useful for xenomonitoring for both LF and malaria.


title: Dietary fatty acids modulate the endocannabinoid system in rat submandibular gland

abstract: The aim of this study was to analyze the influence of dietary fatty acids on endocannabinoid system components in rat submandibular gland. 15 male Wistar rats were fed on commercial diet until the 8th week of life. They were then divided into three dietary groups: Control, continuing with chow diet, and two experimental groups receiving for 30 days a diet containing corn oil or chia oil as lipid source (7%). At that time, animals were sacrificed and salivary glands obtained. Anandamide and 2-arachidonylglycerol endogenous ligands (high performance liquid chromatography) and cannabinoid receptors CB1 and CB2 (immunofluorescence) were quantified. Fatty acid amide hydrolase enzyme activity was analyzed (spectrophotometry). Kruskal Wallis test was applied. 2-Arachidonylglycerol was higher in Corn oil group than in Control and Chia oil groups. The greatest CB1 and the lowest CB2 receptor positively-marked area percentage were found in Corn oil and in Chia oil, respectively. Fatty acid amide hydrolase enzyme activity was higher in Corn oil than in Chia oil. 18:2 n-6 (Corn oil) and 18:3 n-3 (Chia oil) dietary fatty acids modulate endocannabinoid system components in rat submandibular gland, what would have influence on salivary secretion. Dietary n-3 fatty acid could be useful in salivary dysfunctions.


title: Aperiodic brain activity and response to anesthesia vary in disorders of consciousness

abstract:
In the human electroencephalogram (EEG), oscillatory power peaks co-exist with non-oscillatory, aperiodic activity. Although EEG analysis has traditionally focused exclusively on oscillatory power, recent investigations have shown that the aperiodic EEG component can distinguish conscious wakefulness from sleep and anesthetic-induced unconsciousness (Lendner et al. 2020). This study investigates the aperiodic EEG component of individuals in a disorder of consciousness (DOC), and how it changes in response to exposure to anesthesia. High-density EEG was recorded from 43 individuals in a DOC. To measure the brains reaction to global perturbation, a subset of n = 16 were also exposed to a targeted infusion of propofol anesthesia. The aperiodic component was defined by the spectral slope and offset in the 1-45 Hz and 30-45 Hz range of the power spectral density. Brain network criticality and complexity were estimated using the pair correlation function (PCF) and Lempel-Ziv complexity, respectively. The level of responsiveness of all individuals in DOC was assessed using the Coma Recovery Scale-Revised (CRS-R). Recovery of consciousness was assessed three months post-EEG. At baseline, the EEG aperiodic component was more strongly correlated to the participants level of consciousness than the oscillatory component. Anesthesia caused a steepening of the spectral slope across participants. Importantly, the change in spectral slope positively correlated with the individual participants level of responsiveness. The spectral slope during exposure to anesthesia contained prognostic value for individuals with DOC. The anesthetic-induced change in aperiodic EEG was accompanied by loss of information-richness and a reduction in network criticality. The aperiodic EEG component in individuals with DOC has been historically neglected; this research highlights the importance of considering this measure for future research investigating brain mechanisms underlying consciousness.

Significance StatementThe analysis of human EEG has traditionally focused on oscillatory power, which is characterized by peaks above a broadband, aperiodic component in the EEG power spectral density. This study is the first to demonstrate the value of the aperiodic EEG component and specifically, its reaction to propofol anesthesia for assessing individuals level of, and capacity for, consciousness. Our results demonstrates that the pharmacological induced change in the aperiodic component accompanies the brains loss of network criticality and complexity. Most importantly, the magnitude of brain response to propofol anesthesia relies on an individuals pre-anesthetic level of consciousness. Whereas the aperiodic EEG component has been historically neglected; this research highlights the necessity of considering this measure for future research that seeks to understand the neurophysiological underpinnings of consciousness.


title: Fine-grained topographic organization within somatosensory cortex during resting-state and emotional face-matching task and its association with ASD traits

abstract:
BACKGROUNDSensory atypicalities are particularly common in autism spectrum disorders (ASD). Nevertheless, our knowledge about the divergence of the underlying somatosensory region and its association with ASD phenotype features is limited.

METHODSWe applied a data-driven approach to map the fine-grained variations in functional connectivity of the primary somatosensory cortex (S1) to the rest of the brain in 240 autistic and 164 neurotypical individuals from the EU-AIMS LEAP dataset, aged between 7 and 30. We estimated the S1 connection topography ( connectopy) during rest and during the emotional face-matching (Hariri) task, an established measure of emotion reactivity, and accessed its association with a set of clinical and behavioral variables.

RESULTSWe demonstrated that the S1 connectopy is organized along a dorsoventral axis, mapping onto the somatotopic organization of S1. We found that its spatial characteristics were linked to the individuals adaptive functioning skills, as measured by the Vineland Adaptive Behavior Scales, across the whole sample. Higher functional differentiation characterized the S1 connectopies of individuals with higher daily life adaptive skills. Notably, we detected significant differences between rest and the Hariri task in the S1 connectopies, as well as their projection maps onto the rest of the brain suggesting a task-modulating effect on S1 due to emotion processing.

CONCLUSIONSVariation of daily life adaptive skills appears to be reflected in the brains mesoscale neural circuitry, as shown by the S1 connectivity profile, which is also differentially modulated during rest and emotional processing.


title: Extensive protected area coverage and an updated global population estimate for the Endangered Madagascar Serpent-eagle identified from species-habitat associations using remote sensing data

abstract: Knowledge gaps regarding distribution, habitat associations, and population size for rare and threatened range-restricted taxa leads to uncertainty in directing conservation action. Quantifying range metrics and species-habitat associations using Species Distribution Models (SDMs) with remote sensing habitat data can overcome these setbacks by establishing baseline estimates for biological parameters critical for conservation assessments. Area of habitat (AOH) is a new range metric developed by the International Union for the Conservation of Nature (IUCN) Red List. AOH seeks to quantify inferred habitat within a species range to inform extinction risk assessments. Here, we use SDMs correlating occurrences with remote-sensing covariates, to calculate a first estimate of AOH for the Endangered Madagascar Serpent-eagle (Eutriorchis astur), and then update additional IUCN range metrics and the current global population estimate. From these baselines we then conduct a gap analysis assessing protected area coverage. Our continuous SDM had robust predictive performance (Continuous Boyce Index = 0.835) and when reclassified to a binary model estimated an AOH = 30,121 km2, 13 % less than the current IUCN range map. We estimate a global population of 533 mature individuals derived from the Madagascar Serpent-eagle AOH metric, which was within the current IUCN population estimates. The current protected area network covered 95 % of AOH, with the binary model identifying three key habitat areas as new protected area designations to fully protect Madagascar Serpent-eagle habitat. Our results demonstrate that correlating presence-only occurrences with remote sensing habitat covariates can fill knowledge gaps useful for informing conservation action. Applying this spatial information to conservation planning would ensure almost full protected area coverage for this endangered raptor. For tropical forest habitat specialists, we recommend that potential predictors derived from remote sensing, such as vegetation indices and biophysical measures are considered as covariates, along with other variables including climate and topography.


title: Differentiation of thermal reaction norms between marginal and core populations of a northward expanding parasitoid

abstract: Understanding the speed of and the type of mechanisms that species use to adapt to rapid change is a central question in evolutionary biology. Classically, the two mechanisms denoted in the literature that allow individuals to address these environmental changes are either phenotypic plasticity or rapid evolutionary changes. However, phenotypic plasticity itself can evolve rapidly. In this study, we investigated the genetic differentiation between marginal and core populations of a high-trophic level insect, Leptopilina boulardi, a Drosophila parasitoid, which has exhibited a very rapid progression northward of its geographical range. Several life history traits have been investigated in different populations according to four fluctuating thermal regimes that mimic the thermal conditions in the field. We found that at low developmental temperature, the two northern marginal populations that have to face a colder winter, survive longer than the two core populations. In addition, the northernmost populations exhibit a higher potential fecundity, a higher starvation resistance and a larger amount of energy at low temperatures. These significant genetic differentiations with genotype-by-environment interactions show that a rapid genetic differentiation of the shape of thermal reaction norms is possible when populations have to cope with new environments.


title: The rediscovery of a relict unlocks the first global phylogeny of whip spiders (Amblypygi)

abstract: Asymmetrical rates of cladogenesis and extinction abound in the Tree of Life, resulting in numerous minute clades that are dwarfed by larger sister groups. Such taxa are commonly regarded as phylogenetic relicts or "living fossils" when they exhibit an ancient first appearance in the fossil record and prolonged external morphological stasis, particularly in comparison to their more diversified sister groups. Due to their special status, various phylogenetic relicts tend to be well-studied and prioritized for conservation. A notable exception to this trend is found within Amblypygi ("whip spiders"), a visually striking order of functionally hexapodous arachnids that are notable for their antenniform first walking leg pair (the eponymous "whips"). Paleoamblypygi, the putative sister group to the remaining Amblypygi, is known from Late Carboniferous and Eocene deposits, but is survived by a single living species, Paracharon caecus Hansen, 1921, that was last collected in 1899. Due to the absence of genomic sequence-grade tissue for this vital taxon, there is no global molecular phylogeny for Amblypygi to date, nor a fossil-calibrated estimation of divergences within the group. Here, we report several individuals of a previously unknown species of Paleoamblypygi from a cave site in Colombia. Capitalizing upon this discovery, we generated the first molecular phylogeny of Amblypygi, integrating ultraconserved element sequencing with legacy Sanger datasets and including described extant genera. To quantify the impact of sampling Paleoamblypygi on divergence time estimation, we performed in silico experiments with pruning of Paracharon. We demonstrate that the omission of relicts has a significant impact on the accuracy of node dating approaches that outweighs the impact of excluding ingroup fossils. Our results underscore the imperative for biodiversity discovery efforts in elucidating the phylogenetic relationships of "dark taxa", and especially phylogenetic relicts in tropical and subtropical habitats.


title: Enhanced recovery of single-cell RNA-sequencing reads for missing gene expression data

abstract: Droplet-based 3 single-cell RNA-sequencing (scRNA-seq) methods have proved transformational in characterizing cellular diversity and generating valuable hypotheses throughout biology1,2. Here we outline a common problem with 3 scRNA-seq datasets where genes that have been documented to be expressed with other methods, are either completely missing or are dramatically under-represented thereby compromising the discovery of cell types, states, and genetic mechanisms. We show that this problem stems from three main sources of sequencing read loss: (1) reads mapping immediately 3 to known gene boundaries due to poor 3 UTR annotation; (2) intronic reads stemming from unannotated exons or pre-mRNA; (3) discarded reads due to gene overlaps3. Each of these issues impacts the detection of thousands of genes even in well-characterized mouse and human genomes rendering downstream analysis either partially or fully blind to their expression. We outline a simple three-step solution to recover the missing gene expression data that entails compiling a hybrid pre-mRNA reference to retrieve intronic reads4, resolving gene collision derived read loss through removal of readthrough and premature start transcripts, and redefining 3 gene boundaries to capture false intergenic reads. We demonstrate with mouse brain and human peripheral blood datasets that this approach dramatically increases the amount of sequencing data included in downstream analysis revealing 20 - 50% more genes per cell and incorporates 15-20% more sequencing reads than with standard solutions5. These improvements reveal previously missing biologically relevant cell types, states, and marker genes in the mouse brain and human blood profiling data. Finally, we provide scRNA-seq optimized transcriptomic references for human and mouse data as well as simple algorithmic implementation of these solutions that can be deployed to both thoroughly as well as poorly annotated genomes. Our results demonstrate that optimizing the sequencing read mapping step can significantly improve the analysis resolution as well as biological insight from scRNA-seq. Moreover, this approach warrants a fresh look at preceding analyses of this popular and scalable cellular profiling technology.


title: Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

abstract:
Metabolomic and proteomic analyses of human plasma and serum samples harbour the power to advance our understanding of disease biology. Pre-analytical factors may contribute to variability and bias in the detection of analytes, especially when multiple labs are involved, caused by sample handling, processing time, and differing operating procedures. To better understand the impact of pre-analytical factors that are relevant to implement a unified proteomic and metabolomic approach in a clinical setting, we assessed the influence of temperature, sitting times, and centrifugation speed on the plasma and serum metabolomes and proteomes from six healthy volunteers.

We used targeted metabolic profiling (497 metabolites) and data-independent acquisition (DIA) proteomics (572 proteins) on the same samples generated with well-defined pre-analytical conditions to evaluate criteria for pre-analytical SOPs for plasma and serum samples. Time and temperature showed the strongest influence on the integrity of plasma and serum proteome and metabolome. While rapid handling and low temperatures (4{degrees}C) are imperative for metabolic profiling, the analysed proteome showed variability when exposed to temperatures of 4{degrees}C for more than 2 hours, highlighting the need for compromises in a combined analysis. We formalised a quality control scoring system to objectively rate sample stability and tested this score using external data sets from other pre-analytical studies.

Stringent and harmonised standard operating procedures (SOPs) are required for pre-analytical sample handling when combining proteomics and metabolomics of clinical samples to yield robust and interpretable data on a longitudinal scale and across different clinics. To ensure an adequate level of practicability in a clinical routine for metabolomics and proteomics studies we suggest to keep blood samples up to 2 hours on ice (4{degrees}C) prior to snap-freezing as a compromise between stability and operability. Finally, we provide the methodology as an open source R package allowing the systematic scoring of proteomics and metabolomics datasets to assess the stability of plasma and serum samples.

category: biochemistry


title: Relationships between post-stroke mediolateral stepping characteristics, walking speed, balance performance, and balance confidence

abstract:
BackgroundMany people with chronic stroke exhibit walking balance deficits, which are linked with increased fall risk and decreased balance confidence. One potential contributor to these deficits is a decreased ability to adjust where the paretic foot is placed based on pelvis motion, which is an important factor in mediolateral walking balance.

ObjectiveThe objective of this study was to investigate altered stepping behavior for steps taken with the paretic leg, and to explore the relationship between this behavior and clinical measures of balance and balance confidence.

Methods.93 individuals with chronic stroke walked on a treadmill and completed a series of common clinical tests. We used partial correlations to quantify the step-by-step relationship between mediolateral pelvis displacement and both step width ({rho}SW) and mediolateral foot placement relative to the pelvis ({rho}FP), a metric that focuses on swing leg repositioning.

Results{rho}SW was weaker for steps taken with the paretic leg, whereas {rho}FP did not differ between non-paretic and paretic steps. Participants who walked faster had larger {rho}SW and {rho}FP values, but instructing participants to walk faster did not consistently increase {rho}SW or {rho}FP for paretic steps. Significant, albeit weak, relationships were observed between paretic {rho}SW and Functional Gait Assessment score, as well as between paretic {rho}FP and Activities-Specific Balance Confidence score, fear of falling, and fall history.

ConclusionsA reduced ability to adjust where the paretic foot lands when taking a step may discourage fast walking speeds after a stroke and contribute to clinical observations of decreased walking balance.


title: A Comparison of Dimension Reduction Methods for Cytometry by Time-of-Flight Data

abstract: Recently developed single-cell profiling technologies, such as single cell sequencing (scRNA-seq) and mass cytometry (CyTOF), provide critical biological insights from a large number of cells and a large number of features. While experimental and informatic techniques around scRNA-seq are much more advanced, research around CyTOF data analysis has severely lagged behind. However, CyTOF profiles the proteomics makeup of the single cells and are more closely related to disease phenotypes than scRNA-seq. CyTOF data are also dramatically different from scRNA-seq data in many aspects. This calls for the evaluation and development of statistical methods for CyTOF data. Dimension reduction (DR) is one of the most critical first steps of analyses of scRNA-seq and CyTOF data. Here, we benchmark 20 of these methods on 110 real and 425 synthetic CyTOF datasets, including 10 Imaging CyTOF datasets, for accuracy, scalability and usability. In particular, we checked the concordance of DR for CyTOF data against scRNA-seq data that were generated from the same samples. We found that SAUCIE and scvis surprisingly perform well across all categories, whereas UMAP particularly excels in downstream analyses and MDS preserves local and global structure well. Our results highlight the complementarity of existing tools, and that the choice of method should depend on the underlying data structure of the single cells. Based on these results, we develop a set of guidelines to help users select the best DR method for their dataset. Our freely available data and evaluation pipeline will aid in the development of improved DR algorithms specifically tailored to analyze data generated from the increasingly popular CyTOF technique.

category: bioinformatics


title: Faster SARS-CoV-2 sequence validation and annotation for GenBank using VADR

abstract:
BackgroundIn 2020 and 2021, more than 1.5 million SARS-CoV-2 sequences were submitted to GenBank. The initial version (v1.0) of the VADR (Viral Annotation DefineR) software package that GenBank uses to automatically validate and annotate incoming viral sequences is too slow and memory intensive to process many thousands of SARS-CoV-2 sequences in a reasonable amount of time. Additionally, long stretches of ambiguous N nucleotides, which are common in many SARS-CoV-2 sequences, prevent VADR from accurate validation and annotation.

ResultsVADR has been updated to more accurately and rapidly annotate SARS-CoV-2 sequences. Stretches of consecutive Ns are now identified and temporarily replaced with expected nucleotides to facilitate processing, and the slowest steps have been overhauled using blastn and glsearch, increasing speed, reducing the memory requirement from 64Gb to 2Gb per thread, and allowing simple, coarse-grained parallelization on multiple processors per host.

ConclusionVADR is now nearly 1000 times faster than it was in early 2020 for processing SARS-CoV-2 sequences submitted to GenBank. It has been used to screen and annotate more than 1.5 million SARS-CoV-2 sequences since June 2020, and it is now efficient enough to cope with the current rate of hundreds of thousands of submitted sequences per month. Version 1.4.1 is freely available (https://github.com/ncbi/vadr) for local installation and use.


title: Prediction of allosterically acting mutations using MD simulations and Rosetta

abstract:
Computationally modeling how mutations affect protein binding not only helps uncover the biophysics of protein interfaces, but also enables the redesign and optimization of protein-protein interactions. Traditional high-throughput methods for estimating binding free energies are currently limited to mutations directly at the interface due to difficulties in accurately modeling how more distant allosterically acting mutations propagate their effects through the protein structure. However, the modeling and design of such allosteric mutations is of substantial interest as it allows for greater control and flexibility in protein design applications. We have developed a method that combines high-throughput Rosetta-based side-chain optimization with conformational sampling using classical molecular dynamics simulations, finding significant improvements in our ability to accurately predict allosterically acting mutational perturbations to protein binding. Our approach uses an analytical framework grounded in rigorous alchemical free energy calculations while enabling exploration of a vastly larger sequence space. When comparing to experimental data, we find that our method can predict allosteric perturbations with a level of accuracy similar to that of traditional methods in predicting the effects of non-allosteric interface mutations. This work represents a new and generalizable approach to optimize protein free energy landscapes for desired biological functions.

Author SummaryProtein-protein interactions are vital to almost all biological processes, and therefore the ability to accurately and efficiently predict how mutations alter protein binding has far-reaching applications in protein analysis and design. Current approaches to predict such mutational free energy changes are limited to mutations directly at the interaction interface. Much research has underlined the prevalence of allosteric protein regulation in biological processes, indicating the importance of understanding and predicting the effects of mutations which act over long distances. In this work we develop a novel method based on theoretically rigorous alchemical free energy calculations and the Rosetta macromolecular modeling suite which can predict the effects of allosteric mutations with levels of accuracy rivaling state of the art interface-specific methods. We hope that our method will serve as a novel framework for high-throughput allosteric mutational analysis and therefore benefit future protein design efforts.

category: biophysics


title: Elevated arginine levels in liver tumors promote metabolic reprogramming and tumor growth

abstract: Arginine auxotropy, due to reduced expression of urea cycle genes, is common in cancer. However, little is known about the levels of arginine in these cancers. Here, we report that arginine levels are elevated in hepatocellular carcinoma (HCC) despite reduced expression of urea cycle enzymes. Liver tumors accumulate high levels specifically of arginine via increased uptake and, more importantly, via suppression of arginine-to-polyamine conversion due to reduced arginase 1 (ARG1) and agmatinase (AGMAT) expression. Furthermore, the high levels of arginine are required for tumor growth. Mechanistically, high levels of arginine promote tumorigenesis via transcriptional regulation of metabolic genes, including upregulation of asparagine synthetase (ASNS). ASNS-derived asparagine further enhances arginine uptake, creating a positive feedback loop to sustain high arginine levels and oncogenic metabolism. Thus, arginine is a novel second messenger-like molecule that reprograms metabolism to promote tumor growth.


title: Discovery of new senolytics using machine learning

abstract: Cellular senescence is a stress response characterised by a permanent cell cycle arrest and a proinflammatory secretome. In addition to its tumour suppressor role, senescence is involved in ageing and promotes many disease processes such as cancer, type 2 diabetes, osteoarthritis, and SARS-CoV-2 infection. There is a growing interest in therapies based on targeted elimination of senescent cells, yet so far only a few such senolytics are known, partly due to the poor grasp of the molecular mechanisms that control the senescence survival programme. Here we report a highly effective machine learning pipeline for the discovery of senolytic compounds. Using solely published data, we trained machine learning algorithms to classify compounds according to their senolytic action. Models were trained on as few as 58 known senolytics against a background of FDA-approved compounds or in late-stage clinical development (2,523 in total). We computationally screened various chemical libraries and singled out top candidates for validation in human lung fibroblasts (IMR90) and lung adenocarcinoma (A549) cell lines. This led to the discovery of three novel senolytics: ginkgetin, oleandrin and periplocin, with potency comparable to current senolytics and a several hundred-fold reduction in experimental screening costs. Our work demonstrates that machine learning can take maximum advantage of existing drug screening data, paving the way for new open science approaches to drug discovery for senescence-associated diseases.


title: MycoPhylo experiment reveals how mycorrhiza types and phylogenetic relationships affect soil biodiversity and functioning

abstract:
O_LINatural forests and abandoned agricultural lands are increasingly replaced by monospecific forest plantations that have poor capacity to support biodiversity and ecosystem services. Natural forests harbour plants belonging to different mycorrhiza types that differ in their microbiome and carbon and nutrient cycling properties.
C_LIO_LIHere we describe the MycoPhylo field experiment that encompasses 116 woody plant species from three mycorrhiza types and 237 plots, with plant diversity and mycorrhiza type diversity ranging from one to four and one to three per plot, respectively.
C_LIO_LIThe MycoPhylo experiment enables us to test hypotheses about the plant species, species diversity, mycorrhiza type, and mycorrhiza type diversity effects and their phylogenetic context on soil microbial diversity and functioning and soil processes.
C_LIO_LIAlongside with other experiments in the TreeDivNet consortium, MycoPhylo will contribute to our understanding of the tree diversity effects on soil biodiversity and ecosystem functioning across biomes, especially from the mycorrhiza type and phylogenetic conservatism perspectives.
C_LI


title: Robustness of organ morphology is associated with modules of co-expressed genes related to plant cell wall

abstract: Reproducibility in organ size and shape is a fundamental trait of living organisms. The mechanisms underlying such robustness remain, however, to be elucidated. Taking the sepal of Arabidopsis as a model, we investigated whether variability of gene expression plays a role in variation of organ morphology. To address this question, we produced a dataset composed of both transcriptomic and morphological information obtained from 27 individual sepals from wild-type plants. Although nearly identical in their genetic background, environment, and developmental stage, these sepals exhibited appreciable variability in both morphology and transcriptome. We identified modules of co-expressed genes in sepals, three of which correlated significantly with morphology, revealing biologically relevant gene regulatory networks. Interestingly, cell-wall related genes were overrepresented in two of these three modules. Additionally, we found that highly variable genes were unexpectedly enriched in cell-wall related processes. We then analyzed sepal morphology from 16 cell-wall mutants and found that the more a gene is expressed in wild-type, the more variable the morphology of the corresponding mutant. Altogether, our work unravels the contribution of cell-wall related genes to the robustness of sepal morphology. More generally, we propose that canalizing traits during development could rely on the modulation of highly expressed genes.


title: Inflammation as a Silent Partner in Opioid Addiction: A Regulatory Logic Model

abstract:
The brain and body consist of complex networks of interconnected feedback and feed forward loops. Because these networks are capable of supporting multiple homeostatic states, a stressor or combination of stressors may cause the network to become "stuck" in a persistent maladaptive state, for example, chronic pain and the potentiation of opioid dependency. The current research uses automated text mining of over 14,000 publications to assemble a regulatory circuit consisting of 44 immune and neurotransmission mediators linked by 188 documented regulatory interactions. Decisional logic parameters dictating the regulatory dynamics available to each network model were estimated such that predicted behavior would adhere to observed pathologies. Analysis of this psycho-neuroimmune network confirmed that a broad family of behavioral kinetics may be equally capable of supporting dynamically stable conditions of chronic pain, persistent depression and addiction behaviors. Despite differences in the predicted course of onset, these models typically point to characteristic patterns of increased inflammatory activity in the brain for each of these pathologies, specifically increased expression of the protein complex NF-kB and inflammatory signaling proteins IL1-B, IL6, and TNF. Potential treatments targeting both addiction and chronic pain may therefore benefit from the use of anti-inflammatory drugs as pharmacological potentiators of current behavioral interventions.

Clinical RelevanceThis work establishes a methodology for understanding both illness-specific and shared mechanisms underlying addiction, chronic pain, and depression, and the corresponding expression profiles of psychoneuroimmune markers that might facilitate screening and treatment design.


title: Approximating Solutions of the Chemical Master Equation using Neural Networks

abstract: The Chemical Master Equation (CME) provides an accurate description of stochastic biochemical reaction networks in well-mixed conditions, but it cannot be solved analytically for most systems of practical interest. While Monte Carlo methods provide a principled means to probe the system dynamics, their high computational cost can render the estimation of molecule number distributions and other numerical tasks infeasible due to the large number of repeated simulations typically required. In this paper we aim to leverage the representational power of neural networks to approximate the solutions of the CME and propose a framework for Neural Estimation of Stochastic Simulations for Inference and Exploration (Nessie). Our approach is based on training a neural network to learn the distributions predicted by the CME from a relatively small number of stochastic simulations, thereby accelerating computationally intensive tasks such as parameter exploration and inference. We show on biologically relevant examples that simple neural networks with one hidden layer are able to capture highly complex distributions across parameter space. We provide a detailed discussion of the neural network implementation and code for easy reproducibility.


title: The arthropod associates of 155 North American cynipid oak galls

abstract: The identities of most arthropod associates of cynipid-induced oak galls in the western Palearctic are generally known. However, a comprehensive accounting of associates has been performed for only a small number of the galls induced by the estimated 700 species of cynipid gall wasp in the Nearctic. This gap in knowledge stymies many potential studies of diversity, coevolution, and community ecology, for which oak gall systems are otherwise ideal models. We report rearing records of insects and other arthropods from more than 527,306 individual galls representing 201 different oak gall types collected from 32 oak tree species in North America. Of the 201 gall types collected, 155 produced one or more animals. A total of 151,075 animals were found in association with these 155 gall types, and of these 61,044 (40.4%) were gall wasps while 90,031 (59.6%) were other arthropods. We identified all animals to superfamily, family, or, where possible, to genus. We provide raw numbers and summaries of collections, alongside notes on natural history, ecology, and previously published associations for each taxon. For eight common gall-associated genera (Synergus, Ceroptres, Euceroptres, Ormyrus, Torymus, Eurytoma, Sycophila, and Euderus), we also connect rearing records to gall wasp phylogeny, geography, and ecology - including host tree and gall location (host organ), and their co-occurrence with other insect genera. Though the diversity of gall wasps and the large size of these communities is such that many Nearctic oak gall-associated insects still remain undescribed, this large collection and identification effort should facilitate the testing of new and varied ecological and evolutionary hypotheses in Nearctic oak galls.

category: zoology


title: Efficacy and Specificity of Melanopsin Reporters for Retinal Ganglion Cells

abstract: Intrinsically photosensitive retinal ganglion cells (ipRGCs) are specialized retinal output neurons that mediate behavioral, neuroendocrine, and developmental responses to environmental light. There are diverse molecular strategies for marking ipRGCs, especially in mice, making them among the best characterized retinal ganglion cells. With the development of more sensitive reporters, new subtypes of ipRGCs have emerged. We therefore tested high-sensitivity reporter systems to see whether we could reveal yet more. Substantial confusion remains about which of the available methods, if any, label all and only ipRGCs. Here, we compared many different methods for labeling of ipRGCs, including anti-melanopsin immunofluorescence, Opn4-GFP BAC transgenic mice, and Opn4cre mice crossed with three different Cre-specific reporters (Z/EG; Ai9; and Ai14) or injected with Cre-dependent (DIO) AAV2. We show that Opn4cre mice, when crossed with sensitive Cre-reporter mice, label numerous ganglion cell types that lack intrinsic photosensitivity. Though other methods label ipRGCs specifically, they do not label the entire population of ipRGCs. We conclude that no existing method labels all and only ipRGCs. We assess the appropriateness of each reporter for particular applications and integrate findings across reporters to estimate that the overall abundance of ipRGCs among mouse retinal ganglion cells may approach 11%.


title: Cortical response variability is driven by local excitability changes with somatotopic organization

abstract: Identical sensory stimuli can lead to different neural responses depending on the instantaneous brain state. Specifically, neural excitability in sensory areas may shape the brains response already from earliest cortical processing onwards. However, whether these dynamics affect sensory domains globally or occur on a spatially local level is largely unknown. We studied this in the somatosensory domain of 38 human participants with EEG, presenting stimuli to the median and tibial nerves alternatingly, and testing the co-variation of initial cortical responses in hand and foot areas, as well as their relation to pre-stimulus oscillatory states. We found that amplitude fluctuations of initial cortical responses to hand and foot stimulation - the N20 and P40 components of the somatosensory evoked potential (SEP), respectively - were not related, indicating local excitability changes in primary sensory regions. In addition, effects of pre-stimulus alpha (8-13 Hz) and beta (18-23 Hz) band amplitude on hand-related responses showed a robust somatotopic organization, thus further strengthening the notion of local excitability fluctuations. However, for foot-related responses, the spatial specificity of pre-stimulus effects was less consistent across frequency bands, with beta appearing to be more foot-specific than alpha. Connectivity analyses in source space suggested this to be due to a somatosensory alpha rhythm that is primarily driven by activity in hand regions while beta frequencies may operate in a more hand-region-independent manner. Altogether, our findings suggest spatially distinct excitability dynamics within the primary somatosensory cortex, yet with the caveat that frequency-specific processes in one sub-region may not readily generalize to other sub-regions.


title: Aquaporin 4 is differentially increased and depolarized in association with tau and amyloid-beta

abstract: Neurovascular-glymphatic dysfunction plays an important role in Alzheimers disease and has been analyzed mainly in association with amyloid-beta (A{beta}) pathology. The neurovascular-glymphatic link with tauopathies has not been well elucidated. Here, we aimed to investigate the alterations in the neurovasculature and map the aquaporin 4 (AQP4) distribution and depolarization associated with tau and A{beta}. Perfusion, susceptibility weighted imaging and structural magnetic resonance imaging (MRI) were performed in the pR5 P301L mouse model of 4-repeat tau and the arcA{beta} mouse model of amyloidosis. Immunofluorescence staining was performed using antibodies against AQP4, CD31, astroglia (GFAP, s100{beta}), phospho-tau (AT-8) and A{beta} (6E10) in brain tissue slices from P301L, arcA{beta} and nontransgenic mice. P301L mice showed regional atrophy, preserved cerebral blood flow and reduced cerebral vessel density compared to nontransgenic mice, while arcA{beta} mice showed cerebral microbleeds and reduced cerebral vessel density. AQP4 depolarization and peri-tau enrichment in the hippocampus and increased AQP4 levels in the forebrain and hippocampus were detected in P301L mice compared to nontransgenic mice. In comparison, cortical AQP4 depolarization and cortical/hippocampal peri-plaque increases were observed in arcA{beta} mice. Increased s100{beta}-GFAP fluorescence intensities indicative of reactive astrocytes were detected surrounding tau inclusions in P301L mice and A{beta} plaques in arcA{beta} mice. In conclusion, we observed a divergent region-specific AQP4 increase and association with phospho-tau and A{beta} pathologies.


title: Fixational eye movements as active sensation for high visual acuity

abstract:
Perception and action are inherently entangled: our world view is shaped by how we explore and navigate our environment through complex and variable self-motion. Even when fixating on a stable stimulus, our eyes undergo small, involuntary movements. Fixational eye movements (FEM) render a stable world jittery on our retinae, which contributes noise to neural coding. Yet, empirical evidence suggests that FEM help rather than harm human perception of fine detail. Here, we elucidate this paradox by uncovering under which conditions FEM improve or impair retinal coding and human acuity. We combine theory and experiment: model accuracy is directly compared to that of healthy human subjects in a visual acuity task. Acuity is modeled by applying an ideal Bayesian classifier to simulations of retinal spiking activity in the presence of FEM. In addition, empirical FEM are monitored using high-resolution eye-tracking by an adaptive optics scanning laser ophthalmoscope. While FEM introduce noise, they also effectively pre-process visual inputs to facilitate retinal information encoding. Based on an interplay of these mechanisms, our model predicts a relation between visual acuity, FEM amplitude, and single-trial stimulus size that quantitatively accounts for experimental observations and captures the beneficial effect of FEM. Moreover, we observe that human subjects FEM statistics vary with stimulus size, and our model suggests that changing eye motion amplitude, as the subjects indeed do, enhances acuity as compared to maintaining eye motion size constant. Overall, our findings indicate that perception benefits from action even at the fine and noise-dominated spatio-temporal scale of FEM.

Significance StatementPerception is inherently active: we need to move our eyes to see the world around us. Yet our eyes also undergo tiny, unconscious movements that can blur out fine visual details. Paradoxically, previous work suggested that these small movements aid fine detail perception. Here, we investigate this paradox to uncover in which contexts small eye movements help or harm visual acuity. Comparing a model of retinal responses with recordings of human visual acuity, we elucidate the mechanisms by which and conditions in which small eye movements support fine detail discrimination. Our results also suggest that varying eye movement amplitude according to stimulus size enhances retinal coding, highlighting that perception is active even at the level of very fine eye movements.


title: Episodic memory retrieval affects the onset and dynamics of evidence accumulation during value-based decisions

abstract: AO_SCPLOWBSTRACTC_SCPLOWIn neuroeconomics, there is much interest in understanding simple value-based choices where agents choose between visually presented goods, comparable to a shopping scenario in a supermarket. However, many everyday decisions are made in the physical absence of the considered goods, requiring agents to recall information about the goods from memory. Here, we asked whether and how this reliance on an internal memory representation affects the temporal dynamics of decision making on a cognitive and neural level. Participants performed a remember-and-decide task, in which they made simple purchasing decisions between money offers and snack items while undergoing EEG. Snack identity was presented either visually (value trials) or had to be recalled from memory (memory trials). Behavioral data indicated comparable choice consistency across both trial types, but considerably longer response times (RT) in memory trials. Drift-diffusion modeling suggested that this RT difference was due to longer non-decision time of decision processes as well as altered evidence accumulation dynamics (lower accumulation rate and higher decision threshold). The non-decision time effect was supported by a delayed onset of the lateralized readiness potential. These results show that both, decision and non-decision processes are prolonged when participants need to resort to internal memory representations during value-based decisions.


title: Neurofeedback training for improving motor performance in healthy adults: A systematic review and meta-analysis

abstract: Neurofeedback training (NFT) refers to a training where the participants voluntarily aim to manipulate their own brain activity using the sensory feedback abstracted from their brain activity. NFT has attracted attention in the field of motor learning for its potential to become an alternative or additional training method for general physical training. In this study, a systematic review of NFT studies for motor performance improvements in healthy adults and a meta-analysis on the effectiveness of NFT were conducted. To identify relevant studies published between January 1st, 1990 to August 3rd, 2021, a computerized search was performed using the databases, Web of Science, Scopus, PubMed, JDreamIII, and Ichushi-Web. Thirty-two studies were identified for the qualitative synthesis and 13 randomized controlled trials (286 subjects) for the meta-analysis. The meta-analysis revealed significant effects of NFT for motor performance improvement examined at the timing after the last NFT session (standardized mean difference = 0.96, 95% CI = 0.40-1.53), but with the existence of publication biases and substantial heterogeneity among the trials. Subsequent subgroup meta-analysis demonstrated reliable benefits when the NFT is performed longer than 1 week. The effectiveness of NFT for each motor performance measurement (e.g., speed, accuracy, and hand dexterity) remains unclear because of high heterogeneity or due to small sample size. Further accumulation of empirical NFT studies for motor performance improvement will be necessary to provide reliable evidence about the NFT effects on specific motor skills and to safely incorporate NFT into real-world scenarios.


title: Mechanisms regulating the frequency of inhibition-based gamma oscillations in primate prefrontal and parietal cortices

abstract:
In primates, the dorsolateral prefrontal (DLPFC) and posterior parietal (PPC) cortices are critical nodes in the network mediating cognitive functions including attention and working memory. Notably, during working memory tasks, gamma oscillations, usually prominent in layer 3 (L3), are induced in both DLPFC and PPC but exhibit higher frequency in DLPFC. These oscillation frequency differences might be crucial for working memory function, but the mechanisms producing different oscillation frequencies in monkey DLPFC and PPC remain poorly understood.

To investigate the basis of the DLPFC-PPC differences in oscillation frequency we studied GABAAR-mediated inhibition, which plays a crucial role in gamma oscillation production, in L3 pyramidal neurons (L3 PNs) from the rhesus monkey DLPFC or PPC. Recordings of GABAAR-mediated synaptic currents from L3 PNs, while suggesting a contribution to network synchronization in both areas, revealed no DLPFC-PPC differences in the strength or kinetics of GABAAR-mediated inhibition. Likewise, the expression of GABAAR genes in L3 PNs did not differ between regions.

In the absence of differences in inhibition, DLPFC L3 PNs showed greater dendritic spine density and higher expression of AMPAR and NMDAR subunit genes relative to PPC L3 PNs, suggesting that the excitatory synaptic drive onto L3 PNs could be stronger in the DLPFC. Simulations in computational models of the cortical microcircuit showed that, with constant synaptic inhibition, increasing the strength of recurrent excitatory synaptic drive increased the network oscillation frequency. Hence, the DLPFC-PPC differences in gamma oscillation frequency could depend on stronger recurrent excitation in the DLPFC relative to PPC.

Significance statementGamma oscillations may contribute to the neural substrate of working memory and exhibit a higher frequency in the prefrontal (DLPFC) than parietal (PPC) areas of primate cortex. To investigate the basis of these oscillation frequency differences which may be crucial for working memory encoding, we studied GABAAR-mediated inhibition on L3 pyramidal neurons (L3 PNs) from rhesus monkey DLPFC or PPC. Our data revealed no DLPFC-PPC differences in GABAAR-mediated inhibition but showed greater dendritic spine density in DLPFC L3 PNs, suggesting stronger excitatory synaptic drive. Simulations in computational network models showed that stronger recurrent excitatory synaptic drive increased the network oscillation frequency, suggesting that the higher oscillation frequency could depend on stronger recurrent excitation in the DLPFC relative to PPC.


title: Dynamic neural reconstructions of attended object location and features using EEG

abstract: We live in a dynamic world and our environment contains far more stimuli than our brain can process at one time. Visual attention allows us to select relevant information and ignore irrelevant information. What happens when attention is shifted from one item to another? To answer this question, it is critical to have tools that can accurately recover neural representations of both feature and location information, and do so across shifts of attention with high temporal resolution. In the current study, we used human electroencephalography (EEG) and machine learning methods to explore how neural representations of object features and locations update across dynamic shifts of attention. We demonstrate that EEG can be used to create simultaneous timecourses of the neural representations of attended features (timepoint-by-timepoint inverted encoding model reconstructions) and attended location (timepoint-by-timepoint decoding) during both stable periods and across dynamic spatial shifts of attention. On each trial two oriented gratings were presented that flickered at the same frequency but had different orientations; participants were cued to attend to one of them, and on half of the trials received a shift cue in the middle of the trial. We trained the models on a stable period from Hold attention trials, and then reconstructed/decoded the attended orientation/location information at each timepoint on Shift attention trials. Our results showed that both feature reconstructions and location decoding dynamically track the shift of attention, and that there may be timepoints during the shifting of attention when (1) feature and location representations become uncoupled, and (2) both the previously-attended and currently-attended orientations are represented with roughly equal strength. The results offer insight into our understanding of attentional shifts, and the noninvasive techniques developed in the current study lend themselves well to a wide variety of future applications.


title: Dynamic Features of Chromosomal Instability during Culture of Induced Pluripotent Stem Cells

abstract: Induced pluripotent stem cells (iPSCs) hold great potential for regenerative medicine. By reprogramming a patients own cells, immunological rejection can be avoided during transplantation. For expansion and gene editing, iPSCs are grown in artificial culture for extended times. Culture affords potential danger for accumulation of genetic aberrations. To study these, two iPS cell lines were cultured and periodically analyzed using advanced optical mapping to detect and classify chromosome numerical and segmental changes that included deletions, insertions, balanced translocations and inversions. In one of the lines, a population trisomic for chromosome 12 gained dominance over a small number of passages. This appearance and dominance of the culture by chromosome 12 trisomic cells was tracked through intermediate passages by analysis of chromosome spreads. Mathematical modeling suggested that the proliferation rates of diploid versus trisomic cells could not account for the rapid dominance of the trisomic population. In addition, optical mapping revealed hundreds of structural variations distinct from those generally found within the human population. Many of these structural variants were detected in samples taken early in the culturing process and were maintained in late passage samples, while others were acquired over the course of culturing.

category: cell biology


title: BioNE: Integration of network embeddings for supervised learning

abstract:
A network embedding approach reduces the analysis complexity of large biological networks by converting them to lowdimensional vector representations (features/embeddings). These lower-dimensional vectors can then be used in machine learning prediction tasks with a wide range of applications in computational biology and bioinformatics. Several network embedding approaches have been proposed with different methods of generating vector representations. These network embedding approaches can be quite diverse in terms of data representation and implementation. Moreover, most were not originally developed for biological networks. Therefore comparing and assessing the performance of these diverse models in practice, in biological contexts, can be challenging. To facilitate such comparisons, we have developed the BioNE framework for integration of different embedding methods in prediction tasks. Using this framework one can easily assess, for instance, whether combined vector representations from multiple embedding methods offer complementary information with regards to the network features and thus better performance on prediction tasks. In this paper, we present the BioNE software suite for embedding integration, which applies network embedding methods following standardised network preparation steps, and integrates the vector representations achieved by these methods using three different techniques. BioNE enables selection of prediction models, oversampling methods, feature selection methods, cross-validation type and cross-validation parameters.

Availability and implementationBioNE pipeline and detailed explanation of implementation is freely available on GitHub, at https://github.com/pooryaparvizi/BioNE


title: Domain motions, dimerization, and membrane interactions of the murine guanylate binding protein 2

abstract: Guanylate-binding proteins (GBPs) are a group of interferon-inducible GTPases that are essential components of cell-autonomous immunity against intracellular pathogens. They restrict the replication of intracellular pathogens by targeting and lysing the membrane of the pathogen-containing vacuole. The aim of our work is to provide a molecular-level understanding of how the GBPs destroy the parasitophorous vacuole membrane. To this end, we use molecular dynamics (MD) simulations to elucidate the domain motions of GBPs and the effects on these motions following GTP binding, GBP multimerization, and membrane binding, assuming that each of these steps plays important roles in the defense mechanism. Here, we present our results for the murine GBP2, one of the eleven GBPs present in mice, obtained from standard and replica exchange MD simulations with an accumulated simulation time of 30 {micro}s. The main findings are that mGBP2 features a large-scale hinge motion in its M/E domain which is not hugely affected by either GTP binding, geranylgeranylation, homodimer formation, or lipid-membrane binding. Our prognosis is that this hinge motion has the potential to destroy the membrane following the formation of supramolecular mGBP2 complexes on the membrane surface.


title: The double round-robin population unravels the genetic architecture of grain size in barley

abstract:
Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characters and observed 84 % or higher heritability across four environments. The results of the quantitative trait locus (QTL) detection indicate that the genetic architecture of grain size is more complex than reported previously. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.

HighlightMulti parent population uncovered the natural allelic series across quantitative loci associated with grain size and weight that will contribute to identifying causal genes and yield improvement in barley.