bluuebunny/crossref_metadata_2025 huggingface dataset:
SCSIM: Jointly simulating correlated single-cell and bulk next-generation DNA sequencing data
Authors: Giguere Collin , Dubey Harsh Vardhan , Sarsani Vishal Kumar , Saddiki Hachem , He Shai , Flaherty Patrick
Published: February 2020

Background

Recently, it has become possible to collect next-generation DNA sequencing data sets that are composed of multiple samples from multiple biological units where each of these samples may be from a single cell or bulk tissue. Yet, there does not yet exist a tool for simulating DNA sequencing data from such a nested sampling arrangement with single-cell and bulk samples so that developers of analysis methods can assess accuracy and precision.

Results

We have developed a tool that simulates DNA sequencing data from hierarchically grouped (correlated) samples where each sample is designated bulk or single-cell. Our tool uses a simple configuration file to define the experimental arrangement and can be integrated into software pipelines for testing of variant callers or other genomic tools.

Conclusions

The DNA sequencing data generated by our simulator is representative of real data and integrates seamlessly with standard downstream analysis tools.
QTG-Finder2: a generalized machine-learning algorithm for prioritizing QTL causal genes in plants
Authors: Lin Fan , Lazarus Elena Z. , Rhee Seung Y.
Published: February 2020

Linkage mapping has been widely used to identify quantitative trait loci (QTL) in many plants and usually requires a time-consuming and labor-intensive fine mapping process to find the causal gene underlying the QTL. Previously, we described QTG-Finder, a machine-learning algorithm to rationally prioritize candidate causal genes in QTLs. While it showed good performance, QTG-Finder could only be used in Arabidopsis and rice because of the limited number of known causal genes in other species. Here we tested the feasibility of enabling QTG-Finder to work on species that have few or no known causal genes by using orthologs of known causal genes as training set. The model trained with orthologs could recall about 64% of Arabidopsis and 83% of rice causal genes when the top 20% ranked genes were considered, which is similar to the performance of models trained with known causal genes. We further extended the algorithm to include polymorphisms in conserved non-coding sequences and gene presence/absence variation as additional features. Using this algorithm, QTG-Finder2, we trained and cross-validatedSorghum bicolorandSetaria viridismodels. TheS. bicolormodel was validated by causal genes curated from the literature and could recall 70% of causal genes when the top 20% ranked genes were considered. In addition, we applied theS. viridismodel and public transcriptome data to prioritize a plant height QTL and identified 13 candidate genes. QTL-Finder2 can accelerate the discovery of causal genes in any plant species and facilitate agricultural trait improvement.
A double role of the Gal80 N-terminus in activation of transcription by Gal4p
Authors: Reinhardt-Tews Annekathrin , Krutyhołowa Rościsław , Günzel Christian , Glatt Sebastian , Breunig Karin D
Published: February 2020

The yeast galactose switch operated by the Gal4p-Gal80p-Gal3p regulatory module is a textbook model of transcription regulation in eukaryotes. The Gal80 protein inhibits Gal4p-mediated transcription activation by binding to the transcription activation domain. Inhibition is relieved by formation of an alternative Gal80-Gal3 complex. In yeasts lacking a Gal3p ortholog the Gal1 protein combines regulatory and enzymatic activity. The data presented here reveal a so-far unknown role of the Gal80 N-terminus in the mechanism of Gal4p activation. The N-terminus contains an NLS, which is responsible for nuclear accumulation of KlGal80p and galactokinase inhibitionin vitro.Herein we propose a model where the N-terminus of KlGal80p reaches into the catalytic center of KlGal1p of the nuclear fraction of KlGal1p triggering dissociation of the KlGal80-KlGal4 complex. We corroborate this model by genetic analyses and structural modelling and provide a rationale for the divergent evolution of the mechanism activating Gal4p.

Summary blurb

Activation of gene expression by Gal4p inK. lactisrequires an element in the N-terminus of KlGal80 that mediates nuclear import, KlGal1 interaction and galactokinase inhibition
Zebrafish Kit ligands cooperate with erythropoietin to promote erythroid cell expansion
Authors: Oltova Jana , Svoboda Ondrej , Machonova Olga , Svatonova Petra , Traver David , Kolar Michal , Bartunek Petr
Published: February 2020

Kit ligand (Kitlg) is pleiotropic cytokine with a prominent role in vertebrate erythropoiesis. Although the role of Kitlg in this process has not yet been reported inDanio rerio(zebrafish), in the present study, we show that its function is evolutionary conserved. Zebrafish possess two copies of Kitlg genes (Kitlga and Kitlgb) due to whole genome duplication. To determine the role of each ligand in zebrafish, we performed a series ofex vivoandin vivogain- and loss-of-function experiments. First, we tested the biological activity of recombinant Kitlg proteins in suspension culture from zebrafish whole kidney marrow and we demonstrate that Kitlga is necessary for expansion of erythroid progenitorsex vivo. To further address the role ofkitlgaandkitlgbin hematopoietic developmentin vivo, we performed gain-of-function experiments in zebrafish embryos, showing that both ligands cooperate with erythropoietin (Epo) to promote erythroid cell expansion. Finally, using thekitamutant (kitab5/b5orsparse), we show that Kita receptor is crucial for Kitlga/b cooperation with Epo in erythroid cells. In summary, using optimized suspension culture conditions with recombinant cytokines (Epo, Kitlga), we are reporting for the first timeex vivosuspension cultures of zebrafish hematopoietic progenitor cells, which can serve as an indispensable tool to study normal and aberrant hematopoiesis in zebrafish. Furthermore, we conclude that although partial functional diversification of Kit ligands has been described in other processes, in erythroid development, both paralogs play a similar role and their function is evolutionary conserved.

Key points:

Kit signaling contributes to erythroid cell development and is conserved from fish to man

Ex vivo expansion and self-renewal of zebrafish erythroid progenitors requires addition of recombinant Kitlga
Gene loss and acquisition in lineages of bacteria evolving in a human host environment
Authors: Gabrielaite Migle , Johansen Helle K. , Molin Søren , Nielsen Finn C. , Marvig Rasmus L.
Published: February 2020

While genome analyses have documented that there are differences in the gene repertoire between evolutionary distant lineages of the same bacterial species, less is known about micro-evolutionary dynamics of gene loss and acquisition within lineages of bacteria as they evolve over the timescale of years. This knowledge is valuable to understand both the basic mutational steps that on long timescales lead to evolutionary distant bacterial lineages, and the evolution of the individual lineages themselves. In the case that lineages evolve in a human host environment, gene loss and acquisition may furthermore have implication for disease.

We analyzed the genomes of 45Pseudomonas aeruginosalineages evolving in the lungs of cystic fibrosis patients to identify genes that are lost or acquired during the first years of infection in each of the different lineages. On average, the lineage genome content changed with 88 genes (range 0–473). Genes were more often lost than acquired, and prophage genes were more variable than bacterial genes. We identified genes that were lost or acquired independently across different clonal lineages, i.e. convergent molecular evolution. Convergent evolution suggests that there is a selection for loss and acquisition of certain genes in the host environment. We find that a significant proportion of such genes are associated with virulence; a trait previously shown to be important for adaptation. Furthermore, we also compared the genomes across lineages to show that within-lineage variable genes more often belonged to genomic content not shared across all lineages. Finally, we used 4,760 genes shared by 446P. aeruginosagenomes to develop a stable and discriminatory typing scheme forP. aeruginosaclone types (Pactyper,https://github.com/MigleSur/Pactyper). In sum, our analysis adds to the knowledge on the pace and drivers of gene loss and acquisition in bacteria evolving over multiple years in a human host environment and provides a basis to further understand how gene loss and acquisition plays a role in lineage differentiation and host adaptation.

Data Summary

P. aeruginosagenome sequencing data has been made publicly available by Marviget al.(2015) and is deposited in Sequence Read Archive (SRA) under accession ERP004853.
High through-put identification of miR-145 targets in human articular chondrocytes
Authors: Martinez-Sanchez Aida , Lazzarano Stefano , Sharma Eshita , Murphy Chris L.
Published: February 2020

Objective

MicroRNAs play a key role in biological processes, including cartilage development and homeostasis and are dysregulated in many diseases, including osteoarthritis. MiR-145 modulation induces profound changes in the human articular chondrocyte (HAC) phenotype, partially through direct repression ofSOX9. Since miRNAs can simultaneously silence multiple targets, we aimed to identify the whole targetome of miR-145 in HACs. This information is critical if miR-145 is to be considered a target for cartilage repair.

Methods

RIP-seq (RNA-immunoprecipitation plus HT-sequencing) of miRISC (miRNA-induced silencing complex) was performed in HACs overexpressing miR-145 to identify miR-145 direct targets. The motif discovery method cWords was used to assess enrichment on miR-145 seed matches in the identified targets. RT-qPCR, Western (immuno-)blot and luciferase assays were used to validate miRNA-target interactions.

Results

MiR-145 overexpression affects the expression of over 350 genes and directly targets more than 50 mRNAs through the 3’UTR or, more commonly, the coding region.

We also demonstrate that miR-145 targets DUSP6, involved in cartilage organization and development, at the translational level. DUSP6 depletion using specific siRNAs lead to MMP13 up-regulation, suggesting that miR-145-mediated DUSP6 depletion contributes to the effect of miR-145 on MMP13 expression.

Conclusion

We demonstrate that miR-145 directly targets several genes in primary chondrocytes including those involved in the expression of the extracellular matrix and inflammation. Thus, we propose miR-145 as an important regulator of chondrocyte function and a new target for cartilage repair.
Prioritizing conservation actions for Pacific salmon in Canada
Authors: Walsh Jessica C. , Connors Katrina , Hertz Eric , Kehoe Laura , Martin Tara G. , Connors Brendan , Bradford Michael J. , Freshwater Cameron , Frid Alejandro , Halverson Jessica , Moore Jonathan W. , Price Michael H.H. , Reynolds John D.
Published: February 2020

Current investment in conservation is insufficient to adequately protect and recover all ecosystems and species. The challenge of allocating limited funds is acute for Pacific salmon (Oncorhynchusspp.) in Canada, which lack a strategic approach to ensure that resources are spent on actions that would cost-effectively recover diminished populations.

We applied the Priority Threat Management framework to prioritize strategies that are most likely to maximize the number of thriving Pacific salmon populations on the Central Coast of British Columbia, Canada. These included 79 genetically, ecologically and spatially distinct population groups called Conservation Units (CUs) for five salmon species. This region has high salmon biodiversity and spans the territories of four First Nations: the Heiltsuk, Nuxalk, Kitasoo/Xai’xais and Wuikinuxv.

Using structured expert elicitation of Indigenous and other experts, we quantified the estimated benefits, costs and feasibility of implementing 10 strategies. Under a business-as-usual scenario (i.e., no additional investments in salmon conservation or management), experts predicted that only one in four CUs would have >50% chance of achieving a thriving status within 20 years. Limiting future industrial development, which was predicted to safeguard CUs from future declines, was identified as the most cost-effective strategy. Investment in three strategies: 1) removal of artificial barriers to fish migration, 2) watershed protection, and 3) stream restoration – at 11.3M CAD per year – was predicted to result in nearly half (34 of 79) of the CUs having a >60% chance of meeting the conservation objective.

If all conservation strategies were implemented, experts estimated a >50% probability of achieving a thriving status for 78 of 79 CUs, at an annual cost of 17.3M CAD. However, even with the implementation of all strategies, most sockeye salmon CUs were unlikely to achieve higher probability targets of reaching the objective.

Policy implications: We illustrate how Priority Threat Management can incorporate the perspectives and expertise of Indigenous peoples and other experts to evaluate and prioritize conservation strategies based on their cost, benefit and feasibility. Timely investment in the strategies outlined in this assessment could help safeguard and recover Pacific salmon in this region of Canada.
DOT1L Methyltransferase Activity Preserves SOX2-Enhancer Accessibility And Prevents Activation of Repressed Genes In Murine Stem Cells
Authors: Ferrari F. , Arrigoni L. , Franz H. , Butenko L. , Trompouki E. , Vogel T. , Manke T.
Published: February 2020

Background

During cellular differentiation, the chromatin landscape changes dynamically and contributes to the activation of cell-type specific transcriptional programs. Disruptor of telomeric silencing 1-like (DOT1L) is a histone methyltransferase that mediates mono-, di- and trimethylation of lysine 79 of histone H3 (H3K79me1, 2, 3). Its enzymatic activity is critical for driving cellular differentiation into cardiomyocytes, chondrocytes and neurons, from embryonic or other type of stem cells in physiological settings. Ectopic localization of DOT1L in MLL-rearranged leukemias is causative for leukemogenesis and relapse. Little is known about the causal relevance of DOT1L methyltransferase activity in the global chromatin context and how its enzymatic function affects transcriptional and global chromatin states. Recent reports conducted in leukemia cell models have suggested that deposition of H3K79me2 may be critical to preserve histone H3K27 acetylation (ac) and enhancer activity, and to sustain expression of highly transcribed genes. If and to what extent DOT1L affects chromatin states and enhancer activity during physiological differentiation processes is currently unknown.

Results

We measure global changes of seven histone modifications during the differentiation process via high-throughput and quantitative ChIP-seq in anin-vitroneuronal differentiation model of mouse embryonic stem cells (mESC). We observe that H3K27ac globally decreases, whereas H3K79me2 globally increases during differentiation, while other modifications remain globally unaltered. Pharmacological inhibition of DOT1L in mESC and mESC-derived neural progenitors results in decreased expression of highly transcribed genes and increased expression of normally repressed genes. Acute DOT1L inhibition primes neural progenitors towards a mature differentiation state. Transcriptional downregulation associates with decreased accessibility of enhancers specifically bound by the master regulator SOX2.

Conclusions

In-vitroneuronal differentiation couples with a genome-wide accumulation of H3K79me2, never described previously in mammalian cells. Acute inhibition of DOT1L is sufficient to initiate a defined transcriptional program, which biases the transcriptome of neural progenitor cells towards neuronal differentiation. H3K79me2 is not generally causative for maintaining transcriptional levels at a genome-wide scale. In contrast, DOT1L inactivation reduces the chromatin accessibility of enhancers bound by SOX2in-vivo, thereby reducing the expression level of a restricted number of genes. Our work establishes that DOT1L activity gates differentiation of progenitors by allowing SOX2-dependent transcription of stemness programs.
Microbial grazers may aid in controlling infections caused by aquatic zoosporic fungi
Authors: Farthing Hazel N. , Jiang Jiamei , Henwood Alexandra J. , Fenton Andy , Garner Trent , Daversa David R. , Fisher Matthew C. , Montagnes David J. S.
Published: February 2020

Free-living eukaryotic microbes may reduce animal diseases. We evaluated the dynamics by which micrograzers (primarily protozoa) apply top-down control on the chytridBatrachochytrium dendrobatidis(Bd) a devastating, panzootic pathogen of amphibians. Although micrograzers consumed zoospores (∼3 µm), the dispersal stage of chytrids, not all species grew monoxenically on zoospores. However, the ubiquitous ciliateTetrahymena pyriformis, which likely co-occurs withBd, grew at near its maximum rate (r= 1.7 d-1). A functional response (ingestion vs. prey abundance) forT. pyriformis, measured using spore-surrogates (microspheres) revealed maximum ingestion (Imax) of 1.63 × 103zoospores d-1, with a half saturation constant (k) of 5.75 × 103zoospores ml-1. Using these growth and grazing data we developed and assessed a population model that incorporated chytrid-host and micrograzer dynamics. Simulations using our data and realistic parameters obtained from the literature suggested that micrograzers could controlBdand potentially prevent chytridiomycosis (defined as 104sporangia host-1). However, simulated inferior micrograzers (0.7 xImaxand 1.5 xk) did not prevent chytridiomycosis, although they ultimately reduced pathogen abundance to below levels resulting in disease. These findings indicate how micrograzer responses can be applied when modelling disease dynamics forBdand other zoosporic fungi.
Signal transfer of visual stimuli to V4 occurs in gamma-rhythmic, pulsed information packages
Authors: Lisitsyn Dmitriy , Grothe Iris , Kreiter Andreas K. , Ernst Udo A.
Published: February 2020

Selective visual attention allows the brain to focus on behaviorally relevant information while ignoring irrelevant signals. As a possible mechanism, routing by synchronization was proposed: neural populations sending attended signals align their gamma-rhythmic activities with receiving populations, such that spikes from the senders arrive at excitability peaks of the receivers, enhancing signal transfer. Conversely, the non-attended signals arrive unaligned to the receiver’s oscillation, reducing signal transfer. Therefore, visual signals should be transferred through periodically pulsed information packages, resulting in a modulation of the stimulus content within the receiver’s activity by its gamma phase and amplitude. To test this prediction, we quantified gamma phase-specific stimulus content within neural activity from area V4 of macaques performing a visual attention task. For the attended stimulus we find enhanced stimulus content reaching its maximum near excitability peaks, with effect magnitude increasing with oscillation amplitude, establishing a functional link between selective processing and gamma activity.
A single-cell RNAseq atlas of the pathogenic stage ofSchistosoma mansoniidentifies a key regulator of blood feeding
Authors: Wendt George , Zhao Lu , Chen Rui , Liu Chenxi , O’Donoghue Anthony J. , Caffrey Conor R. , Collins James J.
Published: February 2020

Schistosomiasis is an ancient and chronic neglected tropical disease that infects over 240 million people and kills over 200,000 of the world’s poorest people every year1, 2. There are no vaccines and because there is only one drug available, the need for new therapeutics is great. The causative agents of this disease are flatworm parasites that dwell inside the host’s circulation, often for decades, where they feed on blood and lay eggs which are primarily responsible for disease pathology. As metazoans comprised of multiple tissue types, understanding the schistosome’s tissues on a molecular level and their functions during what can be decades of successful parasitism could suggest novel therapeutic strategies. Here, we employ single-cell RNAseq to characterize 43,642 cells from the pathogenic (adult) stage of the schistosome lifecycle. From these data, we characterize 68 molecularly distinct cell populations that comprise nearly all tissues described morphologically, including the nervous and reproductive systems. We further uncover a lineage of somatic stem cells responsible for producing and maintaining the parasite’s gut – the primary tissue responsible for digestion of host blood. Finally, we show that a homologue ofhepatocyte nuclear factor 4(hnf4) is expressed in this gut lineage and required for gut maintenance, blood feeding and inducing egg-associated pathologyin vivo. Together, the data highlight the utility of this single-cell RNAseq atlas to understand schistosome biology and identify potential therapeutic interventions.
EslB is required for cell wall biosynthesis and modification inListeria monocytogenes
Authors: Rismondo Jeanine , Schulz Lisa M. , Yacoub Maria , Wadhawan Ashima , Hoppert Michael , Dionne Marc S. , Gründling Angelika
Published: February 2020

Lysozyme is an important component of the innate immune system. It functions by hydrolysing the peptidoglycan (PG) layer of bacteria. The human pathogenListeria monocytogenesis intrinsically lysozyme resistant. The peptidoglycanN-deacetylase PgdA andO-acetyltransferase OatA are two known factors contributing to its lysozyme resistance. Furthermore, it was shown that the absence of components of an ABC transporter, here referred to as EslABC, leads to reduced lysozyme resistance. How its activity is linked to lysozyme resistance is still unknown. To investigate this further, a strain with a deletion ineslB, coding for a membrane component of the ABC transporter, was constructed inL. monocytogenesstrain 10403S. TheeslBmutant showed a 40-fold reduction in the minimal inhibitory concentration to lysozyme. Analysis of the PG structure revealed that theeslBmutant produced PG with reduced levels ofO-acetylation. Using growth and autolysis assays, we show that the absence of EslB manifests in a growth defect in media containing high concentrations of sugars and increased endogenous cell lysis. A thinner PG layer produced by theeslBmutant under these growth conditions might explain these phenotypes. Furthermore, theeslBmutant had a noticeable cell division defect and formed elongated cells. Microscopy analysis revealed that an early cell division protein still localized in theeslBmutant indicating that a downstream process is perturbed. Based on our results, we hypothesize that EslB affects the biosynthesis and modification of the cell wall inL. monocytogenesand is thus important for the maintenance of cell wall integrity.

IMPORTANCE

The ABC transporter EslABC is associated with the intrinsic lysozyme resistance ofListeria monocytogenes. However, the exact role of the transporter in this process and in the physiology ofL. monocytogenesis unknown. Using different assays to characterize aneslBdeletion strain, we found that the absence of EslB not only affects lysozyme resistance, but also endogenous cell lysis, cell wall biosynthesis, cell division and the ability of the bacterium to grow in media containing high concentrations of sugars. Our results indicate that EslB is by a yet unknown mechanism an important determinant for cell wall integrity inL. monocytogenes.
Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback
Authors: Minchington Thomas G , Griffiths-Jones Sam , Papalopulu Nancy
Published: February 2020

Concepts from dynamical systems theory, including multi-stability, oscillations, robustness and stochasticity, are increasingly implicated in the control of gene expression during cell fate decisions, inflammation and stem cell heterogeneity. However, the prevalence of the underlying structures within gene networks which drive these dynamical behaviours, such as direct autoregulation or feedback by microRNAs, is unknown.

We integrate transcription factor binding site (TFBS) and microRNA target data to generate a gene interaction network across 28 human tissues. This network was interrogated to identify network motifs capable of driving dynamical gene expression, in particular oscillations. Autoregulatory motifs were identified in 56% of transcription factors (TFs) investigated, 89% of which were also found in dual feedback motifs with a microRNA. Both the autoregulatory and dual feedback motifs were enriched in the network. TFs that autoregulate were found to be highly conserved between tissues. Dual feedback motifs with microRNAs were also conserved, but less so. Such dual feedback motifs were conserved between tissues, although TFs regulate different combinations of microRNAs in a tissue-dependent manner.

TFs which autoregulate are prevalent among human TFs and have more interactions with microRNAs than non-autoregulatory genes. The enrichment of such motifs within the human transcriptional network indicates that more genes may have interesting expression dynamics than previously thought. These data provide a resource for the identification of TFs which regulate the dynamical properties of human gene expression. These findings support the development of dynamical conceptual frameworks for the study of fundamental biological processes.
Mining Whole Genome Sequence data to efficiently attribute individuals to source populations
Authors: Pérez-Reche Francisco J. , Rotariu Ovidiu , Lopes Bruno S. , Forbes Ken J. , Strachan Norval J.C.
Published: February 2020

Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that effectively mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.
The parasiteSchistocephalus solidussecretes proteins with putative host manipulation functions
Authors: Berger Chloé Suzanne , Laroche Jérôme , Maaroufi Halim , Martin Hélène , Moon Kyung-Mee , Landry Christian R. , Foster Leonard J. , Aubin-Horth Nadia
Published: February 2020

Background

Manipulative parasites are thought to liberate molecules in their external environment acting as manipulation factors with biological functions implicated in their host’s physiological and behavioural alterations. These manipulation factors are part of a complex mixture called the secretome. While the secretomes of various parasites have been described, there is very little data for a putative manipulative parasite. It is necessary to study the molecular interaction between a manipulative parasite and its host to better understand how such alterations evolve.

Methods

Here, we used proteomics to characterize the secretome of a model cestode with a complex life cycle based on trophic transmission. We studiedSchistocephalus solidusduring the life stage in which behavioural changes take place in its obligatory intermediate fish host, the threespine stickleback (Gasterosteus aculeatus). We produced a novel genome sequence and assembly ofS. solidusto improve protein coding gene prediction and annotation for this parasite. We then described the whole worm’s proteome and its secretome during fish host infection using LC-MS/MS.

Results

A total of 2 290 proteins were detected in the proteome ofS. solidus, and 30 additional proteins were detected specifically in the secretome. We found that the secretome contains proteases, proteins with neural and immune functions, as well as proteins involved in cell communication. We detected Receptor-type tyrosine-protein phosphatases, which were reported in other parasitic systems to be manipulation factors. We also detected 12S. solidus-specific proteins in the secretome that may play important roles in host-parasite interactions.

Conclusions

Our results suggest thatS. solidusliberates molecules with putative host manipulation functions in the host and that many of them are species specific.
FAN-C: A Feature-rich Framework for the Analysis and Visualisation of C data
Authors: Kruse Kai , Hug Clemens B. , Vaquerizas Juan M.
Published: February 2020

Chromosome conformation capture data, particularly from high-throughput approaches such as Hi-C and its derivatives, are typically very complex to analyse. Existing analysis tools are often single-purpose, or limited in compatibility to a small number of data formats, frequently making Hi-C analyses tedious and time-consuming. Here, we present FAN-C, an easy-to-use command-line tool and powerful Python API with a broad feature set covering matrix generation, analysis, and visualisation for C-like data (https://github.com/vaquerizaslab/fanc). Due to its comprehensiveness and compatibility with the most prevalent Hi-C storage formats, FAN-C can be used in combination with a large number of existing analysis tools, thus greatly simplifying Hi-C matrix analysis.
Cross-platform genetic discovery of small molecule products of metabolism and application to clinical outcomes
Authors: Lotta Luca A. , Pietzner Maik , Stewart Isobel D. , Wittemans Laura B.L. , Li Chen , Bonelli Roberto , Raffler Johannes , Biggs Emma K. , Oliver-Williams Clare , Auyeung Victoria P.W. , Luan Jian’an , Wheeler Eleanor , Paige Ellie , Surendran Praveen , Michelotti Gregory A. , Scott Robert A. , Burgess Stephen , Zuber Verena , Sanderson Eleanor , Koulman Albert , Imamura Fumiaki , Forouhi Nita G. , Khaw Kay-Tee ,   MacTel Consortium, Griffin Julian L. , Wood Angela M. , Kastenmüller Gabi , Danesh John , Butterworth Adam S. , Gribble Fiona M. , Reimann Frank , Bahlo Melanie , Fauman Eric , Wareham Nicholas J. , Langenberg Claudia
Published: February 2020

Circulating levels of small molecules or metabolites are highly heritable, but the impact of genetic differences in metabolism on human health is not well understood. In this cross-platform, genome-wide meta-analysis of 174 metabolite levels across six cohorts including up to 86,507 participants (70% unpublished data), we identify 499 (362 novel) genome-wide significant associations (p<4.9×10-10) at 144 (94 novel) genomic regions. We show that inheritance of blood metabolite levels in the general population is characterized by pleiotropy, allelic heterogeneity, rare and common variants with large effects, non-linear associations, and enrichment for nonsynonymous variation in transporter and enzyme encoding genes. The majority of identified genes are known to be involved in biochemical processes regulating metabolite levels and to cause monogenic inborn errors of metabolism linked to specific metabolites, such asASNS(rs17345286, MAF=0.27) and asparagine levels. We illustrate the influence of metabolite-associated variants on human health including a shared signal at GLP2R (p.Asp470Asn) associated with higher citrulline levels, body mass index, fasting glucose-dependent insulinotropic peptide and type 2 diabetes risk, and demonstrate beta-arrestin signalling as the underlying mechanism in cellular models. We link genetically-higher serine levels to a 95% reduction in the likelihood of developing macular telangiectasia type 2 [odds ratio (95% confidence interval) per standard deviation higher levels 0.05 (0.03-0.08; p=9.5×10-30)]. We further demonstrate the predictive value of genetic variants identified for serine or glycine levels for this rare and difficult to diagnose degenerative retinal disease [area under the receiver operating characteristic curve: 0.73 (95% confidence interval: 0.70-0.75)], for which low serine availability, through generation of deoxysphingolipids, has recently been shown to be causally relevant. These results show that integration of human genomic variation with circulating small molecule data obtained across different measurement platforms enables efficient discovery of genetic regulators of human metabolism and translation into clinical insights.
High MHC gene copy number maintains diversity despite homozygosity in a Critically Endangered single-island endemic bird, but no evidence of MHC-based mate choice
Authors: Stervander Martin , Dierickx Elisa G. , Thorley Jack , Brooke M. de L. , Westerdahl Helena
Published: February 2020

Abstract

Small population sizes can, over time, put species at risk due to the loss of genetic variation and the deleterious effects of inbreeding. Losing diversity in the major histocompatibility complex (MHC) could be particularly harmful, given its key role in the immune system. Here, we assess MHC class I (MHC-I) diversity and its effects on mate choice and survival in the Critically Endangered Raso larkAlauda razae, a species restricted to the 7 km2islet of Raso (Cape Verde) since ~1460, whose population size has dropped as low as 20 pairs. Exhaustively genotyping 122 individuals, we find no effect of MHC-I genotype/diversity on mate choice or survival. However, we demonstrate that MHC-I diversity has been maintained through extreme bottlenecks by retention of a high number of gene copies (at least 14), aided by co-segregation of multiple haplotypes comprising 2–8 linked MHC-I loci. Within-locus homozygosity is high, contributing to comparably low population-wide diversity. Conversely, each individual had comparably many alleles, 6–16 (average 11), and the large and divergent haplotypes occur at high frequency in the population, resulting in high within-individual MHC-I diversity. This functional immune gene diversity will be of critical importance for this highly threatened species’ adaptive potential.
PxdA interacts with the DipA phosphatase to regulate endosomal hitchhiking of peroxisomes
Authors: Salogiannis John , Christensen Jenna R. , Aguilar-Maldonado Adriana , Shukla Nandini , Reck-Peterson Samara L.
Published: February 2020

In canonical microtubule-based transport, adaptor proteins link cargos to the molecular motors dynein and kinesin. Recently, an alternative mode of transport known as ‘hitchhiking’ was discovered, in which a cargo achieves motility by hitching a ride on an already-motile cargo, rather than attaching to a motor protein. Hitchhiking has been best-studied in two filamentous fungi,Aspergillus nidulansandUstilago maydis. InU. maydis, ribonucleoprotein complexes, peroxisomes, lipid droplets, and endoplasmic reticulum all hitchhike on early endosomes. InA. nidulans, peroxisomes hitchhike using a putative molecular linker, PxdA, that associates with early endosomes. However, whether other organelles use PxdA to hitchhike on early endosomes is unclear, as are the molecular mechanisms that regulate hitchhiking inA. nidulans. Here we find that the proper distribution of lipid droplets, mitochondria and autophagosomes do not require PxdA, suggesting that PxdA is a molecular linker specific to peroxisomes. We also identify two newpxdAalleles, including a point mutation (R2044P) that disrupts PxdA’s ability to associate with early endosomes and reduces peroxisome movement. Finally, we identify a novel regulator of peroxisome hitchhiking, the phosphatase DipA. DipA co-localizes with early endosomes and its early endosome-association relies on PxdA.
Genome-Wide Identification and Characterization of MLO Gene Family in Octoploid Strawberry (Fragaria ×ananassa)
Authors: Tapia Ronald R. , Barbey Christopher R. , Chandra Saket , Folta Kevin M. , Whitaker Vance M. , Lee Seonghee
Published: February 2020

Powdery mildew (PM) caused by Podosphaera aphanis is a major fungal disease in cultivated strawberry. Mildew Resistance Locus O (MLO) is a gene family described for having conserved seven-transmembrane domains. Induced loss-of-function in specific MLO genes can confer durable and broad resistance against PM pathogens. However, the underlying biological role of MLO genes in strawberry is still unknown. In the present study, the genomic structure of MLO genes were characterized in both diploid (Fragaria vesca) and octoploid strawberry (Fragaria ×ananassa), and the potential sources of MLO-mediated susceptibility were identified. Twenty MLO-like sequences were identified in F. vesca, with sixty-eight in F. ×ananassa. Phylogenetic analysis divides strawberry MLO genes into eight different clades, in which three FveMLO and ten FaMLO genes were grouped together with the functionally known MLO susceptibility. Out of ten FaMLO genes, FaMLO17-2 and FaMLO17-3 showed the highest similarity to the known susceptibility MLO proteins. Gene expression analysis of FaMLO genes was conducted using a multi-parental segregating population. Three expression quantitative trait loci (eQTL) were substantially associated with MLO transcript levels in mature fruits, suggesting discrete genetic control of susceptibility. These results are a critical first step in understanding allele function of MLO genes, and are necessary for further genetic studies of PM resistance in cultivated strawberry.
Microtubule Assembly and Pole Coalescence: Early Steps inC. elegansOocyte Meiosis I Spindle Assembly
Authors: Chuang Chien-Hui , Schlientz Aleesa J. , Yang Jie , Bowerman Bruce
Published: February 2020

How oocytes assemble bipolar meiotic spindles in the absence of centrosomes as microtubule organizing centers remains poorly understood. We have used live cell imaging inC. elegansto investigate requirements for the nuclear lamina and for conserved regulators of microtubule dynamics during oocyte meiosis I spindle assembly, assessing these requirements with respect to recently identified spindle assembly steps. We show that the nuclear lamina is required for microtubule bundles to form a cage-like structure that appears shortly after oocyte nuclear envelope breakdown and surrounds the oocyte chromosomes, although bipolar spindles still assembled in its absence. Although two conserved regulators of microtubule nucleation, RAN-1 and γ-tubulin, are not required for bipolar spindle assembly, both contribute to normal levels of spindle-associated microtubules and spindle assembly dynamics. Finally, the XMAP215 ortholog ZYG-9 and the nearly identical minus-end directed kinesins KLP-15/16 are required for proper assembly of the early cage-like structure of microtubule bundles, and for early spindle pole foci to coalesce into a bipolar structure. Our results provide a framework for assigning molecular mechanisms to recently described steps inC. elegansoocyte meiosis I spindle assembly.
Profiling of Human Gut Virome with Oxford Nanopore Technology
Authors: Cao Jiabao , Zhang Yuqing , Dai Min , Xu Jiayue , Chen Liang , Zhang Faming , Zhao Na , Wang Jun
Published: February 2020

Human gut virome play critical roles in maintaining gut microbial composition and functionality, as well as host physiology and immunology. Yet, there are insufficient amount of studies on this topic mainly due to methodological limitations, including enrichment of viruses (phages and host viruses) as well as short read-length from current sequencing technology. Here we developed a full working protocol for analyzing human gut virome using physical enrichment, reverse transcription and random amplification, and eventually the state-of-art single-molecule real-time sequencing (SMRT) platform of Oxford Nanopore Technology (ONT). We demonstrate that sequencing viral DNA directly, or viral DNA/cDNA after amplification using ONT achieves much longer reads and provides more information regarding virome diversity, many of the virome sequences do not have match in current databases. Moreover, direct DNA sequencing of virome provides first insights into the epigenetic modifications on phages, where signals of methylations can be directly detected. Our study demonstrates that progressing sequencing technology and bioinformatic improvements will bring more knowledge into virome composition, diversity and potentially their important functions.

Highlights

Virus-like particles were enriched from human stool samples;

Viral nucleotides were sequenced with Oxford Nanopore Technology with and without amplification;

Gut virome in humans showed highly individualized composition;

Novel sequences and contigs were found to be the majority in the resulted sequences;

Epigenetic modifications were detected directly on virus genomes.
Mesoscopic Liquid Clusters Represent a Distinct Condensate of Mutant p53
Authors: Yang David S. , Saeedi Arash , Davtyan Aram , Fathi Mohsen , Safari Mohammad S. , Klindziuk Alena , Barton Michelle C. , Varadarajan Navin , Kolomeisky Anatoly B. , Vekilov Peter G.
Published: February 2020

The oncogenic properties of mutant p53 have been ascribed to destabilization of the p53 conformation, followed by aggregation into insoluble fibrils. Here we combine immunofluorescent 3D confocal microscopy of breast cancer cells expressing the p53 mutant Arg248Gln (R248Q) with light scattering from solutions of the purified protein and molecular simulations to probe the mechanisms that govern phase behaviors of the mutant across multiple length scales, from cellular to molecular. We establish that p53 R248Q forms mesoscopic protein-rich clusters, an anomalous liquid phase with several unique properties. We demonstrate that the clusters host and facilitate the nucleation of amyloid fibrils. The distinct characteristics of the clusters of R248Q and wild-type p53 and theoretical models indicate that p53 condensation into clusters is driven by the structural destabilization of the core domain and not by interactions of its extensive disordered region. Two-step nucleation of mutant p53 amyloids suggests means to control fibrillization and the associated pathologies through modifying the cluster behaviors. In a broader context, our findings exemplify interactions between distinct protein phases that activate complex physicochemical mechanisms operating in biological systems.
Enhancement of Target Specificity of CRISPR-Cas12a by Using a Chimeric DNA-RNA Guide
Authors: Kim Hanseop , Lee Wi-jae , Kang Seung-Hun , Hur Junho K. , Lee Hyomin , Song WooJeung , Lim Kyung-Seob , Park Young-Ho , Song Bong-Seok , Jin Yeung Bae , Jun Bong-Hyun , Lee Dong-Seok , Kim Sun-Uk , Lee Seung Hwan
Published: February 2020

The CRISPR-Cas9 system is widely used for target-specific genome engineering. Cpf1 is one of the CRISPR effectors that controls target genes by recognizing thymine-rich protospacer adjacent motif (PAM) sequences. Cpf1 has a higher sensitivity to mismatches in the guide RNA than does Cas9; therefore, off-target sequence recognition and cleavage are lower. However, it tolerates mismatches in regions distant from the PAM sequence (TTTN or TTN) in the protospacer, and off-target cleavage issues may become more problematic when Cpf1 activity is improved for therapeutic purposes. In our study, we investigated off-target cleavage by Cpf1 and modified the Cpf1 (cr)RNA to address the off-target cleavage issue. We developed a CRISPR-Cpf1 that can induce mutations in target DNA sequences in a highly specific and effective manner by partially substituting the (cr)RNA with DNA to change the energy potential of base pairing to the target DNA. A model to explain how chimeric (cr)RNA guided CRISPR-Cpf1 and SpCas9 nickase effectively work in the intracellular genome is suggested. In our results, CRISPR-Cpf1 induces less off-target mutations at the cell level, when chimeric DNA-RNA guide was used for genome editing. This study has a potential for therapeutic applications in incurable diseases caused by genetic mutation.
Electrophysiology prediction of single neurons based on their morphology
Authors: Michiels Mario
Published: February 2020

Electrophysiology data acquisition of single neurons represents a key factor for the understanding of neuronal dynamics. However, the traditional method to acquire this data is through patch-clamp technology, which presents serious scalability flaws due to its slowness and complexity to record at fine-grained spatial precision (dendrites and axon).

In silico biophysical models are therefore created for simulating hundreds of experiments that would be impractical to recreate in vitro. The optimal way to create these models is based on the knowledge of the morphological and electrical features for each neuron. Since large-scale data acquisition is often unfeasible for electrical data, previous expert knowledge can be used but it must have an acceptable degree of similarity with the type of neurons that we are trying to model.

Here, we present a data-driven machine learning approach to predict the electrophysiological features of single neurons in case of only having their morphology available. To solve this multi-output regression problem, we use an artificial neural network that has the particularity of providing a probability distribution for every output feature, to incorporate uncertainty. Input data to train the model is obtained from from the Allen Cell Types database. The electrical properties can depend on the morphology, whose acquisition technology is highly automated and scalable so there exist large data sets of them. We also provide integrations with the BluePyOpt library to create a biophysical model using the original morphology and the predicted electrical features. Finally, we connect the resulting biophysical model with the Geppetto UI software to run all the simulations in a sophisticated user interface.
N-[(E)-Quinolin-2-ylmethylidene]-1,2,4-triazol-4-amine hemihydrate
Authors: Shahri Nurulizzatul Ningsheh M. , Omar Ali Nur Halilatul Sadiqin , Sheikh Abdul Hamid Malai Haniti , Mirza Aminul Huq , Usman Anwar , Hoq Md Rejaul , Karim Mohammad R.
Published: February 2020

The title hemihydrate, C12H9N5·0.5H2O, was isolated from the condensation reaction of quinoline-2-carbaldehyde with 4-amino-4H-1,2,4-triazole. The Schiff base molecule adopts an E configuration about the C=N bond and is approximately planar, with a dihedral angle between the quinoline ring system and the 1,2,4-triazole ring of 12.2 (1)°. In the crystal, one water molecule bridges two Schiff base molecules via O—H...N hydrogen bonds. The Schiff base molecules are interconnected by π–π stacking interactions [centroid-centroid distances of 3.7486 (7) and 3.9003 (7) Å] into columns along [1\overline{1}0].
Job rotation scheduling in the Seru system: shake enforced invasive weed optimization approach
Authors: Ayough Ashkan , Hosseinzadeh Mohammad , Motameni Alireza
Published: February 2020

Purpose

Line–cell conversion and rotation of operators between cells are common in lean production systems. Thus, the purpose of this study is to provide an integrated look at these two practices through integrating job rotation scheduling and line-cell conversion problems, as well as investigating the effect of rotation frequency on flow time of a Seru system.

Design/methodology/approach

First, a nonlinear integer programming model of job rotation scheduling problem and line–cell conversion problem (Seru-JRSP) was presented. Then, because Seru-JRSP is NP-hard, an efficient and effective invasive weed optimization (IWO) algorithm was developed. Exploration process of IWO was enhanced by enforcing two shake mechanisms.

Findings

Computations of various sample problems showed shorter flow time and less number of assigned operators in a Seru system scheduled through job rotation. Also, nonlinear behavior of flow time versus number of rotation periods was shown. It was demonstrated that, setting number of rotation frequency to one in line with the literature leads to inferior flow time. In addition, ability of developed algorithm to generate clusters of equivalent solutions in terms of flow time was shown.

Originality/value

In this research, integration of job rotation scheduling and line–cell conversion problems was introduced, considering lack of an integrated look at these two practices in the literature. In addition, a new improved IWO equipped with shake enforcement was introduced.