bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Evolution of the Sex Peptide Network in Drosophila
Authors: McGeary Meaghan K. , Findlay Geoffrey D.
Published: November 2019

Successful reproduction depends on interactions between numerous proteins beyond those involved directly in gamete fusion. While such reproductive proteins evolve in response to sexual selection pressures, how networks of interacting proteins arise and evolve as reproductive phenotypes change remains an open question. Here, we investigated the molecular evolution of the “sex peptide network” of Drosophila melanogaster, a functionally well-characterized reproductive protein network. In this species, the peptide hormone sex peptide (SP) and its interacting proteins cause major changes in female physiology and behavior after mating. In contrast, females of more distantly related Drosophila species do not respond to SP. In spite of these phenotypic differences, we detected orthologs of all network proteins across 22 diverse Drosophila species and found evidence that most orthologs likely function in reproduction throughout the genus. Within SP-responsive species, we detected the recurrent, adaptive evolution of several network proteins, consistent with sexual selection acting to continually refine network function. We also found some evidence for adaptive evolution of several proteins along two specific phylogenetic lineages that correspond with increased expression of the SP receptor in female reproductive tracts or increased sperm length, respectively. Finally, we used gene expression profiling to examine the likely degree of functional conservation of the paralogs of an SP network protein that arose via gene duplication. Our results suggest a dynamic history for the SP network in which network members arose before the onset of robust SP-mediated responses and then were shaped by both purifying and positive selection.
Diachronic monitoring of snow leopards at Sarychat-Ertash State Reserve (Kyrgyzstan) through scat genotyping: a pilot study
Authors: Rode Julie , Pelletier Agnès , Fumey Julien , Rode Stéphane , Cabanat Anne-Lise , Ouvrard Anne , Chaix Bastien , White Bradley , Harnden Matthew , Xuan Nguyen Thi , Vereshagin Alexander , Casane Didier
Published: November 2019

Snow leopards (Panthera uncia) are a keystone species of Central Asia’s high mountain ecosystem. The species is listed as vulnerable and is elusive, preventing accurate population assessments that could inform conservation actions. Non-invasive genetic monitoring conducted by citizen scientists offers avenues to provide key data on this species that would otherwise be inaccessible. From 2011 to 2015, OSI-Panthera citizen science expeditions tracked signs of presence of snow leopards along transects in the main valleys and crests of the Sarychat-Ertash State Reserve (Kyrgyzstan). Scat samples were genotyped at seven autosomal microsatellite loci and at a X/Y locus for sex identification, which allowed estimating a minimum of 11 individuals present in the reserve from 2011 to 2015. The genetic recapture of 7 of these individuals enabled diachronic monitoring, providing indications of individuals’ movements throughout the reserve. We found putative family relationships between several individuals. Our results demonstrate the potential of this citizen science program to get a precise description of a snow leopard population through time.
A deep learning-based model of normal histology
Authors: Sing Tobias , Hoefling Holger , Hossain Imtiaz , Boisclair Julie , Doelemeyer Arno , Flandre Thierry , Piaia Alessandro , Romanet Vincent , Santarossa Gianluca , Saravanan Chandrassegar , Sutter Esther , Turner Oliver , Wuersch Kuno , Moulin Pierre
Published: November 2019

Deep learning models have been applied on various tissues in order to recognize malignancies. However, these models focus on relatively narrow tissue context or well-defined pathologies. Here, instead of focusing on pathologies, we introduce models characterizing the diversity of normal tissues. We obtained 1,690 slides with rat tissue samples from the control groups of six preclinical toxicology studies, on which tissue regions were outlined and annotated by pathologists into 46 different tissue classes. From these annotated regions, we sampled small patches of 224 × 224 pixels at six different levels of magnification. Using four studies as training set and two studies as test set, we trained VGG-16, ResNet-50, and Inception-v3 networks separately at each of these magnification levels. Among these models, Inception-v3 consistently outperformed the other networks and attained accuracies up to 83.4% (top-3 accuracy: 96.3%). Further analysis showed that most tissue confusions occurred within clusters of histologically similar tissues. Investigation of the embedding layer using the UMAP method revealed not only pronounced clusters corresponding to the individual tissues, but also subclusters corresponding to histologically meaningful structures that had neither been annotated nor trained for. This suggests that the histological representation learned by the normal histology network could also be used to flag abnormal tissue as outliers in the embedding space without a need to explicitly train for specific types of abnormalities. Finally, we found that models trained on rat tissues can be used on non-human primate and minipig tissues with minimal retraining.

Author contribution

T.S. and H.H. contributed equally to this work.

Significance statement

Like many other scientific disciplines, histopathology has been profoundly impacted by recent advances in machine learning with deep neural networks. In this field, most deep learning models reported in the literature are trained on pathologies in specific tissues/contexts. Here, we aim to establish a model of normal tissues as a foundation for future models of histopathology. We build models that are specific to histopathology images and we show that their embeddings are better feature vectors for describing the underlying images than those of off-the shelf CNN models. Therefore, our models could be useful for transfer learning to improve the accuracy of other histopathology models.
Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury
Authors: Renthal William , Tochitsky Ivan , Yang Lite , Cheng Yung-Chih , Li Emmy , Kawaguchi Riki , Geschwind Daniel H. , Woolf Clifford J.
Published: November 2019

Primary somatosensory neurons are specialized to transmit specific types of sensory information through differences in cell size, myelination, and the expression of distinct receptors and ion channels, which together define their transcriptional and functional identity. By transcriptionally profiling sensory ganglia at single-cell resolution, we find that different somatosensory neuronal subtypes undergo a remarkably consistent and dramatic transcriptional response to peripheral nerve injury that both promotes axonal regeneration and suppresses cell identity. Successful axonal regeneration leads to a restoration of neuronal cell identity and the deactivation of the growth program. This injury-induced transcriptional reprogramming requires Atf3, a transcription factor which is induced rapidly after injury and is necessary for axonal regeneration and functional recovery. While Atf3 and other injury-induced transcription factors are known for their role in reprogramming cell fate, their function in mature neurons is likely to facilitate major adaptive changes in cell function in response to damaging environmental stimuli.
RsQTL: correlation of expressed SNVs with splicing using RNA-sequencing data
Authors: Sein Justin , Spurr Liam F. , Bousounis Pavlos , Prashant N M , Liu Hongyu , Alomran Nawaf , Bernot Jimmy , Ibeawuchi Helen , Reece-Stremtan Dacian , Horvath Anelia
Published: November 2019

RsQTL is a tool for identification of splicing quantitative trait loci (sQTLs) from RNA-sequencing (RNA-seq) data by correlating the variant allele fraction at expressed SNV loci in the transcriptome (VAFRNA) with the proportion of molecules spanning local exon-exon junctions at loci with differential intron excision (percent spliced in, PSI). We exemplify the method on sets of RNA-seq data from human tissues obtained though the Genotype-Tissue Expression Project (GTEx). RsQTL does not require matched DNA and can identify a subset of expressed sQTL loci. Due to the dynamic nature of VAFRNA, RsQTL is applicable for the assessment of conditional and dynamic variation-splicing relationships.

Availability and implementation

https://github.com/HorvathLab/RsQTL.

Contact

horvatha@gwu.edu or jsein@gwmail.gwu.edu

Supplementary Information

RsQTL_Supplementary_Data.zip
Effective downregulation of BCR-ABL tumorigenicity by RNA targeted CRISPR-Cas13a
Authors: Singh Aditya , Bhatia Prateek
Published: November 2019

Aim

To induce BCR-ABL gene silencing using CRISPR Cas13a.

Background

CML is a clonal myeloproliferative disorder of pluripotent stem cells driven by a reciprocal translocation between chromosome 9 and 22, forming a BCR-ABL fusion gene. Tyrosinekinase inhibitor drugs like imatinib are the mainstay of treatment and cases resistant to these drugs have a poor prognosis in the absence of a compatible stem-cell donor. However, with rapid advancements in gene-editing technologies, most studies are now focusing on developing a translational model targeting single-gene disorders with a prospective permanent cure.

Objective

To explore the potential application of the RNA targeting CRISPR-Cas13a system for effective knockdown of BCR-ABL fusion transcript in a CML cell line, K562.

Method

CRISPR Cas13a crRNA was designed specific to the chimeric BCR-ABL gene and the system was transfected as a two-plasmid system into a CML cell line, K562. The effects were enumerated by evaluating the expression levels of downstream genes dependent on the expression of the BCR-ABL gene. Also, next-generation sequencing was used to ascertain the effects of CRISPR on the gene.

Results

The CRISPR system was successfully able to lower the expression of downstream genes (pCRKL and pCRK) dependent on the activated BCR-ABL kinase signal by up-to 4.3 folds. The viability of the CRISPR treated cells were also significantly lowered by 373.83-fold (p-value= 0.000891196). The time-dependent kinetics also highlighted the significant in-vitro suppressive activity to last up to 8 weeks (p-value: 0.025). As per the cDNA sequencing data from Oxford MinION next-generation sequencer, the CRISPR treated cells show 62.37% suspected cleaved reads.

Conclusion

These preliminary results highlight an excellent potential application of RNA targeting CRISPRs in Haematological neoplasms like CML and should pave way for further research in this direction.
Manipulating synthetic optogenetic odors reveals the coding logic of olfactory perception
Authors: Chong Edmund , Moroni Monica , Wilson Christopher , Shoham Shy , Panzeri Stefano , Rinberg Dmitry
Published: November 2019

How does neural activity generate perception? The spatial identities and temporal latencies of activated units correlate with external sensory features, but finding the principal activity subspace that is consequential for perception, remains challenging. We trained mice to recognize synthetic odors constructed from parametrically-defined patterns of optogenetic activation, then measured perceptual changes during extensive and controlled perturbations across spatio-temporal dimensions. We modelled recognition as the matching of patterns to learned templates, finding that perceptually-meaningful templates are sequences of spatially-identified units, ordered by latencies relative to each other (with minimal effects of sniff). Within templates, individual units contribute additively, with larger contributions from earlier-activated units. Our synthetic approach reveals the fundamental logic of the olfactory code, and provides a general framework for testing links between sensory activity and perception.
Rapid Recalibration of Peri-Personal Space; Psychophysical, Electrophysiological, and Neural Network Modeling Evidence
Authors: Noel Jean-Paul , Bertoni Tommaso , Terrebonne Emily , Pellencin Elisa , Herbelin Bruno , Cascio Carissa , Blanke Olaf , Magosso Elisa , Wallace Mark T. , Serino Andrea
Published: November 2019

Interactions between individuals and the environment are mediated by the body and occur within the peri-personal space (PPS) – the space surrounding the body. The multisensory encoding of this space plastically adapts to different bodily constraints and stimuli features. However, these remapping effects have only been demonstrated on the time-scale of days, hours, or minutes. Yet, if PPS mediates human-environment interactions in an adaptive manner, its representation should be altered by sensory history on trial-to-trial timescale. Here we test this idea first via a visuo-tactile reaction time paradigm in augmented reality where participants are asked to respond as fast as possible to touch, as visual object approach them. Results demonstrate that reaction times to touch are facilitated as a function of visual proximity, and the sigmoidal function describing this facilitation shifts closer to the body if the immediately precedent trial had indexed a smaller visuo-tactile disparity (i.e., positive serial dependency). Next, we derive the electroencephalographic correlates of PPS and demonstrate that this measure is equally shaped by recent sensory history. Finally, we demonstrate that a validated neural network model of PPS is able to account for the present results via a simple Hebbian plasticity rule. The present findings suggest that PPS encoding remaps on a very rapid time-scale and is sensitive to recent sensory history.
ZODIAC: database-independent molecular formula annotation using Gibbs sampling reveals unknown small molecules
Authors: Ludwig Marcus , Nothias Louis-Félix , Dührkop Kai , Koester Irina , Fleischauer Markus , Hoffmann Martin A. , Petras Daniel , Vargas Fernando , Morsy Mustafa , Aluwihare Lihini , Dorrestein Pieter C. , Böcker Sebastian
Published: November 2019

1

The confident high-throughput identification of small molecules remains one of the most challenging tasks in mass spectrometry-based metabolomics. SIRIUS has become a powerful tool for the interpretation of tandem mass spectra, and shows outstanding performance for identifying the molecular formula of a query compound, being the first step of structure identification. Nevertheless, the identification of both molecular formulas for large compounds above 500 Daltons and novelmolecular formulasremains highly challenging. Here, we present ZODIAC, a network-based algorithm for thede novoestimation of molecular formulas. ZODIAC reranks SIRIUS’ molecular formula candidates, combining fragmentation tree computation with Bayesian statistics using Gibbs sampling. Through careful algorithm engineering, ZODIAC’s Gibbs sampling is very swift in practice. ZODIAC decreases incorrect annotations 16.2-fold on a challenging plant extract dataset with most compounds above 700 Dalton; we then show improvements on four additional, diverse datasets. Our analysis led to the discovery of compounds with novel molecular formulas such as C24H47BrNO8P which, as of today, is not present in any publicly available molecular structure databases.
Functional Connectivity Evoked by Orofacial Tactile Perception of Velocity
Authors: Wang Yingying , Sibaii Fatima , Custead Rebecca , Oh Hyuntaek , Barlow Steven M.
Published: November 2019

The cortical representation of orofacial pneumotactile stimulation involves a complex network, which is still unknown. This study aims to identify the characteristics of functional connectivity (FC) elicited by different saltatory velocities over the perioral and buccal surface of the lower face using functional magnetic resonance imaging (fMRI) in twenty neurotypical adults. Our results showed 25 cm/s evoked more functional coupling in the right hemisphere, suggesting 25 cm/s might be optimal velocity if bilateral brain damages occur. The decreased FC between the right secondary somatosensory cortex and right posterior parietal cortex for 5 cm/s versus All-on showed that the relatively slow velocity evoked less coupling in the ipsilateral hemisphere, which suggesting functional coupling in the contralateral hemisphere is in charge of orofacial tactile perception of velocity. The increased FC between the right thalamus and bilateral secondary somatosensory cortex for 65 cm/s versus All-on indicated that the neural encoding of relatively fast tactile velocity is more coupling between the right thalamus and bilateral secondary somatosensory cortex. Our results have shown different characteristics of FC for each seed at various velocity contrasts (5 > 25 cm/s, 5 > 65 cm/s, and 25 > 65 cm/s), suggesting the neuronal networks encoding the orofacial tactile perception of velocity. The difference of functional connectivity among three velocities may indicate the optimal stimulation setting for better therapeutic effects on stroke recovery.
Functional connectome analyses reveal a highly optimized human olfactory network
Authors: Arnold T. Campbell , You Yuqi , Ding Mingzhou , Zuo Xi-Nian , de Araujo Ivan , Li Wen
Published: November 2019

The olfactory system is uniquely heterogeneous, performing multifaceted functions (beyond basic sensory processing) across diverse, widely distributed neural substrates. While knowledge of human olfaction continues to grow, it remains unclear how the olfactory network is organized to serve this unique set of functions. Leveraging a large and high-quality resting-state functional magnetic resonance imaging (rs-fMRI) dataset of nearly 900 participants from the Human Connectome Project (HCP), we identified a human olfactory network encompassing cortical and subcortical regions across the temporal and frontal lobes. Highlighting its reliability and generalizability, the connectivity matrix of this olfactory network mapped closely onto that extracted from an independent rs-fMRI dataset. Graph theoretical analysis further explicated the organizational principles of the network. The olfactory network exhibits a functionally advantageous modular composition of three (i.e., thesensory,limbic, andfrontal) subnetworks and demonstrates strong small-world properties, high in both global integration and local segregation (i.e., circuit specialization). This network organization thus ensures the segregation of local circuits, which are nonetheless integrated via connecting hubs (i.e., amygdala and anterior insula), thereby enabling the specialized, yet integrative, functions of olfaction. In particular, the degree of local segregation positively predicted olfactory discrimination performance in the independent sample. In sum, an olfactory functional network has been identified through the large HCP dataset, affording a representative template of the human olfactory functional neuroanatomy. Importantly, the topological analysis of the olfactory network provides network-level insights into the remarkable functional specialization and spatial segregation of the olfactory system.

Significance Statement

Olfaction is an intriguing multifunctional system, playing key roles in regulating emotions, autonomic tone, and feeding, beyond basic sensory perception. However, it is unclear how the neuroanatomy of olfaction is organized in humans to subserve these functions. Functional connectivity analysis of the HCP dataset combined with graph theoretical analysis revealed an optimized large-scale network consisting of three subnetworks—the sensory, limbic, and frontal subnetworks. Distributed across frontal and temporal lobes in well segregated fashion, these olfactory structures are also highly integrated, linked through hub nodes of the amygdala and anterior insula. Our independent dataset replicated the HCP-derived olfactory network and, importantly, highlighted a direct association between the degree of network segregation and olfactory perception.
hTFtarget: a comprehensive database for regulations of human transcription factors and their targets
Authors: Zhang Qiong
Published: November 2019

Transcription factors (TFs) as key regulators play crucial roles in biological processes. The identification of TF-target regulatory relationships is a key step for revealing functions of TFs and their regulations on gene expression. The accumulated data of Chromatin immunoprecipitation sequencing (ChIP-Seq) provides great opportunities to discover the TF-target regulations across different conditions. In this study, we constructed a database named hTFtarget, which integrated huge human TF target resources (7,190 ChIP-Seq samples of 659 TFs and high confident TF binding sites of 699 TFs) and epigenetic modification information to predict accurate TF-target regulations. hTFtarget offers the following functions for users to explore TF-target regulations: 1) Browse or search general targets of a query TF across datasets; 2) Browse TF-target regulations for a query TF in a specific dataset or tissue; 3) Search potential TFs for a given target gene or ncRNA; 4) Investigate co-association between TFs in cell lines; 5) Explore potential co-regulations for given target genes or TFs; 6) Predict candidate TFBSs on given DNA sequences; 7) View ChIP-Seq peaks for different TFs and conditions in genome browser. hTFtarget provides a comprehensive, reliable and user-friendly resource for exploring human TF-target regulations, which will be very useful for a wide range of users in the TF and gene expression regulation community. hTFtarget is available at http://bioinfo.life.hust.edu.cn/hTFtarget.
Effects of technical noise on bulk RNA-seq differential gene expression inference
Authors: Sheerin Dylan , O’Connor Daniel , Pollard Andrew J , Mohorianu Irina
Published: November 2019

Motivation

Inconsistent, analytical noise introduced either by the sequencing technology or by the choice of read-processing tools can bias bulk RNA-seq analyses by shifting the focus to the variation in expression of low-abundance transcripts; as a consequence these highly-variable genes are often included the differential expression (DE) call and impact the interpretation of results.

Results

To illustrate the effects of “noise”, we present simulated datasets following closely the characteristics of aH.sapiensand aM.musculusdataset, respectively, highlighting the extent of technical-noise in both a high inter-individual variability (H. sapiens) and reduced variability (M. Musculus) setup. The sequencing-induced noise is assessed using correlations of distributions of expression across transcripts; analytical noise is evaluated through side-by-side comparisons of several standard choices. The proportion of genes in the noise-range differs for each tool combi-nation. Data-driven, sample-specific noise-thresholds were applied to reduce the impact of low-level variation. Noise-adjustment reduced the number of significantly DE genes and gave rise to convergent calls across tool combinations.

Availability

The code for determining the sequence-derived noise is available for download from:https://github.com/yry/noiseAnalysis/tree/master/noiseDetection_mRNA; the code for running the analysis is available for download from:https://github.com/sheerind/noise_detection.
Muscle synergies are associated with intermuscular coherence in an isometric upper limb task
Authors: Ortega-Auriol Pablo , Byblow Winston D , McMorland Angus JC
Published: November 2019

To elucidate the underlying physiological mechanism of muscle synergies, we investigated the functional corticomuscular and intermuscular binding during an isometric upper limb task in 14 healthy participants. Cortical activity was recorded using 32-channel encephalography (EEG) and muscle activity using 16-channel electromyography (EMG). Using non-negative matrix factorization (NMF), we calculated muscle synergies from two different tasks. A preliminary multidirectional task was used to identify synergy preferred directions. A subsequent coherence task, consisting of generating forces isometrically in the synergy PDs, was used to assess the functional connectivity properties of synergies. Functional connectivity was estimated using corticomuscular coherence (CMC) and intermuscular coherence (IMC). Overall, we were able to extract four different synergies from the multidirectional task. A significant alpha band IMC was present consistently in all extracted synergies. Moreover, alpha band IMC was higher between muscles with higher weights within a synergy. In contrast, no significant CMC was found between the motor cortex area and synergy muscles. In addition, there is a relationship between a synergy muscle weight and the level of IMC. Our findings suggest the existence of a consistent shared input between muscles of each synergy. Finally, the existence of a shared input onto synergistic muscles within a synergy supports the idea of neurally-derived muscle synergies that build human movement.
Beyond taxonomic identification: integration of ecological responses to a soil bacterial 16S rRNA gene database
Authors: Jones Briony A. , Goodall Tim , George Paul B.L. , Gweon Soon , Puissant Jeremy , Read Daniel , Emmett Bridget A. , Robinson David A. , Jones Davey L. , Griffiths Robert I.
Published: November 2019

High-throughput sequencing 16S rRNA gene surveys have enabled new insights into the diversity of soil bacteria, and furthered understanding of the ecological drivers of abundances across landscapes. However, current analytical approaches are of limited use in formalising syntheses of the ecological attributes of taxa discovered, because derived taxonomic units are typically unique to individual studies and sequence identification databases only characterise taxonomy. To address this, we used sequences obtained from a large nationwide soil survey (GB Countryside Survey, henceforth “CS”) to create a comprehensive soil specific 16S reference database, with coupled ecological information derived from the survey metadata. Specifically, we modelled taxon responses to soil pH at the OTU level using hierarchical logistic regression (HOF) models, to provide information on putative landscape scale pH-abundance responses. We identify that most of the soil OTUs examined exhibit predictable abundance responses across soil pH gradients, though with the exception of known acidophilic lineages, the pH optima of OTU relative abundance was variable and could not be generalised by broad taxonomy. This highlights the need for tools and databases to predict ecological traits at finer taxonomic resolution. We further demonstrate the utility of the database by testing against geographically dispersed query 16S datasets; evaluating efficacy by quantifying matches, and accuracy in predicting pH responses of query sequences from a separate large soil survey. We found that the CS database provided good coverage of dominant taxa; and that the taxa indicating soil pH in a query dataset corresponded with the pH classifications of top matches in the CS database. Furthermore we were able to predict query dataset community structure, using predicted abundances of dominant taxa based on query soil pH data and the HOF models of matched CS database taxa. The database with associated HOF model outputs is released as an online portal for querying single sequences of interest (https://shiny-apps.ceh.ac.uk/ID-TaxER), and as a DADA2 database for use in bioinformatics pipelines. The further development of advanced informatics infrastructures incorporating modelled ecological attributes along with new functional genomic information will likely facilitate large scale exploration and prediction of soil microbial functional biodiversity under current and future environmental change scenarios.
A precision medicine approach uncovers a unique signature of neutrophils in patients with brushite kidney stones
Authors: Makki Mohammad Shahidul , Winfree Seth , Lingeman James E. , Witzmann Frank , Worcester Elaine M. , Krambeck Amy , Coe Fred , Evan Andrew P. , Bledsoe Sharon , Bergsland Kristin , Khochare Suraj , Barwinska Daria , Williams James C. , El-Achkar Tarek M.
Published: November 2019

Background

We have previously found that papillary histopathology differs greatly between calcium oxalate and brushite stone formers (SF); the latter have much more papillary mineral deposition, tubular cell injury and tissue fibrosis.

Methods

In this study, we applied unbiased orthogonal “omics” approaches on biopsied renal papillae and extracted stones from patients with brushite or calcium oxalate (CaOx) stones. Our goal was to discover stone type-specific molecular signatures to advance our understanding of the underlying pathogenesis.

Results

Brushite SF did not differ from CaOx SF with respect to metabolic risk factors for stones, but did exhibit increased tubule plugging in their papillae. Brushite SF had upregulation of inflammatory pathways in papillary tissue, and increased neutrophil markers in stone matrix compared to those with CaOx stones. Large-scale 3D tissue cytometry on renal papillary biopsies showed an increase in the number and density of neutrophils in the papillae of brushite vs. CaOx patients, thereby linking the observed inflammatory signatures to the neutrophils in the tissue. To explain how neutrophil proteins appear in the stone matrix, we measured neutrophil extracellular trap (NET) formation, NETosis, and found it significantly increased in the papillae of brushite compared to CaOx patients.

Conclusions

We show that increased neutrophil infiltration and NETosis is an unrecognized factor that differentiates brushite and CaOx SF, and may explain the markedly increased scarring and inflammation seen in the papillae of brushite patients. Given the increasing prevalence of brushite stones, the role of neutrophil activation in brushite stone formation requires further study.
A scalable random walk with restart on heterogeneous networks with Apache Spark for ranking disease-causing genes using type-2 fuzzy data fusion
Authors: Joodaki Mehdi , Ghadiri Nasser , Maleki Zeinab , Shahreza Maryam Lotfi
Published: November 2019

Prediction and discovery of disease-causing genes are among the main missions of biology and medicine. In recent years, researchers have developed several methods based on gene/protein networks for the detection of causative genes. However, because of the presence of false positives in these networks, the results of these methods often lack accuracy and reliability. This problem can be solved by using multiple genomic sources to reduce noise in data. However, network integration can also affect the quality of the integrated network. In this paper, we present a method named RWRHN (random walk with restart on a heterogeneous network) with fuzzy fusion or RWRHN-FF. In this method, first, four gene-gene similarity networks are constructed based on different genomic sources and then integrated using the type-II fuzzy voter scheme. The resulting gene-gene network is then linked to a disease-disease similarity network, which itself is constructed by the integration of four sources, through a two-part disease-gene network. The product of this process is a reliable heterogeneous network, which is analyzed by the RWRHN algorithm. The results of the analysis with the leave-one-out cross-validation method show that RWRHN-FF outperforms both RWRHN and RWRH. The proposed method is used to predict new genes for prostate, breast, gastric and colon cancers. To reduce the algorithm run time, Apache Spark is used as a platform for parallel execution of the RWRHN algorithm on heterogeneous networks. In the test conducted on heterogeneous networks of different sizes, this solution results in faster convergence than other non-distributed modes of implementations.
A complete time-calibrated multi-gene phylogeny of the European butterflies
Authors: Wiemers Martin , Chazot Nicolas , Wheat Christopher W. , Schweiger Oliver , Wahlberg Niklas
Published: November 2019

With the aim of supporting ecological analyses in butterflies, the third most species-rich superfamily of Lepidoptera, this paper presents the first time-calibrated phylogeny of all 496 extant butterfly species in Europe, including 18 very localized endemics for which no public DNA sequences had been available previously. It is based on a concatenated alignment of the mitochondrial gene COI and up to 11 nuclear gene fragments, using Bayesian inference of phylogeny. To avoid analytical biases that could result from our region-focus sampling, our European tree was grafted upon a global genuslevel backbone butterfly phylogeny for analyses. In addition to a consensus tree, we provide the posterior distribution of trees and the fully-concatenated alignment for future analyses.
A representational asymmetry for composition in the human left-middle temporal gyrus
Authors: Frankland Steven M. , Greene Joshua D.
Published: November 2019

Natural language is notable amongst representational systems for the rich internal structure of phrase and sentence-level expressions. Here, we provide evidence from two fMRI studies that a region of the left Middle Temporal Gyrus (MTG) exhibits a surprising representational asymmetry: verbs and patients (to whom was it done?) are bound to form a representation, but verbs and agents (who did it?) are not. Within MTG, BOLD signal to novel combinations of familiar components can be modeled by combining learned verb-patient conjunctive representations with more general agent representations, but not by the converse (verb-agent + patient). This asymmetry is not predicted by an abstract propositional representation of the event (e.g., chased(dog,cat), nor by a theory which derives conjunctions from the experienced statistical co-occurences between verbs and nouns. However, this asymmetry is predicted by various linguistic accounts of the internal structure of event descriptions (e.g., Williams, 1981; Marantz,1984; Grimshaw, 1990; Kratzer, 1996). These results provide evidence for the time-varying instantiation of re-usable representations of structure in MTG, consistent with the principle of compositionality, as well as accounts of verb-argument structure.
Enhancers predominantly regulate gene expression in vivo via transcription initiation
Authors: Larke Martin S. C. , Nojima Takayuki , Telenius Jelena , Sharpe Jacqueline A. , Sloane-Stanley Jacqueline A. , Butler Sue , Beagrie Robert A. , Downes Damien J. , Schwessinger Ron , Marieke Oudelaar A. , Truch Julia , Crompton Bryony , Bender M. A. , Proudfoot Nicholas J. , Higgs Douglas R. , Hughes Jim R.
Published: November 2019

Gene transcription occurs via a cycle of linked events including initiation, promoter proximal pausing and elongation of RNA polymerase II (Pol II). A key question is how do transcriptional enhancers influence these events to control gene expression? Here we have used a new approach to quantify transcriptional initiation and pausing in vivo, while simultaneously identifying transcription start sites (TSSs) and pause-sites (TPSs) from single RNA molecules. When analyzed in parallel with nascent RNA-seq, these data show that differential gene expression is achieved predominantly via changes in transcription initiation rather than Pol II pausing. Using genetically engineered mouse models deleted for specific enhancers we show that these elements control gene expression via Pol II recruitment and/or initiation rather than via promoter proximal pause release. Together, our data show that enhancers, in general, control gene expression predominantly by Pol II recruitment and initiation rather than via pausing.
ESI mutagenesis: A one-step method for introducing point mutations into bacterial artificial chromosome transgenes
Authors: Rondelet Arnaud , Pozniakovsky Andrei , Leuschner Marit , Poser Ina , Ssykor Andrea , Berlitz Julian , Schmidt Nadine , Hyman Anthony A , Bird Alexander W
Published: November 2019

Bacterial artificial chromosome (BAC)-based transgenes have emerged as a powerful tool for controlled and conditional interrogation of protein function in higher eukaryotes. While homologous recombination-based recombineering methods have streamlined the efficient integration of protein tags onto BAC transgenes, generating precise point mutations has remained less efficient and time-consuming. Here we present a simplified method for inserting point mutations into BAC transgenes requiring a single recombineering step followed by antibiotic selection. This technique, which we call ESI (Exogenous/Synthetic Intronization) mutagenesis, relies on co-integration of a mutation of interest along with a selectable marker gene, the latter of which is harboured in an artificial intron adjacent to the mutation site. Cell lines generated from ESI-mutated BACs express the transgenes equivalently to the endogenous gene, and all cells efficiently splice out the synthetic intron. Thus, ESI-mutagenesis provides a robust and effective single-step method with high precision and high efficiency for mutating BAC transgenes.
Neural dysfunction correlates with heat coma and CTmax in Drosophila but does not set the boundaries for heat stress survival
Authors: Jørgensen Lisa B. , Meldrum Robertson R. , Overgaard Johannes
Published: November 2019

When heated, insects loose coordinated movement followed by the onset of heat coma (CTmax). These phenotypes are popular measures to quantify inter- and intraspecific differences in insect heat tolerance, and CTmax correlate well with current species distributions. Here we examined the function of the central nervous system (CNS) in five species of Drosophila with different heat tolerances, while they were exposed to either constant high temperature or a gradual increasing temperature (ramp). Tolerant species were able to preserve CNS function at higher temperatures and for longer durations than sensitive species and similar differences were found for the behavioral indices (loss of coordination and onset of heat coma). Furthermore, the timing and temperature (constant and ramp exposure, respectively) for loss of coordination or complete coma coincided with the occurrence of spreading depolarisation (SD) events in the CNS. These SD events disrupt neurological function and silence the CNS suggesting that CNS failure is the primary cause of impaired coordination and heat coma. Heat mortality occurs soon after heat coma in insects and to examine if CNS failure could also be the proximal cause of heat death, we used selective heating of the head (CNS) and abdomen (visceral tissues). When comparing the temperature causing 50% mortality (LT50) of each body part to that of the whole animal, we found that the head was not particularly heat sensitive compared to the abdomen. Accordingly, it is unlikely that nervous failure is the principal/proximate cause of heat mortality in Drosophila.

Summary statement

Hyperthermic failure of the Drosophila central nervous system causes heat coma, a phenotype varying in temperature between drosophilids, but neural failure is likely not the primary cause of heat mortality.
Surface Sensing Stimulates Cellular Differentiation inCaulobacter crescentus
Authors: Snyder Rhett A. , Ellison Courtney K. , Severin Geoffrey B. , Waters Christopher M. , Brun Yves V.
Published: November 2019

Cellular differentiation is a fundamental strategy used by cells to generate specialized functions at specific stages of development. The bacteriumC. crescentusemploys a specialized dimorphic life cycle consisting of two differentiated cell types. How environmental cues, including mechanical inputs such as contact with a surface, regulate this cell cycle remain unclear. Here, we find that surface sensing by the physical perturbation of retracting extracellular pilus filaments accelerates cell cycle progression and cellular differentiation. We show that physical obstruction of dynamic pilus activity by chemical perturbation or by a mutation in the outer membrane pilus pore protein, CpaC, stimulates early initiation of chromosome replication. In addition, we find that surface contact stimulates cell cycle progression by demonstrating that surface-stimulated cells initiate early chromosome replication to the same extent as planktonic cells with obstructed pilus activity. Finally, we show that obstruction of pilus retraction stimulates the synthesis of the cell cycle regulator, cyclic diguanylate monophosphate (c-di-GMP) through changes in the activity and localization of two key regulatory histidine kinases that control cell fate and differentiation. Together, these results demonstrate that surface contact and mechanosensing by alterations in pilus activity stimulateC. crescentusto bypass its developmentally programmed temporal delay in cell differentiation to more quickly adapt to a surface-associated lifestyle.

Significance

Cells from all domains of life sense and respond to mechanical cues [1–3]. In eukaryotes, mechanical signals such as adhesion and surface stiffness are important for regulating fundamental processes including cell differentiation during embryonic development [4]. While mechanobiology is abundantly studied in eukaryotes, the role of mechanical influences on prokaryotic biology remains under-investigated. Here, we demonstrate that mechanosensing mediated through obstruction of the dynamic extension and retraction oftightadherence (tad) pili stimulates cell differentiation and cell cycle progression in the dimorphic α-proteobacteriumCaulobacter crescentus. Our results demonstrate an important intersection between mechanical stimuli and the regulation of a fundamental aspect of cell biology.
Retrieval of the Complete Coding Sequence of the UK-Endemic Tatenale Orthohantavirus Reveals Extensive Strain Variation and Supports its Classification as a Novel Species
Authors: Chappell Joseph G. , Tsoleridis Theocharis , Onianwa Okechukwu , Drake Gabby , Ashpole Ian , Dobbs Phillipa , Edema William , Kumi-Ansah Frederick , Bennett Malcolm , Tarlinton Rachael E , Ball Jonathan K , McClure C. Patrick
Published: November 2019

Hantaviruses are a diverse group of single-stranded, negative-sensed RNA viruses, known to cause sporadic outbreaks of potentially fatal human disease. To date, only two Orthohantavirus species have been detected in the UK - Seoul virus and Tatenale. Whilst Seoul is known to be pathogenic in humans, only partial fragments of Tatenale have been recovered, precluding any accurate analysis of its phylogeny or potential pathogenicity. To overcome this shortfall we used a degenerate primer PCR method to identify Tatenale-infection in rodents living in two separate locations in the UK. PCR positive samples were then subjected to either unbiased high-throughput sequencing or overlapping PCR product sequencing to recover the complete coding sequence of the Tatenale virus. This analysis provided in-depth insight into the evolutionary origins of this recently identified UK Orthohantavirus and unequivocally showed that Tatenale virus meets the established criteria for classification as a novel species. Crucially, our data will facilitate in vitro investigation into the zoonotic potential of Tatenale virus.
Comprehensive analysis of horizontal gene transfer among multidrug-resistant bacterial pathogens in a single hospital
Authors: Evans Daniel R. , Griffith Marissa P. , Mustapha Mustapha M. , Marsh Jane W. , Sundermann Alexander J. , Cooper Vaughn S. , Harrison Lee H. , Van Tyne Daria
Published: November 2019

Multidrug-resistant bacterial pathogens pose a serious public health threat, especially in hospital settings. Horizontal gene transfer (HGT) of mobile genetic elements (MGEs) contributes to this threat by facilitating the rapid spread of genes conferring antibiotic resistance, enhanced virulence, and environmental persistence between nosocomial pathogens. Despite recent advances in microbial genomics, studies of HGT in hospital settings remain limited in scope. The objective of this study was to identify and track the movement of MGEs within a single hospital system using unbiased methods. We screened the genomes of 2,173 bacterial isolates from healthcare-associated infections collected over an 18-month time period to identify nucleotide regions that were identical in the genomes of bacteria belonging to distinct genera. These putative MGEs were found in 196 isolates belonging to 11 different genera; they grouped into 51 clusters of related elements, and they were most often shared between related genera. To resolve the genomic locations of the most prevalent MGEs, we performed long-read sequencing on a subset of representative isolates and generated highly contiguous, hybrid-assembled genomes. Many of these genomes contained plasmids and chromosomal elements encoding one or more of the MGEs we identified, which were often arranged in a mosaic fashion. We then tracked the appearance of ten MGE-bearing plasmids in all 2,173 genomes, and found evidence supporting the transfer of plasmids between patients independent from bacterial transmission. Finally, we identified two instances of likely plasmid transfer across genera within individual patients. In one instance, the plasmid appeared to have subsequently transferred to a second patient. By surveying a large number of bacterial genomes sampled from infections at a single hospital in a systematic and unbiased manner, we were able to track the independent transfer of MGEs over time. This work expands our understanding of HGT in healthcare settings, and can inform efforts to limit the spread of drug-resistant pathogens in hospitals.
Bi-allelic MCM10 mutations cause telomere shortening with immune dysfunction and cardiomyopathy
Authors: Baxley Ryan M. , Leung Wendy , Schmit Megan M. , Matson Jacob Peter , Oram Marissa K. , Wang Liangjun , Taylor John , Yin Lulu , Hedberg Jack , Rogers Colette B. , Harvey Adam J. , Basu Debashree , Taylor Jenny C. , Pagnamenta Alistair T. , Dreau Helene , Craft Jude , Ormondroyd Elizabeth , Watkins Hugh , Hendrickson Eric A. , Mace Emily M. , Orange Jordan S. , Aihara Hideki , Stewart Grant S. , Blair Edward , Cook Jeanette Gowen , Bielinsky Anja-Katrin
Published: November 2019

Minichromosome maintenance protein 10 (Mcm10) is essential for eukaryotic DNA replication. Here, we describe compound heterozygous MCM10 mutations in patients with distinctive but overlapping clinical phenotypes – natural killer (NK) cell deficiency (NKD) and restrictive cardiomyopathy (RCM) with hypoplasia of the spleen and thymus. To understand the mechanism of Mcm10-associated disease, we modeled these mutations in human cell lines. Mcm10 deficiency causes chronic replication stress that reduces cell viability due to increased genomic instability and telomere erosion. Our data suggest that loss of Mcm10 function constrains telomerase activity by accumulating abnormal replication fork structures enriched with single-stranded DNA. Terminally-arrested replication forks in Mcm10-deficient cells require endonucleolytic processing by Mus81, as MCM10:MUS81 double mutants display decreased viability and accelerated telomere shortening. We propose that these bi-allelic mutations in MCM10 predispose specific cardiac and immune cell lineages to prematurely arrest during differentiation, causing the clinical phenotypes in both NKD and CM patients.