bluuebunny/crossref_metadata_2025 huggingface dataset:
An all-to-all approach to the identification of sequence-specific readers for epigenetic DNA modifications on cytosine
Authors: Song Guang , Wang Guohua , Luo Ximei , Cheng Ying , Song Qifeng , Wan Jun , Moore Cedric , Song Hongjun , Jin Peng , Qian Jiang , Zhu Heng
Published: May 2019

The authors have withdrawn their manuscript whilst they perform additional experiments to test some of their conclusions further. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
A dynamical systems framework to uncover the drivers of large-scale cortical activity
Authors: Ashourvan Arian , Pequito Sérgio , Bertolero Maxwell , Kim Jason Z. , Bassett Danielle S. , Litt Brian
Published: May 2019

A fundamental challenge in neuroscience is to uncover the principles governing complex interactions between the brain and its external environment. Over the past few decades, the development of functional neuroimaging techniques and tools from graph theory, network science, and computational neuroscience have markedly expanded opportunities to study the intrinsic organization of brain activity. However, many current computational models are fundamentally limited by little to no explicit assessment of the brain’s interactions with external stimuli. To address this limitation, we propose a simple scheme that jointly estimates the intrinsic organization of brain activity and extrinsic stimuli. Specifically, we adopt a linear dynamical model (intrinsic activity) under unknown exogenous inputs (e.g., sensory stimuli), and jointly estimate the model parameters and exogenous inputs. First, we demonstrate the utility of this scheme by accurately estimating unknown external stimuli in a synthetic example. Next, we examine brain activity at rest and task for 99 subjects from the Human Connectome Project, and find significant task-related changes in the identified system, and task-related increases in the estimated external inputs showing high similarity to known task regressors. Finally, through detailed examination of fluctuations in the spatial distribution of the oscillatory modes of the estimated system during the resting state, we find an apparent non-stationarity in the profile of modes that span several brain regions including the visual and the dorsal attention systems. The results suggest that these brain structures display a time-varying relationship, or alternatively, receive non-stationary exogenous inputs that can lead to apparent system non-stationarities. Together, our embodied model of brain activity provides an avenue to gain deeper insight into the relationship between cortical functional dynamics and their drivers.
Task-Based Functional Connectomes Predict Cognitive Phenotypes Across Psychiatric Disease
Authors: Barron Daniel S. , Gao Siyuan , Dadashkarimi Javid , Greene Abigail S. , Spann Marisa N. , Noble Stephanie , Lake Evelyn , Krystal John , Constable R. Todd , Scheinost Dustin
Published: May 2019

Importance

We show that three common approaches to clinical deficits (cognitive phenotype, disease group, disease severity) each offer useful and perhaps complimentary explanations for the brain’s underlying functional architecture as affected by psychiatric disease.

Objective

To understand how different clinical frameworks are represented in the brain’s functional connectome.

Design

We use an openly available dataset to create predictive models based on multiple connectomes built from task-based functional MRI data. We use these models to predict individual traits corresponding to multiple cognitive constructs across disease category. We also show that these same connectomes statistically differ depending on disease category and symptom burden.

Setting

This was a population-based study with data collected in UCLA.

Participants

Healthy adults were recruited by community advertisements from the Los Angeles area. Participants with adult ADHD, bipolar disorder, and schizophrenia were recruited using a patient-oriented strategy involving outreach to local clinics and online portals (separate from the methods used to recruit healthy volunteers)
OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine
Authors: López-Cortés Andrés , Paz-y-Miño César , Guerrero Santiago , Cabrera-Andrade Alejandro , Barigye Stephen J. , Munteanu Cristian R. , González-Díaz Humberto , Pazos Alejandro , Pérez-Castillo Yunierkis , Tejera Eduardo
Published: May 2019

Breast cancer (BC) is a heterogeneous disease where each OncoOmics approach needs to be fully understood as a part of a complex network. Therefore, the main objective of this study was to analyze genetic alterations, signaling pathways, protein-protein interaction networks, protein expression, dependency maps and enrichment maps in 230 previously prioritized genes by the Consensus Strategy, the Pan-Cancer Atlas, the Pharmacogenomics Knowledgebase and the Cancer Genome Interpreter, in order to reveal essential genes to accelerate the development of precision medicine in BC. The OncoOmics essential genes were rationally filtered to 144, 48 (33%) of which were hallmarks of cancer and 20 (14%) were significant in at least three OncoOmics approaches: RAC1, AKT1 CCND1, PIK3CA, ERBB2, CDH1, MAPK14, TP53, MAPK1, SRC, RAC3, PLCG1, GRB2, MED1, TOP2A, GATA3, BCL2, CTNNB1, EGFR and CDK2. According to the Open Targets Platform, there are 111 drugs that are currently being analyzed in 3151 clinical trials in 39 genes. Lastly, there are more than 800 clinical annotations associated with 94 genes in BC pharmacogenomics.
Bayesian multivariate reanalysis of large genetic studies identifies many new associations
Authors: Turchin Michael C. , Stephens Matthew
Published: May 2019

Genome-wide association studies (GWAS) have now been conducted for hundreds of phenotypes of relevance to human health. Many such GWAS involve multiple closely-related phenotypes collected on the same samples. However, the vast majority of these GWAS have been analyzed using simple univariate analyses, which consider one phenotype at a time. This is de-spite the fact that, at least in simulation experiments, multivariate analyses have been shown to be more powerful at detecting associations. Here, we conduct multivariate association analyses on 13 different publicly-available GWAS datasets that involve multiple closely-related phenotypes. These data include large studies of anthropometric traits (GIANT), plasma lipid traits (GlobalLipids), and red blood cell traits (HaemgenRBC). Our analyses identify many new associations (433 in total across the 13 studies), many of which replicate when follow-up samples are available. Overall, our results demonstrate that multivariate analyses can help make more effective use of data from both existing and future GWAS.

1

Author Summary

Genome-wide association studies (GWAS) have become a common and powerful tool for identifying significant correlations between markers of genetic variation and physical traits of interest. Often these studies are conducted by comparing genetic variation against single traits one at a time (‘univariate’); however, it has previously been shown that it is possible to increase your power to detect significant associations by comparing genetic variation against multiple traits simultaneously (‘multivariate’). Despite this apparent increase in power though, researchers still rarely conduct multivariate GWAS, even when studies have multiple traits readily available. Here, we reanalyze 13 previously published GWAS using a multivariate method and find >400 additional associations. Our method makes use of univariate GWAS summary statistics and is available as a software package, thus making it accessible to other researchers interested in conducting the same analyses. We also show, using studies that have multiple releases, that our new associations have high rates of replication. Overall, we argue multivariate approaches in GWAS should no longer be overlooked and how, often, there is low-hanging fruit in the form of new associations by running these methods on data already collected.
Century long fertilization reduces stochasticity controlling grassland microbial community succession
Authors: Liang Yuting , Ning Daliang , Lu Zhenmei , Zhang Na , Hale Lauren , Wu Liyou , Clark Ian M. , McGrath Steve P. , Storkey Jonathan , Hirsch Penny R. , Sun Bo , Zhou Jizhong
Published: May 2019

Determining the drivers underlying ecological succession is a fundamental goal of ecological research and essential for predicting ecosystem functioning in response to human-induced environmental changes. Although various studies have examined the impacts of nitrogen (N) addition on plant and microbial community diversity, structure and activities, it remains unknown how long-term anthropogenic fertilization affects the ecological succession of microbial functional guilds and its underlying community assembly mechanisms. Here, using archived soils, we examined more than a century’s succession in soil microbial functional communities (from 1870 to 2008) from the Park Grass Experiment at Rothamsted Experimental Station, the longest running ecological experiment in the world. Long-term fertilization was found to significantly alter soil functional community structure and led to increasingly convergent succession of soil microbial communities. Meta-analysis indicated that microbial temporal turnover (w) was highly time scale-dependent, and the w value threshold was estimated as 0.0025 with a threshold time point of approximately 160 years. In addition, the importance of stochastic assembly varied greatly in regulating the succession of different microbial guilds. Fertilization had large to medium effects on reducing ecological stochasticity for microbial guilds involved in carbon (C) fixation and degradation, N fixation and mineralization, and denitrification. This century long-term study elucidated the differing influences of assembly mechanisms on soil microbial functional communities involved in C and N cycling, which could not be derived from taxonomic or phylogenetic approaches.
Efficient horizontal transmission without viral super-spreaders may cause the high prevalence of STLV-1 infection in Japanese macaques
Authors: Murata Megumi , Yasunaga Jun-ichirou , Washizaki Ayaka , Seki Yohei , Tan Wei Keat , Mizukami Takuo , Matsuoka Masao , Akari Hirofumi
Published: May 2019

Abstracts

Simian T-cell leukemia virus type-1 (STLV-1) is disseminated among various non-human primate species and is closely related to human T-cell leukemia virus type-1 (HTLV-1), the causative agent of adult T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis. Notably, the prevalence of STLV-1 infection in Japanese macaques (JMs) is estimated to be much greater than that in other non-human primates; however, the mechanism and mode of STLV-1 transmission remain unknown. We hypothesized that a substantial proportion of infected macaques may play a critical role as viral super-spreaders for efficient inter-individual transmission leading to the high prevalence of infection. To address this, we examined a cohort of 280 JMs reared in a free-range facility for levels of anti-STLV-1 antibody titers (ABTs) and STLV-1 proviral loads (PVLs). We found that the prevalence of STLV-1 in the cohort reached up to 65% (180/280), however, the ABTs and PVLs were normally distributed with mean values of 4076 and 0.62%, respectively, which were comparable to those of HTLV-1-infected humans. Contrary to our expectations, we did not observe the macaques with abnormally high PVLs and poor ABTs, and therefore, the possibility of viral super-spreaders was unlikely. Results from further analyses regarding age-dependent changes in STLV-1 prevalence and a longitudinal follow-up of STLV-1 seroconversion strongly suggest that frequent horizontal transmission is a major route of STLV-1 infection, probably due to the unique social ecology of JMs associated with environmental adaptation.

Importance

We investigated the cause of the high prevalence of STLV-1 infection in the studied JMs cohort. Contrary to our expectations, the potential viral super-spreaders as shown by abnormally high PVLs and poor ABTs were not observed among the JMs. Rather, the ABTs and PVLs among the infected JMs were comparable to those of HTLV-1-infected humans although the prevalence of HTLV-1 in humans is much less than the macaques. Further analyses demonstrate that the prevalence drastically increased over one year of age and most of these animals over 6 years of age were infected with STLV-1, and that in the longitudinal follow-up study frequent seroconversion occurred in not only infants but also in juvenile and adult seronegative monkeys (around 20% per year). This is the first report showing that frequent horizontal transmission without viral super-spreaders may cause high prevalence of STLV-1 infection in JMs.
Carbon starvation induces the expression of PprB-regulated genes inPesudomonas aeruginosa
Authors: Wang Congcong , Chen Wenhui , Xia Aiguo , Zhang Rongrong , Huang Yajia , Yang Shuai , Ni Lei , Jin Fan
Published: May 2019

Pseudomonas aeruginosacan cause severe infections in humans. This bacteria often adopt a biofilm lifestyle that is hard to treat. In several previous studies, the PprA-PprB two-component system (TCS), which controls the expression of type IVb pili, BapA adhesin, and CupE fimbriae, was shown to be involved in biofilm formation. However, signals or environmental conditions that can trigger the PprA-PprB TCS are still unknown, and the molecular mechanisms of PprB-mediated biofilm formation are poorly characterized. Here we report that carbon starvation stress (CCS) can induce the expression ofpprBand genes in the PprB regulon. The stress response sigma factor RpoS, rather than the two-component sensor PprA, was determined to mediate the induction ofpprBtranscription. We also observed a strong negative regulation of PprB to the transcription of itself. Further experiments showed that PprB overexpression greatly enhanced cell-cell adhesion (CCA) and cell-surface adhesion (CSA) inP. aeruginosa. Specially, under the background of PprB overexpression, both of the BapA adhesin and CupE fimbriae displayed positive effect on CCA and CSA, while the type IVb pili showed an unexpected negative effect on CCA and no effect on CSA. In addition, expression of the PprB regulon genes displayed significant increases in 3-day colony biofilms, indicating a possible carbon limitation state in these biofilms. The CSS-RpoS-PprB-Bap/Flp/CupE/Tad pathway identified in this study provides a new perspective on the process of biofilm formation under carbon-limited environments.

IMPORTANCE

Typically, determining the external signals that can trigger a regulatory system is crucial to understand the regulatory logic and inward function of that system. The PprA-PprB two-component system was reported to be involved in biofilm formation inPseudomonas aeruginosa, but the signals that can trigger this system are unknown. In this study, we found that carbon starvation stress (CSS) can induce the transcription ofpprBand genes in PprB regulon, through an RpoS dependent pathway. Increase of PprB expression leads to enhanced cell-cell and cell-surface adhesions inP. aeruginosa,both of which are dependent mainly on the Bap adhesin secretion system and partially on the CupE fimbriae. Our findings suggest that PprB reinforces the structure of biofilms under carbon-limited conditions, and the Bap secretion system and CupE fimbriae are two potential targets for biofilm treatment.
The Polycomb group protein Ring1 regulates dorsoventral patterning of the mouse telencephalon
Authors: Eto Hikaru , Kishi Yusuke , Koseki Haruhiko , Gotoh Yukiko
Published: May 2019

Patterning of the dorsal-ventral (D-V) axis of the mammalian telencephalon is fundamental to the formation of distinct functional regions including the neocortex and ganglionic eminences. Morphogenetic signaling by bone morphogenetic protein (BMP), Wnt, Sonic hedgehog (Shh), and fibroblast growth factor (FGF) pathways determines regional identity along this axis. It has remained unclear, however, how region-specific expression patterns of these morphogens along the D-V axis are established, especially at the level of epigenetic (chromatin) regulation. Here we show that epigenetic regulation by Ring1, an essential Polycomb group (PcG) protein, plays a key role in formation of ventral identity in the mouse telencephalon. Deletion of theRing1bor bothRing1aandRing1bgenes in neuroepithelial cells of the mouse embryo attenuated expression of the gene for Shh, a key morphogen for induction of ventral identity, and induced misexpression of dorsal marker genes including those for BMP and Wnt ligands in the ventral telencephalon. PcG protein–mediated trimethylation of histone H3 on lysine-27 (H3K27me3) was also apparent at BMP and Wnt ligand genes in wild-type embryos. Importantly, forced activation of Wnt or BMP signaling repressed the expression ofShhin organotypic and dissociated cultures of the early-stage telencephalon. Our results thus indicate that epigenetic regulation by PcG proteins—and, in particular, that by Ring1— confers a permissive state for the induction ofShhexpression through suppression of BMP and Wnt signaling pathways, which in turn allows the development of ventral identity in the telencephalon.
Tracking of antibiotic resistance transfer and rapid plasmid evolution in a hospital setting by Nanopore sequencing
Authors: Peter Silke , Bosio Mattia , Gross Caspar , Bezdan Daniela , Gutierrez Javier , Oberhettinger Philipp , Liese Jan , Vogel Wichard , Dörfel Daniela , Berger Lennard , Marschal Matthias , Willmann Matthias , Gut Ivo , Gut Marta , Autenrieth Ingo , Ossowski Stephan
Published: May 2019

Background

Infection of patients with multidrug-resistant (MDR) bacteria often leave very limited or no treatment options. The transfer of antimicrobial resistance genes (ARG) carrying plasmids between bacterial species by horizontal gene transfer represents an important mode of expansion of ARGs. Here, we evaluated the application of Nanopore sequencing technology in a hospital setting for monitoring the transfer and rapid evolution of antibiotic resistance plasmids within and across multiple species.

Results

In 2009 we experienced an outbreak with an extensively multidrug resistant P. aeruginosa harboring the carbapenemase enzyme blaIMP-8, and in 2012 the first Citrobacter freundii and Citrobacter werkmanii harboring the same enzyme were detected. Using Nanopore and Illumina sequencing we conducted a comparative analysis of all blaIMP-8 bacteria isolated in our hospital over a 6-year period (n = 54). We developed the computational platforms pathoLogic and plasmIDent for Nanopore-based characterization of clinical isolates and monitoring of ARG transfer, comprising de-novo assembly of genomes and plasmids, polishing, QC, plasmid circularization, ARG annotation, comparative genome analysis of multiple isolates and visualization of results. Using plasmIDent we identified a 40 kb plasmid carrying blaIMP-8 in P. aeruginosa and C. freundii, verifying that plasmid transfer had occurred. Within C. freundii the plasmid underwent further evolution and plasmid fusion, resulting in a 164 kb mega-plasmid, which was transferred to C. werkmanii. Moreover, multiple rearrangements of the multidrug resistance gene cassette were detected in P. aeruginosa, including deletions and translocations of complete ARGs.

Conclusion

Plasmid transfer, plasmid fusion and rearrangement of the multidrug resistance gene cassette mediated the rapid evolution of opportunistic pathogens in our hospital. We demonstrated the feasibility of tracking plasmid evolution dynamics and ARG transfer in clinical settings in a timely manner. The approach will allow for successful countermeasures to contain not only clonal, but also plasmid mediated outbreaks.
Development of the first low nanomolar Liver Receptor Homolog-1 agonist through structure-guided design
Authors: Mays Suzanne G. , Flynn Autumn R. , Cornelison Jeffery L. , Okafor C. Denise , Wang Hongtao , Wang Guohui , Huang Xiangsheng , Donaldson Heather N. , Millings Elizabeth J. , Polavarapu Rohini , Moore David D. , Calvert John W. , Jui Nathan T. , Ortlund Eric A.
Published: May 2019

As a key regulator of metabolism and inflammation, the orphan nuclear hormone receptor, Liver Receptor Homolog-1 (LRH-1), has potential as a therapeutic target for diabetes, nonalcoholic fatty liver disease, and inflammatory bowel diseases. Discovery of LRH-1 modulators has been difficult, in part due to the tendency for synthetic compounds to bind unpredictably within the lipophilic binding pocket. Using a structure-guided approach, we exploited a newly-discovered polar interaction to lock agonists in a consistent orientation. This enabled the discovery of the first low nanomolar LRH-1 agonist, one hundred times more potent than the best previous modulator. We elucidate a novel mechanism of action that relies upon specific polar interactions deep in the LRH-1 binding pocket. In an organoid model of inflammatory bowel disease, the new agonist increases expression of LRH-1-conrolled steroidogenic genes and promotes anti-inflammatory gene expression changes. These studies constitute major progress in developing LRH-1 modulators with potential clinical utility.
Ultrastructural details of mammalian chromosome architecture
Authors: Krietenstein Nils , Abraham Sameer , Venev Sergey V. , Abdennur Nezar , Gibcus Johan , Hsieh Tsung-Han S. , Parsi Krishna Mohan , Yang Liyan , Maehr René , Mirny Leonid A. , Dekker Job , Rando Oliver J.
Published: May 2019

Over the past decade, 3C-related methods, complemented by increasingly detailed microscopic views of the nucleus, have provided unprecedented insights into chromosome folding in vivo. Here, to overcome the resolution limits inherent to the majority of genome-wide chromosome architecture mapping studies, we extend a recently-developed Hi-C variant, Micro-C, to map chromosome architecture at nucleosome resolution in human embryonic stem cells and fibroblasts. Micro-C maps robustly capture well-described features of mammalian chromosome folding including A/B compartment organization, topologically associating domains (TADs), and cis interaction peaks anchored at CTCF binding sites, while also providing a detailed 1-dimensional map of nucleosome positioning and phasing genome-wide. Compared to high-resolution in situ Hi-C, Micro-C exhibits substantially improved signal-to-noise with an order of magnitude greater dynamic range, enabling not only localization of domain boundaries with single-nucleosome accuracy, but also resolving more than 20,000 additional looping interaction peaks in each cell type. Intriguingly, many of these newly-identified peaks are localized along stripe patterns and form transitive grids, consistent with their anchors being pause sites impeding the process of cohesin-dependent loop extrusion. Together, our analyses provide the highest resolution maps of chromosome folding in human cells to date, and provide a valuable resource for studies of chromosome folding mechanisms.
Frontoparietal connectivity correlates with working memory performance in multiple sclerosis
Authors: Figueroa-Vargas Alejandra , Cárcamo Claudia , Henríquez-Ch Rodrigo , Zamorano Francisco , Ciampi Ethel , Uribe Reinaldo , Vásquez Macarena , Aboitiz Francisco , Billeke Pablo
Published: May 2019

Working Memory (WM) impairment is the most common cognitive deficit of Multiple Sclerosis (MS) patients. However, evidence of its neurobiological mechanisms is scarce. Here we recorded electroencephalographic activity of twenty patients with relapsing-remitting MS and minimal cognitive deficit, and 20 healthy control (HC) subjects while they solved a WM task. In spite of similar performance, the HC group demonstrated both a correlation between temporoparietal theta activity and memory load, and a correlation between medial frontal theta activity and successful memory performances. MS patients did not show theses correlations leading significant differences between groups. Moreover, cortical connectivity analyses using granger causality and phase-amplitude coupling between theta and gamma revealed that HC group, but not MS group, presented a load-modulated progression of the frontal-to-parietal connectivity. This connectivity correlated with working memory capacity in MS groups. This early alterations in the oscillatory dynamics underlaying working memory could be useful for plan therapeutic interventions
Testing implications of the polygenic model for the genetic analysis of loci identified through genome-wide association
Authors: Zhang Wenyu , Reeves R. Guy , Tautz Diethard
Published: May 2019

It has been proposed that many loci with no significant association in GWA studies can nonetheless contribute to the phenotype through modifier interactions with the core genes, implying a polygenic determination of quantitative traits. We have tested this hypothesis by using Drosophila pupal phenotypes. We identified candidate genes for pupal length determination in a GWA and show for disrupted versions of the genes that most are indeed involved in the phenotype, presumably forming a core pathway. We then randomly chose genes below the GWA threshold and found that three quarters of them had also an effect on the trait. We further tested the effects of these knockout lines on an independent behavioral pupal trait (pupation site choice) and found that a similar, but non-correlated fraction of them had a significant effect as well. Our data thus confirm the prediction that a large number of genes can influence independent quantitative traits.

Impact statement

Quantitative traits are similarly likely influenced by randomly picked loci as by loci identified in a genome-wide association study.
DNA accessibility is not the primary determinant of chromatin-mediated gene regulation
Authors: Chereji Răzvan V. , Eriksson Peter R. , Ocampo Josefina , Clark David J.
Published: May 2019

DNA accessibility is thought to be of major importance in regulating gene expression. We test this hypothesis using a restriction enzyme as a probe of chromatin structure and as a proxy for transcription factors. We measured the digestion rate and the fraction of accessible DNA at all genomicAluI sites in budding yeast and mouse liver nuclei. Hepatocyte DNA is more accessible than yeast DNA, consistent with longer linkers between nucleosomes, and indicating that nucleosome spacing is a major determinant of accessibility. DNA accessibility varies from cell to cell, such that essentially no sites are accessible or inaccessible in every cell.AluI sites in inactive mouse promoters are accessible in some cells, implying that transcription factors could bind without activating the gene. Euchromatin and heterochromatin have very similar accessibilities, suggesting that transcription factors can penetrate heterochromatin. Thus, DNA accessibility is not likely to be the primary determinant of gene regulation.
High-Throughput Single-Molecule R-loop Footprinting Reveals Principles of R-loop Formation
Authors: Malig Maika , Hartono Stella R. , Giafaglione Jenna M. , Sanz Lionel A. , Chedin Frederic
Published: May 2019

R-loops are a prevalent class of non-B DNA structures that form during transcription upon reannealing of the nascent RNA to the template DNA strand. R-loops have been profiled using the S9.6 antibody to immunoprecipitate DNA:RNA hybrids. S9.6-based DNA:RNA immunoprecipitation (DRIP) techniques revealed that R-loops form dynamically over conserved genic hotspots. We developed an orthogonal profiling methodology that queries R-loops via the presence of long stretches of single-stranded DNA on the looped-out strand. Non-denaturing sodium bisulfite treatment catalyzes the conversion of unpaired cytosines to uracils, creating permanent genetic tags for the position of an R-loop. Long read, single-molecule PacBio sequencing allows the identification of R-loop ‘footprints’ at near nucleotide resolution in a strand-specific manner on single DNA molecules and at ultra-deep coverage. Single-molecule R-loop footprinting (SMRF-seq) revealed a strong agreement between S9.6-and bisulfite-based R-loop mapping and confirmed that R-loops form from unspliced transcripts over genic hotspots. Using the largest single-molecule R-loop dataset to date, we show that individual R-loops generate overlapping sets of molecular clusters that pile-up through larger R-loop-prone zones. SMRF-seq further established that R-loop distribution patterns are driven by both intrinsic DNA sequence features and DNA topological constraints, revealing the principles of R-loop formation.
Three-dimensional morphological analysis of the dynamic digestive system in the green brittle star
Authors: Wakita Daiki , Naniwa Keisuke , Aonuma Hitoshi
Published: May 2019

Brittle stars (Echinodermata: Ophiuroidea) digest a great diversity of food in their stomach, which widely lies in the central disk. As for a possible digestive activity, the green brittle starOphiarachna incrassata(Lamarck, 1816) is known to show a dynamic movement at the disk. This phenomenon would deeply involve the morphological structure of the stomach. However, past anatomical studies have shown the digestive system in two dimensions after wide incision of the body wall anchoring the stomach. This methodology restrains us from understanding how the stomach actually shapes inside a brittle star. We aim to visualize the morphology of brittle stars’ digestive system in a non-destructive and three-dimensional way, with a comparison between a relaxed specimen and a specimen fixed at the very moment of the disk’s movement. Employing X-ray micro-computed tomography (micro-CT) and introducing an instant freezing method with cryogenic ethanol, we found the stomach wholly transformed during the movement. We here brought transparency to thein vivoposition of gut contents to hint the mechanism and digestive function of the movement. Our outcome spotlights a dynamic digestive process in echinoderms and a widely applicable method for probing into its relation with body structure.
When will the cancer start? Elucidating the correlations between cancer initiation times and lifetime cancer risks
Authors: Teimouri Hamid , Kochugaeva Maria , Kolomeisky Anatoly B.
Published: May 2019

Cancer is a genetic disease that results from accumulation of unfavorable mutations. As soon as genetic and epigenetic modifications associated with these mutations become strong enough, the uncontrolled tumor cell growth is initiated, eventually spreading through healthy tissues. Clarifying the dynamics of cancer initiation is thus critically important for understanding the molecular mechanisms of tumorigenesis. Here we present a new theoretical method to evaluate the dynamic processes associated with the cancer initiation. It is based on a discrete-state stochastic description of the formation of tumors as a fixation of unfavorable mutations in tissues. Using a first-passage analysis the probabilities for the cancer to appear and the times before it happens, which are viewed as fixation probabilities and fixation times, respectively, are explicitly calculated. It is predicted that the slowest cancer initiation dynamics is observed for neutral mutations, while it is fast for both advantageous and, surprisingly, disadvantageous mutations. The method is applied for estimating the cancer initiation times from experimentally available lifetime cancer risks for different types of cancer. It is found that the higher probability of the cancer to occur does not necessary lead to the fast times of starting the cancer. Our theoretical analysis helps to clarify microscopic aspects of cancer initiation processes.
Variability in human drug metabolizing cytochrome P450 CYP2C9, CYP2C19 and CYP3A5 activities caused by genetic variations in cytochrome P450 oxidoreductase
Authors: Velazquez Maria Natalia Rojas , Parween Shaheena , Udhane Sameer S , Pandey Amit V
Published: May 2019

A broad spectrum of human diseases are caused by mutations in the NADPH cytochrome P450 oxidoreductase (POR). Cytochrome P450 proteins perform several reactions, including the metabolism of steroids, drugs, and other xenobiotics. In 2004 the first human patients with defects in POR were reported, and over 250 variations in POR are known. Information about the effects of POR variants on drug metabolizing enzymes is limited and has not received much attention. By analyzing the POR sequences from genomics databases, we identified potentially disease-causing variations and characterized these by in vitro functional studies using recombinant proteins. Proteins were expressed in bacteria and purified for activity assays. Activities of cytochrome P450 enzymes were tested in vitro using liposomes prepared with lipids into which P450 and P450 reductase proteins were embedded. Here we are reporting the effect of POR variants on drug metabolizing enzymes CYP2C9, CYP2C19, and CYP3A5 which are responsible for the metabolism of many drugs. POR Variants A115V, T142A, A281T, P284L, A287P, and Y607C inhibited activities of all P450 proteins tested. Interestingly, the POR variant Q153R showed a reduction of 20-50% activities with CYP2C9 and CYP2C19 but had a 400% increased activity with CYP3A5. The A287P is most common POR mutation found in patients of European origin, and significantly inhibited drug metabolism activities which has important consequences for monitoring and treatment of patients. In vitro, functional assays using recombinant proteins provide a useful model for establishing the metabolic effect of genetic mutations. Our results indicate that detailed knowledge about POR variants is necessary for correct diagnosis and treatment options for persons with POR deficiency and the role of changes in drug metabolism and toxicology due to variations in POR needs to be addressed.
Cooperation and spatial self-organization determine ecosystem function for polysaccharide-degrading bacteria
Authors: Ebrahimi Ali , Schwartzman Julia , Cordero Otto X.
Published: May 2019

The recycling of particulate organic matter (POM) by microbes is a key part of the global carbon cycle, one which is mediated by the extracellular hydrolysis of polysaccharides and the production of public goods that can trigger social behaviors in bacteria. Despite the potential importance of these microbial interactions, their role in regulating of ecosystem function remains unclear. In this study, we developed a computational and experimental model system to address this challenge and studied how POM depolymerization rate and its uptake efficiency –two main ecosystem function parameters– depended on social interactions and spatial self-organization on particle surfaces. We found an emergent trade-off between rate and efficiency resulting from the competition between oligosaccharide diffusion and cellular uptake, with low rate and high efficiency being achieved through cell-to-cell cooperation between degraders. Bacteria cooperated by aggregating in cell-clusters of ~10-20μm, where cells were able to share public goods. This phenomenon, which was independent of any explicit group-level regulation, led to the emergence of critical cell concentrations below which degradation did not occur, despite all resources being available in excess. By contrast, when particles were labile and turnover rates were high, aggregation promoted competition and decreased the efficiency of carbon utilization. Our study shows how social interactions and cell aggregation determine the rate and efficiency of particulate carbon turnover in environmentally relevant scenarios.

Significance Statement

Microorganisms can cooperate by secreting public goods that benefit local neighbors, however, the impact of cooperation on ecosystem functions remains poorly constrained. We here pair computation and experiment to show that bacterial cooperation mediates the degradation of polysaccharide particles recalcitrant to hydrolysis in aquatic environments. On particle surfaces, cooperation emerges through the self-organization of cells into ~10-20μm clusters that promote cooperative uptake of hydrolysis products. The transition between cooperation and competition in aggregates is mitigated by individual cell behaviors such as motility and chemotaxis, that promote reorganization on the particle surface. When cooperation is required, the degradation of recalcitrant biopolymers can only take place when degraders exceed a critical cell concentration, underscoring the importance of microbial interactions for ecosystem function.
The role of ATP hydrolysis in conformational changes of human P-glycoprotein in living cells
Authors: Futamata Ryota , Ogasawara Fumihiko , Ichikawa Takafumi , Kodan Atsushi , Kimura Yasuhisa , Kioka Noriyuki , Ueda Kazumitsu
Published: May 2019

P-glycoprotein (P-gp; also known as MDR1 or ABCB1) is an ATP-driven multidrug transporter that extrudes various hydrophobic toxic compounds to the extracellular space. P-gp consists of two transmembrane domains (TMDs) that form the substrate translocation pathway and two nucleotide-binding domains (NBDs) that bind and hydrolyze ATP. P-gp takes at least two states during transport; the inward-facing (pre-drug transport) conformation, in which the two NBDs are separated and the two TMDs are open to the intracellular side, and the outward-facing (post-drug transport) conformation, in which the NBDs are dimerized and the TMDs are slightly open to the extracellular side. ATP binding and hydrolysis cause conformational changes between the inward-facing and the outward-facing conformations to translocate substrates across the membrane. However, it remains unclear how ATP is used during these conformational changes in living cells. In this study, we investigated the role of ATP binding and hydrolysis during the conformational changes of human P-gp in living cells by using fluorescence resonance energy transfer (FRET). We show that ATP binding causes the conformational change to the outward-facing state and that ATP hydrolysis and subsequent release of γ-phosphate from both NBDs allow the outward-facing state to return to the original inward-facing state.
A bacterial effector protein prevents MAPK-mediated phosphorylation of SGT1 to suppress plant immunity
Authors: Yu Gang , Xian Liu , Xue Hao , Yu Wenjia , Rufian Jose S. , Sang Yuying , Morcillo Rafael J. L. , Wang Yaru , Macho Alberto P.
Published: May 2019

Nucleotide-binding domain and leucine-rich repeat-containing (NLR) proteins function as sensors that perceive pathogen molecules and activate immunity. In plants, the accumulation and activation of NLRs is regulated by SUPPRESSOR OF G2 ALLELE OF skp1 (SGT1). In this work, we found that an effector protein named RipAC, secreted by the plant pathogen Ralstonia solanacearum, associates with SGT1 to suppress NLR-mediated SGT1-dependent immune responses, including those triggered by another R. solanacearum effector, RipE1. RipAC does not affect the accumulation of SGT1 or NLRs, or their interaction. However, RipAC inhibits the interaction between SGT1 and MAP kinases, and the phosphorylation of a MAPK target motif in the C-terminal domain of SGT1. Such phosphorylation is enhanced upon activation of immune signaling, leads to the release of the interaction between SGT1 and NLRs, and contributes to the activation of NLR-mediated responses. Additionally, SGT1 phosphorylation contributes to resistance against R. solanacearum, and this is particularly evident in the absence of RipAC. Our results shed light onto the mechanism of activation of NLR-mediated immunity, and suggest a positive feedback loop between MAPK activation and SGT1-dependent NLR activation.
High-resolution and High-accuracy Topographic and Transcriptional Maps of the Nucleosome Barrier
Authors: Chen Zhijie , Gabizon Ronen , Brown Aidan I. , Lee Antony , Song Aixin , Celis César Díaz , Koslover Elena F. , Yao Tingting , Bustamante Carlos
Published: May 2019

Nucleosomes represent mechanical and energetic barriers that RNA Polymerase II (Pol II) must overcome during transcription. A high-resolution description of the barrier topography, its modulation by epigenetic modifications, and their effects on Pol II nucleosome crossing dynamics, is still missing. Here, we obtain topographic and transcriptional (Pol II residence time) maps of canonical, H2A.Z, and monoubiquitinated H2B (uH2B) nucleosomes at near base-pair resolution and accuracy. Pol II crossing dynamics are complex, displaying pauses at specific loci, backtracking, and nucleosome hopping between wrapped states. While H2A.Z widens the barrier, uH2B heightens it, and both modifications greatly lengthen Pol II crossing time. Using the dwell times of Pol II at each nucleosomal position we extract the energetics of the barrier. The orthogonal barrier modifications of H2A.Z and uH2B, and their effects on Pol II dynamics rationalize their observed enrichment in +1 nucleosomes and suggest a mechanism for selective control of gene expression.

Highlights

A single-molecule unzipping assay mimics DNA unwinding by Pol II and maps the topography of human canonical, H2A.Z and uH2B nucleosome barriers at high resolution

Real-time dynamics and full molecular trajectories of Pol II crossing the nucleosomal barrier reveal the transcriptional landscape of the barrier at high accuracy

H2A.Z enhances the width and uH2B the height of the barrier

A unified mechanical model links position-dependent dwell times of Pol II on the nucleosome with energetics of the barrier
A multi-level society comprised of one-male and multi-male core units in an African colobine (Colobus angolensis ruwenzorii)
Authors: Stead Samantha M. , Teichroeb Julie A.
Published: May 2019

A few mammalian species exhibit complex, nested social organizations, termed multi-level societies. Among nonhuman primates, multi-level societies have been confirmed in several African papionin and Asian colobine species. Using data on individually-recognized Rwenzori Angolan colobus at Lake Nabugabo, Uganda, we document the first multi-level society in an African colobine. The study band comprised up to 135 individuals living in 12 socially and spatially distinct core units that ranged in size from 4 to 23 individuals. These core units shared a home range, and fissioned and fused throughout the day. Using the association indices between core units, we employed hierarchical cluster analyses and permutation tests to show that some core units clustered into clans. Thus, we confirm three tiers of social organization for Rwenzori Angolan colobus: core unit, clan, and band. The social organization of this subspecies is unlike any reported previously in a nonhuman primate, with about half the core units containing a single adult male and the others containing multiple reproductive adult males. Preliminary data show males to transfer within the band and female to transfer outside of the band, which suggests that, like Hamadryas baboons, this subspecies could provide insight into the selective pressures underlying hominin social organization.
Changes in the microbial community of Lubomirskia baicalensis affected by Brown Rot Disease
Authors: Colin ROREX , Sergej BELIKOV , Natalia BELKOVA , Lubov Chernogor , Igor Khanaev , Armen Nalian , Alexandra Martynova-Van Kley
Published: May 2019

Sponge diseases occur globally and the resulting reduction of sponge populations has negative effects on other organisms within the ecosystems due to loss of nutrient enrichment and loss of bioremediation. In Lake Baikal, the predominate sponge species Lubomirskia baicalensis is currently being infected with an unidentified pathogen resulting in a sharp decline in population. The current hypothesis is that the recent increase in methane concentration in the lake has caused dysbiosis within the bacterial community of L. baicalensis resulting in the disease outbreak. In this study we investigated the changes in the bacterial community between healthy and sick sponges using 16S bacterial profiling targeting veritable regions 3-5. Here we present data that the bacterial communities of the healthy sponge samples were significantly different from sick samples and several poorly classified organisms were identified by Indicator Species Analysis as significant. Organisms identified from the sick samples classified within taxonomic units that contain acidophilic bacteria which suggest pH may play a role. There was also an observed decrease in the number of identified methyltropic bacteria present in the sick sponge samples compared to the healthy.
A helminth chitinase structurally similar to mammalian chitinase displays immunomodulatory properties
Authors: Ebner Friederike , Balster Katja , Janek Katharina , Niewienda Agathe , Malecki Piotr H. , Weiss Manfred S. , Sutherland Tara E. , Heuser Arnd , Kühl Anja A. , Zentek Jürgen , Hofmann Andreas , Hartmann Susanne
Published: May 2019

Previously, we reported significant immunomodulatory effects of the entire excretory-secretory (ES) proteins of the first larval stage (L1) of the gastrointestinal nematodeTrichuris suisin a rodent model of allergic hyperreactivity. In the present study, we aimed to identify the proteins accounting for the modulatory effects of theT. suisL1 ES proteins and thus studied selected components for their immunomodulatory efficacy in an OVA-induced allergic airway disease model. In particular, an enzymatically activeT. suischitinase mediated amelioration of airway hyperreactivity, primarily associated with suppression of eosinophil recruitment into the lung. The three-dimensional structure of theT. suischitinase as determined by high-resolution X-ray crystallography revealed significant similarities to mouse acidic mammalian chitinase (AMCase). In addition, the unique ability ofT. suischitinase to form dimers, as well as acidic surface patches within the dimerization region may contribute to the formation of cross-reactive antibodies to the mouse homologs. This hypothesis is supported by the observation thatT. suischitinase treatment induced cross-reactive antibodies to mouse AMCase and chitinase-like protein BRP-39 in the AHR model. In conclusion, a biologically activeT. suischitinase exhibits immunomodulatory properties despite its structural similarity to the mammalian counterpart.

Author summary

Experimental immunotherapy via reintroduction of intestinal worms to treat and prevent autoimmune, chronic inflammatory or allergic diseases is being discussed but the underlying mechanisms are still not fully understood. Here, we investigated the immunomodulatory potential of specific proteins of the whipwormTrichuris suisthat are secreted very early during larval development. Using a murine model of allergic lung disease, we show that in particular oneT. suisprotein, functionally characterized as an active chitinase, is reducing the lung inflammation. TheT. suischitinases three-dimensional protein structure revealed remarkable similarities to the hosts’ chitinase, an enzyme known to play a pivotal role in lung allergy. We also show that treatment with the helminth chitinase induced cross-reactive antibody responses against murine chitinase and chitinase-like proteins, both being inflammatory marker and regulators of type 2 immunity. Thus, our study provides a novel mechanism of immunomodulation by helminth components and may contribute to a better understanding of clinical responses of patients receiving helminthic therapy.