bluuebunny/crossref_metadata_2025 huggingface dataset:
DISTINCT ACTIN-DEPENDENT NANOSCALE ASSEMBLIES UNDERLIE THE DYNAMIC AND HIERARCHICAL ORGANIZATION OF E-CADHERIN
Authors: Chandran Rumamol , Kale Girish , Philippe Jean-Marc , Lecuit Thomas , Mayor Satyajit
Published: November 2019

Intercellular adhesion mediated by E-cadherin is pivotal in maintaining epithelial tissue integrity and for tissue morphogenesis. Adhesion requires homophilic interactions between extracellular domains of E-cadherin molecules from neighboring cells. The interaction of its cytoplasmic domains with the cortical acto-myosin network, appears to strengthen adhesion, although, it is unclear how cortical actin affects the organization and function of E-cadherin dynamically. Here we use the ectopic expression ofDrosophilaE-cadherin (E-cad) in larval hemocytes, which lack endogenous E-cad, to recapitulate functional cell-cell junctions in a convenient model system. We used fluorescence emission anisotropy-based microscopy and Fluorescence Correlation Spectroscopy (FCS) to probe the nanoscale organization of E-cad. We find that E-cad at cell-cell junctions in hemocytes exhibits a clusteredtrans-paired organization, similar to that reported for the adherens junction in the developing embryonic epithelial tissue. Further, we find that extra-junctional E-cad is also organized as relatively immobile nanoclusters as well as diffusive and more loosely packed oligomers and monomers. These oligomers are promoted bycis-interactions of the ectodomain and, strikingly, their growth is constantly counteracted by cortical actomyosin. Oligomers in turn assist in generating nanoclusters that are stabilized by cortical acto-myosin. Thus, actin remodels oligomers and stabilizes nanoclusters, revealing a requirement for actin in the dynamic organization of E-cad at the nanoscale. This dynamic organization is also present at cell-cell contacts (junction), and its disruption affects junctional integrity in the hemocyte system, as well as in the embryo. Our observations uncover a hierarchical mechanism for the nanoscale organization of E-cad, which is necessary for dynamic adhesion and maintaining junctional integrity in the face of extensive remodeling.
CtcfHaploinsufficiency Mediates Intron Retention in A Tissue-specific Manner
Authors: Alharbi Adel B , Schmitz Ulf , Marshall Amy D , Vanichkina Darya , Nagarajah Rajini , Vellozzi Melissa , Wong Justin JL , Bailey Charles G , Rasko John EJ
Published: November 2019

CTCF is a master regulator of gene transcription and chromatin organization with occupancy at thousands of DNA target sites. CTCF is essential for embryonic development and somatic cell viability and has been characterized as a haploinsufficient tumor suppressor. Increasing evidence demonstrates CTCF as a key player in several alternative splicing (AS) regulatory mechanisms, including transcription elongation, regulation of splicing factors, and epigenetic regulation. However, the genome-wide impact ofCtcfdosage on AS has not been investigated. We examined the effect ofCtcfhaploinsufficiency on gene expression and AS in multiple tissues fromCtcfhemizygous (Ctcf+/-) mice. Distinct tissue-specific differences in gene expression and AS were observed inCtcf+/-mice compared to wildtype mice. We observed a surprisingly large number of increased intron retention (IR) events inCtcf+/-liver and kidney, specifically in genes associated with cytoskeletal organization, splicing and metabolism. This study provides further evidence forCtcfdose-dependent and tissue-specific regulation of gene expression and AS. Our data provide a strong foundation for elucidating the mechanistic role of CTCF in AS regulation and its biological consequences.
A natural antisense to brain-derived neurotrophic factor impairs extinction of drug seeking
Authors: Youngson Neil A. , Castino Matthew R. , Stuart Angela , Kershaw Kelly A. , Holmes Nathan M. , Waters Paul D. , Morris Kevin V. , Clemens Kelly J.
Published: November 2019

BACKGROUND

Brain derived neurotrophic factor (BDNF) is critical for the extinction of drug-seeking. Expression of the Bdnf gene is highly regulated via interactions with non-coding RNA, which themselves are altered following drug exposure. Here we investigate whether a novel long non-coding RNA antisense to Bdnf prevents extinction of drug-seeking. METHODS: Strand-specific RNA sequencing identified a novel long non-coding RNA antisense to exon IV of the Bdnf gene in the ventromedial prefrontal cortex of 8 adult male rats. We then assessed asBdnf-IV expression using strand-specific reverse transcription and quantitative polymerase chain reaction following acquisition, extinction or abstinence from intravenous nicotine self-administration (N = 116). A functional role of the asBdnf-IV in extinction of nicotine-seeking was established by infusing gapmer oligonucleotides into the infralimbic cortex prior to extinction and testing for the effect of these infusions on reinstatement and reacquisition of nicotine-seeking (N = 36).

RESULTS

RNA sequencing identified the presence of a novel long non-coding RNA antisense to exon IV of the Bdnf gene (asBdnf-IV). Expression of asBdnf-IV was elevated following intravenous nicotine self-administration but not experimenter-administered nicotine. Elevated asBdnf-IV persisted across abstinence and to a greater extent following extinction training, suggesting an interaction between abstinence and extinction learning. In support of this, knockdown of the asBdnf-IV across extinction, but not abstinence, significantly attenuated nicotine-primed reinstatement of nicotine-seeking.

CONCLUSIONS

asBdnf-IV accumulates in the infralimbic cortex across self-administration training, interferes with the inhibitory learning that underpins extinction of drug-seeking, and predisposes animals to drug relapse.
Histone chaperone Nucleophosmin regulates transcription of key genes involved in oral tumorigenesis
Authors: Senapati Parijat , Dey Suchismita , Sudarshan Deepthi , Bhattacharya Aditya , G Shyla , Das Sadhan , Sudevan Surabhi , Maliekal Tessy Thomas , Kundu Tapas K.
Published: November 2019

Nucleophosmin (NPM1) is a multifunctional histone chaperone that can activate RNA Polymerase II-driven chromatin transcription. Acetylation of NPM1 by acetyltransferase p300 has been shown to further enhance its transcription activation potential. Moreover, its total and acetylated pools are increased in oral squamous cell carcinoma. However, the role of NPM1 or its acetylated form (AcNPM1) in transcriptional regulation in cells is not fully elucidated. Using ChIP-seq analyses, we show that AcNPM1 co-occupies marks of active transcription at promoters and DNase I hypersensitive sites at enhancers. Moreover, NPM1 interacts with proteins involved in transcription, including RNA Pol II, general transcription factors, mediator subunits, histone acetyltransferase complexes, and chromatin remodelers. Moreover, its histone chaperone also contributes to transcriptional activation. We further show that AcNPM1 regulates key genes required for proliferation, migration and invasion potential of oral cancer cells and knockdown of NPM1 mitigates these processes in cells as well as orthotopic tumors in mice. Collectively, these results establish that AcNPM1 functions as a coactivator and regulates the expression of key genes involved in oral tumorigenesis.
Low membrane fluidity triggers lipid phase separation and protein segregation in vivo
Authors: Gohrbandt Marvin , Lipski André , Grimshaw James W. , Buttress Jessica A. , Baig Zunera , Herkenhoff Brigitte , Walter Stefan , Kurre Rainer , Deckers-Hebestreit Gabriele , Strahl Henrik
Published: November 2019

All living organisms adapt their membrane lipid composition in response to changes in their environment or diet. These conserved membrane-adaptive processes have been studied extensively. However, key concepts of membrane biology linked to regulation of lipid composition including homeoviscous adaptation maintaining stable levels of membrane fluidity, and gel-fluid phase separation resulting in domain formation, heavily rely upon in vitro studies with model membranes or lipid extracts. Using the bacterial model organisms Escherichia coli and Bacillus subtilis, we now show that inadequate in vivo membrane fluidity interferes with essential complex cellular processes including cytokinesis, envelope expansion, chromosome replication/segregation and maintenance of membrane potential. Furthermore, we demonstrate that very low membrane fluidity is indeed capable of triggering large-scale lipid phase separation and protein segregation in intact, protein-crowded membranes of living cells; a process that coincides with the minimal level of fluidity capable of supporting growth. Importantly, the in vivo lipid phase separation is not associated with a breakdown of the membrane diffusion barrier function, thus explaining why the phase-separation process induced by low fluidity is biologically reversible.
mity: A highly sensitive mitochondrial variant analysis pipeline for whole genome sequencing data
Authors: Puttick Clare , Kumar Kishore R , Davis Ryan L , Pinese Mark , Thomas David M , Dinger Marcel E , Sue Carolyn M , Cowley Mark J
Published: November 2019

Motivation

Mitochondrial diseases (MDs) are the most common group of inherited metabolic disorders and are often challenging to diagnose due to extensive genotype-phenotype heterogeneity. MDs are caused by mutations in the nuclear or mitochondrial genome, where pathogenic mitochondrial variants are usually heteroplasmic and typically at much lower allelic fraction in the blood than affected tissues. Both genomes can now be readily analysed using unbiased whole genome sequencing (WGS), but most nuclear variant detection methods fail to detect low heteroplasmy variants in the mitochondrial genome.

Results

We present mity, a bioinformatics pipeline for detecting and interpreting heteroplasmic SNVs and INDELs in the mitochondrial genome using WGS data. In 2,980 healthy controls, we observed on average 3,166× coverage in the mitochondrial genome using WGS from blood. mity utilises this high depth to detect pathogenic mitochondrial variants, even at low heteroplasmy. mity enables easy interpretation of mitochondrial variants and can be incorporated into existing diagnostic WGS pipelines. This could simplify the diagnostic pathway, avoid invasive tissue biopsies and increase the diagnostic rate for MDs and other conditions caused by impaired mitochondrial function.

Availability

mity is available from https://github.com/KCCG/mityunder an MIT license.

Contact

clare.puttick@crick.ac.uk, carolyn.sue@sydney.edu.au, MCowley@ccia.org.au
Large-scale transgenicDrosophilaresource collections for loss- and gain-of-function studies
Authors: Zirin Jonathan , Hu Yanhui , Liu Luping , Yang-Zhou Donghui , Colbeth Ryan , Yan Dong , Ewen-Campen Ben , Tao Rong , Vogt Eric , VanNest Sara , Cavers Cooper , Villalta Christians , Comjean Aram , Sun Jin , Wang Xia , Jia Yu , Zhu Ruibao , Peng Pin , Yu Jinchao , Shen Da , Qiu Yuhao , Ayisi Limmond , Ragoowansi Henna , Fenton Ethan , Efrem Senait , Parks Annette , Saito Kuniaki , Kondo Shu , Perkins Liz , Mohr Stephanie E. , Ni Jianquan , Perrimon Norbert
Published: November 2019

The Transgenic RNAi Project (TRiP), aDrosophilafunctional genomics platform at Harvard Medical School, was initiated in 2008 to generate and distribute a genome-scale collection of RNAi fly stocks. To date, the TRiP has generated >15,000 RNAi fly stocks. As this covers mostDrosophilagenes, we have largely transitioned to development of new resources based on CRISPR technology. Here, we present an update on our libraries of publicly available RNAi and CRISPR fly stocks, and focus on the TRiP-CRISPR overexpression (TRiP-OE) and TRiP-CRISPR knockout (TRiP-KO) collections. TRiP-OE stocks express sgRNAs targeting upstream of a gene transcription start site. Gene activation is triggered by co-expression of catalytically dead Cas9 (dCas9) fused to an activator domain, either VP64-p65-Rta (VPR) or Synergistic Activation Mediator (SAM). TRiP-KO stocks express one or two sgRNAs targeting the coding sequence of a gene or genes, allowing for generation of indels in both germline and somatic tissue. To date, we have generated more than 5,000 CRISPR-OE or -KO stocks for the community. These resources provide versatile, transformative tools for gene activation, gene repression, and genome engineering.
Improved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions
Authors: Lees John A. , Tien Mai T. , Galardini Marco , Wheeler Nicole E. , Corander Jukka
Published: November 2019

Discovery of influential genetic variants and prediction of phenotypes such as antibiotic resistance are becoming routine tasks in bacterial genomics. Genome-wide association study (GWAS) methods can be applied to study bacterial populations, with a particular emphasis on alignment-free approaches, which are necessitated by the more plastic nature of bacterial genomes. Here we advance bacterial GWAS by introducing a computationally scalable joint modeling framework, where genetic variants covering the entire pangenome are compactly represented by unitigs, and the model fitting is achieved using elastic net penalization. In contrast to current leading GWAS approaches, which test each genotype-phenotype association separately for each variant, our joint modelling approach is shown to lead to increased statistical power while maintaining control of the false positive rate. Our inference procedure also delivers an estimate of the narrow-sense heritability, which is gaining considerable interest in studies of bacteria. Using an extensive set of state-of-the-art bacterial population genomic datasets we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. We expect that these advances will pave the way for the next generation of high-powered association and prediction studies for an increasing number of bacterial species.
De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells
Authors: Jasmer Douglas P. , Rosa Bruce A. , Tyagi Rahul , Bulman Christina A. , Beerntsen Brenda , Urban Joseph F. , Sakanari Judy , Mitreva Makedonka
Published: November 2019

Efforts to identify new drugs for therapeutic and preventive treatments against parasitic nematodes have gained increasing interest with expanding pathogen omics databases and drug databases from which new anthelmintic compounds might be identified. Here, a novel approach focused on integrating a pan-Nematoda multi-omics data targeted to a specific nematode organ system (the intestinal tract) with evidence-based filtering and chemogenomic screening was undertaken. Based onde novocomputational target prioritization of the 3,564 conserved intestine genes inA. suum, exocytosis was identified as a high priority pathway, and predicted inhibitors of exocytosis were tested using the large roundworm (Ascaris suumlarval stages), a filarial worm (Brugia pahangiadult and L3), a whipworm (Trichuris murisadult), and the non-parasitic nematodeCaenorhabditis elegans. 10 of 13 inhibitors were found to cause rapid immotility inA. suumL3 larvae, and five inhibitors were effective against the three phylogenetically diverse parasitic nematode species, indicating potential for a broad spectrum anthelmintics. Several distinct pathologic phenotypes were resolved related to molting, motility, or intestinal cell and tissue damage using conventional and novel histologic methods. Pathologic profiles characteristic for each inhibitor will guide future research to uncover mechanisms of the anthelmintic effects and improve on drug designs. This progress firmly validates the focus on intestinal cell biology as a useful resource to develop novel anthelmintic strategies.

Author summary

The intestinal cells of parasitic nematodes are not known to regenerate, therefore disruption of essential processes that cause irreparable damage to intestinal cells is expected to promote worm expulsion. To facilitate improved methods of therapy we need to better understand the basic intestinal cell and tissue functions of this critical organ. To that end have undertaken a comprehensive analysis of multi-omics omics data and identify and prioritize intestinal genes/pathways with essential functions and associated drugs and established a foundational model of the STH intestinal system using the large roundwormAscaris suumto test and validate inhibitors of these functions. We found 10 inhibitors to impacted motility, and seven of those showed severe pathology and an apparent irreparable damage to intestinal cells. Furthermore, five inhibitors were effective against the three phylogenetically diverse parasitic nematode species, indicating potential for a broad spectrum anthelmintics. Our results firmly validate the focus on intestinal cell biology as a useful resource to develop novel anthelmintic strategies.
Confirmation of local transmission of Orientia tsutsugamushi during scrub typhus outbreaks in Nepal
Authors: Dhimal Meghnath , Dumre Shyam Prakhas , Sharma Guna Niddhi , Khanal Pratik , Ranabhat Kamal , Shah Lalan Prasad , Lal Bibek Kumar , Jha Runa , Upadhyaya Bishnu Prasad , Acharya Bhim , Shrestha Sanjaya Kumar , Davidson Silas A. , Charoensinphon Piyada , Karki Khem B.
Published: November 2019

Background

Scrub typhus is a severely ignored tropical disease and a leading cause of undifferentiated febrile illness worldwide caused by infection of an obligate intracellular bacteria Orientia tsutsugamushi. It has been rapidly expanding in South Asian countries, although clear epidemiological information is not available from Nepal. After the 2015 earthquake in Nepal, a sudden upsurge in scrub typhus cases was reported. The objective of this study was to investigate scrub typhus and its causative agents in human, rodent and chigger mites to better understand the ongoing transmission ecology.

Methods

Scrub typhus cases with confirmed diagnosis throughout the country were included in the analysis. Studies were concentrated in the Chitwan district, the site of a major outbreak in 2016. Additional country-wide data from 2015 to 2017 was made available from the government database to analyse the disease distribution using geographical mapping.

Results

During 2015-2017, 1,239 scrub typhus cases were confirmed with the largest outbreak occurring in 2016 with 831 (67.1%) cases. The remainder 267 cases were reported in 2017. The case fatality rate was 5.7% in 2015 and declined to 1.1% in 2017. Nationwide outbreak of scrub typhus was identified as the cases were found from 52 of the 75 districts of Nepal. A seasonal trend was observed with a peak during August and September (p = 0.01). In addition to the human cases, the presence of O. tsutsugamushi was also confirmed in rodents and chigger mites from the outbreak areas of southern Nepal.

Conclusion

The detection of O. tsutsugamushi in human, rodent, and chigger mites from outbreak locations and wide-spread reports of scrub typhus throughout the country over two years confirms the ongoing transmission of O. tsutsugamushi with a firmly established ecology in Nepal. The country’s health system needs to be strengthened for systematic surveillance, early outbreaks detection, and immediate response actions including treatment and preventive measures.

Author Summary

Scrub typhus is a disease caused by a bacteria called Orientia tsutsugamushi and transmitted to people through bites of infected chiggers (larval mites). After the 2015 Gorkha earthquake in Nepal, a sudden upsurge in scrub typhus cases was reported with repeated outbreaks from different parts of the country. This study has documted epidemiology of scrub typhus and its causative agents in human, rodent and chigger mites confimring the local transmission O. tsutsugamushi with a firmly established ecology in Nepal. The local transmission of the diseases from most parts of the country demands strengthening for systematic surveillance, early outbreaks detection, and immediate response actions including treatment and preventive measures.
High Prevalence of Strongyloidiasis in Spain: A Hospital-Based Study
Authors: Requena-Méndez Ana , Salas-Coronas Joaquin , Salvador Fernando , Gomez-Junyent Joan , Villar-Garcia Judith , Santin Miguel , Muñoz Carme , Gonzalez-Cordon Ana , Cabezas Fernández Maria Teresa , Sulleiro Elena , del Mar Arenas Maria , Somoza Dolors , Vazquez-Villegas Jose , Treviño Begoña , Rodríguez Esperanza , Valls Maria Eugenia , Subirá Carme , Muñoz Jose ,   on behalf of the STRONG-SEMTSI working group
Published: November 2019

Strongyloidiasis is a prevailing helminth infection ubiquitous in tropical and subtropical areas. However, prevalence data are scarce in migrant populations.

This study aims at evaluating the prevalence of S. stercoralis at hospital level in migrant populations or long term travellers being attended in out-patient and in-patient units as part of a systematic screening implemented in 6 Spanish hospitals. A cross-sectional study was conducted and systematic screening for S. stercoralis infection using serological tests was offered to all eligible participants. The overall seroprevalence of S. stercoralis was 9.04% (95% confidence interval [95%CI] 7.76 −10.31). The seroprevalence of people with a risk of infection acquired in Africa and Latin America was 9.35% (95%CI 7.01-11.69), 9.22% (7.5-10.93), respectively. The number of individuals coming from Asian countries was significantly smaller and the overall prevalence in these countries was 2.9% (95%CI −0.3; −6.2). There was only one case (1/14 (7.14%) from an individual from East European countries. The seroprevalence in units attending potentially immunosuppressed patients was significantly lower (5.64%) compared with the seroprevalence in other units of the hospital (10.20%) or Tropical diseases units (13.33%) (p<0.001). Conclusions: We report a hospital-based systematic screening of strongyloidiasis with a seroprevalence of almost 10% in a mobile population coming from endemic areas suggesting the need of implementing strongyloidiasis screening in hospitalized patients coming from endemic areas, particularly if they are at risk of immunosuppression.

Author summary

Strongyloidiasis is an infection caused by the helminth Strongyloides stercoralis which is ubiquitous in tropical and subtropical areas. In the rest of the countries, it is also frequent in migrants coming from tropical and subtropical areas. The disease is more severe when an infected subject has an impaired immune system. Within this study we have evaluated the prevalence of this infection in people being attended in six Spanish hospitals. The prevalence was around 9%, being higher in Africa and Latin America compared with other regions. In addition, the prevalence in patients with an impaired immune system (immunosuppression) was lower compared with people non suffering immunosuppression. These results suggest that the prevalence of strongyloidiasis is quite high among migrants living in Spain and that a screening programme should be designed, particularly in immunosuppressed patients that are at more risk of suffering severe complications of the infection.
Complementary Performances of Convolutional and Capsule Neural Networks on Classifying Microfluidic Images of Dividing Yeast Cells
Authors: Ghafari Mehran , Clark Justin , Guo Hao-Bo , Yu Ruofan , Sun Yu , Dang Weiwei , Qin Hong
Published: November 2019

Microfluidic-based assays have become effective high-throughput approaches to examining replicative aging of budding yeast cells. Deep learning may offer an efficient way to analyze a large number of images collected from microfluidic experiments. Here, we compare three deep learning architectures to classify microfluidic time-lapsed images of dividing yeast cells into categories that represent different stages in the yeast replicative aging process. We found that convolutional neural networks outperformed capsule networks in terms of accuracy, precision, and recall. The capsule networks had the most robust performance at detecting one specific category of cell images. An ensemble of three best-fitted single-architecture models achieves the highest overall accuracy, precision, and recall due to complementary performances. In addition, extending classification classes and augmentation of the training dataset can improve the predictions of the biological categories in our study. This work lays a useful framework for sophisticated deep-learning processing of microfluidics-based assays of yeast replicative aging.
CXCR4 and MIF are required for neutrophil extracellular trap release triggered byPlasmodium-infected erythrocytes
Authors: Rodrigues Danielle S. A. , Prestes Elisa B. , de Souza Silva Leandro , Pinheiro Ana Acácia S. , Ribeiro Jose Marcos C. , Dicko Alassane , Duffy Patrick E. , Fried Michal , Francischetti Ivo M. B. , Saraiva Elvira M. , Paula Neto Heitor A. , Bozza Marcelo T.
Published: November 2019

Neutrophil extracellular traps (NETs) evolved as a unique effector mechanism contributing to resistance against infection that can also promote tissue damage in inflammatory conditions. Malaria infection can trigger NET release, but the mechanisms and consequences of NET formation in this context remain poorly characterized. Here we show, similarly to previous reports, that patients suffering from severe malaria had increased amounts of circulating DNA and increased neutrophil elastase (NE) levels in plasma. We used cultured erythrocytes and isolated human neutrophils to show thatPlasmodium-infected red blood cells release MIF, which in turn caused NET formation by neutrophils in a mechanism dependent on the C-X-C chemokine receptor type 4 (CXCR4). NET production was dependent on histone citrulination by PAD4 and independent of reactive oxygen species (ROS), myeloperoxidase (MPO) or NE. In vitro, NETs functioned to restrain parasite dissemination in a mechanism dependent on MPO and NE activities. Finally, C57/B6 mice infected withP. bergheiANKA, a well-established model of cerebral malaria, presented high amounts of circulating DNA, while treatment with DNAse increased parasitemia and accelerated mortality, indicating a role for NETs in resistance againstPlasmodiuminfection.

Author summary

Protozoans of the Plasmodium genre infect red blood cells and cause malaria in humans and various other mammalian species. Estimated malaria cases are at more than 200 million, with 450,000 deaths per year, being cerebral malaria a serious complication that accounts for the majority of deaths. Neutrophils are cells that participate in host defense against pathogens. These cells use various mechanisms to kill invading microrganisms, including the release of webs of DNA, called neutrophil extracellular traps (NETs). These NETs can help control infections but can also induce tissue damage and their role in malaria and the mechanisms of NET production during malaria infection are starting to be understood. Here we show that infected red blood cells produce a cytokine, macrophage migration inhibitory factor (MIF) that stimulates neutrophils to release NETs. These NETs function to limitPlasmodiumdissemination and, thus, digestion of NETs with DNAse treatment causes increased parasitemia and accelerated death in an experimental model of cerebral malaria. Our study uncovers the mechanism by which infected red blood cells stimulate neutrophils to release NETs and suggest an important participation of this process in malaria control.
Bacteriophages can be used as infection control agents: A proof-of concept study involving anti-Acinetobacter baumannii phage
Authors: Hussain Aamir , Manzoor Amna , Ullah Ihsan , Aziz Atif , Aziz Mubashar , Saeed Muhammad Qamar
Published: November 2019

Hospital acquired infections are responsible for morbidity and mortality worldwide. Acinetobacter spp. infections are particularly notorious for complicating patient management in ICU settings. Extremely high mortality rates are associated with Acinetobacter infections because of their resistance to first- and second-line drugs. There is imminent need to develop infections control systems that are specific and environment friendly. Here, we report a proof-of-concept anti-Acinetobacter spp. bacteriophage-based infection control assay that is very target specific as well as innocuous to environment. extensively drug resistant (XDR) Acinetobacter baumannii strain was inoculated at various solid surfaces. A bacteriophage, enriched in the same strain, was applied on the inoculated surfaces. Phenol (carbolic acid) was used as a positive control. We show that bacteriophages can be used as infection control agents. In our assay, they killed XDR Acinetobacter baumannii present on solid surfaces. Our bacteriophage was extremely effective at reducing the CFU of inoculated strain to almost undetectable levels.
The heparan sulfate proteoglycan Syndecan-1 influences local bone cell communication via the RANKL/OPG axis
Authors: Timmen Melanie , Hidding Heriburg , Götte Martin , El Khassawna Thaqif , Kronenberg Daniel , Stange Richard
Published: November 2019

The heparan sulfate proteoglycan Syndecan-1, a mediator of signals between the extracellular matrix and cells involved is able to interact with OPG, one of the major regulators of osteoclastogenesis. The potential of osteoblasts to induce osteoclastogenesis is characterized by a switch of OPG (low osteoclastogenic potential) towards RANKL production (high osteoclastogenic potential).

In the present study, we investigated the influence of endogenous Syndecan-1 on local bone-cell-communication via the RANKL/OPG-axis in murine osteoblasts and osteoclasts in wild type and Syndecan-1 lacking cells. Syndecan-1 expression and secretion was increased in osteoblasts with high osteoclastogenic potential. Syndecan-1 deficiency led to increased OPG release by osteoblasts that decreased the availability of RANKL. In co-cultures of Syndecan-1 deficient osteoblasts with osteoclast these increased OPG in supernatant caused decreased development of osteoclasts. Syndecan-1 and RANKL level were increased in serum of aged WT mice, whereas Syndecan-1 deficient mice showed high serum OPG concentration. However, bone structure of Syndecan-1 deficient mice was not different compared to wild type.

In conclusion, Syndecan-1 could be regarded as a new modulator of bone-cell-communication via RANKL/OPG axis. This might be of high impact during bone regeneration or bone diseases like cancer where Syndecan-1 expression is known to be even more prevalent.
VADR: validation and annotation of virus sequence submissions to GenBank
Authors: Schäffer Alejandro A , Hatcher Eneida L , Yankie Linda , Shonkwiler Lara , Brister J Rodney , Karsch-Mizrachi Ilene , Nawrocki Eric P
Published: November 2019

Background

GenBank contains over 3 million viral sequences. The National Center for Biotechnology Information (NCBI) previously made available a tool for validating and annotating influenza virus sequences that is used to check submissions to GenBank. Before this project, there was no analogous tool in use for non-influenza viral sequence submissions.

Results

We developed a system called VADR (Viral Annotation DefineR) that validates and annotates viral sequences in GenBank submissions. The annotation system is based on the analysis of the input nucleotide sequence using models built from curated RefSeqs. Hidden Markov models are used to classify sequences by determining the RefSeq they are most similar to, and feature annotation from the RefSeq is mapped based on a nucleotide alignment of the full sequence to a covariance model. Predicted proteins encoded by the sequence are validated with nucleotide-to-protein alignments using BLAST. The system identifies 43 types of “alerts” that (unlike the previous BLAST-based system) provide deterministic and rigorous feedback to researchers who submit sequences with unexpected characteristics. VADR has been integrated into GenBank’s submission processing pipeline allowing for viral submissions passing all tests to be accepted and annotated automatically, without the need for any human (GenBank indexer) intervention. Unlike the previous submission-checking system, VADR is freely available (https://github.com/nawrockie/vadr) for local installation and use. VADR has been used for Norovirus submissions since May 2018 and for Dengue virus submissions since January 2019. Other viruses with high numbers of submissions will be added incrementally.

Conclusion

VADR improves the speed with which non-flu virus submissions to GenBank can be checked and improves the content and quality of the GenBank annotations. The availability and portability of the software allow researchers to run the GenBank checks prior to submitting their viral sequences, and thereby gain confidence that their submissions will be accepted immediately without the need to correspond with GenBank staff. Reciprocally, the adoption of VADR frees GenBank staff to spend more time on services other than checking routine viral sequence submissions.
Nanopore sequencing undergoes catastrophic sequence failure at inverted duplicated DNA sequences
Authors: Spealman Pieter , Burrell Jaden , Gresham David
Published: November 2019

Inverted duplicated sequences are a common feature of structural variants (SVs) and copy number variants (CNVs). Analysis of CNVs containing inverted duplicated sequences using nanopore sequencing identified recurrent aberrant behavior characterized by incorrect and low confidence base calls that result from a systematic elevation in the current recorded by the sequencing pore. The coincidence of inverted duplicated sequences with catastrophic sequence failure suggests that secondary DNA structures may impair transit through the nanopore.
Zygotic pioneer factor activity of Odd-paired/Zic is necessary for establishing theDrosophilaSegmentation Network
Authors: Soluri Isabella V. , Zumerling Lauren M. , Payan Parra Omar A. , Clark Eleanor G. , Blythe Shelby A.
Published: November 2019

Because regulatory networks of transcription factors drive embryonic patterning, it is possible that chromatin accessibility states impact how networks interact with information encoded in DNA. To determine the interplay between chromatin states and regulatory network function, we performed ATAC seq onDrosophilaembryos over the period spanning the establishment of the segmentation network, from zygotic genome activation to gastrulation. Chromatin accessibility states are dynamic over this period, and establishment of the segmentation network requires maturation of the ground chromatin state. Elimination of all maternal patterning information allows identification of patterning-dependent and -independent dynamic chromatin regions. A significant proportion of patterning-dependent accessibility stems from pioneer activity of the pair-rule factor Odd-paired (opa). Whileopais necessary to drive late opening of segmentation network cis-regulatory elements, competence foropato pioneer is regulated over time. These results indicate that dynamic systems for chromatin regulation directly impact the interpretation of embryonic patterning information.
A multiple-trait Bayesian Lasso for genome-enabled analysis and prediction of complex traits
Authors: Gianola Daniel , Fernando Rohan L.
Published: November 2019

1

A multiple-trait Bayesian LASSO (MBL) for genome-based analysis and prediction of quantitative traits is presented and applied to two real data sets. The data-generating model is a multivariate linear Bayesian regression on possibly a huge number of molecular markers, and with a Gaussian residual distribution posed. Each (one per marker) of theT× 1 vectors of regression coefficients (T: number of traits) is assigned the sameT–variate Laplace prior distribution, with a null mean vector and unknown scale matrixΣ. The multivariate prior reduces to that of the standard univariate Bayesian LASSO whenT= 1. The covariance matrix of the residual distribution is assigned a multivariate Jeffreys prior andΣis given an inverse-Wishart prior. The unknown quantities in the model are learned using a Markov chain Monte Carlo sampling scheme constructed using a scale-mixture of normal distributions representation. MBL is demonstrated in a bivariate context employing two publicly available data sets using a bivariate genomic best linear unbiased prediction model (GBLUP) for benchmarking results. The first data set is one where wheat grain yields in two different environments are treated as distinct traits. The second data set comes from genotypedPinustrees with each individual was measured for two traits, rust bin and gall volume. In MBL, the bivariate marker effects are shrunk differentially, i.e., “short” vectors are more strongly shrunk towards the origin than in GBLUP; conversely, “long” vectors are shrunk less. A predictive comparison was carried out as well where, in wheat, the comparators of MBL where bivariate GBLUP and bivariate Bayes Cπ, a variable selection procedure. A training-testing layout was used, with 100 random reconstructions of training and testing sets. For the wheat data, all methods produced similar predictions. InPinus, MBL gave better predictions that either a Bayesian bivariate GBLUP or the single trait Bayesian LASSO. MBL has been implemented in the Julia language package JWAS and is now available for the scientific community to explore with different traits, species and environments. It is well known that there is no universally best prediction machine and MBL represents a new piece in the armamentarium for genome-enabled analysis and prediction of complex traits.
The transition state and regulation of γ-TuRC-mediated microtubule nucleation revealed by single molecule microscopy
Authors: Thawani Akanksha , Rale Michael J , Coudray Nicolas , Bhabha Gira , Stone Howard A , Shaevitz Joshua W , Petry Sabine
Published: November 2019

Determining how microtubules (MTs) are nucleated is essential for understanding how the cytoskeleton assembles. While the MT nucleator, γ-tubulin ring complex (γ-TuRC) has been identified, precisely how γ-TuRC nucleates a MT remains poorly understood. Here we developed a single molecule assay to directly visualize nucleation of a MT from purifiedXenopus laevisγ-TuRC. We reveal a high γ-/αβ-tubulin affinity, which facilitates assembly of a MT from γ-TuRC. Whereas spontaneous nucleation requires assembly of 8 αβ-tubulins, nucleation from γ-TuRC occurs efficiently with a cooperativity of 4 αβ-tubulin dimers. This is distinct from pre-assembled MT seeds, where a single dimer is sufficient to initiate growth. A computational model predicts our kinetic measurements and reveals the rate-limiting transition where laterally-associated αβ-tubulins drive γ-TuRC into a closed conformation. Putative activation domain of CDK5RAP2, NME7 and TPX2 do not enhance γ-TuRC-mediated nucleation, while XMAP215 drastically increases the nucleation efficiency by strengthening the longitudinal γ-/αβ-tubulin interaction.
Odd-paired is a late-acting pioneer factor coordinating with Zelda to broadly regulate gene expression in early embryos
Authors: Koromila Theodora , Gao Fan , Iwasaki Yasuno , He Peng , Pachter Lior , Gergen J. Peter , Stathopoulos Angelike
Published: November 2019

Pioneer factors such as Zelda help initiate zygotic transcription inDrosophilaearly embryos, but whether other factors support this dynamic process is unclear. Odd-paired (Opa), a zinc-finger transcription factor expressed at cellularization, controls transition of genes from pair-rule to segmental patterns along the anterior-posterior axis. Finding that Opa also regulates late expression through enhancersog_Distal,along the dorso-ventral axis, we hypothesized that Opa acts as a general timing factor. Chromatin-immunoprecipitation (ChIP-seq) confirmed Opain vivobinding tosog_Distalbut also identified widespread binding throughout the genome, comparable to Zelda. Furthermore, chromatin assays (ATAC-seq) demonstrate that Opa, like Zelda, influences chromatin accessibility genome-wide, suggesting both are pioneer factors with common as well as distinct targets. Lastly, embryos lackingopaexhibit widespread, late patterning defects spanning both axes. Collectively, these data suggest Opa, a general timing factor and likely a late-acting pioneer factor, heralds in a secondary wave of zygotic gene expression.
Low redundancy and complementarity shape ecosystem functioning in a low‐diversity ecosystem
Authors: Henderson Christopher J. , Gilby Ben L. , Schlacher Thomas A. , Connolly Rod M. , Sheaves Marcus , Maxwell Paul S. , Flint Nicole , Borland Hayden P. , Martin Tyson S. H. , Olds Andrew D.
Published: November 2019

Ecosystem functioning is positively linked to biodiversity on land and in the sea. In high‐diversity systems (e.g. coral reefs), species coexist by sharing resources and providing similar functions at different temporal or spatial scales. How species combine to deliver the ecological function they provide is pivotal for maintaining the structure, functioning and resilience of some ecosystems, but the significance of this is rarely examined in low‐diversity systems such as estuaries.

We tested whether an ecological function is shaped by biodiversity in a low‐diversity ecosystem by measuring the consumption of carrion by estuarine scavengers. Carrion (e.g. decaying animal flesh) is opportunistically fed on by a large number of species across numerous ecosystems. Estuaries were chosen as the model system because carrion consumption is a pivotal ecological function in coastal seascapes, and estuaries are thought to support diverse scavenger assemblages, which are modified by changes in water quality and the urbanization of estuarine shorelines.

We used baited underwater video arrays to record scavengers and measure the rate at which carrion was consumed by fish in 39 estuaries across 1,000 km of coastline in eastern Australia.

Carrion consumption was positively correlated with the abundance of only one species, yellowfin bream Acanthopagrus australis, which consumed 58% of all deployed carrion. The consumption of carrion by yellowfin bream was greatest in urban estuaries with moderately hardened shorelines (20%–60%) and relatively large subtidal rock bars (>0.1 km2).

Our findings demonstrate that an ecological function can be maintained across estuarine seascapes despite both limited redundancy (i.e. dominated by one species) and complementarity (i.e. there is no spatial context where the function is delivered significantly when yellowfin bream are not present) in the functional traits of animal assemblages. The continued functioning of estuaries, and other low‐diversity ecosystems, might therefore not be tightly linked to biodiversity, and we suggest that the preservation of functionally dominant species that maintain functions in these systems could help to improve conservation outcomes for coastal seascapes.
Interactive range‐limit theory (iRLT): An extension for predicting range shifts
Authors: Sirén Alexej P. K. , Morelli Toni Lyn
Published: November 2019

A central theme of range‐limit theory (RLT) posits that abiotic factors form high‐latitude/altitude limits, whereas biotic interactions create lower limits. This hypothesis, often credited to Charles Darwin, is a pattern widely assumed to occur in nature. However, abiotic factors can impose constraints on both limits and there is scant evidence to support the latter prediction. Deviations from these predictions may arise from correlations between abiotic factors and biotic interactions, as a lack of data to evaluate the hypothesis, or be an artifact of scale. Combining two tenets of ecology—niche theory and predator–prey theory—provides an opportunity to understand how biotic interactions influence range limits and how this varies by trophic level.

We propose an expansion of RLT, interactive RLT (iRLT), to understand the causes of range limits and predict range shifts. Incorporating the main predictions of Darwin's hypothesis, iRLT hypothesizes that abiotic and biotic factors can interact to impact both limits of a species’ range. We summarize current thinking on range limits and perform an integrative review to evaluate support for iRLT and trophic differences along range margins, surveying the mammal community along the boreal‐temperate and forest‐tundra ecotones of North America.

Our review suggests that range‐limit dynamics are more nuanced and interactive than classically predicted by RLT. Many (57 of 70) studies indicate that biotic factors can ameliorate harsh climatic conditions along high‐latitude/altitude limits. Conversely, abiotic factors can also mediate biotic interactions along low‐latitude/altitude limits (44 of 68 studies). Both scenarios facilitate range expansion, contraction or stability depending on the strength and the direction of the abiotic or biotic factors. As predicted, biotic interactions most often occurred along lower limits, yet there were trophic differences. Carnivores were only limited by competitive interactions (n = 25), whereas herbivores were more influenced by predation and parasitism (77%; 55 of 71 studies). We highlight how these differences may create divergent range patterns along lower limits.

We conclude by (a) summarizing iRLT; (b) contrasting how our model system and others fit this hypothesis and (c) suggesting future directions for evaluating iRLT.
Stigma, trauma and sexuality: the experiences of women hospitalised with serious mental illness
Authors: Frieh Emma C.
Published: November 2019

Women with serious mental illness (SMI) occupy a social position in which their experiences are simultaneously influenced by stigmatisation, institutionalisation and gendered dimensions of trauma and power. Women with SMI are stigmatised in society, pushed to the margins and left vulnerable to victimisation and rejection, particularly if hospitalised in psychiatric institutions. Using modified labelling theory, I investigate how women hospitalised with SMI, especially those who have histories of sexual abuse and trauma, experience sexuality and perceive men and masculinity. I extend modified labelling theory by empirically analysing the role of social status and power in the labelling process. Specifically, I focus on gender, and analyse interviews with 55 women in US psychiatric hospitals, focusing on gendered experiences of trauma, stigma and attitudes about sexuality. I show how trauma increases the salience of stigma and potential for retraumatisation, both of which are amplified by the institutional setting. I find meaningful differences in the narratives of women who have experienced trauma and those who have not. Modified labelling theory helps explain how labelling can perpetuate self‐stigma, which threatens women's self‐esteem, safety and trust in others. The intersection of these experiences extends modified labelling theory and may have profound implications for recovery.
Efficiency and Shareholder Value in Australian Banking
Authors: Hoang Van H. T. , Hoang Nam T. , Yarram Subba R.
Published: November 2019

This paper investigates the influences of efficiency, concentration and market power on the shareholder value of 73 Australian authorised deposit‐taking institutions over the 2000–15 period. Four alternative proxies for shareholder value (net interest margin, return on equity, Tobin’s q ratio and economic value‐added ratio) are employed to test two competing hypotheses, the structure–conduct–performance hypothesis and the efficient structure hypothesis. Results from panel data analysis show that both hypotheses are applicable to varying degrees to the different aspects of shareholder value. First, the inference that high concentration results in oligopolistic behaviour and collusive arrangements may not apply to the Australian banking sector. Second, enhancement of market power tends to promote economic returns but impedes other facets of performance. Third, technical efficiency has a positive impact on returns on equity, while scale efficiency has a positive influence on market value and a negative influence on interest and returns on equity. Finally, the outcomes indicate that additional control factors, such as size, non‐interest income, operating costs, capitalisation, credit risk, inflation, and GDP growth rate, impact significantly on different views of shareholder value.