bluuebunny/crossref_metadata_2025 huggingface dataset:
The monothiol glutaredoxin Grx4 interacts with the Cryptococcus iron regulator Cirl and regulates iron homeostasis and virulence in the Cryptococcus neoformans
Authors: Attarian Rodgoun , Hu Guanggan , Caza Melissa , Sanchez-Leon Eddy , Croll Daniel , Do Eunsoo , Bach Horacio , Missall Tricia , Lodge Jennifer , Jung Won Hee , Kronstad James W.
Published: July 2018

The acquisition of iron and the maintenance of iron homeostasis are important aspects of the virulence in the pathogenic fungus Cryptococcus neoformans. In this study, we identified the monothiol glutaredoxin Grx4 as a binding partner of Cir1, a master regulator of iron-responsive genes and virulence factor elaboration in C. neoformans. Monothiol glutaredoxins are important regulators of iron homeostasis because of their conserved roles in [2Fe-2S] cluster sensing and trafficking. We confirmed that Grx4 binds Cir1 and demonstrated that iron repletion promotes the relocalization of Grx4 from the nucleus to the cytoplasm. Nuclear retention is partially dependent on Cir1 and also influenced by treatment with the proteasome inhibitor bortezomib. Cir1 remains in the nucleus in both iron replete and iron limiting conditions. We also found that a grx4Δ mutant displayed iron-related phenotypes similar to those of a cir1Δ mutant, including poor growth upon iron deprivation. Importantly, a grx4Δ mutant was avirulent in mice, a phenotype consistent with observed defects in the key virulence determinants, capsule and melanin, and poor growth at 37°C. A comparative transcriptome analysis of a grx4Δ mutant and the WT strain in low iron and iron-replete conditions confirmed a central role for Grx4 in iron homeostasis. Dysregulation of iron-related metabolism was consistent with grx4Δ mutant phenotypes related to oxidative stress, mitochondrial function, and DNA repair. Overall, the phenotypes of the grx4Δ mutant and the RNA-Seq analysis support the hypothesis that Grx4 functions as a sensor of iron levels, in part through an interaction with Cir1, to extensively regulate iron homeostasis and contribute to virulence.
Type I-E CRISPR-Cas system as an immune system in a eukaryote
Authors: Rath Devashish , Amlinger Lina , Bindal Gargi , Lundgren Magnus
Published: July 2018

Defense against viruses and other mobile genetic elements (MGEs) is important in many organisms. The CRISPR-Cas systems found in bacteria and archaea constitute adaptive immune systems that acquire the ability to recognize MGEs by introducing nucleic acid samples, spacers, in the CRISPR locus. The CRISPR is transcribed and processed, and the produced CRISPR RNAs guide Cas proteins to degrade matching nucleic acid sequences. No CRISPR-Cas system is found to occur naturally in eukaryotic cells but here we demonstrate interference by type I-E CRISPR-Cas system from Escherichia coli introduced in Saccharomyces cerevisiae. The designed CRISPR arrays are properly expressed and processed in S. cerevisiae. Targeted plasmids display reduced transformation efficiency, indicative of DNA cleavage. Unlike e.g. Cas9-based systems, which can be used to inactivate MGEs in eukaryotes by introducing specific mutations, type I-E systems processively degrade the target. The type I-E system thus allows for defense without knowledge of MGE gene function. The reconstituted CRISPR-Cas system in S. cerevisiae can also function as a basic research platform for testing the role of various factors in the interference process.
The reovirus μ1 protein contributes to the environmental stability of virions
Authors: Snyder Anthony J. , Wang Joseph Che-Yen , Danthi Pranav
Published: July 2018

The mammalian orthoreovirus (reovirus) outer capsid is composed of 200 μ1-σ3 heterohexamers and a maximum of 12 σ1 trimers. During cell entry, σ3 is degraded by luminal or intracellular proteases to generate a metastable intermediate, called infectious subviral particle (ISVP). Prior to disassembly, σ3 stabilizes the virion by capping μ1. Reovirus fails to establish a productive infection when σ3 degradation is prevented, suggesting proteolytic priming is required for entry. Once uncovered, ISVPs are converted to ISVP*s, which is accompanied by a μ1 rearrangement. Nonetheless, whether σ3 degradation can be bypassed for virions to adopt an altered conformation is undetermined. In this report, we utilized the T1L/T3D M2 reassortant, which encodes a mismatched outer capsid, to further investigate the determinants of reovirus stability. When μ1-σ3 were derived from different strains, virions resembled wild type in structure and protease sensitivity. Using heat as a surrogate for environmental assault, T1L/T3D M2 ISVPs were more susceptible to inactivation than wild type ISVPs. In contrast, virions of each strain were equally stable. Surprisingly, virion associated μ1 rearranged into an ISVP*-like conformation concurrent with loss of infectivity. Despite the presence σ3, a hyperstable variant of μ1 also contributed to heat resistance. The dual layered architecture of reovirus allowed for differential sensitivity to inactivating agents; the inner capsid (core) displayed exceptional resistance to heating. Together, these findings reveal a previously undefined contribution from μ1 in maintaining virion stability.
Schizophrenia risk and reproductive success: A Mendelian randomization study
Authors: Lawn Rebecca B , Sallis Hannah M , Taylor Amy E , Wootton Robyn E , Smith George Davey , Davies Neil M , Hemani Gibran , Fraser Abigail , Penton-Voak Ian S , Munafò Marcus R
Published: July 2018

Schizophrenia is a debilitating and heritable mental disorder associated with lower reproductive success. However, the prevalence of schizophrenia is stable over populations and time, resulting in an evolutionary puzzle: how is schizophrenia maintained in the population given its apparent fitness costs? One possibility is that increased genetic liability for schizophrenia, in the absence of the disorder itself, may confer some reproductive advantage. We assessed the correlation and causal effect of genetic liability for schizophrenia with number of children and age at first birth using data from the Psychiatric Genomics Consortium and UK Biobank. Linkage disequilibrium score regression showed little evidence of genetic correlation between genetic liability for schizophrenia and number of children (rg=0.002,p=0.84) or age at first birth (rg=-0.007,p=0.45). Mendelian randomization indicated no robust evidence of a causal effect of genetic liability for schizophrenia on number of children (mean difference: 0.003 increase in number of children per doubling in the natural log odds ratio of schizophrenia risk, 95% CI: −0.003 to 0.009,p=0.39) or age at first birth (−0.004 years lower age at first birth, 95% CI: −0.043 to 0.034,p=0.82). These results suggest that increased genetic liability for schizophrenia does not confer a reproductive advantage.
Draft genome sequences ofHirudo medicinalisand salivary transcriptome of three closely related medicinal leeches
Authors: Babenko Vladislav V. , Podgorny Oleg V. , Manuvera Valentin A. , Kasianov Artem S. , Manolov Alexander I. , Grafskaia Ekaterina N. , Shirokov Dmitriy A. , Kurdyumov Alexey S. , Vinogradov Dmitriy V. , Nikitina Anastasia S. , Kovalchuk Sergey I. , Anikanov Nickolay A. , Butenko Ivan O. , Pobeguts Olga V. , Matushkina Daria S. , Rakitina Daria V. , Kostryukova Elena S. , Zgoda Victor G. , Baskova Isolda P. , Trukhan Vladimir M. , Gelfand Mikhail S. , Govorun Vadim M. , Schiöth Helgi B. , Lazarev Vassili N.
Published: July 2018

Salivary cell secretion (SCS) plays a critical role in blood feeding by medicinal leeches, making them of use for certain medical purposes even today. We annotated theHirudo medicinalisgenome and performed RNA-seq on salivary cells isolated from three closely related leech species,H. medicinalis, Hirudo orientalis,andHirudo verbana.Differential expression analysis verified by proteomics identified salivary cell-specific genes, many of which encode previously unknown salivary components. However, the genes encoding known anticoagulants were not differentially expressed in the salivary cells. The function-related analysis of the unique salivary cell genes enabled an update of the concept of interactions between salivary proteins and components of haemostasis. Thus, our study provides one of the most comprehensive knowledge of the genetic fundamentals of the blood-sucking lifestyle in leeches.
Single-embryo and single-blastomere immunoblotting reports protein expression heterogeneity in early-stage preimplantation embryos
Authors: Rosàs-Canyelles Elisabet , Modzelewski Andrew J. , He Lin , Herr Amy E.
Published: July 2018

Understanding how a zygote develops from a single cell into a multicellular organism has benefitted from single-cell tools, including RNA sequencing (RNA-Seq) and immunofluorescence (IF). However, scrutinizing inter- and intra-embryonic phenotypic variation is hindered by two fundamental limitations; the loose correlation between transcription and translation and the cross-reactivity of immunoreagents. To address these challenges, we describe a high-specificity microfluidic immunoblot optimized to quantify protein expression from all stages of mouse preimplantation development. Despite limited availability of isoform-specific immunoreagents, the immunoblot resolves inter-embryonic heterogeneity of embryo-specific isoforms (i.e., DICER-1). We observed significantly higher DICER-1 isoform expression in oocytes when compared to two-cell embryos, and further find that protein expression levels follow the same trend as mRNA for both the full-length and truncated DICER-1 isoforms. At the morula stage, we assayed both whole and disaggregated embryos for loading controls (β-tubulin, GAPDH) and markers that regulate cell fate decisions (CDX-2, SOX-2). In disaggregated morula, we found that cell volume showed positive, linear correlation with expression of β-tubulin and SOX-2. In dissociated two-cell and four-cell blastomeres, we detect significant inter-blastomeric variation in GADD45a expression, corroborating suspected cellular heterogeneity even in the earliest multicellular stage of preimplantation embryos. As RNA-Seq and other transcript-centric approaches continue to further probe preimplantation development, the demand for companion protein-based techniques rises. The reported microfluidic immunoblot serves as an essential tool for understanding mammalian development by providing high-specificity and direct measurements of protein targets at single-embryo and single-blastomere resolution.
Finding the difference between periosteal and endocortical bone adaptation by using Artificial Neural Networks
Authors: Tiwari Abhishek Kumar , Prasad Jitendra
Published: July 2018

In silico models of bone adaptation successfully simulated in vivo periosteal bone apposition, however, there are instances where these models may have limited success in predicting the new bone formation at endocortical surface. In vivo studies have highlighted that cortical bone surfaces may have differences in their modeling or remodeling responses to mechanical loading. However, the principle which the two cortical surfaces follow in bone adaptation is not very clear. This work accordingly attempts to understand how periosteal and endocortical surfaces accommodate loading-induced new bone formation. A neural network model is used to serve the purpose. A relationship is established to compute new bone thickness as a function of mechanical parameters (normal and shear strains) and non-mechanical parameters (distances from the neutral axis and the centroid) at the two surfaces. Analytical results indicate that two cortical surfaces behave opposite to each other in order to achieve optimal distribution of newly formed bone. The outcomes may be useful in establishing a unifying principle to predict site-specific new bone formation.
Modelling the brain response to arbitrary visual stimulation patterns for a flexible high-speed BCI
Authors: Nagel Sebastian , Spüler Martin
Published: July 2018

Visual evoked potentials (VEPs) can be measured in the EEG as response to a visual stimulus. Commonly, VEPs are displayed by averaging multiple responses to a certain stimulus or a classifier is trained to identify the response to a certain stimulus. While the traditional approach is limited to a set of predefined stimulation patterns, we present a method that models the general process of VEP generation and thereby can be used to predict arbitrary visual stimulation patterns from EEG and predict how the brain responds to arbitrary stimulation patterns. We demonstrate how this method can be used to model single-flash VEPs, steady state VEPs (SSVEPs) or VEPs to complex stimulation patterns. It is further shown that this method can also be used in a BCI to allow information transfer rates of more than 470 bit/min and lead to more flexible BCIs with a virtually unlimited amount of targets and any desired trial duration.
Chromatin Condensation Fluctuations Rather than Steady-State Predict Chromatin Accessibility
Authors: Audugé Nicolas , Padilla-Parra Sergi , Tramier Marc , Borghi Nicolas , Coppey-Moisan Maïté
Published: July 2018

Chromatin accessibility to protein factors is critical for genome activities. Dynamic changes in nucleosomal DNA compaction and higher order chromatin structures are expected to allow specific sites to be accessible to regulatory factors and the transcriptional machinery. However, the dynamic properties of chromatin that regulate its accessibility are poorly understood. Here, we took advantage of the microenvironment sensitivity of the fluorescence lifetime of EGFP-H4 histone incorporated in chromatin to map in the nucleus of live cells the dynamics of chromatin condensation and its direct interaction with a tail acetylation recognition domain (the double bromodomain module of human TAFII250, dBD). We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation. Fluctuations are spontaneous, yet their amplitudes are affected by their sub-nuclear localization and by distinct and competing mechanisms dependent on histone acetylation, ATP, and both. Moreover, we show that accessibility of acetylated histone H4 to dBD is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.

Significance

In higher eukaryotes, the structure and compaction of chromatin are considered as barriers to genome activities. Epigenetic marks such as post-translational modifications of histones can modify the structure and compaction of chromatin. The accessibility of protein factors to these epigenetic marks is therefore of paramount importance for genome activities. We reveal chromatin condensation fluctuations supported by mechanisms fundamentally distinct from that of condensation itself. We show that accessibility of acetylated histone H4 to double bromodomains is not restricted by chromatin condensation nor predicted by acetylation, rather, it is predicted by chromatin condensation fluctuations.

Classification

Biological Sciences, Cell Biology
Diallel Analysis for Morphological and Biochemical Traits in Tomato Cultivated Under the Influence of Tomato Leaf Curl Virus
Authors: Kaushik Prashant , Dhaliwal Major Singh
Published: July 2018

Eloquent information about the genetic basis of inheritance is important for any breeding program. Therefore, a diallel study was conducted under the influence of tomato leaf curl virus (TLCV) disease, using the eleven advanced lines of tomato. Firstly, the information regarding percent disease index (PDI) was determined via artificial screening with viruliferous whiteflies. Later, these lines were crossed in half diallel mating design to produce fifty-five one-way hybrids. These hybrids and parental genotypes were evaluated for seven morphological and three biochemical traits under open field conditions. Using the Griffing approach (Method II and Model I) basis of inheritance of traits were determined. Also, a Bayesian model was applied to the total yield descriptor. Correlations data indicated that total yield was not correlated with any other trait. The significant general combining ability (GCA) and specific combining ability (SCA) values indicates exploitable genetic variation. The broad-sense heritability values were larger than narrow-sense heritability, showing that selection will be efficient for the improvement of these traits. Hybrid combinations H23, H42 and H49 can be considered efficient for the selection of multiple traits, including yield. Overall, this study provides a useful information regarding the genetics of important traits of tomato under TLCV infestation.
Antiviral Response by Plasmacytoid Dendritic Cells via Interferogenic Synapse with Infected Cells
Authors: Assil Sonia , Coléon Séverin , Décembre Elodie , Sherry Lee , Allatif Omran , Webster Brian , Dreux Marlene
Published: July 2018

Type I interferon (IFN-I) is critical for protection against viral infections. Plasmacytoid dendritic cells (pDCs) massively produce IFN-I against viruses. Physical contacts are required for pDC-mediated sensing of cells infected by genetically distant viruses. How and why these contacts are established remains enigmatic. Using dengue, hepatitis C, zika viruses, we demonstrate that the pDC/infected cell interface is a specialized platform for viral immunostimulatory-RNA transfer, which we named interferogenic synapse and required for pDC-mediated antiviral response. This synapse is an exquisitely differentiated territory with polarized adhesion complexes and regulators of actin network and endocytosis. Toll-like receptor 7-induced signaling in pDCs promotes the interferogenic synapse establishment, thus providing a feed-forward regulation that sustains contacts with infected cells. We propose that the interferogenic synapse is crucial to pDC function as it allows scanning of infected cells to locally secrete IFN-I at the infection site, thereby confining a response potentially deleterious to the host.

Highlights

pDCs adhere to infected cells via αLβ2integrin/ICAM-1

Regulators of actin network and endocytosis polarize at contact

TLR7-induced signaling potentiates pDC polarity

Infected cells activate pDCs by interferogenic synapse
LRScaf: Improving Draft Genomes Using Long Noisy Reads
Authors: Qin Mao , Wu Shigang , Li Alun , Zhao Fengli , Feng Hu , Ding Lulu , Chang Yuxiao , Ruan Jue
Published: July 2018

Background

The advent of Third Generation Sequencing (TGS) technologies opens the door to improve genome assembly. Long reads are promised to enhance the quality of fragmental draft assemblies constructed from Next Generation Sequencing (NGS) technologies. To date, a few of algorithms, i.e., SSPACE-LongRead, OPERA-LG, SMIS, npScarf, DBG2OLC, Unicycler, and LINKS, have been released that are capable of improving draft assemblies. However, hybrid assembly on large genomes is still challenging.

Results

We develop a scalable and computationally efficient scaffolder, Long Reads Scaffolder (LRScaf), that is capable of boosting assembly contiguity to a large extent using long reads. In our experiment, our method significantly improves the contiguity of human draft assemblies, increasing the NG50 value of CHM1 from 127.5 Kb to 10.4 Mb using 20-fold coverage PacBio dataset and the NG50 value of NA12878 from 115.7 Kb to 17.4 Mb using 35-fold coverage Nanopore dataset. The run time for the scaffolding procedure using LRScaf is the shortest in all cases of our experiment. Compared with the run time of SSPACE-LongRead, LRScaf is faster 300 times for S. cerevisiae and 2,300 times for D. melanogaster. The peak RAM of LRScaf, by contrast, is more efficient than LINKS in our test. For the rice case, the peak RAM of LINKS (877.72 Gb) is about 196 times higher than LRScaf. For the experiment of human assembly, the peak RAM of LINKS is beyond the capacity of system memory (1 Tb) whereas LRScaf takes 20.28 and 41.20 Gb on CHM1 and NA12878 datasets.

Conclusions

The new method, LRScaf, yields the best or at least moderate contiguity and accuracy of scaffolds in the shortest run time compared with the state-of-the-art methods. Furthermore, it offers a new opportunity for the hybrid assembly of large genomes.
Integrated sequence and gene expression analysis of mouse models of breast cancer reveals critical events with human parallels
Authors: Rennhack Jonathan P , Swiatnicki Matthew , Zhang Yueqi , Li Caralynn , Bylett Evan , Ross Christina , Szczepanek Karol , Hanrahan William , Jayatissa Muthu , Hunter Kent , Andrechek Eran R.
Published: July 2018

Mouse models have an essential role in cancer research, yet little is known about how various models resemble human cancer at a genomic level. However, the shared genomic alterations in each model and corresponding human cancer are critical for translating findings in mice to the clinic. We have completed whole genome sequencing and transcriptome profiling of two widely used mouse models of breast cancer, MMTV-Neu and MMTV-PyMT. This genomic information was integrated with phenotypic data and CRISPR/Cas9 studies to understand the impact of key events on tumor biology. Despite the engineered initiating transgenic event in these mouse models, they contain similar copy number alterations, single nucleotide variants, and translocation events as human breast cancer. Through integrative in vitro and in vivo studies, we identified copy number alterations in key extracellular matrix proteins including Collagen 1 Type 1 alpha 1 (Col1a1) and Chondroadherin (CHAD) that drive metastasis in these mouse models. Importantly this amplification is also found in 25% of HER2+ human breast cancer and is associated with increased metastasis. In addition to copy number alterations, we observed a propensity of the tumors to modulate tyrosine kinase mediated signaling through mutation of phosphatases. Specifically, we found that 81% of MMTV-PyMT tumors have a mutation in the EGFR regulatory phosphatase, PTPRH. Mutation in PTPRH led to increased phospho-EGFR levels and decreased latency. Moreover, PTPRH mutations increased response to EGFR kinase inhibitors. Analogous PTPRH mutations are present in lung cancer patients and together this data suggests that a previously unidentified population of human lung cancer patients may respond to EGFR targeted therapy. These findings underscore the importance of understanding the complete genomic landscape of a mouse model and illustrate the utility this has in understanding human cancers.
Scedar: a scalable Python package for single-cell RNA-seq exploratory data analysis
Authors: Zhang Yuanchao , Kim Man S. , Reichenberger Erin R. , Stear Ben , Taylor Deanne M.
Published: July 2018

In single-cell RNA-seq (scRNA-seq) experiments, the number of individual cells has increased exponentially, and the sequencing depth of each cell has decreased significantly. As a result, analyzing scRNA-seq data requires extensive considerations of program efficiency and method selection. In order to reduce the complexity of scRNA-seq data analysis, we present scedar, a scalable Python package for scRNA-seq exploratory data analysis. The package provides a convenient and reliable interface for performing visualization, imputation of gene dropouts, detection of rare transcriptomic profiles, and clustering on large-scale scRNA-seq datasets. The analytical methods are efficient, and they also do not assume that the data follow certain statistical distributions. The package is extensible and modular, which would facilitate the further development of functionalities for future requirements with the open-source development community. The scedar package is distributed under the terms of the MIT license at https://pypi.org/project/scedar.
Development of a vanillate biosensor for the vanillin biosynthesis pathway in E. coli
Authors: Kunjapur Aditya M. , Prather Kristala L. J.
Published: July 2018

Genetically encoded small molecule sensors can facilitate metabolic engineering by enabling high-throughput detection of metabolite concentrations, directed evolution of host and pathway enzymes, and dynamic regulation. The engineered de novo vanillin biosynthesis pathway assembled in Escherichia coli is industrially relevant and ideal for biosensor deployment given that the pathway requires only three heterologous enzyme-catalyzed reactions, generates naturally occurring metabolites, and may benefit from dynamic regulation. However, pathway flux is stalled and diverted by the activity of the Homo sapiens catechol O-methyltransferase, which is intended to catalyze the conversion of protocatechuate to vanillate. To confront this challenge, we constructed and applied a vanillate sensor based on the Caulobacter crescentus VanR-VanO system. Using components from a previously characterized E. coli promoter library, we achieved greater than 14-fold dynamic range in our best rationally constructed sensor. We characterized sensor substrate specificity and found that this construct and an evolved variant are remarkably selective, exhibiting no detectable response to the regioisomer byproduct isovanillate. We then harnessed the evolved biosensor to conduct rapid bioprospecting of natural catechol O-methyltransferases. We identified eight that appear to have greater desired activity than the originally used variant, including three previously uncharacterized O-methyltransferases. Collectively, these efforts enrich our knowledge of how biosensing can aid metabolic engineering and constitute the foundation for future improvements in vanillin pathway productivity.
Kipoi: accelerating the community exchange and reuse of predictive models for genomics
Authors: Avsec Žiga , Kreuzhuber Roman , Israeli Johnny , Xu Nancy , Cheng Jun , Shrikumar Avanti , Banerjee Abhimanyu , Kim Daniel S. , Urban Lara , Kundaje Anshul , Stegle Oliver , Gagneur Julien
Published: July 2018

Advanced machine learning models applied to large-scale genomics datasets hold the promise to be major drivers for genome science. Once trained, such models can serve as a tool to probe the relationships between data modalities, including the effect of genetic variants on phenotype. However, lack of standardization and limited accessibility of trained models have hampered their impact in practice. To address this, we present Kipoi, a collaborative initiative to define standards and to foster reuse of trained models in genomics. Already, the Kipoi repository contains over 2,000 trained models that cover canonical prediction tasks in transcriptional and post-transcriptional gene regulation. The Kipoi model standard grants automated software installation and provides unified interfaces to apply and interpret models. We illustrate Kipoi through canonical use cases, including model benchmarking, transfer learning, variant effect prediction, and building new models from existing ones. By providing a unified framework to archive, share, access, use, and build on models developed by the community, Kipoi will foster the dissemination and use of machine learning models in genomics.
DNA Methylation by Restriction Modification Systems Affects the Global Transcriptome Profile inBorrelia burgdorferi
Authors: Casselli Timothy , Tourand Yvonne , Scheidegger Adam , Arnold William K. , Proulx Anna , Stevenson Brian , Brissette Catherine A.
Published: July 2018

Prokaryote restriction modification (RM) systems serve to protect bacteria from potentially detrimental foreign DNA. Recent evidence suggests that DNA methylation by the methyltransferase (MTase) components of RM systems can also have effects on transcriptome profiles. The causative agent of Lyme disease,Borrelia burgdorferi, encodes two RM systems with N6-Methyladenosine (m6A) MTase activity. The specific recognition and/or methylation sequences have not been identified for eitherB. burgdorferiMTase, and it is not currently known whether these RM systems influence transcriptome profiles. In the current study, Single Molecule Real Time sequencing was utilized to map genome-wide m6A sites, and to identify consensus modified motifs in wild-typeB. burgdorferias well as isogenic MTase mutants. Four conserved m6A motifs were identified, and were fully attributable to the presence of specific MTases. Whole-genome transcriptome changes were observed in conjunction with the loss of MTase enzymes, indicating that DNA methylation by RM systems has effects on gene expression inB. burgdorferi. The results of this study provide a comprehensive view of the DNA methylation pattern inB. burgdorferi, and the accompanying gene expression profiles add to the emerging body of research on RM systems and gene regulation in bacteria.

IMPORTANCE

Lyme disease is the most prevalent vector-borne disease in North America, and is classified by the Centers for Disease Control and Prevention (CDC) as an emerging infectious disease with an expanding geographical area of occurrence. Previous studies have shown that the causative bacterium,Borrelia burgdorferi, methylates its genome using restriction modification systems that allow for the distinction of self from foreign DNA. Although much research has focused on the regulation of gene expression inB. burgdorferi, the effects of DNA methylation on gene regulation has not been evaluated. The current study characterizes the patterns of DNA methylation by restriction modification systems inB. burgdorferi, and evaluates the resulting effects on gene regulation in this important pathogen.
Rootstocks shape the rhizobiome: Rhizosphere and endosphere bacterial communities in the grafted tomato system
Authors: Poudel Ravin , Jumpponen Ari , Kennelly Megan M. , Rivard Cary L. , Gomez-Montano Lorena , Garrett Karen A.
Published: July 2018

Root-associated microbes are critical to plant health and performance, although understanding of the factors that structure these microbial communities and theory to predict microbial assemblages are still limited. Here we use a grafted tomato system to study the effects of rootstock genotypes and grafting in endosphere and rhizosphere microbiomes that were evaluated by sequencing 16S rRNA. We compared the microbiomes of nongrafted tomato cultivar BHN589, selfgrafted BHN589, and BHN589 grafted to Maxifort or RST-04-106 hybrid rootstocks. OTU-based bacterial diversity was greater in Maxifort compared to nongraft controls, whereas bacterial diversity in the controls (selfgraft and nongraft) and the other rootstock (RST-04-106) was similar. Grafting itself did not affect bacterial diversity; diversity in the selfgraft was similar to the nongraft. Bacterial diversity was higher in the rhizosphere than in the endosphere for all treatments. However, despite the lower overall diversity, there was a greater number of differentially abundant OTUs (DAOTUs) in the endosphere, with the greatest number of DAOTUs associated with Maxifort. In a PERMANOVA analysis, there was evidence for an effect of rootstock genotype on bacterial communities. The endosphere-rhizosphere compartment and study site explained a high percentage of the differences among bacterial communities. Further analyses identified OTUs responsive to rootstock genotypes in both the endosphere and the rhizosphere. Our findings highlight the effects of rootstocks on bacterial diversity and composition. The influence of rootstock and plant compartment on microbial communities indicates opportunities for the development of designer communities and microbiome-based breeding to improve future crop production.

Importance

Understanding factors that control microbial communities is essential for designing and supporting microbiome-based agriculture. In this study, we used a grafted tomato system to study the effect of rootstock genotypes and grafting on bacterial communities colonizing the endosphere and the rhizosphere. Comparing the bacterial communities in control treatments (nongraft and selfgraft plants) with the hybrid rootstocks used by farmers, we evaluated the effect of rootstocks on overall bacterial diversity and composition. These findings indicate the potential for using plant genotype to indirectly select bacterial taxa. In addition, we identify taxa responsive to each rootstock treatments, which may represent candidate taxa useful for biocontrol and in biofertilizers.
Microfluidic study of effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength in microchannels
Authors: Liu Na , Skauge Tormod , Landa-Marbán David , Hovland Beate , Thorbjørnsen Bente , Radu Florin Adrain , Vik Bartek Florczyk , Baumann Thomas , Bødtker Gunhild
Published: July 2018

Biofilm accumulation in the porous media can cause plugging and change many physical properties of porous media. Up to now, applications of desired biofilm growth and its
subsequent bioplugging have been attempted for various practices. A deeper understanding of the relative influences of hydrodynamic conditions including flow velocity and nutrient concentration, on biofilm growth and detachment is necessary to plan and analyze bioplugging experiments and field trials. The experimental results by means of microscopic imaging over a T-shape microchannel show that flow velocity and nutrient concentrations can have significant impacts on biofilm accumulation and adhesive strength in both flowing and stagnant microchannels. Increase in fluid velocity could facilitate biofilm growth, but that above a velocity threshold, biofilm detachment and inhibition of biofilm formation due to high shear stress were observed. High nutrient concentration prompts the biofilm growth, but was accompanied by a relatively weak adhesive strength. This research provides an overview of biofilm development in a hydrodynamic environment for better predicting and modelling the bioplugging associated with porous system in petroleum industry, hydrogeology, and water purification.

IMPORTANCE

In the recent decade, the use of bacteria has become more and more important in many applications. Bioplugging caused by bacteria growth in porous media has been explored as a viable technique for some applications, such as bioremediation, water purification and microbial enhanced oil recovery (MEOR). In order to control biofilms/biomasses selectively/directionally plugging in desirable places, the role of hydrodynamic conditions on biofilm growth and detachment is essential to investigate. Herein, a T-shape microchannel was prepared to study effects of flow velocity and nutrient concentration on biofilm accumulation and adhesive strength at pore scale. Our results suggest that flow velocity and nutrient concentration could control biofilm accumulation in microchannels. The finding helps explain and predict the engineering bioplugging in porous media, especially for the selective plugging strategy of a MEOR field trial.
Activation of 2,4-diaminoquinazoline in Mycobacterium tuberculosis by Rv3161c, a putative dioxygenase
Authors: Melief Eduard , Bonnett Shilah A. , Zuniga Edison S. , Parish Tanya
Published: July 2018

The diaminoquinazoline series has good potency against Mycobacterium tuberculosis. Resistant isolates have mutations in Rv3161c, a putative dioxygenase. We carried out metabolite analysis on wild-type and an Rv3161c mutant strain after exposure to a diaminoquinazoline. The parental compound was found in intracellular extracts from the mutant, but not the wild-type. A metabolite consistent with a mono-hydroxylated form was identified in the wild-type. These data support the hypothesis that Rv3161c metabolizes diaminoquinazolines in M. tuberculosis.
CexE Is A Virulence Factor ofCitrobacter rodentiumAnd Present In Enteric Pathogens Of Humans
Authors: Rivas Zachary , McCormack Ryan M. , Adkins Becky , Munson George P.
Published: July 2018

CexE is a 12 kDa protein that was originally reported to be present in just three strains of enterotoxigenicEscherichia coli(ETEC); a frequent causes of diarrheal illnesses worldwide. However, an examination of recently sequenced genomes has revealed that CexE is actually present in a majority of ETEC strains. Homologs of CexE are also present in enteroaggregativeE. coli(EAEC) and other enteric pathogens includingYersinia enterocolitica, Providencia alcalifaciens, andCitrobacter rodentium. CexE and its homologs are expressed within virulence regulons of ETEC, EAEC, andC. rodentium. This, along with its distribution across several species of enteric pathogens, suggest that CexE confers a selective advantage to these pathogens. However, this hypothesis has yet to be testedin vivo. Here we demonstrate that CexE is conditionally secreted to the external leaf of the outer membrane of ETEC. Although CexE does not appear to play a role in adherencein vitro, it does facilitate colonization of murine intestinal tissues byC. rodentium in vivo. In adult mice wild-type bacteria reached significantly higher loads and were shed in higher numbers than acexE::kanmutant. A similar trend was observed in neonatal mice. In addition, all of the neonates infected with the wild-type strain succumbed to infection within 16 days of inoculation. In contrast, 45% of the neonates infected with thecexE::kanstrain survived for the 30 day duration of the experiment. These finding indicate that CexE is a conditionally secreted virulence factor that increases the colonization of hosts by enteric pathogens.
A genome-wide screen identifies genes in rhizosphere-associatedPseudomonasrequired to evade plant defenses
Authors: Liu Zhexian , Beskrovnaya Polina , Melnyk Ryan A. , Hossain Sarzana S. , Khorasani Sophie , O’Sullivan Lucy R. , Wiesmann Christina L. , Bush Jen , Richard Joël D. , Haney Cara H.
Published: July 2018

Pseudomonas fluorescensand related plant root- (“rhizosphere”) associated species contribute to plant health by modulating defenses and facilitating nutrient uptake. To identify bacterial fitness determinants in the rhizosphere of the model plantArabidopsis thaliana, we performed a Tn-Seq screen using the biocontrol and growth-promoting strainPseudomonassp. WCS365. The screen, which was performed in parallel on wild-type and an immunocompromisedArabidopsis, identified 231 genes that positively affect fitness in the rhizosphere of wild-type plants. A subset of these genes negatively affect fitness in the rhizosphere of immunocompromised plants. We postulated that these genes might be involved in avoiding plant defenses and verified 7Pseudomonassp. WCS365 candidate genes by generating clean deletions. We found that two of these deletion strains, ΔmorA(encodes a putative diguanylate cyclase/phosphodiesterase) and ΔspuC(encodes a putrescine aminotransferase) formed enhanced biofilms and inhibited plant growth. Inhibition of plant growth by ΔspuCand ΔmorAwas the result of pattern triggered immunity (PTI) as measured by induction of anArabidopsisPTI reporter andFLS2/BAK1-dependent inhibition of plant growth. We found that MorA acts as a phosphodiesterase to inhibit biofilm formation suggesting a possible role in biofilm dispersal. We found that both putrescine and its precursor arginine promote biofilm formation that is enhanced in the ΔspuCmutant, which cannot break down putrescine suggesting that putrescine might serve as a signaling molecule in the rhizosphere. Collectively, this work identified novel bacterial factors required to evade plant defenses in the rhizosphere.

Importance

While rhizosphere bacteria hold the potential to improve plant health and fitness, little is known about the bacterial genes required to evade host immunity. Using a model system consisting ofArabidopsisand a beneficialPseudomonassp. isolate, we identified bacterial genes required for both rhizosphere fitness and for evading host immune responses. This work advances our understanding of how evasion of host defenses contributes to survival in the rhizosphere.
Influence of food and Nosema ceranae infection on the gut microbiota of Apis cerana workers
Authors: Huang Shao K. , Ye Kun T. , Huang Wei F. , Ying Bi H. , Su Xin , Lin Li H. , Li Jiang H. , Chen Yan P. , Li Ji L. , Bao Xiu L. , Hu Jian Z.
Published: July 2018

Background

Gut microbiota plays an essential role in bee’s health. To elucidate the effect of food and Nosema ceranae infection on the gut microbiota of honeybee Apis cerana, we used 16S rRNA sequencing to survey the gut microbiota of honeybee workers fed with sugar water or beebread and inoculated with or without N. ceranae.

Results

The gut microbiota of A. cerana is dominated by Serratia, Snodgrassella, and Lactobacillus genera. The overall gut microbiota diversity was significantly differential by food type. The N. ceranae infection significantly affects the gut microbiota only at bees fed with sugar water. Higher abundance of Lactobacillus, Gluconacetobacter and Snodgrassella and lower abundance of Serratia were found in bees fed with beebread than with sugar water. N. ceranae infection led to higher abundance of Snodgrassella and lower abundance of Serratia in sugar-fed bees. Imputed bacterial KEGG pathways showed the significant metagenomics functional differences by feeding and N. ceranae infections. Furthermore, A. cerana workers fed with sugar water showed lower N. ceranae spore loads but higher mortality than those fed with beebread. The cumulative mortality was strongly positive correlated (rho=0.61) with the changes of overall microbiota dissimilarities by N. ceranae infection.

Conclusions

Both food and N. ceranae infection significantly affect the gut microbiota in A. cerana workers. Beebread feeding not only provide better nutrition but also help establish a more stabled gut microbiota therefore protect bee in response to N. ceranae infection.

Abstract Importance

Gut microbiota plays an essential role in bee’s health. Scientific evidence suggests the diet and infection can affect the gut microbiota and modulate the gut health, however the interplay between those two factors and bee gut microbiota is not well known. In this study, we used high-throughput sequencing method to monitor the changes of gut microbiota by both food intake and the Nosema ceranae infection. Our result showed that the gut microbiota composition and diversity of Asia Honeybee was significantly associated with both food intake and the N. ceranae infection. More interestingly, bees fed with beebread showed higher microbiota stability and less mortality than those fed with sugar water when infected by N. ceranae. Those data suggest the potential role of beebread, not only providing better nutrition but also helping establish a more stabled gut microbiota to protect bee against N. ceranae infection.
Experimental demonstration that screening can enable the environmental recruitment of a defensive microbiome
Authors: Innocent Tabitha , Holmes Neil , Bassam Mahmoud Al , Schiøtt Morten , Scheuring István , Wilkinson Barrie , Hutchings Matthew I , Boomsma Jacobus J , Yu Douglas W
Published: July 2018

Many animals and plants recruit beneficial microbes from the environment, enhancing their defence against pathogens. However, we have only a limited understanding of the assembly mechanisms involved. A game-theoretical concept from economics, screening, potentially explains how a host selectively recruits mutualistic microbes from the environment by fomenting and biasing competition among potential symbionts in such a way that the more likely winners are antibiotic producers. The cuticular microbiomes of Acromyrmex leaf-cutting ants inspired one of the first applications of screening theory, and here we simulate this system in vitro to test screening. On agar infused with antibacterial metabolites from Acromyrmex’s vertically transmitted Pseudonocardia bacteria, we show that antibiotic-producing Streptomyces bacteria exhibit higher growth rates than do non-antibiotic-producer strains and are more likely to win in direct competition. Our results demonstrate how game-theoretical concepts can provide powerful insight into host-microbiome coevolution.
Outcome contingency selectively affects the neural coding of outcomes but not of tasks
Authors: Wisniewski David , Forstmann Birte , Brass Marcel
Published: July 2018

Value-based decision-making is ubiquitous in every-day life, and critically depends on the contingency between choices and their outcomes. Only if outcomes are contingent on our choices can we make meaningful value-based decisions. Here, we investigate the effect of outcome contingency on the neural coding of rewards and tasks. Participants performed a reversal-learning task in which reward outcomes were contingent on trial-by-trial choices, and performed a ‘free choice’ task in which rewards were random and not contingent on choices. We hypothesized that contingent outcomes enhance the neural coding of rewards and tasks, which was tested using multivariate pattern analysis of fMRI data. Reward outcomes were encoded in a large network including the striatum, dmPFC and parietal cortex, and these representations were indeed amplified for contingent rewards. Tasks were encoded in the dmPFC at the time of decision-making, and in parietal cortex in a subsequence maintenance phase. We found no evidence for contingency-dependent modulations of task signals, demonstrating highly similar coding across contingency conditions. Our findings suggest selective effects of contingency on reward coding only, and further highlight the role of dmPFC and parietal cortex in value-based decision-making, as these were the only regions strongly involved in both reward and task coding.
Are we overestimating the utility of hair glucocorticoids? A systematic review exploring the empirical evidence supporting hair glucocorticoids as a measure of stress
Authors: Kalliokoski Otto , Jellestad Finn K. , Murison Robert
Published: July 2018

Quantitating glucocorticoids (GCs) in hairs is a popular method for assessing chronic stress in studies of humans and animals alike. The cause-and-effect relationship between stress and elevated GC levels in hairs, sampled weeks later, is however hard to prove. This systematic review evaluated the evidence supporting hair glucocorticoids (hGCs) as a biomarker of stress.

Only a relatively small number of controlled studies employing hGC analyses have been published, and the quality of the evidence is compromised by unchecked sources of bias. Subjects exposed to stress mostly demonstrate elevated levels of hGCs, and these concentrations correlate significantly with GC concentrations in serum, saliva and feces. This supports hGCs as a biomarker of stress, but the dataset provided no evidence that hGCs are a marker of historical stress. Only in cases where the stressor persisted at the time of hair sampling could a clear link between stress and hGCs be established.
Regional Collapsing of Rare Variation Implicates Specific Genic Regions in ALS
Authors: Gelfman Sahar , Dugger Sarah , Martins Moreno Cristiane de Araujo , Ren Zhong , Wolock Charles J. , Shneider Neil A. , Phatnani Hemali , Cirulli Elizabeth T. , Lasseigne Brittany N. , Harris Tim , Maniatis Tom , Rouleau Guy A. , Brown Robert H. , Gitler Aaron D. , Myers Richard M. , Petrovski Slavé , Allen Andrew , Harms Matthew B. , Goldstein David B.
Published: July 2018

Large-scale sequencing efforts in amyotrophic lateral sclerosis (ALS) have implicated novel genes using gene-based collapsing methods. However, pathogenic mutations may be concentrated in specific genic regions. To address this, we developed two collapsing strategies, one focuses rare variation collapsing on homology-based protein domains as the unit for collapsing and another gene-level approach that, unlike standard methods, leverages existing evidence of purifying selection against missense variation on said domains. The application of these two collapsing methods to 3,093 ALS cases and 8,186 controls of European ancestry, and also 3,239 cases and 11,808 controls of diversified populations, pinpoints risk regions of ALS genes including SOD1, NEK1, TARDBP and FUS. While not clearly implicating novel ALS genes, the new analyses not only pinpoint risk regions in known genes but also highlight candidate genes as well.