bluuebunny/crossref_metadata_2025 huggingface dataset:
hts-nim: scripting high-performance genomic analyses
Authors: Pedersen Brent S. , Quinlan Aaron R.
Published: February 2018

Motivation

Extracting biological insight from genomic data inevitably requires custom software. In many cases, this is accomplished with scripting languages, owing to their accessibility and brevity. Unfortunately, the ease of scripting languages typically comes at a substantial performance cost that is especially acute with the scale of modern genomics datasets.

Results

We present hts-nim, a high-performance library written in the Nim programming language that provides a simple, scripting-like syntax without sacrificing performance.

Availability

hts-nim is available at https://github.com/brentp/hts-nim and the example tools are at https://github.com/brentp/hts-nim-tools both under the MIT license.

Contact

bpederse@gmail.com

Supplementary information

Supplementary data are available at Bioinformatics online.
Improving Metagenomic Assemblies Through Data Partitioning: a GC content approach
Authors: Miranda Fábio , Batista Cassio , Silva Artur , Morais Jefferson , Neto Nelson , Ramos Rommel
Published: February 2018

Assembling metagenomic data sequenced by NGS platforms poses significant computational challenges, especially due to large volumes of data, sequencing errors, and variations in size, complexity, diversity and abundance of organisms present in a given metagenome. To overcome these problems, this work proposes an open-source, bioinfor-matic tool called GCSplit, which partitions metagenomic sequences into subsets using a computationally inexpensive metric: the GC content. Experiments performed on real data show that preprocessing short reads with GCSplit prior to assembly reduces memory consumption and generates higher quality results, such as an increase in the N50 metric and the reduction in both the L50 value and the total number of contigs produced in the assembly. GCSplit is available at https://github.com/mirand863/gcsplit.
Example of Methylome Analysis with MethylIT using Cancer Datasets
Authors: Sanchez Robersy , Mackenzie Sally
Published: February 2018

Methyl-IT, a novel methylome analysis procedure based on information thermodynamics and signal detection was recently released. Methylation analysis involves a signal detection problem, and the method was designed to discriminate methylation regulatory signal from background noise induced by thermal fluctuations. Methyl-IT enhances the resolution of genome methylation behavior to reveal network-associated responses, offering resolution of gene pathway influences not attainable with previous methods. Herein, an example of MethylIT application to the analysis of breast cancer methylomes is presented.
Lentiviral co-packaging mitigates the effects of intermolecular recombination and multiple integrations in pooled genetic screens
Authors: Feldman David , Singh Avtar , Garrity Anthony J. , Blainey Paul C.
Published: February 2018

Lentiviral vectors are widely used for functional genomic screens, enabling efficient and stable transduction of target cells with libraries of genetic elements. Unfortunately, designs that rely on integrating multiple variable sequences, such as combinatorial perturbations or perturbations linked to barcodes, may be compromised by unintended consequences of lentiviral packaging. Intermolecular recombination between library elements and integration of multiple perturbations (even at limiting virus dilution) can negatively impact the sensitivity of pooled screens. Here, we describe a simple approach to prevent recombination between lentiviral vectors containing multiple linked variable elements, such as the recently reported CRISP-seq, Perturb-seq, and Mosaic-seq designs. We show that modifying the packaging protocol by diluting the perturbation library with a carrier plasmid increases the fraction of correct, single integrations from <60% to >90%, at the cost of reducing titer by 100-fold.
Co-occurrence history increases ecosystem temporal stability and recovery from a flood in experimental plant communities
Authors: van Moorsel Sofia J. , Hahl Terhi , Petchey Owen L. , Ebeling Anne , Eisenhauer Nico , Schmid Bernhard , Wagg Cameron
Published: February 2018

Understanding factors that increase ecosystem stability is critical in the face of environmental change. Experiments simulating species loss from grassland ecosystems have shown that losing biodiversity decreases the ability of ecosystems to buffer negative effects of disturbances. However, as the originally sown experimental communities with reduced biodiversity develop, plant evolutionary processes or the assembly of interacting soil organisms may allow them to develop stability and resilience over time. We explored such effects in a long-term grassland biodiversity experiment with plant communities with either a history of co-occurrence (selected communities) or no such history (naïve communities) over a four-year period in which a major flood disturbance occurred.

We found selected communities had temporally more stable biomass than the same communities of naïve plants, especially at low species richness. Furthermore, selected communities showed greater short-term biomass recovery after flooding, resulting in more stable post-flood productivity. In contrast to a previous study, the positive diversity–stability relationship was maintained after the flooding. Our results were consistent across three soil treatments simulating the presence or absence of co-selected microbial communities. We suggest that prolonged exposure of plant populations to a particular community context and abiotic site conditions can increase ecosystem temporal stability and resistance to disturbance. We argue that selection during the course of a biodiversity experiment is the most parsimonious explanation for these effects. A history of co-occurrence can in part compensate for species loss, as can high plant diversity in part compensate for the missing opportunity of such adaptive adjustments.
Engineering of new-to-nature halogenated indigo precursors in plants
Authors: Frabel Sabine , Wagner Bastian , Krischke Markus , Schmidts Volker , Thiele Christina M , Staniek Agata , Warzecha Heribert
Published: February 2018

Plants are versatile chemists producing a tremendous variety of specialized compounds. Here, we describe the engineering of entirely novel metabolic pathways in planta enabling generation of halogenated indigo precursors as non-natural plant products. Indican (indolyl-beta-D-glucopyranoside) is a secondary metabolite characteristic of a number of dyers plants. Its deglucosylation and subsequent oxidative dimerization leads to the blue dye, indigo. Halogenated indican derivatives are commonly used as detection reagents in histochemical and molecular biology applications; their production, however, relies largely on chemical synthesis. To attain the de novo biosynthesis in a plant-based system devoid of indican, we employed a sequence of enzymes from diverse sources, including three microbial tryptophan halogenases substituting the amino acid at either C5, C6, or C7 of the indole moiety. Subsequent processing of the halotryptophan by bacterial tryptophanase TnaA in concert with a mutant of the human cytochrome P450 monooxygenase 2A6 and glycosylation of the resulting indoxyl derivatives by an endogenous tobacco glucosyltransferase yielded corresponding haloindican variants in transiently transformed Nicotiana benthamiana plants. Accumulation levels were highest when the 5-halogenase PyrH was utilized, reaching 0.93 +/-0.089 mg/g dry weight of 5-chloroindican. The identity of the latter was unambiguously confirmed by NMR analysis. Moreover, our combinatorial approach, facilitated by the modular assembly capabilities of the GoldenBraid cloning system and inspired by the unique compartmentation of plant cells, afforded testing a number of alternative subcellular localizations for pathway design. In consequence, chloroplasts were validated as functional biosynthetic venues for haloindican, with the requisite reducing augmentation of the halogenases as well as the cytochrome P450 monooxygenase fulfilled by catalytic systems native to the organelle. Thus, our study puts forward a viable alternative production platform for halogenated fine chemicals, eschewing reliance on fossil fuel resources and toxic chemicals. We further contend that in planta generation of halogenated indigoid precursors previously unknown to nature offers an extended view on and, indeed, pushes forward the established frontiers of biosynthetic capacity of plants.
Spatio-temporal relays control layer identity of direction-selective neuron subtypes inDrosophila
Authors: Apitz Holger , Salecker Iris
Published: February 2018

Visual motion detection in sighted animals is essential to guide behavioral actions ensuring their survival. InDrosophila, motion direction is first detected by T4/T5 neurons. Their axons innervate one of four lobula plate layers. How T4/T5 neurons with layer-specific representation of motion-direction preferences are specified during development is unknown. We show that diffusible Wingless (Wg) between adjacent neuroepithelia induces its own expression to form secondary signaling centers. These activate Decapentaplegic (Dpp) signaling in adjacent lateral tertiary neuroepithelial domains dedicated to producing layer 3/4-specific T4/T5 neurons. T4/T5 neurons derived from the core domain devoid of Dpp signaling adopt the default layer 1/2 fate. Dpp signaling induces the expression of the T-box transcription factor Optomotor-blind (Omb), serving as a relay to postmitotic neurons. Omb-mediated repression of Dachshund transforms layer 1/2-into layer 3/4-specific neurons. Hence, spatio-temporal relay mechanisms, bridging the distances between neuroepithelial domains and their postmitotic progeny, implement T4/T5 neuron-subtype identity.
Mycobacterium tuberculosis-specific CD4+and CD8+T cells differ in their capacity to recognize infected macrophages
Authors: Yang Jason , Mott Daniel , Sutiwisesak Rujapak , Lu Yu Jung , Raso Fiona , Stowell Britni , Babunovic Greg , Lee Jinhee , Carpenter Steve , Way Sing Sing , Fortune Sarah , Behar Sam
Published: February 2018

Containment ofMycobacterium tuberculosis(Mtb) infection requires T cell recognition of infected macrophages. Mtb has evolved to tolerate, evade, and subvert host immunity. Despite a vigorous and sustained CD8+T cell response during Mtb infection, CD8+T cells make limited contribution to protection. Here, we ask whether the ability of Mtb-specific T cells to restrict Mtb growth is related to their capacity to recognize Mtb-infected macrophages.

We derived CD8+T cell lines that recognized the Mtb immunodominant epitope TB10.44-11and compared them to CD4+T cell lines that recognized Ag85b240-254 or ESAT63-17. While the CD4+T cells recognized Mtb-infected macrophages and inhibited Mtb growth in vitro, the TB10.4-specific CD8+T cells neither recognized Mtb-infected macrophages nor restricted Mtb growth. TB10.4-specific CD8+T cells recognized macrophages infected withListeria monocytogenesexpressing TB10.4. However, over-expression of TB10.4 in Mtb did not confer recognition by TB10.4-specific CD8+T cells. Importantly, CD8+T cells recognized macrophages pulsed with irradiated Mtb, indicating that macrophages can efficiently cross-present the TB10.4 protein and raising the possibility that viable bacilli might suppress cross-presentation. Importantly, polyclonal CD8+T cells specific for Mtb antigens other than TB10.4 recognized Mtb-infected macrophages in a MHC-restricted manner.

As TB10.4 elicits a dominant CD8+T cell response that poorly recognizes Mtb-infected macrophages, we propose that TB10.4 acts as a decoy antigen. Moreover, it appears that this response overshadows subdominant CD8+T cell response that can recognize Mtb-infected macrophages. The ability of Mtb to subvert the CD8+T cell response may explain why CD8+T cells make a disproportionately small contribution to host defense compared to CD4+T cells. The selection of Mtb antigens for vaccines has focused on antigens that generate immunodominant responses. We propose that establishing whether vaccine-elicited, Mtb-specific T cells recognize Mtb-infected macrophages could be a useful criterion for preclinical vaccine development.
Generative adversarial networks simulate gene expression and predict perturbations in single cells
Authors: Ghahramani Arsham , Watt Fiona M. , Luscombe Nicholas M.
Published: February 2018

Recent advances have enabled gene expression profiling of single cells at lower cost. As more data is produced there is an increasing need to integrate diverse datasets and better analyse underutilised data to gain biological insights. However, analysis of single cell RNA-seq data is challenging due to biological and technical noise which not only varies between laboratories but also between batches. Here for the first time, we apply a new generative deep learning approach called Generative Adversarial Networks (GAN) to biological data. We apply GANs to epidermal, neural and hematopoietic scRNA-seq data spanning different labs and experimental protocols. We show that it is possible to integrate diverse scRNA-seq datasets and in doing so, our generative model is able to simulate realistic scRNA-seq data that covers the full diversity of cell types. In contrast to many machine-learning approaches, we are able to interpret internal parameters in a biologically meaningful manner. Using our generative model we are able to obtain a universal representation of epidermal differentiation and use this to predict the effect of cell state perturbations on gene expression at high time-resolution. We show that our trained neural networks identify biological state-determining genes and through analysis of these networks we can obtain inferred gene regulatory relationships. Finally, we use internal GAN learned features to perform dimensionality reduction. In combination these attributes provide a powerful framework to progress the analysis of scRNA-seq data beyond exploratory analysis of cell clusters and towards integration of multiple datasets regardless of origin.
Shared Nucleotide Flanks Confer Transcriptional Competency to bZip Core Motifs
Authors: Cohen Daniel M. , Lim Hee-Woong , Won Kyoung-Jae , Steger David J.
Published: February 2018

Sequence-specific DNA binding recruits transcription factors (TFs) to the genome to regulate gene expression. Here, we perform high resolution mapping of CEBP proteins to determine how sequence dictates genomic occupancy. We demonstrate a fundamental difference between the sequence repertoire utilized by CEBPs in vivo versus the palindromic sequence preference reported by classical in vitro models, by identifying a palindromic motif at less than 1% of the genomic binding sites. On the native genome, CEBPs bind a diversity of related 10 bp sequences resulting from the fusion of degenerate and canonical half-sites. Altered DNA specificity of CEBPs in cells occurs through heterodimerization with other bZip TFs, and approximately 40% of CEBP-binding sites in primary human cells harbor motifs characteristic of CEBP heterodimers. In addition, we uncover an important role for sequence bias at core-motif-flanking bases for CEBPs and demonstrate that flanking bases regulate motif function across mammalian bZip TFs. Favorable flanking bases confer efficient TF occupancy and transcriptional activity, and DNA shape may explain how the flanks alter TF binding. Importantly, motif optimization within the 10-mer is strongly correlated with cell-type-independent recruitment of CEBPβ, providing key insight into how sequence sub-optimization affects genomic occupancy of widely expressed CEBPs across cell types.
Effect of environment on the evolutionary trajectories and growth characteristics of antibiotic-resistant Escherichia coli mutants
Authors: Hubbard Alasdair T. M. , Jafari Nazila V. , Feasey Nicholas , Rohn Jennifer L. , Roberts Adam P.
Published: February 2018

In the face of an accelerating global antimicrobial resistance crisis, the determination of bacterial fitness following acquisition of resistance is an expanding area of research, and increased understanding of this process will be crucial to translate in vitro fitness data to successful therapies. Given that crucial clinical treatment situations are guided by in vitro diagnostic testing in an artificial environment far removed from human physiological niches, we used Escherichia coli and amoxicillin-clavulanic acid (AMC) resistance as a model to understand how such environments could affect the emergence of resistance, associated fitness costs and the predictive value of this data when strains were grown in the more physiologically relevant environments of urine and urothelial organoids. Resistant E. coli isolates were selected for following 24-hour exposure to sub-inhibitory concentrations of AMC in either M9, ISO or LB broth, followed by growth on LB agar containing AMC. No resistant colonies emerged following growth in M9, whereas resistant isolates were detected from cultures grown in ISO and LB broth. We observed both within and between media-type variability in the levels of resistance and fitness of the resistant mutants grown in LB. MICs and fitness of these resistant strains in different media (M9, ISO, LB, human urine and urothelial organoids) showed considerable variation. Media can therefore have a direct effect on the isolation of mutants that confer resistance to AMC and these mutants can exhibit unpredictable MIC and fitness profiles under different growth conditions. This study highlights the risks in relying on a single culture protocol to predict the behaviour and treatment response of bacteria in vivo and highlights the importance of developing comprehensive experimental designs to ensure effective translation of diagnostic procedures to successful clinical outcomes.
First nuclear genome assembly of an extinct moa species, the little bush moa (Anomalopteryx didiformis)
Authors: Cloutier Alison , Sackton Timothy B. , Grayson Phil , Edwards Scott V. , Baker Allan J.
Published: February 2018

Abstract

High throughput sequencing (HTS) has revolutionized the field of ancient DNA (aDNA) by facilitating recovery of nuclear DNA for greater inference of evolutionary processes in extinct species than is possible from mitochondrial DNA alone. We used HTS to obtain ancient DNA from the little bush moa (Anomalopteryx didiformis), one of the iconic species of large, flightless birds that became extinct following human settlement of New Zealand in the 13 th century. In addition to a complete mitochondrial genome at 249.9X depth of coverage, we recover almost 900 Mb of the moa nuclear genome by mapping reads to a high quality reference genome for the emu (Dromaius novaehollandiae). This first nuclear genome assembly for moa covers approximately 75% of the 1.2 Gb emu reference with sequence contiguity sufficient to identify more than 85% of bird universal single-copy orthologs. From this assembly, we isolate 40 polymorphic microsatellites to serve as a community resource for future population-level studies in moa. We also compile data for a suite of candidate genes associated with vertebrate limb development and show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization among this candidate set. We also identify potential function-altering coding sequence variants in moa for future experimental assays.
DNA methylation dynamics during embryonic development and postnatal maturation of the mouse auditory organ of Corti
Authors: Yizhar-Barnea Ofer , Valensisi Cristina , Kishore Kamal , Doni Jayavelu Naresh , Andrus Colin , Koffler-Brill Tal , Ushakov Kathy , Perl Kobi , Noy Yael , Bhonker Yoni , Pelizzola Mattia , Hawkins R. David , Avraham Karen B.
Published: February 2018

Background

The mammalian inner ear is a complex morphological structure responsible for hearing and balance, and its pathology is associated with deafness and balance disorders. To evaluate the role of epigenomic dynamics in the development and maturation of mouse inner ear sensory epithelium, we performed whole-genome bisulfite sequencing on inner ear tissue, yielding temporal base-pair resolution methylomes at key developmental time points.

Results

We found a late accumulation of non-CpG methylation, indicating a similarity between the inner ear sensory epithelium and neuronal tissue. Moreover, annotation of both unmethylated and low methylated regions pointed to regulatory elements active in the inner ear in proximity of and distal from transcriptional units. Finally, we identified differentially methylated regions across the transition periods. An analysis of these regions led us to identify several novel candidate regulatory factors, connecting regulatory elements from specific time points in development to molecular features that drive the development and maturation of the inner ear sensory epithelium. The GJB6 locus putative regulatory region was shown to upregulate distal GJB6 gene expression and a non-coding RNA.

Conclusions

Our analysis of inner ear sensory epithelium DNA methylation sheds light on novel regulatory regions in the hearing organ, and may help boost diagnostic capabilities and guide the development of therapeutics for hearing loss, by providing multiple intervention points for manipulation of the auditory system.
TFmapper: A tool for searching putative factors regulating gene expression using ChIP-seq data
Authors: Zeng Jianming , Li Gang
Published: February 2018

Background

Next-generation sequencing coupled to chromatin immunoprecipitation (ChIP-seq), DNase I hypersensitivity (DNase-seq) and the transposase-accessible chromatin assay (ATAC-seq) has generated enormous amounts of data, markedly improved our understanding of the transcriptional and epigenetic control of gene expression. To take advantage of the availability of such datasets and provide clues on what factors, including transcription factors, epigenetic regulators and histone modifications, potentially regulates the expression of a gene of interest, a tool for simultaneous queries of multiple datasets using symbols or genomic coordinates as search terms is needed.

Results

In this study, we annotated the peaks of thousands of ChIP-seq datasets generated by ENCODE project, or ChIP-seq/DNase-seq/ATAC-seq datasets deposited in Gene Expression Omnibus and curated by CistromeDB; We built a MySQL database called TFmapper containing the annotations and associated metadata, allowing users without bioinformatics expertise to search across thousands of datasets to identify factors targeting a genomic region/gene of interest in a specified sample through a web interface. Users can also visualize multiple peaks in genome browsers and download the corresponding sequences.

Conclusion

TFmapper will help users explore the vast amount of publicly available ChIP-seq/DNase-seq/ATAC-seq data, and perform integrative analyses to understand the regulation of a gene of interest. The web server is freely accessible at http://www.tfmapper.org/.
KrakenHLL: Confident and fast metagenomics classification using unique k-mer counts
Authors: Breitwieser FP , Salzberg SL
Published: February 2018

False positive identifications are a significant problem in metagenomic classification. We present KrakenHLL, a novel metagenomic classifier that combines the fast k-mer based classification of Kraken with an efficient algorithm for assessing the coverage of unique k-mers found in each species in a dataset. On various test datasets, KrakenHLL gives better recall and F1-scores than other methods, and effectively classifies and distinguishes pathogens with low abundance from false positives in infectious disease samples. By using the probabilistic cardinality estimator HyperLogLog (HLL), KrakenHLL is as fast as Kraken and requires little additional memory.
SMRT-Cappable-seq reveals complex operon variants in bacteria
Authors: Yan Bo , Boitano Matthew , Clark Tyson , Ettwiller Laurence
Published: February 2018

Current methods for genome-wide analysis of gene expression requires shredding original transcripts into small fragments for short-read sequencing. In bacteria, the resulting fragmented information hides operon complexity. Additionally,in-vivoprocessing of transcripts confounds the accurate identification of the 5’ and 3’ ends of operons. Here we developed a novel methodology called SMRT-Cappable-seq that combines the isolation of unfragmented primary transcripts with single-molecule long read sequencing. Applied toE. coli, this technology results in an unprecedented definition of the transcriptome with 34% of the known operons being extended by at least one gene. Furthermore, 40% of transcription termination sites have read-through that alters the gene content of the operons. As a result, most of the bacterial genes are present in multiple operon variants reminiscent of eukaryotic splicing. By providing an unprecedented granularity in the operon structure, this study represents an important resource for the study of prokaryotic gene network and regulation.
Subtle left-right asymmetry of gene expression profiles in embryonic and foetal human brains
Authors: de Kovel Carolien G.F. , Lisgo Steven N. , Fisher Simon E. , Francks Clyde
Published: February 2018

Left-right laterality is an important aspect of human brain organization for which the genetic basis is poorly understood. Using RNA sequencing data we contrasted gene expression in left- and right-sided samples from several structures of the anterior central nervous systems of post mortem human embryos and fetuses. While few individual genes stood out as significantly lateralized, most structures showed evidence of laterality of their overall transcriptomic profiles. These left-right differences showed overlap with age-dependent changes in expression, indicating lateralized maturation rates, but not consistently in left-right orientation over all structures. Brain asymmetry may therefore originate in multiple locations, or if there is a single origin, it is earlier than 5 weeks post conception, with structure-specific lateralized processes already underway by this age. This pattern is broadly consistent with the weak correlations reported between various aspects of adult brain laterality, such as language dominance and handedness.
Specific Eph Receptor-Cytoplasmic Effector Signaling Mediated by SAM-SAM Domain Interactions
Authors: Wang Yue , Shang Yuan , Li Jianchao , Chen Weidi , Li Gang , Wan Jun , Liu Wei , Zhang Mingjie
Published: February 2018

The Eph receptor tyrosine kinase (RTK) family is the largest subfamily of RTKs playing critical roles in many developmental processes such as tissue patterning, neurogenesis and neuronal circuit formation, angiogenesis, etc. How the 14 Eph proteins, via their highly similar cytoplasmic domains, can transmit diverse and sometimes opposite cellular signals upon engaging ephrins is a major unresolved question. Here we systematically investigated the bindings of each SAM domain of Eph receptors to the SAM domains from SHIP2 and Odin, and uncover a highly specific SAM-SAM interaction-mediated cytoplasmic Eph-effector binding pattern. Comparative X-ray crystallographic studies of several SAM-SAM heterodimer complexes, together with biochemical and cell biology experiments, not only revealed the exquisite specificity code governing Eph/effector interactions but also allowed us to identify SAMD5 as a new Eph binding partner. Finally, these Eph/effector SAM heterodimer structures can explain numerous Eph SAM mutations identified in patients suffering from cancers and other diseases.
TCR-MHC Interaction Strength Defines Trafficking and Resident Memory Status of CD8 T cells in the Brain
Authors: Sanecka Anna , Yoshida Nagisa , Kolawole Elizabeth Motunrayo , Patel Harshil , Evavold Brian D. , Frickel Eva-Maria
Published: February 2018

T cell receptor-Major histocompatibility complex (TCR-MHC) affinities span a wide range in a polyclonal T cell response, yet it is undefined how affinity shapes long-term properties of CD8 T cells during chronic infection with persistent antigen. Here, we investigate how the affinity of the TCR-MHC interaction shapes the phenotype of memory CD8 T cells in the chronicallyToxoplasma gondii-infectedbrain. We employed CD8 T cells from three lines of transnuclear (TN) mice that harbour in their endogenous loci different T cell receptors specific for the sameToxoplasmaantigenic epitope ROP7. The three TN CD8 T cell clones span a wide range of affinities to MHCI-ROP7. These three CD8 T cell clones have a distinct and fixed hierarchy in terms of effector function in response to the antigen measured as proliferation capacity, trafficking, T cell maintenance and memory formation. In particular, the T cell clone of lowest affinity does not home to the brain. The two higher affinity T cell clones show differences in establishing resident memory populations (CD103+) in the brain with the higher affinity clone persisting longer in the host during chronic infection. Transcriptional profiling of naïve and activated ROP7-specific CD8 T cells revealed thatKlf2encoding a transcription factor that is known to be a negative marker for T cell trafficking is upregulated in the activated lowest affinity ROP7 clone. Our data thus suggest that TCR-MHC affinity dictates memory CD8 T cell fate at the site of infection.
New insights on adaptation and population structure of cork oak using genotyping by sequencing
Authors: Pina-Martins F. , Baptista J. , Pappas G. , Paulo O. S.
Published: February 2018

Species respond to global climatic changes in a local context. Understanding this process is paramount due to the pace of these changes. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species’ evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. The potential response of Q. suber to global climatic changes has also been studied, under ecological modelling. In this work, “Genotyping by Sequencing” (GBS) is used to derive 2,547 SNP markers to assess the species’ evolutionary history from a nuclear DNA perspective, gain insights on how local adaptation may be shaping the species’ genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal an essentially unstructured species, where a balance between gene flow and local adaptation keeps the species’ gene pool somewhat homogeneous across its distribution, but at the same time allows variation clines for the individuals to cope with local conditions. “Risk of Non-Adaptedness” (RONA) analyses, suggest that for the considered variables and most sampled locations, the cork oak does not require large shifts in allele frequencies to survive the predicted climatic changes. However, more research is required to integrate these results with those of ecological modelling.
A critical role for Dna2 at unwound telomeres
Authors: Markiewicz-Potoczny Marta , Lisby Michael , Lydall David
Published: February 2018

Dna2 is a nuclease and helicase that functions redundantly with other proteins in Okazaki fragment processing, double strand break (DSB) resection and checkpoint kinase activation. Dna2 is an essential enzyme, required for yeast and mammalian cell viability. Here we report that numerous mutations affecting the DNA damage checkpoint suppressdna2Δ lethality inSaccharomyces cerevisiae.dna2Δ cells are also suppressed by deletion of helicases,PIF1andMPH1, and by deletion ofPOL32, a subunit of DNA polymerase δ. Alldna2Δ cells are temperature sensitive, have telomere length defects, and low levels of telomeric 3’ single stranded DNA (ssDNA). Interestingly, Rfa1, a subunit of the major ssDNA binding protein RPA, and the telomere specific ssDNA binding protein Cdc13, often co-localize indna2Δ cells. This suggests that telomeric defects often occur indna2Δ cells. There are several plausible explanations for why the most critical function of Dna2 is at telomeres. Telomeres modulate the DNA damage response (DDR) at chromosome ends, inhibiting resection, ligation and cell cycle arrest. We suggest that Dna2 nuclease activity contributes to modulating the DNA damage response at telomeres by removing telomeric C-rich ssDNA and thus preventing checkpoint activation.
Structural insights into the recognition of mono- and di-acetylated histones by the ATAD2B bromodomain
Authors: Lloyd Jonathan T. , McLaughlin Kyle , Lubula Mulu Y. , Gay Jamie C. , Dest Andrea , Gao Cong , Phillips Margaret , Tonelli Marco , Cornilescu Gabriel , Marunde Matthew R. , Evans Chiara M. , Boyson Samuel P. , Carlson Samuel , Keogh Michael-Christopher , Markley John L. , Frietze Seth , Glass Karen C.
Published: February 2018

Bromodomains are chromatin reader modules that recognize acetylated lysine. Different bromodomains exhibit a preference for specific patterns of lysine acetylation marks on core and variant histone proteins, however, the functional relationships that exist between histone acetyllysine ligands and bromodomain recognition remain poorly understood. In this study, we examined the ligand specificity of the ATAD2B bromodomain and compared it to its closely related paralog in ATAD2. We show that the ATAD2B bromodomain selects for mono- and di-acetylated histones, and structural analysis identified key residues in the acetyllysine binding pocket that dictate ligand binding specificity. The X-ray crystal structure of the ATAD2B bromodomain in complex with an ATAD2 bromodomain inhibitor was solved at 2.4 Å resolution. This structure demonstrated that critical contacts required for bromodomain inhibitor coordination are conserved between the ATAD2/B bromodomains, and many of these residues play a dual role in acetyllysine recognition. We further characterized a variant of the ATAD2B bromodomain that through alternative splicing loses critical amino acids required for histone ligand and inhibitor coordination. Altogether our results outline the structural and functional features of the ATAD2B bromodomain and identify a novel mechanism important for regulating the interaction of the ATAD2B protein with chromatin.

HIGHLIGHTS

The ATAD2B bromodomain recognizes mono- and di-acetylated histone ligands.

Chemical shift perturbations outline the ATAD2B bromodomain acetyllysine binding pocket.

An ATAD2B bromodomain-inhibitor complex reveals important binding contacts.

An alternate splice variant in the ATAD2B bromodomain abolishes histone and inhibitor binding.
Postsynaptic Pannexin-1 Facilitates Anandamide Uptake to Modulate Glutamate Release and Enhance Network Excitability
Authors: Bialecki Jennifer , Weilinger Nicholas L. , Lohman Alexander W. , Vecchiarelli Haley A. , Robinson Jordan H.B. , Egaña Jon , Medizabal-Zubiaga Juan , Werner Allison C. , Grandes Pedro , Teskey G. Campbell , Hill Matthew N. , Thompson Roger J.
Published: February 2018

Prolonged neurotransmitter release following synaptic stimulation extends the time window for postsynaptic neurons to respond to presynaptic activity. This can enhance excitability and increase synchrony of outputs, but the prevalence of this at normally highly synchronous synapses is unclear. We show that the postsynaptic channel, pannexin-1 (Panx1) regulates prolonged glutamate release onto CA1 neurons. Block of postsynaptic (CA1 neuronal) Panx1 increased the frequency of glutamate neurotransmission and action potentials in these neurons following Schaffer collateral stimulation. When Panx1 was blocked, anandamide levels increase and activated transient receptor potential vanilloid 1 (TRPV1)-mediated glutamate release. This TRPV1-induced synaptic acitvity enhanced excitability and translated into a faster rate of TRPV1-dependent epileptogenesis induced by kindling. We conclude that Panx1 facilitates AEA clearance to maintain synchronous release onto CA1 neurons so that when AEA clearance is reduced, TRPV1 channels prolong glutamate neurotransmission to enhance network output to promote epileptiform activity.
Evolutionary rescue of sphericalmreBdeletion mutants of the rod-shape bacteriumPseudomonas fluorescensSBW25
Authors: Yulo P. Richard J. , Desprat Nicolas , Gerth Monica L. , Ritzl- Rinkenberger Barbara , Farr Andrew D. , Liu Yunhao , Zhang Xue-Xian , Miller Michael , Cava Felipe , Rainey Paul B. , Hendrickson Heather L.
Published: February 2018

Maintenance of rod-shape in bacterial cells depends on the actin-like protein MreB. Deletion ofmreBfromPseudomonas fluorescensSBW25 results in viable spherical cells of variable volume and reduced fitness. Using a combination of time-resolved microscopy and biochemical assay of peptidoglycan synthesis, we show that reduced fitness is a consequence of perturbed cell size homeostasis that arises primarily from differential growth of daughter cells. A 1,000-generation selection experiment resulted in rapid restoration of fitness with derived cells retaining spherical shape. Mutations in the peptidoglycan synthesis protein Pbp1A were identified as the main route for evolutionary rescue with genetic reconstructions demonstrating causality. Compensatorypbp1Amutations that targeted transpeptidase activity enhanced homogeneity of cell wall synthesis on lateral surfaces and restored cell size homeostasis. Mechanistic explanations require enhanced understanding of why deletion ofmreBcauses heterogeneity in cell wall synthesis. We conclude by presenting two testable hypotheses, one of which posits that heterogeneity stems from non-functional cell wall synthesis machinery, while the second posits that the machinery is functional, albeit stalled. Overall, our data provide support for the second hypothesis and draw attention to the importance of balance between transpeptidase and glycosyltransferase functions of peptidoglycan building enzymes for cell shape determination.
3′ UTR lengthening as a novel mechanism in regulating cellular senescence
Authors: Chen Meng , Lyu Guoliang , Han Miao , Nie Hongbo , Shen Ting , Chen Wei , Niu Yichi , Song Yifan , Li Xueping , Li Huan , Chen Xinyu , Wang Ziyue , Xia Zheng , Li Wei , Tian Xiao-Li , Ding Chen , Gu Jun , Zheng Yufang , Liu Xinhua , Hu Jinfeng , Wei Gang , Tao Wei , Ni Ting
Published: February 2018

Cellular senescence has been viewed as a tumor suppression mechanism and also as a contributor to individual aging. Widespread shortening of 3′ untranslated regions (3′ UTRs) in messenger RNAs (mRNAs) by alternative polyadenylation (APA) has recently been discovered in cancer cells. However, the role of APA in the process of cellular senescence remains elusive. Here, we found that hundreds of genes in senescent cells tended to use distal poly(A) (pA) sites, leading to a global lengthening of 3′ UTRs and reduced gene expression. Genes that harbor longer 3′ UTRs in senescent cells were enriched in senescence-related pathways. Rras2, a member of the Ras superfamily that participates in multiple signal transduction pathways, preferred longer 3′ UTR usage and exhibited decreased expression in senescent cells. Depletion of Rras2 promoted senescence, while rescue of Rras2 reversed senescence-associated phenotypes. Mechanistically, splicing factor TRA2B bound to a core “AGAA” motif located in the alternative 3′ UTR of Rras2, thereby reducing the RRAS2 protein level and causing senescence. Both proximal and distal poly(A) signals showed strong sequence conservation, highlighting the vital role of APA regulation during evolution. Our results revealed APA as a novel mechanism in regulating cellular senescence.
Surface morphology studies and kinetic-thermodynamic characterization of steels treated in 5.0 M HCl medium: hot-dip galvanizing application
Authors: El Kacimi Younes , Galai Mouhsine , Alaoui Khaoula , Touir Rachid , Ebn Touhami Mohamed
Published: February 2018

Purpose

The purpose of this paper is to study the effect of silicon and phosphorus content in steel suitable for galvanizing on its corrosion and inhibitor adsorption processes in steels/cetyltrimethylammonium bromide combined and KI (mixture)/5.0 M hydrochloric acid systems has been studied in relation to the temperature using chemical (weight loss), Tafel polarization, electrochemical impedance spectroscopy (EIS), scanning electronic microscope (SEM) analysis and Optical 3D profilometry characterization. All the methods used are in reasonable agreement. The kinetic and thermodynamic parameters for each steels corrosion and inhibitor adsorption, respectively, were determined and discussed. Results show that the adsorption capacity for Steel Classes A and B are better than Steel Class C surfaces depending on their silicon and phosphorus content. Surface analyses via SEM and Optical 3D profilometry was used to investigate the morphology of the steels before and after immersion in 5.0 M HCl solution containing mixture. Surface analysis revealed improvement of corrosion resistance of Steels Classes A and B in the presence of mixture more than Classes C. It has been determined that the adsorbed protective film on the steels surface heterogeneity markedly depends on steels compositions, that is, the heterogeneity increases with decreasing silicon and phosphorus content.

Design/methodology/approach

The effect of silicon and phosphorus content in Steels Classes A, B and C on its corrosion and inhibitor mixture adsorption processes in 5.0 M HCl solution has been studied by weight loss, potentiodynamic polarization, EIS and surface analysis.

Findings

The inhibition efficiency of mixture follows the order: (Steel Class A) > (Steel Class B) > Steel Class C) and depends on their compositions in the absence of mixture according on their silicon and phosphorus content, that is, the corrosion rate increases with increasing of the silicon and phosphorus content. A potentiodynamic polarization measurement indicates that the mixture acts as mixed-type inhibitor without changing the mechanism of corrosion process for the three classes of mild steels.

Originality/value

Corrosion rate mild steels in 5.0 M HCl depends on their compositions in the absence of mixture according to their silicon and phosphorus content, that is, the corrosion rate increases with increasing silicon and phosphorus content. The adsorbed protective film on the steels surface heterogeneity markedly depends on steels class’s compositions, that is, the heterogeneity increases with decreasing silicon and phosphorus content.
Entrepreneurial financing relationships: how does gender matter?
Authors: Kim Grace
Published: February 2018

Purpose

Financing is cited as the major obstacle for entrepreneurs. However, data limitations have prevented study of entrepreneurs’ own impact on their financing relationships. Gender-based studies have concerned lender constraints and discriminatory outcomes. Others which are generally examined are borrowers’ fear of denial and non-pursuit of credit. To more fully explain the financing obstacle, the purpose of this study is to uniquely examine entrepreneurial borrowers’ evaluation of and actions in their existing financing relationship. This study also captures those businesses with equal ownership gender concentration, to contribute to a deeper understanding of gender impact.

Design/methodology/approach

This study uses a cross-sectional sample of several thousand US small enterprises from the NFIB’s proprietary credit survey. The data set offers links between owners’ perceptions and financing behavior. Robust univariate analysis examines differences across gender ownership groups. Multivariate regression analyzes how gender, business environment and other factors determine the entrepreneurs’ financing relationships.

Findings

This study highlights how entrepreneurs affect their own financing outcomes. Findings suggest that switching lenders, seeking multiple relationships and other actions determine financing satisfaction. Growth intent, business performance and characteristics of the entrepreneur are among significant posited factors influencing perception and behavior of entrepreneurs in their financing relationships that drive business performance. Furthermore, equal ownership concentration firms appear to be similar to those primarily owned by men. This study indicates that researchers need to further delineate among entrepreneurs. The results of this study also have implications for policy-makers in their assessment of gender discrimination and government entrepreneurial financing initiatives.

Originality/value

Financing is cited as the major obstacle for entrepreneurs. However, data limitations have prevented study of entrepreneurs’ own impact on their financing relationships. Gender-based studies have concerned lender constraints and discriminatory outcomes. Others which are generally examined are borrowers’ fear of denial and non-pursuit of credit. To more fully explain the financing obstacle, this study uniquely examines entrepreneurial borrowers’ evaluation of and actions in their existing financing relationship. This study also captures those businesses with equal ownership gender concentration, to contribute to a deeper understanding of gender impact.
The service recovery paradox in B2B relationships
Authors: Hübner Denis , Wagner Stephan M. , Kurpjuweit Stefan
Published: February 2018

Purpose

This study aims to explore the service recovery paradox (SRP) in business to business (B2B) relationships. Previously, this phenomenon has been identified in consumer-facing industries. The research advances the marketing literature by highlighting the ways in which the antecedents of the service recovery paradox differ between B2B and consumer markets.

Design/methodology/approach

This research draws upon findings on the SRP in the consumer setting and service failure literature in business to consumer and B2B contexts. For the analysis, interview data were collected from 43 informants among clients and service providers in the aftermath of a service failure.

Findings

The authors propose an exploratory model of the SRP for B2B relationships. In the B2B setting the propensity of eliciting the SRP depends on (1) the characteristics of the service failure, (2) the attributes of the service recovery and (3) the shared subjective perceptions among boundary spanners.

Practical implications

Empowered operating-level employees, straightforward communication, immediate responses and action plans that ensure future conformance are the key factors to turn service failures into increased customer satisfaction.

Originality/value

This study is the first to transfer the SRP from consumer marketing into the B2B domain. Moreover, it derives an exploratory model of the SRP, which can be refined by future research.