bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient exact associative structure for sequencing data
Authors: Marchet Camille , Kerbiriou Mael , Limasset Antoine
Published: February 2019

Motivation

A plethora of methods and applications share the fundamental need to associate information to words for high throughput sequence analysis. Doing so for billions of k-mers is commonly a scalability problem, as exact associative indexes can be memory expensive. Recent works take advantage of overlaps between k-mers to leverage this challenge. Yet existing data structures are either unable to associate information to k-mers or are not lightweight enough.

Results

We present BLight, a static and exact data structure able to associate unique identifiers to k-mers and determine their membership in a set without false positive, that scales to huge k-mer sets with a low memory cost. This index combines an extremely compact representation along with very fast queries. Besides, its construction is efficient and needs no additional memory. Our implementation achieves to index the k-mers from the human genome using 8GB of RAM (23 bits per k-mer) within 10 minutes and the k-mers from the large axolotl genome using 63 GB of memory (27 bits per k-mer) within 76 minutes. Furthermore, while being memory efficient, the index provides a very high throughput: 1.4 million queries per second on a single CPU or 16.1 million using 12 cores. Finally, we also present how BLight can practically represent metagenomic and transcriptomic sequencing data to highlight its wide applicative range.

Availability

We wrote the BLight index as an open source C++ library under the AGPL3 license available at github.com/Malfoy/BLight. It is designed as a user-friendly library and comes along with code usage samples.
Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update
Authors: Cruz-Morales Pablo , Orellana Camila A. , Moutafis George , Moonen Glenn , Rincon Gonzalo , Nielsen Lars K , Marcellin Esteban
Published: February 2019

Clostridiumis a large genus of obligate anaerobes belonging to theFirmicutesphylum of bacteria, most of which have a Gram-positive cell wall structure. The genus includes significant human and animal pathogens, causative of potentially deadly diseases such as tetanus and botulism. Despite their relevance and many studies suggesting that they are not a monophyletic group, the taxonomy of the group has largely been neglected. Currently, species belonging to the genus are placed in the unnatural order defined asClostridiales, which includes the classClostridia. Here we used genomic data from 779 strains to study the taxonomy and evolution of the group. This analysis allowed us to; (i) confirm that the group is composed of more than one genus (ii), detect major differences between pathogens classified as a single species within the group of authenticClostridiumspp. (sensu stricto), identify inconsistencies between taxonomy and toxin evolution that reflect on the pervasive misclassification of strains and, (iv) identify differential traits within central metabolism of members of what has been defined earlier and confirmed by us as cluster I. Our analysis shows that the current taxonomic classification ofClostridiumspecies hinders the prediction of functions and traits, suggests a new classification for this fascinating class of bacteria and highlights the importance of phylogenomics for taxonomic studies.
Extensive loss of cell cycle and DNA repair genes in an ancient lineage of bipolar budding yeasts
Authors: Steenwyk Jacob L. , Opulente Dana A. , Kominek Jacek , Shen Xing-Xing , Zhou Xiaofan , Labella Abigail L. , Bradley Noah P. , Eichman Brandt F. , Čadež Neža , Libkind Diego , DeVirgilio Jeremy , Hulfachor Amanda Beth , Kurtzman Cletus P. , Hittinger Chris Todd , Rokas Antonis
Published: February 2019

Cell cycle checkpoints and DNA repair processes protect organisms from potentially lethal mutational damage. Compared to other budding yeasts in the subphylum Saccharomycotina, we noticed that a lineage in the genusHanseniasporaexhibited very high evolutionary rates, low GC content, small genome sizes, and lower gene numbers. To better understandHanseniasporaevolution, we analyzed 25 genomes, including 11 newly sequenced, representing 18 / 21 known species in the genus. Our phylogenomic analyses identify twoHanseniasporalineages, the fast-evolving lineage (FEL), which began diversifying ∼87 million years ago (mya), and the slow-evolving lineage (SEL), which began diversifying ∼54 mya. Remarkably, both lineages lost genes associated with the cell cycle and genome integrity, but these losses were greater in the FEL. For example, all species lost the cell cycle regulatorWHI5, and the FEL lost components of the spindle checkpoint pathway (e.g.,MAD1, MAD2) and DNA damage checkpoint pathway (e.g.,MEC3, RAD9). Similarly, both lineages lost genes involved in DNA repair pathways, including the DNA glycosylase geneMAG1, which is part of the base excision repair pathway, and the DNA photolyase genePHR1, which is involved in pyrimidine dimer repair. Strikingly, the FEL lost 33 additional genes, including polymerases (i.e.,POL4andPOL32) and telomere-associated genes (e.g.,RIF1, RFA3, CDC13, PBP2). Echoing these losses, molecular evolutionary analyses reveal that, compared to the SEL, the FEL stem lineage underwent a burst of accelerated evolution, which resulted in greater mutational loads, homopolymer instabilities, and higher fractions of mutations associated with the common endogenously damaged base, 8-oxoguanine. We conclude thatHanseniasporais an ancient lineage that has diversified and thrived, despite lacking many otherwise highly conserved cell cycle and genome integrity genes and pathways, and may represent a novel system for studying cellular life without them.
Nanoscopic Clustering of Neuroligin-3 and Neuroligin-4X Regulates Growth Cone Organization and Size
Authors: Gatford Nicholas J. F. , Michael Deans P. J. , Duarte Rodrigo R.R. , Chennell George , Raval Pooja , Srivastava Deepak P.
Published: February 2019

The cell-adhesion proteins neuroligin-3 and neuroligin-4X (NLGN3/4X) have well described roles in synapse formation. NLGN3/4X are also expressed highly during neurodevelopment. However, the role these proteins play during this period is unknown. Here we show that NLGN3/4X localized to the leading edge of growth cones where itpromoted neuritogenesis in immature human neurons. Super-resolution microscopyrevealed that NLGN3/4X clustering induced growth cone enlargement and influenced actin filament organization. Critically, these morphological effects were not induced by Autism spectrum condition (ASC)-associated NLGN3/4X variants. Finally, actin regulators p21-activated kinase 1 (PAK1) and cofilin were found to be activated by NLGN3/4X and involved in mediating the effects of these adhesion proteins on actin filaments, growth cones, and neuritogenesis. These data reveal a novel role for NLGN3 and NLGN4X in the development of neuronal architecture, which may be altered in the presence of ASD-associated variants.
High resolution single-cell chromatin 3D modeling reveals coherent chromatin aggregation with varied structures in controlling genome function stability
Authors: Meng Luming , Shi Yi , Wang Chenxi
Published: February 2019

The genome 3D architecture is thought to be related to regulating gene expression levels in cells and can be explained by genome-wide chromatin interactions which have been explored by chromosome conformation capture based techniques, especially Hi-C. Based on single-cell Hi-C data, we developed a new method in constructing experimental consistent 3D intact genome structures for individual cells with a resolution of 10kb or higher. The modeled structures showed marked variations of 3D genome organization across different cells. However, chromosome loci marked by different proteins, such as CTCF and post-translationally modified histones, are consistently non-specifically aggregated in space. Interestingly, similar aggregations between active enhancers and active promoters were observed, especially for those separated by genomic regions of the scale of megabase or larger. Such long-range associations between active enhancers and promoters are strongly correlated with spatial aggregation of chromosome loci marked by different proteins. Through analyzing the 3D structures of intact genome, we proposed that coherent gene activation profiles among individual cells can be achieved by the consistent aggregation of protein marked loci instead of maintaining identical folded conformations.
Neural activity during a simple reaching task in macaques is counter to gating and rebound in basal ganglia-thalamic communication
Authors: Schwab Bettina C. , Kase Daisuke , Zimnik Andrew , Rosenbaum Robert , Codianni Marcello G. , Rubin Jonathan E. , Turner Robert S.
Published: February 2019

Task-related activity in the ventral thalamus, a major target of basal ganglia output, is often assumed to be permitted or triggered by changes in basal ganglia activity through gating- or rebound-like mechanisms. To test those hypotheses, we sampled single-unit activity from connected basal ganglia output and thalamic nuclei (globus pallidus-internus, GPi, and ventrolateral-anterior nucleus, VLa) in monkeys performing a reaching task. Rate increases were the most common peri-movement change in both nuclei. Moreover, peri-movement changes generally began earlier in VLa than in GPi. Simultaneously-recorded GPi-VLa pairs rarely showed short-timescale spike-to-spike correlations or slow across-trials covariations and both were equally positive and negative. Finally, spontaneous GPi bursts and pauses were both followed by small, slow reductions in VLa rate. These results appear incompatible with standard gating and rebound models. Still, gating or rebound may be possible in other physiological situations: Simulations show how GPi-VLa communication can scale with GPi synchrony and GPi-to-VLa convergence, illuminating how synchrony of basal ganglia output during motor learning or in pathological conditions may render this pathway effective. Thus, in the healthy state, basal ganglia-thalamic communication during learned movement is more subtle than expected, with changes in firing rates possibly being dominated by a common external source.
Assessment of Dried Blood Spots for DNA Methylation Profiling
Authors: Walker Rosie M. , MacGillivray Louise , McCafferty Sarah , Wrobel Nicola , Murphy Lee , Kerr Shona M. , Morris Stewart W. , Campbell Archie , McIntosh Andrew M. , Porteous David J. , Evans Kathryn L.
Published: February 2019

Background

DNA methylation reflect health-related environmental exposures and genetic risk, providing insights into aetiological mechanisms and potentially predicting disease onset, progression and treatment response. An increasingly recognised need for large-scale, longitudinally-profiled samples collected world-wide has made the development of efficient and straightforward sample collection and storage procedures a pressing issue. An alternative to the low-temperature storage of EDTA tubes of venous blood samples, which are frequently the source of the DNA used in such studies, is to collect and store at room temperature blood samples using filter paper engineered for the purpose, such as Whatman FTA®cards. Our goal was to determine whether DNA stored in this manner can be used to generate DNA methylation profiles comparable to those generated using blood samples frozen in EDTA tubes.

Methods

DNA methylation profiles were obtained from matched EDTA tube and Whatman FTA®card whole-blood samples from 62 Generation Scotland: Scottish Family Health Study participants using the Infinium HumanMethylation450 BeadChip. Multiple quality control procedures were implemented, the relationship between the two sample types assessed, and EWASs performed for smoking status, age and the interaction between these variables and sample storage method. Results: Dried blood spot (DBS) DNA methylation profiles were of good quality and DNA methylation profiles from matched DBS and EDTA tube samples were highly correlated (mean r = 0.991) and could distinguish between participants. EWASs replicated established associations for smoking and age, with no evidence for moderation by storage method.

Conclusions

Our results support the use of Whatman FTA®cards for collecting and storing blood samples for DNA methylation profiling. This approach is likely to be particularly beneficial for large-scale studies and those carried out in areas where freezer access is limited. Furthermore, our results will inform consideration of the use of newborn heel prick DBSs for research use.
SyRI: identification of syntenic and rearranged regions from whole-genome assemblies
Authors: Goel Manish , Sun Hequan , Jiao Wen-Biao , Schneeberger Korbinian
Published: February 2019

Here, we present SyRI, an efficient tool for genome-wide structural rearrangement identification from genome graphs, which are build up from pair-wise whole-genome alignments. Instead of searching for differences, SyRI starts by finding all co-linear regions between the genomes. As all remaining regions are SRs by definition, they just have to be classified as inversions, translocations, or duplications based on their positions in convoluted networks of repetitive alignments. Finally, SyRI reports local variations like SNPs and indels within syntenic and rearranged regions. We show SyRI’s broad applicability to multiple species and genetically validate the presence of ~100 translocations identified in Arabidopsis.
Oligoribonuclease functions as a diribonucleotidase to bypass a key bottleneck in RNA degradation
Authors: Kim Soo-Kyoung , Lormand Justin D. , Weiss Cordelia A. , Eger Karin A. , Turdiev Husan , Turdiev Asan , Winkler Wade C. , Sondermann Holger , Lee Vincent T.
Published: February 2019

Degradation of RNA polymers is a multistep process catalyzed by specific subsets of RNases. In all cases, degradation is completed by exoribonucleases that recycle RNA fragments into nucleotide monophosphate. In γ-proteobacteria, a group of up to eight 3’-5’ exoribonucleases have been implicated in RNA degradation. Oligoribonuclease (Orn) is unique among them as its activity is required for clearing short RNA fragments, a function important for cellular fitness. However, the mechanistic basis for this substrate selectivity remained unclear. Here we show that Orn’s activity as a general exoribonuclease has been vastly overestimated by demonstrating that the enzyme exhibits a much narrower substrate preference for diribonucleotides. Co-crystal structures of Orn with substrates reveal an active site optimized for diribonucleotides that does not accommodate longer substrates. While other cellular RNases process oligoribonucleotides down to diribonucleotide entities, our functional studies demonstrate that Orn is the one and only diribonucleotidase that completes the final stage of the RNA degradation pathway. Together, these results indicate that Orn is a dedicated diribonucleotidase that clears the diribonucleotide pool that otherwise affects cellular physiology and viability.
Evidence for Similar Structural Brain Anomalies in Youth and Adult Attention-Deficit/Hyperactivity Disorder: A Machine Learning Analysis
Authors: Zhang-James Yanli , Helminen Emily C , Liu Jinru ,   The ENIGMA-ADHD Working Group, Franke Barbara , Hoogman Martine , Faraone Stephen V
Published: February 2019

ADHD affects 5% of children world-wide. Of these, two-thirds continue to have impairing symptoms of ADHD into adulthood. Although a large literature implicates structural brain differences in the pathophysiology of the disorder, it is not clear if adults with ADHD have similar neuroanatomical impairments as those seen in children with recent reports from the large ENIGMA-ADHD consortium finding structural abnormalities for children but not for adults. This paper uses deep learning neural network classification models to determine if there are neuroanatomical changes in the brains of children with ADHD that are also observed for adult ADHD, and vice versa. We found that structural MRI data can significantly separate ADHD from control participants for both children and adults. Consistent with the prior reports from ENIGMA-ADHD, prediction performance and effect sizes were better for the child than the adult samples. The model trained on adult samples significantly predicted ADHD in the child sample, suggesting that our model learned anatomical features that common to ADHD in childhood and adulthood. These results support the continuity of ADHD’s pathophysiology from childhood to adulthood. In addition, our work demonstrates a novel use of neural network classification models to test hypotheses about developmental continuity.
Exploring the influence of surface proteins on probiotic activity of Lactobacillus pentosus HC-2 in Litopenaeus vannamei midgut via Label-free quantitative proteomic analysis
Authors: Du Yang , Fang Han , Liu Mei , Jiang Keyong , Wang Mengqiang , Wang Baojie , Wang Lei
Published: February 2019

Our previously work showed that Lactobacillus pentosus HC-2 as probiotic could improve the growth performance, immune response, gut bacteria diversity and disease resistance of Litopenaeus vannamei. However, the probiotic mechanism of was not fully characterized. In the present study, histology and proteomic analysis was performed to explore the influence of HC-2 surface protein on its probiotic effects to L. vannamei after feeding the intact surface proteins or the probiotic treated with lithium chloride (LiCl) to remove non-covalently bound surface proteins or no probiotic for four weeks. Histological observation found that feeding with normal HC-2 obviously improved the intestinal histology and enhanced the protective effect against pathogens damages, but fed with LiCl-treated HC-2 didn’t improve the intestinal environment. A total over 2,764 Peptides and 1,118 uniproteins were identified from L. vannamei midgut, 211 proteins were significant differentially expressed normal HC-2 group compared with control, 510 proteins were significant differentially expressed in LiCl-tread HC-2 group compared with control, and 458 proteins were significant differentially expressed in LiCl-tread HC-2 group compared with normal HC-2 group. GO/KEGG enrichment analysis of the significantly different proteins demonstrated that fed with normal HC-2 mainly induced immune response, metabolic, cell adhesion and cell-cell signaling related proteins up-regulation, which were contributed to bacteria adhesion and colonization in midgut to improve shrimp immune system and growth, but these proteins were suppressed after feeding with deprived surface proteins bacteria. Taken together, these results indicating that the surface proteins were indispensable for HC-2 to execute probiotic effects in midgut of shrimp.
Environmental specificity and evolution in Drosophila-bacteria symbiosis
Authors: Guilhot Robin , Rombaut Antoine , Xuéreb Anne , Howell Kate , Fellous Simon
Published: February 2019

Environmentally acquired microbial symbionts could contribute to host adaptation to local adaptation like vertically transmitted symbionts do. This scenario necessitates symbionts to have different effects in different environments. In Drosophila melanogaster, communities of extracellular bacterial symbionts vary largely among environments, which could be due to variable effects on phenotype. We investigated this idea with four bacterial strains isolated from the feces of a D. melanogaster lab strain, and tested their effects in two environments: the environment of origin (i.e. the laboratory medium) and a new one (i.e. fresh fruit with live yeast). All bacterial effects on larval and adult traits differed among environments, ranging from very beneficial to marginally deleterious. The joint analysis of larval development speed and adult size further suggests bacteria would affect developmental plasticity more than resource acquisition in males. The context-dependent effects of bacteria we observed, and its underlying mechanisms, sheds light on how environmentally acquired symbionts may contribute to host evolution.
Full-length mRNA sequencing reveals principles of poly(A) tail length control
Authors: Legnini Ivano , Alles Jonathan , Karaiskos Nikos , Ayoub Salah , Rajewsky Nikolaus
Published: February 2019

Although mRNAs are key molecules for understanding life, there exists no method to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although poly(A) tails can be modified in functionally important ways, there also exists no method to accurately sequence them. Here, we present FLAM-seq, a rapid and simple method for high-quality sequencing of entire mRNAs. We report a cDNA library preparation method coupled to single-molecule sequencing to perform FLAM-seq. Using human cell lines, brain organoids, andC. eleganswe show that FLAM-seq delivers high-quality full-length mRNA sequences for thousands of different genes per sample. We find that (a) 3’ UTR length is correlated with poly(A) tail length, (b) alternative polyadenylation sites and alternative promoters for the same gene are linked to different tail lengths, (c) tails contain a significant number of cytosines. Thus, we provide a widely useful method and fundamental insights into poly(A) tail regulation.
Respiratory syncytial virus activates Rab5a to suppress IRF1-dependent IFN-λ production, subverting the antiviral defense of airway epithelial cells
Authors: Gao Leiqiong , Tang Wei , Xie Jun , Chen Sisi , Ren Luo , Zang Na , Xie Xiaohong , Deng Yu , Liu Enmei
Published: February 2019

Human respiratory syncytial virus (RSV) is a negative-strand RNA virus that causes severe acute pediatric respiratory tract infections worldwide. The limited effective antiviral options and lack of an effective vaccine against RSV highlight the need for a novel anti-viral therapy. One alternative is to identify and target the host factors required for viral infection. All viruses, including RSV, utilize cellular trafficking machinery to fulfill their life cycle in the infected host cells. Rab proteins mediate specific steps in intracellular membrane trafficking through the recruitment and tethering of fusion factors, and docking with actin- or microtubule-based motor proteins. Using RNA interference to knock down Rab proteins, we document that the micropinocytosis-associated Rab5a is required for RSV infection. RSV infection itself induces activation of Rab5a, and inhibition of this activation reduces RSV infection, but the mechanism for this effect remains unknown. Interferon (IFN) signaling plays an important role in innate immunity, and recent studies have identified IFN-λ (lambda), a type III IFN, as the most important IFN for antiviral immune in response to RSV infection of mucosal epithelium. However, how the RSV-induced Rab5a suppresses airway epithelial antiviral immunity has not been unraveled. Here, we show that activated Rab5a inhibits IRF1-induced IFN-λ production and IFN-λ-mediated signal transduction via JAK-STAT1, thereby increasing viral replication. Rab5a knockdown by siRNA resulted in stimulation of IRF1, IFN-λ and JAK-STAT1 expression, and suppressed viral growth. Our results highlight new role for Rab5a in RSV infection, such that its depletion inhibits RSV infection by stimulating the endogenous respiratory epithelial antiviral immunity, which suggests that Rab5a is a potential target for novel therapeutics against RSV infection.

Author summary

RSV is the leading cause of lower respiratory tract infection in under 5 years old children. Worldwide. We identified Rab5a as a host factor involved in RSV infection via RNA interference to knock down familiar Rab proteins in human lung epithelial A549 cells infected with RSV. Rab5a belongs to Rab GTPases subfamily, which contributes to intracellular trafficking to promote virus infection. Knockdown or inactive (GDP-bound) Rab5a results in low infection and replication through stimulating IRF1, IFN-λ and JAK-STAT1 expression, and suppressed viral growth. Besides, we propose that the regulation of Rab5a expression during RSV infection might be a viral strategy to promote its infectivity.
A single dose of antibody-drug conjugate cures a stage 1 model of African trypanosomiasis
Authors: MacGregor Paula , Gonzalez-Munoz Andrea L. , Jobe Fatoumatta , Taylor Martin C. , Rust Steven , Sandercock Alan M. , Macleod Olivia J.S. , Van Bocxlaer Katrien , Francisco Amanda F. , D’Hooge Francois , Tiberghien Arnaud , Barry Conor S. , Howard Philip , Higgins Matthew K. , Vaughan Tristan J. , Minter Ralph , Carrington Mark
Published: February 2019

Infections of humans and livestock with African trypanosomes are treated with drugs introduced decades ago that are not always fully effective and often have severe side effects. Here, the trypanosome haptoglobin-haemoglobin receptor (HpHbR) has been exploited as a route of uptake for an antibody-drug conjugate (ADC) that is completely effective againstTrypanosoma bruceiin the standard mouse model of infection. Recombinant human anti-HpHbR monoclonal antibodies were isolated and shown to be internalised in a receptor-dependent manner. Antibodies were conjugated to a pyrrolobenzodiazepine (PBD) toxin and killedT. brucei in vitroat picomolar concentrations. A single therapeutic dose (0.25 mg/kg) of a HpHbR antibody-PBD conjugate completely cured aT. bruceimouse infection within 2 days with no re-emergence of infection over a subsequent time course of 77 days. These experiments provide a demonstration of how ADCs can be exploited to treat protozoal diseases that desperately require new therapeutics.

Author Summary

Here we show that antibody-drug conjugates (ADCs) can be re-purposed from cancer immunotherapeutics to anti-protozoals by changing the specificity of the immunoglobulin to target a trypanosome cell surface receptor. Trypanosomes were used as a model system due to the availability of receptor null cell lines that allowed the unambiguous demonstration that ADCs targeted to a parasite surface receptor could be specifically internalised via receptor-mediated endocytosis. A single low dose of the resulting ADC was able to cure a stage 1 mouse model of trypanosome infection. We have used toxins and conjugation chemistry that are identical to anti cancer ADCs demonstrating the ability to piggy-back onto the huge research efforts and resources that are being invested in the development of such ADCs.

The potential for development of ADCs against a wide range of human pathogens is vast, where only epitope binding sites need vary in order to provide selectivity. This provides a far-reaching opportunity for the rapid development of novel anti-protozoals for the targeted killing of a wide range of pathogens that cause disease worldwide, especially in developing countries.
3D Microstructure of Tendon Collagen Fibrils using Serial Block-Face SEM and a Mechanical Model for Load Transfer
Authors: Safa Babak N. , Peloquin John M. , Natriello Jessica R. , Caplan Jeffrey L. , Elliott Dawn M.
Published: February 2019

Tendon’s hierarchical structure allows for load transfer between its fibrillar elements at multiple length scales. Tendon microstructure is particularly important, because it includes the cells and their surrounding collagen fibrils, where mechanical interactions can have potentially important physiological and pathological contributions. However, the three-dimensional microstructure and the mechanisms of load transfer in that length scale are not known. It has been postulated that interfibrillar matrix shear or direct load transfer via the fusion/branching of small fibrils are responsible for load transfer, but the significance of these mechanisms is still unclear. Alternatively, the helical fibrils that occur at the microstructural scale in tendon may also mediate load transfer, however, these structures are not well studied due to the lack of a three-dimensional visualization of tendon microstructure. In this study, we used serial block-face scanning electron microscopy (SBF-SEM) to investigate the threedimensional microstructure of fibrils in rat tail tendon. We found that tendon fibrils have a complex architecture with many helically wrapped fibrils. We studied the mechanical implications of these helical structures using finite element modeling and found that frictional contact between helical fibrils can induce load transfer even in the absence of matrix bonding or fibril fusion/branching. This study is significant in that it provides a three-dimensional view of the tendon microstructure and suggests friction between helically wrapped fibrils as a mechanism for load transfer, which is an important aspect of tendon biomechanics.
Ephrin-A5 potentiates netrin-1 axon guidance by enhancing Neogenin availability
Authors: Croteau L.-P. , Kao T.-J. , Kania A.
Published: February 2019

Axonal growth cones are guided by molecular cues in the extracellular environment. The mechanisms of combinatorial integration of guidance signals at the growth cone cell membrane are still being unravelled. Limb-innervating axons of vertebrate spinal lateral motor column (LMC) neurons are attracted to netrin-1 via its receptor, Neogenin, and are repelled from ephrin-A5 through its receptor EphA4. The presence of both cues elicits synergistic guidance of LMC axons, but the mechanism of this effect remains unknown. Using fluorescence immunohistochemistry, we show that ephrin-A5 increases LMC growth cone Neogenin protein levels and netrin-1 binding. This effect is enhanced by overexpressing EphA4 and is inhibited by blocking ephrin-A5-EphA4 binding. These effects have a functional consequence on LMC growth cone responses since bath addition of ephrin-A5 increases the responsiveness of LMC axons to netrin-1. Surprisingly, the overexpression of EphA4 lacking its cytoplasmic tail, also enhances Neogenin levels at the growth cone and potentiates LMC axon preference for growth on netrin-1. Since netrins and ephrins participate in a wide variety of biological processes, the enhancement of netrin-1 signalling by ephrins may have broad implications.
Transposable elements contribute to dynamic genome content in maize
Authors: Anderson Sarah N , Stitzer Michelle C , Brohammer Alex B. , Zhou Peng , Noshay Jaclyn M , Hirsch Cory D. , Ross-Ibarra Jeffrey , Hirsch Candice N. , Springer Nathan M
Published: February 2019

Transposable elements (TEs) are ubiquitous components of eukaryotic genomes and can create variation in genomic organization. The majority of maize genomes are composed of TEs. We developed an approach to define shared and variable TE insertions across genome assemblies and applied this method to four maize genomes (B73, W22, Mo17, and PH207). Among these genomes we identified 1.6 Gb of variable TE sequence representing a combination of recent TE movement and deletion of previously existing TEs. Although recent TE movement only accounted for a portion of the TE variability, we identified 4,737 TEs unique to one genome with defined insertion sites in all other genomes. Variable TEs are found for all superfamilies and are distributed across the genome, including in regions of recent shared ancestry among individuals. There are 2,380 genes annotated in the B73 genome located within variable TEs, providing evidence for the role of TEs in contributing to the substantial differences in gene content among these genotypes. The large scope of TE variation present in this limited sample of temperate maize genomes highlights the major contribution of TEs in driving variation in genome organization and gene content.

Significance Statement

The majority of the maize genome is comprised of transposable elements (TEs) that have the potential to create genomic variation within species. We developed a method to identify shared and non-shared TEs using whole genome assemblies of four maize inbred lines. Variable TEs are found throughout the maize genome and in comparisons of any two genomes we find ~20% of the genome is due to non-shared TEs. Several thousand maize genes are found within TEs that are variable across lines, highlighting the contribution of TEs to gene content variation. This study creates a comprehensive resource for genomic studies of TE variability among four maize genomes, which will enable studies on the consequences of variable TEs on genome function.
A rare variant on a common risk haplotype of HFE causes increased risk of hereditary hemochromatosis
Authors: Glazer Andrew M. , Bastarache Lisa , Hall Lynn , Short Laura , Shields Tiffany , Kroncke Brett M. , Denny Joshua C. , Roden Dan M.
Published: February 2019

Hereditary hemochromatosis (HH) is an autosomal recessive disorder of excess iron absorption. The most common form, HH1, is caused by loss of function variants in HFE. HFE encodes a cell surface protein that binds to the Transferrin Receptor (TfR1), reducing TfR1’s affinity for the transferrin/iron complex and thereby limiting cellular iron uptake. Two common missense alleles for HH1 have been identified, HFE C282Y and HFE H63D; H63D is considered to be a less penetrant allele. When we deployed Phenotype Risk Scores (PheRS), a method that aggregates multiple symptoms together in Electronic Health Records (EHRs), we identified HFE E168Q as a novel variant associated with HH. E168Q is on the same haplotype as H63D, and in a crystal structure HFE E168 lies at the interface of the HFE-TfR1 interaction and makes multiple salt bridge connections with TfR1. In in vitro cell surface abundance experiments, the HFE E168Q+H63D double mutation surprisingly increased cell surface abundance of HFE by 10-fold compared to wildtype. In coimmunoprecipitation experiments, however, HFE C282Y, E168Q, and E168Q+H63D completely abolished the interaction between HFE and TfR1, while H63D alone only partially reduced binding. These findings provide mechanistic insight to validate the PheRS result that HFE E168Q is an HH1-associated allele and lead to the reclassification of E168Q from a variant of uncertain significance to a pathogenic variant, according to ACMG guidelines. HFE E168Q results in loss of HFE function by disrupting the HFE-TfR1 interaction. In addition, some disease manifestations attributed to H63D may reflect the functional effects of E168Q.
Exercise twice-a-day potentiates skeletal muscle signalling responses associated with mitochondrial biogenesis in humans, which are independent of lowered muscle glycogen content
Authors: Andrade-Souza Victor A. , Ghiarone Thaysa , Sansonio Andre , Silva Kleiton Augusto Santos , Tomazini Fabiano , Arcoverde Lucyana , Fyfe Jackson , Perri Enrico , Saner Nicholas , Kuang Jujiao , Bertuzzi Romulo , Leandro Carol Gois , Bishop David J. , Lima-Silva Adriano E.
Published: February 2019

Endurance exercise begun with reduced muscle glycogen stores seems to potentiate skeletal muscle protein abundance and gene expression. However, it is unknown whether this greater signalling responses is due to low muscle glycogenper seor to performing two exercise sessions in close proximity - as a first exercise session is necessary to reduce the muscle glycogen stores. In the present study, we manipulated the recovery duration between a first muscle glycogen-depleting exercise and a second exercise session, such that the second exercise session started with reduced muscle glycogen in both approaches but was performed either two or 15 h after the first exercise session (so-called “twice-a-day” and “once-daily” approaches, respectively). We found that exercise twice-a-day increased the nuclear abundance of transcription factor EB (TFEB) and nuclear factor of activated T cells (NFAT) and potentiated the transcription of peroxisome proliferator-activated receptor-coactivator 1 alpha (PGC-1α), peroxisome proliferator-activated receptor alpha (PPARα) and peroxisome proliferator-activated receptor beta/delta (PPARβ/δ) genes, in comparison with the once-daily exercise. These results suggest that the elevated molecular signalling reported with previous “train-low” approaches can be attributed to performing two exercise sessions in close proximity rather than the reduced muscle glycogen contentper se.The twice-a-day approach might be an effective strategy to induce adaptations related to mitochondrial biogenesis and fat oxidation.
Dynamic architecture of the Escherichia coli Structural Maintenance of Chromosomes (SMC) complex, MukBEF
Authors: Rajasekar Karthik V. , Tang Minzhe , Baker Rachel , Zawadzka Katarzyna , Koczy Oliwia , Wagner Florence , Bolla Jani Reddy , Robinson Carol V. , Arciszewska Lidia K. , Sherratt David J.
Published: February 2019

Structural Maintenance of Chromosomes (SMC) complexes use a proteinaceous ring-shaped architecture to organise chromosomes, thereby facilitating chromosome segregation. They utilise cycles of ATP binding and hydrolysis to transport themselves rapidly with respect to DNA, a process requiring protein conformational changes and multiple DNA contacts. We have analysed changes in the architecture of the Escherichia coli SMC complex, MukBEF, as a function of nucleotide binding to MukB and subsequent ATP hydrolysis. This builds upon previous work showing that MukF kleisin directs formation of a MukBEF tripartite ring as a consequence of functional interactions between the C- and N-terminal domains of MukF with the MukB head and neck, respectively (Zawadzka et al., 2018). Using both model truncated substrates and complexes containing full length MukB, we now demonstrate formation of MukBEF ‘dimers of dimers’, dependent on MukF dimerization, MukB head-engagement and MukE, which plays an essential role in organizing MukBEF complexes.
Changes in Ovary Transcriptome and Alternative splicing at estrus from Xiang pigs with Large and Small Litter Size
Authors: Zhang Fuping , Tang Liangting , Ran Xueqin , Mao Ning , Ruan Yiqi , Yi Fanli , Liu Chang , Niu Xi , Huang Shihui , Li Sheng , Wang Jiafu
Published: February 2019

Background/Aims

Litter size is one of the most important reproductive traits in pig breeding, which is affected by multiple genes and the environment. Ovaries are the most important reproductive organs and have a profound impact on the reproduction efficiency. Therefore, genetic differences in the ovaries may contribute to the observed differences in litter size. Although QTLs and candidate genes have been reported to affect the litter size in many pig breeds, however, the findings cannot elucidate the marked differences of the reproductive traits between breeds. The aim of present work is to elucidate the mechanisms of the differences for the reproductive traits and identify candidate genes associated with litter size in Xiang pig breed.

Methods

The changes in ovary transcriptome and alternative splicing were investigated at estrus between Xiang pigs with large and small litter size by RNA-seq technology. The RNA-seq results were confirmed by RT-qPCR method.

Results

We detected 16,219 - 16,285 expressed genes and 12 types of alternative splicing (AS) events in Xiang pig samples. A total of 762 differentially expressed genes were identified by XL (Xiang pig group with larger litter size) vs XS (Xiang pig group with small litter size) sample comparisons. A total of 34 genes were upregulated and 728 genes were downregulated in XL ovary samples compared with the XS samples. Alternative splicing (AS) rates in XL samples were slightly lower than that observed in XS samples. Most of differentially expressed genes were differentially regulated on AS level. Eleven candidate genes were potentially identified to be related to Xiang pig fecundity and litter size, which may be closely related to the gonad development, oocyte maturation or embryo quality.

Conclusion

The significant changes in the expression of the protein-coding genes and the level of alternative splicing in estrus ovarian transcriptome between XL and XS groups probably are the molecular mechanisms of phenotypic variation in litter size.
A semiautomated whole-exome sequencing workflow leads to increased diagnostic yield and identification of novel candidate variants
Authors: Ji Jianling , Shen Lishuang , Bootwalla Moiz , Quindipan Catherine , Tatarinova Tatiana , Maglinte Dennis T. , Buckley Jonathan , Raca Gordana , Saitta Sulagna C. , Biegel Jaclyn A. , Gai Xiaowu
Published: February 2019

Advancing the clinical utility of whole-exome sequencing (WES) for patients with suspected genetic disorders is largely driven by bioinformatics approaches that streamline data processing and analysis. Herein, we describe our experience with implementing a semiautomated and phenotype-driven WES diagnostic workflow, incorporating both the DRAGEN pipeline and the Exomiser variant prioritization tool, at an academic children's hospital with an ethnically diverse pediatric patient population. We achieved a 41% molecular diagnostic rate for 66 duo-, quad-, or trio-WES cases, and 28% for 40 singleton-WES cases. Preliminary results were returned to ordering physicians within 1 wk for 12 of 38 (32%) probands with positive findings, which were instrumental in guiding the appropriate clinical management for a variety of patients, especially in critical care settings. The semiautomated and streamlined WES workflow also enabled us to identify novel variants in candidate disease genes in patients with developmental delay and autism and immune disorders and cancer, including ANK2, BPTF, BCL11A, FOXN1, PLAA, ATRX, DNAJC21, and RAD50. Together, we demonstrated the implementation of a streamlined WES workflow that was successfully applied for both clinical and research purposes.
SyLMAND: a microfabrication beamline with wide spectral and beam power tuning range at the Canadian Light Source
Authors: Wells Garth , Achenbach Sven , Subramanian Venkat , Jacobs Michael , Klymyshyn David , Iyer Swathi , Moazed Banafsheh , Hanson Jack , Shen Chen , Haluzan Darcy
Published: February 2019

SyLMAND, the Synchrotron Laboratory for Micro and Nano Devices, is a recently commissioned microfabrication bend magnet beamline with ancillary cleanroom facilities at the Canadian Light Source. The synchrotron radiation is applied to pattern high-aspect-ratio polymer microstructures used in the area of micro-electro-mechanical systems (MEMS). SyLMAND particularly focuses on spectral and beam power adjustability and large exposable area formats in an inert gas atmosphere; a rotating-disk intensity chopper allows for independent beam-power reduction, while continuous spectral tuning between 1–2 keV and >15 keV photon energies is achieved using a double-mirror system and low-atomic-number filters. Homogeneous exposure of samples up to six inches in diameter is performed in the experimental endstation, a vertically scanning precision stage (scanner) with tilt and rotation capabilities under 100 mbar helium. Commissioning was completed in late 2017, and SyLMAND is currently ramping up its user program, mostly in the areas of RF MEMS, micro-fluidics/life sciences and micro-optics.
The typical crystal structures of a few representative α-aryl-α-hydroxyphosphonates
Authors: Rádai Zita , Kiss Nóra Zsuzsa , Czugler Mátyás , Karaghiosoff Konstantin , Keglevich György
Published: February 2019

The crystal structures of seven α-aryl-α-hydroxyphosphonates synthesized by the Pudovik reaction of substituted benzaldehydes and dialkyl phosphites, namely dimethyl [(hydroxy)(phenyl)methyl]phosphonate, C9H13O4P, dimethyl [(3,4-dimethoxyphenyl)(hydroxy)methyl]phosphonate, C11H17O6P, dimethyl (1-hydroxy-1-phenylethyl)phosphonate, C10H15O4P, dimethyl [1-hydroxy-1-(4-nitrophenyl)ethyl]phosphonate, C10H14NO6P, dibenzyl [hydroxy(2-nitrophenyl)methyl]phosphonate, C21H20NO6P, dibenzyl [(3-chlorophenyl)(hydroxy)methyl]phosphonate, C21H20ClO4P, and dibenzyl [hydroxy(4-methylphenyl)methyl]phosphonate, C22H23O4P, were studied to gain a better understanding of the organization in this type of molecule in the solid state. The crystals obtained for this series of compounds show a balance between C—OH...O=P chain-linked packing and the dimeric types of hydrogen-bond bridges of intermolecular pairs of such functions. The description is based on primary graph-set descriptors. Using graph-set descriptors one level deeper (i.e. secondary graph sets of the C—H...O type) revealed a similarity in the graph-set descriptors, suggesting a fine interplay of substituent- and shape-dependent effects on strong–weak interactions. It seems that the formation of chains or dimers is governed not only by the presence of a tertiary Cα atom, but also by the nature and crowding of the ortho substituents of the α-aryl group.
Crystal structure of chlorido{tris[2-(isopropylsulfanyl)phenyl]phosphane-κ4
P,S,S′,S′′}nickel(II) trifluoromethanesulfonate
Authors: Takeda Nobuhiro , Oma Rin , Unno Masafumi
Published: February 2019

The complex cation of the title compound, [NiCl{P(C6H4-2-S-i-Pr)3}](CF3SO3), has a slightly distorted trigonal–bipyramidal coordination geometry in which three S atoms are located in the equatorial plane, and one P and one Cl atom in the apical positions. In the cation, there are two intramolecular C—H...S hydrogen bonds. In the crystal, there are some intermolecular C—H...O and C—H...F hydrogen bonds formed between the cation and the anion. The trifluoromethanesulfonate anion and one of the methyl groups are both disordered over two sets of sites with occupancies of 0.629 (17):0.371 (17) and 0.786 (14):0.214 (14), respectively.
Influences of airfoil profile on lateral-directional stability of aircraft with flying wing layout
Authors: Pan Yalin , Huang Jun
Published: February 2019

Purpose

The purpose of this study is to analyze influence of airfoil profile on lateral-directional flying quality of flying wing aircraft. The lateral-directional stability is always insufficient for aircraft with the layout due to the absence of vertical stabilizer. A flying wing aircraft with double-swept wing is used as research object in the paper.

Design/methodology/approach

The 3D model is established for the aircraft with flying wing layout, and parametric modeling is carried out for airfoil mean camber line of the aircraft to analyze lateral-directional stability of the aircraft with different camber line parameters. To increase computational efficiency, vortex lattice method is adopted to calculate aerodynamic coefficients and aerodynamic derivatives of the aircraft.

Findings

It is found from the research results that roll mode and spiral mode have a little effect on lateral-directional stability of the aircraft but Dutch roll mode is the critical factor affecting flying quality level of such aircraft. Even though changes of airfoil mean line parameters can greatly change assessment parameters of aircraft lateral-directional flying quality, that is kind of change cannot have a fundamental impact on level of flying quality of the aircraft. In case flat shape parameters are determined, the airfoil profile has a limited impact on Dutch roll mode.

Originality/value

Influences of airfoil profile on lateral-directional flying quality of aircraft with double-swept flying wing layout are revealed in the thesis and some important rules and characteristics are also summarized to lay a theoretical basis for design of airfoil and flight control system of aircraft with the layout.