bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptomic analysis of Rhizobium leguminosarum bacteroids in determinate and indeterminate nodules
Authors: Green R. T. , East A. K. , Karunakaran R. , Downie J. A. , Poole P. S.
Published: February 2019

Two common classes of nitrogen-fixing legume root nodules are those that have determinate or indeterminate meristems, as in Phaseolus bean and pea, respectively. In indeterminate nodules, rhizobia terminally differentiate into bacteroids with endoreduplicated genomes, whereas bacteroids from determinate nodules are less differentiated and can regrow. We used RNA sequencing to compare bacteroid gene expression in determinate and indeterminate nodules using two

Rhizobium leguminosarum

strains whose genomes differ due to replacement of the symbiosis (Sym) plasmid pRP2 (strain Rlp4292) with pRL1 (strain RlvA34), thereby switching symbiosis hosts from Phaseolus bean (determinate nodules) to pea (indeterminate nodules). Both bacteroid types have gene expression patterns typical of a stringent response, a stressful environment and catabolism of dicarboxylates, formate, amino acids and quaternary amines. Gene expression patterns were indicative that bean bacteroids were more limited for phosphate, sulphate and iron than pea bacteroids. Bean bacteroids had higher levels of expression of genes whose products are predicted to be associated with metabolite detoxification or export. Pea bacteroids had increased expression of genes associated with DNA replication, membrane synthesis and the TCA (tricarboxylic acid) cycle. Analysis of bacteroid-specific transporter genes was indicative of distinct differences in sugars and other compounds in the two nodule environments. Cell division genes were down-regulated in pea but not bean bacteroids, while DNA synthesis was increased in pea bacteroids. This is consistent with endoreduplication of pea bacteroids and their failure to regrow once nodules senesce.
Low birth weight in Bangladesh and associated maternal and socioeconomic factors: results from a recent nationally-representative survey
Authors: Hossain Fariha Binte , Adhikary Gourab , Arafat Yasir , Shawon Md Shajedur Rahman
Published: February 2019

Objectives

Little is known about the relative contributions of maternal and socioeconomic factors on low birth weight in Bangladesh and whether they differ by sex. We examined the prevalence and associated maternal and socioeconomic factors of low birth weight separately among boys and girls.

Design and settings

This is a cross-sectional study based on the Bangladesh Demographic and Health Survey 2014.

Participants

A total of 4728 children with information on birth size were included in this study.

Outcome measure

Low birth weight was defined according to mother’s perception of birth size of their children. Logistic regression analysis was used to estimate the association between maternal and socioeconomic factors with low birth weight.

Results

The overall prevalence of low birth weight was 17.8% among boys and 22.4% among girls. Low birth weight was associated with maternal factors like maternal age of <20 years at birth (adjusted OR vs. 20-29 years: 1.40, 95% CI 1.09-1.78), and maternal undernutrition (adjusted OR 1.33, 95% CI 1.05-1.69) among boys while only the association with maternal undernutrition was significant among girls. The association for no antenatal care visit was explained by socioeconomic factors. Lower level of mother’s education and poorest wealth index were found to be associated with low birth weight in both sexes.

Conclusion

Our study identifies that maternal factors are associated with increased risk of having low birth weight babies, which cannot be explained by socioeconomic factors, and vice versa. Community-based interventions to reduce low birth weight in Bangladesh should focus on these factors.

Strengths and limitations of this study

To the best of our knowledge our study is the first study in Bangladesh that has looked at the factors for low birth weight separately among boys and girls.

We used multiple logistic regression to examine the associations of maternal and socioeconomic factors with low birth weight in a large and nationally-representative sample.

This study is limited because we used mother’s perception of child’s size at birth to define low birth weight.

We did not have information about gestational age and thereby could not take prematurity into account in our study.
Trait-based life-history strategies explain succession scenario for complex bacterial communities under varying disturbance
Authors: Santillan Ezequiel , Seshan Hari , Constancias Florentin , Wuertz Stefan
Published: February 2019

Trait-based approaches are increasingly gaining importance in community ecology, as a way of finding general rules for the mechanisms driving changes in community structure and function under the influence of perturbations. Frameworks for life-history strategies have been successfully applied to describe changes in plant and animal communities upon disturbance. To evaluate their applicability to complex bacterial communities, we operated replicated wastewater treatment bioreactors for 35 days and subjected them to eight different disturbance frequencies of a toxic pollutant (3-chloroaniline), starting with a mixed inoculum from a full-scale treatment plant. Relevant ecosystem functions were tracked and microbial communities assessed through metagenomics and 16S rRNA gene sequencing. Combining a series of ordination, statistical and network analysis methods, we associated different life-history strategies with microbial communities across the disturbance range. These strategies were evaluated using tradeoffs in community function and genotypic potential, and changes in bacterial genus composition. We further compared our findings with other ecological studies and adopted a semi-quantitative CSR (competitors, ruderals, stress-tolerants) classification. The framework reduces complex datasets of microbial traits, functions, and taxa into ecologically meaningful components to help understand the system response to disturbance, and hence represents a promising tool for managing microbial communities.

Originality-Significance Statement

This study establishes, for the first time, CSR life-history strategies in the context of bacterial communities. This framework is explained using community aggregated traits in an environment other than soil, also a first, using a combination of ordination methods, network analysis, and genotypic information from shotgun metagenomics and 16S rRNA gene amplicon sequencing.
Delineating and validating higher-order dimensions of psychopathology in the Adolescent Brain Cognitive Development (ABCD) study
Authors: Michelini Giorgia , Barch Deanna M. , Tian Yuan , Watson David , Klein Daniel N. , Kotov Roman
Published: February 2019

Hierarchical dimensional systems of psychopathology promise more informative descriptions for understanding risk and predicting outcome than traditional diagnostic systems, but it is unclear how many major dimensions they should include. We delineated the hierarchy of childhood and adult psychopathology and validated it against clinically-relevant measures. Participants were 4,524 9- and 10-year-old children and their parents from the Adolescent Brain Cognitive Development (ABCD) study. Factor analyses on items from the Child Behavior Checklist and Adult Self-Report characterized a dimensional hierarchy. We examined the familial aggregation of the psychopathology dimensions, and the ability of different factor solutions to account for risks factors, social, educational and cognitive functioning, and physical and mental health service utilization. A hierarchical structure with a general psychopathology (‘p’) factor at the apex and five specific factors (internalizing, somatoform, detachment, neurodevelopmental, and externalizing) emerged in children. Adult factors were similar, but externalizing behaviors separated into disinhibited and antagonistic factors. Child and parent p-factors correlated highly (r=.61, P<.001), and smaller but significant correlations emerged for convergent dimensions between parents and children after controlling for p-factors (r=.10-20, P<.001). A model with childhood p-factor alone explained mental health service utilization (R2=.13, P<.001), but up to five dimensions provided incremental validity to account for developmental risk and current functioning (R2=.03-.20, P<.001). In this first investigation comprehensively mapping the psychopathology hierarchy in children and adults, we delineated a hierarchy of higher-order dimensions associated with a range of clinically-relevant validators. These findings hold important implications for psychiatric nosology and future research in this sample.
Deconvolution of bulk blood eQTL effects into immune cell subpopulations
Authors: Aguirre-Gamboa R. , de Klein N. , di Tommaso J. , Claringbould A. , Võsa U. , Zorro M. , Chu X. , Bakker O.B. , Borek Z. , Ricaño-Ponce I. , Deelen P. , Xu C.J. , Swertz M. , Jonkers I. , Withoff S. , Joosten I. , Sanna S. , Kumar V. , Koenen H.J.P.M. , Joosten L.A.B. , Netea M.G. , Wijmenga C. ,   BIOS Consortium, Franke L. , Li Y.
Published: February 2019

Expression quantitative trait loci (eQTL) studies are used to interpret the function of disease-associated genetic risk factors. To date, most eQTL analyses have been conducted in bulk tissues, such as whole blood and tissue biopsies, which are likely to mask the cell type context of the eQTL regulatory effects. Although this context can be investigated by generating transcriptional profiles from purified cell subpopulations, the current methods are labor-intensive and expensive. Here we introduce a new method, Decon2, a statistical framework for estimating cell proportions using expression profiles from bulk blood samples (Decon-cell) and consecutive deconvolution of cell type eQTLs (Decon-eQTL). The estimated cell proportions from Decon-cell agree with experimental measurements across cohorts (R ≥ 0.77). Using Decon-cell we can predict the proportions of 34 circulating cell types for 3,194 samples from a population-based cohort. Next we identified 16,362 whole blood eQTLs and assign them to a cell type with Decon-eQTL using the predicted cell proportions from Decon-cell. Deconvoluted eQTLs show excellent allelic directional concordance with those of eQTL(≥ 96%) and chromatin mark QTL (≥87%) studies that used either purified cell subpopulations or single-cell RNA-seq. Our new method provides a way to assign cell type effects to eQTLs from bulk blood, which is useful in pinpointing the most relevant cell type for a certain complex disease. Decon2 is available as an R package and Java application (https://github.com/molgenis/systemsgenetics/tree/master/Decon2), and as a web tool (www.molgenis.org/deconvolution).
Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli
Authors: Alikhan Nabil-Fareed , Bachmann Nathan L. , Zakour Nouri L. Ben , Petty Nicola K. , Stanton-Cook Mitchell , Gawthorne Jayde A. , Easton Donna M. , Mahony Timothy J. , Cobbold Rowland , Schembri Mark A. , Beatson Scott A.
Published: February 2019

Background

Shiga toxigenic Escherichia coli (STEC) is an emerging global pathogen and remains a major cause of food-borne illness with more severe symptoms including hemorrhagic colitis and hemolytic-uremic syndrome. Since the characterization of the archetypal STEC serotype, E. coli O157:H7, more than 250 STEC serotypes have been defined. Many of these non-O157 STEC are associated with clinical cases of equal severity as O157. In this study, we utilize whole genome sequencing of 44 STEC strains from eight serogroups associated with human infection to establish their evolutionary relationships and contrast this with their virulence gene profiles and established typing methods.

Results

Our phylogenomic analysis delineated these STEC strains into seven distinct lineages, each with a characteristic repertoire of virulence factors. Some lineages included commensal or other E. coli pathotypes. Multiple independent acquisitions of the Locus for Enterocyte Effacement were identified, each associated with a distinct repertoire of effector genes. Lineages were inconsistent with O-antigen typing in several instances, consistent with lateral gene transfer within the O-antigen locus. STEC lineages could be defined by the conservation of clustered regularly interspaced short palindromic repeats (CRISPRs), however, no CRISPR profile could differentiate STEC from other E. coli strains. Six genomic regions (ranging from 500 bp - 10 kbp) were found to be conserved across all STEC in this dataset and may dictate interactions with Stx phage lysogeny.

Conclusions

The genomic analyses reported here present non-O157 STEC as a diverse group of pathogenic E. coli emerging from multiple lineages that independently acquired mobile genetic elements that promote pathogenesis.
Ordered Hexagonal Patterns via Notch-Delta Signaling
Authors: Teomy Eial , Kessler David A. , Levine Herbert
Published: February 2019

Many developmental processes in biology utilize Notch-Delta signaling to construct an ordered pattern of cellular differentiation. This signaling modality is based on nearest-neighbor contact, as opposed to the more familiar mechanism driven by the release of diffusible ligands. Here, we show that this “juxtracrine” property allows for an exact treatment of the pattern formation problem via a system of nine coupled ordinary differential equations. Furthermore, we show that the possible patterns that are realized can be analyzed by considering a co-dimension 2 pitchfork bifurcation of this system. This analysis explains the observed prevalence of hexagonal patterns with high Delta at their center, as opposed to those with central high Notch levels. Also, our theory suggests a simple strategy for producing defect-free patterns.
TNFR2 induced priming of NLRP3-inflammasome via RIPK1 leads to pyroptosis in XIAP deficient cells
Authors: Knop Janin , Spilgies Lisanne M. , Rufli Stefanie , Reinhart Ramona , Vasilikos Lazaros , Yabal Monica , Jost Philipp J. , Wajant Harald , Robinson Mark D. , Kaufmann Thomas , Wong W. Wei-Lynn
Published: February 2019

Recent data suggests that LPS stimulation can trigger inflammasome activation through a TNFR2/TNF/TNFR1 mediated loop inxiap−/−macrophages. Yet, the direct role TNFR2-specific activation plays in the absence of XIAP is unknown. We found TNFR2-specific activation lead to cell death inxiap−/−myeloid cells, particularly in the absence the RING domain. RIPK1/TAK1 kinase activity downstream of TNFR2 resulted in a TNF/TNFR1 cell death independent of necroptosis. TNFR2-specific activation lead to a similar inflammatory NF-kB driven transcriptional profile as TNFR1 activation with the exception of up-regulation of NLRP3 and caspase-11. Activation and up-regulation of the canonical inflammasome was mediated by RIPK1 kinase activity and ROS production. While both RIPK1 kinase activity and ROS production reduced cell death as well as release of IL-1β, the release of IL-18 was not reduced to basal levels. This study supports, targeting TNFR2 specifically to reduce IL-18 release in XIAP deficient (XLP-2) patients.
A Novel Taxon of RNA Viruses Endemic to Planarian Flatworms
Authors: Burrows Jeffrey , Depierreux Delphine , Nibert Max L. , Pearson Bret J.
Published: February 2019

The phylum Platyhelminthes is composed of both parasitic and non-parasitic flatworms. While the parasitic species have drawn attention for their wide effects on human and livestock heath, free-living flatworms, such as freshwater planarians, have become molecular models of regeneration and stem cell biology in the laboratory. However, one aspect of planarian biology that remains understudied is the relationship between host and any endemic viruses. Here we used searches of multiple transcriptomes from Schmidtea mediterranea asexual strain CIW4 and detected a novel, double-stranded RNA (dsRNA) virus, named S. mediterranea tricladivirus (SmedTV), which represents a distinct taxon (proposed new genus) within a larger taxon of monosegmented dsRNA viruses of diverse hosts. Experimental evidence for SmedTV in S. mediterranea CIW4 was obtained through whole-mount in situ hybridization (WISH). SmedTV “expression” (detected by both sense and anti-sense probes) was discrete yet variable from worm to worm and cell type to cell type, suggesting a persistent infection. Single-cell RNA sequencing (scRNAseq) further supported that SmedTV expression was low in stem cells, but substantially higher in multiple, though not all, differentiated tissues, with notable neural enrichment.

Interestingly, knockdown of SmedTV by RNA-interference resulted in a “cure” of SmedTV after 10 RNAi doses, and expression remained undetectable by WISH even after 90 days. Due to being able to evade host defenses and the endogenous RNAi pathway, we believe SmedTV represents a novel animal model to study host-virus evolution.

Statement of significance

Planarians are freshwater flatworms and emerging models to study the molecular mechanisms of adult stem cell and regenerative biology. However, they also live in aquatic environments with high amounts of viruses, bacteria, fungi, and protist pathogens. How the planarian immune system copes with all of these is largely unknown and only 2 types of virus have been described. Here we find a novel dsRNA virus, endemic to multiple types of flatworms. We show that it is a persistent infection, and likely transmits from stem cell to differentiated cell in the planarian, while avoiding endogenous RNA-interference machinery and mechanisms used to suppress viruses. We present this as a new model to study host-virus defense and evolution.
Differences in word learning: bilingualism or linguistic experience?
Authors: Borragan Maria , de Bruin Angela , Havas Viktoria , de Diego-Balaguer Ruth , Vulchanova Mila Dimitrova , Vulchanov Valentin , Duñabeitia Jon Andoni
Published: February 2019

Bilinguals may be better than monolinguals at word learning due to their increased experience with language learning. In addition, bilinguals that have languages that are orthotactically different could be more used to dissimilar orthotactic patterns. The current study examines how bilinguals with languages that are orthotactically similar and dissimilar and monolinguals learn novel words that violate or respect the orthotactic legality of the languages they know and how this learning may be affected by the similarity between the bilinguals’ two languages. In Experiment 1, three groups of children were tested: monolinguals, Spanish-Basque bilinguals (dissimilar orthotactic languages), and Spanish-Catalan bilinguals (similar orthotactic languages). After an initial word learning phase, they were tested in a recall task and a recognition task. Results showed that Spanish-Basque bilingual children performed differently than the other two groups. While Spanish monolinguals and Spanish-Catalan bilinguals recognized illegal words worse than legal words, Spanish-Basque bilinguals showed equal performance in learning illegal and legal patterns. A replication study conducted with two new groups of Spanish-Basque children (one group with high Basque proficiency and one group with a lower proficiency) indicated that the effects were not driven by the proficiency in the second language since a similar performance on legal and illegal patterns was observed in both groups. In Experiment 2, two groups of adults, monolinguals and Spanish-Basque bilinguals, were tested with the same task used in Experiment 1. The effect seen in children seems to be absent in adults. Spanish-Basque bilingual adults showed better overall learning performance than monolinguals, irrespective of the illegality of the items. Differences between groups could be due to the effect of having acquired literacy and linguistic competence.
Graph Signal Processing of Low and High-Order Dynamic Functional Connectivity Networks Using EEG Resting-State for Schizophrenia: A Whole Brain Breakdown
Authors: Dimitriadis Stavros I.
Published: February 2019

Conventional static or dynamic functional connectivity graph (FCG/DFCG) referred to as low-order FCG focusing on temporal correlation estimates of the resting-state electroencephalography (rs-EEG) time series between any potential pair of brain areas. A DFCG is first constructed from multichannel recordings by adopting the methodology of sliding-window and a proper functional connectivity estimator. However, low-order FC ignores the high-level inter-relationship of brain areas. Recently, a high-order version of FCG has emerged by estimating the correlations of the time series that describe the fluctuations of the functional strength of every pair of ROIs across experimental time.

In the present study, a dynamic functional connectivity graph (DFCG) has been estimated using the imaginary part of phase lag value (iPLV). We analyzed DFCG profiles of electroencephalographic resting state (eyes-closed) recordings of healthy controls subjects (n=39) and subjects with symptoms of schizophrenia (n=45) in basic frequency bands {δ,θ,α1,α2,β1,β2,γ}. In our analysis, we incorporated both intra and cross-frequency coupling modes. Adopting our recent Dominant Intrinsic Coupling Mode (DICM) model leads to the construction of an integrated DFCG (iDFCG) that encapsulates both the functional strength but also the DICM of every pair of brain areas. Based on the LO - IDFCG, we constructed the HO- IDFCG by adopting the cosine similarity between the time-series derived from the LO-DIFCG. At a second level, we estimated the laplacian transformations of both LO and HO-IDFCG and by calculating the temporal evolution of Synchronizability (Syn), four network metric time series (NMTSSyn) were produced. Following, a machine learning approach based on multi-kernel SVM with the four NMTSSynused as potential features and appropriate kernels, we succeeded a superior classification accuracy (∼98%). DICM and flexibility index (FI) achieved a classification with absolute performance (100 %)

Schizophrenic subjects demonstrated a hypo-synchronization compared to healthy control group which can be interpreted as a low global synchronization of co-fluctuate functional patterns. Our analytic pathway could be helpful both for the design of reliable biomarkers and also for evaluating non-intervention treatments tailored to schizophrenia. EEG offers a low-cost environment for applied neuroscience and the transfer of research knowledge from neuroimaging labs to daily clinical practice.
Changes in Anterior and Posterior Hippocampus Differentially Predict Item-Space, Item-Time, and Item-Item Memory Improvement
Authors: Lee Joshua K. , Fandakova Yana , Johnson Elliott G. , Cohen Neal J. , Bunge Silvia A. , Ghetti Simona
Published: February 2019

Relational memory requires the hippocampus, but whether distinct hippocampal mechanisms along the anterior-posterior axis are required for different types of relations is debated. We investigated the contribution of structural changes in hippocampal head, body, and tail subregions to the capacity to remember item-space, item-time, and item-item relations. Memory for each relation and volumes of hippocampal subregions were assessed longitudinally in 171 participants across 3 time points (Mage at T1= 9.45 years; Mage at T2= 10.86 years, Mage at T3=12.12 years; comprising 393 behavioral assessments and 362 structural scans). Among older children, volumetric growth in: (a) head and body predicted improvements in item-time memory, (b) head predicted improvements in item-item memory; and (c) right tail predicted improvements in item-space memory. The present research establishes that volumetric changes in hippocampal subregions differentially predict changes in different aspects of relational memory, underscoring a division of labor along the hippocampal anterior-posterior axis.
Electrophysiology and transcriptomics reveal two photoreceptor classes and complex visual integration inHirudo verbana
Authors: Stowasser Annette , Stahl Aaron , Benoit Joshua B. , Wagenaar Daniel A.
Published: February 2019

Among animals with complex visual processing mechanisms, the leechHirudo verbanais a rare example in which all neurons can be identified. However, little is known about its visual system, which is composed of several pigmented head eyes and photosensitive non-pigmented sensilla that are distributed across its entire body. Although several interneurons are known to respond to visual stimuli, their response properties are poorly understood. Among these, the S cell system is especially intriguing: It is multimodal, spans the entire body of the leech, and is thought to be involved in complex sensory integration. To improve our understanding of the role of this system, we tested its spectral sensitivity, spatial integration, and adaptation properties. The response of the S cell system to visual stimuli was found to be strongly dependent on the size of the area stimulated, and adaptation was local. Furthermore, a “bleaching experiment” demonstrated that at least two color channels contributed to the response, and that their contribution was dependent on the adaptation to the background. The existence of at least two color channels was further supported by transcriptomic evidence, which indicated the existence of at least two distinct groups of putative opsins for leeches. Taken together, our results show that the S cell system has highly sophisticated response properties, and could be involved in the processing of complex visual stimuli. We propose the leech as a novel system to understand visual processing mechanisms with many practical advantages.

Summary statement

Detailed quantitative analysis of light responses in the medicinal leechHirudo verbanaunequivocally demonstrates the existence of parallel visual pathways processing visual and UV stimuli. Responses to spatially complex stimuli indicate relatively sophisticated information processing.
Retinoic acid promotes in vitro development of haploid germ cells from pre-pubertal porcine spermatogenic cells
Authors: Yu Kun , Zhang Yi , Zhang Bao-Lu , Wu Han-Yu , Wang Su-Tian , Han De-Ping , Lian Zheng-Xing , Liu Yi-Xun , Deng Shou-Long
Published: February 2019

Spermatogonial stem cells (SSCs) self-renew and contribute genetic information to the next generation. Inducing directional differentiation of porcine SSCs may be an important strategy in exploring the mechanisms of spermatogenesis and developing better treatment methods for male sterility. Here, we established an in vitro culture model for porcine small seminiferous tubule segments, to induce SSCs to differentiate into single-tail haploid spermatozoa. The culture model subsequently enabled spermatozoa to express the sperm-specific protein acrosin, and oocytes to develop to blastocyst stage after round spermatid injection. The addition of retinoic acid (RA) to the differentiation media promoted the efficiency of haploid differentiation. RT-PCR analysis indicated that RA stimulated the expression of Stra8 but reduced the expression of NANOS2 in spermatogonia. Genes involved in post-meiotic development, Prm1 and Tnp1, were up-regulated in the presence of RA. The addition of RAR inhibitor, BMS439, showed that RA enhanced the expression of cAMP responsive-element binding protein through RAR, and promoted the formation of round spermatids.
Modelling the Perception of Colour Patterns in Vertebrates with HMAX
Authors: Renoult Julien P. , Guyl Bastien , Mendelson Tamra C. , Percher Alice , Dorignac Jérôme , Geniet Fredéric , François Molino
Published: February 2019

In order to study colour signals as animals perceive them, visual ecologists usually rely on models of colour vision that do not consider patterns–the spatial arrangement of features within a signal.

HMAX describes a family of models that are used to study pattern perception in human vision research, and which have inspired many artificial intelligence algorithms. In this article, we highlight that the sensory and brain mechanisms modelled in HMAX are widespread, occurring in most if not all vertebrates, thus offering HMAX models a wide range of applications in visual ecology.

We begin with a short description of the neural mechanisms of pattern perception in vertebrates, emphasizing similarities in processes across species. Then, we provide a detailed description of HMAX, highlighting how the model is linked to biological vision. We further present sparse-HMAX, an extension of HMAX that includes a sparse coding scheme, in order to make the model even more biologically realistic and to provide a tool for estimating efficiency in information processing. In an illustrative analysis, we then show that HMAX performs better than two other reference methods (manually-positioned landmarks and the SURF algorithm) for estimating similarities between faces in a nonhuman primate species.

This manuscript is accompanied with MATLAB codes of an efficient implementation of HMAX and sparse-HMAX that can be further flexibly parameterized to model non-human colour vision, with the goal to encourage visual ecologists to adopt tools from computer vision and computational neuroscience.
Fastq-pair: efficient synchronization of paired-end fastq files
Authors: Edwards John A. , Edwards Robert A.
Published: February 2019

Paired end DNA sequencing provides additional information about the sequence data that is used in sequence assembly, mapping, and other downstream bioinformatics analysis. Paired end reads are usually provided as two fastq-format files, with each file representing one end of the read. Many commonly used downstream tools require that the sequence reads appear in each file in the same order, and reads that do not have a pair in the corresponding file are placed in a separate file of singletons. Although most sequencing instruments capable of generating paired end reads produce files where each read has a corresponding mate, many downstream bioinformatics manipulations break the one-to-one correspondence between reads, and paired-end sequence files loose synchronicity, and contain either unordered sequences or sequences in one or other file without a mate. Trivial solutions to this problem require reading one or both of the DNA sequence files into memory but quickly become limited by computational resources for moderate to large sized sequence files that are common nowadays. Here, we introduce a fast and memory efficient solution, written in C for portability, that synchronizes paired-end fastq files for subsequent analysis and places unmatched reads into singleton files.

Fastq-pair is freely available from https://github.com/linsalrob/fastq-pair and is released under the MIT license.
Robust archaeal and bacterial communities inhabit shallow subsurface sediments of the Bonneville Salt Flats
Authors: McGonigle Julia M. , Bernau Jeremiah A. , Bowen Brenda B. , Brazelton William J.
Published: February 2019

We report the first census of natural microbial communities of the Bonneville Salt Flats (BSF), a perennial salt pan at the Utah–Nevada border. Environmental DNA sequencing of archaeal and bacterial 16S rRNA genes was conducted on samples from multiple evaporite sediment layers of the surface salt crust. Our results show that at the time of sampling (September 2016), BSF hosted a robust microbial community dominated by diverse Halobacteriaceae andSalinibacterspecies. Desulfuromonadales from GR-WP33-58 are also abundant in all samples. We identified taxonomic groups enriched in each layer of the salt crust sediment and revealed that the upper gypsum sediment layer found immediately under the uppermost surface halite contains a robust microbial community. We found an increased presence of Thermoplasmatales, Nanohaloarchaeota, Woesearchaeota, Acetothermia, Halanaerobium, Parcubacteria, Planctomycetes, Clostridia, Gemmatimonadetes, Marinilabiaceae and other Bacteroidetes in this upper gypsum layer. This study provides insight into the diversity, spatial heterogeneity, and geologic context of a surprisingly complex microbial ecosystem within this macroscopically-sterile landscape.

IMPORTANCE

Over the last ∼13,000 years the Pleistocene Lake Bonneville, which covered a large portion of Utah, drained and desiccated leaving behind the Bonneville Salt Flats (BSF). Today BSF is famous for its use as a speedway, which has hosted many land-speed records and a community that greatly values this salty landscape. Additionally, the salts that saturate BSF basin are extracted and sold as an additive for agricultural fertilizers. The salt crust is a well-known recreational and economic commodity, but the roles of microbes in the formation and maintenance of the salt crust are generally unknown. This study is the first geospatial analysis of microbial diversity at this site using cultivation-independent environmental DNA sequencing methods. Identification of the microbes present within this unique, dynamic, and valued sedimentary evaporite environment is an important step toward understanding the potential consequences of perturbations to the microbial ecology on the surrounding landscape and ecosystem.
Cancer gene therapy by NF-κB-activated cancer cell-specific expression of CRISPR/Cas9 targeting to telomere
Authors: Dai Wei , Wu Jian , Wang Danyang , Wang Jinke
Published: February 2019

NF-κB has been a luring target for cancer therapy due to its over activation in all tumors. In this study, we showed that a gene therapy named as NF-κB-activated gene expression (Nage) could be used to induce cancer cell deathin vitroandin vivoby utilizing the NF-κB activity in cancer cells; however, it had no effect on normal cells. In this gene therapy, we constructed a NF-κB-specific promoter by fusing a NF-κB decoy sequence to a minimal promoter, which could be bound by the intracellular over activated NF-κB and thus activate the expression of downstream effector gene in a NF-κB-specific manner. In this study, we firstly demonstrated the cancer cell-specific activation of NF-κB. We then demonstrated the cancer cell specificity of Nage vector expression by introducing a Nage vector that could express a reporter gene ZsGreen in various cell lines. We next demonstrated that a Nage vector that could express CRISPR/Cas9 protein and a telomere-targeting sgRNA could be used to specifically induce death of cancer cells. We finally showed that the Cas9/sgRNA Nage vector packaged into the adeno-associated virus (AAV) could be used to inhibit the growth of xenografted tumors in mouse by intravenously injecting recombinant AAV.
Adaptive introgression during environmental change can weaken reproductive isolation
Authors: Owens Gregory L. , Samuk Kieran
Published: February 2019

Anthropogenic climate change is an urgent threat to species diversity. One aspect of this threat is the collapse of species reproductive barriers through increased hybridization. The primary mechanism for this collapse is thought to be the weakening of ecologically-mediated reproductive barriers, as demonstrated in many cases of “reverse speciation” . Here, we expand on this idea and show that adaptive introgression between species adapting to a shared, moving climatic optimum can readily weakenanyreproductive barrier, including those that are completely independent of the climatic variable. Using genetically explicit forward-time simulations, we show that genetic linkage between alleles conferring adaptation to a changing climate and alleles conferring reproductive isolation can lead to adaptive introgression facilitating the homogenization of reproductive isolation alleles. This effect causes the decay of species boundaries across a broad and biologically-realistic parameter space. We explore how the magnitude of this effect depends upon the rate of climate change, the genetic architecture of adaptation, the initial degree of reproductive isolation and the mutation rate. These results highlight a previously unexplored effect of rapid climate change on species diversity.
In situstructures of periplasmic flagella inBorreliareveals conformational changes essential for flagellar rotation
Authors: Chang Yunjie , Moon Kihwan , Zhao Xiaowei , Steven J. Norris , Motaleb Md A. , Liu Jun
Published: February 2019

The bacterial flagellar motor is a molecular machine that rotates the flagellar filament at high speed. Torque is generated by the stator-rotor interaction coupled to an ion flux through the torque-generating stator. Here, we employed cryo-electron tomography to visualize the intact flagellar motor in the Lyme disease spirocheteBorrelia burgdorferi. By analysis of the motor structures of wild-type and stator mutants, we localize the torque-generating units precisely and determine three-dimensional structure of the stator and its interactions with the rotor. Our study shows that the cytoplasmic domains of the stator are packed regularly around the circumference of the flagellar C-ring. The stator-rotor interaction induces a profound conformational change in the C-ring. Analysis of the motors of a less motilemotB-D24E mutant and a non-motilemotB-D24N mutant, in which the proton translocation is reduced and blocked, respectively, provides evidence that the conformational change of the C-ring is essential for flagellar rotation.
Auto-inhibition of myoblast fusion by cyclic receptor signalling
Authors: Sieiro Daniel , Melendez Julie , Morin Valérie , Salgado David , Marcelle Christophe
Published: February 2019

Fusion of nascent myoblasts to pre-existing myofibres is critical for skeletal muscle growth and repair. The vast majority of molecules known to regulate myoblast fusion are necessary in this process. Here we uncover, through high-throughputin vitroassays andin vivostudies in the chicken embryo, that TGFβ (SMAD2/3-dependent) signalling acts as a molecular brake on muscle fusion. While constitutive activation of the pathway arrests fusion, its inhibition leads to a striking over-fusion phenotype. This dynamic control of TGFβ signalling in the embryonic muscle relies on a unique receptor complementation mechanism, prompted by the merging of myoblasts with myofibres, each carrying one component of the heterodimer receptor complex. The competence of myofibres to fuse is restored through endocytic degradation of activated receptors. Altogether, this study shows that muscle fusion is a self-regulated process that relies on cyclic TGFβ signalling to regulate its pace.
Perturbation of the gut microbiota by antibiotics results in accelerated breast tumour growth and metabolic dysregulation
Authors: Kirkup Benjamin M , McKee Alastair , Makin Kate A , Paveley Jack , Caim Shabhonam , Alcon-Giner Cristina , Leclaire Charlotte , Dalby Matthew , Le Gall Gwenaelle , Andrusaite Anna , Kreuzaler Peter , Ghanate Avinash , Driscoll Paul , MacRae James , Calvani Enrica , Milling Simon WF , Yuneva Mariia , Weilbaecher Katherine N , Korcsmáros Tamas , Hall Lindsay J , Robinson Stephen D
Published: February 2019

Background

Breast cancer is the second most prevalent cancer worldwide with around 1.7 million new cases diagnosed every year. Whilst prognosis is generally favourable in early stages, this worsens significantly in advanced disease. Therefore, it is pertinent to focus on mitigating factors that may slow growth or progression. Recently, the gut microbiome has been implicated in a wide-range of roles in tumour biology. Through modulation of immunity, the gut microbiota can improve the efficacy of several immunotherapies. However, despite the prevalence of breast cancer, there is still a lack of microbiota studies in this field, including exploring the influence of external microbiome-modulating factors such as antibiotics. We describe herein how disruption of the gut microbiota via antibiotics may be detrimental to patient outcomes through acceleration of tumour growth.

Results

Supplementing animals with a cocktail of antibiotics leads to gut microbiota alterations and is accompanied by significant acceleration of tumour growth. Surprisingly, and distinct from previous microbiome-tumour studies, the mechanism driving these effects do not appear to be due to gross immunological changes. Analysis of intratumoural immune cell populations and cytokine production are not affected by antibiotic administration. Through global tumour transcriptomics, we have uncovered dysregulated gene expression networks relating to protein and lipid metabolism that are correlated with accelerated tumour growth. Fecal metabolomics revealed a reduction of the microbial-derived short-chain fatty acid butyrate that may contribute to accelerated tumour growth. Finally, through use of a routinely administered antibiotic in breast cancer patients, Cephalexin, we have shown that tumour growth is also significantly affected. Metataxanomic sequencing and analysis highlighted significant antibiotic-associated reductions in the butyrate producing generaOdoribacterandAnaeotruncus, and increased abundance ofBacteroides.

Conclusions

Our data indicate that perturbation of the microbiota by antibiotics may have negative impacts on breast cancer patient outcomes. This is of importance as antibiotics are regularly prescribed to breast cancer patients undergoing mastectomy or breast reconstruction. We have also shown that the metabolic impact of disruption to the microbiome should be considered alongside the potent immunological effects. We believe our work lays the foundation for improving the use of antibiotics in patients, and with further investigation could potentially inform clinical practice.
A quantitative tri-fluorescent yeast two-hybrid system: from flow cytometry to in-cellula affinities
Authors: Cluet David , Amri Ikram , Vergier Blandine , Léault Jérémie , Grosjean Clémence , Calabresi Dylan , Spichty Martin
Published: February 2019

We present a technological advancement for the estimation of the affinities of Protein-Protein Interactions (PPIs) in living cells. A novel set of vectors is introduced that enables a quantitative yeast two-hybrid system based on fluorescent fusion proteins. The vectors allow simultaneous quantification of the reaction partners (Bait and Prey) and the reporter at the single-cell level by flow cytometry. We validate the applicability of this system on PPIs with different affinities. After only two hours of reaction, expression of the reporter can easily be detected even for the weakest PPI. Through a simple gating analysis, it is possible to select only cells with identical expression levels of the reaction partners. As a result of this standardization of expression levels, the mean reporter levels directly reflects the affinities of the studied PPIs. With a set of PPIs with known affinities, it is straightforward to construct an affinity ladder that permits rapid classification of PPIs with thus far unknown affinities. Conventional software can be used for this analysis. To permit automated high-throughput analysis, we provide a graphical user interface for the Python-based FlowCytometryTools package.
Micro-indentation and optical coherence tomography for the mechanical characterization of embryos: Experimental setup and measurements on fixed chicken embryos
Authors: Marrese Marica , Antonovaité Nelda , Nelemans Ben K.A. , Smit Theodoor H. , Iannuzzi Davide
Published: February 2019

Summary statement

We introduce an experimental technique that combines micro-indentation and optical coherence tomography to map the viscoelastic properties of embryonic tissue and investigate correlations between local mechanical features and tissue morphology.

The investigation of the mechanical properties of embryos is expected to provide valuable information on the phenomenology of morphogenesis. It is thus believed that, by mapping the viscoelastic features of an embryo at different stages of growth, it may be possible to shed light on the role of mechanics in embryonic development. To contribute to this field, we present a new instrument that can determine spatiotemporal distributions of mechanical properties of embryos over a wide area and with unprecedented accuracy. The method relies on combining ferrule-top micro-indentation, which provides local measurements of viscoelasticity, with Optical Coherence Tomography, which can reveal changes in tissue morphology and help the user to localize the indentation locations. To prove the working principle, we have collected viscoelasticity maps of fixed HH11-HH12 chicken embryos. Our study highlights the nonlinear behavior of the tissue and qualitatively shows the correlation between local mechanical properties and tissue morphology for different regions of interest.
QTL and genetic analysis controlling fiber quality traits using paternal backcross population in Upland Cotton
Authors: Ma Lingling , Su Ying , Wang Yumei , Nie Hushai , Cui Yupeng , Cheng Cheng , Wang Meiyan , Hua Jinping
Published: February 2019

In present study, F14recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one Upland cotton hybrid. Three repetitive BC/P field trials and one BC/M field trial were performed including both two BC populations and the original RIL population. Totally, for fiber quality traits, 24 novel QTLs were detected and 13 QTLs validated previous results. And 19 quantitative trait loci (QTL) in BC/P populations explained 5.01% - 22.09% of phenotype variation (PV). Among the 19 QTLs, three QTLs were detected simultaneously in BC/M population. The present study provided novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly,qFS-Chr3-1controlling fiber strength explained 22.09% of PV in BC/P population, which increased 0.48 cN/tex for fiber strength. A total of seven, two, eight, two and six QTLs explained over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In the RIL population, six common QTLs detected in more than one environment such asqFL-Chr1-2,qFS-Chr5-1,qFS-Chr9-1,qFS-Chr21-1,qFM-Chr9-1andqFM-Chr9-2. Two common QTLs ofqFE-Chr2-2(TMB2386-SWU12343) andqFM-Chr9-1(NAU2873-CGR6771) explained 22.42% and 21.91% of PV. In addition, a total of 142 and 46 epistatic QTLs and QTL × environments (E-QTLs and QQEs) were identified in RIL-P and BC/P populations, respectively.