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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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bioRxiv2019

Phylogenetic inference of changes in amino acid propensities with single-position resolution

Fitness conferred by the same allele may differ between genotypes, and these differences shape variation and evolution. Changes in amino acid propensities at protein sites over the course of evolution have been inferred from sequence alignments statistically, but the existing methods are data-intensive and aggregate multiple sites. Here, we develop an approach to detect individual amino acids that confer different fitness in different groups of species from combined sequence and phylogenetic data. Using the fact that the probability of a substitution to an amino acid depends on its fitness, our method looks for amino acids such that substitutions to them occur more frequently in one group of lineages than in another. We validate our method using simulated evolution of a protein site under different scenarios and show that it has high specificity for a wide range of assumptions regarding the underlying changes in selection, while its sensitivity differs between scenarios. We apply our method to the env gene of two HIV-1 subtypes, A and B, and to the HA gene of two influenza A subtypes, H1 and H3, and show that the inferred fitness changes are consistent with the fitness differences observed in deep mutational scanning experiments. We find that changes in relative fitness of different amino acid variants within a site do not always trigger episodes of positive selection and therefore may not result in an overall increase in the frequency of substitutions, but can still be detected from changes in relative frequencies of different substitutions. Author summaryWhich amino acids are acceptable at a certain protein site can change with time. In viruses, for example, this can be due to changes in mechanisms of drug resistance and immune escape in the course of evolution. Here, we develop a method for detecting such changes from how evolutionary events are distributed over an evolutionary tree. Informally, we infer that a certain amino acid is favored in a certain group of lineages if substitutions giving rise to it repeatedly occur in the evolution of this group, and disfavored if such substitutions are rare. In surface proteins of HIV-1 and influenza A, we find that changes in preferences detected with d-test match those observed in deep mutational scanning experiments. Our purely bioinformatic approach allows inference of changes in selection between lineages from sequences alone, shedding light on the functional differences between strains or species even in the absence of any structural or functional data.

evolutionary biology↗

bioRxiv2019

Relative performance of Oxford Nanopore MinION vs. Pacific Biosciences Sequel third-generation sequencing platforms in identification of agricultural and forest pathogens

Culture-based molecular characterization methods have revolutionized detection of pathogens, yet these methods are either slow or imprecise. The second-generation sequencing tools have much improved precision and sensitivity of detection, but the analysis processes are costly and take several days. Of third-generation techniques, the portable Oxford Nanopore MinION device has received much attention because of its small size and possibility of rapid analysis at reasonable cost. Here, we compare the relative performance of two third-generation sequencing instruments, MinION and Pacific Biosciences Sequel in identification and diagnostics of pathogens from conifer needles and potato leaves and tubers. We demonstrate that Sequel is efficient in metabarcoding of complex samples, whereas MinION is not suited for this purpose due to the high error rate and multiple biases. However, we find that MinION can be utilized for rapid and accurate identification of dominant pathogenic organisms from plant tissues following both amplicon-based and metagenomics-based approaches. Using the PCR-free approach with shortened extraction and incubation times, we performed the entire MinION workflow from sample preparation through DNA extraction, sequencing, bioinformatics and interpretation in two and half hours. We advocate the use of MinION for rapid diagnostics of pathogens, but care needs to be taken to control or account for all potential technical biases.\n\nIMPORTANCEWe develop new and rapid protocols for MinION-based third-generation diagnostics of plant pathogens that greatly improves the speed and precision of diagnostics. Due to high error rate and technical biases in MinION, PacBio Sequel platform is more useful for amplicon-based metabarcoding from complex biological samples.

microbiology↗

bioRxiv2019

Gene Cascade Finder: A tool for identification of gene cascades and its application in Caenorhabditis elegans

Obtaining a comprehensive understanding of the gene regulatory networks, or gene cascades, involved in cell fate determination and cell lineage segregation in Caenorhabditis elegans is a long-standing challenge. Although RNA-sequencing (RNA-Seq) is a promising technique to resolve these questions, the bioinformatics tools to identify associated gene cascades from RNA-Seq data remain inadequate. To overcome these limitations, we developed Gene Cascade Finder (GCF) as a novel tool for building gene cascades by comparison of mutant and wild-type RNA-Seq data along with integrated information of protein-protein interactions, expression timing, and domains. Application of GCF to RNA-Seq data confirmed that SPN-4 and MEX-3 regulate the canonical Wnt pathway during embryonic development. Moreover, lin-35, hsp-3, and gpa-12 were found to be involved in MEX-1-dependent neurogenesis, and MEX-3 was found to control the gene cascade promoting neurogenesis through lin-35 and apl-1. Thus, GCF could be a useful tool for building gene cascades from RNA-Seq data.

genomics↗

bioRxiv2019

Genomic analysis reveals selection signatures of Yucatan miniature pig on its X chromosome during domestication

Yucatan miniature pig (YMP), a naturally small breed, has been domesticated in the hot and arid Yucatan Peninsula for a long time. However, its selection signatures on the X chromosome remain poorly understood. In this study, we focused on elucidating the selection signatures of YMP on the X chromosome during its domestication and breeding, using the whole-genome sequencing data. We performed population admixture analyses to determine its genetic relationships with other domesticated breeds and wild boars. Subsequently, we used two approaches, the fixation index (Fst) and {pi} ratios, to identify the selection signatures with 100 kb windows sliding in 10 kb steps. As a result, we found that the ectodysplasin A (EDA) gene was related with hypoplasia or absence of hair and sweat glands. This could uncover the relative lack of odor in YMP and the presence of hypoplasia or absence of hair in pigs. Furthermore, we found several genes under selection in other animals. A bioinformatics analysis of the genes in selection regions showed that they were associated with growth, lipid metabolism, reproduction, and immune system. Our findings will lead to a better understanding of the unique genetic and phenotypic characteristics of YMP and offer a plausible method for their utilization as an animal model for hair and odor disease research.

genomics↗

bioRxiv2019

A new massively-parallel transposon mutagenesis approach comparing multiple datasets identifies novel mechanisms of action and resistance to triclosan

The mechanisms by which antimicrobials exert inhibitory effects against bacterial cells and by which bacteria display resistance vary under different conditions. Our understanding of the full complement of genes which can influence sensitivity to many antimicrobials is limited and often informed by experiments completed in a small set of exposure conditions. Capturing a broader suite of genes which contribute to survival under antimicrobial stress will improve our understanding of how antimicrobials work and how resistance can evolve. Here, we apply a new version of TraDIS (Transposon Directed Insert Sequencing); a massively parallel transposon mutagenesis approach to identify different responses to the common biocide triclosan across a 125-fold range of concentrations. We have developed a new bioinformatic tool AlbaTraDIS allowing both predictions of the impacts of individual transposon inserts on gene function to be made and comparisons across multiple TraDIS data sets. This new TraDIS approach allows essential genes as well as non-essential genes to be assayed for their contribution to bacterial survival and growth by modulating their expression. Our results demonstrate that different sets of genes are involved in survival following exposure to triclosan under a wide range of concentrations spanning bacteriostatic to bactericidal. The identified genes include those previously reported to have a role in triclosan resistance as well as a new set of genes not previously implicated in triclosan sensitivity. Amongst these novel genes are those involved in barrier function, small molecule uptake and integrity of transcription and translation. These data provide new insights into potential routes of triclosan entry and bactericidal mechanisms of action. Our data also helps to put recent work which has demonstrated the ubiquitous nature of triclosan in people and the built environment into context in terms of how different triclosan exposures may influence evolution of bacteria. We anticipate the approach we show here that allows comparisons across multiple experimental conditions of TraDIS data will be a starting point for future work examining how different drug conditions impact bacterial survival mechanisms.

microbiology↗

bioRxiv2019

MicroRNAs expressed from FSHR and aromatase genes target important ovarian functions

MicroRNAs (miRNAs) have known roles in the post-transcriptional regulation of various biological processes including ovarian follicle development. We have previously identified miRNAs from human pre-ovulatory granulosa cells that are expressed from the intronic regions of two key genes in normal follicular development: FSH receptor (FSHR) and CYP19A1, the latter encoding the aromatase enzyme. In the present study, we aim to identify the targets regulated by those two miRNAs: hsa-miR-548ba and hsa-miR-7973, respectively. The miRNAs of interest were endogenously expressed in KGN cell-line, gene expression changes were analyzed by Affymetrix microarray and confirmed by RT-qPCR. Potential miRNA-regulated sequences were further filtered from the obtained results by bioinformatic target prediction algorithms and validated for direct miRNA:mRNA binding by luciferase reporter assay. Our results verified Leukemia inhibitory factor receptor (LIFR), Phosphatase and tensin homolog (PTEN), Neogenin 1 (NEO1) and SP110 nuclear body protein (SP110) as target genes for hsa-miR-548ba. Hsa-miR-7973 target genes ADAM metallopeptidase domain 19 (ADAM19), Peroxidasin (PXDN) and Formin like 3 (FMNL3) also passed all verification steps. In conclusion we propose that hsa-miR-548ba may be involved in the regulation of follicle growth and activation via LIFR and PTEN. Hsa-miR-7973 may be implicated in the modulation of extracellular matrix and cell-cell interactions. Taken together, our results suggest that those two miRNAs of interest have important regulatory roles in granulosa cells and in follicle development in general.\n\nSummary sentenceConfirmed targets of miRNAs hsa-miR-548ba and hsa-miR-7973 are involved in follicle recruitment, apoptosis, intercellular interactions and extracellular matrix remodeling pathways in KGN cells.

molecular biology↗

bioRxiv2019

Regulation of adenylyl cyclase 5 in striatal neurons confers the ability to detect coincident neuromodulatory signals

Long-term potentiation and depression of synaptic activity in response to stimuli is a key factor in reinforcement learning. Strengthening of the corticostriatal synapses depends on the second messenger cAMP, whose synthesis is catalysed by the enzyme adenylyl cyclase 5 (AC5), which is itself regulated by the stimulatory Golf and inhibitory Gi proteins. AC isoforms have been suggested to act as coincidence detectors, promoting cellular responses only when convergent regulatory signals occur close in time. However, the mechanism for this is currently unclear, and seems to lie in their diverse regulation patterns. Despite attempts to isolate the ternary complex, it is not known if Golf and Gi can bind to AC5 simultaneously, nor what activity the complex would have. Using protein structure-based molecular dynamics simulations, we show that this complex is stable and inactive. These simulations, along with Brownian dynamics simulations to estimate protein association rates constants, constrain a kinetic model that shows that the presence of this ternary inactive complex is crucial for AC5s ability to detect coincident signals, producing a synergistic increase in cAMP. These results reveal some of the prerequisites for corticostriatal synaptic plasticity, and explain recent experimental data on cAMP concentrations following receptor activation. Moreover, they provide insights into the regulatory mechanisms that control signal processing by different AC isoforms.\n\nAuthor summaryAdenylyl cyclases (ACs) are enzymes that can translate extracellular signals into the intracellular molecule cAMP, which is thus a 2nd messenger of extracellular events. The brain expresses nine membrane-bound AC variants, and AC5 is the dominant form in the striatum. The striatum is the input stage of the basal ganglia, a brain structure involved in reward learning, i.e. the learning of behaviors that lead to rewarding stimuli (such as food, water, sugar, etc). During reward learning, cAMP production is crucial for strengthening the synapses from cortical neurons onto the striatal principal neurons, and its formation is dependent on several neuromodulatory systems such as dopamine and acetylcholine. It is, however, not understood how AC5 is activated by transient (subsecond) changes in the neuromodulatory signals. Here we combine several computational tools, from molecular dynamics and Brownian dynamics simulations to bioinformatics approaches, to inform and constrain a kinetic model of the AC5-dependent signaling system. We use this model to show how the specific molecular properties of AC5 can detect particular combinations of co-occuring transient changes in the neuromodulatory signals which thus result in a supralinear/synergistic cAMP production. Our results also provide insights into the computational capabilities of the different AC isoforms.

neuroscience↗

bioRxiv2019

Translation and Transforming Activity of a Circular RNA from Human Papillomavirus

Bioinformatics and in vitro studies have revealed that single-stranded circular RNAs (circRNAs), generated through backsplicing, occur more extensively than initially appreciated. While the functions of most circRNAs are unknown, binding of microRNAs (miRNA), regulation of splicing and transcription, and translation into proteins have all been demonstrated for specific circRNAs. Virally-derived circRNAs have recently been described in gamma-herpesviruses. Here, we report that oncogenic human papillomaviruses (HPV) generate circRNAs, including ones which encompass the entire coding region of the E7 oncogene (circE7). HPV16 circE7 can be detected by both inverse RT-PCR and Northern blots of HPV16-transformed cell lines. CircE7 is N6-methyladenosine (m6A) modified, preferentially localized to the cytoplasm, and can be translated to produce E7 oncoprotein. Specific disruption of circE7 in CaSki cervical carcinoma cells decreased E7 protein levels, inhibited cell proliferation, and inhibited the ability of the cells to form colonies in soft agar. Analysis of TCGA RNA-seq data demonstrates that HPV-positive cancers have abundant circE7 RNAs. These results provide evidence that virally-derived, protein-encoding circular RNAs have biologically important functions with relevance to the transforming properties of HPV.

molecular biology↗

bioRxiv2019

Multi-disease associated risk locus in IL6 represses the anti-inflammatory gene GPNMB through chromatin looping and recruiting MEF2-HDAC complex

We have previously revealed a genetic association between Takayasu arteritis and a non-coding genetic variant in an enhancer region within IL6 (rs2069837 A/G). The risk allele in this variant (allele A) has a protective effect against chronic viral infection and cancer. Using a combination of experimental and bioinformatics tools, we identified the monocyte/macrophage anti-inflammatory gene GPNMB, [~]520kb away, as a target gene regulated by rs2069837. We revealed preferential recruitment of myocyte enhancer factor 2-histone deacetylase (MEF2-HDAC) repressive complex to the Takayasu arteritis risk allele. Further, we demonstrated suppression of GPNMB expression in monocyte-derived macrophages from healthy individuals with the AA compared to AG genotype, which was reversed by histone deacetylase inhibition. Our data suggest that the A allele in rs2069837 represses the expression of GPNMB by recruiting MEF2-HDAC complex, enabled through a long-range intra-chromatin looping mediated by CTCF. Suppression of this anti-inflammatory gene might mediate increased susceptibility in Takayasu arteritis and enhance protective immune responses in chronic infection and cancer. Our data highlight long-range chromatin interactions in functional genomic studies.

genetics↗

bioRxiv2019

Exploring the link between adenine DNA methylation and 3D genome organization in the parasite Trichomonas vaginalis

Trichomonas vaginalis is a common sexually transmitted parasite that colonizes the human urogenital tract causing infections that range from asymptomatic to highly inflammatory. Recent works have highlighted the importance of histone modifications in the regulation of transcription and parasite pathogenesis. However, the nature of DNA methylation in the parasite remains unexplored. Using a combination of immunological techniques and UHPLC, we analyzed the abundance of DNA methylation in strains with differential pathogenicity demonstrating that N6-methyladenine (6mA), and not 5-methylcytosine (5mC), is the main DNA methylation mark in T. vaginalis. Genome-wide distribution of 6mA reveals that this mark is enriched at intergenic regions, with a preference for certain super-families of DNA transposable elements. We show that 6mA in T. vaginalis is associated with silencing when present on genes. Interestingly, bioinformatics analysis revealed the presence of transcriptionally active or repressive intervals flanked by 6mA-enriched regions and results from chromatin conformation capture (3C) experiments suggest these 6mA flanked regions are in close spatial proximity. These associations were disrupted when parasites were treated with the demethylation activator ascorbic acid. This finding revealed a new role for 6mA in modulating 3D chromatin structure and gene expression in this divergent member of the Excavata.\n\nSIGNIFICANCE STATEMENTTrichomonas vaginalis causes the most common non-viral sexually transmitted infection yet little is known about the regulation of gene expression in this eukaryotic parasite. We demonstrate that N6-methyladenine (6mA) is the main methylation mark in the T. vaginalis genome. 6mA is widespread in DNA of eubacterial genera, but uncommon in genomes of most eukaryotes. Examination of the genome-wide distribution of 6mA reveals a preference for intergenic regions. Transcriptionally active or repressive intervals are found to be flanked by 6mA-enriched regions and data suggest 6mA flanked regions are in close 3D spatial proximity. Our findings describe for the first time the presence of DNA methylation in T. vaginalis and reveal a new role for 6mA in modulating 3D chromatin architecture.

microbiology↗

bioRxiv2019

Start from Scratch: Precisely Identify Massive Active Enhancers by Sequencing

Enhancer loci identified by ChIP-Seq or other experimental methods occupy hundreds of base pairs on the genome. It is the paradox comparing with the motif analysis, which usually contains only a few or tens nucleotides, achieved by bioinformatics analysis. To address this issue, we develop an experimental method, termed as massive active enhancer sequencing (MAE-Seq), to designate active enhancer sequences from arbitrary sources of 25bp random DNA libraries. These sequences are constructed in a mini-promoter vector with fluorescent reporter. After transfection, positive cells are sorted out and for sequencing. With the results, we successfully identify hundreds known accurate active enhancer sequences as expected. Besides that, large amounts of unmarked regulatory elements (UREs) without epigenetic features are also been spotted. In conclusion, MAE-Seq would be useful to refine enhancer sequences and precisely annotate the genome in eukaryotes.

genomics↗

bioRxiv2019

MiR-219 deficiency in Alzheimer’s disease contributes to neurodegeneration and memory dysfunction through post-transcriptional regulation of tau-kinase network

Intracellular accumulation of hyperphosphorylated misfolded tau proteins is one of the main neuropathological hallmarks in Alzheimers disease (AD) and related tauopathies. Hence, knowledge and understanding of disease mechanisms altering tau proteostasis and inducing cytotoxicity is critical. MicroRNAs (miRNAs) are capable of binding to and silencing many target transcripts, providing an additional level of regulation that complements canonical transcriptional pathways. Therefore, observed abnormalities in their expression patterns in neurodegeneration suggest alterations of microRNA-target networks as drivers of cellular dysfunction in the disease. Strikingly, here we have found in autopsy brain tissue that miRNA miR-219 expression levels are decreased in a brain region early affected in AD patients, the entorhinal cortex. Our bioinformatics analysis indicates miR-219 is predicted to target Calcium/calmodulin-dependent protein kinase 2 gamma subunit (CAMK2{gamma}), Tau tubulin kinase 1 (TTBK1) and Glycogen synthase kinase 3 beta (GSK3{beta}), which are all implicated in the generation of abnormal hyperphosphorylated tau. We reveal human proteomic data supporting dysregulation in the levels of predicted miR-219 targets in the entorhinal cortex. In mammalian cellular models, we found that downregulation of miR-219 de-repress synthesis of three tau kinases, CAMK2{gamma}, TTBK1 and GSK3{beta} on the post-transcriptional level resulting in tau phosphorylation and cell toxicity. Finally, we show that deficiency of miR-219 in vivo promotes age dependent neurodegeneration in the adult brain, with enhanced alterations in tau proteostasis, presynaptic terminals and memory impairment. Taken together, our data implicate miRNA dysregulation central to AD etiopathogenesis and suggest potential targets for the treatment of AD and related tauopathies.

neuroscience↗

bioRxiv2019

THE PROTO-ONCOGENE FYN INHIBITS THE ANTI-GLIOBLASTOMA IMMUNE RESPONSE

BackgroundHigh grade gliomas are aggressive and immunosuppressive brain tumors. Molecular mechanisms that regulate the inhibitory immune tumor microenvironment (TME) and glioma progression remain poorly understood. FYN tyrosine kinase is a downstream target of the oncogenic receptor tyrosine kinases pathway and is overexpressed in human gliomas. FYNs role in vivo in glioma growth remains unknown. We investigated whether FYN regulates glioma initiation, growth and invasion. MethodsWe evaluated the role of FYN using genetically engineered mouse glioma models (GEMM). We also generated FYN knockdown stem cells to induce gliomas in immune-competent and immune-deficient mice (NSG, CD8-/-, CD4-/-). We analyzed molecular mechanism by RNA-Seq and bioinformatics analysis. Flow cytometry was used to characterize immune cellular infiltrates in the FYN knockdown glioma TME. ResultsWe demonstrate that FYN knockdown in diverse immune-competent GEMMs of glioma reduced tumor progression and significantly increased survival. Gene ontologies (GOs) analysis of differentially expressed genes in wild type vs. FYN knockdown gliomas showed enrichment of GOs related to immune reactivity. However, in NSG, CD8-/- and CD4-/- immune-deficient mice, FYN knockdown gliomas failed to show differences in survival. These data suggest that the expression of FYN in glioma cells reduces anti-glioma immune activation. Examination of glioma immune infiltrates by flow-cytometry displayed reduction in the amount and activity of immune suppressive myeloid derived cells (MDSCs) in the FYN glioma TME. ConclusionsGliomas employ FYN mediated mechanisms to enhance immune-suppression and promote tumor progression. We propose that FYN inhibition within glioma cells could improve the efficacy of anti-glioma immunotherapies. Key pointsInhibition of FYN tyrosine kinase in genetically engineered mouse glioma models delays tumor initiation and progression. The oncogenic effects of FYN in vivo are mediated by downregulation of anti-glioma immunity. Importance of the StudyFYN is an effector of receptor tyrosine kinases (RTK) signaling in glioma. However, its role in vivo remains unknown. Our study demonstrates that FYN tyrosine kinase is a novel regulator of the anti-glioma immune response. We show that FYN inactivation suppresses glioma growth, increases survival, and enhances anti-tumor immune reactivity. Our findings suggest that suppressing the expression of FYN in glioma cells could provide a novel therapeutic target.

cancer biology↗

bioRxiv2019

PSX: Protein-Solvent Exchange - Software for calculation of deuterium-exchange effects in SANS measurements from protein coordinates

Recent developments in neutron scattering instrumentation and sample handling have enabled studies of more complex biological samples and measurements at shorter exposure times. The experiments are typically conducted in D2O-based buffers to emphasize or diminish scattering from a particular components or to minimize background noise in the experiment. To extract most information from such experiments it is thus desirable to determine accurate estimates of how and when closely bound hydrogen atoms from the biomolecule exchange with the deuterium in the solvent. We introduce and document software, PSX, for exploring the effect of hydrogen-deuterium exchange for proteins solubilized in D2O as well as the underlying bioinformatical models. The software aims to be generally applicable for any atomistic structure of a protein and its surrounding environment, and thus captures effects of both heterogenous exchange rates throughout the protein structure and by varying the experimental conditions such as pH and temperature. The paper concludes with examples of applications and estimates of the effect in typical scenarios emerging in small-angle neutron scattering on biological macromolecules in solution. Our analysis suggests that the common assumption of 90% exchange is in many cases an overestimate with the rapid sample handling systems currently available, which leads to fitting and calibration issues when analysing the data. Source code for the presented software is available from an online repository in which it is published under version 3 of the GNU publishing license.

biophysics↗

bioRxiv2019

Metrics for Graph Comparison: A Practitioner’s Guide

Comparison of graph structure is a ubiquitous task in data analysis and machine learning, with diverse applications in fields such as neuroscience [1], cyber security [2], social network analysis [3], and bioinformatics [4], among others. Discovery and comparison of structures such as modular communities, rich clubs, hubs, and trees in data in these fields yields insight into the generative mechanisms and functional properties of the graph.\n\nOften, two graphs are compared via a pairwise distance measure, with a small distance indicating structural similarity and vice versa. Common choices include spectral distances (also known as{lambda} distances) and distances based on node affinities (such as DeltaCon [5]). However, there has of yet been no comparative study of the efficacy of these distance measures in discerning between common graph topologies and different structural scales.\n\nIn this work, we compare commonly used graph metrics and distance measures, and demonstrate their ability to discern between common topological features found in both random graph models and empirical datasets. We put forward a multi-scale picture of graph structure, in which the effect of global and local structure upon the distance measures is considered. We make recommendations on the applicability of different distance measures to empirical graph data problem based on this multi-scale view. Finally, we introduce the Python library NetComp which implements the graph distances used in this work.

neuroscience↗

bioRxiv2019

Single cell RNA sequencing reveals cellular diversity of trisomy 21 retina

Retina is a crucial tissue for the capturing and processing of light stimulus. Characterization of the retina at single cell level is essential for the understanding of its biological functions. A variety of abnormalities in terms of morphology and function were reported in T21 retina. To evaluate the effects of chromosome aneuploidy on retina development, we characterized single cell transcriptional profiles of a T21 fetus and performed comprehensive bioinformatic analyses. Our data revealed the diversity and heterogeneity of cellular compositions in T21 retina. In total, we identified seven major cell types, and detected several subtypes within each cell type, followed by the detection of corresponding molecular markers including previously reported ones and a series of novel markers. Our analyses identified extensive communication networks between distinct cellular types, among which a few ligand-receptor interactions were associated with the development of retina and immunoregulatory interactions. Taken together, our data provided the first single cell transcriptome profile for human T21 retina which facilitates our understanding on the dosage effects of chromosome 21 on the development of retina.

cell biology↗

bioRxiv2019

Integrated analysis of the miRNA-mRNA network associated with LMP1 gene in nasopharyngeal carcinoma

Epstein-Barr virus oncogenic latent membrane protein 1 (LMP1) has been known to play important roles in nasopharyngeal carcinoma (NPC). LMP1 gene also induced a variety of microRNAs (miRNAs) which bear pivotal roles in regulation of mRNAs expression. However, little was known about the global change of mRNAs and miRNAs induced by LMP1 gene in NPC. In our study, one NPC tissue microarray profile and two LMP1-associated microarray expression profiles data were downloaded from the Gene Expression Omnibus database. A protein-protein interaction network was constructed by using bioinformatics platform Gene-Cloud of Biotechnology Information (GCBI). 78 differentially expressed miRNAs and 3322 differentially expressed genes were identified in order to generate a macroscopic network between miRNAs and mRNAs associated with LMP1 gene. In addition, two significant models were generated to illustrate the expression tendency. Our study provided a way to reveal the interaction between miRNAs and mRNAs in LMP1 axis, bringing insights into the pathogenesis of NPC.

microbiology↗

bioRxiv2019

Raw wastewater irrigation for urban agriculture in Africa increases the diversity of transferable antibiotic resistances genes in soil, including those encoding ESBLs

A metagenomic study was conducted to investigate the impact of raw wastewater use for irrigation in urban agriculture on the development of bacterial resistance in soil. Soil samples were collected in two African countries, from three different cities (each with irrigated and non-irrigated plots). Basic physical and chemical analysis were conducted, and the presence of selected antibiotic residues was assessed. Microbial DNA was extracted, quantified and sequenced. Microbial population structure and function, presence of horizontally transferable antibiotic resistance genes and Enterobacteriaceae plasmids replicons were analysed using bioinformatics. The relative prevalence of Proteobacteria and Bacteroidetes and sequence reads coding for microbial adaptation and growth were higher in irrigated fields; 33 and 26 transferable ARGs were found in irrigated and non-irrigated fields sequence reads, respectively. Extended spectrum {beta}-lactam genes identified in irrigated fields included blaCARB-3, blaOXA-347, blaOXA-5 and blaRm3. Concentration of sulfamethoxazole, ciprofloxacin and enrofloxacin in soils influenced the selection of antibiotic resistance genes encoding resistance against amphenicol, {beta}-lactams, and tetracyclines. Ten Enterobacteriaceae plasmid amplicon groups were identified in the fields, five were common to both, two (IncW and IncP1) and three (IncY, IncFIB and IncFIA) were found in irrigated and non-irrigated fields, respectively.\n\nIn conclusion, wastewater irrigation affected both soil microbial diversity and functions. Irrigated fields have more diverse transferable antibiotic resistance genes, including ESBL genes that encode resistance to {beta}-lactams antibiotics, except cephamycins and carbapenems. Even more, critical concentrations of antibiotic residues select for multiple and cross resistance. The findings from African cities show that wastewater irrigation in urban agriculture presents a serious public health risk for farmworkers and consumers by spread of bacterial resistance.

microbiology↗