Biology subjects

Islam, T.

Publications and source records attributed to Islam, T..

45 records · Page 3Linked to original sources

bioRxiv2020

Diversity and genomic determinants of the microbiomes associated with COVID-19 and non-COVID respiratory diseases

The novel coronavirus disease 2019 (COVID-19) is a rapidly emerging and highly transmissible disease caused by the Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2). Understanding the microbiomes associated with the upper respiratory tract infection (URTI), chronic obstructive pulmonary disease (COPD) and COVID-19 diseases has clinical interest. We hypothesized that the diversity of microbiome compositions and their genomic features are associated with different pathological conditions of these human respiratory tract diseases (COVID-19 and non-COVID; URTI and COPD). To test this hypothesis, we analyzed 21 whole metagenome sequences (WMS) including eleven COVID-19 (BD = 6 and China = 5), six COPD (UK = 6) and four URTI (USA = 4) samples to unravel the diversity of microbiomes, their genomic features and relevant metabolic functions. The WMS data mapped to 534 bacterial, 60 archaeal and 61 viral genomes with distinct variation in the microbiome composition across the samples (COVID-19>COPD>URTI). Notably, 94.57%, 80.0% and 24.59% bacterial, archaeal and viral genera shared between the COVID-19 and non-COVID samples, respectively, however, the COVID-19 related samples had sole association with 16 viral genera other than SARS-CoV-2. Strain-level virome profiling revealed 660 and 729 strains in COVID-19 and non-COVID sequence data, respectively and of them 34.50% strains shared between the conditions. Functional annotation of metagenomics sequences of thevCOVID-19 and non-COVID groups identified the association of several biochemical pathways related to basic metabolism (amino acid and energy), ABC transporters, membrane transport, replication and repair, clustering-based subsystems, virulence, disease and defense, adhesion, regulation of virulence, programmed cell death, and primary immunodeficiency. We also detected 30 functional gene groups/classes associated with resistance to antibiotics and toxic compounds (RATC) in both COVID-19 and non-COVID microbiomes. Furthermore, a predominant higher abundance of cobalt-zinc-cadmium resistance (CZCR) and multidrug resistance to efflux pumps (MREP) genes were detected in COVID-19 metagenome. The profiles of microbiome diversity and associated microbial genomic features found in both COVID-19 and non-COVID (COPD and URTI) samples might be helpful for developing the microbiome-based diagnostics and therapeutics for COVID-19 and non-COVID respiratory diseases. However, future studies might be carried out to explore the microbiome dynamics and the cross-talk between host and microbiomes employing larger volume of samples from different ethnic groups and geoclimatic conditions.

genomics↗

bioRxiv2020

Oligomycins Inhibit Magnaporthe oryzae Triticum and suppress wheat blast disease

Oligomycins are macrolide antibiotics, produced by Streptomyces spp., show biological activities to several microorganisms like bacteria, fungi, nematodes and peronosporomycetes. Conidiogenesis, germination of conidia and formation of appressoria are crucial for a successful disease cycle and pathogenicity of the filamentous fungal phytopathogen. The goal of this research was to evaluate the effects of two oligomycins, oligomycin B and oligomycin F along with a commercial fungicide Nativo(R) 75WG on hyphal growth, conidiogenesis, conidia germination, appressoria formation, and disease development of a worrisome wheat blast fungus, Magnaporthe oryzae Triticum (MoT) pathotype. Both oligomycins suppressed the growth of MoT mycelia depending on the dose. Between the two natural products, oligomycin F displayed the maximum inhibition of MoT hyphal growth accompanied by oligomycin B with minimum inhibitory concentrations (MICs) of 0.005 and 0.05 g/disk, respectively. The application of the compounds also completely halted the conidia formation in the MoT mycelia in agar medium. A further bioassay showed that these compounds significantly inhibited MoT conidia germination and induced lysis; if germinated, induced abnormal germ tube and suppressed appressoria formation. Interestingly, the application of these macrolides significantly inhibited wheat blast disease on detached leaves of wheat. This is a first report on the inhibition of mycelial growth, process of conidia formation, germination of conidia, morphological changes in germinated conidia, and suppression of blast disease of wheat by oligomycins from Streptomyces spp. A further study is needed to evaluate the mode of action and field trials of these natural compounds to consider them as biopesticides for controlling this devastating wheat killer.

microbiology↗

bioRxiv2019

Future state prediction errors guide active avoidance behavior by adult zebrafish.

Human predicts future. To ask if fish also has this capacity, we established the virtual reality training system with live imaging of the telencephalic neurons of adult zebrafish in the active avoidance and found that, at the onset of the trial, learned fish conceives two future conditions as the favorable status on its way to the safe goal, i.e. one with the backwardly moving landscape and the other with the color of the safe goal. And the two different neural ensembles monitor the discrepancy between these predictions and the perceived real external status. Once fish reaches the goal, another ensemble is set to work to monitor whether fish keeps staying in the safe goal. The manipulation to artificially enhance these prediction errors elevated the activities of these ensembles and induced fish to behave to correct errors, revealing that fish sets behavioral strategy to actively realize these predictions.

neuroscience↗

bioRxiv2018

Blood-based molecular biomarker signatures in Alzheimer’s disease: Insights from systems biomedicine analyses

Background and objectivesAlzheimers disease (AD) is the progressive neurodegenerative disease characterized by dementia, but no peripheral biomarkers available yet that can detect the AD. This study aimed to identify systems biomarker signatures in the AD through integrative analyses.\n\nMaterials and MethodsWe used two microarray transcriptomics datasets of blood from AD patients to identify differentially expressed genes (DEGs). Geneset and protein overrepresentation analysis, protein-protein interaction (PPI), DEGs-Transcription Factor interactions, DEGs-MicroRNAs interactions, protein-drug interactions, and protein subcellular localizations analyses were done on common DEGs.\n\nResultsTotal 25 DEGs were detected between the two datasets. Integration of DEGs with biomolecular networks revealed hub proteins (TUBB, ATF3, NOL6, UQCRC1, SND1, CASP2, BTF3, INPP5K, VCAM1, and CSTF1), TFs (FOXC1, ZNF3, GEMIN7, and SMG9), miRNAs (mir-20a-5p, mir-93-5p, mir-16-5p, let-7b-5p, mir-708-5p, mir-24-3p, mir-26b-5p, mir-17-5p, mir-4270, and mir-4441). The analyses revealed candidate blood based biomarkers in the AD. We evaluated the histone modifications of the identified biomolecules. The hub genes and transcription factors (TFs) revealed that they possess several histone modification sites associated with Alzheimers disease. The protein-drug interactions revealed 10 candidate drugs consisting of antineoplastic (Vinorelbine, Vincristine, Vinblastine, Epothilone D, Epothilone B, CYT997, and ZEN-012), dermatologicals (Podofilox), and immunosuppressive agents (Colchicine) that may target the candidate systems biomarkers. The subcellular localization analysis revealed the interactions of the DEGs range from nucleus to plasma membrane through cytosol.\n\nConclusionsThis study presents blood based systems molecular biomarker signatures at RNA and protein levels which might be useful as peripheral biomarkers in the AD. The candidate drugs, histone modification sites, and subcellular localizations will be useful in future drug design in the AD.

systems biology↗

bioRxiv2018

Common molecular biomarker signatures in blood and brain of Alzheimers disease

BackgroundAlzheimers disease (AD) is a progressive neurodegenerative disease characterized by memory loss and confusion. Neuroimaging and cerebrospinal fluid-based early detection is limited in sensitivity and specificity as well as by cost. Therefore, detecting AD from blood cell analysis could improve early diagnosis and treatment of the disease. The present study aimed to identify blood cell transcripts that reflect brain expression levels of factors linked to AD progression.\n\nMethodsWe analyzed blood cell and brain microarray gene expression datasets from NCBI-GEO for AD association and expression in blood and brain. We also used eQTL and epigenetics data to identify AD-related genes that were regulated similarly in blood and brain.\n\nResultsWe identified 9 differentially expressed genes (DEG; AD versus controls) common to blood cells and brain (CNBD1, SUCLG2-AS1, CCDC65, PDE4D, MTMR1, C3, SLC6A15, LINC01806, and FRG1JP) and 18 genes (HSD17B1, GAS5, RPS5, VKORC1, GLE1, WDR1, RPL12, MORN1, RAD52, SDR39U1, NPHP4, MT1E, SORD, LINC00638, MCM3AP-AS1, GSDMD, RPS9, and GNL2) that were commonly dysregulated between AD blood and brain tissues using SNP and cis-eQTL data. This data revealed significant neurodegeneration-associated molecular pathways in the ribosomal and complement systems. Integration of these different analyses revealed dys-regulation of hub transcription factors (SREBF2, NR1H2, NR1H3, PRDM1, XBP1) and microRNAs (miR-518e, miR-518a-3p, miR-518b, miR-518c, miR-518d-3p and miR-518f) in AD. Several significant histone modification sites in DEGs were also identified.\n\nConclusionWe have identified new putative links between pathological processes in brain and transcripts in blood cells in AD subjects that may enable the use of blood to diagnose and monitor AD onset and progression.

neuroscience↗

bioRxiv2018

Wide and Deep Imaging of Neuronal Activities by a Wearable NeuroImager Reveals Premotor Activity in the Whole Motor Cortex

Wearable technologies for functional whole brain imaging in freely moving animals would advance our understanding of cognitive processing and adaptive behavior. Fluorescence imaging can visualize the activity of individual neurons in real time, but conventional microscopes have limited sample coverage in both the width and depth of view. Here we developed a novel head-mounted laser camera (HLC) with macro and deep-focus lenses that enable fluorescence imaging at cellular resolution for comprehensive imaging in mice expressing a layer- and cell type-specific calcium probe. We visualized orientation selectivity in individual excitatory neurons across the whole visual cortex of one hemisphere, and cell assembly expressing the premotor activity that precedes voluntary movement across the motor cortex of both hemispheres. Including options for multiplex and wireless interfaces, our wearable, wide- and deep-imaging HLC technology could enable simple and economical mapping of neuronal populations underlying cognition and behavior.

neuroscience↗

bioRxiv2018

The contribution of parent-to-offspring transmission of telomeres to the heritability of telomere length in humans

Leukocyte telomere length (LTL) is a heritable trait with two potential sources of heritability (h2): inherited variation in non-telomeric regions (e.g., SNPs that influence telomere maintenance) and variability in the lengths of telomeres in gametes that produce offspring zygotes (i.e., \"direct\" inheritance). Prior studies of LTL h2 have not attempted to disentangle these two sources. Here, we use a novel approach for detecting the direct inheritance of telomeres by studying the association between identity-by-descent (IBD) sharing at chromosome ends and phenotypic similarity in LTL. We measured genome-wide SNPs and LTL for a sample of 5,069 Bangladeshi adults with substantial relatedness. For each of the 7,254 relative pairs identified, we used SNPs near the telomeres to estimate the number of chromosome ends shared IBD, a proxy for the number of telomeres shared IBD (Tshared). We then estimated the association between Tshared and the squared pairwise difference in LTL (({Delta}LTL)2) within various classes of relatives (siblings, avuncular, cousins, and distant), adjusting for overall genetic relatedness ({phi}). The association between Tshared and ({Delta}LTL)2 was inverse among all relative pair types. In a meta-analysis including all relative pairs ({phi} >0.05), the association between Tshared and ({Delta}LTL)2 (P=0.002) was stronger than the association between {phi} and ({Delta}LTL)2 (P=0.45). Our results provide strong evidence that telomere length (TL) in parental germ cells impacts TL in offspring cells and contributes to LTL h2 despite telomere \"reprogramming\" during embryonic development. Applying our method to larger studies will enable robust estimation of LTL h2 attributable to direction transmission.

genetics↗

bioRxiv2018

Dynamic embedding of salience coding in hippocampal spatial maps

Hippocampal CA1 neurons participate in dynamic ensemble codes for space and memory. Prominent features of the environment are represented by an increased density of place cells, but cellular principles governing the formation and plasticity of such disproportionate maps are unknown. We thus imaged experience-dependent long-term changes in spatial representations at the cellular level in the CA1 deep sublayer in mice learning to navigate in a virtual-reality environment. The maps were highly dynamic but gradually stabilized as over-representations for motivational (reward) and environmental (landmark) salience emerged in different time courses by selective consolidation of relevant spatial representations. Relocation of the reward extensively reorganized pre-formed maps by a mechanism involving rapid recruitment of cells from the previous location followed by their re-stabilization, indicating that a subset of neurons encode reward-related information. The distinct properties of these CA1 cells may provide a substrate by which salient experience forms lasting and adaptable memory traces.

neuroscience↗

bioRxiv2016

Co-occurring eQTLs and mQTLs: detecting shared causal variants and shared biological mechanisms

Inherited genetic variation impacts local gene expression and DNA methylation in humans. Expression and methylation quantitative trait loci (cis-eQTLs and cis-mQTLs) often occur at the same genomic location, suggesting a common causal variant and shared mechanism. Using DNA and RNA from peripheral blood of Bangladeshi individuals, we use \"co-localization\" methods to identify 3,695 eQTL-mQTL pairs that are likely to share a causal variant. Using partial correlation analysis and mediation analysis, we identify >500 pairs with evidence of a causal relationships between expression and methylation (i.e., shared mechanism) with many additional pairs that we are underpowered to detect. These co-localized pairs are enriched for SNPs showing opposite effects on expression and methylation, although a many affect multiple CpGs in opposite directions. Evidence of shared SNP-age interaction also supports shared mechanisms for two eQTL-mQTL pairs. This work demonstrates the pervasiveness of co-regulated expression and methylation traits in the human genome. This approach can be applied to other types of molecular QTLs to enhance our understanding of regulatory mechanisms.

genomics↗