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bioRxiv2026

Integrated 16S rRNA Bioinformatics Analysis of Gut Microbiota, Predicted Pathways, and Candidate Biomarkers in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is associated with changes in gut microbiota composition and predicted microbial functions that may relate to intestinal immune processes. This study compared gut microbiota profiles between individuals with IBD and healthy controls and examined predicted microbial pathways and their associations with bacterial genera. Publicly available 16S rRNA amplicon sequencing data from 22 stool samples (11 IBD and 11 healthy controls) were analysed. Taxonomic profiling, diversity analysis, differential abundance testing, and PICRUSt2-based functional prediction were performed. Microbe-pathway associations were examined using Spearman correlation and Cytoscape. Extended analyses integrated differential abundance with machine-learning feature importance to prioritize candidate genera, evaluated a three-genus signature, assessed selected findings in an independent dataset, and compared predicted fermentation- and acetate-related pathways. Alpha diversity was significantly lower in the IBD group (Shannon index, p = 0.003), and Bray-Curtis PCoA showed separation of the two groups mainly along PC1 (PERMANOVA pseudo-F = 6.125, p < 0.001), although this separation may partly reflect differences between the source cohorts. DESeq2 identified 44 significantly differentially abundant genera among 186 tested (FDR-adjusted p < 0.05), of which 32 were lower and 12 were higher in the IBD group relative to healthy controls; 27 of these genera were detected in only one of the two groups. PICRUSt2 predicted lipopolysaccharide and peptidoglycan biosynthesis pathways; after normalising pathway abundances for sequencing depth, Spearman analysis identified 84 significant microbe-pathway associations, 47 with lipopolysaccharide biosynthesis (44 positive; rho up to 0.90) and 37 with peptidoglycan biosynthesis (33 negative; rho down to -0.82). Five genera were prioritized by integrated biomarker analysis. The combined three-genus signature achieved an ROC-AUC of 0.959. External validation was limited to Bifidobacterium, whose abundance direction was concordant with the discovery analysis. Of the two SCFA-related pathways examined, the predicted acetate-related pathway (methanogenesis from acetate) was lower in the IBD group (FDR = 0.002), whereas the predicted fermentation pathway did not differ significantly between groups (FDR = 0.076). These findings provide an integrated view of microbial composition and predicted functional potential in IBD. The small sample size, differences in cohort and sequencing characteristics between the IBD and control samples, limited external validation, and reliance on predicted rather than directly measured functions mean that the results are exploratory and require confirmation in larger independent cohorts and through direct functional or metabolomic analyses.

bioinformatics↗

bioRxiv2026

FastaGuard: FASTA preflight QC for modern bioinformatics pipelines

Summary: FastaGuard is a streaming, explainable FASTA preflight QC tool that validates assembly FASTA files, detects structural and composition red flags, and emits a versioned multi-format report with an explicit pipeline gate before expensive downstream analysis. We evaluated v1.1.0 in four analyses whose design was fixed before data collection. On 700 public NCBI assemblies the pipeline gate stopped 19.7% (1.9% weighted to the population), always on its high-N rule and mostly in scaffold-level genomes; the NCBI submission gate stopped 2.0%, and an independent recount confirmed every stop. Among 1,040 faults injected into real assemblies, the NCBI gate flagged 520 of 520 in 13 error classes (table2asn: 280 at error level) and blocked none of 120 benign changes. Across seven downstream tools, 46 of 182 defect cells failed and 12 altered the records without a warning, all in classes the pipeline gate blocks. Stopping a mismatched reference at the gate avoided about 54-62 s of mapping and sorting at a cost of 0.05-0.06 s. Availability and Implementation: Source code and documentation are freely available under the MIT license at https://github.com/ehsanestaji/FastaGuard (release tag v1.1.0: https://github.com/ehsanestaji/FastaGuard/releases/tag/v1.1.0; archived at doi:10.5281/zenodo.23728753). Install via Bioconda (mamba install -c conda-forge -c bioconda fastaguard=1.1.0), BioContainers, or GitHub release binaries. Implemented in Rust; supported on Linux and macOS, including Bioconda builds for linux-64, linux-aarch64, osx-64, and osx-arm64. Contact: ehsan.estaji@umu.se; jianfeng.mao@umu.se Supplementary information: Supplementary Note (designs, all results, deviations from the pre-registered protocol); scripts, manifests and result tables at Zenodo, doi:10.5281/zenodo.23729530.

bioinformatics↗

bioRxiv2015

Novel bioinformatics approach to investigate quantitative phenotype-genotype associations in neuroimaging studies

Imaging genetics is an emerging field in which the association between genes and neuroimaging-based quantitative phenotypes are used to explore the functional role of genes in neuroanatomy and neurophysiology in the context of healthy function and neuropsychiatric disorders. The main obstacle for researchers in the field is the high dimensionality of the data in both the imaging phenotypes and the genetic variants commonly typed. In this article, we develop a novel method that utilizes Gene Ontology, an online database, to select and prioritize certain genes, employing a stratified false discovery rate (sFDR) approach to investigate their associations with imaging phenotypes. sFDR has the potential to increase power in genome wide association studies (GWAS), and is quickly gaining traction as a method for multiple testing correction. Our novel approach addresses both the pressing need in genetic research to move beyond candidate gene studies, while not being overburdened with a loss of power due to multiple testing. As an example of our methodology, we perform a GWAS of hippocampal volume using the Alzheimers Disease Neuroimaging Initiative sample.

Genetics↗

bioRxiv2017

Laboratory cultivation of acidophilic nanoorganisms. Physiological and bioinformatic dissection of a stable laboratory co-culture.

This study describes the laboratory cultivation of ARMAN (Archaeal Richmond Mine Acidophilic Nanoorganisms). After 2.5 years of successive transfers in an anoxic medium containing ferric sulfate as an electron acceptor, a consortium was attained that is comprised of two members of the order Thermoplasmatales, a member of a proposed ARMAN group, as well as a fungus. The 16S rRNA of one archaeon is only 91.6% identical to Thermogymnomonas acidicola as most closely related isolate. Hence, this organism is the first member of a new genus. The enrichment culture is dominated by this microorganism and the ARMAN. The third archaeon in the community seems to be present in minor quantities and has a 100% 16S rRNA identity to the recently isolated Cuniculiplasma divulgatum. The enriched ARMAN species is most probably incapable of sugar metabolism because the key genes for sugar catabolism and anabolism could not be identified in the metagenome. Metatranscriptomic analysis suggests that the TCA cycle funneled with amino acids is the main metabolic pathway used by the archaea of the community. Microscopic analysis revealed that growth of the ARMAN is supported by the formation of cell aggregates. These might enable cross feeding by other community members to the ARMAN.

microbiology↗

bioRxiv2020

Candidate targets for immune responses to 2019-Novel Coronavirus (nCoV): sequence homology- and bioinformatic-based predictions

Effective countermeasures against the recent emergence and rapid expansion of the 2019-Novel Coronavirus (2019-nCoV) require the development of data and tools to understand and monitor viral spread and immune responses. However, little information about the targets of immune responses to 2019-nCoV is available. We used the Immune Epitope Database and Analysis Resource (IEDB) resource to catalog available data related to other coronaviruses, including SARS-CoV, which has high sequence similarity to 2019-nCoV, and is the best-characterized coronavirus in terms of epitope responses. We identified multiple specific regions in 2019-nCoV that have high homology to SARS virus. Parallel bionformatic predictions identified a priori potential B and T cell epitopes for 2019-nCoV. The independent identification of the same regions using two approaches reflects the high probability that these regions are targets for immune recognition of 2019-nCoV. ONE SENTENCE SUMMARYWe identified potential targets for immune responses to 2019-nCoV and provide essential information for understanding human immune responses to this virus and evaluation of diagnostic and vaccine candidates.

immunology↗

bioRxiv2020

Evaluation of whole genome amplification and bioinformatic methods for the characterization of Leishmania genomes at a single cell level

Here, we report a pilot study paving the way for further single cell genomics studies in Leishmania. First, the performances of two commercially available kits for Whole Genome Amplification (WGA), PicoPlex and RepliG was compared on small amounts of Leishmania donovani DNA, testing their ability to preserve specific genetic variations, including aneuploidy levels and SNPs. We show here that the choice of WGA method should be determined by the planned downstream genetic analysis, Picoplex and RepliG performing better for aneuploidy and SNP calling, respectively. This comparison allowed us to evaluate and optimize corresponding bio-informatic methods. As PicoPlex was shown to be the preferred method for studying single cell aneuploidy, this method was applied in a second step, on single cells of L. braziliensis, which were sorted by fluorescence activated cell sorting (FACS). Even sequencing depth was achieved in 28 single cells, allowing accurate somy estimation. A dominant karyotype with three aneuploid chromosomes was observed in 25 cells, while two different minor karyotypes were observed in the other cells. Our method thus allowed the detection of aneuploidy mosaicism, and provides a solid basis which can be further refined to concur with higher-throughput single cell genomic methods.

microbiology↗

bioRxiv2020

Identification of key candidate genes and pathways in axial Spondyloarthritis through integrated bioinformatics analysis

BackgroundRadiographic axial Spondyloarthritis (r-axSpA) is the prototypic form of seronegative spondyloarthritis (SpA). In the present study, we evaluated the key genes related with r-axSpA, and then elucidated the possible molecular mechanisms of r-axSpA. Material/MethodsThe gene expression GSE13782 was downloaded from the GEO database contained five proteoglycan-induced spondylitis mice and three naive controls. The differentially expressed genes (DEGs) were identified with the Bioconductor affy package in R. Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were built with the DAVID program followed by construction of a protein-protein interaction (PPI) network performed with Cytoscape. WebGestalt was performed to construct transcriptional regulatory network and microRNAs-target regulatory networks. RT-PCR and immunohistochemical staining were performed to testify the expression of hub genes, transcription factors (TFs) and microRNAs. ResultsA total of 230 DEGs were identified. PPI networks were constructed by mapping DEGs into STRING, in which 20 hub proteins were identified. KEGG pathway analyses revealed that the chemokine, NOD-like receptor, IL-17, and TNF signalling pathways were altered. GO analyses revealed that DEGs were extensively involved in the regulation of cytokine production, the immune response, the external side of the plasma membrane, and G-protein coupled chemoattractant receptor activity. The results of RT-PCR and immunohistochemical staining demonstrated that the expression of DEGs, TFs and microRNAs in our experiment were basically consistent with the predictions. ConclusionsThe results of this study offer insight into the pathomechanisms of r-axSpA and provide potential research directions.

molecular biology↗

bioRxiv2020

Bioinformatic and experimental evidence for suicidal and catalytic plant THI4s

Like fungi and some prokaryotes, plants use a thiazole synthase (THI4) to make the thiazole precursor of thiamin. Fungal THI4s are suicide enzymes that destroy an essential active-site Cys residue to obtain the sulfur atom needed for thiazole formation. In contrast, certain prokaryotic THI4s have no active-site Cys, use sulfide as sulfur donor, and are truly catalytic. The presence of a conserved active-site Cys in plant THI4s and other indirect evidence implies that they are suicidal. To confirm this, we complemented the Arabidopsis tz-1 mutant, which lacks THI4 activity, with a His-tagged Arabidopsis THI4 construct. LC-MS analysis of tryptic peptides of the THI4 extracted from leaves showed that the active-site Cys was predominantly in desulfurated form, consistent with THI4 having a suicide mech-anism in planta. Unexpectedly, transcriptome datamining and deep proteome profiling showed that barley, wheat, and oat have both a widely expressed canonical THI4 with an active-site Cys, and a THI4-like paralog (non-Cys THI4) that has no active-site Cys and is the major type of THI4 in devel-oping grains. Transcriptomic evidence also indicated that barley, wheat, and oat grains synthesize thiamin de novo, implying that their non-Cys THI4s synthesize thiazole. Structure modeling supported this inference, as did demonstration that non-Cys THI4s have significant capacity to complement thia-zole auxotrophy in Escherichia coli. There is thus a prima facie case that non-Cys cereal THI4s, like their prokaryotic counterparts, are catalytic thiazole synthases. Bioenergetic calculations show that, relative to suicide THI4s, such enzymes could save substantial energy during the grain filling period. AbbreviationsDHAla, dehydroalanine; EST, expressed sequence tag; FDR, false discovery rate; IPTG, {beta}-D-1-thiogalactopyranoside

plant biology↗

bioRxiv2020

Bioinformatics approach reveals Nur77-regulated genes common to the central nervous and immune systems

Neurons and immune cells have similar mechanisms for cell to cell communication. Exists active crosstalk between neurons and immune cells. Neurotransmitters can activate or inhibit immune cells, and cytokines modulate neuronal activity. The transcription factor Nur77 (NR4A1) is highly and transiently induced by several stimuli in neurons and T-lymphocytes, suggesting that Nur77 is involved in the coordination of the genetics response in both cell types. By analyzing publicly available databases, we found Nur77 target genes common to the nervous and immune systems. Functions as cell adhesion and anchoring appear as processes regulated by Nur77 in neurons and immune cells.

neuroscience↗

bioRxiv2020

Bioinformatic analysis of shared B and T cell epitopes amongst relevant coronaviruses to human health: Is there cross-protection?

Within the last 30 years 3 coronaviruses, SARS-CoV, MERS-CoV and SARS-CoV-2, have evolved and adapted to cause disease and spread amongst the human population. From the three, SARS-CoV-2 has spread world-wide and to July 2020 it has been responsible for more than 11 million confirmed cases and over half a million deaths. In the absence of an effective treatment or vaccine, social distancing has been the most effective measure to control the pandemic. However it has become evident that as the virus spreads the only tool that will allow us to fully control it is an effective vaccine. There are currently more than 150 vaccine candidates in different stages of development using a variety of viral antigens, with the S protein being the most targeted antigen. Although some new experimental evidence suggests cross-reacting responses between coronaviruses are present in the population, it remains unknown whether potential shared antigens between different coronaviruses could provide cross-protection. Given that coronaviruses are emerging pathogens and continue to represent a threat to global health, the development of a SARS-Cov-2 vaccine that could provide universal protection against other coronaviruses should be pushed forward. Here we present a thorough review of reported B and T cell epitopes shared between SARS-CoV-2 and other relevant coronaviruses, in addition we used web-based tools to predict novel B and T cell epitopes that have not been reported before. Analysis of experimental evidence that is constantly emerging complemented with the findings of this study allow us support the hypothesis that cross-reactive responses, particularly those coming from T cells, might play a key role in controlling infection by SARS-CoV-2. We hope that with the evidence presented in this manuscript we provide arguments to encourage the study of cross-reactive responses in order to elucidate their role in immunity to SARS-CoV-2. Finally we expect our findings will aid targeted analysis of antigen-specific immune responses and guide future vaccine design aiming to develop a cross reactive effective vaccine against respiratory diseases caused by coronaviruses.

immunology↗

bioRxiv2021

Non-invasive sex genotyping of paiche Arapaima gigas by qPCR: An applied bioinformatic approach to identify sex differences

Arapaima gigas, one of the largest freshwater fish in the world, is suffering from high fishing pressure and habitat loss, which threaten the conservation status of its natural populations. Of great cultural importance to Amazonian people, the paiche or pirarucu A. gigas is in high demand for its meat, ornamental uses and other byproducts such as scales. Aquaculture is a feasible solution to this dilemma. However, the fact that A. gigas presents no sexual dimorphism until it is 5 years old and its long period to sexual maturity are major obstacles for brood-stock management and fingerling production. Thus, the aim of this study was to develop a molecular tool for non-invasive genotypic sexing of paiche throughout its life cycle. We collected samples from gonads, fins and gill mucus of juvenile specimens from local facilities for histological and molecular analysis. Based on the recently available genome sequence of the paiche and making use of current NGS method, we implemented a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. We found a Male-Specific Region (MSR), identified as MSR_3728, to be present only in males. Next, we designed two specific sets of primers on this region to identify genotypic sex by qPCR assays. Both primer sets, MSR_107 and MSR_129, detected males with 100% accuracy. Then we developed a duplex qPCR reaction for each primer set along a reference gene, analyzed the melting curves and detected males by observing two distinct peaks, one for MSR_107 or MSR_129 and one for the reference, while females only presented the reference peak. The same results were obtained for gonads, fins and interestingly, a non-invasive source from gill mucus samples. Finally, the gonads were evaluated histologically in a double-blind test, showing 100% accuracy with qPCR assay for identifying males and females. Data clearly demonstrated a novel pipeline approach for identifying DNA sex markers, followed by a quick, non-invasive, cost-effective duplex qPCR method for sexing A. gigas. These results may be valuable to efficient paiche aquaculture and conservation studies, helping to reduce the fishing pressure on its natural populations. Highlights of the manuscript- Implementation of a novel approach, called Genome Differences by Unmapped Reads, to identify DNA sex markers. - Finding of a Male-Specific Region (MSR), present only in males. - Development of a duplex qPCR to identify genotypic sex through non-invasive sampling.

genomics↗

bioRxiv2021

Bioinformatic analysis deciphers the molecular toolbox in the endophytic/pathogenic behaviour in F. oxysporum f. sp. vanillae - V. planifolia Jacks interaction

BackgroundF. oxysporum as a species complex (FOSC) possesses the capacity to specialize into host-specific pathogens known as formae speciales. This with the help of horizontal gene transfer (HGT) between pathogenic and endophytic individuals of FOSC. From these pathogenic forma specialis, F. oxysporum f. sp. vanillae (Fov) is the causal agent of fusarium wilt producing root and stem rot (RSR) and is positioned as the main phytosanitary problem in vanilla plantations worldwide. Nonetheless, the origin of this forma speciales and the behavioral genetics dictating the endophytic/pathogenic Fusarium lifestyles still unknown. To elucidate the underlying molecular mechanisms that establish these behaviors we analyzed the RNA-seq libraries of two-times frames of vanilla-Fov interactions. ResultsOur analyses identified the sets of transcripts corresponding to Fov pathogenic strain JAGH3 during the two-times frames of the infection as the sets of the transcripts belonging to endophytic Fox in vanilla. Functional predictions of de novo annotated transcripts as the enriched GO terms with the overrepresented metabolic pathways, allowed us to identify the processes that establish the pathogenic lifestyle in Fov being virulence, hypervirulence, sporulation, conidiation, necrosis and fusaric acid related genes with the carbohydrates, amino acids, proteins, glycerophospholipids and autophagy metabolic pathways that are key regulators of spores germination and pathogenicity establishment as the underlying mechanisms behind this behavior. As the absence of these were found in the vanilla endophytic Fox. ConclusionsThis work reveals the main players of the behavioral genetics in pathogenic Fov/endophytic Fox in V. planifolia Jacks. Its pathogenic strategy allows Fov to infect in a SIX genes-independent manner. As the other pathogenic elements found in this study could be explained by the presence of pathogenicity islands and genomic regions associated with supernumerary chromosomes in Fov. These play a central role as carriers of genes involved with pathogenic activity and could be obtained through HGT.

genomics↗

bioRxiv2021

Experimental and Bioinformatic upgrade for genome-wide mapping of nucleosomes in Trypanosoma cruzi

1In Trypanosoma cruzi, as in every eukaryotic cell, DNA is packaged into chromatin by octamers of histone proteins that constitute nucleosomes. Besides compacting DNA, nucleosomes control DNA dependent processes by modulating the access of DNA binding proteins to regulatory elements on the DNA; or by providing the platform for additional layers of regulation given by histone variants and histone post-translational modifications. In trypanosomes, protein coding genes are constitutively transcribed as polycistronic units. Therefore, gene expression is controlled mainly post transcriptionally. However, chromatin organization and the histone code influence transcription, cell cycle progression, replication and DNA repair. Hence, determining nucleosome position is of uppermost importance to understand the peculiarities of these processes in trypanosomes. Digestion of chromatin with micrococcal nuclease followed by deep sequencing has been widely applied for genome-wide mapping of nucleosomes in several organisms. Nonetheless, this parasite presents numerous singularities. On one hand, special growth conditions and cell manipulation are required. On the other hand, chromatin organization shows some uniqueness that demands a specially designed analytical approach. An additional entanglement is given by the nature of its genome harboring a large content of repetitive sequences and the poor quality of the genome assembly and annotation of many strains. Here, we adapted this broadly used method to the hybrid reference strain, CL Brener. Particularly, we developed an exhaustive and thorough computational workflow for data analysis, highlighting the relevance of using its whole genome as a reference instead of the commonly used Esmeraldo-like haplotype. Moreover, the performance of two aligners, Bowtie2 and HISAT2 was tested to find the most appropriate tool to map any genomic read to reference genomes bearing this complexity.

genomics↗

bioRxiv2021

Identification of key genes and immune infiltration modulated by CPAP in Obstructive sleep apnea by integrated bioinformatics analysis

Patients with obstructive sleep apnea (OSA) experience partial or complete upper airway collapses during sleep resulting in nocturnal hypoxia-normoxia cycling. And continuous positive airway pressure (CPAP) is the golden treatment for OSA. Nevertheless, the exact mechanisms of action, especially the transcriptome effect of CPAP on OSA patients, remains elusive. The goal of this study was to evaluate the longitudinal alterations in peripheral blood mononuclear cells transcriptome profiles of OSA patients in order to identify the hub gene and immune response. GSE133601 were downloaded from Gene Expression Omnibus (GEO). We identified black module via weighted gene co-expression network analysis (WGCNA), the genes in which were correlated significantly with the clinical trait of CPAP treatment. Finally, eleven hub genes (TRAV10, SNORA36A, RPL10, OBP2B, IGLV1-40, H2BC8, ESAM, DNASE1L3, CD22, ANK3, ACP3) were traced and used to construct a random forest model to predict therapeutic efficacy of CPAP in OSA with a good performance with AUC of 0.92. We further studied the immune cells infiltration in OSA patients with CIBERSORT, and monocytes were found to be related with the remission of OSA and partially correlated with the hub genes identified. In conclusion, these key genes and immune infiltration may be of great importance in the remission of OSA and related research of these genes may provide a new therapeutic target for OSA in the future.

genomics↗

bioRxiv2021

Conserved T-cell epitopes predicted by bioinformatics in SARS-COV-2 variants

BackgroundFinding conservative T cell epitopes in the proteome of numerous variants of SARS-COV-2 is required to develop T cell activating SARS-COV-2 capable of inducing T cell responses against SARS-COV-2 variants. MethodsA computational workflow was performed to find HLA restricted CD8+ and CD4+ T cell epitopes among conserved amino acid sequences across the proteome of 474727 SARS-CoV-2 strains. ResultsA batch of covserved regions in the amino acid sequences were found in the proteome of the SARS-COV-2 strains. 2852 and 847 peptides were predicted to have high binding affinity to distint HLA class I and class II molecules. Among them, 1456 and 484 peptides are antigenic. 392 and 111 of the antigenic peptides were found in the conseved amino acid sequences. Among the antigenic-conserved peptides, 6 CD8+ T cell epitopes and 7 CD4+ T cell epitopes were identifed. The T cell epitopes could be presented to T cells by high-affinity HLA molecules which are encoded by the HLA alleles with high population coverage. ConclusionsThe T cell epitopes are conservative, antigenic and HLA presentable, and could be constructed into SARS-COV-2 vaccines for inducing protective T cell immunity against SARS-COV-2 and their variants.

immunology↗

bioRxiv2021

CDK1 and HSP90AA1 appears as novel regulatory gene in Non-Small Cell Lung Cancer: A Bioinformatics Approach

Lung cancer is one of the most invasive cancer affecting over a million of population. Non-small cell lung cancer constitutes up to 85% of all lung cancer cases. Therefore, it is important to identify prognostic biomarkers of NSCLC for therapeutic purpose. The complex behaviour of the NSCLC gene-regulatory network interaction is investigated using a network theoretical approach. We used eight NSCLC microarray datasets GSE19188, GSE118370, GSE10072, GSE101929, GSE7670, GSE33532, GSE31547, GSE31210 and meta analyse them to find differentially expressed genes (DEGs), construct protein-protein interaction (PPI) network, analysed its topological properties, significant modules using network analyser with MCODE, construct a PPI-MCODE network using the genes of the significant modules. We used topological properties such as Maximal Clique Centrality (MCC) and bottleneck from the PPI-MCODE network. We compare them with hub genes (those with highest degrees) to find key regulator (KR) gene. This result is also validated by finding of common genes among top twenty hub genes, genes with highest betweenness, closeness centrality and eigenvector values. It was found that two genes, CDK1 and HSP90AA1 were common in PPI-MCODE combined analysis, and it was also found that CDK1, HSP90AA1 and HSPA8 were common among hub and bottle neck properties and suggesting significant regulatory role of CDK1 in non-small cell lung cancer. After validation, the common genes among top twenty hubs and centrality values like Betweenness Centrality, Closeness Centrality and eigen vector properties, CDK1 again appeared as the common gene. Our study as a summary suggested CDK1 as key regulator gene in complex NSCLC network interaction using network theoretical approach and described the complex topological properties of the network.

systems biology↗

bioRxiv2021

Ionotropic glutamate receptors in the retina - a bioinformatical meta-analysis

Glutamate is an essential neurotransmitter for signal processing in the vertical pathway of the mammalian retina, where it is involved in the distribution of visual information into several parallel channels. The excitatory effects of glutamate are mediated by AMPA-, kainate-, and NMDA-type ionotropic glutamate receptors (iGluRs). The expression patterns of these receptors in the vertebrate retina have been investigated so far with mainly immunocytochemical, in-situ hybridization, and electrophysiological/pharmacological techniques. Here, we have used scRNA sequencing data from chicken, mouse, macaque, and human retina to describe and compare the profile of iGluR expression in major retinal cell types across species. Our results suggest that major retinal cell types each express a unique set of iGluRs with substantial differences between non-mammalian and mammalian retinae. Expression of iGluRs has been investigated in more detail for amacrine and bipolar cell types of the human retina, each showing minor variations of a common pattern. The differential expression of iGluRs is likely to convey unique signal processing properties to individual elements of the retinal circuitry.

neuroscience↗

bioRxiv2021

BESFA: Bioinformatics based Evolutionary, Structural & Functional Analysis of Prostrate, Placenta, Ovary, Testis, and Embryo (POTE) Paralogs

The POTE family comprises 14 paralogues and is primarily expressed in Prostrate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins structure, function, and Adaptive Divergence. Our result discerns that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this studys outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.

cancer biology↗