Avian Immunome DB: an example of a user-friendly interface for extracting genetic information

Abstract Background Genomic and genetic studies often require a target list of genes before conducting any hypothesis testing or experimental verification. With the ever-growing number of sequenced genomes and a variety of different annotation strategies, comes the potential for ambiguous gene symbols, making it cumbersome to capture the “correct” set of genes. In this article, we present and describe the Avian Immunome DB (Avimm) for easy gene property extraction as exemplified by avian immune genes. The avian immune system is characterised by a cascade of complex biological processes underlaid by more than 1000 different genes. It is a vital trait to study particularly in birds considering that they are a significant driver in spreading zoonotic diseases. With the completion of phase II of the B10K (“Bird 10,000 Genomes”) consortium’s whole-genome sequencing effort, we have included 363 annotated bird genomes in addition to other publicly available bird genome data which serve as a valuable foundation for Avimm. Construction and content A relational database with avian immune gene evidence from Gene Ontology, Ensembl, UniProt and the B10K consortium has been designed and set up. The foundation stone or the “seed” for the initial set of avian immune genes is based on the well-studied model organism chicken (Gallus gallus). Gene annotations, different transcript isoforms, nucleotide sequences and protein information, including amino acid sequences, are included. Ambiguous gene names (symbols) are resolved within the database and linked to their canonical gene symbol. Avimm is supplemented by a command-line interface and a web front-end to query the database. Utility and discussion The internal mapping of unique gene symbol identifiers to canonical gene symbols allows for an ambiguous gene property search. The database is organised within core and feature tables, which makes it straightforward to extend for future purposes. The database design is ready to be applied to other taxa or biological processes. Currently, the database contains 1170 distinct avian immune genes with canonical gene symbols and 612 synonyms across 363 bird species. While the command-line interface readily integrates into bioinformatics pipelines, the intuitive web front-end with download functionality offers sophisticated search functionalities and tracks the origin for each record. Avimm is publicly accessible at https://avimm.ab.mpg.de.

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Transcriptome sequencing of black grouse ( Tetrao tetrix ) for immune gene discovery and microsatellite development

Open Biology ◽

10.1098/rsob.120054 ◽

2012 ◽

Vol 2 (4) ◽

pp. 120054 ◽

Cited By ~ 25

Author(s):

Biao Wang ◽

Robert Ekblom ◽

Todd A. Castoe ◽

Eleanor P. Jones ◽

Radoslav Kozma ◽

...

Keyword(s):

Large Scale ◽

Expressed Sequence Tag ◽

Gene Discovery ◽

Bird Species ◽

Preliminary Test ◽

Immune Gene ◽

Large Set ◽

Black Grouse ◽

Immune Genes ◽

Tetrao Tetrix

The black grouse ( Tetrao tetrix ) is a galliform bird species that is important for both ecological studies and conservation genetics. Here, we report the sequencing of the spleen transcriptome of black grouse using 454 GS FLX Titanium sequencing. We performed a large-scale gene discovery analysis with a focus on genes that might be related to fitness in this species and also identified a large set of microsatellites. In total, we obtained 182 179 quality-filtered sequencing reads that we assembled into 9035 contigs. Using these contigs and 15 794 length-filtered (greater than 200 bp) singletons, we identified 7762 transcripts that appear to be homologues of chicken genes. A specific BLAST search with an emphasis on immune genes found 308 homologous chicken genes that have immune function, including ten major histocompatibility complex-related genes located on chicken chromosome 16. We also identified 1300 expressed sequence tag microsatellites and were able to design suitable flanking primers for 526 of these. A preliminary test of the polymorphism of the microsatellites found 10 polymorphic microsatellites of the 102 tested. Genomic resources generated in this study should greatly benefit future ecological, evolutionary and conservation genetic studies on this species.

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Identification and development of an independent immune-related genes prognostic model for breast cancer

BMC Cancer ◽

10.1186/s12885-021-08041-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Lin Chen ◽

Yuxiang Dong ◽

Yitong Pan ◽

Yuhan Zhang ◽

Ping Liu ◽

...

Keyword(s):

Breast Cancer ◽

Regression Analysis ◽

Cox Regression ◽

Gene Set Enrichment Analysis ◽

Risk Scores ◽

Validation Dataset ◽

Immune Gene ◽

Cox Regression Analysis ◽

Immune Genes ◽

Immune Related Genes

Abstract Background Breast cancer is one of the main malignant tumors that threaten the lives of women, which has received more and more clinical attention worldwide. There are increasing evidences showing that the immune micro-environment of breast cancer (BC) seriously affects the clinical outcome. This study aims to explore the role of tumor immune genes in the prognosis of BC patients and construct an immune-related genes prognostic index. Methods The list of 2498 immune genes was obtained from ImmPort database. In addition, gene expression data and clinical characteristics data of BC patients were also obtained from the TCGA database. The prognostic correlation of the differential genes was analyzed through Survival package. Cox regression analysis was performed to analyze the prognostic effect of immune genes. According to the regression coefficients of prognostic immune genes in regression analysis, an immune risk scores model was established. Gene set enrichment analysis (GSEA) was performed to probe the biological correlation of immune gene scores. P < 0.05 was considered to be statistically significant. Results In total, 556 immune genes were differentially expressed between normal tissues and BC tissues (p < 0. 05). According to the univariate cox regression analysis, a total of 66 immune genes were statistically significant for survival risk, of which 30 were associated with overall survival (P < 0.05). Finally, a 15 immune genes risk scores model was established. All patients were divided into high- and low-groups. KM survival analysis revealed that high immune risk scores represented worse survival (p < 0.001). ROC curve indicated that the immune genes risk scores model had a good reliability in predicting prognosis (5-year OS, AUC = 0.752). The established risk model showed splendid AUC value in the validation dataset (3-year over survival (OS) AUC = 0.685, 5-year OS AUC = 0.717, P = 0.00048). Moreover, the immune risk signature was proved to be an independent prognostic factor for BC patients. Finally, it was found that 15 immune genes and risk scores had significant clinical correlations, and were involved in a variety of carcinogenic pathways. Conclusion In conclusion, our study provides a new perspective for the expression of immune genes in BC. The constructed model has potential value for the prognostic prediction of BC patients and may provide some references for the clinical precision immunotherapy of patients.

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A family of pathogen-induced cysteine-rich transmembrane proteins is involved in plant disease resistance

Planta ◽

10.1007/s00425-021-03606-3 ◽

2021 ◽

Vol 253 (5) ◽

Author(s):

Marciel Pereira Mendes ◽

Richard Hickman ◽

Marcel C. Van Verk ◽

Nicole M. Nieuwendijk ◽

Anja Reinstädler ◽

...

Keyword(s):

Arabidopsis Thaliana ◽

Plasma Membrane ◽

Disease Resistance ◽

Plant Disease Resistance ◽

Transmembrane Proteins ◽

Series Data ◽

Immune Gene ◽

Biological Processes ◽

Hypocotyl Growth ◽

Enhanced Resistance

Abstract Main conclusion Overexpression of pathogen-induced cysteine-rich transmembrane proteins (PCMs) in Arabidopsis thaliana enhances resistance against biotrophic pathogens and stimulates hypocotyl growth, suggesting a potential role for PCMs in connecting both biological processes. Abstract Plants possess a sophisticated immune system to protect themselves against pathogen attack. The defense hormone salicylic acid (SA) is an important player in the plant immune gene regulatory network. Using RNA-seq time series data of Arabidopsis thaliana leaves treated with SA, we identified a largely uncharacterized SA-responsive gene family of eight members that are all activated in response to various pathogens or their immune elicitors and encode small proteins with cysteine-rich transmembrane domains. Based on their nucleotide similarity and chromosomal position, the designated Pathogen-induced Cysteine-rich transMembrane protein (PCM) genes were subdivided into three subgroups consisting of PCM1-3 (subgroup I), PCM4-6 (subgroup II), and PCM7-8 (subgroup III). Of the PCM genes, only PCM4 (also known as PCC1) has previously been implicated in plant immunity. Transient expression assays in Nicotiana benthamiana indicated that most PCM proteins localize to the plasma membrane. Ectopic overexpression of the PCMs in Arabidopsis thaliana resulted in all eight cases in enhanced resistance against the biotrophic oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Additionally, overexpression of PCM subgroup I genes conferred enhanced resistance to the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. The PCM-overexpression lines were found to be also affected in the expression of genes related to light signaling and development, and accordingly, PCM-overexpressing seedlings displayed elongated hypocotyl growth. These results point to a function of PCMs in both disease resistance and photomorphogenesis, connecting both biological processes, possibly via effects on membrane structure or activity of interacting proteins at the plasma membrane.

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ESIS ON THE WORLD WIDE WEB

International Journal of Modern Physics C ◽

10.1142/s0129183194000921 ◽

1994 ◽

Vol 05 (05) ◽

pp. 805-809 ◽

Cited By ~ 1

Author(s):

SALIM G. ANSARI ◽

PAOLO GIOMMI ◽

ALBERTO MICOL

Keyword(s):

World Wide Web ◽

Web Application ◽

World Wide ◽

Markup Language ◽

Command Line ◽

Command Line Interface ◽

The World ◽

Hypertext Transfer Protocol ◽

Hypertext Markup Language ◽

Near Future

On 3rd November, 1993, ESIS announced its Homepage on the World Wide Web (WWW) to the user community. Ever since then, ESIS has steadily increased its Web support to the astronomical community to include a bibliographic service, the ESIS catalogue documentation and the ESIS Data Browser. More functionality will be added in the near future. All these services share a common ESIS structure that is used by other ESIS user paradigms such as the ESIS Graphical User Interface (Giommi and Ansari, 1993), and the ESIS Command Line Interface. A forms-based paradigm, each ESIS-Web application interfaces to the hypertext transfer protocol (http) translating queries from/to the hypertext markup language (html) format understood by the NCSA Mosaic interface. In this paper, we discuss the ESIS system and show how each ESIS service works on the World Wide Web client.

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Deficiency of innate immunity against P. aeruginosa enhances behavioral avoidance via the HECW-1/NPR-1 module in C. elegans

Infection and Immunity ◽

10.1128/iai.00067-21 ◽

2021 ◽

Author(s):

Hua Bai ◽

Wei Zou ◽

Wenhui Zhou ◽

Keqin Zhang ◽

Xiaowei Huang

Keyword(s):

Innate Immunity ◽

Pathogenic Bacteria ◽

Immune Gene ◽

Biological Processes ◽

Defensive Strategy ◽

C Elegans ◽

Defensive Strategies ◽

Behavioral Avoidance ◽

Neuropeptide Y Receptor ◽

G Protein Coupled

To antagonize infection of pathogenic bacteria in soil and confer increased survival, Caenorhabditis elegans employs innate immunity and behavioral avoidance synchronously as the two main defensive strategies. Although both biological processes and their individual signaling pathways have been partially elucidated, knowledge of their interrelationship remains limited. The current study reveals that deficiency of innate immunity triggered by mutation of the classic immune gene pmk-1 promotes avoidance behavior in C. elegans ; and vice versa. Restoration of pmk-1 expression using the tissue-specific promoters suggested that the functional loss of both intestinal and neuronal pmk-1 is necessary for the enhanced avoidance. Additionally, PMK-1 co-localized with the E3 ubiquitin ligase HECW-1 in OLL neurons and regulated the expressional level of the latter, which consequently affected the production of NPR-1, a G-protein-coupled receptor homologous to the mammalian neuropeptide Y receptor, in RMG neurons in a non-cell-autonomous manner. Collectively, our study illustrates, once the innate immunity is impaired when C. elegans antagonizes bacterial infection, the other defensive strategy of behavioral avoidance can be enhanced accordingly via the HECW-1/NPR-1 module, suggesting that GPCRs in neural circuits may receive the inputs from immune system and integrate those two systems for better adapting to the real-time status.

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UCEasy: A software package for automating and simplifying the analysis of ultraconserved elements (UCEs)

Biodiversity Data Journal ◽

10.3897/bdj.9.e78132 ◽

2021 ◽

Vol 9 ◽

Author(s):

Caio Ribeiro ◽

Lucas Oliveira ◽

Romina Batista ◽

Marcos De Sousa

Keyword(s):

Best Practices ◽

Software Package ◽

Phylogenetic Trees ◽

Computational Analysis ◽

Data Matrix ◽

Command Line ◽

Command Line Interface ◽

Ultraconserved Elements ◽

Research Software ◽

Different Levels

The use of Ultraconserved Elements (UCEs) as genetic markers in phylogenomics has become popular and has provided promising results. Although UCE data can be easily obtained from targeted enriched sequencing, the protocol for in silico analysis of UCEs consist of the execution of heterogeneous and complex tools, a challenge for scientists without training in bioinformatics. Developing tools with the adoption of best practices in research software can lessen this problem by improving the execution of computational experiments, thus promoting better reproducibility. We present UCEasy, an easy-to-install and easy-to-use software package with a simple command line interface that facilitates the computational analysis of UCEs from sequencing samples, following the best practices of research software. UCEasy is a wrapper that standardises, automates and simplifies the quality control of raw reads, assembly and extraction and alignment of UCEs, generating at the end a data matrix with different levels of completeness that can be used to infer phylogenetic trees. We demonstrate the functionalities of UCEasy by reproducing the published results of phylogenomic studies of the bird genus Turdus (Aves) and of Adephaga families (Coleoptera) containing genomic datasets to efficiently extract UCEs.

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Efficient Transfer of data from RDBMS to HDFS and conversion to JSON format

International Journal for Research in Applied Science and Engineering Technology ◽

10.22214/ijraset.2021.38710 ◽

2021 ◽

Vol 9 (10) ◽

pp. 1869-1871

Author(s):

Dr. C. K. Gomathy

Keyword(s):

Data Warehouse ◽

Relational Databases ◽

Command Line ◽

Command Line Interface ◽

Apache Hadoop ◽

Enterprise Data Warehouse ◽

Efficient Transfer ◽

Efficient Execution

Abstract: Apache Sqoop is mainly used to efficiently transfer large volumes of data between Apache Hadoop and relational databases. It helps to certain tasks, such as ETL (Extract transform load) processing, from an enterprise data warehouse to Hadoop, for efficient execution at a much less cost. Here first we import the table which presents in MYSQL Database with the help of command-line interface application called Sqoop and there is a chance of addition of new rows and updating new rows then we have to execute the query again. So, with the help of our project there is no need of executing queries again for that we are using Sqoop job, which consists of total commands for import and next after import we retrieve the data from hive using Java JDBC and we convert the data to JSON Format, which consists of data in an organized way and easy to access manner by using GSON Library. Keywords: Sqoop, Json, Gson, Maven and JDBC

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Intraspecific variation in immune gene expression and heritable symbiont density

PLoS Pathogens ◽

10.1371/journal.ppat.1009552 ◽

2021 ◽

Vol 17 (4) ◽

pp. e1009552

Author(s):

Holly L. Nichols ◽

Elliott B. Goldstein ◽

Omid Saleh Ziabari ◽

Benjamin J. Parker

Keyword(s):

Gene Expression ◽

Acyrthosiphon Pisum ◽

Aphid Species ◽

F1 Hybrids ◽

Immune Gene ◽

Immune Genes ◽

Immune Mechanisms ◽

Immune Gene Expression ◽

Host Microbe Interactions ◽

And Function

Host genetic variation plays an important role in the structure and function of heritable microbial communities. Recent studies have shown that insects use immune mechanisms to regulate heritable symbionts. Here we test the hypothesis that variation in symbiont density among hosts is linked to intraspecific differences in the immune response to harboring symbionts. We show that pea aphids (Acyrthosiphon pisum) harboring the bacterial endosymbiontRegiella insecticola(but not all other species of symbionts) downregulate expression of key immune genes. We then functionally link immune expression with symbiont density using RNAi. The pea aphid species complex is comprised of multiple reproductively-isolated host plant-adapted populations. These ‘biotypes’ have distinct patterns of symbiont infections: for example, aphids from theTrifoliumbiotype are strongly associated withRegiella. Using RNAseq, we compare patterns of gene expression in response toRegiellain aphid genotypes from multiple biotypes, and we show thatTrifoliumaphids experience no downregulation of immune gene expression while hostingRegiellaand harbor symbionts at lower densities. Using F1 hybrids between two biotypes, we find that symbiont density and immune gene expression are both intermediate in hybrids. We propose that in this system,Regiellasymbionts are suppressing aphid immune mechanisms to increase their density, but that some hosts have adapted to prevent immune suppression in order to control symbiont numbers. This work therefore suggests that antagonistic coevolution can play a role in host-microbe interactions even when symbionts are transmitted vertically and provide a clear benefit to their hosts. The specific immune mechanisms that we find are downregulated in the presence ofRegiellahave been previously shown to combat pathogens in aphids, and thus this work also highlights the immune system’s complex dual role in interacting with both beneficial and harmful microbes.

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Development of a Multi-gene-based Immune Prognostic Signature in Ovarian Cancer

10.21203/rs.3.rs-52624/v1 ◽

2020 ◽

Author(s):

tiefeng cao ◽

huimin shen

Keyword(s):

Ovarian Cancer ◽

Network Analysis ◽

Prognostic Biomarkers ◽

Survival Prediction ◽

Immune Gene ◽

Prognostic Signature ◽

Data Set ◽

Cox Regression Analysis ◽

Immune Genes ◽

Immune Related Genes

Abstract Background：Chemotherapeutic resistance is responsible for treatment failure. Immunotherapy is important in ovarian cancer (OC). Systematic exploration of immunogenic landscape and reliable immune gene-based prognostic biomarkers or signature is necessary to be identified. This study aims to identify the immune gene-based prognostic biomarkers and regulatory factors, further to develop an individualized prediction signature.Methods: This study systematically explored the gene expression profiles from RNA-seq data set for The Cancer Genome Atlas (TCGA) ovarian cancer. Differentially expressed and survival-associated immune genes and transcription factors (TFs) were identified using immune genes from ImmPort dataset and TFs from Cistoma database. We developed the prognostic signature based on survival associated immune genes with LASSO (Least absolute shrinkage and selection operator) Cox regression analysis. Further, Network analysis was performed to uncover the potential molecular mechanisms of immune-related genes with the help of computational biology. Results: The prognostic signature, a weighted combination of the 21 immune-related genes, performed moderately in survival prediction with AUC was 0.746, 0.735, and 0.749 for 1, 3, and 5 year overall survival, respectively. Network analysis uncovered the regulatory role of TFs in immune genes. Intriguingly, the prognostic signature reflected infiltration of some immune cell subtypes.Conclusions: We first constructed a signature with 21 immune genes of clinical significance, which showed promising predictive value in the surveillance, prognosis, even immunotherapy response of OC patients.

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Model-Centric Fulfillment Operations and Maintenance Automation

Advances in Wireless Technologies and Telecommunication - Emerging Automation Techniques for the Future Internet ◽

10.4018/978-1-5225-7146-9.ch001 ◽

2018 ◽

pp. 1-20

Author(s):

Patrick Moore

Keyword(s):

Support Systems ◽

Dynamic Capability ◽

Command Line ◽

Command Line Interface ◽

Business Support ◽

Service Models ◽

Operations And Maintenance ◽

Operational Models ◽

Multiple Templates

As networks have evolved, there has been an evolution in how they are managed as well. This evolution has seen a move from manual configuration via command line interface (CLI) to script-based automation and eventually to a template-based approach with workflow to coordinate multiple templates and scripts. The next step in this evolution is the introduction of models to provide a more dynamic capability than is in place today. This chapter will discuss three major layers of modelling that should be considered during implementation of this approach: device models focused on the configuration of the hardware itself; service models focused on the customer or network facing services that leverage the hardware level configuration; and operational models focused on people, processes, and tools involved in application of device and service models. This includes the orchestration of activities with other tools, such as operational support systems (OSS) and business support systems (BSS).

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