4.7 Article

Transcriptomes of Zebrafish in Early Stages of Multiple Viral Invasions Reveal the Role of Sterols in Innate Immune Switch-On

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022

Yongbiao Xue et al.

Summary: The National Genomics Data Center (NGDC) of China National Center for Bioinformation (CNCB) provides database resources to support global research, with a focus on single-cell omics and precision medicine. They continuously scale up and update core database resources, daily update SARS-CoV-2 genome data, and establish OpenLB and update Database Commons.

NUCLEIC ACIDS RESEARCH (2022)

Article Developmental Biology

Nrf2 dictates the neuronal survival and differentiation of embryonic zebrafish harboring compromised alanyl-tRNA synthetase

Binbin Jin et al.

Summary: tRNA synthetase deficiency leads to unfolded protein responses in neuronal disorders. This study identified a mutant zebrafish allele that showed increased neuronal apoptosis and compromised neurogenesis. The aberration in gene expression resulted in protein overloading and activated Perk.

DEVELOPMENT (2022)

Article Cell Biology

Opposing effects of deubiquitinase OTUD3 in innate immunity against RNA and DNA viruses

Xiaolian Cai et al.

Summary: OTUD3 plays opposite roles in response to RNA and DNA virus infection by removing distinct types of ubiquitination from RIG-I/MDA5 and cGAS, thereby regulating immune responses. OTUD3 can suppress RNA virus-triggered immunity and enhance DNA virus-triggered immunity.

CELL REPORTS (2022)

Article Microbiology

Fish female-biased gene cyp19a1a leads to female antiviral response attenuation between sexes by autophagic degradation of MITA

Long-Feng Lu et al.

Summary: From insects to mammals, females generally have higher innate and adaptive immune response than males. This study investigates the role of the autosomal gene cyp19a1a in the antiviral response of zebrafish. Results show that females with high expression of cyp19a1a exhibit a weaker antiviral response, and this gene mediates autophagic degradation of MITA to suppress interferon expression. These findings broaden our understanding of sex differences in the immune response.

PLOS PATHOGENS (2022)

Article Biochemistry & Molecular Biology

A systematic evaluation of bioinformatics tools for identification of long noncoding RNAs

You Duan et al.

Summary: An investigation comparing the performance of 41 analysis models for lncRNA identification revealed that no single model excelled under all test conditions. The efficiency of different models depended largely on the source of transcripts and the quality of assemblies. Recommendations were summarized for lncRNA identification under different situations, emphasizing the need for careful selection of appropriate tools based on actual data.
Review Immunology

Influence of chronic stress on the mechanism of the cytotoxic system in common carp (Cyprinus carpio)

Mazal Shimon-Hophy et al.

Summary: Aquaculture conditions can make fish more vulnerable to illness and death due to internal and environmental stressors. The brain processes stress signals based on intensity and type, leading to release of catecholamines and glucocorticoids which affect immune system functions. Chronic stress may cause deterioration of cytotoxic functions, increasing morbidity and mortality risk.

IMMUNOLOGY (2021)

Article Fisheries

Genome-wide characterization of Toll-like receptors in Japanese meagre Argyrosomus japonicus and their response to poly (I:C) injection

Fei Han et al.

Summary: The study identified 12 members of the TLR gene family in the Japanese meagre genome, distributed across 10 chromosomes. Evolutionary analysis placed the TLR genes into different subfamilies, with highly consistent conserved motifs. qRT-PCR assays revealed higher expression levels of TLRs in immune tissues of Japanese meagre.

AQUACULTURE (2021)

Article Fisheries

Recognition of MDP and activation of NF-KB by cytosolic sensor NOD2 in Oreochromis niloticus

Jianan He et al.

Summary: Nile tilapia NOD2, a member of NLR family, is highly conserved and plays a significant role in innate immune defense against bacterial infection. It is widely and highly expressed in immune-related tissues and can recognize MDP intracellularly to activate the NF-KB signaling pathway.

AQUACULTURE (2021)

Article Immunology

Zebrafish otud6b Negatively Regulates Antiviral Responses by Suppressing K63-Linked Ubiquitination of irf3 and irf7

Ziwen Zhou et al.

Summary: OTUD6B gene is induced upon viral infection and functions to suppress cellular antiviral response. It interacts with irf3 and irf7, diminishing their polyubiquitination, thereby impacting the IFN-1 signaling pathway.

JOURNAL OF IMMUNOLOGY (2021)

Editorial Material Immunology

(Sterol)ized Immunity: Could PI3K/AKT3 Be the Answer?

Xun Chi et al.

IMMUNITY (2020)

Article Biochemistry & Molecular Biology

Zebrafish prmt3 negatively regulates antiviral responses

Junji Zhu et al.

FASEB JOURNAL (2020)

Article Biochemistry & Molecular Biology

Structural Basis of Low-pH-Dependent Lysosomal Cholesterol Egress by NPC1 and NPC2

Hongwu Qian et al.

Article Biotechnology & Applied Microbiology

Alignment and mapping methodology influence transcript abundance estimation

Avi Srivastava et al.

GENOME BIOLOGY (2020)

Article Biochemical Research Methods

Salmon provides fast and bias-aware quantification of transcript expression

Rob Patro et al.

NATURE METHODS (2017)

Article Biochemistry & Molecular Biology

CPC2: a fast and accurate coding potential calculator based on sequence intrinsic features

Yu-Jian Kang et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Pharmacology & Pharmacy

Modelling viral infections using zebrafish: Innate immune response and antiviral research

Monica Varela et al.

ANTIVIRAL RESEARCH (2017)

Review Biotechnology & Applied Microbiology

Spring viraemia of carp virus: recent advances

Usama Ashraf et al.

JOURNAL OF GENERAL VIROLOGY (2016)

Article Biotechnology & Applied Microbiology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

Mihaela Pertea et al.

NATURE BIOTECHNOLOGY (2015)

Article Biochemical Research Methods

HISAT: a fast spliced aligner with low memory requirements

Daehwan Kim et al.

NATURE METHODS (2015)

Article Biochemistry & Molecular Biology

Steroids in teleost fishes: A functional point of view

Janina Tokarz et al.

STEROIDS (2015)

Article Fisheries

Neuroendocrine mechanisms for immune system regulation during stress in fish

Gino Nardocci et al.

FISH & SHELLFISH IMMUNOLOGY (2014)

Review Pharmacology & Pharmacy

Polarization of the Innate Immune Response by Prostaglandin E-2: A Puzzle of Receptors and Signals

Mario Rodriguez et al.

MOLECULAR PHARMACOLOGY (2014)

Article Biotechnology & Applied Microbiology

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

Michael I. Love et al.

GENOME BIOLOGY (2014)

Article Biochemistry & Molecular Biology

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

Liguo Wang et al.

NUCLEIC ACIDS RESEARCH (2013)

Review Fisheries

Molecular regulation of interferon antiviral response in fish

Yi-Bing Zhang et al.

DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY (2012)

Article Multidisciplinary Sciences

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

Ravi K. Patel et al.

PLOS ONE (2012)

Article Fisheries

Stress and immune modulation in fish

Lluis Tort

DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY (2011)

Review Fisheries

Lysozyme: an important defence molecule of fish innate immune system

Shailesh Saurabh et al.

AQUACULTURE RESEARCH (2008)

Article Biochemical Research Methods

WGCNA: an R package for weighted correlation network analysis

Peter Langfelder et al.

BMC BIOINFORMATICS (2008)

Article Fisheries

Innate immunity of fish (overview)

B Magnadóttir

FISH & SHELLFISH IMMUNOLOGY (2006)

Article Biochemistry & Molecular Biology

Toll-like receptor gene family and TIR-domain adapters in Danio rerio

C Jault et al.

MOLECULAR IMMUNOLOGY (2004)

Review Immunology

Modulation of the fish immune system by hormones

J Harris et al.

VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY (2000)