New persistent plant RNA virus carries mutations to weaken viral suppression of antiviral RNA interference.

Persistent plant viruses are widespread in natural ecosystems. However, little is known about why persistent infection with these viruses may cause little or no harm to their host. Here, we discovered a new polerovirus that persistently infected wild rice plants by deep sequencing and assembly of virus-derived small-interfering RNAs (siRNAs).

Protein-coding circular RNA enhances antiviral immunity via JAK/STAT pathway in .

RNA interference (RNAi) drives powerful antiviral immunity in plants and animals so that many viruses must express viral suppressor of RNAi (VSR) to establish virulent infection. However, little is known about the immune responses conferring resistance against viruses that have evolved the counter-defensive strategy to suppress antiviral RNAi. In this study, we discover that cells infected with C virus (DCV), a natural viral pathogen of known to harbor a potent VSR, exhibit heightened expression of circular RNA circZfh1.

Unraveling metabolic characteristics and clinical implications in gastric cancer through single-cell resolution analysis.

Gastric cancer is a highly prevalent malignant neoplasm. Metabolic reprogramming is intricately linked to both tumorigenesis and cancer immune evasion. The advent of single-cell RNA sequencing technology provides a novel perspective for evaluating cellular metabolism.

Regulation of ubiquitination and antiviral activity of Cactin by deubiquitinase Usp14 in .

Cactin, a highly conserved protein, plays a crucial role in various physiological processes in eukaryotes, including innate immunity. Recently, the function of Cactin in the innate immunity of has been explored, revealing that Cactin regulates a non-canonical signaling pathway associated with the Toll and Imd pathways the Cactin-Deaf1 axis. In addition, Cactin exhibits specific antiviral activity against the C virus (DCV) in , with an unknown mechanism.

Regulation of phase separation and antiviral activity of Cactin by glycolytic enzyme PGK via phosphorylation in .

Unlabelled: Liquid-liquid phase separation (LLPS) plays a crucial role in various biological processes in eukaryotic organisms, including immune responses in mammals. However, the specific function of LLPS in immune responses in remains poorly understood. Cactin, a highly conserved protein in eukaryotes, is involved in a non-canonical signaling pathway associated with Nuclear factor-κB (NF-κB)-related pathways in .

Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera.

Sogatella furcifera is a destructive agricultural pest causing large threats to rice production in China and Southeast Asian countries. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in S. furcifera.

Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing.

A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens.

Phylogenomics of five Pseudanabaena cyanophages and evolutionary traces of horizontal gene transfer.

Background: Along with the fast development and urbanization in developing countries, the waterbodies aside the growing cities become heavily polluted and highly eutrophic, thus leading to the seasonal outbreak of cyanobacterial bloom. Systematic isolation and characterization of freshwater cyanophages might provide a biological solution to control the awful blooms. However, genomic sequences and related investigations on the freshwater cyanophages remain very limited to date.

Complete genome sequence of a new badnavirus infecting a tea plant in China.

The complete genome of a novel virus, provisionally named "Camellia sinensis badnavirus 1" (CSBV1), was identified in tea plant (Camellia sinensis) leaves collected in Anhui Province, China. The genome of CSBV1 consists of 8,195 bp and possesses three open reading frames (ORFs), sharing 68.6 % nucleotide sequence identity with the genome of Camellia lemon glow virus (CLGV) from Camellia japonica.

A Deep Neural Network for Gastric Cancer Prognosis Prediction Based on Biological Information Pathways.

Background: Gastric cancer (GC) is one of the deadliest cancers in the world, with a 5-year overall survival rate of lower than 20% for patients with advanced GC. Genomic information is now frequently employed for precision cancer treatment due to the rapid advancements of high-throughput sequencing technologies. As a result, integrating multiomics data to construct predictive models for the GC patient prognosis is critical for tailored medical care.

Profiling the Tumor-Infiltrating Lymphocytes in Gastric Cancer Reveals Its Implication in the Prognosis.

Gastric cancer is the fifth most common malignancy and the third leading cause of cancer-related mortality worldwide. Immunotherapy offers promising new treatment options for gastric cancer patients; however, it is only effective in a limited fraction of patients. In this study, we evaluated the composition of 22 tumor-infiltrating lymphocytes (TILs) in TCGA Stomach Adenocarcinoma (STAD) using deconvolution-based method by analyzing the publicly available bulk tumor RNA-seq data.

Diagnosis of Viral Diseases Using Deep Sequencing and Metagenomics Analyses.

Viruses are ubiquitous in nature and exist in a variety of habitats. The advancement in sequencing technologies has revolutionized the understanding of viral biodiversity associated with plant diseases. Deep sequencing combined with metagenomics is a powerful approach that has proven to be revolutionary in the last decade and involves the direct analysis of viral genomes present in a diseased tissue sample.

Culture-Independent Discovery of Viroids by Deep Sequencing and Computational Algorithms.

Viroids are single-stranded circular RNA molecules that cause diseases in plants and do not encode any protein. Classical approaches for the identification of new viroids are challenging for many plant pathology laboratories as viroid cDNA synthesis and sequencing require purification and enrichment of the naked viroid RNA by two-dimensional gel electrophoresis. Conventional metagenomic approaches are not effective for viroid discovery because the total number of known viroids is small, and distinct viroids share limited nucleotide sequence similarity.

Energy stress-induced linc01564 activates the serine synthesis pathway and facilitates hepatocellular carcinogenesis.

Cancer cells undergo metabolic adaption to sustain their survival and growth under metabolic stress conditions, yet the underlying mechanism remains largely unclear. It is also not known if lncRNAs contribute to this metabolic adaption of cancer cells. Here we show that linc01564 is induced in response to glucose deprivation by the transcription factor ATF4.

Integrated analysis of whole genome and transcriptome sequencing in a young patient with gastric cancer provides insights for precision therapy.

Gastric cancer is a leading cause of cancer-associated deaths worldwide and is considered to be an age-related disease. In younger patients, gastric cancer is biologically more aggressive, and prognosis is worse compared with that in elderly patients. In the present case report, the whole genome and transcriptome was sequenced in a 26-year-old patient with gastric cancer who presented with gastric cancer-related symptoms and was admitted to the First Affiliated Anhui Medical Hospital (Hefei, China) in December 2016.

Exploration of the genomic landscape of a long-term surviving stage III colorectal cancer patient identifies recurrent and rare mutations: a case report.

A 40-year old female patient from the Chinese Han population presented colorectal cancer (CRC) related symptoms including abdominal discomfort, tenesmus and severe back pain, and was admitted to the First Affiliated Anhui Medical University in October, 2008. The size of her tumor was 3 cm × 3 cm, and the carcinoma had invaded the serosa layer, covering 3/4 of the intestine tube. She was diagnosed with stage III CRC after examination.

Virome Identification and Characterization of and : Causative Agents of Pokkah Boeng Disease in Sugarcane.

and are two devastating sugarcane pathogens that cause pokkah boeng disease (PBD) in China. RNA_Seq was conducted to identify mycoviruses in and isolates collected from PBD symptom-showing sugarcane plants across China. Fifteen isolates with a normal, debilitated, or abnormal phenotype in colony morphology were screened out for the existence of dsRNA from 104 isolates.

lncRNA Sensing of a Viral Suppressor of RNAi Activates Non-canonical Innate Immune Signaling in Drosophila.

Antiviral immunity in insects is mediated by the RNA interference (RNAi) pathway. Viruses evade antiviral RNAi by expressing virulence factors known as viral suppressors of RNAi (VSR). Here, we report the identification of VINR, a Drosophila VSR-interacting long non-coding (lnc) RNA that activates non-canonical innate immune signaling upon detection of the dsRNA-binding VSR of Drosophila C virus (DCV).

Clinicopathological risk factors for gastric cancer: a retrospective cohort study in China.

Objective: To examine the potential clinicopathological factors affecting the prognosis of patients with gastric cancer after surgical treatment in China.

Methods: Between 1 January 2001 and 31 December 2012, a total of 716 patients aged 22-84 years with gastric cancer were enrolled in the study. Survival analysis techniques including log rank test and Cox proportional hazard regression model were applied to evaluate the prognostic significance of clinicopathological characteristics in terms of survival time.

Functional analysis of the congenital heart disease‑associated GATA4 H436Y mutation in vitro.

Congenital heart disease (CHD) is the most common type of developmental defect, with high rates of morbidity in infants. The transcription factor GATA‑binding factor 4 (GATA4) has been reported to serve a critical role in embryogenesis and cardiac development. Our previous study reported a heterozygous GATA4 c.

Identification of genes underlying phenotypic plasticity of wing size via insulin signaling pathway by network-based analysis in Sogatella furcifera.

Background: Phenotypic plasticity is a common and highly adaptive phenomenon where the same genotype produces different phenotypes in response to environmental cues. Sogatella furcifera, a migratory pest of rice exhibits wing dimorphism, is a model insect for studying phenotypic plasticity of wing size. The Insullin-PI3K-Akt-FOXO signaling pathway plays a crucial role in the manipulation of wing size in the migratory insects.

NMT1 inhibition modulates breast cancer progression through stress-triggered JNK pathway.

Myristoylation is one of key post-translational modifications that involved in signal transduction, cellular transformation and tumorigenesis. Increasing evidence demonstrates that targeting myristoylation might provide a new strategy for eliminating cancers. However, the underlying mechanisms are still yielded unclear.