Circular RNA circ_0004470 accelerates the occurrence of lung cancer by promoting DNA damage and cell cycle arrest.

Defects in the DNA damage response are associated with tumorigenesis, and circular RNAs (circRNAs) can also affect the occurrence and progression of cancer by regulating gene expression. However, the relationship between DNA damage in lung cancer and circRNAs remains unexplored. In this study, circ_0004470 was significantly upregulated in various lung cancer cells (H446, A549, H1299) as well as in carcinogenic animal models and clinical lung cancer samples.

Integrative mapping of human CD8 T cells in inflammation and cancer.

CD8 T cells exhibit remarkable phenotypic diversity in inflammation and cancer. However, a comprehensive understanding of their clonal landscape and dynamics remains elusive. Here we introduce scAtlasVAE, a deep-learning-based model for the integration of large-scale single-cell RNA sequencing data and cross-atlas comparisons.

Comprehensive assessment of mRNA isoform detection methods for long-read sequencing data.

The advancement of Long-Read Sequencing (LRS) techniques has significantly increased the length of sequencing to several kilobases, thereby facilitating the identification of alternative splicing events and isoform expressions. Recently, numerous computational tools for isoform detection using long-read sequencing data have been developed. Nevertheless, there remains a deficiency in comparative studies that systemically evaluate the performance of these tools, which are implemented with different algorithms, under various simulations that encompass potential influencing factors.

CRISPR-TE: a web-based tool to generate single guide RNAs targeting transposable elements.

Background: The CRISPR/Cas systems have emerged as powerful tools in genome engineering. Recent studies highlighting the crucial role of transposable elements (TEs) have stimulated research interest in manipulating these elements to understand their functions. However, designing single guide RNAs (sgRNAs) that are specific and efficient for TE manipulation is a significant challenge, given their sequence repetitiveness and high copy numbers.

MSdb: An integrated expression atlas of human musculoskeletal system.

The global prevalence and burden of musculoskeletal (MSK) disorders are immense. Advancements in next-generation sequencing (NGS) have generated vast amounts of data, accelerating the research of pathological mechanisms and the development of therapeutic approaches for MSK disorders. However, scattered datasets across various repositories complicate uniform analysis and comparison.

Selective binding of retrotransposons by ZFP352 facilitates the timely dissolution of totipotency network.

Acquisition of new stem cell fates relies on the dissolution of the prior regulatory network sustaining the existing cell fates. Currently, extensive insights have been revealed for the totipotency regulatory network around the zygotic genome activation (ZGA) period. However, how the dissolution of the totipotency network is triggered to ensure the timely embryonic development following ZGA is largely unknown.

Resistance Risk and Resistance-Related Point Mutation in SdhB and SdhC of Cyclobutrifluram in .

Cyclobutrifluram is a novel succinate dehydrogenase inhibitor (SDHI) developed by Syngenta and helps to inhibit . Here, the potential for cyclobutrifluram resistance in and the resistance mechanism involved were evaluated. Baseline sensitivity of to cyclobutrifluram was determined with a mean EC value of 0.

Untargeted lipidomics reveals lipid metabolism disorders induced by oxathiapiprolin in Phytophthora sojae.

Background: Oxathiapiprolin, an oxysterol-binding protein inhibitor (OSBPI), shows unexceptionable inhibitory activity against plant pathogenic oomycetes. FRAC (Fungicide Resistance Action Committee) classifies it into the mode of action group F9 (lipid homeostasis and transfer/storage), but very little is known about the lipid metabolism of oomycete pathogens when subjected to oxathiapiprolin.

Results: In this study, seven lipid categories and 1435 lipid molecules were identified in Phytophthora sojae, among which glycerolipids, glycerophospholipids, and sphingolipids account for 30.

Pathogen Identification: Ultrasensitive Nucleic Acid Detection via a Dynamic DNA Nanosystem-Integrated Ratiometric Electrochemical Sensing Strategy.

Sensitively determining trace nucleic acid is of great significance for pathogen identification. Herein, a dynamic DNA nanosystem-integrated ratiometric electrochemical biosensor was proposed to determine human immunodeficiency virus-associated DNA fragment (HIV-DNA) with high sensitivity and selectivity. The dynamic DNA nanosystem was composed of a target recycling unit and a multipedal DNA walker unit.

Baseline sensitivity and control efficacy of a new QiI fungicide, florylpicoxamid, against Botrytis cinerea.

Background: Gray mold caused by Botrytis cinerea is an airborne plant pathogen with a necrotrophic lifestyle that infects more than 200 crops worldwide. Florylpicoxamid is a second-generation picolinamide fungicide inspired by a natural product. Florylpicoxamid targets the Qi site of the mitochondrial cytochrome bc1 complex and is currently being registered in China for the control of gray mold in a variety of crops.

Resistance Risk and Novel Resistance-Related Point Mutations in Target Protein PiORP1 of Fluoxapiprolin in .

Fluoxapiprolin is a new oxysterol binding protein inhibitor (OSBPI), which showed excellent inhibitory activity to plant pathogenic oomycetes. Its resistance risk and mechanism in are unclear. In the current study, the sensitivities of 103 isolates to fluoxapiprolin were investigated, and a unimodal distribution with a mean EC value of 0.

huARdb: human Antigen Receptor database for interactive clonotype-transcriptome analysis at the single-cell level.

T-cell receptors (TCRs) and B-cell receptors (BCRs) are critical in recognizing antigens and activating the adaptive immune response. Stochastic V(D)J recombination generates massive TCR/BCR repertoire diversity. Single-cell immune profiling with transcriptome analysis allows the high-throughput study of individual TCR/BCR clonotypes and functions under both normal and pathological settings.

Identification of SRSF3 target mRNAs using inducible TRIBE.

Serine and arginine-rich splicing factor 3 (SRSF3), the smallest member of the Ser/Arg-rich (SR) RNA-binding protein family, regulates multiple aspects of post-transcriptional gene expression program. Although SRSF3 is essential for early embryo development, reprogramming, and pluripotency maintenance, the RNA targets and specificity of RNA recognition of SRSF3 are not well understood in human pluripotent stem cells. In this study, we used inducible TRIBE (targets of RNA binding sites by editing) to identify RNA targets and binding motifs of SRSF3 in human embryonic stem cells (hESCs).

RAD: a web application to identify region associated differentially expressed genes.

Summary: With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually less focused, largely due to the lack of reliable tools to link these regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes (DEGs).