Comprehensive Time-Course Transcriptome Reveals the Crucial Biological Pathways Involved in the Seasonal Branch Growth in Siberian Elm ().

Timber, the most prevalent organic material on this planet, is the result of a secondary xylem emerging from vascular cambium. Yet, the intricate processes governing its seasonal generation are largely a mystery. To better understand the cyclic growth of vascular tissues in elm, we undertook an extensive study examining the anatomy, physiology, and genetic expressions in Ulmus pumila.

Lactobacillus spp. in the reproductive system of female moths and mating induced changes and possible transmission.

Background: The microbiome in the insect reproductive tract is poorly understood. Our previous study demonstrated the presence of Lactobacillus spp. in female moths, but their distribution and function remain unclear.

Comparative Transcriptome Analysis Identifies Key Defense Genes and Mechanisms in Mulberry () Leaves against Silkworms ().

As a consequence of long-term coevolution and natural selection, the leaves of mulberry () trees have become the best food source for silkworms (). Nevertheless, the molecular and genomic basis of defense response remains largely unexplored. In the present study, we assessed changes in the transcriptome changes of mulberry in response to silkworm larval feeding at 0, 3, and 6 h.

Mating Leads to a Decline in the Diversity of Symbiotic Microbiomes and Promiscuity Increased Pathogen Abundance in a Moth.

Mating may promote microbial diversity through sexual transmission, while mating-induced immune responses may decrease it. Therefore, the study of mating-induced microbiomes changes under different mating systems is informative to unravel its biological relevance and evolutionary significance. Here, we studied the microbiomes in a community context within the abdomen of females using 16S rDNA sequences by setting virgin females, and females mated once, twice, or thrice with the same or different males.

Comparative Transcriptome Analysis Reveals Candidate Genes and Pathways for Potential Branch Growth in Elm () Cultivars.

Wood plays a vital role in human life. It is important to study the thickening mechanism of tree branches and explore the mechanism of wood formation. Elm () is a strong essential wood, and it is widely used in cabinets, sculptures, and ship making.

Comprehensive Time-Course Transcriptome and Co-expression Network Analyses Identify Salt Stress Responding Mechanisms in Strain GY-D55.

It is highly necessary to understand the molecular mechanism underlying the salt stress response in green algae, which may contribute to finding the evolutionary cues of abiotic stress response in plants. Here, we reported a comprehensive temporal investigation of transcriptomes using data at eight different time points, from an early stage (2 h) to a late stage (up to 96 h) in GY-D55 cells. The principal component analysis (PCA) of transcriptome profiles showed that the samples of the early and late stages were well separated.

Characterization of the complete plastome of (Rosaceae), a perennial shrub.

The complete plastome of , a shrub, is determined. The plastome is 155,981 bp in length and comprises a large single-copy region (84,417 bp), a small single-copy region (18,878 bp), and a pair of inverted repeats regions (26,343 bp). A total of 113 unique genes are annotated for the plastome of , containing 79 protein coding genes (PCGs), 30 tRNAs, and four rRNAs.

Characterization and phylogenetic analysis of the complete plastome of (Convolvulaceae), an edible vegetable.

, commonly known as water spinach, is an edible annual vegetable in the genus ,. In this study, the complete plastome of was determined using the Illumina sequencing platform. The plastome size was 162,663 bp.

Screening of Salt Stress Responsive Genes in (L.) Beauv. by Transcriptome Analysis.

As one of the most common abiotic stresses, salt stress seriously impairs crop yield. (L.) Beauv.

Exosomal miR-1246 and miR-155 as predictive and prognostic biomarkers for trastuzumab-based therapy resistance in HER2-positive breast cancer.

Purpose: This study aimed to investigate the predictive and prognostic roles of circulating exosomal miRNAs in breast cancer treated with trastuzumab-based chemotherapy.

Methods: Circulating exosomal miRNAs from trastuzumab-resistant (n = 4) and -sensitive (n = 4) patients were profiled using miRNA microarray. The predictive and prognostic roles of filtered miRNAs were validated in 107 early-stage and 68 metastatic patients treated with trastuzumab-based chemotherapy through receiver-operating characteristic (ROC) curve analysis, logistic regression and Cox proportional hazards regression analysis, and Kaplan-Meier survival analysis.

Novel module and hub genes of distinctive breast cancer associated fibroblasts identified by weighted gene co-expression network analysis.

Background: As abundant and heterogeneous stromal cells in tumor microenvironment, carcinoma-associated fibroblasts (CAFs) are critically involved in cancer progression.

Methods: To identify co-expression module and hub genes of distinctive breast CAFs, weighted gene co-expression network analysis (WGCNA) was conducted based on the expression array results of CAFs from seven chemo-sensitive breast cancer (BC) patients and seven chemo-resistant ones before neo-adjuvant chemotherapy.

Results: A total of 4916 genes were included in WGCNA, and 12 modules were determined.

Comparative Transcriptome Analysis of Halophyte in Response to Salinity Stress.

As one of the most severe environmental stresses, salt stress can cause a series of changes in plants. In salt tolerant plant Zoysia macrostachya, germination, physiology, and genetic variation under salinity have been studied previously, and the morphology and distribution of salt glands have been clarified. However, no study has investigated the transcriptome of such species under salt stress.

Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves.

Salinity is a critical abiotic stress, which significantly impacts the agricultural yield worldwide. Identification of the molecular mechanisms underlying the salt tolerance in euhalophyte Suaeda salsa is conducive to the development of salt-resistant crops. In the present study, high-throughput RNA sequencing was performed after S.

Identification of modules and hub genes associated with platinum-based chemotherapy resistance and treatment response in ovarian cancer by weighted gene co-expression network analysis.

High-grade serous ovarian carcinoma (HGSOC) is the most prevalent and malignant ovarian tumor.To identify co-expression modules and hub genes correlated with platinum-based chemotherapy resistant and sensitive HGSOC, we performed weighted gene co-expression network analysis (WGCNA) on microarray data of HGSOC with 12 resistant samples and 16 sensitive samples of GSE51373 dataset.A total of 5122 genes were included in WGCNA, and 16 modules were identified.

MiR-337-3p suppresses proliferation of epithelial ovarian cancer by targeting PIK3CA and PIK3CB.

Epithelial ovarian cancer (EOC) is responsible for nearly 140,000 deaths worldwide each year. MicroRNAs play critical roles in cancer development and progression. The function of microRNA miR-337-3p has been described in various cancers.

RNF144B inhibits LPS-induced inflammatory responses via binding TBK1.

Innate immune responses need to be precisely controlled to avoid prolonged inflammation and prevent unwanted damage to the host. Here, we report that RNF144B responded dynamically to LPS stimulation and negatively regulated LPS-induced inflammation. We found that RNF144B interacted with the scaffold/dimerization domain (SDD) of TANK binding kinase 1 (TBK1) through the in between RING (IBR) domain to inhibit its phosphorylation and K63-linked polyubiquitination, which led to TBK1 inactivation, IRF3 dephosphorylation, and IFN-β reduction.

The complete chloroplast genome of an annual halophyte herb, (Amaranthaceae).

The complete chloroplast genome (plastome) of , an annual halophytic herb, was determined in this study. The plastome was 149,807 bp in size, containing a large single-copy region (82,162 bp), a small single-copy region (18,191 bp), and two inverted repeats regions (24,727 bp). The overall GC content of this plastome was 36.

Characterization of the complete plastome of (Chenopodiaceae), an annual halophytic herb.

, an annual halophytic herb, is one of the most important Chinese herbal medicines, forages and indicator plants for saline-alkali soil. In this study, we report the complete plastome of . The plastome was 152,237 bp in length and comprises a large single-copy region (83,721 bp), a small single-copy region (18,096 bp), and a pair of inverted repeats (25,210 bp).

Characterization of the complete chloroplast genome of (Amaranthaceae/Chenopodiaceae), an annual succulent halophyte.

, an annual succulent halophytic herb, is one of the major halophyte widely distributed in both saline inland and the intertidal zone. In this study, we report the complete chloroplast genome (plastome) of . The plastome was 151,642 bp in length and comprises a large single-copy region (83,502 bp), a small single-copy region (17,780 bp), and a pair of inverted repeats (25,180 bp).

Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer.

Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV.

Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii.

Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga , physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge.

A biological network-based regularized artificial neural network model for robust phenotype prediction from gene expression data.

Background: Stratification of patient subpopulations that respond favorably to treatment or experience and adverse reaction is an essential step toward development of new personalized therapies and diagnostics. It is currently feasible to generate omic-scale biological measurements for all patients in a study, providing an opportunity for machine learning models to identify molecular markers for disease diagnosis and progression. However, the high variability of genetic background in human populations hampers the reproducibility of omic-scale markers.