Southwest University

About: Southwest University is a education organization based out in Chongqing, China. It is known for research contribution in the topics: Population & Bombyx mori. The organization has 29772 authors who have published 27755 publications receiving 409441 citations. The organization is also known as: Southwest University in Chongqing & SWU.

Systematic Identification and Characterization of Long Non-Coding RNAs in the Silkworm, Bombyx mori

Abstract: Long noncoding RNAs (lncRNAs) are emerging as important regulators in various biological processes. However, to date, no systematic characterization of lncRNAs has been reported in the silkworm Bombyx mori. In the present study, we generated eighteen RNA-seq datasets with relatively high depth. Using an in-house designed lncRNA identification pipeline, 11,810 lncRNAs were identified for 5,556 loci. Among these lncRNAs, 474 transcripts were intronic lncRNAs (ilncRNAs), 6,250 transcripts were intergenic lncRNAs (lincRNAs), and 5,086 were natural antisense lncRNAs (lncNATs). Compared with protein-coding mRNAs, silkworm lncRNAs are shorter in terms of full length but longer in terms of exon and intron length. In addition, lncRNAs exhibit a lower level of sequence conservation, more repeat sequences overlapped and higher tissue specificity than protein-coding mRNAs in the silkworm. We found that 69 lncRNA transcripts from 33 gene loci may function as miRNA precursors, and 104 lncRNA transcripts from 72 gene loci may act as competing endogenous RNAs (ceRNAs). In total, 49.47% of all gene loci (2,749/5,556) for which lncRNAs were identified showed sex-biased expression. Co-expression network analysis resulted in 19 modules, 12 of which revealed relatively high tissue specificity. The highlighted darkgoldenrod module was specifically associated with middle and posterior silk glands, and the hub lncRNAs within this module were co-expressed with proteins involved in translation, translocation, and secretory processes, suggesting that these hub lncRNAs may function as regulators of the biosynthesis, translocation, and secretion of silk proteins. This study presents the first comprehensive genome-wide analysis of silkworm lncRNAs and provides an invaluable resource for genetic, evolutionary, and genomic studies of B. mori.

First Succinyl-Proteome Profiling of Extensively Drug-Resistant Mycobacterium tuberculosis Revealed Involvement of Succinylation in Cellular Physiology

Abstract: Protein lysine succinylation, an emerging protein post-translational modification widespread among eukaryotic and prokaryotic cells, represents an important regulator of cellular processes. However, the extent and function of lysine succinylation in Mycobacterium tuberculosis, especially extensively drug-resistant strain, remain elusive. Combining protein/peptide prefractionation, immunoaffinity enrichment, and LC–MS/MS analysis, a total of 686 succinylated proteins and 1739 succinylation sites of M. tuberculosis were identified, representing the first global profiling of M. tuberculosis lysine succinylation. The identified succinylated proteins are involved in a variety of cellular functions such as metabolic processes, transcription, translation, and stress responses and exhibit different subcellular localization via GO, protein interaction network, and other bioinformatic analysis. Notably, proteins involved in protein biosynthesis and carbon metabolism are preferred targets of lysine succinylation. Mo...

Model-Based Analysis of the Long-Term Effects of Fertilization Management on Cropland Soil Acidification.

Abstract: Agricultural soil acidification in China is known to be caused by the over-application of nitrogen (N) fertilizers, but the long-term impacts of different fertilization practices on intensive cropl...

Long-Term Fertilizer Experiment Network in China: Crop Yields and Soil Nutrient Trends

Abstract: Results are summarized for the first 15 yr of an eight-site, long-term experimental network in China designed to assess the sustainability of cropping systems in environments representing 70% of Chinese cropland. Systems were wheat–maize double cropping (two crops per year) at four sites, wheat–rice double cropping, rice-based triple cropping, and wheat or maize single cropping. Without fertilizers, wheat yields were mainly ≤1 t ha⁻¹, and maize yields were ≥2 t ha⁻¹ With NPK fertilizer (rates averaging 154, 33, and 54 kg ha⁻¹ per crop of N, P, and K, respectively), wheat yields mainly ranged from 5 to 7 t ha⁻¹, and maize yields ranged from 6 to 9 t ha⁻¹ Without P fertilizer, yields declined (up to 4 t ha⁻¹ less than with NPK), and Olsen-P values in soil declined, although rates differed between sites. Decreasing yields from withholding K usually emerged more slowly. The results emphasize the value of long-term experiments to reveal trends in soil fertility not apparent within a few years and the need for research in these environments to define “critical concentrations” of plant-available P and K in soil for maintaining maximum crop yields. Results with manures show the risk of overfertilization and water pollution with N and P if inorganic fertilizer applications are not decreased to take account of nutrients from manure. At two sites, there was evidence of significant N and P inputs from irrigation water. At one site, the addition of N fertilizer gradually caused soil acidification; this caused inefficient utilization of nutrients and led to crop failure.