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The significance of CP29 reversible phosphorylation in thylakoids of higher plants under environmental stresses

Reversible phosphorylation of proteins is a key event in many fundamental cellular processes. Under stressful conditions, many thylakoid membrane proteins in photosynthetic apparatus of higher plants undergo rapid phosphorylation and dephosphorylation in response to environmental changes. CP29 is the most frequently phosphorylated protein among three minor antennae complexes in...

Association of vitamin D receptor gene polymorphisms with metabolic syndrome: a case–control design of population-based cross-sectional study in North China

management: YZ, YHZ; Data management: YZ, ZYH; Data analysis and drafting paper: SL, YZ. All authors read and approved the final manuscript. Authors information Yi Zhao and Sha Liao Co-first authors

Efficacy and safety of electroacupuncture with different acupoints for chemotherapy-induced nausea and vomiting: study protocol for a randomized controlled trial

Background Many patients experience nausea and vomiting during chemotherapy treatment. Evidence demonstrates that electroacupuncture is beneficial for controlling chemotherapy-induced nausea and vomiting (CINV). However, the acupoint or matching acupoint with the best efficacy for controlling CINV still remains unidentified. Methods/Design This study consists of a randomized...

Contribution of moderate overall coal-bearing basin uplift to tight sand gas accumulation: case study of the Xujiahe Formation in the Sichuan Basin and the Upper Paleozoic in the Ordos Basin, China

Tight sand gas is an important unconventional gas resource occurring widely in different petroleum basins. In coal-bearing formations of the Upper Triassic in the Sichuan Basin and the Carboniferous and Permian in the Ordos Basin, coal measure strata and tight sandstone constitute widely distributed source–reservoir assemblages and form the basic conditions for the formation of...

Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts

It is a challenge to classify protein-coding or non-coding transcripts, especially those re-constructed from high-throughput sequencing data of poorly annotated species. This study developed and evaluated a powerful signature tool, Coding-Non-Coding Index (CNCI), by profiling adjoining nucleotide triplets to effectively distinguish protein-coding and non-coding sequences...

The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex

Background The whiteflies under the name Bemisia tabaci (Gennadius) (Aleyrodidae: Hemiptera) are species complex of at least 31 cryptic species some of which are globally invasive agricultural pests. Previously, the mitochondrial genome (mitogenome) of the indigenous New World B. tabaci species was sequenced and major differences of gene order from the postulated whitefly...

Genome-wide identification of cancer-related polyadenylated and non-polyadenylated RNAs in human breast and lung cell lines

Eukaryotic mRNAs consist of two forms of transcripts: poly(A)+ and poly(A)−, based on the presence or absence of poly(A) tails at the 3′ end. Poly(A)+ mRNAs are mainly protein coding mRNAs, whereas the functions of poly(A)− mRNA are largely unknown. Previous studies have shown that a significant proportion of gene transcripts are poly(A)− or bimorphic (containing both poly(A...

Dr.VIS v2.0: an updated database of human disease-related viral integration sites in the era of high-throughput deep sequencing

Dr.VIS is a database of human disease-related viral integration sites (VIS). The number of VIS has grown rapidly since Dr.VIS was first released in 2011, and there is growing recognition of the important role that viral integration plays in the development of malignancies. The updated database version, Dr.VIS v2.0 (http://www.bioinfo.org/drvis or bminfor.tongji.edu.cn/drvis_v2...

Photoresponse and carrier transport of protocrystalline silicon multilayer films

Alternating multilayer films of hydrogen diluted hydrogenated protocrystalline silicon (pc-Si:H) were prepared using a plasma- enhanced chemical vapor deposition technique. The microstructure of the deposited films and photoresponse characteristics of their Schottky diode structures were investigated by Raman scattering spectroscopy, Fourier transform infrared spectroscopy and...

Ion annotation-assisted analysis of LC-MS based metabolomic experiment

Background Analysis of multiple LC-MS based metabolomic studies is carried out to determine overlaps and differences among various experiments. For example, in large metabolic biomarker discovery studies involving hundreds of samples, it may be necessary to conduct multiple experiments, each involving a subset of the samples due to technical limitations. The ions selected from...

Dietary intake and risk of rheumatoid arthritis—a cross section multicenter study

Environmental factors play an important role in the development of rheumatoid arthritis (RA). Among these factors, smoking is generally considered to be an established risk factor for RA. Data regarding the impact of diet on risk of RA development is limited. This study assessed the impact of dietary patterns on RA susceptibility in Chinese populations. This was a large scale...

CpG oligodeoxynucleotides enhance chemosensitivity of 5-fluorouracil in HepG2 human hepatoma cells via downregulation of the antiapoptotic factors survivin and livin

Background Recent studies indicated that a synthetic oligonucleotide containing un-methylated CpG oligodeoxynucleotides (CpG-ODN) has a potential function for cancer therapy. In this study, we evaluated the chemosensitizing effects of CpG-ODN in 5-fluorouracil (5-FU)-treated HepG2 human hepatoma cells. Methods Cell viability assay were utilized to evaluate the direct cytotoxicity...

Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study

Background With the fast advances in nextgen sequencing technology, high-throughput RNA sequencing has emerged as a powerful and cost-effective way for transcriptome study. De novo assembly of transcripts provides an important solution to transcriptome analysis for organisms with no reference genome. However, there lacked understanding on how the different variables affected...

Characterization of the Partitioning System of Myxococcus Plasmid pMF1

pMF1 is the only autonomously replicating plasmid that has been recently identified in myxobacteria. This study characterized the partitioning (par) system of this plasmid. The fragment that significantly increased the retaining stability of plasmids in Myxococcus cells in the absence of selective antibiotics contained three open reading frames (ORFs) pMF1.21-pMF1.23 (parCAB...

Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species

Background Genomic divergence between invasive and native species may provide insight into the molecular basis underlying specific characteristics that drive the invasion and displacement of closely related species. In this study, we sequenced the transcriptome of an indigenous species, Asia II 3, of the Bemisia tabaci complex and compared its genetic divergence with the...

A Comparative Study of Techniques for Differential Expression Analysis on RNA-Seq Data

Recent advances in next-generation sequencing technology allow high-throughput cDNA sequencing (RNA-Seq) to be widely applied in transcriptomic studies, in particular for detecting differentially expressed genes between groups. Many software packages have been developed for the identification of differentially expressed genes (DEGs) between treatment groups based on RNA-Seq data...

A Computational Method Based on the Integration of Heterogeneous Networks for Predicting Disease-Gene Associations

The identification of disease-causing genes is a fundamental challenge in human health and of great importance in improving medical care, and provides a better understanding of gene functions. Recent computational approaches based on the interactions among human proteins and disease similarities have shown their power in tackling the issue. In this paper, a novel systematic and...

Identifying Schistosoma japonicum Excretory/Secretory Proteins and Their Interactions with Host Immune System

Schistosoma japonicum is a major infectious agent of schistosomiasis. It has been reported that large number of proteins excreted and secreted by S. japonicum during its life cycle are important for its infection and survival in definitive hosts. These proteins can be used as ideal candidates for vaccines or drug targets. In this work, we analyzed the protein sequences of S...

The Choice of Regimens Based on Bortezomib for Patients with Newly Diagnosed Multiple Myeloma

Introduction Bortezomib has significantly improved multiple myeloma (MM) response rates, but strategies for choosing bortezomib-based regimens for initial MM therapy are not standardized. Here, we describe four bortezomib-based therapies in Chinese MM patients to determine the optimal chemotherapeutic approach. Methods Newly diagnosed symptomatic MM patients at three...