[Experimental] List of manuscripts available for review volunteers
3 manuscripts available for review volunteers
December 5, 2017
The basic helix-loop-helix transcription factor gene family is one of the largest gene families and extensively involved in plant growth, development, and stress responses. However, limited studies are available on the gene family in poplar. In this study, we focused on 202 bHLH genes, exploring their DNA and protein sequences and physicochemical properties. According to their protein sequence similarities and the bootstrap values, the genes can be classified into 25 groups with specific motif structures each. In addition, we performed gene expression profiling using RNA-Seq and identified 19 genes that display tissue-differential expression patterns before salt treatment. Furthermore, under salt stress, we found 74 differentially expressed genes, which are responsive to the treatment. Eighteen of the 19 genes correspond well to the differentially expressed genes. Besides, we validated the results using quantitative real-time PCR. This study lays the foundation for future work in gene cloning, transgenes, and biological mechanisms.
November 30, 2017
Occlusive artery disease (CAD) is the leading cause of death worldwide. Bypass graft surgery remains the prevalently performed treatments for occlusive arterial disease, and veins are the most frequently used conduits for surgical revascularization. However, clinical efficacy is highly affected by the long-term potency rates of vein grafts, and there are no optimal treatments available for the prevention of vein graft restenosis (VGR) until today. Hence, there is an urgent need to improve our understanding of the molecular mechanisms involved in mediating VGR. The past decade has seen the rapid development of genomic technologies, such as the genomic sequencing and microarray technologies, which will definitely provide novel insights into potential molecular mechanisms involved in VGR program. Ironically, high-through put data associated with VGR is extremely scarce until today. The main goal of the current study was to explore potential crucial genes and pathways associated with VGR and provide valid biological information for further investigation of VGR. Based on high-throughput gene expression data, a further comprehensive bioinformatics analysis was performed. The differentially expressed genes (DEGs) were identified using R and Bioconductor packages. After functional enrichment analyses of DEGs, protein–protein interaction (PPI) network and sub-PPI network analyses were performed. Finally, 9 potential hub genes and 14 pathways were found out. In conclusion, these results not only may explain the causes of VGR, but could also open new avenues for therapeutic strategies of VGR. Despite its exploratory nature, this work offers valuable insights into our knowledge of the molecular mechanism involved in VGR.
November 16, 2017
Effective approaches for assessing mitochondrial DNA (mtDNA) variation are important to multiple scientific disciplines. Mitochondrial haplogroups characterize branch points in the phylogeny of mtDNA. Several tools exist for mitochondrial haplogroup classification. However, most require full or partial mtDNA sequence which is often cost prohibitive for studies with large sample sizes. The purpose of this study was to develop Hi-MC, a high-throughput method for mitochondrial haplogroup classification that is cost effective and applicable to large sample sizes making mitochondrial analysis more accessible in genetic studies. Using rigorous selection criteria, we defined and validated a custom panel of mtDNA single nucleotide polymorphisms (SNPs) that allows for accurate classification of European, African, and Native American mitochondrial haplogroups at broad resolution with minimal genotyping and cost. We demonstrate that Hi-MC performs well in samples of European, African, and Native American ancestries, and that Hi-MC performs comparably to a commonly used classifier. Implementation as a software package in R enables users to download and run the program locally, grants greater flexibility in the number of samples that can be run, and allows for easy expansion in future revisions. The source code is freely available at https://github.com/vserch/himc .


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