Identification of Differentially Expressed Genes Associated with the Prognosis and Diagnosis of Hepatocellular Carcinoma by Integrated Bioinformatics Analysis.

Objective: The goal of this study was to understand the possible core genes associated with hepatocellular carcinoma (HCC) pathogenesis and prognosis. Methods: GEO contains datasets of gene expression, miRNA, and methylation patterns of diseased and healthy/control patients. The GSE62232 dataset was selected by employing the server Gene Expression Omnibus. A total of 91 samples were collected, including 81 HCC and 10 healthy samples as control. GSE62232 was analysed through GEO2R, and Functional Enrichment Analysis was performed to extract rational information from a set of DEGs. The Protein-Protein Relationship Networking search method has been used for extracting the interacting genes. MCC method was used to calculate the top 10 genes according to their importance. Hub genes in the network were analysed using GEPIA to estimate the effect of their differential expression on cancer progression. Results: We identified the top 10 hub genes through CytoHubba plugin. These included BUB1, BUB1B, CCNB1, CCNA2, CCNB2, CDC20, CDK1 and MAD2L1, NCAPG, and NDC80. NCAPG and NDC80 reported for the first time in this study while the remaining from a recently reported literature. The pathogenesis of HCC may be directly linked with the aforementioned genes. In this analysis, we found critical genes for HCC that showed recommendations for future prognostic and predictive biomarkers studies that could promote selective molecular therapy for HCC.

Correction: In silico screening and identification of deleterious missense SNPs along with their effects on CD-209 gene: An insight to CD-209 related-diseases.

[This corrects the article DOI: 10.1371/journal.pone.0247249.].

Purification, characterization, and determination of biological activities of water-soluble polysaccharides from Mahonia bealei.

Mahonia bealei is one of the important members of the genus Mahonia and Traditional Chinese Medicine (TCM). Several compounds isolated from this plant have exhibited useful biological activities. Polysaccharides, an important biomacromolecule have been underexplored in case of M. bealei. In this study, hot water extraction and ethanol precipitation were used for the extraction of polysaccharides from the stem of M. bealei, and then extract was purified using ultrafiltration membrane at 50,000 Da cut off value. Characterization of the purified M. bealei polysaccharide (MBP) was performed using Fourier Transform Infrared Spectroscopy (FT-IR), along with Scanning Electron Microscopy (SEM), X-ray crystallography XRD analysis and Thermal gravimetric analysis (TGA). The purified polysaccharide MBP was tested for antioxidant potential by determining its reducing power, besides determining the DPPH, ABTS, superoxide radical, and hydroxyl radical scavenging along with ferrous ion chelating activities. An increased antioxidant activity of the polysaccharide was reported with increase in concentration (0.5 to 5 mg/ml) for all the parameters. Antimicrobial potential was determined against gram positive and gram-negative bacteria. 20 µg/ml MBP was found appropriate with 12 h incubation period against Escherichia coli and Bacillus subtilis bacteria. We conclude that polysaccharides from M. bealei possess potential ability of biological importance; however, more studies are required for elucidation of their structure and useful activities.

In silico screening and identification of deleterious missense SNPs along with their effects on CD-209 gene: An insight to CD-209 related-diseases.

DC-SIGN receptor articulated by macrophages and dendritic cells is encoded by CD209 gene and plays a role to activate and proliferate the T-lymphocytes in response of virus attack. The dysfunctional activity of DC-SIGN receptor because of missense SNPs can lead to cause dengue haemorrhage fever, HIV-1 infection etc. Out of 11 transcripts of CD209, all missense SNPs of canonical transcript were retrieved from Ensembl database and evaluated by their deleteriousness by using Polyphen-2, PMut, SIFT, MutPred, PROVEAN and PhD-SNP together with stimulation of its complete 3D structure. 10 nsSNPs were chosen depending on both the significance value of nsSNP and their prediction among SNPs evaluating servers which are based on different algorithms. Moreover, the position and native role of 10 nsSNPs in wild 3D model has been described which assist to acknowledge their importance. This study urges the researcher's community to experimentally validate these SNPs and their association in causing the diseases like dengue fever, Tuberculosis etc.

Structure, function, and pathology of protein O-glucosyltransferases.

Protein O-glucosylation is a crucial form of O-glycosylation, which involves glucose (Glc) addition to a serine residue within a consensus sequence of epidermal growth factor epidermal growth factor (EGF)-like repeats found in several proteins, including Notch. Glc provides stability to EGF-like repeats, is required for S2 cleavage of Notch, and serves to regulate the trafficking of Notch, crumbs2, and Eyes shut proteins to the cell surface. Genetic and biochemical studies have shown a link between aberrant protein O-glucosylation and human diseases. The main players of protein O-glucosylation, protein O-glucosyltransferases (POGLUTs), use uridine diphosphate (UDP)-Glc as a substrate to modify EGF repeats and reside in the endoplasmic reticulum via C-terminal KDEL-like signals. In addition to O-glucosylation activity, POGLUTs can also perform protein O-xylosylation function, i.e., adding xylose (Xyl) from UDP-Xyl; however, both activities rely on residues of EGF repeats, active-site conformations of POGLUTs and sugar substrate concentrations in the ER. Impaired expression of POGLUTs has been associated with initiation and progression of human diseases such as limb-girdle muscular dystrophy, Dowling-Degos disease 4, acute myeloid leukemia, and hepatocytes and pancreatic dysfunction. POGLUTs have been found to alter the expression of cyclin-dependent kinase inhibitors (CDKIs), by affecting Notch or transforming growth factor-ß1 signaling, and cause cell proliferation inhibition or induction depending on the particular cell types, which characterizes POGLUT's cell-dependent dual role. Except for a few downstream elements, the precise mechanisms whereby aberrant protein O-glucosylation causes diseases are largely unknown, leaving behind many questions that need to be addressed. This systemic review comprehensively covers literature to understand the O-glucosyltransferases with a focus on POGLUT1 structure and function, and their role in health and diseases. Moreover, this study also raises unanswered issues for future research in cancer biology, cell communications, muscular diseases, etc.

A review on polysaccharides from Artemisia sphaerocephala Krasch seeds, their extraction, modification, structure, and applications.

Artemisia sphaerocephala Krasch (ASK) is an important member of Compositae (Asteraceae) family. Its seeds have been widely used as traditional medicine and to improve the quality of food. Water soluble and water insoluble polysaccharides are found in the seeds of this plant. Research has been conducted on the extraction of polysaccharides, their modification and determination of their structure. To date different techniques for extraction purposes have been applied which are reviewed here. Antioxidant, antidiabetic, anti-obesogenic, antitumor, and immunomodulatory activities have been explored using in vivo and in vitro methods. Moreover, these polysaccharides have been used as packaging material and as a sensing component for monitoring the freshness of packaged food. Some experimental results have shown that the quality of foods is also improved by using them as a food additive. We have also indicated some of the potential areas that are needed to be explored.

Identification and functional characterization of a novel selenocysteine methyltransferase from Brassica juncea L.

Organic selenium (Se), specifically Se-methylselenocysteine (MeSeCys), has demonstrated potential effects in human disease prevention including cancer and the emerging ameliorating effect on Alzheimer's disease. In plants, selenocysteine methyltransferase (SMT) is the key enzyme responsible for MeSeCys formation. In this study, we first isolated a novel SMT gene, designated as BjSMT, from the genome of a known Se accumulator, Brassica juncea L. BjSMT shows high sequence (amino acid) similarity with its orthologues from Brassica napus and Brassica oleracea var. oleracea, which can use homocysteine (HoCys) and selenocysteine (SeCys) as substrates. Similar to its closest homologues, BjSMT also possesses a conserved Thr187 which is involved in transferring a methyl group to HoCys by donating a hydrogen bond, suggesting that BjSMT can methylate both HoCys and SeCys substrates. Using quantitative real-time PCR (qRT-PCR) technology and BjSMT-transformed tobacco (Nicotiana tabacum) plants, we observed how BjSMT responds to selenite [Se(IV)] and selenate [Se(VI)] stress in B. juncea, and how the phenotypes of BjSMT-overexpressing tobacco cultured under selenite stress are affected. BjSMT expression was nearly undetectable in the B. juncea plant without Se exposure, but in the plant leaves it can be rapidly and significantly up-regulated upon a low level of selenite stress, and enormously up-regulated upon selenate treatment. Overexpression of BjSMT in tobacco substantially enhanced tolerance to selenite stress manifested as significantly higher fresh weight, plant height, and chlorophyll content than control plants. In addition, transgenic plants exhibited low glutathione peroxidase activity in response to a lower dose of selenite stress (with a higher dose of selenite stress resulting in a high activity response) compared with the controls. Importantly, the BjSMT-transformed tobacco plants accumulated a high level of Se upon selenite stress, and the plants also had significantly increased MeSeCys production potential in their leaves. This first study of B. juncea SMT demonstrates its potential applications in crop MeSeCys biofortification and phytoremediation of Se pollution.

In-Silico analysis of missense SNPs in Human HPPD gene associated with Tyrosinemia type III and Hawkinsinuria.

HPPD gene codes a dioxygenase enzyme involved in catalysis of different molecules such as tyrosine and phenylalanine by oxidizing them to produce energy. A single change in protein can trigger serious genetic disorders like Tyrosinemia type III and Hawkinsinuria. This study aims to identify the functional missense SNPs of the HPPD gene by using multiple computational tools. All deleterious missense SNPs retrieved from Ensembl and OMIM database were evaluated through six different software. Ultimately, out of 148 missense SNPs, only 27 were confirmed as diseasecausing SNPs by developing a consensus approach. These damaging SNPs were further examined to evaluate their impact on protein stability and energy including their evolutionary conservation. Native and mutated proteins structures were also designed and superimposed by I-TASSER and PyMol respectively. This work results in narrowing down missense SNPs which are still not confirmed experimentally and demands the confirmation by GWAS data. Thus, these missense SNPs could directly or indirectly destabilize the amino acid interactions causing functional deviations of protein.

In-silico analysis of putative HCV epitopes against Pakistani human leukocyte antigen background: An approach towards development of future vaccines for Pakistani population.

Mounting burden of HCV-infected individuals and soaring cost of treatment is a serious source of unease for developing countries. Numbers of various approaches have been anticipated to develop a vaccine against HCV but the majority of them proved ineffective. Development of vaccine by considering geographical distribution of HCV genotypes and host genetics shows potential. In this research article, we have tried to predict most putative HCV epitopes which are efficiently restricted by most common HLA alleles in Pakistani population through different computational algorithms. Thirteen selected, experimentally identified epitopes sequences were used to derived consensus sequences in all genotypes of HCV. Obtained consensus sequences were used to predict their binding affinities with most prevalent HLA alleles in Pakistani population. Two Class-I epitopes from NS4B region, one from Class-I epitope from NS5A and one Class-II epitope from NS3 region showed effective binding and proved to be highly putative to boost immune response. A cocktail of these four have been checked for population coverage and they gave 75.53% for Pakistani Asian and 70.77% for Pakistani Mixed populations with no allergenic response. Computational algorithms are robust way to shortlist potential candidate epitopes for vaccine development but further, in vivo and in-vitro studies are required to confirm their immunogenic properties.