Hub genes identification and association of key pathways with hypoxia in cancer cells: A bioinformatics analysis.

Three human cancer cell lines (A549, HCT116, and HeLa) were used to investigate the molecular mechanisms and potential prognostic biomarkers associated with hypoxia. We obtained gene expression data from Gene Expression Omnibus (GEO) datasets GSE11704, GSE147384, and GSE38061, which included 5 hypoxic and 8 control samples. Using the GEO2R tool and Venn diagram software, we identified common differentially expressed genes (cDEGs). The cDEGs were then subjected to Gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis by employing DAVID. The hub genes were identified from critical PPI subnetworks through CytoHuba plugin and these genes' prognostic significance and expression were verified using Kaplan-Meier analysis and Gene Expression Profiling Interactive Analysis (GEPIA), respectively. The research showed 676 common DEGs (cDEGs), with 207 upregulated and 469 downregulated genes. The STRING analysis showed 673 nodes and 1446 edges in the PPI network. We identified 4 significant modules and 19 downregulated hub genes. GO analysis revealed all of them were majorly involved in ribosomal large subunit assembly and biogenesis, rRNA processing, ribosome biogenesis, translation, RNA & protein binding frequently at the sites of nucleolus and nucleoplasm while 11 were significantly associated with a better prognosis of hypoxic tumors. Our research sheds light on the molecular mechanisms that underpin hypoxia in human cancer cell lines and identifies potential prognostic biomarkers for hypoxic tumors.

Integration of OMICS Technologies for Crop Improvement.

Sustainable crop improvement can help to feed the exploding human population in an era of shrinking cultivable lands and dwindling water resources. In this scenario, crop improvement using OMICS technologies may help to ensure food security and alleviate the rural poverty in poor countries. Additionally, the improved crops may help to cope with the problem of malnutrition in the different parts of the world, especially Africa. OMICS technologies are based on the knowledge gained through genomics, transcriptomics, proteomics, metabolomics, interactomics and phenomics. This expert review article congregates recent knowledge of the emerging OMICS technologies and evaluates how their integrated application is improving important crops and the potential of these technologies in bringing a revolution in agriculture. Moreover, we have provided an analysis of various technical challenges and difficulties arising during application of OMICS technologies to crop plants which pose major restrictions to the implementation of these strategies.

In silico epitope prediction and immunogenic analysis for penton base epitope-focused vaccine against hydropericardium syndrome in chicken.

Certain strains of fowl adenovirus serotype 4 (FAdV-4) of the family Adenoviridae are recognized to be the causative agents of Hydropericardium Syndrome (HPS) in broiler chicken. Despite the significantly spiking mortality in broilers due to HPS, not much effort has been made to design an effective vaccine against FAdV-4. The combination of immuno- and bioinformatics tools for immunogenic epitope prediction is the most recent concept of vaccine design. It reduces the time and effort required for hunting a potent vaccine candidate and is economical. Previously, we have reported the penton base protein of FAdV-4 to be a candidate for subunit vaccine against HPS. In the present study, we have computationally pre-screened promising B- and T-cell epitopes of the penton base. Multiple methods were employed for linear B-cell epitope identification; BepiPred and five other methods based on physicochemical properties of the amino acids. The penton base was homology modeled by means of Modeller 9.17 and after refinement of the model (by GalaxyRefine web server) ElliPro web tool was used to predict the discontinuous epitopes. NetMHCcons 1.1 and NetMHCIIpan 3.1 servers were used for the likelihood of peptide binding to Major Histocompatibility Complex (MHC) class I & II molecules respectively for T-cell epitope forecast. As a result, we identified the peptide stretch of 1-225  as the most promiscuous B- and T-cell epitope region in penton base Full Length (FL) protein sequence. Escherichia coli based expression vectors were generated containing cloned peptide stretch 1-225 (penton base1-225) and penton base FL gene sequence. The recombinant penton base1-225 and penton base FL proteins were expressed and purified using Escherichia coli-based expression system. Purification yield of penton base1-225 was 3-fold higher compared to penton base FL. These proteins were injected in chickens to determine their competence in protection against HPS. The results showed equal protection level of the two proteins and the commercial inactivated vaccine against FAdV-4 infection. The results suggest the peptide stretch 1-225 of penton base as a valuable candidate for developing an epitope-driven vaccine to combat HPS.

Unfiltered Nanofat Injections Rejuvenate Postburn Scars of Face.

The aim of this study was to compare the quality of postburn facial scars before and after injection of unfiltered nanofat. The study was performed in the Plastic Surgery Department of Mayo Hospital, Lahore, Pakistan, from January 2015 to December 2016. Forty-eight patients with postburn facial scars were included; age range was 4 to 32 years with Fitzpatrick skin types between 3 and 4. Patients with hypertrophic scars, contractures, or keloids were excluded. Scars were assessed by a senior plastic surgeon and the patient on the POSAS (Patient Observer Scar Assessment Scale). Fat was harvested from the abdomen and/or thighs with a 3-mm multiport liposuction cannula (containing several sharp side holes of 1 mm) using Coleman technique. The harvested fat was emulsified and transferred into 1-mL Luer-Lock syringes for injection into the subdermal or intradermal plane. Final follow-up was scheduled at 6 months, and scar was rated by the patient and the same surgeon on the POSAS. Preoperative and postoperative scar scores were compared, and P values were calculated. Results indicated that after nanofat grafting, there was a statistically significant improvement in scar quality. The most significant improvements on the observer scale were seen in pigmentation and pliability (P < 0.0001). Thickness and relief were the least improved variables (P = of 0.785 and 0.99, respectively). ImageJ scanning also showed pigmentation change (P = 0.076). A statistically significant improvement was seen in all parameters of the patient section of the POSAS (P < 0.0001). In conclusion, unfiltered nanofat grafting seems to be a promising and effective therapeutic approach in postburn facial scars, showing significant improvement in scar quality. The trial was registered on www.clinicaltrials.gov with following ID NCT03352297.

Screening for Del 185 AG and 4627C>A BRCA1 Mutations in Breast Cancer Patients from Lahore, Pakistan.

Breast cancer contributes to approximately 23% of the cancer cases identified and 14% of cancer related deaths worldwide. Including a strong association between genetic and environmental factors, breast cancer is a complex and multi factorial disorder. Two high penetration breast cancer susceptibility genes (BRCA1 and BRCA2) have been identified, and germ line mutations in these are thought to account for between 5% and 10% of all breast cancer cases. The human BRCA1 gene, located on 17q, is involved in the regulation of cell proliferation by aiding in DNA repair, transcriptional responses to DNA damage and cell cycle check points. Mutations in this gene enhance cell proliferation and facilitate formation of tumors. Two mutations, the 185 deletion of AG and the 4627 substitution from C to A, are founder mutations in the BRCA1 gene for breast cancer in Asian populations. Allele specific PCR was performed to detect these selected mutations in 120 samples. No mutation of 4627 C to A was detected in the samples and only one of the patients had the 185 del AG mutation in the heterozygous condition. Our collected samples had lower consanguinity and family history indicating the greater involvement of environmental as compared to genetic factors.