Bioinformatics and Biology Insights

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is one of the most common cancers worldwide. Intense efforts have been made to elucidate the molecular pathogenesis, but the molecular mechanisms of PDAC are still not well understood. The purpose of this study is to further explore the molecular mechanism of PDAC through integrated bioinformatics analysis. METHODS: To identify the candidate genes in the carcinogenesis and progression of PDAC, next-generation sequencing (NGS) data set GSE133684 was downloaded from Gene Expression Omnibus (GEO) database...

The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant and its subvariants have a unique set of mutations. Two of those mutations (N679 K and P681 H) reside close to the S1 /S2 furin cleavage site (FCS; 685-686). When these mutations reside together, they exert less-efficient membrane fusion than wild type and most other variants of concern such as the Delta variant. Here, we in silico targeted these mutations to find out which of the amino acids and interactions change plays the key role in fusion...

The COVID-19 coronavirus, which primarily affects the lungs, is the source of the disease known as SARS-CoV-2. According to "Smoking and COVID-19: a scoping review," about 32% of smokers had a severe case of COVID-19 pneumonia at their admission time and 15% of non-smokers had this case of COVID-19 pneumonia. We were able to determine which genes were expressed differently in each group by comparing the expression of gene transcriptomic datasets of COVID-19 patients, smokers, and healthy controls. In all, 37 dysregulated genes are common in COVID-19 patients and smokers, according to our analysis...

The increased transmissibility of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has generated variants of concern (VOCs) throughout the pandemic, responsible for waves of cases worldwide. To monitor mutations in the S gene of SARS-CoV-2 in different variants, we evaluated 1497 individuals with COVID-19 in western Amazonia in the period April 2021 to July 2022. The epidemiological and clinical data of the individuals were collected; subsequently, the samples were extracted using a commercial kit, the viral load was assessed, and viral genomes were sequenced...

Genomes may now be sequenced in a matter of weeks, leading to an influx of "hypothetical" proteins (HP) whose activities remain a mystery in GenBank. The information included inside these genes has quickly grown in prominence. Thus, we selected to look closely at the structure and function of an HP (AFF25514.1; 246 residues) from Pasteurella multocida (PM) subsp. multocida str. HN06. Possible insights into bacterial adaptation to new environments and metabolic changes might be gained by studying the functions of this protein...

The activation of the Wnt signaling pathway is implicated in a neuroprotective mechanism against the Alzheimer disease. When this pathway is blocked, it activates GSK3 beta, leading to tau hyperphosphorylation and the apoptosis of neurons. Dickkopf-related protein 1 (DKK1) is a protein that competes with the Wnt ligand for the low-density lipoprotein receptor-related protein 6 (LRP6) receptor's binding, interrupting the Wnt-induced Fzd-Wnt-LRP6 complex. This counteracts Wnt's neuroprotective effect and contributes to the progression of the Alzheimer disease...

The ecological deterioration caused by the continuous and excessive use of synthetic inputs in agriculture has prompted the search for environmentally favorable resources for crop production. Many have advocated for the use of soils from termite mounds to improve soil and plant health; therefore, the purpose of this study was to characterize the microbiome multifunctionalities that are important for plant health and growth in termite mound soil. The metagenomics of soil from termite mounds revealed taxonomic groups with functional potentials associated with promoting the growth and health of plants in nutrient-poor, virtually dry environments...

The search for effective therapeutics to combat COVID-19 has led to the exploration of the biological activity of numerous compounds. In this study, hydrazones derived from oseltamivir intermediate, methyl 5-(pentan-3-yloxy)-7-oxabicyclo[4.1.0]hept-3-ene-3-carboxylate have been investigated for their potential as drug candidates against the COVID-19 virus using computational methods, including density functional theory (DFT) studies, molecular docking, and absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis...

AIM: Antibiotics treat various diseases by targeting microorganisms by killing them or reducing their multiplication rate. New Delhi Metallo-beta-lactamase-1 (NDM-1) is produced by bacteria possessing the resistance gene blaNDM-1, the enzyme that makes bacteria resistant to beta-lactams. Bacteriophages, especially Lactococcus, have shown their ability to break down lactams. Hence, the current study computationally evaluated the binding potential of Lactococcus bacteriophages with NDM using Molecular docking and dynamics...

Targeted delivery of therapeutic anticancer chimeric molecules enhances the efficacy of drug by improving cellular uptake and circulation time. Engineering the molecules to facilitate the specific interaction between chimeric protein and its receptor is critical to elucidate biological mechanism as well as accuracy in modeling of complexes. A theoretically designed novel protein-protein interfaces can serve as a bottom-up method for comprehensive understanding of interacting protein residues. This study was aimed for in silico analyses of a chimeric fusion protein against breast cancer...

The increasing commercialization of new gene panels based on next-generation sequencing for clinical research has significantly improved our understanding of breast cancer genetics and has led to the discovery of new mutation variants. The study included 16 unselected Moroccan breast cancer patients tested with multi-gene panel (HEVA screen panel) using Illumina Miseq, followed by Sanger sequencing to validate the most relevant mutation. Mutational analysis revealed the presence of 13 mutations (11 single-nucleotide polymorphisms [SNPs] and 2 indels), and 6 of 11 identified SNPs were predicted as pathogenic...

Reutealis trisperma belonging to the family Euphorbiaceae is currently used for biodiesel production, and rapid development in plant-based biofuel production has led to its increasing demand. However, massive utilization of bio-industrial plants has led to conservation issues. Moreover, genetic information on R trisperma is still limited, which is crucial for developmental, physiological, and molecular studies. Studying gene expression is essential to explain plant physiological processes. Nonetheless, this technique requires sensitive and precise measurement of messenger RNA (mRNA)...

Non-typhoidal Salmonella (NTS) infections occur globally with high morbidity and mortality. The public health challenge caused is exacerbated by increasing rate of antibiotic resistance and absence of NTS vaccine. In this study, we characterized the outer membrane protein C ( OmpC ) serovars isolated from different food animals and predicted antigenicity. ompC of 27 NTS serovars were amplified by polymerase chain reaction (PCR) and sequenced. Sequence data were analysed and B-cell epitope prediction was done by BepiPred tool...

Human papillomavirus 16 (HPV16) is considered to be strongly correlated with the development of cervical cancer. Among the 8 HPV16 genes, the E6 constitutes a remarkable marker to follow the evolutionary history and spatial phylodynamics of HPV16 in the Mediterranean basin. Thus, this work aims to decipher the major evolutionary events and crosstalks in the Mediterranean basin with a focus on Tunisian strains regarding the E6 oncogene. In this study, we first extracted the available and annotated Mediterranean strains of HPV16 E6 gene sequences (n = 155) from the NCBI nucleotide database...

Several genes influence sheep's reproductive performance, among them the paired-like homeodomain transcription factor 2 ( PITX2 ) gene. Thus, this study aimed to examine whether the variability within the PITX2 gene is associated with the reproductive performance of Awassi ewes. A total of 123 single-progeny ewes and 109 twin ewes were used to extract genomic DNA. An amplicon of 4 sequence fragments from exons 2, 4, 5 (upstream portion), and 5 (downstream portion) of the PITX2 gene was generated by polymerase chain reaction (PCR), 228, 304, 381, and 382 bp, respectively...

Multi-omic data mining has the potential to revolutionize synthetic biology especially in non-model organisms that have not been extensively studied. However, tangible engineering direction from computational analysis remains elusive due to the interpretability of large datasets and the difficulty in analysis for non-experts. New omics data are generated faster than our ability to use and analyse results effectively, resulting in strain development that proceeds through classic methods of trial-and-error without insight into complex cell dynamics...

One of the most valuable traits in production and breeding is a sheep's prolificacy which is influenced by several genes, one of which is the osteopontin ( OPN ) gene. Thus, this study aimed to determine the effect of genetic variation within the OPN gene on Awassi ewe prolificacy. Genomic DNA was extracted from 123 single-progeny ewes and 109 twin ewes. Polymerase chain reaction (PCR) was used to amplify 4 sequence fragments (289, 275, 338, and 372 bp), representing exons 4, 5, 6, and 7 of the OPN gene...

Drug-resistant tuberculosis (TB), which results mainly from the selection of naturally resistant strains of Mycobacterium tuberculosis (MTB) due to mismanaged treatment, poses a severe challenge to the global control of TB. Therefore, screening novel and unique drug targets against this pathogen is urgently needed. The metabolic pathways of Homo sapiens and MTB were compared using the Kyoto Encyclopedia of Genes and Genomes tool, and further, the proteins that are involved in the metabolic pathways of MTB were subtracted and proceeded to protein-protein interaction network analysis, subcellular localization, drug ability testing, and gene ontology...

Dihydrofolate reductase (DHFR) is a crucial enzyme that catalyzes the conversion of folic acid. Its reserved properties and significance in both human (h-DHFR) and mycobacterium (mt-DHFR) make it a challenging target for developing drugs against cancer and bacterial infections. Although methotrexate (MTX) is commonly used for cancer therapy and bacterial infections, it has a toxic profile. In this study, we aimed to identify selective and non-toxic inhibitors against h-DHFR and mt-DHFR using an in silico approach...

The Parkinson disease (PD) is the second most common neurodegenerative disorder affecting the central nervous system and motor functions. The biological complexity of PD is yet to reveal potential targets for intervention or to slow the disease severity. Therefore, this study aimed to compare the fidelity of blood to substantia nigra (SN) tissue gene expression from PD patients to provide a systematic approach to predict role of the key genes of PD pathobiology. Differentially expressed genes (DEGs) from multiple microarray data sets of PD blood and SN tissue from GEO database are identified...