A GLOBAL COMPARISON AND ANALYSIS OF NEURAMINIDASE H1N1 STRAIN OF INFLUENZA A

Objective: To evaluate the variation of neuraminidase (NA) protein from various H1N1 strain for drug designing.Methods: In this study we have used 12 sequences of NA protein from various countries, retrieved from UniprotKB database. We have performed structural analysis, antigenic and glycosylation site prediction between NA proteins of influenza A strains.Results: Antigenic variants in sequence of NA H1N1 strain from Italy were found to be unique and were not present in any other NA H1N1. Strains from Italy and Thailand were found to be distantly related while others are closely related. We observed the maximum similarity from position 84 to 448 using disorder prediction analysis of different strains. Sequences from 1 to 83 and 449 to 469 showed the maximum dissimilarity among the NA Proteins.Conclusion: This study focuses on the regions of sequence similarity and dissimilarity of NA in H1N1 strains from different countries. The results in this paper are based on currently available sequences for NA of H1N1 strains and bioinformatic tools. Our study will help in understanding of the regions of high variability due to mutations and conserved domains that can be potential targets for drug development

DUCTAL CARCINOMA IN SITU AND INVASIVE BREAST CANCER-BASED DIFFERENTIAL GENE EXPRESSION STUDY FOR THERAPEUTIC DEVELOPMENT

ABSTRACTObjective: Breast cancer is the second most common cancer in women globally. Multiple inherited mutations in genes are predominantly associatedwith breast cancer. The gene expression profiling of breast tumors generated by DNA microarray analysis provides molecular phenotyping thatdetermines and characterizes the classifications of these tumors.Methods: In this work, we used gene expression profiling of breast cancer samples from Gene Expression Omnibus (GEO) database. The datasetGSE41194, retrieved from GEO, was used to investigate differential gene expression in ductal carcinoma in situ (DCIS) and invasive breast cancer (IBC).The dataset contains 26 DCIS and 24 IBC samples. The data were analyzed in R and Bioconductor. To normalize the data Robust Multiarray Average(RMA) method was applied, limma software was used to identify the differentially expressed genes (DEGs) in DCIS and IBC; an adjusted p value ≤0.05was used to filter differentially expressed probe sets, and a fold change (FC) ≥ 2 to identify upregulated and ≤−2 for downregulated genes. The DEGsretrieved were clustered and annotated using Database for Annotation, Visualization and Integrated Discovery (DAVID) Bioinformatics Resourceswith an EASE score ≤0.1 and count 2.Results: The analysis obtained 72 DEGs with a p≤0.05. The FC≥2 identified 38 upregulated probesets and FC≤−2 identified 34 downregulated probesets. The up and downregulated genes obtained in various comparisons were characterized based on gene ontology (GO) and pathway analyses inDAVID, which retrieved six genes that had principal pathways targeting breast cancer.Conclusion: Identification of these genes and pathways enhances the knowledge and progression of DCIS to IBC; paving a novel way for developingnew therapies for treating patients with breast cancer.Keywords: Molecular phenotyping, Gene Expression, Ductal carcinoma in situ, Invasive breast cancer

Knockdown of CD-74 in the Proliferative and Apoptotic Activity of Breast Cancer Cells.

BACKGROUND:The cluster of differentiation (CD) 74 is known for its immunological functions and its elevated level was reported in various cancer cells. AIM:The aim of the present study was to investigate the expression and potential roles of CD74 in the proliferative and apoptotic activity of breast cancer. METHODS:Expression of CD74, macrophage migration inhibitory factor (MIF) and CD44 was assayed in CAMA-1 and MDA-MB-231 cell lines using flow cytometry. CD74 was knocked down using CD74 siRNA-transfection in CAMA-1, and MDA-MB-231 cells and proliferation and apoptosis were determined in the transfected breast cancer cells. RESULTS:The data showed that CD74, MIF and CD44 were expressed in breast cancer cell lines and were associated with cell proliferation and apoptosis. Correlation analysis revealed that CD74 was positively correlated and colocalised with MIF on the cell-surface of CAMA-1 and MDA-MB-231. The knockdown of CD74 significantly reduced CAMA-1 and MDA-MB-231 cell proliferation and increased the level of apoptotic cells. CONCLUSION:We concluded that the interactions of CD74 with MIF and CD74 with CD44 could be a potential tumour marker for breast cancer cells. Moreover, the level of co-expression of MIF and CD74 or CD44 could be a surrogate marker for the efficacy of anti-angiogenic drugs, particularly in breast cancer tumours. In short, the study revealed the potential roles of CD74 in the proliferation and apoptosis of breast cancer which may serve as a potential therapeutic target for breast cancer

In Vitro and In Silico Screening and Characterization of Antimicrobial Napin Bioactive Protein in Brassica juncea and Moringa oleifera

The study aimed to investigate the antibacterial activity of Mustard (Brassica juncea) and Moringa (Moringa oleifera) leaf extracts and coagulant protein for their potential application in water treatment. Bacterial cell aggregation and growth kinetics studies were employed for thirteen bacterial strains with different concentrations of leaf extracts and coagulant protein. Moringa oleifera leaf extract (MOS) and coagulant protein showed cell aggregation against ten bacterial strains, whereas leaf extract alone showed growth inhibition of five bacterial strains for up to 6 h and five bacterial strains for up to 3 h. Brassica juncea leaf extract (BJS) showed growth inhibition for up to 6 h, and three bacterial strains showed inhibition for up to 3 h. The highest inhibition concentration with 2.5 mg/mL was 19 mm, and furthermore, the minimum inhibitory concentration (MIC) (0.5 mg/mL) and MBC (1.5 mg/mL) were determined to have a higher antibacterial effect for <3 KDa peptides. Based on LCMS analysis, napin was identified in both MOS and BJS; furthermore, the mode of action of napin peptide was determined on lipoprotein X complex (LpxC) and four-chained structured binding protein of bacterial type II topoisomerase (4PLB). The docking analysis has exhibited moderate to potent inhibition with a range of dock score −912.9 Kcal/mol. Thus, it possesses antibacterial-coagulant potential bioactive peptides present in the Moringa oleifera purified protein (MOP) and Brassica juncea purified protein (BJP) that could act as an effective antimicrobial agent to replace currently available antibiotics. The result implies that MOP and Brassica juncea purified coagulant (BJP) proteins may perform a wide degree of antibacterial functions against different pathogens

Multiplexed Post-Experimental Monoisotopic Mass Refinement (<i>m</i>PE-MMR) to Increase Sensitivity and Accuracy in Peptide Identifications from Tandem Mass Spectra of Cofragmentation

Mass spectrometry (MS)-based proteomics, which uses high-resolution hybrid mass spectrometers such as the quadrupole-orbitrap mass spectrometer, can yield tens of thousands of tandem mass (MS/MS) spectra of high resolution during a routine bottom-up experiment. Despite being a fundamental and key step in MS-based proteomics, the accurate determination and assignment of precursor monoisotopic masses to the MS/MS spectra remains difficult. The difficulties stem from imperfect isotopic envelopes of precursor ions, inaccurate charge states for precursor ions, and cofragmentation. We describe a composite method of utilizing MS data to assign accurate monoisotopic masses to MS/MS spectra, including those subject to cofragmentation. The method, “multiplexed post-experiment monoisotopic mass refinement” (<i>m</i>PE-MMR), consists of the following: multiplexing of precursor masses to assign multiple monoisotopic masses of cofragmented peptides to the corresponding multiplexed MS/MS spectra, multiplexing of charge states to assign correct charges to the precursor ions of MS/MS spectra with no charge information, and mass correction for inaccurate monoisotopic peak picking. When combined with MS-GF+, a database search algorithm based on fragment mass difference, <i>m</i>PE-MMR effectively increases both sensitivity and accuracy in peptide identification from complex high-throughput proteomics data compared to conventional methods

Proteogenomic landscape of human pancreatic ductal adenocarcinoma in an Asian population reveals tumor cell-enriched and immune-rich subtypes

We report a proteogenomic analysis of pancreatic ductal adenocarcinoma (PDAC). Mutation–phosphorylation correlations identified signaling pathways associated with somatic mutations in significantly mutated genes. Messenger RNA–protein abundance correlations revealed potential prognostic biomarkers correlated with patient survival. Integrated clustering of mRNA, protein and phosphorylation data identified six PDAC subtypes. Cellular pathways represented by mRNA and protein signatures, defining the subtypes and compositions of cell types in the subtypes, characterized them as classical progenitor (TS1), squamous (TS2–4), immunogenic progenitor (IS1) and exocrine-like (IS2) subtypes. Compared with the mRNA data, protein and phosphorylation data further classified the squamous subtypes into activated stroma-enriched (TS2), invasive (TS3) and invasive-proliferative (TS4) squamous subtypes. Orthotopic mouse PDAC models revealed a higher number of pro-tumorigenic immune cells in TS4, inhibiting T cell proliferation. Our proteogenomic analysis provides significantly mutated genes/biomarkers, cellular pathways and cell types as potential therapeutic targets to improve stratification of patients with PDAC. © 2022, The Author(s), under exclusive licence to Springer Nature America, Inc.FALS