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In Silico Analysis of the Dextransucrase Obtained From Leuconostoc mesenteroides Strain IBUN 91.2.98
Bioinform Biol Insights. 2023 Nov 28;17:11779322231212751. doi: 10.1177/11779322231212751. eCollection 2023.ABSTRACTThe DSR-IBUN dextransucrase produced by Leuconostoc mesenteroides strain IBUN 91.2.98 has a short production time (4.5 hours), an enzymatic activity of 24.8 U/mL, and a specific activity of purified enzyme 2 times higher (331.6 U/mg) than that reported for similar enzymes. The aim of this study was to generate a structural model that, from an in silico approach, allows a better understanding, from the structural point of view, of the activity obtained by the enzyme of interest, which is key to continue with i...
Source: Bioinformatics and Biology Insights - November 30, 2023 Category: Bioinformatics Authors: Luisa Alejandra Garc ía Galindo Martha Margarita Gonz ález Jairo Alonso Cer ón Salamanca Sonia Amparo Ospina S ánchez Source Type: research

A Systems Biology Approach for Investigating Significant Biomarkers and Drug Targets Common Among Patients with Gonorrhea, Chlamydia, and Prostate Cancer: A Pilot Study
In this study, we studied RNA-seq gene expression profiles using computational biology methods to find out potential biomarkers that could help us in understanding the patho-biological mechanisms of gonorrhea, chlamydia, and prostate cancer. Using statistical methods on the Gene Expression Omnibus (GEO) data sets, it was found that a total of 22 distinct differentially expressed genes were shared among these 3 diseases of which 14 were up-regulated (PGRMC1, TSC22D1, SH3BGRL, NNT, CTSC, FRMD3, CCR2, FAM210B, VCL, PTGS1, SLFN11, SLC40A1, PROS1, and DSE) and the remaining 8 genes were down-regulated (PRNP, HINT3, MARCKSL1, TM...
Source: Bioinformatics and Biology Insights - November 30, 2023 Category: Bioinformatics Authors: Abdulla Al Noman Md Kobirul Islam Tasmiah Feroz Md Monir Hossain Md Shahariar Kabir Shakil Source Type: research

A Comprehensive Bioinformatics Approach to Identify Molecular Signatures and Key Pathways for the Huntington Disease
This study combined bioinformatics analysis and network-based system biology approaches to discover the biomarker, pathways, and drug targets related to molecular mechanism of HD etiology. The gene expression profile data sets GSE64810 and GSE95343 were analyzed to predict the molecular markers in HD where 162 mutual differentially expressed genes (DEGs) were detected. Ten hub genes among them (DUSP1, NKX2-5, GLI1, KLF4, SCNN1B, NPHS1, SGK2, PITX2, S100A4, and MSX1) were identified from protein-protein interaction (PPI) network which were mostly expressed as down-regulated. Following that, transcription factors (TFs)-DEGs ...
Source: Bioinformatics and Biology Insights - November 30, 2023 Category: Bioinformatics Authors: Tahera Mahnaz Meem Umama Khan Md Bazlur Rahman Mredul Md Abdul Awal Md Habibur Rahman Md Salauddin Khan Source Type: research

 In Silico Identification of Natural Food Compounds as Potential Quorum-Sensing Inhibitors Targeting the LasR Receptor of Pseudomonas aeruginosa 
In this study, we performed a structure-based virtual screening of a natural food database of 10 997 compounds against the crystal structure of the ligand-binding domain of the LasR receptor (PDB ID: 3IX4). This allowed us to identify four molecules, namely ZINC000001580795, ZINC000014819517, ZINC000014708292, and ZINC000004098719, that exhibited a favorable binding mode and docking scores greater than -13 kcal/mol. Furthermore, the molecular dynamics simulation showed that these four molecules formed stable complexes with LasR during the 150-ns molecular dynamics (MD) simulation, indicating their potential for use as inhi...
Source: Bioinformatics and Biology Insights - November 29, 2023 Category: Bioinformatics Authors: Meryam Magri El Mehdi Bouricha Mohammed Hakmi Rachid El Jaoudi Lahcen Belyamani Azeddine Ibrahimi Source Type: research

Integrated Transcriptomics and Network Analysis of Potential Mechanisms and Health Effects of Convalescent COVID-19 Patients
In this study, we aimed to explore the molecular mechanism, disease association, and possible health risks in convalescent COVID-19 patients. Gene expression data from a human convalescent COVID-19 data set was compared with a data set from healthy normal individuals in order to identify differentially expressed genes (DEGs). To determine biological function and potential pathway alterations, the GO and KEGG databases were used to analyze the DEGs. Disease association, tissue, and organ-specific analyses were used to identify possible health effects. A total of 250 DEGs were identified between healthy and convalescent COVI...
Source: Bioinformatics and Biology Insights - October 26, 2023 Category: Bioinformatics Authors: Suthipong Chujan Watanyoo Nakareangrit Tawit Suriyo Jutamaad Satayavivad Source Type: research