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Functional Enrichment Analysis of Tumor Microenvironment-Driven Molecular Alterations That Facilitate Epithelial-to-Mesenchymal Transition and Distant Metastasis
This study investigated the molecular differences between tumor border cells and tumor core cells or internal tumor cells in HCC for specific EMT genes. Expression of NOTCH1, ID1, and LST1 genes showed a significant increase at the HCC tumor border. Targeting these genes can be considered as a useful therapeutic strategy to prevent distant metastasis in HCC patients.PMID:38318286 | PMC:PMC10840405 | DOI:10.1177/11779322241227722 (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - February 6, 2024 Category: Bioinformatics Authors: Mahnaz Abdolahi Parnian Ghaedi Talkhounche Mohammad Hossein Derakhshan Nazari Haniyeh Sadat Hosseininia Niloofar Khoshdel-Rad Amin Ebrahimi Sadrabadi Source Type: research

Evaluation of the Antidiabetic Activities of the Fruit of Parquetina nigrescens (Afzel.) Bullock and In Silico Identification of Its Antidiabetic Agent
Bioinform Biol Insights. 2024 Jan 26;18:11779322231223857. doi: 10.1177/11779322231223857. eCollection 2024.ABSTRACTThe study investigated the antidiabetic potentials of the fruit extract of Parquetina nigrescens with the aim of justifying its folkloric antidiabetic usage in some part of Nigeria. Acute toxicity test of the plant extract was assessed using Lorke's method. Its antidiabetic activities were assayed in α-amylase, α-glucosidase, glucose, and streptozotocin-induced diabetic rats' models at various doses with acarbose and glibenclamide (5 mg/kg) as positive controls. Molecular docking studies were performed to i...
Source: Bioinformatics and Biology Insights - January 29, 2024 Category: Bioinformatics Authors: Marcus D Ayoola Yetunde B Ogundeko Temiloluwa D Obanleowo Deborah O Omole Blessing N Chukwu Kolade O Faloye Source Type: research

Revealing Propolis Potential Activity on Inhibiting Estrogen Receptor and Heat Shock Protein 90 Overexpressed in Breast Cancer by Bioinformatics Approaches
This study revealed the positive correlation between ERα and HSP90 genes in breast cancer disease development. Furthermore, we also found novel potential bioactive compounds of propolis against breast cancer through binding with ERα and HSP90; they were 3',4',7-trihydroxyisoflavone and baicalein-7-O-β-D glucopyranoside, respectively. Further research on these compounds is needed to elucidate deeper mechanisms and activity in the real biological system to develop new breast cancer drug treatments.PMID:38274992 | PMC:PMC10809879 | DOI:10.1177/11779322231224187 (Source: Bioinformatics and Biology Insights)
Source: Bioinformatics and Biology Insights - January 26, 2024 Category: Bioinformatics Authors: Masriana Vivi Simanjuntak Muhammad Miftah Jauhar Putri Hawa Syaifie Adzani Gaisani Arda Etik Mardliyati Wervyan Shalannanda Beni Rio Hermanto Isa Anshori Source Type: research

Neomangiferin, a Naturally Occurring Mangiferin Congener, Inhibits Sodium-Glucose Co-transporter-2: An In silico Approach
This study sought to investigate the inhibitory property of naturally occurring mangiferin congeners on sodium-glucose co-transporter 2 protein (SGLT-2) using comprehensive computational methods. The naturally occurring mangiferin congeners were subjected to molecular docking, molecular dynamics (MDs) simulation (100 ns), molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) binding free energy, density functional theory calculations (B3LYP 6-31G basis set), and ADMET approaches to identify potential SGLT-2 inhibitor. The molecular docking studies revealed neomangiferin (-9.0 kcal/mol) as the hit molecule compared w...
Source: Bioinformatics and Biology Insights - January 22, 2024 Category: Bioinformatics Authors: Ayobami J Olusola Samson O Famuyiwa Kolade O Faloye Oluwaseun E Olatunji Uduak I Olayemi Abiodun A Adeyemi John O Balogun Seun B Ogundele Blessing O Babamuyiwa Rajesh B Patil Source Type: research

Phylogenetic Characterization of Resistant Salmonella Strains in Typhoid Fever Patients in Nigeria
In this study, the distribution of broad-spectrum β-lactamase regulatory genes and genetic relatedness of isolates was determined. Stool samples (400) were collected from patients with fever in Dalhatu Araf Specialist Hospital (DASH), Lafia, Nigeria, between March 2020 and April 2021. Salmonella species were isolated and extended-spectrum β-lactamase distribution was determined among resistant isolates using polymerase chain reaction (PCR). Genetic relatedness of Salmonella species resistant to the 10 first-line antibiotics administered was determined among S typhi isolated. Of the 60 isolates that were confirmed to belo...
Source: Bioinformatics and Biology Insights - January 12, 2024 Category: Bioinformatics Authors: Olukayode Olugbenga Orole Jebes Ngolo Lamini Aleruchi Chuku 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 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