Bioinformatics and Biology Insights最新文献

{"title":"Potential Biomarkers for Parkinson Disease from Functional Enrichment and Bioinformatic Analysis of Global Gene Expression Patterns of Blood and Substantia Nigra Tissues.","authors":"Ramu Elango,&nbsp;Babajan Banaganapalli,&nbsp;Abdulrahman Mujalli,&nbsp;Nuha AlRayes,&nbsp;Sarah Almaghrabi,&nbsp;Majid Almansouri,&nbsp;Ahmed Sahly,&nbsp;Gada Ali Jadkarim,&nbsp;Md Zubbair Malik,&nbsp;Hussam Ibrahim Kutbi,&nbsp;Noor Ahmad Shaik,&nbsp;Eman Alefishat","doi":"10.1177/11779322231166214","DOIUrl":"https://doi.org/10.1177/11779322231166214","url":null,"abstract":"<p><p>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. Using the theoretical network approach and variety of bioinformatic tools, we prioritized the key genes from DEGs. A total of 540 and 1024 DEGs were identified in blood and SN tissue samples, respectively. Functional pathways closely related to PD such as ERK1 and ERK2 cascades, mitogen-activated protein kinase (MAPK) signaling, Wnt, nuclear factor-κB (NF-κB), and PI3K-Akt signaling were observed by enrichment analysis. Expression patterns of 13 DEGs were similar in both blood and SN tissues. Comprehensive network topological analysis and gene regulatory networks identified additional 10 DEGs functionally connected with molecular mechanisms of PD through the mammalian target of rapamycin (mTOR), autophagy, and AMP-activated protein kinase (AMPK) signaling pathways. Potential drug molecules were identified by chemical-protein network and drug prediction analysis. These potential candidates can be further validated in vitro/in vivo to be used as biomarkers and/or novel drug targets for the PD pathology and/or to arrest or delay the neurodegeneration over the years, respectively.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231166214"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/59/b3/10.1177_11779322231166214.PMC10155030.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10289663","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Association of Novel C319T Variant of <i>PITX2</i> Gene 3'UTR Region With Reproductive Performance in Awassi Sheep.","authors":"Ahmed H Alkhammas,&nbsp;Tahreer M Al-Thuwaini,&nbsp;Mohammed Baqur S Al-Shuhaib,&nbsp;Neam M Khazaal","doi":"10.1177/11779322231179018","DOIUrl":"https://doi.org/10.1177/11779322231179018","url":null,"abstract":"<p><p>Several genes influence sheep's reproductive performance, among them the paired-like homeodomain transcription factor 2 (<i>PITX2</i>) gene. Thus, this study aimed to examine whether the variability within the <i>PITX2</i> 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 <i>PITX2</i> gene was generated by polymerase chain reaction (PCR), 228, 304, 381, and 382 bp, respectively. Three genotypes of 382 bp amplicons were identified: CC, CT, and TT. Sequence analysis revealed a novel mutation in the CT genotype 319C > T. Statistical analysis revealed that single-nucleotide polymorphism (SNP) 319C > T was associated with reproductive performance. Single-nucleotide polymorphism 319C > T-carrying ewes had significantly (<i>P</i> ⩽ .01) lower litter sizes, twinning rates, lambing rates, and more days to lambing than those carrying CT and CC genotypes. Based on a logistic regression analysis, it was confirmed that the 319C > T SNP decreased litter size. Ewes with TT genotype produced fewer lambs than ewes with CT and CC genotypes. According to these results, the variant 319C> T SNP negatively affects the reproductive performance of Awassi sheep. Ewes carrying the 319C > T SNP have a lower litter size and are less prolific than those without the SNP.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231179018"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/a1/43/10.1177_11779322231179018.PMC10259137.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9988197","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Indigenous Oral and Gut Phages Defeat the Deadly NDM-1 Superbug.","authors":"Pradeep Kumar Yadalam,&nbsp;Raghavendra Vamsi Anegundi,&nbsp;Ramya Ramadoss,&nbsp;M Saravanan,&nbsp;AshokKumar Veeramuthu,&nbsp;Artak Heboyan","doi":"10.1177/11779322231182767","DOIUrl":"https://doi.org/10.1177/11779322231182767","url":null,"abstract":"<p><strong>Aim: </strong>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.</p><p><strong>Methods: </strong>Modelling of NDM I-TASSER for Main tail protein gp19 OS=Lactococcus phage LL-H or Lactobacillus delbrueckii subsp. lactis after downloading from UNIPROT ID- Q38344. Cluspro tool helps in Understanding cellular function and organization with protein-protein interactions. MD simulations(19) typically compute atom movements over time. Simulations were used to predict the ligand binding status in the physiological environment.</p><p><strong>Results: </strong>The best binding affinity score was found -1040.6 Kcal/mol compared to other docking scores. MD simulations show in RMSD values for target remains within 1.0 Angstrom, which is acceptable. The ligand-protein fit to receptor protein RMSD values of 2.752 fluctuates within 1.5 Angstrom after equilibration.</p><p><strong>Conclusions: </strong>Lactococcus bacteriophages showed a strong affinity to the NDM. Hence, this hypothesis, supported by evidence from a computational approach, will solve this life-threatening superbug problem.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231182767"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/14/aa/10.1177_11779322231182767.PMC10291530.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9729772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Novel Inhibitor of DKK1/LRP6 Interactions Against the Alzheimer Disease: An Insilco Approach.","authors":"Manisha Prajapat,&nbsp;Harvinder Singh,&nbsp;Gajendra Chaudhary,&nbsp;Phulen Sarma,&nbsp;Gurjeet Kaur,&nbsp;Ajay Prakash Patel,&nbsp;Bikash Medhi","doi":"10.1177/11779322231183762","DOIUrl":"https://doi.org/10.1177/11779322231183762","url":null,"abstract":"<p><p>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 aim of this study was to use in silico approach to develop new agents that can combat the Alzheimer disease by targeting the interaction between DKK1 and LRP6. To achieve this, we conducted a virtual screening (Vsw) of the Asinex-CNS database library (n = 54 513) compounds against a generated grid in LRP6 protein. From this screening, we selected 6 compounds based on their docking score and performed molecular mechanics-generalized Born surface area (MM-GBSA) binding energy calculations on the selected ligands. Next, we evaluated the Absorption, Distribution, Metabolism, and Excretion (ADME) results of the 6 screened compounds using the Quick prop module of Schrödinger. We then employed several computational techniques, including PCA (Principal Component Analysis), DCCM (Dynamic Cross-Correlation Map), molecular dynamics simulation, and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA)-based negative binding free energy (BFE) calculation, to further analyze the compounds. Our extensive computational analysis resulted in the identification of 3 potential hits, LAS 29757582, LAS 29984441, and LAS 29757942. These compounds were found to block the interaction of DKK1 with LRP6 (A and B interface) protein, and their potential as therapeutic agents was supported by negative BFE calculation. Therefore, these compounds show potential as possible therapeutic agents for treating the Alzheimer disease through targeting the interaction between DKK1 and LRP6.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231183762"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/b4/e3/10.1177_11779322231183762.PMC10328054.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9799561","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"MicroRNAs Regulate Tumorigenesis by Downregulating SOCS3 Expression: An <i>In silico</i> Approach.","authors":"Sura Al-Asadi,&nbsp;Hiba Mansour,&nbsp;Ahmed Jwaid Ataimish,&nbsp;Rusul Al-Kahachi,&nbsp;Jamila Rampurawala","doi":"10.1177/11779322231193535","DOIUrl":"https://doi.org/10.1177/11779322231193535","url":null,"abstract":"<p><p>Tumor microenvironment is characterized by the occurrence of significant changes due to disrupted signaling pathways that affect a broad spectrum of cellular activities such as proliferation, differentiation, signaling, invasiveness, migration, and apoptosis. Similarly, a downregulated suppressor of cytokine signaling 3 (SOCS3) promotes increased JAK/STAT function due to aberrant cytokine signaling, which results in increased cell proliferation, differentiation, and migration. Multiple carcinomas including breast cancer, prostate cancer, hepatocellular carcinoma, pancreatic cancer, and colorectal cancer involve the disruption of SOCS3 expression due to microRNA overexpression. MicroRNAs are small, conserved, and non-coding RNA molecules that regulate gene expression through post-transcriptional inhibition and mRNA destabilization. The aim of this study was to identify putative microRNAs that interact with SOCS3 and downregulate its expression. In this study, miRWalk, TargetScan, and miRDB were used to identify microRNAs that interact with SOCS3, whereas RNA22 was utilized to identify the binding sites of 238 significant microRNAs. The tertiary structures of shortlisted microRNAs and SOCS3 regions were predicted through MC Sym and RNAComposer, respectively. For molecular docking, HDOCK was used, which predicted 80 microRNA-messengerRNA complexes and the interactions of the top 5 shortlisted complexes were assessed. The complexes were shortlisted on the basis of least binding affinity score and maximum confidence score. This study identifies the interactions of known (miR-203a-5p) and novel (miR-6756-5p, miR-6732-5p, miR-1203, miR-6887-5p) microRNAs with SOCS3 regions due to their maximum interactions. Identifying the interactions of these microRNAs with SOCS3 will significantly advance the understanding of oncomiRs (miRNAs that are associated with cancer development) in tumor development due to their influence on SOCS3 expression. These insights will assist in future studies to understand the significance of miRNA-SOCS3-associated tumor development and progression.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231193535"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/1d/a0/10.1177_11779322231193535.PMC10493049.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10295523","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics Analysis to Uncover the Potential Drug Targets Responsible for <i>Mycobacterium tuberculosis</i> Peptidoglycan and Lysine Biosynthesis.","authors":"Dian Ayu Eka Pitaloka,&nbsp;Afifah Izzati,&nbsp;Siti Rafa Amirah,&nbsp;Luqman Abdan Syakuran,&nbsp;Lalu Muhammad Irham,&nbsp;Athika Darumas Putri,&nbsp;Wirawan Adikusuma","doi":"10.1177/11779322231171774","DOIUrl":"https://doi.org/10.1177/11779322231171774","url":null,"abstract":"<p><p>Drug-resistant tuberculosis (TB), which results mainly from the selection of naturally resistant strains of <i>Mycobacterium tuberculosis</i> (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 <i>Homo sapiens</i> 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. The study aims to identify enzymes for the unique pathways for further screening to determine the feasibility of the therapeutic targets. The qualitative characteristics of 28 proteins identified as drug target candidates were studied. The results showed that 12 were cytoplasmic, 2 were extracellular, 12 were transmembrane, and 3 were unknown. Furthermore, druggability analysis revealed 14 druggable proteins, of which 12 were novel and responsible for MTB peptidoglycan and lysine biosynthesis. The novel targets obtained in this study are used to develop antimicrobial treatments against pathogenic bacteria. Future studies should further shed light on the clinical implementation to identify antimicrobial therapies against MTB.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231171774"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/d1/13/10.1177_11779322231171774.PMC10176782.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10299669","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pyridine Derivatives as Potential Inhibitors for Coronavirus SARS-CoV-2: A Molecular Docking Study.","authors":"Kamaraj Karthick,&nbsp;Kalaiyar Swarnalatha","doi":"10.1177/11779322221146651","DOIUrl":"https://doi.org/10.1177/11779322221146651","url":null,"abstract":"<p><p>Coronavirus SARS-CoV-2, a causative agent for the global epidemic disease COVID-19, which has a highest modality rate. Several initiatives have been undertaken to repurpose current antiviral medications and tested the classic pyridine derivatives (PyDev), which have showed substantial therapeutic potential against a variety of illnesses and also have several biological functions such as, antibacterial, antiviral, and anti-inflammatory. However, limited reports are available for the treatment of Coronavirus SARS-CoV-2 using PyDev. Hence, the possibilities of the best-described PyDev molecules of powerful Coronavirus SARS-CoV-2 inhibitors have been attempted in this investigation. This study primarily focused on blocking four key targets of Coronavirus SARS-CoV-2 proteins. Terpyridine has shown the greatest inhibitory potential (with a binding energy of -8.8 kcal/mol) against all four coronavirus targets. This study results would pave the potential lead medication for Coronavirus SARS-CoV-2 therapeutic strategies.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322221146651"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/04/d9/10.1177_11779322221146651.PMC10076986.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9289132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In Silico Characterization of the Physicochemical and Biological Properties of the Pink (<i>Pleurotus djamor</i> var. <i>salmoneostramineus</i>) Oyster Mushroom Chromoprotein.","authors":"Mónica A Valdez-Solana,&nbsp;Erica K Ventura-García,&nbsp;Iván A Corral-Guerrero,&nbsp;Atahualpa Guzmán de Casa,&nbsp;Claudia Avitia-Domínguez,&nbsp;Alfredo Téllez-Valencia,&nbsp;Erick Sierra-Campos","doi":"10.1177/11779322231154139","DOIUrl":"https://doi.org/10.1177/11779322231154139","url":null,"abstract":"<p><p>Cap color is an important commercial trait for oyster mushrooms. Various pigment constituents determine a diverse color. However, the pigments of oyster mushrooms are still ambiguous. The pink oyster mushroom (<i>Pleurotus salmoneostramineus</i> or <i>Pleurotus djamor</i>) chromoprotein is one of the few proteins belonging to this fungus that has a record of its sequence of amino acid residues. However, even though there are studies about this chromoprotein isolation, purification, and crystallization, the current information focused on its 3-dimensional model and the cofactor and prosthetic group (3H-indol-3-one) binding sites is unreliable and fragmented. Therefore, in this study, using free online servers such as Prot pi, GalaxyWEB, MIB, and CB-Dock2, a structural analysis and the prediction of its physicochemical and biological properties were conducted, to understand the possible function of this chromoprotein. The obtained results showed that this molecule is a protein with a molecular weight of 23 712.5 Da, an isoelectric point of 7.505, with oligomerization capacity in a dimer and glycation in the Ser6 residue. In addition, the participation of the residues Leu5, Leu8, Lys211, Ala214, and Gln215 in the binding of the prosthetic group to the protein was highlighted; as well as Ser6 and Pro7 are important residues for the interaction of the Mg²⁺ ion and eumelanin. Likewise, morphological changes based on different culture conditions (light/dark) showed that this protein is constitutive expressed and independent of blue light. The findings in this study demonstrate that pink chromoprotein is a melanosomal protein, and it possibly has a critical role in melanogenesis and the melanin polymerization. However, more experimental studies are needed to predict a possible mechanism of action and type of enzymatic activity.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231154139"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/0f/ea/10.1177_11779322231154139.PMC9912552.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10707878","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Potential Inhibitory Biomolecular Interactions of Natural Compounds With Different Molecular Targets of Diabetes.","authors":"Precious A Akinnusi,&nbsp;Samuel O Olubode,&nbsp;Adebowale A Alade,&nbsp;Aderemi A Ashimi,&nbsp;Olamide L Onawola,&nbsp;Abigail O Agbolade,&nbsp;Adaobi P Emeka,&nbsp;Sidiqat A Shodehinde,&nbsp;Olawole Y Adeniran","doi":"10.1177/11779322231167970","DOIUrl":"https://doi.org/10.1177/11779322231167970","url":null,"abstract":"<p><p>Type II diabetes is an endemic disease and is responsible for approximately 90% to 95% of diabetes cases. The pathophysiological distortions are majorly β-cell dysfunction, insulin resistance, and long-term inflammation, which all progressively unsettle the control of blood glucose levels and trigger microvascular and macrovascular complications. The diverse pathological disruptions which patients with type II diabetes mellitus exhibit precipitate the opinion that different antidiabetic agents, administered in combination, might be required to curb this menace and maintain normal blood glucose. To this end, natural compounds were screened to identify small molecular weight compounds with inhibitory effects on protein tyrosine phosphatase 1B (PTP1B), dipeptidyl-peptidase-4 (DPP-4), and α-amylase. From the result, the top 5 anthocyanins with the highest binding affinity are reported herein. Further ADMET profiling showed moderate pharmacokinetic profiles for these compounds as well as insignificant toxicity. Cyanidin 3-(p-coumaroyl)-diglucoside-5-glucoside (-15.272 kcal/mol), cyanidin 3-O-(6\"-malonyl-3\"-glucosyl-glucoside) (-9.691 kcal/mol), and delphinidin 3,5-O-diglucoside (-12.36 kcal/mol) had the highest binding affinities to PTP1B, DPP-4, and α-amylase, respectively, and can be used in combination to control glucose fluctuations. However, validations must be carried out through further <i>in vitro</i> and <i>in vivo</i> tests.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231167970"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/e2/f6/10.1177_11779322231167970.PMC10134171.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9392846","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"miR-6087 Might Regulate Cell Cycle-Related mRNAs During Cardiomyogenesis of hESCs.","authors":"Hellen Cristine Machado,&nbsp;Saloe Bispo,&nbsp;Bruno Dallagiovanna","doi":"10.1177/11779322231161918","DOIUrl":"https://doi.org/10.1177/11779322231161918","url":null,"abstract":"MicroRNAs (miRNAs) are small noncoding RNAs that act as negative regulators of gene expression at the post-transcriptional level, promoting mRNA degradation or translation repression. Despite the well-described presence of miRNAs in various human tissues, there is still a lack of information about the relationship between miRNAs and the translation regulation in human embryonic stem cells (hESCs) during cardiomyogenesis. Here, we investigate RNA-seq data from hESCs, focusing on distinct stages of cardiomyogenesis and searching for polysome-bound miRNAs that could be involved in translational regulation. We identify miR-6087 as a differentially expressed miRNA at latest steps of cardiomyocyte differentiation. We analyzed the coexpression pattern between the differentially expressed mRNAs and miR-6087, evaluating whether they are predicted targets of the miRNA. We arranged the genes into an interaction network and identified BLM, RFC4, RFC3, and CCNA2 as key genes of the network. A post hoc analysis of the key genes suggests that miR-6087 could act as a regulator of the cell cycle in hESC during cardiomyogenesis.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"17 ","pages":"11779322231161918"},"PeriodicalIF":5.8,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/c7/ab/10.1177_11779322231161918.PMC10069004.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9612101","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}