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Phenazine Scaffolds as a Potential Allosteric Inhibitor of LasR Protein in Pseudomonas aeruginosa. 非那嗪支架作为铜绿假单胞菌LasR蛋白的潜在变构抑制剂。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2025-02-20 eCollection Date: 2025-01-01 DOI: 10.1177/11779322251319594
Prisca Baah Nketia, Prince Manu, Priscilla Osei-Poku, Alexander Kwarteng
{"title":"Phenazine Scaffolds as a Potential Allosteric Inhibitor of LasR Protein in <i>Pseudomonas aeruginosa</i>.","authors":"Prisca Baah Nketia, Prince Manu, Priscilla Osei-Poku, Alexander Kwarteng","doi":"10.1177/11779322251319594","DOIUrl":"10.1177/11779322251319594","url":null,"abstract":"<p><p>Millions of individuals suffer from chronic infections caused by bacterial biofilms, resulting in significant loss of life. <i>Pseudomonas aeruginosa</i> stands out as a major culprit in causing such chronic infections, largely due to its antibiotic resistance. This pathogen poses a considerable threat in healthcare settings, particularly to critically ill and immunocompromised patients. The persistence of chronic and recurrent bacterial infections is often attributed to bacterial biofilms. Therefore, there is an urgent need to discover novel small molecules capable of efficiently eliminating biofilms independent of bacterial growth. In this project, an <i>in silico</i> drug discovery approach was employed to identify nine halogenated-phenazine compounds as allosteric inhibitors of the LasR protein. The LasR is a key transcription factor that triggers other quorum-sensing systems and plays a crucial role in biofilm formation and activation of virulence genes. By inhibiting LasR, specifically targeting its allosteric site, the dimerization of LasR and subsequent biofilm formation could be prevented. Molecular docking and simulations, coupled with binding energy calculations, identified five compounds with potential as anti-biofilm agents. These compounds exhibited higher binding affinities to the distal site, suggesting their structural capability to interact with allosteric site residues of the LasR protein. Based on these findings, it is proposed that these compounds could serve as promising leads for the treatment of biofilm and quorum-sensing-related infections.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251319594"},"PeriodicalIF":2.3,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11843726/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143482212","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}
引用次数: 0
In Silico Analysis and Characterization of the Immunogenicity of Toxoplasma gondii Rhoptry Protein 18. 刚地弓形虫虫体蛋白18免疫原性的计算机分析与表征。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2025-02-07 eCollection Date: 2025-01-01 DOI: 10.1177/11779322251315924
Masoud Foroutan, Amir Karimipour-Saryazdi, Ali Dalir Ghaffari, Hamidreza Majidiani, Arezo Arzani Birgani, Elaheh Karimzadeh-Soureshjani, Shahrzad Soltani, Hany M Elsheikha
{"title":"<i>In Silico</i> Analysis and Characterization of the Immunogenicity of <i>Toxoplasma gondii</i> Rhoptry Protein 18.","authors":"Masoud Foroutan, Amir Karimipour-Saryazdi, Ali Dalir Ghaffari, Hamidreza Majidiani, Arezo Arzani Birgani, Elaheh Karimzadeh-Soureshjani, Shahrzad Soltani, Hany M Elsheikha","doi":"10.1177/11779322251315924","DOIUrl":"10.1177/11779322251315924","url":null,"abstract":"<p><p>Rhoptry protein 18 (ROP18) is a key virulence factor secreted into host cells during the invasion of <i>Toxoplasma gondii</i> (<i>T. gondii</i>) and plays an important role in the pathogenesis of infection. Due to its potential as a vaccine candidate, this study aimed to characterize several properties of the <i>T. gondii</i> ROP18 (TgROP18) protein to support its inclusion in vaccine formulations. Using a range of bioinformatics tools, we investigated its T-cell and B-cell epitopes, physicochemical properties, subcellular localization, transmembrane domains, and tertiary and secondary structures. Our analysis revealed 48 post-translational modification sites in TgROP18. The secondary structure was composed of 4.87% beta-turns, 38.45% random coils, 42.42% alpha helices, and 14.26% extended strands. Several potential T- and B-cell epitopes were identified on ROP18. The Ramachandran plot of both crude and refined models showed that 85.8% and 95.3% of the amino acid residues, respectively, fell within favored regions, indicating energetically stable conformations. Allergenicity and antigenicity assessments indicated that TgROP18 is a nonallergenic, immunogenic protein. Predictions using the C-ImmSim server suggest that TgROP18 can stimulate humoral and cell-mediated immune responses, based on antibody titers and cytokine profiles following antigen administration. These findings provide baseline data for future investigations focused on the potential of TgROP18 in developing therapeutic strategies against toxoplasmosis.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251315924"},"PeriodicalIF":2.3,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11806494/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143381466","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}
引用次数: 0
Molecular Docking Appraisal of Pleurotus ostreatus Phytochemicals as Potential Inhibitors of PI3K/Akt Pathway for Breast Cancer Treatment. 平耳植物化学物质作为PI3K/Akt通路潜在抑制剂治疗乳腺癌的分子对接评价
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2025-02-03 eCollection Date: 2025-01-01 DOI: 10.1177/11779322251316864
Magdalene Eno Effiong, Mercy Bella-Omunagbe, Israel Sunmola Afolabi, Shalom Nwodo Chinedu
{"title":"Molecular Docking Appraisal of <i>Pleurotus ostreatus</i> Phytochemicals as Potential Inhibitors of PI3K/Akt Pathway for Breast Cancer Treatment.","authors":"Magdalene Eno Effiong, Mercy Bella-Omunagbe, Israel Sunmola Afolabi, Shalom Nwodo Chinedu","doi":"10.1177/11779322251316864","DOIUrl":"10.1177/11779322251316864","url":null,"abstract":"<p><strong>Introduction: </strong>Breast cancer (BC) is a heterogeneous disease involving a network of numerous extracellular signal transduction pathways. The phosphoinositide 3-kinase (PI3K)/serine/threonine kinase (Akt)/mechanistic target of rapamycin (mTOR) pathway is crucial for understanding the BC development. Phosphoinositide 3-kinase, phosphatase and tensin homolog (PTEN), mTOR, Akt, 3-phosphoinositide-dependent kinase 1 (PDK1), FoxO1, glycogen synthase kinase 3 (GSK-3), mouse double minute 2 (MDM2), H-Ras, and proapoptotic B-cell lymphoma 2 (BCL-2) family protein (BAD) proteins are key drivers of this pathway and potential therapeutic targets. <i>Pleurotus ostreatus</i> is an edible mushroom that is rich in flavonoids and phenols that can serve as potential inhibitors of proteins in the PI3K/Akt/mTOR pathway.</p><p><strong>Aim: </strong>This study evaluated the anticancer properties of <i>P ostreatus</i> through a structure-based virtual screening of 22 biologically active compounds present in the mushroom.</p><p><strong>Method: </strong>Model optimization was carried out on PI3K, PTEN, mTOR, Akt, PDK1, FoxO1, GSK-3, MDM2, H-Ras, and BAD proteins in the PI3K/Akt/mTOR pathway and molecular docking of compounds/control inhibitors in the binding pocket were simulated AutoDock Vina in PyRx. The drug likeness, pharmacokinetic, and pharmacodynamic features of prospective docking leads were all anticipated.</p><p><strong>Result: </strong>Several potent inhibitors of the selected key driver proteins in PI3K/Akt/mTOR pathway were identified from <i>P ostreatus</i>. Ellagic acid with binding affinities of -8.0, -8.0, -8.1, -8.2, -6.2, and -7.1 kcal/mol on PI3K, Akt, PDK1, GSK-3, MDM2, and BAD, respectively, had better binding affinity compared with their reference drugs. Likewise, apigenin (-7.8 kcal/mol), chrysin (-7.8 kcal/mol), quercetin (-6.4 kcal/mol), and chlorogenic acid (-6.2 kcal/mol) had better binding affinities to PTEN, mTOR, FoxO1, and H-Ras proteins, respectively.</p><p><strong>Conclusion: </strong>Ellagic acid, apigenin, luteolin, quercetin, chlorogenic acid, chrysin, and naringenin phytochemicals are seen as the better lead molecules due to their ability to strongly bind to the proteins under study in this pathway. Analogs of these compounds can also be designed as potential drugs.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251316864"},"PeriodicalIF":2.3,"publicationDate":"2025-02-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143188279","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}
引用次数: 0
Cliotide U1, a Novel Antimicrobial Peptide Isolated From Urtica Dioica Leaves. 从荨麻疹叶片中分离的新型抗菌肽Cliotide U1。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2025-01-29 eCollection Date: 2025-01-01 DOI: 10.1177/11779322251315291
Mahnaz Nasre Taheri, Sima Sadat Seyedjavadi, Mehdi Goudarzi, Gholamhossein Ebrahimipour, Ali Hashemi
{"title":"Cliotide U1, a Novel Antimicrobial Peptide Isolated From <i>Urtica Dioica</i> Leaves.","authors":"Mahnaz Nasre Taheri, Sima Sadat Seyedjavadi, Mehdi Goudarzi, Gholamhossein Ebrahimipour, Ali Hashemi","doi":"10.1177/11779322251315291","DOIUrl":"10.1177/11779322251315291","url":null,"abstract":"<p><strong>Aims: </strong>Antibiotic resistance is currently a major challenge to scientists. Thus, attempts have been made to develop new compounds with antimicrobial activity. In this research, a new antimicrobial peptide with antibacterial activity was isolated from the plant <i>Urtica dioica</i>.</p><p><strong>Methods: </strong>A new antimicrobial peptide, named cliotide U1, was purified through precipitation with ammonium sulfate and reverse-phase high-performance liquid chromatography. In silico methods analyzed the physicochemical properties of cliotide U1. The properties of the peptide, including antibacterial activity, pH stability, heat stability, cytotoxicity, and hemolytic activity, were also examined.</p><p><strong>Findings: </strong>The purified peptide was composed of 35 amino acids with a hydrophobicity ratio of 63% and a net charge of + 5. The antibacterial activity of cliotide U1 was observed against gram-negative and gram-positive bacteria with a minimum inhibitory concentration (MIC) of 1 to 4 µM. Cliotide U1 had less than 2% cytotoxic activity at the MIC range against the human embryonic kidney cell line 293 with no clear hemolytic activity. The stability of cliotide U1 was preserved at various temperatures (10-60°C) and pH (6-9).</p><p><strong>Conclusion: </strong>Our results demonstrated that cliotide U1 had potent antibacterial potential against gram-negative and gram-positive bacteria. Considering its properties, cliotide U1 can be introduced as a novel antibacterial candidate for expanding new therapeutic drugs.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251315291"},"PeriodicalIF":2.3,"publicationDate":"2025-01-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11780632/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143063581","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}
引用次数: 0
Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae. 抵抗:一种新的NLR分类器,揭示了茄科与helitron相关的NLR扩展。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2025-01-22 eCollection Date: 2025-01-01 DOI: 10.1177/11779322241308944
Moray Smith, John T Jones, Ingo Hein
{"title":"Resistify: A Novel NLR Classifier That Reveals Helitron-Associated NLR Expansion in Solanaceae.","authors":"Moray Smith, John T Jones, Ingo Hein","doi":"10.1177/11779322241308944","DOIUrl":"10.1177/11779322241308944","url":null,"abstract":"<p><p>Nucleotide-binding domain leucine-rich repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes, NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying novel sources of disease resistance. While several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322241308944"},"PeriodicalIF":2.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11752215/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143021974","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}
引用次数: 0
Advancing Regulatory Genomics With Machine Learning. 用机器学习推进调控基因组学。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2024-12-24 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241249562
Laurent Bréhélin
{"title":"Advancing Regulatory Genomics With Machine Learning.","authors":"Laurent Bréhélin","doi":"10.1177/11779322241249562","DOIUrl":"10.1177/11779322241249562","url":null,"abstract":"<p><p>In recent years, several machine learning (ML) approaches have been proposed to predict gene expression signal and chromatin features from the DNA sequence alone. These models are often used to deduce and, to some extent, assess putative new biological insights about gene regulation, and they have led to very interesting advances in regulatory genomics. This article reviews a selection of these methods, ranging from linear models to random forests, kernel methods, and more advanced deep learning models. Specifically, we detail the different techniques and strategies that can be used to extract new gene-regulation hypotheses from these models. Furthermore, because these putative insights need to be validated with wet-lab experiments, we emphasize that it is important to have a measure of confidence associated with the extracted hypotheses. We review the procedures that have been proposed to measure this confidence for the different types of ML models, and we discuss the fact that they do not provide the same kind of information.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241249562"},"PeriodicalIF":2.3,"publicationDate":"2024-12-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11672376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142902309","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}
引用次数: 0
Bioinformatic Annotation of Transposon DNA Processing Genes on the Long-Read Genome Assembly of Caenorhabditis elegans. 秀丽隐杆线虫长读基因组组装转座子DNA加工基因的生物信息学注释。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2024-12-20 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241304668
Yukinobu Arata, Peter Jurica, Nicholas Parrish, Yasushi Sako
{"title":"Bioinformatic Annotation of Transposon DNA Processing Genes on the Long-Read Genome Assembly of <i>Caenorhabditis elegan</i>s.","authors":"Yukinobu Arata, Peter Jurica, Nicholas Parrish, Yasushi Sako","doi":"10.1177/11779322241304668","DOIUrl":"10.1177/11779322241304668","url":null,"abstract":"<p><p>Transposable elements (TEs) or transposons are thought to play roles in animal physiological processes, such as germline, early embryonic, and brain development, as well as aging. However, their roles have not been systematically investigated through experimental studies. In this study, we created a catalog of genes directly involved in replication, excision, or integration of transposon-coding DNA, which we refer to as transposon DNA processing genes (TDPGs). Specifically, to bridge the gap to experimental studies, we sought potentially functional TDPGs which maintain intact open reading frames and the amino acids at their catalytic cores on the latest long-read genome assembly of <i>Caenorhabditis elegans</i>, VC2010. Among 52 519 TE loci, we identified 145 potentially functional TDPGs encoded in long terminal repeat elements, long interspersed nuclear elements, terminal inverted repeat elements, Helitrons, and Mavericks/Polintons. Our TDPG catalog, which contains a feasible number of genes, allows for the experimental manipulation of TE mobility <i>in vivo</i>, regardless of whether the TEs are autonomous or non-autonomous, thereby potentially promoting the study of the physiological functions of TE mobility.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241304668"},"PeriodicalIF":2.3,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662393/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142875910","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}
引用次数: 0
The Alteration of Proteomic Profiles in Hippocampus of Type 2 Diabetic Mice Associated With Cognitive Impairment. 认知障碍相关2型糖尿病小鼠海马蛋白质组谱的改变
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241306290
Yoottana Janthakhin, Sirikran Juntapremjit, Karin Hummel, Ebrahim Razzazi-Fazeli, Sutin Kingtong
{"title":"The Alteration of Proteomic Profiles in Hippocampus of Type 2 Diabetic Mice Associated With Cognitive Impairment.","authors":"Yoottana Janthakhin, Sirikran Juntapremjit, Karin Hummel, Ebrahim Razzazi-Fazeli, Sutin Kingtong","doi":"10.1177/11779322241306290","DOIUrl":"10.1177/11779322241306290","url":null,"abstract":"<p><p>Clinical and experimental studies have demonstrated that type 2 diabetes mellitus (T2DM) affects the brain structure and function, in particular the hippocampus, leading to cognitive impairments. However, the molecular mechanisms underlying cognitive deficits induced by T2DM are not fully understood. In this study, we aimed to investigate the effects of T2DM on behavior, the proteome profile in the hippocampus, and the potential molecular pathways involved in the development of cognitive dysfunction in T2DM mice. We found that the diabetic mice exhibited cognitive impairment in the novel object location recognition test and the novel object recognition test. The proteomic analysis revealed that various molecular pathways were involved in this context. These included the upregulation of proteins in the protein synthesis and folding pathway (EIF5A, RSP24, and PPIB), endocytosis and cellular trafficking (VPS24, SNX12, and ARP2/3), cannabinoid receptor interacting (CRIP1), ubiquitination (SKP1), and oxidative stress response (NUDT3). Downregulated proteins were related to mitochondria function (ANT1), neuronal development (ELP1), protein glycosylation (RPN2), and endocytosis (VPS4). Our study shows that T2DM mice exhibit neurocognitive impairment, which is linked to the dysregulation of hippocampal proteins involved in various molecular pathways. These findings contribute to a better understanding of the pathophysiology of T2DM-related cognitive impairment and may identify molecular targets for drug development to treat T2DM-associated cognitive impairment conditions.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241306290"},"PeriodicalIF":2.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11656429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863154","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}
引用次数: 0
Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats. 全基因组工具的敏感从头鉴定和可视化的穿插和串联重复序列。
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241306391
Ruslan Kalendar, Ulykbek Kairov
{"title":"Genome-Wide Tool for Sensitive de novo Identification and Visualisation of Interspersed and Tandem Repeats.","authors":"Ruslan Kalendar, Ulykbek Kairov","doi":"10.1177/11779322241306391","DOIUrl":"10.1177/11779322241306391","url":null,"abstract":"<p><p>Genomic repeats are functionally ubiquitous structural units found in all genomes. Studying these repeats of different origins is essential for understanding the evolution and adaptation of a given organism. These repeating patterns have manifold signatures and structures with varying degrees of homology, making their identification challenging. To address this challenge, we developed a new algorithm and software that can rapidly and accurately detect any repeated sequences de novo with varying degrees of homology in genomic sequences in interspersed or clustered repeats. Numerous forms of repeated sequences and complex patterns can be identified, even for complex sequence variants and implicit or mixed types of repeat blocks. Direct and inverted-repeat elements, perfect and imperfect microsatellite repeats, and any short or long tandem repeat belonging to a wide range of higher-order repeat structures of telomeres or large satellite sequences can be detected. By combining precision and versatility, our tool contributes significantly to elucidating the intricate landscape of genomic repeats.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241306391"},"PeriodicalIF":2.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11656428/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863153","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}
引用次数: 0
Variations in Furin SNPs, a Major Concern of SARS-CoV-2 Susceptibility Among Different Populations: An In-Silico Approach. 不同人群对 SARS-CoV-2 易感性的主要关注点--Furin SNPs 的变异:内模拟方法
IF 2.3
Bioinformatics and Biology Insights Pub Date : 2024-12-18 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241306388
Md Nasir Uddin, Md Arzo Mia, Yasmin Akter, Mohammad Al-Baruni Chowdhury, Md Hadisur Rahman, Hafsa Siddiqua, Umme Salma Shathi, Abdullah Al-Mamun, Farida Siddika, Lolo Wal Marzan
{"title":"Variations in Furin SNPs, a Major Concern of SARS-CoV-2 Susceptibility Among Different Populations: An <i>In</i>-<i>Silico</i> Approach.","authors":"Md Nasir Uddin, Md Arzo Mia, Yasmin Akter, Mohammad Al-Baruni Chowdhury, Md Hadisur Rahman, Hafsa Siddiqua, Umme Salma Shathi, Abdullah Al-Mamun, Farida Siddika, Lolo Wal Marzan","doi":"10.1177/11779322241306388","DOIUrl":"10.1177/11779322241306388","url":null,"abstract":"<p><p>COVID-19 caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) had an adverse effect globally because it caused a global pandemic with several million deaths. This virus possesses spike protein that is cleaved or activated by Furin-like protease enzymes occurring by mammalian lung or respiratory cells to enter the mammalian body. The addition of the Furin cleavage site in SARS-CoV-2 makes it a more infectious and emerging virus than its ancestor's viruses. Phylogenetic relationships of coronavirus spike proteins have analyzed and mapped Furin recognition motif on the tree using bioinformatics tools such as GTEx, KEGG, GO, NCBI, PolyPhen-2, SNAP2, PANTHER, Hidden Markov Models (Fathmm), Phd-single-nucleotide polymorphism (SNP), I-TASSER, Modpred, Phobius, SIFT, iPTREE-STAB, and PROVEAN. During this study, it has been found that in certain regions, <i>Furin</i> SNPs have some relation with the susceptibility to SARS-CoV-2. Whereas in other regions, the effects are very negligible. Finally, our study demonstrates that <i>Furin</i> SNPs have a strong relationship with susceptibility to SARS-CoV-2. As it helps to cleave the spike protein of the virus, thus it can be targeted to inhibit at a particular site to prevent the SARS-CoV-2 from the entrance into the body.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241306388"},"PeriodicalIF":2.3,"publicationDate":"2024-12-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11656424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142863155","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}
引用次数: 0
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