Bioinformatics and Biology Insights最新文献_第6页

Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk. 大动脉间差异表达的基因富含内皮功能障碍相关基因组：动脉间动脉粥样硬化相对风险的意义。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-05-16 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241251563

Paul A Brown

{"title":"Genes Differentially Expressed Across Major Arteries Are Enriched in Endothelial Dysfunction-Related Gene Sets: Implications for Relative Inter-artery Atherosclerosis Risk.","authors":"Paul A Brown","doi":"10.1177/11779322241251563","DOIUrl":"10.1177/11779322241251563","url":null,"abstract":"Atherosclerosis differs across major arteries. Although the biological basis is not fully understood, limited evidence of genetic differences has been documented. This study, therefore, was aimed to identify differentially expressed genes between clinically relevant major arteries and investigate their enrichment in endothelial dysfunction-related gene sets. A bioinformatic analysis of publicly available gene-level read counts for coronary, aortic, and tibial arteries was performed. Differential gene expression was conducted with DeSeq2 at a false discovery rate of 0.05. Differentially expressed genes were then subjected to over-representation analysis and active-subnetwork-oriented enrichment analysis, both at a false discovery rate of 0.005. Enriched terms common to both analyses were categorized for each contrast into immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related terms, and the top differentially expressed genes validated against Swiss Institute of Bioinformatics' Bgee database. There was mostly upregulation of differentially expressed genes for the coronary/tibial and aorta/tibial contrasts, but milder changes for the coronary/aorta contrast. Transcriptomic differences between coronary or aortic versus tibial samples largely involved immunity/inflammation-, membrane biology-, lipid metabolism-, and coagulation-related genes, suggesting potential to modulate endothelial dysfunction and atherosclerosis. These results imply atheroprone coronary and aortic environments compared with tibial artery tissue, which may explain observed relative inter-artery atherosclerosis risk.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241251563"},"PeriodicalIF":5.8,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11100403/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064719","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

Human Pose Estimation for Clinical Analysis of Gait Pathologies. 用于步态病症临床分析的人体姿势估计。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-05-15 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241231108

Manal Mostafa Ali, Maha Medhat Hassan, M Zaki

{"title":"Human Pose Estimation for Clinical Analysis of Gait Pathologies.","authors":"Manal Mostafa Ali, Maha Medhat Hassan, M Zaki","doi":"10.1177/11779322241231108","DOIUrl":"https://doi.org/10.1177/11779322241231108","url":null,"abstract":"Gait analysis serves as a critical diagnostic tool for identifying neurologic and musculoskeletal damage. Traditional manual analysis of motion data, however, is labor-intensive and heavily reliant on the expertise and judgment of the therapist. This study introduces a binary classification method for the quantitative assessment of gait impairments, specifically focusing on Duchenne muscular dystrophy (DMD), a prevalent and fatal neuromuscular genetic disorder. The research compares spatiotemporal and sagittal kinematic gait features derived from 2D and 3D human pose estimation trajectories against concurrently recorded 3D motion capture (MoCap) data from healthy children. The proposed model leverages a novel benchmark dataset, collected from YouTube and publicly available datasets of their typically developed peers, to extract time-distance variables (e.g. speed, step length, stride time, and cadence) and sagittal joint angles of the lower extremity (e.g. hip, knee, and knee flexion angles). Machine learning and deep learning techniques are employed to discern patterns that can identify children exhibiting DMD gait disturbances. While the current model is capable of distinguishing between healthy subjects and those with DMD, it does not specifically differentiate between DMD patients and patients with other gait impairments. Experimental results validate the efficacy of our cost-effective method, which relies on recorded RGB video, in detecting gait abnormalities, achieving a prediction accuracy of 96.2% for Support Vector Machine (SVM) and 97% for the deep network.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241231108"},"PeriodicalIF":5.8,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11097739/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140955771","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

Investigating the Antimicrobial Effects of a Novel Peptide Derived From Listeriolysin S on S aureus, E coli, and L plantarum: An In Silico and In Vitro Study. 调查从李斯特溶菌素 S 中提取的一种新型多肽对金黄色葡萄球菌、大肠杆菌和植物大肠杆菌的抗菌作用：一项硅学和体外研究。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-05-15 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241252513

Mojgan Sarabi Nobakht, Kaveh Bazyar, Mohammad Sadegh Ghalyanchi Langeroudi, Mandana Mirzaei, Mehdi Goudarzi, Ali Shivaee

{"title":"Investigating the Antimicrobial Effects of a Novel Peptide Derived From Listeriolysin S on S aureus, E coli, and L plantarum: An In Silico and In Vitro Study.","authors":"Mojgan Sarabi Nobakht, Kaveh Bazyar, Mohammad Sadegh Ghalyanchi Langeroudi, Mandana Mirzaei, Mehdi Goudarzi, Ali Shivaee","doi":"10.1177/11779322241252513","DOIUrl":"10.1177/11779322241252513","url":null,"abstract":"Aims: The emergence of antibiotic resistance is one of the most significant issues today. Modifying antimicrobial peptides (AMPs) can improve their effects. In this study, the active region of Listeriolysin S (LLS) as a peptidic toxin has been recognized, and its antibacterial properties have been evaluated by modifying that region.Methods: After extracting the sequence, the structure of LLS was predicted by PEP-FOLD3. AntiBP and AMPA servers identified its antimicrobial active site. It was modified by adding arginine residue to its 3- and N-terminal regions. Its antimicrobial properties on Staphylococcus aureus, Escherichia coli, and Lactobacillus Plantarum were estimated.Findings: The results of AntiBP and AntiBP servers demonstrated that a region of 15 amino acids has the most antimicrobial properties (score = 1.696). After adding arginine to the chosen region, the physicochemical evaluation and antimicrobial properties revealed that the designed peptide is a stable AMP with a positive charge of 4, which is not toxic to human erythrocyte cells and has antigenic properties. The results of in vitro and colony counting indicated that at different hours, it caused a significant reduction in the count of S aureus, E coli, and L Plantarum compared with the control sample.Conclusions: Upcoming research implies that identifying and enhancing the active sites of natural peptides can help combat bacteria.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241252513"},"PeriodicalIF":5.8,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11100392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141064723","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

DENV-2 Outbreak Associated With Cosmopolitan Genotype Emergence in Western Brazilian Amazon. 巴西亚马孙河流域西部与世界性基因型出现有关的 DENV-2 爆发。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-05-11 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241251581

Jessiane Rodrigues Ribeiro, Tárcio Peixoto Roca, Gleense Dos Santos Cartonilho, Ana Maísa Passos-Silva, Hillquias Monteiro Moreira, Karolaine Santos Teixeira, André Luiz Ferreira da Silva, Celina Aparecida Bertoni Lugtenburg, Alcione Oliveira Dos Santos, Juan Miguel Villalobos Salcedo, Valdinete Alves do Nascimento, Victor Costa de Souza, Rosemary Aparecida Roque, Marco Aurélio Krieger, Felipe Gomes Naveca, Rita de Cássia Pontello Rampazzo, Deusilene Souza Vieira

{"title":"DENV-2 Outbreak Associated With Cosmopolitan Genotype Emergence in Western Brazilian Amazon.","authors":"Jessiane Rodrigues Ribeiro, Tárcio Peixoto Roca, Gleense Dos Santos Cartonilho, Ana Maísa Passos-Silva, Hillquias Monteiro Moreira, Karolaine Santos Teixeira, André Luiz Ferreira da Silva, Celina Aparecida Bertoni Lugtenburg, Alcione Oliveira Dos Santos, Juan Miguel Villalobos Salcedo, Valdinete Alves do Nascimento, Victor Costa de Souza, Rosemary Aparecida Roque, Marco Aurélio Krieger, Felipe Gomes Naveca, Rita de Cássia Pontello Rampazzo, Deusilene Souza Vieira","doi":"10.1177/11779322241251581","DOIUrl":"10.1177/11779322241251581","url":null,"abstract":"Background: Dengue virus (DENV) causes an important disease and directly affects public health, being the arbovirus that presents the highest number of infections and deaths in the Western Brazilian Amazon. This virus is divided into 4 serotypes that have already circulated in the region.Methodology: Molecular characterization of a cohort containing 841 samples collected from febrile patients between 2021 and 2023 was analyzed using a commercial kit to detect the main arboviruses circulating in Brazil: Zika, DENV-1, DENV-2, DENV-3, DENV-4 and, Chikungunya. Subsequently, Sanger sequencing was performed for positive samples.Results: The cohort detected 162 positive samples, 12 for DENV-1 and 150 identified as DENV-2, indicating co-circulation of serotypes. The samples were subjected to sequencing and the analysis of the sequences that obtained good quality revealed that 5 samples belonged to the V genotype of DENV-1 and 46 were characterized as DENV-2 Cosmopolitan genotype-lineage 5.Conclusion: The results allowed us to identify for the first time the Cosmopolitan genotype in Rondônia, Brazilian Western Amazon, and its fast spread dispersion.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241251581"},"PeriodicalIF":5.8,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11088811/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140911134","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 Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress. 对刺阿干树（Argania spinosa L. Skeels）脂肪酸去饱和酶（FAD）基因的硅学鉴定和特征描述：对油质和非生物压力的影响。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-05-05 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241248908

Abdelmoiz El Faqer, Karim Rabeh, Mohammed Alami, Abdelkarim Filali-Maltouf, Bouchra Belkadi

{"title":"In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress.","authors":"Abdelmoiz El Faqer, Karim Rabeh, Mohammed Alami, Abdelkarim Filali-Maltouf, Bouchra Belkadi","doi":"10.1177/11779322241248908","DOIUrl":"10.1177/11779322241248908","url":null,"abstract":"Fatty acid desaturase (FAD) is the key enzyme that leads to the formation of unsaturated fatty acids by introducing double bonds into hydrocarbon chains, and it plays a critical role in plant lipid metabolism. However, no data are available on enzyme-associated genes in argan trees. In addition, a candidate gene approach was adopted to identify and characterize the gene sequences of interest that are potentially involved in oil quality and abiotic stress. Based on phylogenetic analyses, 18 putative FAD genes of Argania spinosa L. (AsFAD) were identified and assigned to three subfamilies: stearoyl-ACP desaturase (SAD), Δ-12 desaturase (FAD2/FAD6), and Δ-15 desaturase (FAD3/FAD7). Furthermore, gene structure and motif analyses revealed a conserved exon-intron organization among FAD members belonging to the various oil crops studied, and they exhibited conserved motifs within each subfamily. In addition, the gene structure shows a wide variation in intron numbers, ranging from 0 to 8, with two highly conserved intron phases (0 and 1). The AsFAD and AsSAD subfamilies consist of three (H(X)2-4H, H(X)2-3HH, and H/Q (X)2-3HH) and two (EEN(K)RHG and DEKRHE) conserved histidine boxes, respectively. A set of primer pairs were designed for each FAD gene, and tested on DNA extracted from argan leaves, in which all amplicons of the expected size were produced. These findings of candidate genes in A spinosa L. will provide valuable knowledge that further enhances our understanding of the potential roles of FAD genes in the quality of oil and abiotic stress in the argan tree.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241248908"},"PeriodicalIF":5.8,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11072076/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858164","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

Analysis of CENP-B Boxes as Anchor of Kinetochores in Centromeres of Human Chromosomes. 分析作为人类染色体中心粒内着丝点锚的 CENP-B 盒。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-04-29 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241248913

Fritz F Parl

{"title":"Analysis of CENP-B Boxes as Anchor of Kinetochores in Centromeres of Human Chromosomes.","authors":"Fritz F Parl","doi":"10.1177/11779322241248913","DOIUrl":"https://doi.org/10.1177/11779322241248913","url":null,"abstract":"The kinetochore is a multiprotein structure that attaches at one end to DNA in the centromere and at the other end to microtubules in the mitotic spindle. By connecting centromere and spindle, the kinetochore controls the migration of chromosomes during cell division. The exact position where the kinetochore assembles on each centromere was uncertain because large sections of centromeric DNA had not been sequenced due to highly repetitive alpha-satellite arrays. Embedded in the arrays is a 17 bp consensus sequence, the so-called CENP-B box, which binds the CENP-B protein, the only protein that binds directly to centromeric DNA. Recently, the Telomere-to-Telomere Consortium published the complete centromeric DNA sequences of all chromosomes including their epigenetic modifications in the T2T-CHM13 map. I used data from the T2T-CHM13 map to locate the CENP-B boxes in the centromeres as anchor of kinetochores. Most of the CENP-B boxes in centromeric DNA are methylated with the exception of the so-called centromere dip region (CDR), where CENP-B protein dimers bind to adjacent unmethylated CENP-B boxes and interact with CENP-A and CENP-C proteins to assemble the kinetochore. The centromeres of all chromosomes combined have a size of 407 Mb of which the kinetochores account for 5.0 Mb or 1.2%. There is no correlation between centromere and kinetochore size (P = .77). While the number of CENP-B boxes varies 4-fold between chromosomes, their density (number/Kb) varies less than 2-fold with a mean of 2.61 ± 0.33. The narrow range ensures a uniform pull of the spindle on the centromeres. I illustrate the findings in a model of the human kinetochore anchored at unmethylated CENP-B boxes in the CDR and present circos plots of chromosomes to show the location of kinetochores in their respective centromeres.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241248913"},"PeriodicalIF":5.8,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11060027/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140853124","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 Novel PTX3 Variant g.22645332G>T Is Strongly Related to Awassi and Hamdani Sheep Litter Size. 新型 PTX3 变体 g.22645332G>T 与阿瓦西羊和哈姆达尼羊的产仔数密切相关。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241248912

Faris S Imran, Tahreer M Al-Thuwaini

{"title":"The Novel PTX3 Variant g.22645332G>T Is Strongly Related to Awassi and Hamdani Sheep Litter Size.","authors":"Faris S Imran, Tahreer M Al-Thuwaini","doi":"10.1177/11779322241248912","DOIUrl":"https://doi.org/10.1177/11779322241248912","url":null,"abstract":"The detection of polymorphisms in genes that control livestock reproduction could be highly beneficial for identifying and enhancing economic traits. One of these genes is pentraxin 3 (PTX3), which affects the reproduction of sheep. Therefore, this study investigated whether the variability of the PTX3 gene was related to the litter size of Awassi and Hamdani ewes. A total of 200 ewes (130 Awassi and 70 Hamdani) were used for genomic DNA extraction. Polymerase chain reaction was used to amplify the sequence fragments of exons 1, 2, 3, and 4 from the PTX3 gene (Oar_v4.0; Chr 1, NC_056054.1), resulting in products of 254, 312, 302, and 253, respectively. Two genotypes, GG and GT, were identified for 302 bp amplicon. A novel mutation was discovered through sequence analysis in the GT genotype at position g.22645332G>T. The statistical analysis revealed a significant association between single nucleotide polymorphism (SNP g.22645332G>T; Oar_v4.0; Chr 1, NC_056054.1) and litter size. The presence of the SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1) genotype in ewes resulted in a significant difference compared to ewes with GG genotypes. The discrepancy became apparent in several aspects, including litter sizes, twinning rates, lambing rates, litter weight at birth, and days to lambing. There were fewer lambs born to ewes with the GG genotype than to ewes with the GT genotype. The variant SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1) has positive effects on the litter size of Awassi and Hamdani sheep. The SNP g.22645332G>T (Oar_v4.0; Chr 1, NC_056054.1 has been associated with an increase in litter size and higher prolificacy in ewes.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241248912"},"PeriodicalIF":5.8,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11047254/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140856533","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 Potential Role of Phytochemicals of Juniperus procera in the Treatment of Ovarian Cancer and the Inhibition of Human Topoisomerase II Alpha Activity. 杜松植物化学物质在治疗卵巢癌和抑制人类拓扑异构酶 II Alpha 活性中的潜在作用。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-04-25 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241248904

Ateeq A Al-Zahrani

{"title":"The Potential Role of Phytochemicals of Juniperus procera in the Treatment of Ovarian Cancer and the Inhibition of Human Topoisomerase II Alpha Activity.","authors":"Ateeq A Al-Zahrani","doi":"10.1177/11779322241248904","DOIUrl":"https://doi.org/10.1177/11779322241248904","url":null,"abstract":"A variety of active chemicals found in medicinal plants can be used to develop new medications with few adverse effects. In vitro and in silico analyses were used to evaluate the anticancer properties of Juniperus procera fruit and leaf extracts. Here, we show that the methanolic extract from J procera fruit and leaf extracts inhibits 2 human ovarian cancer cell lines, A2780CP and SKOV-3. The leaf extract demonstrated strong cytotoxicity against A2780CP with an IC50 of 1.2 μg/mL, almost matching the IC50 of the anticancer medication doxorubicin (0.9 μg/mL). Higher antioxidant activity was observed in the fruit than leaf extract. The molecular docking results showed that the active component, podocarpusflavone A, was the best-docked chemical with the human topoisomerase II alpha enzyme. According to our knowledge, this is the first in vitro study to show the cytotoxicity of J procera extracts against the 2 previously described human ovarian cancer cell lines. The fact that the podocarpusflavone A molecule may have an inhibitory effect on the human topoisomerase II alpha enzyme was also revealed by this first in silico analysis. Our findings imply that the J procera fruit and leaf methanolic extract has anticancer characteristics that may guide future in vivo studies.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241248904"},"PeriodicalIF":5.8,"publicationDate":"2024-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11047251/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140847870","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

Enzymatic Performance of Aspergillus oryzae α-Amylase in the Presence of Organic Solvents: Activity, Stability, and Bioinformatic Studies. 有机溶剂存在下的黑曲霉α-淀粉酶的酶性能：活性、稳定性和生物信息学研究。

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-04-23 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241234767

Khomaini Hasan, Umi Baroroh, Indri Novia Madhani, Zahra Silmi Muscifa, Mia Tria Novianti, Muhamad Abidin, Muhammad Yusuf, Toto Subroto

{"title":"Enzymatic Performance of Aspergillus oryzae α-Amylase in the Presence of Organic Solvents: Activity, Stability, and Bioinformatic Studies.","authors":"Khomaini Hasan, Umi Baroroh, Indri Novia Madhani, Zahra Silmi Muscifa, Mia Tria Novianti, Muhamad Abidin, Muhammad Yusuf, Toto Subroto","doi":"10.1177/11779322241234767","DOIUrl":"https://doi.org/10.1177/11779322241234767","url":null,"abstract":"Enzymatic reactions can be modulated by the incorporation of organic solvents, leading to alterations in enzyme stability, activity, and reaction rates. These solvents create a favorable microenvironment that enables hydrophobic reactions, facilities enzyme-substrate complex formation, and reduces undesirable water-dependent side reactions. However, it is crucial to understand the impact of organic solvents on enzymatic activity, as they can also induce enzyme inactivation. In this study, the enzymatic performance of Aspergillus oryzae α-amylase (Taka-amylase) in various organic solvents both experimentally and computationally was investigated. The results demonstrated that ethanol and ether sustain Taka-amylase activity up to 20% to 25% of the organic solvents, with ether providing twice the stability of ethanol. Molecular dynamics simulations further revealed that Taka-amylase has a more stable structure in ether and ethanol relative to other organic solvents. In addition, the analysis showed that the loop located near the active site in the AB-domain is a vulnerable site for enzyme destabilization when exposed to organic solvents. The ability of Taka-amylase to preserve the secondary loop structure in ether and ethanol contributed to the enzyme's activity. In addition, the solvent accessibility surface area of Taka-amylase is distributed throughout all enzyme structures, thereby contributing to the instability of Taka-amylase in the presence of most organic solvents.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241234767"},"PeriodicalIF":5.8,"publicationDate":"2024-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11041543/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140858163","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

Computer-Assisted Discovery of Salvia fruticosa Compounds With Schistosomicidal Activity. 计算机辅助发现具有杀血吸虫活性的丹参化合物

IF 5.8

Bioinformatics and Biology Insights Pub Date : 2024-03-27 eCollection Date: 2024-01-01 DOI: 10.1177/11779322241240651

Ryman Shoko, Farirai Mandivenga

{"title":"Computer-Assisted Discovery of Salvia fruticosa Compounds With Schistosomicidal Activity.","authors":"Ryman Shoko, Farirai Mandivenga","doi":"10.1177/11779322241240651","DOIUrl":"10.1177/11779322241240651","url":null,"abstract":"Schistosomiasis, otherwise known as bilharzia or snail fever, is a disease that usually affects poor people and people exposed to poor sanitation. The disease affects over 200 million people worldwide annually. Schistosomiasis has been treated using a single drug, praziquantel, since the 1970s and this is resulting in schistosomes becoming resistant. Therefore, there is an urgent need to develop new antischistosoma drugs and vaccines. This study focuses on identifying potential antischistosomal compounds from the plant Salvia fruticosa. We virtually screened a library of 163 S fruticosa compounds by docking against Schistosoma mansoni sulfotransferase (SmSULT) using the PyRx software. Docking scores ranged from -4.7 to -9.3 kcal/mol. Compounds with binding affinity of -7.6 or stronger were subjected to drug-likeness assessments using the DataWarrior software. We also employed the PAINS removal tool to filter off false-positive results. Twelve compounds passed the drug-likeness screen, and these were subjected to in silico toxicity predictions to determine their mutagenic, tumorigenic and reproductive potential. Seven compounds were predicted to be nontoxic. After considering the toxicity analysis results and drug scores of the compounds, we identified rosmarinic acid and hispidulin as qualifying for further evaluation as potential drugs against schistosomiasis. Free energy calculations using the fastDRH webserver and molecular dynamics simulations using CABS-flex showed that the receptor-ligand complexes for the 2 lead compounds are stable under physiological conditions. We recommend that rosmarinic acid and hispidulin be used as hit compounds for the development of potential antischistosomal drugs.","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"18 ","pages":"11779322241240651"},"PeriodicalIF":5.8,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10976507/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140317759","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}

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