Journal, genetic engineering & biotechnology最新文献

{"title":"Targeting apoptotic anticancer response with natural glucosinolates from cell suspension culture of Lepidium sativum.","authors":"Mona M Ibrahim,&nbsp;Marwa M Mounier,&nbsp;Shawky A Bekheet","doi":"10.1186/s43141-023-00511-y","DOIUrl":"https://doi.org/10.1186/s43141-023-00511-y","url":null,"abstract":"<p><strong>Background: </strong>Finding natural products with anticancer activity is an effective strategy to fight this disease. In this respect, Lepidium sativum or garden cress (family Brassicaceae) has been widely used worldwide for its wide therapeutic application, including anticancer and chemoprotective agents. Plant tissue culture techniques hold great promise for natural product enhancement without any climatic boundaries. In this study, glucosinolates and petroleum ether fractions were isolated from in vitro cell cultures and used against different carcinoma cell lines to investigate their anticancer potential.</p><p><strong>Methods: </strong>In this study, callus cultures from leaf and root explants were initiated, cell suspension cultures were established, and cell growth and viability profiles were characterized. Different amino acids were added as precursors to the cell suspension cultures to enhance glucosinolates accumulation. Gas chromatography-mass spectrometric analysis (GC-MS) of glucosinolates and petroleum ether fractions was performed, and all fractions were tested against different carcinoma cell lines.</p><p><strong>Results: </strong>The findings clarified that the maximum callus initiation percentage was obtained in the medium containing 1.0 mg/l 2,4-dichlorophenoxy acetic acid (2,4-D) + 1.0 mg/l kinetin (Kin) (C1). The viable cell number of cell suspension cultures from leaves and roots increased until it reached the maximum values on day 15. Adding tyrosine and methionine to the cell suspension cultures was the most influential and recorded high glucosinolate percentages. 1H-Cyclopenta (b) pyridine-3-carbonitrile-4,5,6,7-tetrahydro-2-methylthio-4-spirocyclohexane was the main glucosinolate compound found in tyrosine-treated leaf suspension (GLT). Fifteen compounds were detected in the petroleum ether fraction in both cell suspensions initiated from the leaf and root (OL and OR). The major compounds were benzene-1,3,5-trimethyl (12.99%) in root cell suspension (OR), and benzene-2-ethyl-1,4-dimethyl (10.66%) in leaf cell suspension (OL). All glucosinolate extracts demonstrated significant anticancer activity against the prostate (PC3), lung (A-549), colorectal (caco2), and liver (HepG2) cell lines. Glucosinolates extracted from leaf cell suspension (GL) were the most active on the hepatocellular carcinoma cell line (HepG2) among all remaining glucosinolate extracts. Treated hepatocellular carcinoma with an IC₅₀ of GL extract (47.5 ug/ml) upregulates pro-apoptotic BAX and downregulates anti-apoptotic BCL2, which disrupts the BAX/BCL2 ratio, leading to activation of caspase 3 inside treated HepG2 cells.</p><p><strong>Conclusions: </strong>The anticancer action of the GL extract was validated by the cell cycle study of its glucosinolates, which successfully promoted apoptosis and reduced hepatocellular growth by causing S-phase arrest.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"53"},"PeriodicalIF":0.0,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151292/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9410004","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":"Whole-genome sequence analysis and probiotic characteristics of Lactococcus lactis Subsp. lactis strain Lac3 isolated from traditional fermented buffalo milk (Dadih).","authors":"Nshimiyimana Sylvere,&nbsp;Apon Zaenal Mustopa,&nbsp;Sri Budiarti,&nbsp;Lita Meilina,&nbsp;Ai Hertati,&nbsp;Ira Handayani","doi":"10.1186/s43141-023-00503-y","DOIUrl":"https://doi.org/10.1186/s43141-023-00503-y","url":null,"abstract":"<p><strong>Background: </strong>Probiotics are live microorganisms that provide beneficial effects on the host's health when exploited in adequate amounts. This study aimed at carrying out whole-genome sequence analysis and in vitro potential probiotic characteristics of Lactococcus lactis subsp. lactis strain Lac3 isolated from the spontaneously fermented buffalo milk named Dadih.</p><p><strong>Results: </strong>The results from de novo assembly indicated that the assembled genome consisted of 55 contigs with a genome size of 2,441,808 bp ~ (2.44 Mb), and GC % content of 34.85%. The evolution history result showed that the strain Lac3 was closely related to Lactococcus lactis species deposited in NCBI with a sequence similarity ≥ 99.93%. L. lactis subsp. lactis Lac3 was non-pathogenic with a probability of 0.21 out of 1 and had a pathogenicity score of zero (0), and neither harbored virulence factors nor acquired antibiotic resistance phenotypes. L. lactis subsp. lactis Lac3 exhibited the potential probiotic characteristics to tolerate acid at pH (2.0 and 5.0), salinity (1-5% NaCl), bile salt of (0.3-1.0%) and had auto-aggregation capacity increased from 6.0 to 13.1%.</p><p><strong>Conclusion: </strong>This study described a novel strain of Lactococcus lactis subsp. lactis called Lac3, which exhibits probiotic properties that could be beneficial in the development of probiotics.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"49"},"PeriodicalIF":0.0,"publicationDate":"2023-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151293/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9410003","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":"16S rRNA gene sequencing and MALDI TOF mass spectroscopy identification of Leuconostoc mesenteroides isolated from Algerian raw camel milk.","authors":"Hanane Fatma Chentouf,&nbsp;Fouzia Rahli,&nbsp;Zineb Benmechernene,&nbsp;Jorge Barros-Velazquez","doi":"10.1186/s43141-023-00500-1","DOIUrl":"https://doi.org/10.1186/s43141-023-00500-1","url":null,"abstract":"<p><strong>Background: </strong>Eighty-three strains of Leuconostoc mesenteroides were isolated from Algerian raw camel milk. Based on morphological, biochemical, and physiological characters tests, strains were identified as Ln. mesenteroides subsp. mesenteroides. Seven strains had a remarkable antagonistic and probiotic characterization. The present study aims at identifying these strains by means of 16 s rRNA gene sequencing and Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), extending phenotypic and genotypic studies done previously.</p><p><strong>Results: </strong>The phyloproteomic dendrograms of the studied strains based on MALDI-TOF MS provided the same identification with more intraspecific information from the 16S rRNA gene sequencing based on phylogenetic analysis. The latter were in agreement with the previous biochemical/physiological identification, the seven isolated strains were Ln. mesenteroides subsp. mesenteroides.</p><p><strong>Conclusions: </strong>Remarkably, MALDI-TOF MS fingerprinting was found to be effective enough as 16S rRNA gene sequencing identification, allowing faster and more reliable analysis than biochemical/physiological methods.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"51"},"PeriodicalIF":0.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151297/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9773388","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":"Optimization, partial purification, and characterization of a novel high molecular weight alkaline protease produced by Halobacillus sp. HAL1 using fish wastes as a substrate.","authors":"Nayer M Fahmy,&nbsp;Bahig El-Deeb","doi":"10.1186/s43141-023-00509-6","DOIUrl":"https://doi.org/10.1186/s43141-023-00509-6","url":null,"abstract":"<p><strong>Background: </strong>Hydrolytic enzymes from halophilic microorganisms have a wide range of industrial applications. Herein, we report the isolation of Halobacillus sp. HAL1, a moderately halophilic bacterium that produces a novel high molecular weight extracellular alkaline protease when grown in fish processing wastes as a substrate.</p><p><strong>Results: </strong>Results showed that the isolated strain belonged to the genus Halobacillus, and it was designated as Halobacillus sp. HAL1 with the GenBank accession number OK001470. The strain secreted an extracellular alkaline protease, and the highest yield was obtained when it was grown in a medium with fish wastes substrate as the sole nutritional source (10 g/L) and incubated at 25 °C under shaking conditions. The enzyme was partially purified by Sephadex G-100 column chromatography. Zymographic analysis showed two casein degrading bands of about 190 and 250 KDa. The optimum enzyme activity was at a temperature of 50 °C at pH 8. The proteolytic activity was enhanced in the presence of metal ions (Ca²⁺, Mg²⁺, and Mn²⁺), surfactants (Tween 80, SDS, and Triton-X100), H₂O₂, and EDTA.</p><p><strong>Conclusion: </strong>Our study indicates that Haobacillus sp. HAL1 is a moderately halophilic strain and secrets a novel high molecular wight alkaline protease that is suitable for detergent formulation.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"48"},"PeriodicalIF":0.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10149429/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9404654","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":"Impacts of ZnO as a nanofertilizer on fenugreek: some biochemical parameters and SCoT analysis.","authors":"Doaa E Elsherif,&nbsp;Eman Abd-ElShafy,&nbsp;Asmaa M Khalifa","doi":"10.1186/s43141-023-00501-0","DOIUrl":"https://doi.org/10.1186/s43141-023-00501-0","url":null,"abstract":"<p><strong>Background: </strong>Zinc oxide nanoparticles (ZnO NPs) can be considered as nanofertilizer providing zinc as an essential micronutrient for plant growth and production at specific safe dose, however, above this dose; ZnO NPs induce oxidative stress. The present research aimed to evaluate some physiological and molecular effects of ZnO NPs on Trigonella foenum-graecum (fenugreek) plant.</p><p><strong>Results: </strong>The ZnO NPs were applied at five different concentrations (10, 20, 30, 40, and 50 mg/l) via soaking fenugreek seeds for 24 h. Fenugreek seedlings were harvested after 14 days for biomass and biochemical analyses. The results revealed that increasing ZnO NPs concentration led to a significant increase in all measured parameters until peaked at 30 mg/l; after that, a decline trend was detected. However, malondialdehyde (MDA) increased significantly just at higher concentrations of ZnO NPs (40 and 50 mg/l). In addition, genetic variation measure using start codon targeted (SCoT) markers revealed that ZnO NP treatments exhibited limited genetic variation.</p><p><strong>Conclusion: </strong>Results showed that treatment with ZnO NPs at 30 mg/l can improve biomass, bioactive compounds, and antioxidant activity of fenugreek seedlings, besides being safe for DNA. So, this concentration could be a decent nanofertilizer for fenugreek plant.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"52"},"PeriodicalIF":0.0,"publicationDate":"2023-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10151287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9403645","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":"Computer-aided analysis of quercetin mechanism of overcoming docetaxel resistance in docetaxel-resistant prostate cancer.","authors":"Victor Omoboyede,&nbsp;Ochapa Ibrahim,&nbsp;Haruna Isiyaku Umar,&nbsp;Grace Ayomide Oke,&nbsp;Olugbenga Samson Onile,&nbsp;Prosper Obed Chukwuemeka","doi":"10.1186/s43141-023-00498-6","DOIUrl":"https://doi.org/10.1186/s43141-023-00498-6","url":null,"abstract":"<p><strong>Background: </strong>Prostate cancer (PC) is a silent but potent killer among men. In 2018, PC accounted for more than 350, 000 death cases while more than 1.2 million cases were diagnosed. Docetaxel, a chemotherapeutic drug belonging to the taxane family of drugs, is one of the most potent drugs in combating advanced PC. However, PC cells often evolve resistance against the regimen. Hence, necessitating the search for complementary and alternative therapies. Quercetin, a ubiquitous phytocompound with numerous pharmacological properties, has been reported to reverse docetaxel resistance (DR) in docetaxel-resistant prostate cancer (DRPC). Therefore, this study aimed to explore the mechanism via which quercetin reverses DR in DRPC using an integrative functional network and exploratory cancer genomic data analyses.</p><p><strong>Results: </strong>The putative targets of quercetin were retrieved from relevant databases, while the differentially expressed genes (DEGs) in docetaxel-resistant prostate cancer (DRPC) were identified by analysing microarray data retrieved from the Gene Expression Omnibus (GEO) database. Subsequently, the protein-protein interaction (PPI) network of the overlapping genes between the DEGs and quercetin targets was retrieved from STRING, while the hub genes, which represent the key interacting genes of the network, were identified using the CytoHubba plug-in of Cytoscape. The hub genes were further subjected to a comprehensive analysis aimed at identifying their contribution to the immune microenvironment and overall survival (OS) of PC patients, while their alterations in PC patients were also revealed. The biological roles played by the hub genes in chemotherapeutic resistance include the positive regulation of developmental process, positive regulation of gene expression, negative regulation of cell death, and epithelial cell differentiation among others.</p><p><strong>Conclusion: </strong>Further analysis revealed epidermal growth factor receptor (EGFR) as the most pertinent target of quercetin in reversing DR in DRPC, while molecular docking simulation revealed an effective interaction between quercetin and EGFR. Ultimately, this study provides a scientific rationale for the further exploration of quercetin as a combinational therapy with docetaxel.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"47"},"PeriodicalIF":0.0,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133427/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9360943","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":"Functional characterization of hypothetical proteins from Monkeypox virus.","authors":"Kajal Gupta","doi":"10.1186/s43141-023-00505-w","DOIUrl":"10.1186/s43141-023-00505-w","url":null,"abstract":"<p><strong>Background: </strong>Monkeypox virus is a small, double-stranded DNA virus that causes a zoonotic disease called Monkeypox. The disease has spread from Central and West Africa to Europe and North America and created havoc in some countries all around the world. The complete genome of the Monkeypox virus Zaire-96-I-16 has been sequenced. The viral strain contains 191 protein-coding genes with 30 hypothetical proteins whose structure and function are still unknown. Hence, it is imperative to functionally and structurally annotate the hypothetical proteins to get a clear understanding of novel drug and vaccine targets. The purpose of the study was to characterize the 30 hypothetical proteins through the determination of physicochemical properties, subcellular characterization, function prediction, functional domain prediction, structure prediction, structure validation, structural analysis, and ligand binding sites using Bioinformatics tools.</p><p><strong>Results: </strong>The structural and functional analysis of 30 hypothetical proteins was carried out in this research. Out of these, 3 hypothetical functions (Q8V547, Q8V4S4, Q8V4Q4) could be assigned a structure and function confidently. Q8V547 protein in Monkeypox virus Zaire-96-I-16 is predicted as an apoptosis regulator which promotes viral replication in the infected host cell. Q8V4S4 is predicted as a nuclease responsible for viral evasion in the host. The function of Q8V4Q4 is to prevent host NF-kappa-B activation in response to pro-inflammatory cytokines like TNF alpha or interleukin 1 beta.</p><p><strong>Conclusions: </strong>Out of the 30 hypothetical proteins of Monkeypox virus Zaire-96-I-16, 3 were annotated using various bioinformatics tools. These proteins function as apoptosis regulators, nuclease, and inhibitors of NF-Kappa-B activator. The functional and structural annotation of the proteins can be used to perform a docking with potential leads to discover novel drugs and vaccines against the Monkeypox. In vivo research can be carried out to identify the complete potential of the annotated proteins.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"46"},"PeriodicalIF":3.6,"publicationDate":"2023-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10133424/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9792569","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":"Assessment of cultivation parameters influencing pectinase production by Aspergillus niger LFP-1 in submerged fermentation.","authors":"Mohd Taufiq Mat Jalil,&nbsp;Nurul Aili Zakaria,&nbsp;Nor Hawani Salikin,&nbsp;Darah Ibrahim","doi":"10.1186/s43141-023-00510-z","DOIUrl":"https://doi.org/10.1186/s43141-023-00510-z","url":null,"abstract":"<p><strong>Background: </strong>Pectinase is helpful in food and beverage industries, particularly in the preparation of fruit juice, the extraction of vegetable oil, and the fermentation of coffee. The current work aimed to screen Aspergillus niger LFP-1, a recently identified fungal strain, for its ability to produce pectinase and to ascertain the contribution of various physicochemical factors to pectinase production.</p><p><strong>Results: </strong>The primary and secondary pectinase activity screenings by Aspergillus niger LFP-1 were performed using pectin screening agar and shake flask system, respectively. The finding revealed that the locally isolated strain is able to secrete favourable pectinase production. Before improvement, the pectinase production was 0.88 ± 0.09 U/mL. However, the improved conditions such as 6 days of the cultivation period, agitation speed of 150 rpm, inoculum size of 1 × 10⁶ spores/mL, 2.5% (w/v) citrus pectin, and 0.4% (w/v) ammonium nitrate could significantly increase pectinase production up to 7.41 ± 0.24 U/mL, representing an 88% increase. In this study, supplementing 2.5% (w/v) citrus pectin to the culture medium as a carbon source increased enzyme production by up to 3.07 ± 0.17 U/mL. Meanwhile, 0.4% (w/v) ammonium nitrate was used as a nitrogen source yielding the highest enzyme activity with a value of 6.86 ± 0.07 U/mL.</p><p><strong>Conclusion: </strong>Thus, the locally isolated fungal strain, A. niger LFP-1 has outstanding pectinase-producing capability and can be utilized for the commercial production of pectinase. The improved cultural conditions significantly increase pectinase production and shorten the incubation period from 8 days (before improvement) to 6 days (after improvement).</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"45"},"PeriodicalIF":0.0,"publicationDate":"2023-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10126171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9394682","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":"Characterization, protein modeling, and molecular docking of factor C from Indonesian horseshoe crab (Tachypleus gigas).","authors":"Apon Zaenal Mustopa, Ayu Fitri Izaki, Suharsono Suharsono, Fatimah Fatimah, Fauziyah Fauziyah, Rahmi Damarani, Arwansyah Arwansyah, Setyanto Tri Wahyudi, Siswi Sekar Sari, Rozirwan Rozirwan, Zubaidi Bachtiar","doi":"10.1186/s43141-023-00496-8","DOIUrl":"10.1186/s43141-023-00496-8","url":null,"abstract":"<p><strong>Background: </strong>Horseshoe crab (Tachypleus gigas) amebocytes are useful biomedical components for endotoxin detection, and their growing needs for biomedical purposes cause the horseshoe crab population to decline. Factor C synthesis via genetic engineering offers a solution to replace natural horseshoe crab's factor C and prevent its excessive harvest from nature. In response to these concerns, this study aimed to characterize the amebocyte lysates and factor C protein modeling of T. gigas originated from Banyuasin South Sumatra Estuary.</p><p><strong>Methods and results: </strong>Sampling of T. gigas was carried out in Banyuasin South Sumatra Estuary, Indonesia. The endotoxin test or TAL (Tachypleus amebocyte lysates) assay was performed using gel coagulation method. Protein characterization of protease enzyme was conducted by protease activity, SDS-PAGE, and zymogram analysis. The cDNA of mitochondrial COI gene was amplified for molecular identification followed by cDNA cloning of factor C. Protein modeling was investigated by molecular docking and molecular dynamic (MD) simulation. Endotoxin test results showed that TAL-35 had endotoxin sensitivity in a range of 0.0156-1 EU/ml, while TAL 36 had a sensitivity between 00,625 and 1 EU/ml. T. gigas amebocytes have protease activity in molecular mass sizes less than 60 kDa, with 367 U/ml for TAL 35 and 430 U/ml for TAL 36. The molecular identification revealed 98.68% identity similarity to T. gigas. The docking results suggested three ligands; i.e., diphosphoryl lipid A, core lipid A, and Kdo2 lipid A can be activators of the factor C protein by binding to the region of the receptor to form a ligand-receptor complex.</p><p><strong>Conclusions: </strong>Endotoxins can be detected using horseshoe crab amebocytes. The presence of proteases is considered responsible for this ability, as evidenced by casein zymogram results. According to docking and MD analysis, we found that lipopolysaccharides (LPS) participate to the binding site of factor C.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"44"},"PeriodicalIF":3.6,"publicationDate":"2023-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10090249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9654759","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":"Identification of conserved miRNAs and their targets in Jatropha curcas: an in silico approach.","authors":"Foeaz Ahmed,&nbsp;Md Nazmul Islam Bappy,&nbsp;Md Shariful Islam","doi":"10.1186/s43141-023-00495-9","DOIUrl":"https://doi.org/10.1186/s43141-023-00495-9","url":null,"abstract":"<p><strong>Background: </strong>MicroRNAs (miRNAs) are small endogenous RNAs with an approximate length of 18-22 nucleotides and involved in the regulation of gene expression in transcriptional or post-transcriptional levels. They were found to be associated with leaf morphogenesis, flowering time, vegetative phase change, and response to environmental cues in plants, where they act as a critical regulatory factor. The nature of high conservancy of plant miRNAs within the plant species made it possible to detect the conserved miRNAs by computational approaches. Expressed Sequence Tags (EST) based comparative genomic approaches provide advantages over wet lab approaches as it is convenient, easy to carry out and less time consuming. EST-based in silico approach can unravel new conserved miRNAs in plants, even when the complete genome sequence is not available.</p><p><strong>Results: </strong>To identify the novel miRNAs, a total of 46,865 ESTs from Jatropha curcas were searched for homology to all available 6746 mature miRNAs of plant eudicotyledons. Finally, we ended up with 12 novel miRNAs in Jatropha that range from 18 to 19 nucleotides where their respective precursor miRNAs had 54.11-71.76% (A + U) content. The putative miRNAs belong to 12 individual miRNA family and most of them have higher (A + U) content ranging from 47.36 to 77.77% than their respective miRNA homologs. Many of the target genes by the newly identified miRNAs were associated with plant growth and development, stress response, defense and hormone signaling, and oil synthesis pathways.</p><p><strong>Conclusion: </strong>These findings have the potential to speed up miRNA identification and expand our understanding of miRNA functions in J. curcas.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"43"},"PeriodicalIF":0.0,"publicationDate":"2023-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10079790/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9625382","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}