Journal, genetic engineering & biotechnology最新文献

{"title":"Estimating the role of single-nucleotide polymorphism (rs1800629)-308 G/A of TNF-alpha gene as genetic marker associated with angina pectoris in a sample of Iraqi patients.","authors":"Shaimaa Y Abdulfattah,&nbsp;Farah Thamer Samawi","doi":"10.1186/s43141-022-00454-w","DOIUrl":"https://doi.org/10.1186/s43141-022-00454-w","url":null,"abstract":"<p><strong>Background: </strong>Angina pectoris (AP) occurs when oxygen and other nutrients are insufficient to meet the metabolic needs of the heart muscle. Stable angina is the most common, while the unstable angina is less frequent. Tumor necrosis factor alpha (TNF-alpha) is a pleiotropic cytokine plays a vital function in the immune response regulation. TNF gene cluster contains many polymorphisms; the most commonly investigated polymorphism is the rs1800629 SNP. This SNP, located at - 308 position with regard to the TNF promoter region, replaces guanine (G) with adenine (A), with the allelic types - 308 G/A, and has been linked to a variety of inflammatory condition and autoimmune diseases. The - 308 G/A SNP was investigated in AP and interconnected to the TNF level to figure out the responsibilities of TNF-alpha gene polymorphism in the pathogenesis of AP.</p><p><strong>Method: </strong>The current work design as a case-control study that involves 300 participant divided to 200 patients evaluated as (stable angina n = 100 and unstable angina n = 100) compared with 100 apparently healthy control subjects. The serum level of TNF-alpha was assessed via enzyme-linked immunosorbent assay (ELISA)/sandwich method. The genotype and allele frequency distribution of TNF-alpha rs1800629 gene polymorphism were investigated by TaqMan probe of allelic discrimination method.</p><p><strong>Results: </strong>The levels of TNF-alpha were significantly higher in patients with stable and unstable angina pectoris in comparison with controls. The deviation from Hardy-Weinberg equilibrium (HWE) of TNF-alpha genotypes was obvious in control and unstable angina pectoris groups. Moreover, the significant differences between patients with AP and controls under the five genetic models consider the association between TNF-alpha (rs1800629) - 308 G/A and AP with OR > 1. However, data analysis of allelic and genotypic of (rs1800629) - 308 G/A revealed higher significantly differences of GG homozygous and GA heterozygous proportions between stable angina patients and control. The A allele was more represented as etiological allele, and G allele was represented as protective allele. The serum levels of TNF-alpha were significantly higher in subjects with genetically mutated AA genotypes than in subjects with wild GG genotypes in the study groups. ROC curve analysis found the best cutoff value of TNF-alpha level was 77.25 pg/ml.</p><p><strong>Conclusion: </strong>As the results, our data observed a linked of TNF-alpha (rs1800629) - 308 G/A genetic variant with angina pectoris patients, and the A allele has been linked to the production or expression of TNF-alpha serum level and represented an etiological factor of angina pectoris.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"2"},"PeriodicalIF":0.0,"publicationDate":"2023-01-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9829927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10557694","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":"Phylogenetic and genetic variation analysis of lesser short-nosed fruit bat Cynopterus brachyotis (Müller 1838) on Java island, Indonesia, inferred from mitochondrial D-loop.","authors":"Husni Mubarok,&nbsp;Niken Satuti Nur Handayani,&nbsp;Ibnu Maryanto,&nbsp;Tuty Arisuryanti","doi":"10.1186/s43141-022-00460-y","DOIUrl":"https://doi.org/10.1186/s43141-022-00460-y","url":null,"abstract":"<p><strong>Background: </strong>Cynopterus brachyotis (Müller 1838) is a generalist and widespread fruit bat species which inhabits different types of habitats in Southeast Asia. This species plays an essential role as a seed disperser and pollinator. Morphological study and phylogenetic analysis using mtDNA markers (cyt-b and D-loop) revealed that this species had two different forms in peninsular Malaysia and Borneo and six lineages in Southeast Asia that lead to new species formation. In addition, this species is also reported to have high genetic diversity in Malaysia and Thailand based on the D-loop sequence. However, a phylogenetic and genetic variation study of C. brachyotis in Indonesia has not been conducted yet. These two studies are important as additional information for taxonomic and population genetic studies of this species. Thus, we performed the phylogenetic and genetic diversity analysis of the C. brachyotis population collected from seven habitats on Java island, including open-fragmented habitats (urban, coffee and rubber plantations, pine forest, secondary forest, mangrove forest) and closed habitats (natural forest) using the mtDNA D-loop marker.</p><p><strong>Results: </strong>The phylogenetic tree using the Bayesian inference (BI) and genetic distance using the Kimura-2 parameter (K-2P) demonstrated that 33 individuals of C. brachyotis from seven habitats on Java island overlapped between habitats and could not be distinguished according to their habitats and lineage. Intrapopulation and intraspecies analysis revealed high haplotype diversity of this species on Java island (Hd = 0.933-1.000). The haplotype network was split into two haplogroups, showing haplotype sharing between habitats. These phylogenetic and genetic variations analysis of C. brachyotis bats on Java island indicated that this species is widespread and adapt to different habitats.</p><p><strong>Conclusions: </strong>This study of C. brachyotis on Java island collected from seven different habitats has overlapped and genetically close and has high genetic variation. Our results provide the first reported study of C. brachyotis on Java island and provide data to understand the phylogenetic and genetic diversity of this species in Indonesia.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"21 1","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2023-01-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9813318/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10540828","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":"Mining and validation of novel simple sequence repeat (SSR) markers derived from coconut (Cocos nucifera L.) genome assembly.","authors":"Reina Esther S Caro,&nbsp;Jesmar Cagayan,&nbsp;Roanne R Gardoce,&nbsp;Anand Noel C Manohar,&nbsp;Alma O Canama-Salinas,&nbsp;Ramon L Rivera,&nbsp;Darlon V Lantican,&nbsp;Hayde F Galvez,&nbsp;Consorcia E Reaño","doi":"10.1186/s43141-022-00354-z","DOIUrl":"https://doi.org/10.1186/s43141-022-00354-z","url":null,"abstract":"<p><strong>Background: </strong>In the past, simple sequence repeat (SSR) marker development in coconut is achieved through microsatellite probing in bacterial artificial chromosome (BAC) clones or using previously developed SSR markers from closely related genomes. These coconut SSRs are publicly available in published literatures and online databases; however, the number is quite limited. Here, we used a locally established, coconut genome-wide SSR prediction bioinformatics pipeline to generate a vast amount of coconut SSR markers.</p><p><strong>Results: </strong>A total of 7139 novel SSR markers were derived from the genome assembly of coconut 'Catigan Green Dwarf' (CATD). A subset of the markers, amounting to 131, were selected for synthesis based on motif filtering, contig distribution, product size exclusion, and success of in silico PCR in the CATD genome assembly. The OligoAnalyzer tool was also employed using the following desired parameters: %GC, 40-60%; minimum ΔG value for hairpin loop, -0.3 kcal/mol; minimum ΔG value for self-dimer, -0.9 kcal/mol; and minimum ΔG value for heterodimer, -0.9 kcal/mol. We have successfully synthesized, optimized, and amplified 131 novel SSR markers in coconut using 'Catigan Green Dwarf' (CATD), 'Laguna Tall' (LAGT), 'West African Tall' (WAT), and SYNVAR (LAGT × WAT) genotypes. Of the 131 SSR markers, 113 were polymorphic among the analyzed coconut genotypes.</p><p><strong>Conclusion: </strong>The development of novel SSR markers for coconut will serve as a valuable resource for mapping of quantitative trait loci (QTLs), assessment of genetic diversity and population structure, hybridity testing, and other marker-assisted plant breeding applications.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"20 1","pages":"71"},"PeriodicalIF":0.0,"publicationDate":"2022-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9110602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10242751","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":"Immunoinformatics approach of epitope prediction for SARS-CoV-2.","authors":"Nourelislam Awad,&nbsp;Rania Hassan Mohamed,&nbsp;Nehal I Ghoneim,&nbsp;Ahmed O Elmehrath,&nbsp;Nagwa El-Badri","doi":"10.1186/s43141-022-00344-1","DOIUrl":"https://doi.org/10.1186/s43141-022-00344-1","url":null,"abstract":"<p><strong>Background: </strong>The novel coronavirus (SARS-CoV-2) caused lethal infections worldwide during an unprecedented pandemic. Identification of the candidate viral epitopes is the first step in the design of vaccines against the viral infection. Several immunoinformatic approaches were employed to identify the SARS-CoV-2 epitopes that bind specifically with the major histocompatibility molecules class I (MHC-I). We utilized immunoinformatic tools to analyze the whole viral protein sequences, to identify the SARS-CoV-2 epitopes responsible for binding to the most frequent human leukocyte antigen (HLA) alleles in the Egyptian population. These alleles were also found with high frequency in other populations worldwide.</p><p><strong>Results: </strong>Molecular docking approach showed that using the co-crystallized MHC-I and T cell receptor (TCR) instead of using MHC-I structure only, significantly enhanced docking scores and stabilized the conformation, as well as the binding affinity of the identified SARS-CoV-2 epitopes. Our approach directly predicts 7 potential vaccine subunits from the available SARS-CoV-2 spike and ORF1ab protein sequence. This prediction has been confirmed by published experimentally validated and in silico predicted spike epitope. On the other hand, we predicted novel epitopes (RDLPQGFSA and FCLEASFNY) showing high docking scores and antigenicity response with both MHC-I and TCR. Moreover, antigenicity, allergenicity, toxicity, and physicochemical properties of the predicted SARS-CoV-2 epitopes were evaluated via state-of-the-art bioinformatic approaches, showing high efficacy of the proposed epitopes as a vaccine candidate.</p><p><strong>Conclusion: </strong>Our predicted SARS-CoV-2 epitopes can facilitate vaccine development to enhance the immunogenicity against SARS-CoV-2 and provide supportive data for further experimental validation. Our proposed molecular docking approach of exploiting both MHC and TCR structures can be used to identify potential epitopes for most microbial pathogens, provided the crystal structure of MHC co-crystallized with TCR.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":"20 1","pages":"60"},"PeriodicalIF":0.0,"publicationDate":"2022-04-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9019534/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9180299","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 statistical strategy for optimizing the production of α-galactosidase by a newly isolated Aspergillus niger NRC114 and assessing its efficacy in improving soymilk properties.","authors":"Ali M Elshafei,&nbsp;Abdelmageed M Othman,&nbsp;Maysa A Elsayed,&nbsp;Gamil E Ibrahim,&nbsp;Mohamed M Hassan,&nbsp;Nayra S Mehanna","doi":"10.1186/s43141-022-00315-6","DOIUrl":"https://doi.org/10.1186/s43141-022-00315-6","url":null,"abstract":"<p><strong>Background: </strong>α-Galactosidase is widely distributed in plants, microorganisms, and animals, and it is produced by different fungal sources. Many studies have confirmed the valuable applications of α-galactosidase enzymes for various biotechnological purposes, like the processing of soymilk.</p><p><strong>Results: </strong>Aspergillus niger NRC114 was exploited to produce the extracellular α-galactosidase. One factor per time (OFT) and central composite design (CCD) approaches were applied to determine the optimum parameters and enhance the enzyme production. The CCD model choices of pH 4.73, 1.25% mannose, 0.959% meat extract, and 6-day incubation period have succeeded in obtaining 25.22 U/mL of enzyme compared to the 6.4 U/mL produced using OFT studies. Treatment of soymilk by α-galactosidase caused an increase in total phenols and flavonoids by 27.3% and 19.9%, respectively. Antioxidant measurements revealed a significant increase in the enzyme-treated soymilk. Through HPLC analysis, the appearance of sucrose, fructose, and glucose in the enzyme-treated soymilk was detected due to the degradation of stachyose and raffinose. The main volatile compounds in raw soymilk were acids (45.04%) and aldehydes (34.25%), which showed a remarkable decrease of 7.82% and 20.03% after treatment by α-galactosidase.</p><p><strong>Conclusions: </strong>To increase α-galactosidase production, the OFT and CCD approaches were used, and CCD was found to be four times more effective than OFT. The produced enzyme proved potent enough to improve the properties of soymilk, avoiding flatulence and undesirable tastes and odors.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"36"},"PeriodicalIF":0.0,"publicationDate":"2022-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881569/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39835685","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":"Spatiotemporal expression pattern of miR-205, miR-26a-5p, miR-17-5p, let-7b-5p, and their target genes during different stages of corpus luteum in Egyptian buffaloes.","authors":"Sally Ibrahim,&nbsp;Mohamed O Taqi,&nbsp;A S A Sosa,&nbsp;Al-Shimaa Al-H H El-Naby,&nbsp;Karima Gh M Mahmoud,&nbsp;Hassan R H Darwish,&nbsp;Amal R Abd El Hameed,&nbsp;M F Nawito","doi":"10.1186/s43141-022-00320-9","DOIUrl":"https://doi.org/10.1186/s43141-022-00320-9","url":null,"abstract":"<p><strong>Background: </strong>No doubt that the corpus luteum (CL) plays a vital role in the regulation of female cyclicity in mammals. The scenarios among microRNAs (miRNAs) and their target genes and steroid hormones {estradiol (E2) and progesterone (P4)} are required for better understanding the molecular regulation of CL during its formation, maturation, and regression. We aimed to (I) study the changes in the relative abundance of miR-205, miR-26a-5p, miR-17-5p, and let-7b-5p and their target genes: LHCGR, CASP3, PCNA, AMH, and PLA2G3, during different stages of corpus luteum in Egyptian buffaloes, and (II) and to address different scenarios between steroid concentrations in the serum and the expression pattern of selected miRNAs and their targets.</p><p><strong>Methods: </strong>The paired ovaries and blood samples were collected from apparently healthy 50 buffalo cows at a private abattoir. The ovaries bearing CL were macroscopically divided according to their morphological structure and color into hemorrhagic (CLH), developing (CLD), mature (CLM), regressed (CLR), and albicans (CLA). Small pieces from different stages of CL (CLH, CLD, CLM, CLR, and CLA) were cut and immediately kept at - 80 °C for total RNA isolation and qRT-PCR. The serum was separated for steroid level estimation.</p><p><strong>Results: </strong>The LHCGR was expressed during different stages of CL, and the peak of expression was at the mid-luteal stage. The CASP3 revealed a stage-specific response at different stages of CL. The PCNA has an essential role in cellular proliferation in buffaloes CL. Both expression patterns of PLA2G3 and AMH were found over the various developmental and regression stages. It was noticed that miR-205 is conserved to target LHCGR and CASP3 transcripts. Moreover, CASP3 and AMH were targeted via miR-26a-5p. Additionally, the CASP3 and PLA2G3 were targeted via let-7b-5p. The P4 level reached its peak during CLM. There were positive and negative strong correlations between miRNAs (miR-26a-5p and miR-205), target genes (LHCGR and CASP3) during different stages of CL, and steroid hormones in the serum.</p><p><strong>Conclusions: </strong>Taken together, the orchestrated pattern among miRNAs, target genes, and steroid hormones is essential for maintaining the proper development and function of CL in buffalo cows.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"37"},"PeriodicalIF":0.0,"publicationDate":"2022-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8881532/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39960876","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":"Screening and identification of potential inhibitor for visceral leishmaniasis (VL) through computational analysis.","authors":"N Shaslinah,&nbsp;P Sangavi,&nbsp;R Sangeetha,&nbsp;S Gowthamkumar,&nbsp;V Sindhu,&nbsp;K Langeswaran","doi":"10.1186/s43141-022-00318-3","DOIUrl":"https://doi.org/10.1186/s43141-022-00318-3","url":null,"abstract":"<p><strong>Aim: </strong>The aim of this investigation is to detect potential inhibitor for visceral leishmaniasis through computational analysis.</p><p><strong>Background: </strong>Leishmaniasis is categorized as a vector born pathogenic infection prevalent in tropical, subtropical, and in Mediterranean zones spread by intra-macrophage protozoa. The clinical syndrome of leishmaniasis is divided into the following type's namely cutaneous leishmaniasis, mucocutaneous leishmaniasis, visceral leishmaniasis, and dermal leishmaniasis. Trypanothione synthetase is a key enzyme involving in glutathione biosynthesis as well as hydrolysis. Trypanothione is one of the promising drug targets for parasites. Parasites are inimitable with concern to their dependence on trypanothione to regulate intracellular thiol-redox balance in fighting against oxidative stress and biochemical anxiety. However, trypanothione synthetase was presumed as the target therapeutic alternate in VL therapy.</p><p><strong>Objective: </strong>The important objective of this current investigation is to identify or analyze the potential inhibitor for V. leishmaniasis through computational approaches which include virtual screening, molecular docking, ADME prediction, and molecular dynamic simulation.</p><p><strong>Methods: </strong>An investigation was performed to develop a 3D protein structure, using computational screening among associated similar structured proteins from popular compound database banks such as Specs, Maybridge, and Enamine, to detect novel staging with a series of validation for emerging innovative drugs molecules. Modeled protein ligand complex was further analyzed to know the binding ability of the complex. Molecular dynamics were performed to ascertain its stability at 50 ns.</p><p><strong>Results: </strong>Trypanothione synthetase overall ability in the outcome of series of analysis. Among three database compounds screened, the compound from the Specs database exhibited the better protein-ligand docking scores and fulfilled the drug-like properties through ADMET analysis, and the docked complexes had better stability throughout the simulation. Besides, the other two database leads fulfilled the pharmacological properties, and the complexes were stable in the simulation.</p><p><strong>Conclusion: </strong>By analyzing the various compounds from different databases, we concluded that the Specs database compound exhibits potential activity against the target protein and is considered a promising inhibitor for trypanothione synthetase.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2022-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8866605/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39821537","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":"Purification, biochemical characterization, and molecular cloning of cellulase from Bacillus licheniformis strain Z9 isolated from soil.","authors":"Zainab E Elsababty,&nbsp;Samir H Abdel-Aziz,&nbsp;Atef M Ibrahim,&nbsp;Adel A Guirgis,&nbsp;Ghada E Dawwam","doi":"10.1186/s43141-022-00317-4","DOIUrl":"https://doi.org/10.1186/s43141-022-00317-4","url":null,"abstract":"<p><strong>Background: </strong>Cellulose is the most prevalent biomass and renewable energy source in nature. The hydrolysis of cellulosic biomass to glucose units is essential for the economic exploitation of this natural resource. Cellulase enzyme, which is largely generated by bacteria and fungus, is commonly used to degrade cellulose. Cellulases are used in a variety of industries, including bioethanol manufacturing, textiles, detergents, drugs, food, and paper. As part of our quest to find an efficient biocatalyst for the hydrolysis of cellulosic biomass, we describe the amplification, cloning, and sequencing of cellulase (cel9z) from Bacillus licheniformis strain Z9, as well as the characterization of the resulting enzyme.</p><p><strong>Results: </strong>Cellulase was partially purified from B. licheniformis strain Z9 using (NH₄)₂SO₄ precipitation and Sephadex G-100 gel column chromatography with 356.5 U/mg specific activity, 2.1-purification fold, and 3.07 % yield. The nucleotide sequence of the cellulase gene was deposited to the GenBank, B. licheniformis strain Z9 cellulase (cel9z) gene, under accession number MK814929. This corresponds to 1453 nucleotides gene and encodes for a protein composed of 484 amino acids. Comparison of deduced amino acids sequence to other related cellulases showed that the enzyme cel9z can be classified as a glycoside hydrolase family 9. SDS-PAGE analysis of the purified enzyme revealed that the molecular mass was 54.5 kDa. The optimal enzyme activity was observed at pH 7.4 and 30 °C. The enzyme was found to be strongly inhibited by Mg²⁺ and Na⁺, whereas strongly activated by Fe³⁺, Cu²⁺, and Ca²⁺.</p><p><strong>Conclusions: </strong>B. licheniformis strain Z9 and its cellulase gene can be further utilized for recombinant production of cellulases for industrial application.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"34"},"PeriodicalIF":0.0,"publicationDate":"2022-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8864052/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39640613","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":"Isolation, molecular identification of lipid-producing Rhodotorula diobovata: optimization of lipid accumulation for biodiesel production.","authors":"Mohamed E Osman,&nbsp;Asharf Bakery Abdel-Razik,&nbsp;Khaled I Zaki,&nbsp;Nesma Mamdouh,&nbsp;Heba El-Sayed","doi":"10.1186/s43141-022-00304-9","DOIUrl":"https://doi.org/10.1186/s43141-022-00304-9","url":null,"abstract":"<p><strong>Background: </strong>The increased demand for oil and fats to satisfy the ever-increasing human needs has enhanced the research in this field. Single-cell oils or microbial lipids produced by oleaginous microorganisms are being utilized as an alternative to traditional oil sources. Oleaginous yeasts can accumulate lipids above 20% of their biomass when they are grown under controlled conditions.</p><p><strong>Results: </strong>In the present study, sixty-five yeasts were isolated from different sources. Using Sudan Black B staining technique, five yeast isolates were selected. Under nitrogen-limited cultivation conditions, the Co1 isolate was the best lipid accumulation potential of 39.79%. Isolate (Co1) was characterized morphologically and identified using the ribosomal DNA internal transcribed spacers regions (rDNA-ITS) from their genomic DNA. The sequence alignment revealed a 99.2% similarity with Rhodotorula diobovata. Under the optimized conditions, Rhodotorula diobovata accumulated lipids up to 45.85% on a dry biomass basis. R. diobovata, when grown on different raw materials, accumulated lipid up to 46.68% on sugar beet molasses medium, and the lipid had a high degree of monounsaturated fatty acids which gives biodiesel better quality.</p><p><strong>Conclusions: </strong>The data suggest that the potent oleaginous yeast, R. diobovata, together with the use of cheap feedstock raw materials such as sugar beet molasses, can be considered as a promising feedstock for biodiesel production.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2022-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861238/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39818081","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":"Dynamic disequilibrium-based pathogenicity model in mutated pyrin's B30.2 domain-Casp1/p20 complex.","authors":"Alaaeldin G Fayez,&nbsp;Ghada Nour Eldeen,&nbsp;Waheba A Zarouk,&nbsp;Khaled Hamed,&nbsp;Abeer Ramadan,&nbsp;Bardees M Foda,&nbsp;Maha M Kobesiy,&nbsp;Mai E Zekrie,&nbsp;Randa S Lotfy,&nbsp;Mona F Sokkar,&nbsp;Hala T El-Bassyouni","doi":"10.1186/s43141-022-00300-z","DOIUrl":"https://doi.org/10.1186/s43141-022-00300-z","url":null,"abstract":"<p><strong>Background: </strong>The B30.2 variants lead to most relevant severity forms of familial Mediterranean fever (FMF) manifestations. The B30.2 domain plays a key role in protein-protein interaction (PPI) of pyrin with other apoptosis proteins and in regulation the cascade of inflammatory reactions. Pyrin-casp1 interaction is mainly responsible for the dysregulation of the inflammatory responses in FMF. Lower binding affinity was observed between the mutant B30.2 pyrin and casp1 without the release of the complete pathogenicity mechanism. The aim of this study was to identify the possible effects of the interface pocked residues in B30.2/SPRY-Casp1/p20 complex using molecular mechanics simulation and in silico analysis.</p><p><strong>Results: </strong>It was found that Lys671Met, Ser703Ile, and Ala744Ser variants led mainly to shift of the binding affinity (∆G), dissociation constant (K_d), and root mean square deviation (RMSD) in B30.2/SPRY-Casp1/p20 complex leading to dynamic disequilibrium of the p20-B30.2/SPRY complex toward its complex form. The current pathogenicity model and its predicted implementation in the relevant colchicine dosage were delineated.</p><p><strong>Conclusion: </strong>The molecular mechanics analysis of B30.2/SPRY-p20 complex harboring Lys671Met, Ser703Ile, and Ala744Ser variants showed dynamic disequilibrium of B30.2/SPRY-casp1/p20complex in context of the studied variants that could be a new computational model for FMF pathogenicity. This study also highlighted the specific biochemical markers that could be useful to adjust the colchicine dose in FMF patients.</p>","PeriodicalId":74026,"journal":{"name":"Journal, genetic engineering & biotechnology","volume":" ","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2022-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8861233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39804551","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}