Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Can human IgG subclasses distinguish between confirmed and unconfirmed SARS-CoV-2 infections?","authors":"Mahmoud Mohamed Bahgat ,&nbsp;Mohamed Hassan Nasraa ,&nbsp;Rola Nadeem ,&nbsp;Khaled Amer ,&nbsp;Wael A. Hassan ,&nbsp;Ahmed Abd EL-Raouf ,&nbsp;Dina Nadeem Abd-Elshafy","doi":"10.1016/j.jgeb.2024.100399","DOIUrl":"10.1016/j.jgeb.2024.100399","url":null,"abstract":"<div><h3>Background</h3><p>Immunoglobulin G (IgG) subclasses play a crucial role in the immune response to viral infections. While total IgG levels can generally provide an indication on the immune response, specific IgG subclasses can offer more detailed information about nature of the immune response and stage of the infection. Herein, we addressed the value of both total (t) and SARS-CoV-2-specific (s) IgG-subclasses in distinguishing between infection-confirmed virus-qRT-PCR-positive (IC; V-qRT-PCR-P) and infection-unconfirmed virus-qRT-PCR-unchecked (IU; V-qRT-PCR-UC) Egyptians.</p></div><div><h3>Results</h3><p>Both the t-IgG2 and 4 means were significantly higher (SH) among the IU subjects, whereas, the s-IgG1 and 3 means were SH among the IC ones. On the gender levels, both the t-IgG2 and 4 means were SH among the IU females, whereas, the mean of the s-IgG1 was SH among the IC females. The t-IgG4 mean was SH among the IU males, whereas, both means of the s-IgG1 and 3 were SH among the IC males. Significant positive correlations (SPC) were recorded between both the t-IgG1 and 3 with the symptom grades (SG) among the IU humans (r² = 0.200 and 0.253, respectively). Also, SPC was noticed between the s-IgG2 and the SG among the IU females (r² = 0.6782). SPC was recorded between both the t-IgG1 and the s-IgG2 with the SG among the IU males (r² = 0.794 and 0.373, respectively). SPC was noticed between the t-IgG3 and the age among the IC males (r² = 0.779).</p></div><div><h3>Conclusion</h3><p>Although the limitation of the small studied sample size, our results suggest some total and SARS-CoV-2-specific IgG-subclasses as both supplemental and gender-specific immune markers to distinguish between confirmed and unconfirmed SARS-CoV-2 infections.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100399"},"PeriodicalIF":3.5,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001021/pdfft?md5=5306b0c0d9b04f02e59420c85290fba4&pid=1-s2.0-S1687157X24001021-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141961787","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":"Genome-wide characterization and expression profiling of FARL (FHY3/FAR1) family genes in Zea mays","authors":"Sharah Jabeen Mou ,&nbsp;Prodipto Bishnu Angon","doi":"10.1016/j.jgeb.2024.100401","DOIUrl":"10.1016/j.jgeb.2024.100401","url":null,"abstract":"<div><p>A significant role of the plant is played by the transcription factor FARL, which is light signal transduction as well as plant growth and development. Despite being transposases, FARL has developed a variety of dominant biological actions in evolution and speciation. On the other hand, little is known about the <em>Zea mays</em> FARL protein family. This study identifies and characterizes fifteen <em>ZmFARL</em> genes genome-wide, and RNA sequencing data was used to profile their expression. 105 FARL proteins from five plant species were classified into five groups based on sequence alignment and phylogeny. The <em>ZmFARL</em> genes’ exon–intron and motif distribution were conserved based on their evolutionary group. The fifteen <em>ZmFARL</em> genes were distributed over seven of the ten <em>Z. mays</em> chromosomes, although no duplication was discovered. <em>Cis</em>-element analysis reveals that <em>ZmFARL</em> genes play a variety of activities, including tissue-specific, stress- and hormone-responsive expressions. Furthermore, the results of the RNA sequencing used to profile expression showed that the genes <em>ZmFARL2</em> and <em>ZmFARL5</em> were much more expressed than other genes in various tissues, particularly in leaf characteristics. The identification of likely genes involved in cellular activity in <em>Z. mays</em> and related species will be aided by the characterization of the <em>FARL</em> genes.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100401"},"PeriodicalIF":3.5,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001045/pdfft?md5=0994da1f5ea3024c87eb9a77ba33d9ab&pid=1-s2.0-S1687157X24001045-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141961786","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":"Bioinformatic and functional analysis of a PHB polymerase (PhbC) from Azospirillum baldaniorum","authors":"Doris del Carmen Fuentes ,&nbsp;Lucía Soto-Urzua ,&nbsp;Lino Javier Martínez-Soto ,&nbsp;Luis Javier Martínez-Morales","doi":"10.1016/j.jgeb.2024.100403","DOIUrl":"10.1016/j.jgeb.2024.100403","url":null,"abstract":"<div><h3>Background</h3><p><em>Azospirillum baldaniorum</em> Sp245 produces poly-β-hydroxybutyrate, a biodegradable polymer with characteristics similar to synthetic thermoplastics, including polypropylene. In the synthesis pathway, the poly-β-hydroxybutyrate synthase enzyme uses thioesters of 3-hydroxy butyryl-CoA as a substrate and catalyzes their polymerization with HS-CoA release.</p></div><div><h3>Methods</h3><p>A study was conducted using <em>in silico</em> analysis of the two <em>phb</em>C genes of <em>A. baldaniorum</em> Sp245. One was selected for amplification and cloning into the pEXP5- CT/TOPO® vector, which was analysed by restriction pattern, polymerase chain reaction, and sequencing. SDS-PAGE analysis determined the molecular weight of the PhbC1 protein from <em>Azospirillum baldaniorum</em> (AbPhbC1). The presence of the protein was confirmed by Western blotting using anti-polyhistidine monoclonal antibodies. The enzymatic activity in the crude extract of AbPhbC1 was determined by measuring the concentration of sulfhydryl groups using the Ellman method. A UV–Vis assay was performed. To confirm the presence of the poly-β-hydroxybutyrate product, an NMR assay was performed.</p></div><div><h3>Results</h3><p><em>In silico</em> analyses, it is revealed that AbPhbC1 and the PhbC2 protein from <em>Azospirillum baldaniorum</em> (AbPhbC2) retain the poly-β-hydroxybutyrate polymerase and α/β hydrolase domain. The Cys-His-Asp catalytic triad is highly conserved in all four polyβ-hydroxyalkanoate synthases in the central subdomain, structurally similar to the reported crystallized proteins. The dimerization subdomain is different; in AbPhbC1, it is in the closed form; in AbPhbC2, it is in the open form; and in AbPhbC2, it lacks the EC region as class III and IV poly-β-hydroxyalcanoate synthases. In vitro, the molecular weight of AbPhbC1 was 68 kDa. The polymerization of PHB by AbPhbC1 was detected by the release of HS-CoA from the quantification of SH. The UV–Vis scan showed a characteristic peak at 264 nm. A comparison of the NMR spectra of the bacterial and commercial poly-β-hydroxybutyrate samples suggested their presence.</p></div><div><h3>Conclusion</h3><p><em>In silico</em> analyses suggested that AbPhbC1 and AbPhbC2 are structurally functional, except that AbPhbC2 might require the PhaR subunit for its activity; this strongly suggests that it could be a class IV poly-β-hydroxyalcanoate synthase. UV–Vis scanning and NMR spectroscopy revealed the synthesis of poly-β-hydroxybutyrate by the <em>A. baldaniorum</em> enzyme AbPhbC1, indicating that the enzyme is functional.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100403"},"PeriodicalIF":3.5,"publicationDate":"2024-07-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001069/pdfft?md5=afe7ad1f4b87cee05942aeb268459c3e&pid=1-s2.0-S1687157X24001069-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141954433","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 of Bacillus amyloliquefaciens strain S2.5 as a potential probiotic for feed supplement in livestock production","authors":"Ha-Anh Nguyen,&nbsp;Thao Tran P.,&nbsp;Hang Thuy Dam,&nbsp;Hai Van Nguyen,&nbsp;Thanh Ha Le,&nbsp;Phu-Ha Ho,&nbsp;Nguyen Lan Huong","doi":"10.1016/j.jgeb.2024.100404","DOIUrl":"10.1016/j.jgeb.2024.100404","url":null,"abstract":"<div><h3>Background</h3><p>Supplementing probiotics in livestock feed is increasing due to concerns over the potential harm caused by antibiotics and other chemical growth promoters. Several <em>Bacillus</em> sp. have been used as probiotic supplements for livestock. In this study, <em>Bacillus amyloliquefaciens</em> S2.5 was isolated from freshwater and its potential probiotic characteristics were evaluated <em>in vitro</em>. The whole genome of strain S2.5 was sequenced, and its probiotic traits were annotated using bioinformatic tools.</p></div><div><h3>Results</h3><p>Both vegetative cells and spores of strain S2.5 remained stable throughout the 1.5 h of gastric juice and 48 h of intestine simulation. The strain S2.5 harbored the ability to produce glucoamylase, carboxymethyl cellulase, protease, and chitinase. It is also susceptible to all six tested antibiotics. The complete genome sequence shows genes related to acid-bile tolerance, environmental stress resistance, hydrolases, and adhesion to gut mucosa, confirming probiotic traits in the <em>in vitro</em> experiments.</p></div><div><h3>Conclusions</h3><p><em>B. amyloliquefaciens</em> S2.5 demonstrated potential probiotic characteristics and its genetic profile in the <em>in vitro</em> experiments. Further <em>in vivo</em> assessments of <em>B. amyloliquefaciens</em> S2.5 on livestock and poultry should be performed to assess its practical application.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100404"},"PeriodicalIF":3.5,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001070/pdfft?md5=a45446593d5bbbcde54f42e5a0b2cbba&pid=1-s2.0-S1687157X24001070-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141954432","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":"Current developments of SELEX technologies and prospects in the aptamer selection with clinical applications","authors":"Danny Jair Chinchilla-Cárdenas ,&nbsp;Juan Sebastian Cruz-Méndez ,&nbsp;Julieth Michel Petano-Duque ,&nbsp;Ramón Ovidio García ,&nbsp;Lyda R Castro ,&nbsp;María Jesús Lobo-Castañón ,&nbsp;Giovanni Orlando Cancino-Escalante","doi":"10.1016/j.jgeb.2024.100400","DOIUrl":"10.1016/j.jgeb.2024.100400","url":null,"abstract":"<div><p>Aptamers are single-stranded oligonucleotide sequences capable of binding to specific ligands with high affinity. In this manner, they are like antibodies but have advantages such as lower manufacturing costs, lower immunogenicity, fewer batch-to-batch differences, a longer shelf life, high tolerance to different molecular milieus, and a greater number of potential targets. Due to their special features, they have been used in drug delivery, biosensor technology, therapy, and diagnostics. The methodology that allowed its production was the “Systematic Evolution of Ligands by Exponential enrichment” (SELEX). Unfortunately, the traditional protocol is time-consuming and laborious. Therefore, numerous variants with considerable optimization steps have been developed, nonetheless, there are still challenges to achieving real applications in the clinical field. Among them, are control of <em>in vivo</em> activities, fast renal filtration, degradation by nucleases and toxicity testing. This review focuses on current technologies based on SELEX, the critical factors for successful aptamer selection, and its upcoming biomedical and biotechnological applications.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100400"},"PeriodicalIF":3.5,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001033/pdfft?md5=8886b18a015cf67f98620836b74bfa7b&pid=1-s2.0-S1687157X24001033-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141954431","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":"Novel domain-structure-containing chitinases A and B of Bacillus velezensis produced by recombinant Escherichia coli cells: Synergism on chitin degradation and their potential in suppressing Candida albicans cell germination","authors":"Dinh Minh Tran,&nbsp;To Uyen Huynh,&nbsp;Tu Oanh Do","doi":"10.1016/j.jgeb.2024.100402","DOIUrl":"10.1016/j.jgeb.2024.100402","url":null,"abstract":"<div><p><em>Bacillus velezensis</em> RB.IBE29 harbors two chitinases belonging to the glycoside hydrolase family 18 and exhibiting a novel domain structure. The roles of these chitinases in crop production have been reported; nevertheless, their contribution to controlling human pathogens is unknown. In this initial work, the chitinases A (BvChiA) and B (BvChiB) of strain RB.IBE29 were produced in recombinant <em>Escherichia coli</em> BL21-CodonPlus (DE3)-RIPL cells and subsequently purified using HisTrap FF column. The purified BvChiA and BvChiB exhibited the highest chitinase and binding activities against colloidal chitin. Combining both chitinases for the hydrolysis of powdered chitin increased the reducing sugar content by 88.7 %. Moreover, the purified chitinases remarkably suppressed the germination of <em>Candida albicans</em> VTCC 20568 (=JCM 2070) cells. These results indicated that the novel domain-structure-containing chitinases of strain RB.IBE29 have great potential and can be further developed as a novel therapeutic agent against human pathogenic <em>C. albicans</em>.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100402"},"PeriodicalIF":3.5,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001057/pdfft?md5=61ce122ba96e17d2dba767dce5a11731&pid=1-s2.0-S1687157X24001057-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141941198","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":"Designing and development of efficient multi-epitope-based peptide vaccine candidate against emerging avian rotavirus strains: A vaccinomic approach","authors":"Mahamudul Hasan ,&nbsp;Shakil Ahmed ,&nbsp;Md. Imranuzzaman ,&nbsp;Rezaul Bari ,&nbsp;Shiplu Roy ,&nbsp;Md. Mahadi Hasan ,&nbsp;Md. Mukthar Mia","doi":"10.1016/j.jgeb.2024.100398","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100398","url":null,"abstract":"<div><h3>Background</h3><p>Enteric avian rotavirus (ARV) is the etiological agent of several health problems that pose a global threat to commercial chickens. Therefore, to avoid these widespread epidemics and high mortality rates, only vaccine and strict biosecurity are required.</p></div><div><h3>Method</h3><p>The present study employs computational techniques to design a unique multi-epitope-based vaccine candidate that successfully activates immune cells against the ARV by combining adjuvant, linker, and B and T-cell epitopes. Starting, homologous sequences in the various ARV serotypes were revealed in the NCBI BLAST database, and then the two surface proteins (VP4 and VP7) of the ARV were retrieved from the UniprotKB database. The Clustal Omega server was then used to identify the conserved regions among the homologous sequences, and the B and T-cell epitopes were predicted using IEDB servers. Then, superior epitopes—2 MHC-1 epitopes, 2 MHC-2 epitopes, and 3B-cell epitopes—were combined with various adjuvants to create a total of four unique vaccine candidates. Afterward, the designed vaccine candidates underwent computational validation to assess their antigenicity, allergenicity, and stability. The vaccine candidate (V2) that demonstrated non-antigenicity, a high VaxiJen score, and non-allergenicity was ultimately chosen for molecular docking and dynamic simulation.</p></div><div><h3>Results</h3><p>Although the V2 and V4 vaccine candidates were highly immunogenic, V2 had a higher solubility rate. The predicted values of the aliphatic index and GRAVY value were 30.4 and 0.417, respectively. In terms of binding energy, V2 outperformed V4. Being successfully docked with TLRs, V2 was praised as the finest. After adaptation, the sequence’s 50.73 % GC content outside of the BglII or ApaI restriction sites indicated that it was equivalently safe to clone. The chosen sequence was then inserted into the pET28a(+) vector within the BglII and ApaI restriction sites. This resulted in a final clone that was 4914 base pairs long, with the inserted sequence accounting for 478 bp and the vector accounting for the remainder.</p></div><div><h3>Conclusions</h3><p>The immune-mediated simulation results for the selected vaccine construct showed significant response; thus, the study confirmed that the selected V2 vaccine candidate could enhance the immune response against ARV.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100398"},"PeriodicalIF":3.5,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X2400101X/pdfft?md5=3b8fdf43686a21b7d0c96f1be737fcae&pid=1-s2.0-S1687157X2400101X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141481812","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":"Lipase activity of recombinant KmYJR107Wp and KmLIP3p enzymes expressed in Saccharomyces cerevisiae BY4742 from Kluyveromyces marxianus L2029","authors":"Ricardo Martínez-Corona ,&nbsp;Renato Canizal-García ,&nbsp;Luis Alberto Madrigal-Perez ,&nbsp;Carlos Cortés-Penagos ,&nbsp;Gustavo Alberto de la Riva de la Riva ,&nbsp;Juan Carlos González-Hernández","doi":"10.1016/j.jgeb.2024.100396","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100396","url":null,"abstract":"<div><p>Lipases are used in many food, energy, and pharmaceutical processes. Thus, new systems have been sought to synthesize alternative lipases with potential biotechnological applications. <em>Kluyveromyces marxianus</em> is a yeast with recognized lipase activity; at least ten putative lipases/esterases in its genome have been detected, and two of them possess a signal peptide for extracellular secretion. The study of extracellular lipases becomes more relevant since they usually have higher activity rates than intracellular lipases and simpler purification mechanisms. For these reasons, this study aimed to characterize the production and lipase activity of the putative extracellular lipases of the <em>K. marxianus</em> L-2029 strain, encoded in the genes <em>LIP3</em> and <em>YJR107W</em>. Both genes were heterologously expressed in <em>Saccharomyces cerevisiae</em> BY4742 (yeast strain without extracellular lipase activity) using a pYES2.1/V5-His-TOPO® plasmid. Herein, we show evidence that the strain transformed with the <em>LIP3</em> gene did not show lipase activity during flask galactose induction. On the other hand, the strain transformed with the <em>YJR107W</em> gene showed a specific activity of 0.397 U/mg, with an optimum temperature of 37 °C and pH 6. For maximum cell production, glucose and yeast extract concentrations were evaluated by a 2² factorial design, followed by the validation of the best concentrations predicted by a statistical model; a 2² factorial design was also carried out to evaluate the concentration of the inducer galactose on the transformed strains, and the intracellular and extracellular lipase specific activities were quantified. Finally, the biomass and lipase production were determined for each strain, which was grown in a stirred tank bioreactor with a working volume of 1.5 L. The specific activities of the transformed strains obtained in the bioreactor were 1.36 U/mg for the <em>LIP3</em> transformant and 1.25 U/mg for the <em>YJR107W</em> transformant, respectively.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100396"},"PeriodicalIF":3.5,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000994/pdfft?md5=c33bff1e56231edb099f714a52407edd&pid=1-s2.0-S1687157X24000994-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141438994","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":"Analysis of promoter region and regulatory elements of Rhizobium giardinii DNA-binding response regulator A3AY_RS01 genes","authors":"Genet Atsbeha ,&nbsp;Mulugeta Kebede ,&nbsp;Behailu Samuel ,&nbsp;Haftom Baraki ,&nbsp;Hailekiros Tadesse ,&nbsp;Desta Berhe Sbhatu","doi":"10.1016/j.jgeb.2024.100397","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100397","url":null,"abstract":"<div><h3>Background</h3><p><em>Rhizobium giardinii</em> has been demonstrated to colonize the roots of a variety of legume species, including common beans, and to increase nitrogen fixation. This suggests that <em>Rhizobium giardinii</em> might be a beneficial tool for sustainable agriculture by lowering dependency on synthetic nitrogen fertilizers and enhancing soil fertility. Understanding the regulatory components in the <em>R. giardinii A3AY_RS01</em> genes might also lead to the creation of innovative ways for increasing the effectiveness of nitrogen fixation in other agriculturally important bacteria. Therefore, this study was aimed to predict regulatory element of <em>R. giardinii DNA-binding response regulator A3AY_RS01</em> genes.</p></div><div><h3>Results</h3><p>The locations for 19 % of the Transcriptional start site (TSSs) were within <strong>−</strong>300 bp relative to the start codon and ten candidate motifs were identified that are shared by at least 50 % of the <em>R. giardinii A3AY_RS01</em> promoter input sequences from both strands. Motif 1 was revealed as the common promoter motif for all of <em>R. giardinii A3AY_RS01</em> genes that serves as binding sites for TFs involved in the expression regulation of these genes. Hence, it was revealed that Motif 1 may serve as the binding site chiefly for Ferric uptake regulator (Fur) transcription factor family to regulate expression of <em>A3AY_RS01</em> genes. High CpG density in the promoter than body regions were observed for most of the genes except for <em>A3AY_RS0102950, A3AY_RS0120195</em> and <em>A3AY_RS0131150</em> genes. Nonetheless, promoter areas were richer than body regions in both techniques.</p></div><div><h3>Conclusions</h3><p>MV1 motif can serve as a binding site for the Fur transcription factor gene family in <em>R. giardinii</em> to regulate the expression of <em>R. giardinii A3AY_RS01</em> genes. <em>R. giardinii A3AY_RS01</em> genes are rich in CpG Islands, and play an important role in the regulation of the gene expression of nitrogen fixing in this bacterium.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100397"},"PeriodicalIF":3.5,"publicationDate":"2024-06-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24001008/pdfft?md5=f836e7833cd3879a4989505fff644ef2&pid=1-s2.0-S1687157X24001008-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141434405","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":"Effect of ginger, chamomile, and green tea extracts on prostate cancer cells","authors":"Aysam M. Fayed ,&nbsp;M.A. Abdelzaher ,&nbsp;Neamah Hassoni Mahdi ,&nbsp;Dina M.R. AlKhafaf ,&nbsp;Mohamed AbdElRahman ,&nbsp;Ahmed Khalid Aldhalmi ,&nbsp;Zahraa Haleem Al-Qaim ,&nbsp;Rania Abd Elmohsen Abo El nour ,&nbsp;Heba G. Abdelzaher ,&nbsp;Alaa Muqbil Alsirhani ,&nbsp;Salwa El. Saied Morsi","doi":"10.1016/j.jgeb.2024.100395","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100395","url":null,"abstract":"<div><p>Prostate cancer (PCa) is a prevalent form of malignancy in males and is a significant contributor to cancer-related mortality worldwide. Because of this, studying the molecular processes of PCa cell growth and death is crucial. Hence, it is imperative to conduct further research on the regulatory mechanism underlying the progression of PCa to enhance our comprehension and identify innovative therapeutic targets. The present study investigates an experimental approach that utilizes cost-effective and environmentally sustainable plant extracts sourced from Egypt, namely ginger, chamomile, and green tea, which have been solubilized in dimethyl sulfoxide (DMSO), then characterized by using different analytical means and techniques, such as HPLC and GC–MS. The present study employed MTT assay, ELISA, and qRT-PCR techniques to assess the possible impact of the investigated extracts on PCa in PC-3 cells. The findings indicate that ginger exhibited a noteworthy cytotoxic impact on PC-3. Remarkably, the treatment of PCa cells with ginger significantly increased relative lactate dehydrogenase (LDH) production compared to those treated with chamomile and green tea extracts. Autophagy may play a crucial role in the context of chemotherapy. Modifying autophagy through its induction or inhibition is a promising and innovative approach to control<!--> <!-->cancer progression. Accordingly, it was found that ginger extract affects protein expression levels of autophagy markers LC3B, ATg12, and pro‐apoptotic signaling, including the Caspase-3 signaling pathway. The ELISA findings revealed a significant rise in the average levels of IL-1β and IL-8 after a 12-hour interval. To conclude, it can be inferred that ginger extract possesses the capability to control the production of inflammatory cytokines. Alternatively, utilizing herbal remedies containing ginger as a viable and secure means of treating PCa as an anticancer agent is possible.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100395"},"PeriodicalIF":3.5,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000982/pdfft?md5=d40cb7e1174e23f829d4854fd6292691&pid=1-s2.0-S1687157X24000982-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141428705","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}