Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality","authors":"Supriya Vaish ,&nbsp;Sumit K. Soni ,&nbsp;Balvindra Singh ,&nbsp;Neelima Garg ,&nbsp;Iffat Zareen Ahmad ,&nbsp;Muthukumar Manoharan ,&nbsp;Ajaya Kumar Trivedi","doi":"10.1016/j.jgeb.2023.100345","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100345","url":null,"abstract":"<div><h3>Background</h3><p>Bacterial community found in biodynamic preparations (BD500–BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.</p></div><div><h3>Results</h3><p>Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.</p></div><div><h3>Conclusion</h3><p>The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100345"},"PeriodicalIF":3.5,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015160/pdfft?md5=9671227402f606283f4f0c7bfa852b28&pid=1-s2.0-S1687157X23015160-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549897","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":"Subtractive genomics study of Xanthomonas oryzae pv. Oryzae reveals repurposable drug candidate for the treatment of bacterial leaf blight in rice","authors":"Ishtiaque Ahammad ,&nbsp;Tabassum Binte Jamal ,&nbsp;Anika Bushra Lamisa ,&nbsp;Arittra Bhattacharjee ,&nbsp;Nayeematul Zinan ,&nbsp;Md. Zahid Hasan Chowdhury ,&nbsp;Shah Mohammad Naimul Islam ,&nbsp;Kazi Md. Omar Faruque ,&nbsp;Zeshan Mahmud Chowdhury ,&nbsp;Mohammad Uzzal Hossain ,&nbsp;Keshob Chandra Das ,&nbsp;Chaman Ara Keya ,&nbsp;Md Salimullah","doi":"10.1016/j.jgeb.2024.100353","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100353","url":null,"abstract":"<div><h3>Background</h3><p><em>Xanthomonas oryzae</em> pv. <em>oryzae</em> is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against <em>X. oryzae</em> pv. <em>oryzae</em>, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants.</p></div><div><h3>Results</h3><p>The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in <em>Xoo</em> proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time.</p></div><div><h3>Conclusion</h3><p>Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by <em>X. oryzae</em> pv. <em>oryzae</em>. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from <em>in silico</em> studies should be validated through further <em>in vitro</em> and <em>in vivo</em> investigation before approval.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100353"},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000520/pdfft?md5=c9355b6b58b7db3e5f5d21d6fd2e7041&pid=1-s2.0-S1687157X24000520-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549102","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":"The role of zygotic genome activation in genetic−related reproductive medicine: Technological perspective, religious and bioethical concerns, challenges and benefits","authors":"Nameer Hashim Qasim ,&nbsp;Abzal Zhumagaliuly ,&nbsp;Rabiga Khozhamkul ,&nbsp;Fakher Rahim","doi":"10.1016/j.jgeb.2023.100340","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100340","url":null,"abstract":"<div><p>Zygotic Genome Activation (ZGA) is a crucial developmental milestone in early embryogenesis, marking the transition from maternal to embryonic control of development. This process, which varies in timing across species, involves the activation of the embryonic genome, paving the way for subsequent cell differentiation and organismal development. Recent advances in genomics and reproductive medicine have highlighted the potential of ZGA in the realm of genetic screening, providing a window into the genetic integrity of the developing embryo at its earliest stages. The intersection of ZGA and genetic screening primarily emerges in the context of preimplantation genetic diagnosis (PGD) and preimplantation genetic screening (PGS). These techniques, often employed during assisted reproductive technologies, aim to detect potential genetic abnormalities or chromosomal imbalances before embryo implantation. Given that ZGA represents the onset of embryonic gene expression, understanding its intricacies can significantly enhance the accuracy and predictive power of these screening processes. With the advent of next-generation sequencing and other high-throughput genomic techniques, detailed mapping of the transcriptomic changes during ZGA has become feasible. Such advancements have deepened our insights into the dynamics of early embryonic development and the onset of genetic disorders. As our knowledge in this realm expands, it promises to revolutionize our capabilities in detecting, understanding, and potentially rectifying genetic anomalies at the earliest stages of human life, thereby optimizing reproductive outcomes.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100340"},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015111/pdfft?md5=e35c9f60af6785557151e565d6527c79&pid=1-s2.0-S1687157X23015111-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549082","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":"Emergence of carbapenem resistant gram-negative pathogens with high rate of colistin resistance in Egypt: A cross sectional study to assess resistance trends during the COVID-19 pandemic","authors":"Fatma A. Afify ,&nbsp;Ahmed H. Shata ,&nbsp;Nirmeen Aboelnaga ,&nbsp;Dina Osama ,&nbsp;Salma W. Elsayed ,&nbsp;Nehal A. Saif ,&nbsp;Shaimaa F. Mouftah ,&nbsp;Sherine M. Shawky ,&nbsp;Ahmed A. Mohamed ,&nbsp;Omar Loay ,&nbsp;Mohamed Elhadidy","doi":"10.1016/j.jgeb.2024.100351","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100351","url":null,"abstract":"<div><p>The current study investigated the temporal phenotypic and genotypic antimicrobial resistance (AMR) trends among multi-drug resistant and carbapenem-resistant <em>Klebsiella pneumoniae</em>, <em>Acinetobacter baumannii,</em> and <em>Pseudomonas aeruginosa</em> recovered from Egyptian clinical settings between 2020 and 2021. Bacterial identification and antimicrobial sensitivity of 111 clinical isolates against a panel of antibiotics were performed. Molecular screening for antibiotic resistance determinants along with integrons and associated gene cassettes was implemented. An alarming rate (98.2%) of these isolates were found to be phenotypically resistant to carbapenem. Although 23.9 % <em>K. pneumoniae</em> isolates were phenotypically resistant to colistin, no mobile colistin resistance (<em>mcr</em>) genes were detected. Among carbapenem-resistant isolates, <em>bla</em>_NDM and <em>bla</em>_OXA-48-like were the most prevalent genetic determinants and were significantly overrepresented among <em>K. pneumoniae</em>. Furthermore, 84.78% of <em>K. pneumoniae</em> isolates co-produced these two carbapenemase genes. The plasmid-mediated quinolone resistance genes (<em>qnrS</em> and <em>qnrB</em>) were detected among the bacterial species and were significantly more prevalent among <em>K. pneumoniae</em>. Moreover, Class 1 integron was detected in 82% of the bacterial isolates. This study alarmingly reveals elevated resistance to last-resort antibiotics such as carbapenems as well as colistin which impose a considerable burden in the health care settings in Egypt. Our future work will implement high throughput sequencing-based antimicrobial resistance surveillance analysis for characterization of novel AMR determinants. This information could be applied as a step forward to establish a robust antibiotic stewardship program in Egyptian clinical settings, thereby addressing the rising challenges of AMR.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100351"},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X2300001X/pdfft?md5=7c5a01d390681c9a96bd6ee36b056005&pid=1-s2.0-S1687157X2300001X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549898","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":"Unveiling the structure and interactions of SOG1, a NAC domain transcription factor: An in-silico perspective","authors":"Kalyan Mahapatra","doi":"10.1016/j.jgeb.2023.100333","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100333","url":null,"abstract":"<div><p>SOG1 is a crucial plant-specific NAC domain family transcription factor and functions as the central regulator of DNA damage response, acting downstream of ATM and ATR kinases. In this study, various <em>in-silico</em> approaches have been employed for the characterization of SOG1 transcription factor in a comparative manner with its orthologues from various plant species. Amino acid sequences of more than a hundred SOG1 or SOG1-like proteins were retrieved and their relationship was determined through phylogenetic and motif analyses. Various physiochemical properties and secondary structural components of SOG1 orthologues were determined in selective plant species including <em>Arabidopsis thaliana</em>, <em>Oryza sativa</em>, <em>Amborella trichopoda</em>, and <em>Physcomitrella patens</em>. Furthermore, fold recognition or threading and homology-based three-dimensional models of SOG1 were constructed followed by subsequent evaluation of quality and accuracy of the generated protein models. Finally, extensive DNA-Protein and Protein-Protein interaction studies were performed using the HADDOCK server to give an insight into the mechanism of how SOG1 binds with the promoter region of its target genes or interacts with other proteins to regulate the DNA damage responses in plants. Our docking analysis data have shown the molecular mechanism of SOG1′s binding with 5′-CTT(N)₇AAG-3′ and 5′-(N)₄GTCAA(N)₄-3′ consensus sequences present in the promoter region of its target genes. Moreover, SOG1 physically interacts and forms a thermodynamically stable complex with NAC103 and BRCA1 proteins, which possibly serve as coactivators or mediators in the transcription regulatory network of SOG1. Overall, our <em>in-silico</em> study will provide meaningful information regarding the structural and functional characterization of the SOG1 transcription factor.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100333"},"PeriodicalIF":3.5,"publicationDate":"2024-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015044/pdfft?md5=f5cfaeeaf4a3f485351fb1973ec071a5&pid=1-s2.0-S1687157X23015044-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549083","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":"The in-silico study of the structural changes in the Arthrobacter globiformis choline oxidase induced by high temperature","authors":"Sonia Kaushik ,&nbsp;Rashmi Rameshwari ,&nbsp;Shilpa S. Chapadgaonkar","doi":"10.1016/j.jgeb.2023.100348","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100348","url":null,"abstract":"<div><h3>Background</h3><p>Choline oxidase, a flavoprotein, is an enzyme that catalyzes the reaction which converts choline into glycine betaine. Choline oxidase started its journey way back in 1933. However, the impact of the high temperature on its structure has not been explored despite the long history and availability of its crystal structure. Both choline oxidase and its product, glycine betaine, have enormous applications spanning across multiple industries. Understanding how the 3D structure of the enzyme will change with the temperature change can open new ways to make it more stable and useful for industry.</p></div><div><h3>Process</h3><p>This research paper presents the <em>in-silico</em> study and analysis of the structural changes of <em>A</em>. <em>globiformis</em> choline oxidase at temperatures from 25 °C to 60 °C. A step-wise process is depicted in <span>Fig. 1</span>.</p></div><div><h3>Results</h3><p>Multiple sequence alignment (MSA) of 11 choline oxidase sequences from different bacteria vs <em>Arthrobacter globiformis</em> choline oxidase showed that active site residues are highly conserved.</p><p>The available crystal structure of <em>A. globiformis</em> choline oxidase with cofactor Flavin Adenine Dinucleotide (FAD) in the dimeric state (PDB ID: 4MJW)<span>¹</span> was considered for molecular dynamics simulations. A simulated annealing option was used to gradually increase the temperature of the system from 25 °C to 60 °C. Analysis of the conserved residues, as well as residues involved in Flavin Adenine Dinucleotide (FAD) binding, substrate binding, substate gating, and dimer formationwas done. At high temperatures, the formation of the inter-chain salt bridge between Arg50 and Glu63 was a significant observation near the active site of choline oxidase.</p></div><div><h3>Conclusion</h3><p>Molecular dynamics studies suggest that an increase in temperature has a significant impact on the extended Flavin Adenine Dinucleotide (FAD) binding region. These changes interfere with the entry of substrate to the active site of the enzyme and make the enzyme inactive.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100348"},"PeriodicalIF":3.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015196/pdfft?md5=d2139446ecb175a114324665201bd32d&pid=1-s2.0-S1687157X23015196-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549899","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 potential antiviral compounds from Egyptian sea stars against seasonal influenza A/H1N1 virus","authors":"Nadia I. Okasha ,&nbsp;Mohamed Abdel Rahman ,&nbsp;Mohammed S. Nafie ,&nbsp;Noura M. Abo Shama ,&nbsp;Ahmed Mostafa ,&nbsp;Dalia A. El-Ebeedy ,&nbsp;Ahmed Z. Abdel Azeiz","doi":"10.1016/j.jgeb.2023.100334","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100334","url":null,"abstract":"<div><h3>Background</h3><p>One of the most dangerous problems that the world faced recently is viral respiratory pathogens. Marine creatures, including <em>Echinodermata,</em> specially <em>Asteroidea</em> class (starfish) have been extensively studied due to their miscellaneous bioactivities, excellent pharmacological properties, and complex secondary metabolites, including steroids, steroidal glycosides, anthraquinones, alkaloids, phospholipids, peptides, and fatty acids. These chemical constituents show antiviral activities against a wide range of viruses, including respiratory viruses.</p></div><div><h3>Results</h3><p>The present study aimed at the identification of potential antiviral compounds from some starfish species. The bioactive compounds from <em>Pentaceraster cumingi, Astropecten polyacanthus,</em> and <em>Pentaceraster mammillatus</em> were extracted using two different solvents (ethyl acetate and methanol). The antiviral activity against influenza A/H1N1 virus showed that ethyl acetate extract from <em>Pentaceraster cumingi</em> has the highest activity, where the selective index was 150.8. The bioactive compounds of this extract were identified by GC/MS analysis. The molecular docking study highlighted the virtual mechanism of binding of the identified compounds towards polymerase basic protein 2 and neuraminidase for H1N1 virus. Interestingly, linoleic acid showed promising binding energy of −10.12 Kcal/mol and −24.20 Kcal/mol for the selected two targets, respectively, and it formed good interactive modes with the key amino acids inside both proteins.</p></div><div><h3>Conclusion</h3><p>The molecular docking analysis showed that linoleic acid was the most active antiviral compound from <em>P. cumingi</em>. Further studies are recommended for <em>in-vitro</em> and <em>in-vivo</em> evaluation of this compound against influenza A/H1N1 virus.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100334"},"PeriodicalIF":3.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015056/pdfft?md5=bd223c2121002d26f5815495e5341cdc&pid=1-s2.0-S1687157X23015056-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549100","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":"SARS-CoV-2 Omicron Spike shows strong binding affinity and favourable interaction landscape with the TLR4/MD2 compared to other variants","authors":"Chiranjib Chakraborty ,&nbsp;Bidyut Mallick ,&nbsp;Manojit Bhattacharya ,&nbsp;Siddappa N. Byrareddy","doi":"10.1016/j.jgeb.2023.100347","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100347","url":null,"abstract":"<div><p>Emergences of SARS-CoV-2 variants have made the pandemic more critical. Toll-like receptor 4 (TLR4) recognizes the molecular patterns of pathogens and activates the production of proinflammatory cytokines to restrain the infection. We have identified a molecular basis of interaction between the Spike and TLR4 of SARS-CoV-2 and its present and past VOCs (variant- of concern) through <em>in silico</em> analysis. The interaction of wild type Spike with TLR4 showed 15 number hydrogen bonds formation. Similarly, the Alpha variants’ Spike with the TLR4 has illustrated that 14 hydrogen bonds participated in the interaction. However, the Delta Spike and TLR4 interaction interface showed that 17 hydrogen bonds were formed during the interaction. Furthermore, Omicron S-glycoprotein and TLR4 interaction interface was depicted (interaction score: −170.3), and 16 hydrogen bonds were found to have been formed in the interaction. Omicron S-glycoprotein shows stronger binding affinity with the TLR4 than wild type, Alpha, and Delta variants. Similarly, the Alpha Spike shows higher binding affinity with TLR4 than the wild type and Delta variant. Now, it is an open question of the molecular basis of the interaction of Spike and TLR4 and the activated downstream signaling events of TLR4 for SARS-CoV-2 and its variants.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100347"},"PeriodicalIF":3.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015184/pdfft?md5=362fc6db583592706851bca3b42e6708&pid=1-s2.0-S1687157X23015184-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549901","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":"Phytocompounds-based therapeutic approach: Investigating curcumin and green tea extracts on MCF-7 breast cancer cell line","authors":"Radwa M. Fawzy,&nbsp;Amal A. Abdel-Aziz,&nbsp;Khalid Bassiouny,&nbsp;Aysam M. Fayed","doi":"10.1016/j.jgeb.2023.100339","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100339","url":null,"abstract":"<div><h3>Background</h3><p>Breast cancer (BC) has transcended lung cancer as the most common cancer in the world. Due to the disease's aggressiveness, rapid growth, and heterogeneity, it is crucial to investigate different therapeutic approaches for treatment. According to the World Health Organization (WHO), Plant-based therapeutics continue to be utilized as safe/non-toxic complementary or alternative treatments for cancer, even in developed countries, regardless of how cutting-edge conventional therapies are. Despite their low bioavailability, curcumin (CUR) and green tea (GT) represent safer therapeutic options. Due to their potent molecular-modulating properties on various cancer-related molecules and signaling pathways, they are considered gold-standard therapeutic agents and have been incorporated into the development of one or more therapeutic strategies of BC treatment.</p></div><div><h3>Methods</h3><p>We investigated the modulatory role of CUR and GT extracts on significant multi molecular targets in MCF-7 BC cell line to assess their potential as BC multi-targeting agents. We analyzed the phytocompounds in GT leaves using High-performance liquid chromatography (HPLC) and Gas chromatography-mass spectrometry (GC-MS) techniques. The mRNA expression levels of Raf-1, Telomerase, Tumor necrosis factor alpha (TNF-α) and Interleukin-8 (IL-8) genes in MCF-7 cells were quantified using quantitative real-time PCR (qRT-PCR). The cytotoxicity of the extracts was assessed by the 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and the released Lactate dehydrogenase (LDH), a valuable marker for identifying the programmed necrosis (necroptosis). Additionally, the concentrations of the necroptosis-related proinflammatory cytokines (TNF-α and IL-8) were measured using enzyme-linked immunosorbent assay (ELISA).</p></div><div><h3>Results</h3><p>In contrast to the GT, the results showed the anticancer and cytotoxic properties of CUR against MCF-7 cells, with a relatively higher level of released LDH. The CUR extract downregulated the oncogenic Raf-1, suppressed the Telomerase and upregulated the TNF-α and IL-8 genes. Results from the ELISA showed a notable increase in IL-8 and TNF-α cytokines levels after CUR treatment, which culminated after 72 h.</p></div><div><h3>Conclusions</h3><p>Among both extracts, only CUR effectively modulated the understudy molecular targets, achieving multi-targeting anticancer activity against MCF-7 cells. Moreover, the applied dosage significantly increased levels of the proinflammatory cytokines, which represent a component of the cytokines-targeting-based therapeutic strategy. However, further investigations are recommended to validate this therapeutic approach.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100339"},"PeriodicalIF":3.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X2301510X/pdfft?md5=34abec42e14be5793c61c226b1dc30a9&pid=1-s2.0-S1687157X2301510X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549902","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":"AraC transcriptional regulator, aspartate semialdehyde dehydrogenase and acyltransferase: Three putative genes in phenol catabolic pathway of Acinetobacter sp. Strain DF4","authors":"Desouky Abd-El-Haleem","doi":"10.1016/j.jgeb.2023.100349","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100349","url":null,"abstract":"<div><p>The objective of this study was to identify genes associated with the biodegradation of phenol by <em>Acinetobacter</em> sp. strain DF4 through the use of differential display (DD) methodology. The bacteria were grown in YEPG medium, and total RNA was extracted and analyzed using labeled primers to detect gene expression differences. Three distinctively expressed cDNA bands (ph1, ph2, and ph3) were identified, cloned, and sequenced. DNA analysis involved searching for open reading frames (ORFs), verifying results with the NCBI database, predicting promoter regions, and constructing phylogenetic trees using bioinformatics tools. The ph1 gene displayed a 97% identity with the AraC transcriptional regulator, suggesting its potential role in regulating the <em>ortho</em>-catabolic pathway of phenol. The ph2 gene showed a 98% identity with aspartate semialdehyde dehydrogenase, which is involved in phenol degradation. The ph3 gene had a 93% identity with acetyltransferase. Essential transcription factors, such as TATA, GTGTGT, CACA, and CTTTT, were detected, and the three genes promoter regions were predicted. This study successfully identified functional genes involved in the metabolism of cyclic chemicals, particularly phenol, using the DD technique. These findings provide insights into the biodegradation pathways of phenol by <em>Acinetobacter</em> sp. Strain DF4 and may contribute to the development of more efficient bioremediation strategies for phenol-contaminated environments.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100349"},"PeriodicalIF":3.5,"publicationDate":"2024-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015202/pdfft?md5=00e5d0081e693e5430f4e26181053f95&pid=1-s2.0-S1687157X23015202-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549900","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}