Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Evaluation of genetic diversity and elucidation of population structure of Lathyrus accessions using agro-morphological characters and ISSR technique","authors":"Reda Helmy Sammour ,&nbsp;Abd EL-Zaher Mohammed Abasery Mustafa ,&nbsp;Hanan Fahad Al-Harbi ,&nbsp;Mohamed Ragab Abdelgawwad ,&nbsp;Fatin Khalid AlShamasi","doi":"10.1016/j.jgeb.2025.100500","DOIUrl":"10.1016/j.jgeb.2025.100500","url":null,"abstract":"<div><div>Genetic diversity and population structure were evaluated for 36 <em>Lathyrus L</em>. accessions using agronomic characters and ISSR markers. The agronomic characters and ISSR markers showed a wide genetic diversity between <em>Lathyrus</em> accessions. The significant association between 1000 seed weight and total seed protein percentage in <em>Lathyrus</em> accessions revealed that both characters were under independent genetic control. The total number of alleles generated by the markers was 336, revealing 100% polymorphism. The polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI), and resolving power (RP) of the markers were 0.75, 16.46, 17.83, and 2.70, respectively, confirming the great variation in <em>Lathyrus</em> accessions. The AMOVA test indicated that 93% of all genetic variation was found within accessions and 7% between accessions. The Ewens–Watterson test for neutrality indicated that the nine markers were neutral, and most of the genetic diversity resided in accessions, with the exception of <em>Lathyrus aphaca</em> from Bulgaria, confirming AMOVA results. The genetic diversity (<em>h</em>) and Shannon’s information index were 0.34 and 0.52, respectively, revealing that maker OPA01-812 was highly recommended for distinguishing <em>Lathyrus</em> accessions. The genetic differentiation among accessions (<em>G_ST</em>) was 0.03, whereas the number of migrants per generation based on Wright’s equation (<em>N_mw</em>) was 18.12. However, the probability (P) of the chi-square values exceeded 0.05 for the nine markers, indicating the low heterogeneity between the investigated accessions. Cluster and correspondence analyses for ISSR results showed that the genetic diversity among <em>Lathyrus</em> accessions was not influenced by their geographical origin. They also revealed that <em>Lathyrus sativus</em> and <em>Lathyrus cicera</em> were not derived from the same ancestor. In conclusion, we recommended (1) <em>Lathyrus sativus</em> PI 179299 for breeding for new cultivars with a high yield and low β-ODAP percentage and (2) ISSR markers for characterizing and differentiating between <em>Lathyrus</em> accessions.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100500"},"PeriodicalIF":3.5,"publicationDate":"2025-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143922959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"TIMELESS as a prognostic biomarker and therapeutic target in gastric cancer","authors":"Xiangrong Meng ,&nbsp;Qi Sun ,&nbsp;Zhongshuang Liu ,&nbsp;Shenqi Cao ,&nbsp;Chunyang Xu ,&nbsp;Longjiang Di ,&nbsp;Yan Wu ,&nbsp;Wenjing Zhang","doi":"10.1016/j.jgeb.2025.100504","DOIUrl":"10.1016/j.jgeb.2025.100504","url":null,"abstract":"<div><h3>Background</h3><div>Gastric cancer (GC), one of the most prevalent malignancies worldwide, is characterized by complex etiological and pathological mechanisms. Emerging evidence on the dysregulation of circadian clock genes has revealed promising opportunities for improving the diagnosis, treatment, and prognosis of patients with GC. Methods: This study utilized a multifaceted approach combining machine learning algorithms, gene set enrichment analysis, immune infiltration profiling, survival prognosis analysis, drug sensitivity testing, and <em>in vitro</em> experiments to investigate the functional roles of core clock genes in GC. Results: By integrating data from The Cancer Genome Atlas, Gene Expression Omnibus datasets, and the National Center for Biotechnology Information database, we identified 29 differentially expressed clock genes in GC. Among these, the application of four distinct machine learning algorithms highlighted TIMELESS (TIM) and BHLHE41 as pivotal genes, with TIM demonstrating notable diagnostic performance (area under the receiver operating characteristic curve = 0.802). Elevated TIM expression was strongly associated with poor clinical prognosis and increased infiltration of immune cells in tumor tissues. Notably, a specific interaction was identified between TIM and the pyroptosis-associated molecule CASP8, indicating a potential synergistic role in GC pathogenesis. Additionally, bortezomib emerged as a potential targeted therapeutic agent capable of modulating TIM activity in GC. Conclusion: TIM is identified as a promising diagnostic biomarker and therapeutic target in GC, offering valuable implications for improving patient prognosis and guiding personalized treatment strategies.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100504"},"PeriodicalIF":3.5,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143912340","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of ionizing radiation and low-energy electrons on DNA functionality: radioprotection and radiosensitization potential of natural products","authors":"Kouass Sahbani Saloua ,&nbsp;Rayan M. Alansari","doi":"10.1016/j.jgeb.2025.100501","DOIUrl":"10.1016/j.jgeb.2025.100501","url":null,"abstract":"<div><div>Ionizing radiation (IR) is a key cancer treatment, but its DNA-damaging effects, particularly double-strand breaks (DSBs) and clustered lesions, pose challenges for therapy. Clustered DNA lesions, often induced by low-energy electrons (LEEs), contribute significantly to genomic instability and repair resistance. Chemotherapeutic agents like cisplatin can enhance IR-induced damage, making tumor cells more susceptible. Emerging strategies in radiation oncology target DNA repair pathways, using inhibitors like poly(ADP-ribose) polymerase (PARP) to sensitize tumors to IR. Natural products, including polyphenols, flavonoids, and alkaloids, offer promising radioprotective effects by scavenging reactive oxygen species and enhancing DNA repair. These agents not only protect normal tissues but also increase tumor sensitivity to IR, improving therapeutic outcomes. Future research should focus on optimizing these natural agents for clinical use, integrating them into radiotherapy protocols for enhanced efficacy and reduced toxicity.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100501"},"PeriodicalIF":3.5,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143900219","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Green synthesis of silver nanoparticles using Padina commersonii: Characterization, hypoglycemic effects, and antimicrobial potential against human pathogenic bacteria","authors":"R. Ragavi ,&nbsp;P. Sachini Sigera ,&nbsp;A.A.E.B. Nirmani ,&nbsp;Milan Rathnayake ,&nbsp;R.A. Pasindu Eranga ,&nbsp;K.K. Dinuhara Theekshana ,&nbsp;Dinithi C. Peiris","doi":"10.1016/j.jgeb.2025.100493","DOIUrl":"10.1016/j.jgeb.2025.100493","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;Nanotechnology is a dynamic field comprising chemistry, physics, biology, and engineering, with a high proficiency in disease treatment delivery methods. Metallic precursors (e.g.,AgNO&lt;sub&gt;3&lt;/sub&gt;) are widely used to synthesize NPs. But, owing to their harmful nature and the cost of these metallic nanoparticles, the focus is shifting toward “green synthesis“ of nanoparticles using fungi, bacteria, plants, and algae. Hence, we used &lt;em&gt;Padina commersonii&lt;/em&gt; to green synthesize NPs. We focused on the antioxidant, hypoglycemic, and antimicrobial efficacy of biologically synthesized AgNPs from &lt;em&gt;P&lt;/em&gt;. &lt;em&gt;commersonii.&lt;/em&gt;&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methods&lt;/h3&gt;&lt;div&gt;Silver NPs (AgNPs) were synthesized using 80% methanol extract of &lt;em&gt;P. commersonii&lt;/em&gt; upon removal of pigments and polysaccharides. Methanol (80%) was selected for higher polyphenol yield (∼30% w/w) compared to aqueous extracts (∼12% w/w), critical for efficient Ag&lt;sup&gt;+&lt;/sup&gt; reduction. Major phytochemicals, including fucoidan, phlorotannins, flavonoids (quercetin), and terpenes, are present in 80% methanol extract of &lt;em&gt;P. Commersonii&lt;/em&gt; The NPs were characterized using ultraviolet–visible spectroscopy, Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, dynamic light scattering, energy dispersive X-ray (X-ray diffraction (XRD), and scanning electron microscopy (SEM). Antioxidant potential was determined using DPPH and ABTS scavenging assays, while hypoglycemic activity was conducted using alpha-glucosidase and alpha-amylase enzyme inhibitory assays. Finally, antimicrobial activities were conducted against S. aureus, E. &lt;em&gt;coli&lt;/em&gt; (bacteria), and the fungal strains &lt;em&gt;Candida albicans&lt;/em&gt; and &lt;em&gt;Aspergillus niger&lt;/em&gt;.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results&lt;/h3&gt;&lt;div&gt;The AgNPs were confirmed by the colour change from yellow to brown. Further, the UV and Raman spectrophotometry peaks, respectively, at 424 nm and 335 cm&lt;sup&gt;-1&lt;/sup&gt;, confirmed the presence of AgNPs. The average AgNPs size of 73.19 nm was obtained using the dynamic light scattering&lt;!--&gt; &lt;!--&gt;(DLS) technique, while the zeta potential indicated its stability at −21.5 mV. The SEM imaging confirmed a smooth surface with no aggregation, whereas the XRD pattern perceived the crystalline nature of these AgNPs. The antioxidant potential of AgNPs was higher than (DPPH: IC&lt;sub&gt;50&lt;/sub&gt;: 271.17 ± 3.992 and ABTS: IC50 195.03 ± 5.7535 µg/mL) the methanol extract. Similar patterns were observed with the hypoglycemic potential with α-glucosidase (IC50:161.74 ± 3.992 µg/mL) and α-amylase inhibitions (IC50: 176.70 ± 5.7535 µg/mL). The antimicrobial efficacy of AgNPs was evident for studied bacterial species (S.aureus:12.77 ± 0.58 mm; E.coli:15.27 ± 0.58 mm) and fungi (A. niger: 18.10 ± 0.15 mm; C.albicans: 17.4 ± 0.57 mm).&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Conclusions&lt;/h3&gt;&lt;div&gt;The AgNPs displayed potent antidiabetic and antimicrobial efficacy, suggesting their potential as viable alternatives to conventional ","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100493"},"PeriodicalIF":3.5,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143900108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The evaluation of a novel multi-epitope vaccine against human papillomavirus and Candida albicans","authors":"Fatemeh Ahmadifar ,&nbsp;Ebrahim Balali ,&nbsp;Ramona Khadivi ,&nbsp;Mehrdad Hashemi ,&nbsp;Ali Jebali","doi":"10.1016/j.jgeb.2025.100489","DOIUrl":"10.1016/j.jgeb.2025.100489","url":null,"abstract":"<div><h3>Purpose</h3><div>The purpose of this study was to design and evaluate a multiepitope peptide vaccine against Human papillomavirus (<em>HPV</em>) and <em>Candida albicans</em> (<em>C. albicans</em>) on human dendritic cells (<em>hDC</em>).</div></div><div><h3>Methods</h3><div>To determine the antigenic epitopes for <em>C. albicans</em> and <em>HPV</em>, the FASTA format of protein targets was extracted from NCBI. Then, all epitopes were analyzed using ABCpred, Vaxijen, AllerTOP, ToxinPred, and molecular docking. Then, selected peptides were first synthesized using the solid phase method, mixed with cationic lipids, and characterized by DLS, Zetasizer, and nanodrop at 280 nm. In the next step, <em>hDC</em>s were obtained from peripheral blood and confirmed by flow cytometry. Then, they were exposed to vaccine candidates at 1 mg/mL. Next, the activation of <em>hDC</em> was checked by the expression and concentration of interleukin-12 (IL-12) and interferon-ɣ (IFN-ɣ). Also, the functionality of <em>hDC</em>s and antigen-loaded <em>hDC</em>s was evaluated by their ability to induce the proliferation of allogeneic T cells by mixed lymphocyte reaction (MLR). Finally, antibody titration against vaccine candidates was investigated on Syrian male mice using the ELISA method.</div></div><div><h3>Results</h3><div>Here, KDIDLDLQEL, GPVLALNVAL, and KDIDLDLQELKKKGPVLALNVAL peptides were selected as E7, HYR1, and merged E7-HYR1 peptides, respectively. We found that more than 85 % of the isolated <em>hDC</em>s were positive for HLA-DR, CD86, and CD209 and less than 5 % were positive for CD14. After treatment of <em>hDC</em>s with vaccine candidates, we found that peptides E7, HYR1, and merged E7-HYR1 could stimulate <em>hDC</em>s to express IL-12 and IFN-ɣ and when the selected peptides integrated into nanoliposomes, they were significantly more capable to stimulate <em>hDC</em> (P &lt; 0.05). Also, we found that the stimulation index of vaccine-loaded <em>hDC</em>s was higher than unloaded <em>hDC</em>s. The antibody titer in mice exposed to nanoliposomes was significantly higher than in mice exposed to specific peptide vaccines. ^a P &lt; 0.05 compared with other groups.</div></div><div><h3>Conclusion</h3><div>Here, a multiepitope peptide vaccine against <em>HPV</em> and <em>C. albicans</em> was designed and evaluated on <em>hDC</em>. Real efficacy and side effects of this vaccine must be analyzed in future studies.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100489"},"PeriodicalIF":3.5,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143895610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-expression of HIF1A with multi-drug transporters (P-GP, MRP1, and BCRP) in chemoresistant breast, colorectal, and ovarian cancer cells","authors":"Sudipta Deb Nath ,&nbsp;Md Tamzid Hossain Tanim ,&nbsp;Md. Mahmudul Hasan Akash ,&nbsp;Mohammad Golam Mostafa ,&nbsp;Abu Ashfaqur Sajib","doi":"10.1016/j.jgeb.2025.100496","DOIUrl":"10.1016/j.jgeb.2025.100496","url":null,"abstract":"<div><div>Therapeutic resistance poses a significant challenge in treating most cancers and often leads to poor clinical outcomes and even treatment failure. One of the primary mechanisms that confer multidrug resistance phenotype to cancer cells is the hyperactivity of certain drug efflux transporters. P-GP, MRP1, and BCRP are the key ABC efflux pumps that collectively extrude a broad spectrum of chemotherapeutic drugs. Besides, HIF1A, a master transcription regulatory protein, is also associated with cancer development and therapeutic resistance. Thereby, this study aimed to delve into the mechanisms of drug resistance, specifically focusing on HIF1A-driven overexpression of ABC transporters. A total of 57 chemoresistant and 57 paired control tissue samples (breast, colorectal, and ovarian) from Bangladeshi cancer patients were analyzed to determine the co-expression level of ABC transporters and HIF1A. Molecular docking was also conducted to evaluate the interactions of HIF1A protein and hypoxia response element (HRE) sequences in the promoter regions transporter genes. This study revealed that HIF1A is significantly overexpressed in chemoresistant tissues, suggesting its pivotal role in chemoresistance mechanisms across malignancies and its potential as a target to overcome therapeutic resistance. The findings from this study also suggest a direct upregulation of <em>ABCB1</em>, <em>ABCC1</em>, and <em>ABCG2</em> transcription by HIF1A in chemoresistant cancer cells by binding to the HRE sequence in the promoter regions. Thus, inhibition of these interactions of HIF1A appears to be a promising approach to reverse chemoresistance. The findings of this study can serve as a foundation for future research, resolving molecular intricacies to improve treatment outcomes in chemoresistant patients.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100496"},"PeriodicalIF":3.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to “Unveiling promising phytocompounds from Moringa oleifera as dual inhibitors of EGFR(T790M/C797S) and VEGFR-2 in non-small cell lung cancer through in silico screening, ADMET, dynamics simulation, and DFT analysis” [J. Genet. Eng. Biotechnol. 22(3) (2024) 100406]","authors":"Md. Masudur Rahman Munna ,&nbsp;Md. Touki Tahamid Tusar ,&nbsp;Saima Sajnin Shanta ,&nbsp;Md. Hossain Ahmed ,&nbsp;Md. Sarafat Ali","doi":"10.1016/j.jgeb.2025.100499","DOIUrl":"10.1016/j.jgeb.2025.100499","url":null,"abstract":"","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100499"},"PeriodicalIF":3.5,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143891662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Multidrug resistance and virulence profile of the commensal Proteus mirabilis isolated from a native Iraqi frozen chicken carcass","authors":"Zaid A. Thabit ,&nbsp;Zahraa A. AlShaheeb ,&nbsp;May Ridha Jaafar ,&nbsp;Safaa A.S. Al-Qaysi ,&nbsp;Sana M.H. Al-Shimmary","doi":"10.1016/j.jgeb.2025.100490","DOIUrl":"10.1016/j.jgeb.2025.100490","url":null,"abstract":"<div><div>This study aimed to determine the prevalence of <em>Proteus mirabilis</em> in frozen chicken carcass from local slaughterhouse. It assesses the activities of nine antimicrobial agents and the presence of antimicrobial resistance genes and virulence genes. Thirty samples were collected from five local Iraqi companies. and then the antibiotic-resistance genes and virulence factor-related genes were detected via polymerase chain reaction (PCR). The results revealed that Nine <em>P. mirabilis</em> isolates were recovered, and the majority of the isolates were resistant to both nalidixic acid and azithromycin at a ratio of (100 %), followed by trimethoprim-sulfamethoxazole (<em>sul1</em>) (88.8 %), whereas the isolates were susceptible to imipenem and meropenem, and both ceftazidime and cefotaxime were efficient at a ratio of (88.8 %). All the isolates (100 %) were resistant to at least three classes of antibiotics and were classified as multidrug resistant. The PCR results indicated that the most common resistance genes were DNA Gyrase Subunit A Gene (<em>gyrA</em>) (100 %), Dihydropteroate Synthase Gene (<em>sul1</em>) (88.8 %), and Florenicol Resistance Gene (<em>floR</em>) (88.8 %), followed by Aminoglycoside N-Acetyltransferase Gene (<em>acc (6′)-lb</em>) (44.4 %) and Macrolide Phosphotransferase Gene (<em>mphA</em>) (33.3 %). In addition, the virulence genes Zinc Metalloprotease A Gene (<em>zapA</em>), Uridine Monophosphate Synthase Gene (<em>uraC</em>), Histone-Modifying Protein A Gene (<em>hpmA</em>), Flagellin A Gene (<em>flaA</em>), Anti-Sigma Factor <em>RsbA</em> Gene (<em>rsbA</em>), and Multidrug Resistance Protein A Gene (<em>mrpA</em>) were found in the same proportion (100 %) of all <em>P. mirabilis</em> isolates. Our study emphasized that <em>Proteus mirabilis</em> has a high frequency of antibiotic resistance as a multidrug resistance pattern and furthermore demonstrated a high level of virulence factor gene detection, which might be a threat to food safety and human health. The phylogenetic tree analysis of the <em>P. mirabilis</em> isolates from chicken meat revealed high similarity to the database strain.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100490"},"PeriodicalIF":3.5,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143873268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic diversity and population structure analysis in Asparagus officinalis","authors":"Gurleen Sidhu ,&nbsp;Travis Banks ,&nbsp;David Wolyn","doi":"10.1016/j.jgeb.2025.100491","DOIUrl":"10.1016/j.jgeb.2025.100491","url":null,"abstract":"<div><div>Asparagus cultivars grown worldwide are thought to have originated from a limited genetic base, however, selection has resulted in variation for climatic adaptation and other traits. Understanding genetic diversity of the crop is important to guide breeding decisions. The objectives of this research were to identify SNPs among 64 cultivated lines from different geographic areas and assess genetic variation, population structure and linkage disequilibrium. More than 55,000 SNPs were identified by GBS and subjected to filtration for minor allele frequency and missing data, resulting in 12,886 markers for all subsequent analysis. Markers exhibited a wide range of Expected Heterozygosity (He), Polymorphic Information Content (PIC) and Observed Heterozygosity (Ho) with mean values of 0.370, 0.310, and 0.450 respectively. Population STRUCTURE analysis indicated that the 64 lines were grouped into two, four, seven, and nine subpopulations. For K = 4, four distinct groups were defined: (1) New Zealand, New Jersey, France, and California; (2) Canada; (3) China, The Netherlands, and Germany; and (4) England, Denmark, Spain, Turkey, and India. The results were further confirmed by PCA, and a phylogenetic tree. LD declined rapidly with an increase in physical distance. A considerable amount of genetic diversity was observed, despite previous suggestions that asparagus cultivars may have originated from one open-pollinated population.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100491"},"PeriodicalIF":3.5,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143877333","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Virtual screening and identification of potent phytoconstituents from Acorus calamus L. as inhibitors of Monkeypox virus infection","authors":"Shivani Lakhani ,&nbsp;Janki V. Rojmala ,&nbsp;Nisarginee M. Chotai ,&nbsp;Bhargav N. Waghela ,&nbsp;Parth Thakor","doi":"10.1016/j.jgeb.2025.100487","DOIUrl":"10.1016/j.jgeb.2025.100487","url":null,"abstract":"<div><h3>Background</h3><div>The threat posed by the Monkeypox (Mpox) disease has re-emerged globally while the world strives to recover from the Corona Virus Disease −19 (COVID-19) pandemic. The World Health Organization has declared Mpox a global health emergency. Monkeypox virus (MPXV), the causative agent of Mpox disease, is a zoonotic, large, enveloped, double-stranded deoxyribonucleic acid (DNA) virus that belongs to the <em>Orthopoxviridae</em> genus. The Food and Drug Administration (FDA), USA has approved repurposed antiviral agents Cidofovir and Tecovirimat as the primary treatment options for Mpox, however, they project systemic toxicity and have underwhelming clinical data. A <!--> <!-->plethora of medicinal plant compounds including flavonoids, phenolics, terpenoids, and alkaloids have a<!--> <!-->wide range of biological activities such as antimicrobial, antioxidant, antiulcer, antineoplastic, anti-inflammatory, and immuno-stimulating potentials. Since many of them are being studied in modern research to discover an active drug candidate, we turned to medicinal plants to explore potent antiviral compounds.</div></div><div><h3>Methods</h3><div>In the present study, we aimed to screen phytoconstituents of<em> <!-->Acorus calamus<!--> </em>L. (AC) against four essential virulence enabling proteins D8L, A48R, D13L, and A42R of MPXV by<em> <!-->in silico</em> <!-->approach. Further, we have elucidated pharmaceutical-relevant parameters of hit compounds through their absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties as well as drug-likeness parameters.</div></div><div><h3>Results</h3><div>Our results revealed that AC phytoconstituents such as β-Sitosterol against A42R and D8L, Lucenin-2 against D13L and Zingiberene against A48R showed the strongest binding affinities, respectively. Moreover, Galangin could prominently interact with all four proteins with lower binding energy and higher affinity. All top phytoconstituents obeyed Lipinski’s RO5 and drug-likeness properties.</div></div><div><h3>Conclusions</h3><div>The phytoconstituents of AC can act as potent inhibitors of essential virulence enabling proteins of MPXV. Thus, we recommend further experimental investigations to validate the promising results of the<!--> <!-->present <em>in silico</em> study.</div></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"23 2","pages":"Article 100487"},"PeriodicalIF":3.5,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143869767","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}