Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Measuring the differential expression of the major hypermethylated tumor suppressor genes in tissues of primary hepatocellular carcinoma","authors":"Khalda Sayed Amr ,&nbsp;Wafaa Mohamed Ezzat ,&nbsp;Ahmed Ibrahim Saleh ,&nbsp;Ahmed Heiba ,&nbsp;Hend Amin ,&nbsp;Refaat Refaat Kamel ,&nbsp;Noha Eltaweel ,&nbsp;Hoda Henery ,&nbsp;Amr Omaia ,&nbsp;Reham Ibrahim Siddik ,&nbsp;Yasser Abdelghany Abdelazeem Elhosary","doi":"10.1016/j.jgeb.2024.100394","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100394","url":null,"abstract":"<div><h3>Background</h3><p>Hepatocarcinogenesis is a multifactorial process that arises from a integration of genetic and epigenetic anomalies leading to abnormal gene expression and function. It is difficult to characterize HCC with a single biomarker. Our study aimed at detecting the expression of a panel of 8 methylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) as regulatory factors among Egyptian patients with HCC.</p></div><div><h3>Methods</h3><p>This study was conducted on HCC tissue samples of 30 Egyptian patients in comparison with their non-cancerous adjacent cirrhotic tissue as a control. Tissue samples were obtained from patients who have undergone living donor liver transplantation (LDLT) or liver resection at El Sahel Teaching Hospital (Cairo, Egypt). A special Custom designed PCR Arrays was used to analyze the expression profiles of chosen methylated genes associated with HCC.</p></div><div><h3>Results</h3><p>Expression of SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2 were lower in the HCC tissue compared to the cirrhotic tissue (<em>p</em>value = 0.015, 0.081, 0.004, 0.027, 0.211, 0.015, 0.025 and 0.0001 respectively). 5 genes (SOCS1, APC, GAdd45b, CDKN1B, and MSH2) showed the ability to be used as diagnostic biomarkers for HCC with high sensitivity and specificity values at cut off values: 1.05, 1.17, 0.995, 0.546, and 0.125 respectively. As for the other 3 genes (P15, PAX6, STAT1), PAX6 gene has the highest sensitivity at a cut off value of 0.3364. A significant negative correlation was shown between alpha fetoprotein (AFP) and 5 of the studied genes (SOCS1, APC, Gadd45b, STAT1, and MSH2).</p></div><div><h3>Conclusions</h3><p>Expression of the selected hypermethylated genes (SOCS1, APC, Gadd45b, CDKN1B, P15, PAX6, STAT1 and MSH2) in HCC tissue samples was lower than adjacent tissue. Their role should be further studied to solve the mystery that surrounds the pathogenesis of HCC.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100394"},"PeriodicalIF":3.5,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000970/pdfft?md5=f06aabfa28b65ccc4c8a7768582c6d2e&pid=1-s2.0-S1687157X24000970-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141264060","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":"De novo transcriptome assembly, annotation and SSR mining data of Hellula undalis (Fabr.) (Lepidoptera: Pyralidae), the cabbage webworm","authors":"Malyaj R. Prajapati ,&nbsp;Pankaj Kumar ,&nbsp;Reetesh Pratap Singh ,&nbsp;Ravi Shanker ,&nbsp;Jitender Singh ,&nbsp;Mahesh Kumar Bharti ,&nbsp;Rajendra Singh ,&nbsp;Harshit Verma ,&nbsp;L.K. Gangwar ,&nbsp;Shailendra Singh Gaurav ,&nbsp;Neelesh Kapoor ,&nbsp;Satya Prakash ,&nbsp;Rekha Dixit","doi":"10.1016/j.jgeb.2024.100393","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100393","url":null,"abstract":"<div><h3>Background</h3><p>The cabbage webworm, <em>Hellula undalis</em> (Fabricius) (Lepidoptera: Pyralidae), is a significant pest of brassicas and other cruciferous plants in warm regions worldwide. Transcriptome analysis is valuable for investigation of molecular mechanisms underlying the insect development and reproduction. <em>De novo</em> assembly is particularly useful for acquiring complete transcriptome information of insect species when there is no reference genome available. In case of <em>Hellula undalis</em>, only 17 nucleotide records are currently available throughout NCBI nucleotide database. Genes associated with metabolic processes, general development, reproduction, defense and functional genomics were not previously predicted in the <em>Hellula undalis</em> at the genomic level.</p></div><div><h3>Methods &amp; Results</h3><p>To address this issue, we constructed <em>Hellula undalis</em> transcriptome using Illumina NovaSeq6000 technology. Approximately 48 million 150 bp paired-end reads were obtained from sequencing. A total of 30,451 contigs were generated by <em>de novo</em> assembly of sample and were compared with the sequences in the NCBI non-redundant protein database (Nr). In total, 71 % of contigs were matched to known proteins in public databases including Nr, Gene Ontology (GO), and Cluster Orthologous Gene Database (COG), and then, contigs were mapped to 123 via functional annotation against the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG). In addition, we compared the ortholog gene family of the <em>Hullula undalis,</em> transcriptome to <em>Spodoptera frugiperda, spodotera litura</em> and <em>spodoptera littoralis</em> and found that 391 orthologous gene families are specific to <em>Hullula undalis</em>. A total of 1,913 potential SSRs was discovered in <em>Hullula undalis</em> contigs.</p></div><div><h3>Conclusions</h3><p>This study is the first transcriptome data for <em>Hullula undalis.</em> Additionally, it serves as a valuable resource for identifying target genes and developing effective and environmentally friendly strategies for pest control.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 3","pages":"Article 100393"},"PeriodicalIF":3.5,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000969/pdfft?md5=d9595f6f619c7d3ec25c547204e59d69&pid=1-s2.0-S1687157X24000969-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141243356","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":"Phytoremediation potential of Brassica oleracea varieties through cadmium tolerance gene expression analysis","authors":"Jasmin Šutković ,&nbsp;Annissa Van Wieren ,&nbsp;Ensar Peljto ,&nbsp;Ahmet Yildirim","doi":"10.1016/j.jgeb.2024.100381","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100381","url":null,"abstract":"<div><h3>Background</h3><p><em>Brassica oleracea</em> var. <em>acephala</em>, commonly referred to as kale, is a well-documented plant species, a food crop but well recognized for its capacity to endure and manage the accumulation of heavy metals. In this research, the phytoremediation potential of kale was evaluated based on cadmium intake, utilizing three distinct kale varieties originating from Bosnia and Herzegovina. All kales were grown in controlled conditions, with different concentrations of cadmium (Cd), a known strong pollutant found in small concentrations in soil under normal environmental conditions. After the root length analysis and cadmium atomic spectrometry, we utilized quantitative PCR (qPCR) and cycle threshold (Ct) values to calculate the expression levels of five genes associated with Cd heavy metal response: Mitogen-activated protein kinase 2 (MAPK₂), Farnesylated protein 26 and 27 (HIPP₂₆, HIPP₂₇), Natural resistance-associated macrophage protein 6 (RAMP₆), and Heavy metal accumulator 2 (HMA₂).</p></div><div><h3>Results</h3><p>The atomic reader's analysis of rising cadmium concentrations revealed a proportional decline in the length of kale roots. The gene expression levels corresponded to cadmium stress differently among varieties, but mostly showing notable up-regulations under Cd stress, indicating the strong Cd presence within the plant.</p></div><div><h3>Conclusions</h3><p>This study demonstrated differences in gene expression behavior among three <em>B. oleracea</em> varieties from Bosnia and Herzegovina, indicating and filtering the Cd-resistant kale, and kale varieties suitable for phytoremediation. For the first time, such a study was conducted on kale varieties from Bosnia and Herzegovina, analyzing the impact of cadmium on the growth and resilience of these species.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100381"},"PeriodicalIF":3.5,"publicationDate":"2024-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000842/pdfft?md5=30ad8512efc7ed67a221c4cc7c1d0a52&pid=1-s2.0-S1687157X24000842-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140905603","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":"Exploring malaria parasite surface proteins to devise highly immunogenic multi-epitope subunit vaccine for Plasmodium falciparum","authors":"Preshita Bhalerao ,&nbsp;Satyendra Singh ,&nbsp;Vijay Kumar Prajapati ,&nbsp;Tarun Kumar Bhatt","doi":"10.1016/j.jgeb.2024.100377","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100377","url":null,"abstract":"<div><h3>Background</h3><p>Malaria has remained a major health concern for decades among people living in tropical and sub-tropical countries. <em>Plasmodium falciparum</em> is one of the critical species that cause severe malaria and is responsible for major mortality. Moreover, the parasite has generated resistance against all WHO recommended drugs and therapies. Therefore, there is an urgent need for preventive measures in the form of reliable vaccines to achieve the target of a malaria-free world. Surface proteins are the preferable choice for subunit vaccine development because they are rapidly detected and engaged by host immune cells and vaccination-induced antibodies. Additionally, abundant surface or membrane proteins may contribute to the opsonization of pathogens by vaccine-induced antibodies.</p></div><div><h3>Results</h3><p>In our study, we have listed all those surface proteins from the literature that could be functionally important and essential for infection and immune evasion of the malaria parasite. Eight <em>Plasmodium</em> surface and membrane proteins from the pre-erythrocyte and erythrocyte stages were shortlisted. Thirty-seven epitopes (B-cell, CTL, and HTL epitopes) from these proteins were predicted using immune-informatic tools and joined with suitable peptide linkers to design a vaccine construct. A TLR-4 agonist peptide adjuvant was added at the N-terminus of the multi-epitope series, followed by the PADRE sequence and EAAAK linker. The TLR-4 receptor was docked with the construct’s anticipated model structure. The complex of vaccine and TLR-4, with the lowest energy −1514, was found to be stable under simulated physiological settings.</p></div><div><h3>Conclusion</h3><p>This study has provided a novel multi-epitope construct that may be exploited further for the development of an efficient vaccine for malaria.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100377"},"PeriodicalIF":3.5,"publicationDate":"2024-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000805/pdfft?md5=a9835dcd8180e78b8cd8702a81572a12&pid=1-s2.0-S1687157X24000805-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824921","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 and analysis of oncogenic non-synonymous single nucleotide polymorphisms in the human NRAS gene: An exclusive in silico study","authors":"Md. Mozibullah ,&nbsp;Hadieh Eslampanah Seyedi ,&nbsp;Marina Khatun ,&nbsp;Md Solayman","doi":"10.1016/j.jgeb.2024.100378","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100378","url":null,"abstract":"<div><h3>Background</h3><p>N-ras protein is encoded by the <em>NRAS</em> gene and operates as GDP-GTP-controlled on/off switching. N-ras interacts with cellular signaling networks that regulate various cellular activities including cell proliferation and survival. The nonsynonymous single nucleotide polymorphism (nsSNPs)-mediated alteration can substantially disrupt the structure and activity of the corresponding protein. N-ras has been reported to be associated with numerous diseases including cancers due to the nsSNPs. A comprehensive study on the <em>NRAS</em> gene to unveil the potentially damaging and oncogenic nsSNPs is yet to be accomplished. Hence, this extensive <em>in silico</em> study is intended to identify the disease-associated, specifically oncogenic nsSNPs of the <em>NRAS</em> gene.</p></div><div><h3>Results</h3><p>Out of 140 missense variants, 7 nsSNPs (I55R, G60E, G60R, Y64D, L79F, D119G, and V152F) were identified to be damaging utilizing 10 computational tools that works based on different algorithms with high accuracy. Among those, G60E, G60R, and D119G variants were further filtered considering their location in the highly conserved region and later identified as oncogenic variants. Interestingly, G60E and G60R variants were revealed to be particularly associated with lung adenocarcinoma, rhabdomyosarcoma, and prostate adenocarcinoma. Therefore, D119G could be subjected to detailed investigation for identifying its association with specific cancer.</p></div><div><h3>Conclusion</h3><p>This <em>in silico</em> study identified the deleterious and oncogenic missense variants of the human <em>NRAS</em> gene that could be utilized for designing further experimental investigation. The outcomes of this study would be worthwhile in future research for developing personalized medicine.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100378"},"PeriodicalIF":3.5,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000817/pdfft?md5=7013281bec3753de6129b1fdcd8780df&pid=1-s2.0-S1687157X24000817-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140824920","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":"Microsatellite marker-based analysis of the genetic diversity and population structure of three Arnebiae Radix in western China","authors":"Jinrong Zhao ,&nbsp;Yanjiao Wang ,&nbsp;Wenhuan Ding ,&nbsp;Haiyan Xu","doi":"10.1016/j.jgeb.2024.100379","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100379","url":null,"abstract":"<div><p><em>Arnebiae Radix</em> is an important medicinal and perennial herb found in Western China, particularly in the Xinjiang region. However, the assessment, utilization and conservation of <em>Arnebiae Radix</em> resources are still unexplored. In this study, we evaluated the genetic diversity of three <em>Arnebiae Radix</em> populations across 47 regions (Ae = 16, Ag = 16, Ad = 15) in Xinjiang, China, using inter-simple sequence repeat (ISSR) molecular markers. In total, 48 alleles were amplified by six pairs of primers screened with ISSR markers. The average number of effective alleles (Ne) was 1.5770. The percentage of interspecific genetic polymorphisms in <em>A. guttata</em> (Ag = 89.58 %) was greater than that in <em>A. euchroma</em>. and <em>A. decumbens</em> (Ae = Ad = 87.50 %). Intraspecific genetic polymorphisms, Bo Le (BL) population of <em>A. euchroma</em> exhibited the highest percentage of polymorphic bands (PPB% =<!--> <!-->58.33 %, Na = 1.313, Ne = 1.467, I = 0.0.366, H = 0.255), which indicated high genetic diversity. In contrast, the Tuo Li (TL) population of <em>A. guttata</em> had the lowest values for these parameters (PPB% =<!--> <!-->0.00 %, Na = 0.313, Ne = 1,000, I = 0.000, H = 0.000). The <em>Arnebiae Radix</em> germplasms were classified into two major groups (I and II) based on UPGMA cluster analysis <strong>(</strong><span>Fig. 8</span><strong>a</strong>) and principal coordinate analysis (PCOA). In addition, <em>A. decumbens</em> is placed in a separate category due to its high differentiation coefficient. The AMOVA and genetic differentiation coefficient results indicated that the genetic variation in <em>Arnebiae Radix</em> was predominantly due to intrapopulation differences (78 %). Additionally, the gene flow index (Nm) between populations was 2.4128, which further indicated that the genetic diversity of <em>Arnebiae Radix</em> was greater at the intrapopulation level. The destruction of the ecological environment leads to the continuous reduction and degradation of the genetic diversity of <em>Arnebiae Radix</em> germplasm resources. In this study, we used ISSR molecular markers to analyze the genetic diversity and relatedness of <em>Arnebiae Radix</em>, which revealed the genetic relationship of <em>Arnebiae Radix</em> germplasm resources at the molecular level and provided a scientific basis for future research on selecting and breeding good varieties, evaluating the quality of <em>Arnebiae Radix</em>, and conserving and utilizing its resources.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100379"},"PeriodicalIF":3.5,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000829/pdfft?md5=7d9a4b01c22620be0790f83b4f6a29a2&pid=1-s2.0-S1687157X24000829-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140822781","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":"CRISPR/Cas9 based genome editing of Phytoene desaturase (PDS) gene in chilli pepper (Capsicum annuum L.)","authors":"Mallesham Bulle ,&nbsp;Ajay Kumar Venkatapuram ,&nbsp;Sadanandam Abbagani ,&nbsp;P.B. Kirti","doi":"10.1016/j.jgeb.2024.100380","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100380","url":null,"abstract":"<div><p>An effective CRISPR/Cas9 reagent delivery system has been developed in a commercially significant crop, the chilli pepper using a construct harboring two distinct gRNAs targeting exons 14 and 15 of the <em>Phytoene desaturase</em> (<em>CaPDS</em>) gene, whose loss-of-function mutation causes a photo-bleaching phenotype and impairs the biosynthesis of carotenoids. The construct carrying two sgRNAs was observed to create visible albino phenotypes in cotyledons regenerating on a medium containing 80 mg/L kanamycin, and plants regenerated therefrom after biolistic-mediated transfer of CRISPR/Cas9 reagents into chilli pepper cells. Analysis of CRISPR/Cas9 genome-editing events, including kanamycin screening of mutants and assessing homozygosity using the T7 endonuclease assay (T7E1), revealed 62.5 % of transformed plants exhibited successful editing at the target region and displayed both albino and mosaic phenotypes. Interestingly, the sequence analysis showed that insertions and substitutions were present in all the plant lines in the targeted <em>CaPDS</em> region. The detected mutations were mostly 12- to 24-bp deletions that disrupted the exon–intron junction, along with base substitutions and the insertion of 1-bp at the protospacer adjacent motif (PAM) region of the target site. The reduction in essential photosynthetic pigments (chlorophyll <em>a</em>, chlorophyll <em>b</em> and carotenoid) in knockout chilli pepper lines provided further evidence that the <em>CaPDS</em> gene had been functionally disrupted. In this present study, we report that the biolistic delivery of CRISPR/Cas9 reagents into chilli peppers is very effective and produces multiple mutation events in a short span of time.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100380"},"PeriodicalIF":3.5,"publicationDate":"2024-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000830/pdfft?md5=fc53916a794176375b5b2e3826ffe5a9&pid=1-s2.0-S1687157X24000830-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140816045","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":"Proteomic analysis of the venom of Conus flavidus from Red Sea reveals potential pharmacological applications","authors":"Mousa O. Germoush ,&nbsp;Maged Fouda ,&nbsp;Hamdy Aly ,&nbsp;Islam Saber ,&nbsp;Barakat M. Alrashdi ,&nbsp;Diaa Massoud ,&nbsp;Sarah Alzwain ,&nbsp;Ahmed E. Altyar ,&nbsp;Mohamed M. Abdel-Daim ,&nbsp;Moustafa Sarhan","doi":"10.1016/j.jgeb.2024.100375","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100375","url":null,"abstract":"<div><h3>Background</h3><p>Venomous marine cone snails produce unique neurotoxins called conopeptides or conotoxins, which are valuable for research and drug discovery. Characterizing <em>Conus</em> venom is important, especially for poorly studied species, as these tiny and steady molecules have considerable potential as research tools for detecting new pharmacological applications. In this study, a worm-hunting cone snail, <em>Conus flavidus</em> inhabiting the Red Sea coast were collected, dissected and the venom gland extraction was subjected to proteomic analysis to define the venom composition, and confirm the functional structure of conopeptides.</p></div><div><h3>Results</h3><p>Analysis of <em>C. flavidus</em> venom identified 117 peptide fragments and assorted them to conotoxin precursors and non-conotoxin proteins. In this procedure, 65 conotoxin precursors were classified and identified to 16 conotoxin precursors and hormone superfamilies. In the venom of <em>C. flavidus</em>, the four conotoxin superfamilies T, A, O2, and M were the most abundant peptides, accounting for 75.8% of the total conotoxin diversity. Additionally, 19 non-conotoxin proteins were specified in the venom, as well as several potentially biologically active peptides with putative applications.</p></div><div><h3>Conclusion</h3><p>Our research displayed that the structure of the <em>C. flavidus</em>-derived proteome is similar to other <em>Conus</em> species and includes toxins, ionic channel inhibitors, insulin-like peptides, and hyaluronidase. This study provides a foundation for discovering new conopeptides from <em>C. flavidus</em> venom for pharmaceutical use.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100375"},"PeriodicalIF":3.5,"publicationDate":"2024-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000787/pdfft?md5=659ba1ea4264d148941f3a5b0c28a2f1&pid=1-s2.0-S1687157X24000787-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140649825","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 resequencing unveils low-temperature stress tolerance specific genomic variations in jute (Corchorus sp.)","authors":"Athoi Ganguly ,&nbsp;Shaheena Amin ,&nbsp;Al-Amin ,&nbsp;Farhana Tasnim Chowdhury ,&nbsp;Haseena Khan ,&nbsp;Mohammad Riazul Islam","doi":"10.1016/j.jgeb.2024.100376","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100376","url":null,"abstract":"<div><p>Jute (<em>Corchorus</em> sp.), a commercially important and eco-friendly crop, is widely cultivated in Bangladesh, India, and China. Some varieties of this tropical plant such as the <em>Corchorus. olitorius</em> variety accession no. 2015 (acc. 2015) has been found to be low-temperature tolerant. The current study was designed to explore the genome-wide variations present in the tolerant plant acc. 2015 in comparison to the sensitive farmer popular variety <em>Corchorus. olitorius</em> var. O9897 using the whole genome resequencing technique. Among different variations, intergenic Single Nucleotide Polymorphism (SNPs) and Insertion-Deletion (InDels) were found in the highest percentage whereas approximately 3% SNPs and 2% InDels were found in exonic regions in both plants. Gene enrichment analysis indicated the presence of acc. 2015 specific SNPs in the genes encoding peroxidase, ER lumen protein retaining receptor, and hexosyltransferase involved in stress response (GO:0006950) which were not present in sensitive variety O9897. Besides, distinctive copy number variation regions (CNVRs) comprising 120 gene loci were found in acc. 2015 with a gain of function from multiple copy numbers but absent in O9897. Gene ontology analysis revealed these gene loci to possess different receptors like kinases, helicases, phosphatases, transcription factors especially Myb transcription factors, regulatory proteins containing different binding domains, annexin, laccase, acyl carrier protein, potassium transporter, and vesicular transporter proteins that are responsible for low temperature induced adaptation pathways in plants. This work of identifying genomic variations linked to cold stress tolerance traits will help to develop successful markers that will pave the way to develop genetically modified cold-resistant jute lines for year-round cultivation to meet the demand for a sustainable fiber crop economy.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100376"},"PeriodicalIF":3.5,"publicationDate":"2024-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000799/pdfft?md5=f57c61a3d080e8e8776dddd2fcd252d1&pid=1-s2.0-S1687157X24000799-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140539765","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":"Validation and optimization of the loop-mediated isothermal amplification (LAMP) technique for rapid detection of wheat stripe mosaic virus, a wheat-infecting pathogen","authors":"Anderson Varela de Andrade,&nbsp;Fernando Sartori Pereira,&nbsp;Fabio Nascimento da Silva,&nbsp;Gustavo Felippe da Silva,&nbsp;Maria de Lourdes Borba Magalhães","doi":"10.1016/j.jgeb.2024.100373","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100373","url":null,"abstract":"<div><h3>Background</h3><p>Wheat stripe mosaic virus (WhSMV) is a significant wheat pathogen that causes substantial yield losses in Brazil and other countries. Although several detection methods are available, reliable and efficient tools for on-site WhSMV detection are currently lacking. In this study, a Loop-Mediated Isothermal Amplification (LAMP) method was developed for rapid and reliable field detection of WhSMV. We designed WhSMV-specific primers for the LAMP assay and optimized reaction conditions for increased sensitivity and specificity using infected plant samples.</p></div><div><h3>Results</h3><p>We have developed a diagnostic method utilizing the Loop-Mediated Isothermal Amplification (LAMP) technique capable of rapidly and reliably detecting WhSMV. The LAMP assay has been optimized to enhance sensitivity, specificity, and cost-effectiveness.</p></div><div><h3>Conclusion</h3><p>The LAMP assay described here represents a valuable tool for early WhSMV detection, serving to mitigate the adverse economic and social impacts of this viral pathogen. By enabling swift and accurate identification, this assay can significantly improve the sustainability of cereal production systems, safeguarding crop yields against the detrimental effects of WhSMV.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 2","pages":"Article 100373"},"PeriodicalIF":3.5,"publicationDate":"2024-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000763/pdfft?md5=141435332207a36ad1e93620d25c3623&pid=1-s2.0-S1687157X24000763-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140344760","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}