Journal of Genetic Engineering and Biotechnology最新文献

{"title":"Bioinformatics approach for prediction and analysis of the Non-Structural Protein 4B (NSP4B) of the Zika virus","authors":"Mohamed E. Hasan ,&nbsp;Aya Samir ,&nbsp;Magdy M. Khalil ,&nbsp;Medhat W. Shafaa","doi":"10.1016/j.jgeb.2023.100336","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100336","url":null,"abstract":"<div><h3>Background</h3><p>The Nonstructural Protein (NSP) 4B of Zika virus of 251 amino acids from (ZIKV/Human/POLG_ZIKVF) with accession number <strong>(A0A024B7W1)</strong>, Induces the production of Endoplasmic Reticulum ER-derived membrane vesicles, which are the sites of viral replication. To understand the physical basis of how proteins fold in nature and to solve the challenge of protein structure prediction, Ab-initio and comparative modeling are crucial tools.</p></div><div><h3>Results</h3><p>The systematic <em>in silico</em> technique, ThreaDom, had only predicted one domain (4 – 190) of NSP4B. I-TASSER, and Alphafold were ranked as the best servers for full-length 3-D protein structure predictions of NSP4B, where the predicted models were evaluated quantitatively using benchmarked metrics including C-score (-3.43), TM-score (0.77949), RMSD (2.73), and Z-score (1.561). The functional and protein binding motifs were realized using motif databases, secondary and surface accessibility predictions combined with Post-Translational Modification Sites (PTMs) prediction. Two highly conserved protein-binding motifs (Flavi NS4B and Bacillus papRprotein), together with three (PTMs) (Casein Kinase II, Myristyl site, and ASN-Glycosylation site) were predicted utilizing the Motif scan and Scanprosite servers. These patterns and PTMs were associated with NSP4B's role in triggering the development of the viral replication complex and its participation in the localization of NS3 and NS5 on the membrane. Only one hit from Structural Classification of Protein (SCOP) matched the protein sequence at positions 10 to 397 and was categorized six-hairpin glycosidases superfamily according to CATH (Class, Architecture, Topology, and Homology). Integrating this NSP4B information with the templates' SCOP and CATH annotations achieves it easier to attribute structure–function/evolution links to both previously known and recently discovered protein structures.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100336"},"PeriodicalIF":3.5,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X2301507X/pdfft?md5=4b2fb844d68c9f3253e820989cf809c7&pid=1-s2.0-S1687157X2301507X-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139674599","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":"Multi-epitope vaccine design against leishmaniasis using IFN-γ inducing epitopes from immunodominant gp46 and g63 proteins","authors":"Amir Dehghani ,&nbsp;Mina Mamizadeh ,&nbsp;Atena Karimi ,&nbsp;Seyyed Amir Hosseini ,&nbsp;Davood Siamian ,&nbsp;Morteza Shams ,&nbsp;Shadan Ghiabi ,&nbsp;Gholam Basati ,&nbsp;Amir Abaszadeh","doi":"10.1016/j.jgeb.2024.100355","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100355","url":null,"abstract":"<div><p>There is no currently approved human vaccine against leishmaniasis. Utilization of immunogenic antigens and their epitopes capable of enhancing immune responses against leishmaniasis is a crucial step for rational <em>in silico</em> vaccine design. The objective of this study was to generate and evaluate a potential vaccine candidate against leishmaniasis, designed by immunodominant proteins from gp46 and gp63 of <em>Leishmania major</em>, which can stimulate helper T-lymphocytes (HTL) and cytotoxic T-lymphocytes (CTL). For this aim, the IFN-γ-inducing MHC-I and MHC-II binders were predicted for each examined protein (gp46 and gp63) and connected with appropriate linkers, along with an adjuvant (<em>Mycobacterium tuberculosis</em> L7/L12) and a histidine tag. The vaccine’s stability, antigenicity, structure, and interaction with the TLR-4 receptor were evaluated <em>in silico</em>. The resulting chimeric vaccine was composed of 344 amino acids and had a molecular weight of 35.64 kDa. Physico-chemical properties indicated that it was thermotolerant, soluble, highly antigenic, and non-allergenic. Predictions of the secondary and tertiary structures were made, and further analyses confirmed that the vaccine construct could interact with the human TLR-4 receptor. Virtual immune simulation demonstrated strong stimulation of T-cell responses, particularly by an increase in IFN-γ, following vaccination. In summary, the <em>in silico</em> data indicated that the vaccine candidate showed high antigenicity in humans. It was also found to trigger significant levels of clearance mechanisms and other components of the cellular immune profile. Nevertheless, further wet experiments are required to properly assess the efficacy of this multi-epitope vaccine candidate against leishmaniasis.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100355"},"PeriodicalIF":3.5,"publicationDate":"2024-02-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000544/pdfft?md5=4d71bd83af7fcafdcc46dc152030ec68&pid=1-s2.0-S1687157X24000544-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675107","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":"Preserving the adaptive salt stress response activity of a tissue-specific promoter with modulating activity","authors":"Elham R.S. Soliman","doi":"10.1016/j.jgeb.2024.100354","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100354","url":null,"abstract":"<div><h3>Background</h3><p>The <em>Arabidopsis</em> “Redox Responsive Transcription Factor1” (<em>RRTF1</em>) promoter is transiently activated by salt stress in roots over 6 h period, followed by an adaptation phase during which its activity returns to baseline levels, even if the salt stress is prolonged. This enables the short-term production of genes that, while initially advantageous to the plant, will have long-term detrimental effects if expressed at high levels indefinitely.</p></div><div><h3>Results</h3><p>In this paper, we demonstrate that the <em>RRTF1</em> promoter salt adaption response is a dominant feature of the promoter, that cannot be overwritten by a strong enhancer. While maintaining the transient activation profile of the <em>RRTF1</em> promoter, linking it to the 35S enhancer results in a significant boost of salt stress induction in roots.</p></div><div><h3>Conclusion</h3><p>The <em>RRTF1</em> promoter’s enhanced and still adaptable activity could become a useful tool in plant biotechnology.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100354"},"PeriodicalIF":3.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000532/pdfft?md5=4db5615c60897fddc7cf2b68ad010f14&pid=1-s2.0-S1687157X24000532-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675105","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phylogenetic and genetic variation of common mudskippers (Periophthalmus kalolo Lesson, 1831) from the southern coast of Java, Indonesia inferred from the COI mitochondrial gene","authors":"Tuty Arisuryanti ,&nbsp;Katon Waskito Aji ,&nbsp;Faizah Nur Shabrina ,&nbsp;Diana Febriyanti ,&nbsp;Budi Setiadi Daryono ,&nbsp;Dwi Sendi Priyono","doi":"10.1016/j.jgeb.2023.100335","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100335","url":null,"abstract":"<div><h3>Background</h3><p>The common mudskipper (<em>Periophthalmus kalolo</em> Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of <em>COI</em> mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected <em>COI</em> sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach).</p></div><div><h3>Results</h3><p>The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events.</p></div><div><h3>Conclusions</h3><p>These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100335"},"PeriodicalIF":3.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015068/pdfft?md5=af30a46616a8f036cb307a7af7512707&pid=1-s2.0-S1687157X23015068-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675106","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":"Role of gene interactions in the pathophysiology of skeletal dysplasias: A case report in Colombia","authors":"Nathalie Yepes Madrid ,&nbsp;Lina Johanna Moreno Giraldo","doi":"10.1016/j.jgeb.2023.100350","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100350","url":null,"abstract":"<div><h3>Background</h3><p>Genome association studies have shown that gene-gene interactions or epistasis play a crucial role in identifying the etiology, prognosis, and treatment response of many complex diseases beyond their main effects. Skeletal dysplasias are a heterogeneous group of congenital bone and cartilage disorders with a genetic and gen-gen interaction etiology. The current classification of skeletal dysplasias distinguishes 461 diseases in 42 groups, and the incidence of all skeletal dysplasias is more than 1 in every 5000 newborns. The objective is to present the case of a patient with four variants that generates gen-gen interactions in the skeletal dysplasia.</p></div><div><h3>Case presentation</h3><p>A 1-year-old male patient was diagnosed with skeletal dysplasia based on prenatal ultrasound showing micromelia and pyelocalyceal dilation. Postnatal physical examination revealed body disproportion and involvement of other organs and systems.</p></div><div><h3>Materials and Methods</h3><p>A sequencing study and deletions/duplications analysis were performed for 358 candidate genes associated with skeletal dysplasia.</p><p>The GeneMANIA interface was used to evaluate the expression network of genes associated with each other for the gen-gen interaction.</p></div><div><h3>Results</h3><p>Four pathogenic variants were obtained two heterozygous variants with pathogenic significance in <em>SLC26A</em>, one heterozygous pathogenic variant in <em>CLCN7</em> and another heterozygous pathogenic variant in <em>CEP120</em>.</p><p>The GeneMANIA interface reveals 77.64% physical interactions, 8.01% co-expression, 5.37% prediction, 3.63% co-localization, 2.87% genetic interactions, 1.88% route of action, and 0.60% shared protein domains.</p></div><div><h3>Discussion and Conclusions</h3><p>These results suggest that the interaction between these genes affects the activity of the inorganic anion exchanger, leading to disorganization of collagen fibers, early mineralization, and decreased assembly of fibronectin in the bone extracellular matrix. Identifying gene-gene interactions is a fundamental step in understanding proper cell function and thus understanding the pathophysiology of many complex human diseases, improving diagnosis, and the possibilities of new personalized therapies.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100350"},"PeriodicalIF":3.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015214/pdfft?md5=5d3dccf35ca6c74daffdd149cc05eac0&pid=1-s2.0-S1687157X23015214-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675120","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":"Efficacy of Event MON 87460 in drought-tolerant maize hybrids under optimal and managed drought-stress in eastern and southern africa","authors":"Caleb O. Obunyali ,&nbsp;Kiru Pillay ,&nbsp;Barbara Meisel ,&nbsp;Eric N. Ndou ,&nbsp;Kingstone Mashingaidze ,&nbsp;Julius Pyton Sserumaga ,&nbsp;Godfrey Asea ,&nbsp;Murenga Mwimali ,&nbsp;Regina Tende ,&nbsp;Yoseph Beyene ,&nbsp;Stephen Mugo ,&nbsp;Emmanuel Okogbenin ,&nbsp;Sylvester O. Oikeh","doi":"10.1016/j.jgeb.2024.100352","DOIUrl":"https://doi.org/10.1016/j.jgeb.2024.100352","url":null,"abstract":"<div><h3>Background</h3><p>Frequent drought events due to climate change have become a major threat to maize (<em>Zea mays</em> L.) production and food security in Africa. Genetic engineering is one of the ways of improving drought tolerance through gene introgression to reduce the impact of drought stress in maize production. This study aimed to evaluate the efficacy of Event MON 87460 (<em>CspB</em>; <em>DroughtGard®</em>) gene in more than 120 conventional drought-tolerant maize hybrids in Kenya, South Africa, and Uganda for 3–6 years under managed drought-stress and optimal conditions and establish any additional yield contribution or yield penalties of the gene in traited hybrids relative to their non-traited isohybrids. Germplasm used in the study were either MON 87460 traited un-adapted (2008–2010), adapted traited <em>DroughtTEGO</em>® (2011–2013) or a mix of both under confined field trials.</p></div><div><h3>Results</h3><p>Results showed significant yield differences (<em>p</em> &lt; 0.001) among MON 87460 traited and non-traited hybrids across well-watered and managed drought-stress treatments. The gene had positive and significant effect on yield by 36–62% in three hybrids (CML312/CML445; WMA8101/CML445; and CML312/S0125Z) relative to non-traited hybrids under drought, and without significant yield penalty under optimum-moisture conditions in Lutzville, South Africa. Five traited hybrids (WMA2003/WMB4401; CML442/WMB4401; CML489/WMB4401; CML511/CML445; and CML395/WMB4401) had 7–13% significantly higher yield than the non-traited isohybrids out of 34 adapted DroughtTEGO® hybrids with same background genetics in the three countries for ≥ 3 years. The positive effect of MON 87460 was mostly observed under high drought-stress relative to low, moderate, or severe stress levels.</p></div><div><h3>Conclusion</h3><p>This study showed that MON 87460 transgenic drought tolerant maize hybrids could effectively tolerate drought and shield farmers against severe yield loss due to drought stress. The study signified that development and adoption of transgenic drought tolerant maize hybrids can cushion against farm yield losses due to drought stress as part of an integrated approach in adaptation to climate change effects.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100352"},"PeriodicalIF":3.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X24000519/pdfft?md5=c71bf960c6713f78b04e98e38d73790d&pid=1-s2.0-S1687157X24000519-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139675124","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 cuproptosis-related lncRNAs signature for predicting the prognosis in patients with kidney renal clear cell carcinoma","authors":"Ya He ,&nbsp;Hongxia Zhang ,&nbsp;Jingang Li ,&nbsp;Hui Zhou ,&nbsp;Fei Wang ,&nbsp;Guangliang Zhang ,&nbsp;Yuetao Wen","doi":"10.1016/j.jgeb.2023.100338","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100338","url":null,"abstract":"<div><h3>Background</h3><p>Kidney renal clear cell carcinoma (KIRC), with low survival rate, is the most frequent subtype of renal cell carcinoma. Recently, more and more studies indicate that cuproptosis-related genes (CRGs) and long non-coding RNAs (lncRNAs) play a vital role in the occurrence and development of many types of cancers. However, the roles of cuproptosis-related lncRNAs (CRlncRNAs) in the KIRC was uncertain.</p></div><div><h3>Results</h3><p>In our study, CRlncRNAs were obtained by coexpression between differentially expressed and prognostic CRGs and differentially expressed and prognostic lncRNAs, and an 8-CRlncRNAs (AC007743.1, AC022915.1, AP005136.4, APCDD1L-DT, HAGLR, LINC02027, MANCR and SMARCA5-AS1) risk model was established according to least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression. This risk model could differentiate immune cell infiltration, immune function and gene mutation.</p></div><div><h3>Conclusions</h3><p>This 8-CRlncRNAs risk model may be promising for the clinical prediction of prognoses, tumor immune, immunotherapy response and chemotherapeutic response in KIRC patients.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100338"},"PeriodicalIF":3.5,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015093/pdfft?md5=1f967c8db9a72fa6cfbb7cd01ca3b887&pid=1-s2.0-S1687157X23015093-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139653146","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":"Aggrecan-related bone disorders; a novel heterozygous ACAN variant associated with spondyloepimetaphyseal dysplasia expanding the phenotypic spectrum and review of literature","authors":"Hoda A. Ahmed ,&nbsp;R. Elhossini ,&nbsp;M. Aglan ,&nbsp;Khalda Amr","doi":"10.1016/j.jgeb.2023.100341","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100341","url":null,"abstract":"<div><h3>Background</h3><p>Spondyloepimetaphyseal dysplasias (SEMD) are a large group of skeletal disorders represented by abnormalities of vertebrae in addition to epiphyseal and metaphyseal areas of bones. Several genes have been identified underlying different forms. <em>ACAN</em> gene mutations were found to cause Aggrecan-related bone disorders (spondyloepimetaphyseal dysplasias,spondyloepiphyseal dysplasias, familial osteochondritis dissecans and short stature syndromes). This study aims to find the disease causing variant in Egyptian patient with SEMD using whole exome sequencing.</p></div><div><h3>Methods</h3><p>Whole-exome sequencing was performed for an Egyptian male patient who presented with short stature, clinical and radiological features suggestive of unclassified SEMD.</p></div><div><h3>Results</h3><p>The study identified a novel de novo heterozygous <em>ACAN</em> gene variant (c.7378G&gt;A; p.Gly2460Arg) in G3 domain. Mutations in <em>ACAN</em> gene have been more commonly associated with short stature than SEMD. The phenotype of our patient was intermediate in severity between spondyloepiphyseal dysplasia presentation; Kimberley type(SEDK) and Spondyloepimetaphyseal dysplasias Aggrecan (SEMDAG)</p></div><div><h3>Conclusions</h3><p>Whole exome sequencing revealed a novel de novo <em>ACAN</em> gene variant in patient with SEDK. The clinical and skeletal phenotype of our patient was much severe than those reported originally and showed more metaphyseal involvement. To the best of our knowledge, two previous studies reported a heterozygous variant in <em>ACAN</em> with spondyloepiphyseal dysplasia presentation; Kimberley type.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100341"},"PeriodicalIF":3.5,"publicationDate":"2024-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015123/pdfft?md5=139b419140ed041fe8c1d1c727bdcc01&pid=1-s2.0-S1687157X23015123-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139653148","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":"Elucidating the evolution of monkeypox virus genomes through phylo-geo-network and haplogroup analysis","authors":"Taslima Nasrin ,&nbsp;Md Samim Hassan ,&nbsp;Muzaffar Iqbal ,&nbsp;Amar Yousif ,&nbsp;Mehboob Hoque ,&nbsp;Nemat Ali ,&nbsp;Safdar Ali","doi":"10.1016/j.jgeb.2023.100346","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100346","url":null,"abstract":"<div><h3>Background</h3><p>As the world settles down from the COVID-19 pandemic, many countries are faced with an unexpected outbreak of monkeypox infection. Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is an enveloped, double stranded DNA virus belonging to the Poxviridae family. Presently, we construct and analyze the phylo-geo-network and the corresponding haplogroups. Presently, we performed the haplogroup analysis with their defining mutations and phylogenetic lineage study along with geographical distributions with the aim to understand the evolutionary path of the MPXV across the world.</p></div><div><h3>Results</h3><p>Information about 719 full length genomes of MPXV were collected from GISAID repository and the sequences extracted from NCBI. The alignment of 719 MPXV genomes and their subsequent analysis revealed a total of 1530 segregating sites of which 330 were parsimony informative (PI) sites. The variations had a positive value of Tajima’s D statistic indicating some mutations being prevalent and hence balancing selection. A total of 39 haplogroups were observed in the phylo-geo-network and their defining mutations along with the evolutionary path has been discussed. The phylo-geo-network revealed the nodal haplogroup is represented by GISAID ID 13889450, haplogroup A1, an isolate from Germany, having a total of 296 identical sequences in the study incident across 22 countries. The localized evolution is highlighted by country specific sequences and haplogroups. USA had a total of 58 genomes and 13 haplogroups as compared to Peru (89 genomes, 7 haplogroups) and Germany (26 genomes, 6 haplogroups).</p></div><div><h3>Conclusions</h3><p>The evolution of MPXV can be happening in a localized manner and hence accumulation of variations in the MPXV genomes needs to be monitored in order to be prepared for any possible threats.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100346"},"PeriodicalIF":3.5,"publicationDate":"2024-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015172/pdfft?md5=2f7565e23bc843bc5a97935c4082175e&pid=1-s2.0-S1687157X23015172-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139653147","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Screening of miRNAs as prognostic biomarkers and their associated hub targets across Hepatocellular carcinoma using survival-based bioinformatics approach","authors":"Prithvi Singh ,&nbsp;Rubi Solanki ,&nbsp;Alvea Tasneem ,&nbsp;Simran Suri ,&nbsp;Harleen Kaur ,&nbsp;Sapna Ratan Shah ,&nbsp;Ravins Dohare","doi":"10.1016/j.jgeb.2023.100337","DOIUrl":"https://doi.org/10.1016/j.jgeb.2023.100337","url":null,"abstract":"<div><h3>Background</h3><p>The hepatocellular carcinoma (HCC) incident rate is gradually increasing yearly despite all the research and efforts taken by scientific communities and governing bodies. Approximately <span><math><mrow><mn>90</mn><mo>%</mo></mrow></math></span> of all liver cancer cases belong to HCC. Usually, HCC patients approach the treatment in the late stages of this malignancy which becomes the primary cause of high mortality rate. The knowledge about molecular pathogenesis of HCC is limited and needs more attention from researchers to identify the driver genes and miRNAs, which causes to translate this information into clinical practice. Therefore, the key regulators identification of miRNA-mRNA regulatory network is essential to identify HCC-associated genes.</p></div><div><h3>Methodology</h3><p>We extracted microRNA (miRNA) and messenger RNA (mRNA) expression datasets of normal and tumor HCC patient samples from UCSC Xena followed by identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Univariate and multivariate cox-proportional hazard models were utilized to identify DEMs having significant association with overall survival (OS). Kaplan-Meier (KM) plotter was used to validate the presence of prognostic DEMs. A risk-score model was used to evaluate the effectiveness of KM-plotter validated DEMs combination on risk of samples. Target DEGs of prognostic miRNAs were identified via sources such as miRTargetLink and miRWalk followed by their validation in an external microarray cohort and enrichment analysis.</p></div><div><h3>Results</h3><p>562 DEGs and 388 DEMs were identified followed by seven prognostic miRNAs (i.e., miR-19a, miR-19b, miR-30d-5p, miR-424-5p, miR-3677-5p, miR-3913-5p, miR-7705) post univariate, multivariate, risk-score model evaluation and KM-plotter analyses. <em>ANLN</em>, <em>MRO</em>, <em>CPEB3</em> were their targets and were also validated in GSE84005 dataset.</p></div><div><h3>Conclusions</h3><p>The findings of this study decipher that most significant miRNAs and their identified target genes have association with apoptosis, inflammation, cell cycle regulation and cancer-related pathways, which appear to contribute to HCC pathogenesis and therefore, the discovery of new targets.</p></div>","PeriodicalId":53463,"journal":{"name":"Journal of Genetic Engineering and Biotechnology","volume":"22 1","pages":"Article 100337"},"PeriodicalIF":3.5,"publicationDate":"2024-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.sciencedirect.com/science/article/pii/S1687157X23015081/pdfft?md5=f3ba9ea0978c27244f33b635ba81f9c4&pid=1-s2.0-S1687157X23015081-main.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139549084","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}