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genetic sequencing</title> <meta name="description" content="Search results for: molecular genetic sequencing"> <meta name="keywords" content="molecular genetic sequencing"> <meta name="viewport" content="width=device-width, initial-scale=1, minimum-scale=1, maximum-scale=1, user-scalable=no"> <meta charset="utf-8"> <link href="https://cdn.waset.org/favicon.ico" type="image/x-icon" rel="shortcut icon"> <link href="https://cdn.waset.org/static/plugins/bootstrap-4.2.1/css/bootstrap.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/plugins/fontawesome/css/all.min.css" rel="stylesheet"> <link href="https://cdn.waset.org/static/css/site.css?v=150220211555" rel="stylesheet"> </head> <body> <header> <div class="container"> <nav class="navbar navbar-expand-lg navbar-light"> <a class="navbar-brand" href="https://waset.org"> <img src="https://cdn.waset.org/static/images/wasetc.png" alt="Open Science Research Excellence" title="Open Science Research Excellence" /> </a> <button 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action="https://publications.waset.org/abstracts/search"> <div id="custom-search-input"> <div class="input-group"> <i class="fas fa-search"></i> <input type="text" class="search-query" name="q" placeholder="Author, Title, Abstract, Keywords" value="molecular genetic sequencing"> <input type="submit" class="btn_search" value="Search"> </div> </div> </form> </div> </div> <div class="row mt-3"> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Commenced</strong> in January 2007</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Frequency:</strong> Monthly</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Edition:</strong> International</div> </div> </div> <div class="col-sm-3"> <div class="card"> <div class="card-body"><strong>Paper Count:</strong> 3845</div> </div> </div> </div> <h1 class="mt-3 mb-3 text-center" style="font-size:1.6rem;">Search results for: molecular genetic sequencing</h1> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3845</span> Application of Molecular Markers for Crop Improvement</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Monisha%20Isaac">Monisha Isaac</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=molecular%20markers" title="molecular markers">molecular markers</a>, <a href="https://publications.waset.org/abstracts/search?q=crop%20productivity" title=" crop productivity"> crop productivity</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20diversity" title=" genetic diversity"> genetic diversity</a>, <a href="https://publications.waset.org/abstracts/search?q=genotype" title=" genotype"> genotype</a> </p> <a href="https://publications.waset.org/abstracts/69621/application-of-molecular-markers-for-crop-improvement" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/69621.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">517</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3844</span> Genomics of Adaptation in the Sea</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Agostinho%20Antunes">Agostinho Antunes</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=marine%20genomics" title="marine genomics">marine genomics</a>, <a href="https://publications.waset.org/abstracts/search?q=evolutionary%20bioinformatics" title=" evolutionary bioinformatics"> evolutionary bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=human%20genome%20sequencing" title=" human genome sequencing"> human genome sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=genomic%20analyses" title=" genomic analyses"> genomic analyses</a> </p> <a href="https://publications.waset.org/abstracts/20910/genomics-of-adaptation-in-the-sea" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/20910.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">611</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3843</span> Development of Microsatellite Markers for Genetic Variation Analysis in House Cricket, Acheta domesticus</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Yash%20M.%20Gupta">Yash M. Gupta</a>, <a href="https://publications.waset.org/abstracts/search?q=Kittisak%20Buddhachat"> Kittisak Buddhachat</a>, <a href="https://publications.waset.org/abstracts/search?q=Surin%20Peyachoknagul"> Surin Peyachoknagul</a>, <a href="https://publications.waset.org/abstracts/search?q=Somjit%20Homchan"> Somjit Homchan</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The house cricket, Acheta domesticus is one of the commonly found species of field crickets. Although it is very commonly used as food and feed, the genomic information of house cricket is still missing for genetic investigation. DNA sequencing technology has evolved over the decades, and it has also revolutionized the molecular marker development for genetic analysis. In the present study, we have sequenced the whole genome of A. domesticus using illumina platform based HiSeq X Ten sequencing technology for searching simple sequence repeats (SSRs) in DNA to develop polymorphic microsatellite markers for population genetic analysis. A total of 112,157 SSRs with primer pairs were identified, 91 randomly selected SSRs used to check DNA amplification, of which nine primers were polymorphic. These microsatellite markers have shown cross-amplification with other three species of crickets which are Gryllus bimaculatus, Gryllus testaceus and Brachytrupes portentosus. These nine polymorphic microsatellite markers were used to check genetic variation for forty-five individuals of A. domesticus, Phitsanulok population, Thailand. For nine loci, the number of alleles was ranging from 5 to 15. The observed heterozygosity was ranged from 0.4091 to 0.7556. These microsatellite markers will facilitate population genetic analysis for future studies of A. domesticus populations. Moreover, the transferability of these SSR makers would also enable researchers to conduct genetic studies for other closely related species. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=cross-amplification" title="cross-amplification">cross-amplification</a>, <a href="https://publications.waset.org/abstracts/search?q=microsatellite%20markers" title=" microsatellite markers"> microsatellite markers</a>, <a href="https://publications.waset.org/abstracts/search?q=observed%20heterozygosity" title=" observed heterozygosity"> observed heterozygosity</a>, <a href="https://publications.waset.org/abstracts/search?q=population%20genetic" title=" population genetic"> population genetic</a>, <a href="https://publications.waset.org/abstracts/search?q=simple%20sequence%20repeats" title=" simple sequence repeats"> simple sequence repeats</a> </p> <a href="https://publications.waset.org/abstracts/109733/development-of-microsatellite-markers-for-genetic-variation-analysis-in-house-cricket-acheta-domesticus" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/109733.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">142</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3842</span> Molecular Detection and Isolation of Benzimidazole Resistant Haemonchus contortus from Pakistan</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=K.%20Ali">K. Ali</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20F.%20Qamar"> M. F. Qamar</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20A.%20Zaman"> M. A. Zaman</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20Younus"> M. Younus</a>, <a href="https://publications.waset.org/abstracts/search?q=I.%20Khan"> I. Khan</a>, <a href="https://publications.waset.org/abstracts/search?q=S.%20Ehtisham-ul-Haque"> S. Ehtisham-ul-Haque</a>, <a href="https://publications.waset.org/abstracts/search?q=R.%20Tamkeen"> R. Tamkeen</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20I.%20Rashid"> M. I. Rashid</a>, <a href="https://publications.waset.org/abstracts/search?q=Q.%20Ali"> Q. Ali</a> </p> <p class="card-text"><strong>Abstract:</strong></p> This study centers on molecular identification of Haemonchus contortus and isolation of Benz-imidazoles (BZ) resistant strains. Different abattoirs’ of two geographic regions of Punjab (Pakistan) were frequently visited for the collection of worms. Out of 1500 (n=1500) samples that were morphologically confirmed as H. contortus, 30 worms were subjected to molecular procedures for isolation of resistant strains. Resistant worms (n=8) were further subjected to DNA gene sequencing. Bio edit sequence alignment editor software was used to detect the possible mutation, deletion, replacement of nucleotides. Genetic diversity was noticed and genetic variation existing in β-tubulin isotype 1 of the H. contortus population of small ruminants of different regions considered in this study. H. contortus showed three different type of genetic sequences. 75%, 37.5%, 25% and 12.5% of the studied samples showed 100% query cover and identity with isolates and clones of China, UK, Australia and other countries, respectively. Interestingly the neighbor countries such as India and Iran haven’t many similarities with the Pakistani isolates. Thus, it suggests that population density of same genetic makeup H. contortus is scattered worldwide rather than clustering in a single region. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Haemonchus%20contortus" title="Haemonchus contortus">Haemonchus contortus</a>, <a href="https://publications.waset.org/abstracts/search?q=Benzimidazole%20resistant" title=" Benzimidazole resistant"> Benzimidazole resistant</a>, <a href="https://publications.waset.org/abstracts/search?q=%CE%B2-tubulin-1%20gene" title=" β-tubulin-1 gene"> β-tubulin-1 gene</a>, <a href="https://publications.waset.org/abstracts/search?q=abattoirs" title=" abattoirs"> abattoirs</a> </p> <a href="https://publications.waset.org/abstracts/86225/molecular-detection-and-isolation-of-benzimidazole-resistant-haemonchus-contortus-from-pakistan" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/86225.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">175</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3841</span> Microarrays: Wide Clinical Utilities and Advances in Healthcare</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Salma%20M.%20Wakil">Salma M. Wakil</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Advances in the field of genetics overwhelmed detecting large number of inherited disorders at the molecular level and directed to the development of innovative technologies. These innovations have led to gene sequencing, prenatal mutation detection, pre-implantation genetic diagnosis; population based carrier screening and genome wide analyses using microarrays. Microarrays are widely used in establishing clinical and diagnostic setup for genetic anomalies at a massive level, with the advent of cytoscan molecular karyotyping as a clinical utility card for detecting chromosomal aberrations with high coverage across the entire human genome. Unlike a regular karyotype that relies on the microscopic inspection of chromosomes, molecular karyotyping with cytoscan constructs virtual chromosomes based on the copy number analysis of DNA which improves its resolution by 100-fold. We have been investigating a large number of patients with Developmental Delay and Intellectual disability with this platform for establishing micro syndrome deletions and have detected number of novel CNV’s in the Arabian population with the clinical relevance. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=microarrays" title="microarrays">microarrays</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20karyotyping" title=" molecular karyotyping"> molecular karyotyping</a>, <a href="https://publications.waset.org/abstracts/search?q=developmental%20delay" title=" developmental delay"> developmental delay</a>, <a href="https://publications.waset.org/abstracts/search?q=genetics" title=" genetics"> genetics</a> </p> <a href="https://publications.waset.org/abstracts/24137/microarrays-wide-clinical-utilities-and-advances-in-healthcare" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/24137.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">458</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3840</span> Evolutionary Genomic Analysis of Adaptation Genomics </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Agostinho%20Antunes">Agostinho Antunes</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of varied species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=adaptation" title="adaptation">adaptation</a>, <a href="https://publications.waset.org/abstracts/search?q=animals" title=" animals"> animals</a>, <a href="https://publications.waset.org/abstracts/search?q=evolution" title=" evolution"> evolution</a>, <a href="https://publications.waset.org/abstracts/search?q=genomics" title=" genomics"> genomics</a> </p> <a href="https://publications.waset.org/abstracts/23726/evolutionary-genomic-analysis-of-adaptation-genomics" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/23726.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">429</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3839</span> Genomics of Aquatic Adaptation</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Agostinho%20Antunes">Agostinho Antunes</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The completion of the human genome sequencing in 2003 opened a new perspective into the importance of whole genome sequencing projects, and currently multiple species are having their genomes completed sequenced, from simple organisms, such as bacteria, to more complex taxa, such as mammals. This voluminous sequencing data generated across multiple organisms provides also the framework to better understand the genetic makeup of such species and related ones, allowing to explore the genetic changes underlining the evolution of diverse phenotypic traits. Here, recent results from our group retrieved from comparative evolutionary genomic analyses of selected marine animal species will be considered to exemplify how gene novelty and gene enhancement by positive selection might have been determinant in the success of adaptive radiations into diverse habitats and lifestyles. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=comparative%20genomics" title="comparative genomics">comparative genomics</a>, <a href="https://publications.waset.org/abstracts/search?q=adaptive%20evolution" title=" adaptive evolution"> adaptive evolution</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title=" bioinformatics"> bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=phylogenetics" title=" phylogenetics"> phylogenetics</a>, <a href="https://publications.waset.org/abstracts/search?q=genome%20mining" title=" genome mining"> genome mining</a> </p> <a href="https://publications.waset.org/abstracts/23727/genomics-of-aquatic-adaptation" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/23727.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">533</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3838</span> Postmortem Genetic Testing to Sudden and Unexpected Deaths Using the Next Generation Sequencing</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Eriko%20Ochiai">Eriko Ochiai</a>, <a href="https://publications.waset.org/abstracts/search?q=Fumiko%20Satoh"> Fumiko Satoh</a>, <a href="https://publications.waset.org/abstracts/search?q=Keiko%20Miyashita"> Keiko Miyashita</a>, <a href="https://publications.waset.org/abstracts/search?q=Yu%20Kakimoto"> Yu Kakimoto</a>, <a href="https://publications.waset.org/abstracts/search?q=Motoki%20Osawa"> Motoki Osawa</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Sudden and unexpected deaths from unknown causes occur in infants and youths. Recently, molecular links between a part of these deaths and several genetic diseases are examined in the postmortem. For instance, hereditary long QT syndrome and Burgada syndrome are occasionally fatal through critical ventricular tachyarrhythmia. There are a large number of target genes responsible for such diseases, the conventional analysis using the Sanger’s method has been laborious. In this report, we attempted to analyze sudden deaths comprehensively using the next generation sequencing (NGS) technique. Multiplex PCR to subject’s DNA was performed using Ion AmpliSeq Library Kits 2.0 and Ion AmpliSeq Inherited Disease Panel (Life Technologies). After the library was constructed by emulsion PCR, the amplicons were sequenced 500 flows on Ion Personal Genome Machine System (Life Technologies) according to the manufacture instruction. SNPs and indels were analyzed to the sequence reads that were mapped on hg19 of reference sequences. This project has been approved by the ethical committee of Tokai University School of Medicine. As a representative case, the molecular analysis to a 40 years old male who received a diagnosis of Brugada syndrome demonstrated a total of 584 SNPs or indels. Non-synonymous and frameshift nucleotide substitutions were selected in the coding region of heart disease related genes of ANK2, AKAP9, CACNA1C, DSC2, KCNQ1, MYLK, SCN1B, and STARD3. In particular, c.629T-C transition in exon 3 of the SCN1B gene, resulting in a leu210-to-pro (L210P) substitution is predicted “damaging” by the SIFT program. Because the mutation has not been reported, it was unclear if the substitution was pathogenic. Sudden death that failed in determining the cause of death constitutes one of the most important unsolved subjects in forensic pathology. The Ion AmpliSeq Inherited Disease Panel can amplify the exons of 328 genes at one time. We realized the difficulty in selection of the true source from a number of candidates, but postmortem genetic testing using NGS analysis deserves of a diagnostic to date. We now extend this analysis to SIDS suspected subjects and young sudden death victims. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=postmortem%20genetic%20testing" title="postmortem genetic testing">postmortem genetic testing</a>, <a href="https://publications.waset.org/abstracts/search?q=sudden%20death" title=" sudden death"> sudden death</a>, <a href="https://publications.waset.org/abstracts/search?q=SIDS" title=" SIDS"> SIDS</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a> </p> <a href="https://publications.waset.org/abstracts/17129/postmortem-genetic-testing-to-sudden-and-unexpected-deaths-using-the-next-generation-sequencing" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/17129.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">359</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3837</span> Genetic Diversity Analysis in Ecological Populations of Persian Walnut</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Masoud%20Sheidai">Masoud Sheidai</a>, <a href="https://publications.waset.org/abstracts/search?q=Fahimeh%20Koohdar"> Fahimeh Koohdar</a>, <a href="https://publications.waset.org/abstracts/search?q=Hashem%20Sharifi"> Hashem Sharifi</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Juglans regia (L.) commonly known as Persian walnut of the genus Juglans L. (Juglandaceae) is one of the most important cultivated plant species due to its high-quality wood and edible nuts. The genetic diversity analysis is essential for conservation and management of tree species. Persian walnut is native from South-Eastern Europe to North-Western China through Tibet, Nepal, Northern India, Pakistan, and Iran. The species like Persian walnut, which has a wide range of geographical distribution, should harbor extensive genetic variability to adapt to environmental fluctuations they face. We aimed to study the population genetic structure of seven Persian walnut populations including three wild and four cultivated populations by using ISSR (Inter simple sequence repeats) and SRAP (Sequence related amplified polymorphism) molecular markers. We also aimed to compare the genetic variability revealed by ISSR neutral multilocus marker and rDNA ITS sequences. The studied populations differed in morphological features as the samples in each population were clustered together and were separate from the other populations. Three wild populations studied were placed close to each other. The mantel test after 5000 times permutation performed between geographical distance and morphological distance in Persian walnut populations produced significant correlation (r = 0.48, P = 0.002). Therefore, as the populations become farther apart, they become more divergent in morphological features. ISSR analysis produced 47 bands/ loci, while we obtained 15 SRAP bands. Gst and other differentiation statistics determined for these loci revealed that most of the ISSR and SRAP loci have very good discrimination power and can differentiate the studied populations. AMOVA performed for these loci produced a significant difference (< 0.05) supporting the above-said result. AMOVA produced significant genetic difference based on ISSR data among the studied populations (PhiPT = 0.52, P = 0.001). AMOVA revealed that 53% of the total variability is due to among population genetic difference, while 47% is due to within population genetic variability. The results showed that both multilocus molecular markers and ITS sequences can differentiate Persian walnut populations. The studied populations differed genetically and showed isolation by distance (IBD). ITS sequence based MP and Bayesian phylogenetic trees revealed that Iranian walnut cultivars form a distinct clade separated from the cultivars studied from elsewhere. Almost all clades obtained have high bootstrap value. The results indicated that a combination of multilpcus and sequencing molecular markers can be used in genetic differentiation of Persian walnut. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=genetic%20diversity" title="genetic diversity">genetic diversity</a>, <a href="https://publications.waset.org/abstracts/search?q=population" title=" population"> population</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20markers" title=" molecular markers"> molecular markers</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20difference" title=" genetic difference"> genetic difference</a> </p> <a href="https://publications.waset.org/abstracts/97640/genetic-diversity-analysis-in-ecological-populations-of-persian-walnut" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/97640.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">162</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3836</span> Transcriptome Analysis of Saffron (crocus sativus L.) Stigma Focusing on Identification Genes Involved in the Biosynthesis of Crocin</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Parvaneh%20Mahmoudi">Parvaneh Mahmoudi</a>, <a href="https://publications.waset.org/abstracts/search?q=Ahmad%20Moeni"> Ahmad Moeni</a>, <a href="https://publications.waset.org/abstracts/search?q=Seyed%20Mojtaba%20Khayam%20Nekoei"> Seyed Mojtaba Khayam Nekoei</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohsen%20Mardi"> Mohsen Mardi</a>, <a href="https://publications.waset.org/abstracts/search?q=Mehrshad%20Zeinolabedini"> Mehrshad Zeinolabedini</a>, <a href="https://publications.waset.org/abstracts/search?q=Ghasem%20Hosseini%20Salekdeh"> Ghasem Hosseini Salekdeh</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Saffron (Crocus sativus L.) is one of the most important spice and medicinal plants. The three-branch style of C. sativus flowers are the most important economic part of the plant and known as saffron, which has several medicinal properties. Despite the economic and biological significance of this plant, knowledge about its molecular characteristics is very limited. In the present study, we, for the first time, constructed a comprehensive dataset for C. sativus stigma through de novo transcriptome sequencing. We performed de novo transcriptome sequencing of C. sativus stigma using the Illumina paired-end sequencing technology. A total of 52075128 reads were generated and assembled into 118075 unigenes, with an average length of 629 bp and an N50 of 951 bp. A total of 66171unigenes were identified, among them, 66171 (56%) were annotated in the non-redundant National Center for Biotechnology Information (NCBI) database, 30938 (26%) were annotated in the Swiss-Prot database, 10273 (8.7%) unigenes were mapped to 141 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, while 52560 (44%) and 40756 (34%) unigenes were assigned to Gen Ontology (GO) categories and Eukaryotic Orthologous Groups of proteins (KOG), respectively. In addition, 65 candidate genes involved in three stages of crocin biosynthesis were identified. Finally, transcriptome sequencing of saffron stigma was used to identify 6779 potential microsatellites (SSRs) molecular markers. High-throughput de novo transcriptome sequencing provided a valuable resource of transcript sequences of C. sativus in public databases. In addition, most of candidate genes potentially involved in crocin biosynthesis were identified which could be further utilized in functional genomics studies. Furthermore, numerous obtained SSRs might contribute to address open questions about the origin of this amphiploid spices with probable little genetic diversity. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=saffron" title="saffron">saffron</a>, <a href="https://publications.waset.org/abstracts/search?q=transcriptome" title=" transcriptome"> transcriptome</a>, <a href="https://publications.waset.org/abstracts/search?q=NGS" title=" NGS"> NGS</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatic" title=" bioinformatic"> bioinformatic</a> </p> <a href="https://publications.waset.org/abstracts/171689/transcriptome-analysis-of-saffron-crocus-sativus-l-stigma-focusing-on-identification-genes-involved-in-the-biosynthesis-of-crocin" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/171689.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">100</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3835</span> Applications of AFM in 4D to Optimize the Design of Genetic Nanoparticles</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Hosam%20Abdelhady">Hosam Abdelhady</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Filming the behaviors of individual DNA molecules in their environment when they interact with individual medicinal nano-polymers in a molecular scale has opened the door to understand the effect of the molecular shape, size, and incubation time with nanocarriers on optimizing the design of robust genetic Nano molecules able to resist the enzymatic degradation, enter the cell, reach to the nucleus and kill individual cancer cells in their environment. To this end, we will show how we applied the 4D AFM as a guide to finetune the design of genetic nanoparticles and to film the effects of these nanoparticles on the nanomechanical and morphological profiles of individual cancer cells. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=AFM" title="AFM">AFM</a>, <a href="https://publications.waset.org/abstracts/search?q=dendrimers" title=" dendrimers"> dendrimers</a>, <a href="https://publications.waset.org/abstracts/search?q=nanoparticles" title=" nanoparticles"> nanoparticles</a>, <a href="https://publications.waset.org/abstracts/search?q=DNA" title=" DNA"> DNA</a>, <a href="https://publications.waset.org/abstracts/search?q=gene%20therapy" title=" gene therapy"> gene therapy</a>, <a href="https://publications.waset.org/abstracts/search?q=imaging" title=" imaging"> imaging</a> </p> <a href="https://publications.waset.org/abstracts/157876/applications-of-afm-in-4d-to-optimize-the-design-of-genetic-nanoparticles" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/157876.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">73</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3834</span> Milk Yield and Fingerprinting of Beta-Casein Precursor (CSN2) Gene in Some Saudi Camel Breeds</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Amr%20A.%20El%20Hanafy">Amr A. El Hanafy</a>, <a href="https://publications.waset.org/abstracts/search?q=Yasser%20M.%20Saad"> Yasser M. Saad</a>, <a href="https://publications.waset.org/abstracts/search?q=Saleh%20A.%20Alkarim"> Saleh A. Alkarim</a>, <a href="https://publications.waset.org/abstracts/search?q=Hussein%20A.%20Almehdar"> Hussein A. Almehdar</a>, <a href="https://publications.waset.org/abstracts/search?q=Elrashdy%20M.%20Redwan"> Elrashdy M. Redwan</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Camels are substantial providers of transport, milk, sport, meat, shelter, fuel, security and capital in many countries, particularly Saudi Arabia. Identification of animal breeds has progressed rapidly during the last decade. Advanced molecular techniques are playing a significant role in breeding or strain protection laws. On the other hand, fingerprinting of some molecular markers related to some productive traits in farm animals represents most important studies to our knowledge, which aim to conserve these local genetic resources, and to the genetic improvement of such local breeds by selective programs depending on gene markers. Milk records were taken two days in each week from female camels of Majahem, Safara, Wathaha, and Hamara breeds, respectively from different private farms in northern Jeddah, Riyadh and Alwagh governorates and average weekly yields were calculated. DNA sequencing for CSN2 gene was used for evaluating the genetic variations and calculating the genetic distance values among four Saudi camel populations which are Hamra(R), Safra(Y), Wadha(W) and Majaheim(M). In addition, this marker was analyzed for reconstructing the Neighbor joining tree among evaluating camel breeds. In respect to milk yield during winter season, result indicated that average weekly milk yield of Safara camel breed (30.05 Kg/week) is significantly (p < 0.05) lower than the other 3 breeds which ranged from 39.68 for Hamara to 42.42 Kg/week for Majahem, while there are not significant differences between these three breeds. The Neighbor Joining analysis that re-constructed based on DNA variations showed that samples are clustered into two unique clades. The first clade includes Y (from Y4 to Y18) and M (from M1, to M9). On the other hand, the second cluster is including all R (from R1 to R6) and W (from W1 to W6). The genetic distance values were equal 0.0068 (between the groups M&Y and R&W) and equal 0 (within each group). <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=milk%20yield" title="milk yield">milk yield</a>, <a href="https://publications.waset.org/abstracts/search?q=beta-casein%20precursor%20%28CSN2%29" title=" beta-casein precursor (CSN2)"> beta-casein precursor (CSN2)</a>, <a href="https://publications.waset.org/abstracts/search?q=Saudi%20camel" title=" Saudi camel"> Saudi camel</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20markers" title=" molecular markers"> molecular markers</a> </p> <a href="https://publications.waset.org/abstracts/74687/milk-yield-and-fingerprinting-of-beta-casein-precursor-csn2-gene-in-some-saudi-camel-breeds" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/74687.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">214</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3833</span> Breast Cancer and BRCA Gene: A Study on Genetic and Environmental Interaction</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Abhishikta%20Ghosh%20Roy">Abhishikta Ghosh Roy</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Breast cancer is the most common malignancy among women globally, including India. Human breast cancer results from the genetic and environmental interaction. The present study attempts to understand the molecular heterogeneity of BRCA1 and BRCA2 genes, as well as to understand the association of various lifestyle and reproductive variables for the Breast Cancer risk. The study was conducted amongst 110 patients and 128 controls with total DNA sequencing of flanking and coding regions of BRCA1 BRCA2 genes that revealed ten Single Nucleotide Polymorphisms (SNPs) (6 novels). The controls selected for the study were age, sex and ethnic group matched. After written and informed consent biological samples were collected from the subjects. After detailed molecular analysis, significant (p < 0.005) molecular heterogeneity is revealed in terms of SNPs in BRCA1 (4 Exonic & 1 Intronic) and BRCA2 (2exonic and 3 Intronic) genes. The augmentation study investigated significant (p < 0.05) association with positive family history, early age at menarche, irregular menstrual periods, menopause, prolong contraceptive use, nulliparity, history of abortions, consumption of alcohol and smoking for breast cancer risk. To the best of authors knowledge, this study is the first of its kind, envisaged that the identification of the SNPs and modification of the lifestyle factors might aid to minimize the risk among the Bengalee Hindu females. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=breast%20cancer" title="breast cancer">breast cancer</a>, <a href="https://publications.waset.org/abstracts/search?q=BRCA" title=" BRCA"> BRCA</a>, <a href="https://publications.waset.org/abstracts/search?q=lifestyle" title=" lifestyle"> lifestyle</a>, <a href="https://publications.waset.org/abstracts/search?q=India" title=" India"> India</a> </p> <a href="https://publications.waset.org/abstracts/99371/breast-cancer-and-brca-gene-a-study-on-genetic-and-environmental-interaction" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/99371.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">114</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3832</span> A Genetic Identification of Candida Species Causing Intravenous Catheter-Associated Candidemia in Heart Failure Patients</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Seyed%20Reza%20Aghili">Seyed Reza Aghili</a>, <a href="https://publications.waset.org/abstracts/search?q=Tahereh%20Shokohi"> Tahereh Shokohi</a>, <a href="https://publications.waset.org/abstracts/search?q=Shirin%20Sadat%20Hashemi%20Fesharaki"> Shirin Sadat Hashemi Fesharaki</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohammad%20Ali%20Boroumand"> Mohammad Ali Boroumand</a>, <a href="https://publications.waset.org/abstracts/search?q=Bahar%20Salmanian"> Bahar Salmanian</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Introduction: Intravenous catheter-associated fungal infection as nosocomial infection continue to be a deep problem among hospitalized patients, decreasing quality of life and adding healthcare costs. The capacity of catheters in the spread of candidemia in heart failure patients is obvious. The aim of this study was to evaluate the prevalence and genetic identification of Candida species in heart disorder patients. Material and Methods: This study was conducted in Tehran Hospital of Cardiology Center (Tehran, Iran, 2014) during 1.5 years on the patients hospitalized for at least 7 days and who had central or peripheral vein catheter. Culture of catheters, blood and skin of the location of catheter insertion were applied for detecting Candida colonies in 223 patients. Identification of Candida species was made on the basis of a combination of various phenotypic methods and confirmed by sequencing the ITS1-5.8S-ITS2 region amplified from the genomic DNA using PCR and the NCBI BLAST. Results: Of the 223 patients samples tested, we identified totally 15 Candida isolates obtained from 9 (4.04%) catheter cultures, 3 (1.35%) blood cultures and 2 (0.90%) skin cultures of the catheter insertion areas. On the base of ITS region sequencing, out of nine Candida isolates from catheter, 5(55.6%) C. albicans, 2(22.2%) C. glabrata, 1(11.1%) C. membranifiaciens and 1 (11.1%) C. tropicalis were identified. Among three Candida isolates from blood culture, C. tropicalis, C. carpophila and C. membranifiaciens were identified. Non-candida yeast isolated from one blood culture was Cryptococcus albidus. One case of C. glabrata and one case of Candida albicans were isolated from skin culture of the catheter insertion areas in patients with positive catheter culture. In these patients, ITS region of rDNA sequence showed a similarity between Candida isolated from the skin and catheter. However, the blood samples of these patients were negative for fungal growth. We report two cases of catheter-related candidemia caused by C. membranifiaciens and C. tropicalis on the base of genetic similarity of species isolated from blood and catheter which were treated successfully with intravenous fluconazole and catheter removal. In phenotypic identification methods, we could only identify C. albicans and C. tropicalis and other yeast isolates were diagnosed as Candida sp. Discussion: Although more than 200 species of Candida have been identified, only a few cause diseases in humans. There is some evidence that non-albicans infections are increasing. Many risk factors, including prior antibiotic therapy, use of a central venous catheter, surgery, and parenteral nutrition are considered to be associated with candidemia in hospitalized heart failure patients. Identifying the route of infection in candidemia is difficult. Non-albicans candida as the cause of candidemia is increasing dramatically. By using conventional method, many non-albicans isolates remain unidentified. So, using more sensitive and specific molecular genetic sequencing to clarify the aspects of epidemiology of the unknown candida species infections is essential. The positive blood and catheter cultures for candida isolates and high percentage of similarity of their ITS region of rDNA sequence in these two patients confirmed the diagnosis of intravenous catheter-associated candidemia. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=catheter-associated%20infections" title="catheter-associated infections">catheter-associated infections</a>, <a href="https://publications.waset.org/abstracts/search?q=heart%20failure%20patient" title=" heart failure patient"> heart failure patient</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20genetic%20sequencing" title=" molecular genetic sequencing"> molecular genetic sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=ITS%20region%20of%20rDNA" title=" ITS region of rDNA"> ITS region of rDNA</a>, <a href="https://publications.waset.org/abstracts/search?q=Candidemia" title=" Candidemia"> Candidemia</a> </p> <a href="https://publications.waset.org/abstracts/60303/a-genetic-identification-of-candida-species-causing-intravenous-catheter-associated-candidemia-in-heart-failure-patients" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/60303.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">332</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3831</span> Unlocking the Genetic Code: Exploring the Potential of DNA Barcoding for Biodiversity Assessment</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mohammed%20Ahmed%20Ahmed%20Odah">Mohammed Ahmed Ahmed Odah</a> </p> <p class="card-text"><strong>Abstract:</strong></p> DNA barcoding is a crucial method for assessing and monitoring species diversity amidst escalating threats to global biodiversity. The author explores DNA barcoding's potential as a robust and reliable tool for biodiversity assessment. It begins with a comprehensive review of existing literature, delving into the theoretical foundations, methodologies and applications of DNA barcoding. The suitability of various DNA regions, like the COI gene, as universal barcodes is extensively investigated. Additionally, the advantages and limitations of different DNA sequencing technologies and bioinformatics tools are evaluated within the context of DNA barcoding. To evaluate the efficacy of DNA barcoding, diverse ecosystems, including terrestrial, freshwater and marine habitats, are sampled. Extracted DNA from collected specimens undergoes amplification and sequencing of the target barcode region. Comparison of the obtained DNA sequences with reference databases allows for the identification and classification of the sampled organisms. Findings demonstrate that DNA barcoding accurately identifies species, even in cases where morphological identification proves challenging. Moreover, it sheds light on cryptic and endangered species, aiding conservation efforts. The author also investigates patterns of genetic diversity and evolutionary relationships among different taxa through the analysis of genetic data. This research contributes to the growing knowledge of DNA barcoding and its applicability for biodiversity assessment. The advantages of this approach, such as speed, accuracy and cost-effectiveness, are highlighted, along with areas for improvement. By unlocking the genetic code, DNA barcoding enhances our understanding of biodiversity, supports conservation initiatives and informs evidence-based decision-making for the sustainable management of ecosystems. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=DNA%20barcoding" title="DNA barcoding">DNA barcoding</a>, <a href="https://publications.waset.org/abstracts/search?q=biodiversity%20assessment" title=" biodiversity assessment"> biodiversity assessment</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20code" title=" genetic code"> genetic code</a>, <a href="https://publications.waset.org/abstracts/search?q=species%20identification" title=" species identification"> species identification</a>, <a href="https://publications.waset.org/abstracts/search?q=taxonomic%20%20resolution" title=" taxonomic resolution"> taxonomic resolution</a>, <a href="https://publications.waset.org/abstracts/search?q=next-generation%20sequencing" title=" next-generation sequencing"> next-generation sequencing</a> </p> <a href="https://publications.waset.org/abstracts/190376/unlocking-the-genetic-code-exploring-the-potential-of-dna-barcoding-for-biodiversity-assessment" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/190376.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">24</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3830</span> Accurate HLA Typing at High-Digit Resolution from NGS Data</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Yazhi%20Huang">Yazhi Huang</a>, <a href="https://publications.waset.org/abstracts/search?q=Jing%20Yang"> Jing Yang</a>, <a href="https://publications.waset.org/abstracts/search?q=Dingge%20Ying"> Dingge Ying</a>, <a href="https://publications.waset.org/abstracts/search?q=Yan%20Zhang"> Yan Zhang</a>, <a href="https://publications.waset.org/abstracts/search?q=Vorasuk%20Shotelersuk"> Vorasuk Shotelersuk</a>, <a href="https://publications.waset.org/abstracts/search?q=Nattiya%20Hirankarn"> Nattiya Hirankarn</a>, <a href="https://publications.waset.org/abstracts/search?q=Pak%20Chung%20Sham"> Pak Chung Sham</a>, <a href="https://publications.waset.org/abstracts/search?q=Yu%20Lung%20Lau"> Yu Lung Lau</a>, <a href="https://publications.waset.org/abstracts/search?q=Wanling%20Yang"> Wanling Yang</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=human%20leukocyte%20antigens" title="human leukocyte antigens">human leukocyte antigens</a>, <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title=" next generation sequencing"> next generation sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=whole%20exome%20sequencing" title=" whole exome sequencing"> whole exome sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=HLA%20typing" title=" HLA typing"> HLA typing</a> </p> <a href="https://publications.waset.org/abstracts/26433/accurate-hla-typing-at-high-digit-resolution-from-ngs-data" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/26433.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">664</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3829</span> Genomic Diversity and Relationship among Arabian Peninsula Dromedary Camels Using Full Genome Sequencing Approach </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=H.%20Bahbahani">H. Bahbahani</a>, <a href="https://publications.waset.org/abstracts/search?q=H.%20Musa"> H. Musa</a>, <a href="https://publications.waset.org/abstracts/search?q=F.%20Al%20Mathen"> F. Al Mathen</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The dromedary camels (Camelus dromedarius) are single-humped even-toed ungulates populating the African Sahara, Arabian Peninsula, and Southwest Asia. The genome of this desert-adapted species has been minimally investigated using autosomal microsatellite and mitochondrial DNA markers. In this study, the genomes of 33 dromedary camel samples from different parts of the Arabian Peninsula were sequenced using Illumina Next Generation Sequencing (NGS) platform. These data were combined with Genotyping-by-Sequencing (GBS) data from African (Sudanese) dromedaries to investigate the genomic relationship between African and Arabian Peninsula dromedary camels. Principle Component Analysis (PCA) and average genome-wide admixture analysis were be conducted on these data to tackle the objectives of these studies. Both of the two analyses conducted revealed phylogeographic distinction between these two camel populations. However, no breed-wise genetic classification has been revealed among the African (Sudanese) camel breeds. The Arabian Peninsula camel populations also show higher heterozygosity than the Sudanese camels. The results of this study explain the evolutionary history and migration of African dromedary camels from their center of domestication in the southern Arabian Peninsula. These outputs help scientists to further understand the evolutionary history of dromedary camels, which might impact in conserving the favorable genetic of this species. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=dromedary" title="dromedary">dromedary</a>, <a href="https://publications.waset.org/abstracts/search?q=genotyping-by-sequencing" title=" genotyping-by-sequencing"> genotyping-by-sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=Arabian%20Peninsula" title=" Arabian Peninsula"> Arabian Peninsula</a>, <a href="https://publications.waset.org/abstracts/search?q=Sudan" title=" Sudan"> Sudan</a> </p> <a href="https://publications.waset.org/abstracts/102448/genomic-diversity-and-relationship-among-arabian-peninsula-dromedary-camels-using-full-genome-sequencing-approach" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/102448.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">205</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3828</span> Molecular Characterization of Chicken B Cell Marker (ChB6) in Native Chicken of Poonch Region from International Borders of India and Pakistan</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mandeep%20Singh%20Azad.Dibyendu%20Chakraborty">Mandeep Singh Azad.Dibyendu Chakraborty</a>, <a href="https://publications.waset.org/abstracts/search?q=Vikas%20Vohra"> Vikas Vohra</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Introduction: Poonch is one of the remotest districts of the Jammu and Kashmir (UT) and situated on international borders. This native poultry population in these areas is quite hardy and thrives well in adverse climatic conditions. Till date, no local breed from this area (Jammu Province) has been characterized thus present study was undertaken with the main objectives of molecular characterization of ChB6 gene in local native chicken of Poonch region located at international borders between India and Pakistan. The chicken B-cell marker (ChB6) gene has been proposed as a candidate gene in regulating B-cell development. Material and Method: RNA was isolated by Blood RNA Purification Kit (HiPura) and Trizol method from whole blood samples. Positive PCR products with size 1110 bp were selected for further purification, sequencing and analysis. The amplified PCR product was sequenced by Sangers dideoxy chain termination method. The obtained sequence of ChB6 gene of Poonchi chicken were compared by MEGAX software. BioEdit software was used to construct phylogenic tree, and Neighbor Joining method was used to infer evolutionary history. In order to compute evolutionary distance Maximum Composite Likelihood method was used. Results: The positively amplified samples of ChB6 genes were then subjected to Sanger sequencing with “Primer Walking. The sequences were then analyzed using MEGA X and BioEdit software. The sequence results were compared with other reported sequence from different breed of chicken and with other species obtained from the NCBI (National Center for Biotechnology Information). ClustalW method using MEGA X software was used for multiple sequence alignment. The sequence results of ChB6 gene of Poonchi chicken was compared with Centrocercus urophasianus, G. gallus mRNA for B6.1 protein, G. gallus mRNA for B6.2, G. gallus mRNA for B6.3, Gallus gallus B6.1, Halichoeres bivittatus, Miniopterus fuliginosus Ferringtonia patagonica, Tympanuchus phasianellus. The genetic distances were 0.2720, 0.0000, 0.0245, 0.0212, 0.0147, 1.6461, 2.2394, 2.0070 and 0.2363 for ChB6 gene of Poonchi chicken sequence with other sequences in the present study respectively. Sequencing results showed variations between different species. It was observed that AT content were higher then GC content for ChB6 gene. The lower AT content suggests less thermostable. It was observed that there was no sequence difference within the Poonchi population for ChB6 gene. The high homology within chicken population indicates the conservation of ChB6 gene. The maximum difference was observed with Miniopterus fuliginosus (Eastern bent-wing bat) followed by Ferringtonia patagonica and Halichoeres bivittatus. Conclusion: Genetic variation is the essential component for genetic improvement. The results of immune related gene Chb6 shows between population genetic variability. Therefore, further association studies of this gene with some prevalent diseases in large population would be helpful to identify disease resistant/ susceptible genotypes in the indigenous chicken population. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=ChB6" title="ChB6">ChB6</a>, <a href="https://publications.waset.org/abstracts/search?q=sequencing" title=" sequencing"> sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=ClustalW" title=" ClustalW"> ClustalW</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20distance" title=" genetic distance"> genetic distance</a>, <a href="https://publications.waset.org/abstracts/search?q=poonchi%20chicken" title=" poonchi chicken"> poonchi chicken</a>, <a href="https://publications.waset.org/abstracts/search?q=SNP" title=" SNP"> SNP</a> </p> <a href="https://publications.waset.org/abstracts/175605/molecular-characterization-of-chicken-b-cell-marker-chb6-in-native-chicken-of-poonch-region-from-international-borders-of-india-and-pakistan" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/175605.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">70</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3827</span> Advances in Sesame Molecular Breeding: A Comprehensive Review</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Micheale%20Yifter%20Weldemichael">Micheale Yifter Weldemichael</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Sesame (Sesamum indicum L.) is among the most important oilseed crops for its high edible oil quality and quantity. Sesame is grown for food, medicinal, pharmaceutical, and industrial uses. Sesame is also cultivated as a main cash crop in Asia and Africa by smallholder farmers. Despite the global exponential increase in sesame cultivation area, its production and productivity remain low, mainly due to biotic and abiotic constraints. Notwithstanding the efforts to solve these problems, a low level of genetic variation and inadequate genomic resources hinder the progress of sesame improvement. The objective of this paper is, therefore, to review recent advances in the area of molecular breeding and transformation to overcome major production constraints and could result in enhanced and sustained sesame production. This paper reviews various researches conducted to date on molecular breeding and genetic transformation in sesame focusing on molecular markers used in assessing the available online database resources, genes responsible for key agronomic traits as well as transgenic technology and genome editing. The review concentrates on quantitative and semi-quantitative studies on molecular breeding for key agronomic traits such as improvement of yield components, oil and oil-related traits, disease and insect/pest resistance, and drought, waterlogging and salt tolerance, as well as sesame genetic transformation and genome editing techniques. Pitfalls and limitations of existing studies and methodologies used so far are identified and some priorities for future research directions in sesame genetic improvement are identified in this review. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=abiotic%20stress" title="abiotic stress">abiotic stress</a>, <a href="https://publications.waset.org/abstracts/search?q=biotic%20stress" title=" biotic stress"> biotic stress</a>, <a href="https://publications.waset.org/abstracts/search?q=improvement" title=" improvement"> improvement</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20breeding" title=" molecular breeding"> molecular breeding</a>, <a href="https://publications.waset.org/abstracts/search?q=oil" title=" oil"> oil</a>, <a href="https://publications.waset.org/abstracts/search?q=sesame" title=" sesame"> sesame</a>, <a href="https://publications.waset.org/abstracts/search?q=shattering" title=" shattering"> shattering</a> </p> <a href="https://publications.waset.org/abstracts/187714/advances-in-sesame-molecular-breeding-a-comprehensive-review" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/187714.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">35</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3826</span> Bioinformatics Approach to Support Genetic Research in Autism in Mali</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=M.%20Kouyate">M. Kouyate</a>, <a href="https://publications.waset.org/abstracts/search?q=M.%20Sangare"> M. Sangare</a>, <a href="https://publications.waset.org/abstracts/search?q=S.%20Samake"> S. Samake</a>, <a href="https://publications.waset.org/abstracts/search?q=S.%20Keita"> S. Keita</a>, <a href="https://publications.waset.org/abstracts/search?q=H.%20G.%20Kim"> H. G. Kim</a>, <a href="https://publications.waset.org/abstracts/search?q=D.%20H.%20Geschwind"> D. H. Geschwind</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Background & Objectives: Human genetic studies can be expensive, even unaffordable, in developing countries, partly due to the sequencing costs. Our aim is to pilot the use of bioinformatics tools to guide scientifically valid, locally relevant, and economically sound autism genetic research in Mali. Methods: The following databases, NCBI, HGMD, and LSDB, were used to identify hot point mutations. Phenotype, transmission pattern, theoretical protein expression in the brain, the impact of the mutation on the 3D structure of the protein) were used to prioritize selected autism genes. We used the protein database, Modeller, and clustal W. Results: We found Mef2c (Gly27Ala/Leu38Gln), Pten (Thr131IIle), Prodh (Leu289Met), Nme1 (Ser120Gly), and Dhcr7 (Pro227Thr/Glu224Lys). These mutations were associated with endonucleases BseRI, NspI, PfrJS2IV, BspGI, BsaBI, and SpoDI, respectively. Gly27Ala/Leu38Gln mutations impacted the 3D structure of the Mef2c protein. Mef2c protein sequences across species showed a high percentage of similarity with a highly conserved MADS domain. Discussion: Mef2c, Pten, Prodh, Nme1, and Dhcr 7 gene mutation frequencies in the Malian population will be very informative. PCR coupled with restriction enzyme digestion can be used to screen the targeted gene mutations. Sanger sequencing will be used for confirmation only. This will cut down considerably the sequencing cost for gene-to-gene mutation screening. The knowledge of the 3D structure and potential impact of the mutations on Mef2c protein informed the protein family and altered function (ex. Leu38Gln). Conclusion & Future Work: Bio-informatics will positively impact autism research in Mali. Our approach can be applied to another neuropsychiatric disorder. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title="bioinformatics">bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=endonucleases" title=" endonucleases"> endonucleases</a>, <a href="https://publications.waset.org/abstracts/search?q=autism" title=" autism"> autism</a>, <a href="https://publications.waset.org/abstracts/search?q=Sanger%20sequencing" title=" Sanger sequencing"> Sanger sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=point%20mutations" title=" point mutations"> point mutations</a> </p> <a href="https://publications.waset.org/abstracts/164430/bioinformatics-approach-to-support-genetic-research-in-autism-in-mali" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/164430.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">83</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3825</span> Mutations in rpoB, katG and inhA Genes: The Association with Resistance to Rifampicin and Isoniazid in Egyptian Mycobacterium tuberculosis Clinical Isolates</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Ayman%20K.%20El%20Essawy">Ayman K. El Essawy</a>, <a href="https://publications.waset.org/abstracts/search?q=Amal%20M.%20Hosny"> Amal M. Hosny</a>, <a href="https://publications.waset.org/abstracts/search?q=Hala%20M.%20Abu%20Shady"> Hala M. Abu Shady</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The rapid detection of TB and drug resistance, both optimizes treatment and improves outcomes. In the current study, respiratory specimens were collected from 155 patients. Conventional susceptibility testing and MIC determination were performed for rifampicin (RIF) and isoniazid (INH). Genotype MTBDRplus assay, which is a molecular genetic assay based on the DNA-STRIP technology and specific gene sequencing with primers for rpoB, KatG, and mab-inhA genes were used to detect mutations associated with resistance to rifampicin and isoniazid. In comparison to other categories, most of rifampicin resistant (61.5%) and isoniazid resistant isolates (47.1%) were from patients relapsed in treatment. The genotypic profile (using Genotype MTBDRplus assay) of multi-drug resistant (MDR) isolates showed missing of katG wild type 1 (WT1) band and appearance of mutation band katG MUT2. For isoniazid mono-resistant isolates, 80% showed katG MUT1, 20% showed katG MUT1, and inhA MUT1, 20% showed only inhA MUT1. Accordingly, 100% of isoniazid resistant strains were detected by this assay. Out of 17 resistant strains, 16 had mutation bands for katG distinguished high resistance to isoniazid. The assay could clearly detect rifampicin resistance among 66.7% of MDR isolates that showed mutation band rpoB MUT3 while 33.3% of them were considered as unknown. One mono-resistant rifampicin isolate did not show rifampicin mutation bands by Genotype MTBDRplus assay, but it showed an unexpected mutation in Codon 531 of rpoB by DNA sequence analysis. Rifampicin resistance in this strain could be associated with a mutation in codon 531 of rpoB (based on molecular sequencing), and Genotype MTBDRplus assay could not detect the associated mutation. If the results of Genotype MTBDRplus assay and sequencing were combined, this strain shows hetero-resistance pattern. Gene sequencing of eight selected isolates, previously tested by Genotype MTBDRplus assay, could detect resistance mutations mainly in codon 315 (katG gene), position -15 in inhA promotes gene for isoniazid resistance and codon 531 (rpoB gene) for rifampicin resistance. Genotyping techniques allow distinguishing between recurrent cases of reinfection or reactivation and supports epidemiological studies. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=M.%20tuberculosis" title="M. tuberculosis">M. tuberculosis</a>, <a href="https://publications.waset.org/abstracts/search?q=rpoB" title=" rpoB"> rpoB</a>, <a href="https://publications.waset.org/abstracts/search?q=KatG" title=" KatG"> KatG</a>, <a href="https://publications.waset.org/abstracts/search?q=inhA" title=" inhA"> inhA</a>, <a href="https://publications.waset.org/abstracts/search?q=genotype%20MTBDRplus" title=" genotype MTBDRplus"> genotype MTBDRplus</a> </p> <a href="https://publications.waset.org/abstracts/115843/mutations-in-rpob-katg-and-inha-genes-the-association-with-resistance-to-rifampicin-and-isoniazid-in-egyptian-mycobacterium-tuberculosis-clinical-isolates" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/115843.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">167</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3824</span> Investigation of Genetic Variation among Anemone narcissiflora L. Population Using PCR-RAPD Molecular Marker</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Somayeh%20Akrami">Somayeh Akrami</a>, <a href="https://publications.waset.org/abstracts/search?q=Habib%20Onsori"> Habib Onsori</a>, <a href="https://publications.waset.org/abstracts/search?q=Elham%20Tahmassebian"> Elham Tahmassebian</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Anemone%20narcissiflora" title="Anemone narcissiflora">Anemone narcissiflora</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20diversity" title=" genetic diversity"> genetic diversity</a>, <a href="https://publications.waset.org/abstracts/search?q=RAPD-PCR" title=" RAPD-PCR"> RAPD-PCR</a> </p> <a href="https://publications.waset.org/abstracts/25060/investigation-of-genetic-variation-among-anemone-narcissiflora-l-population-using-pcr-rapd-molecular-marker" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/25060.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">475</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3823</span> Resequencing and Genomic Study of Wild Coffea Arabica Unveils Genetic Groups at Its Origin and Their Geographic Distribution</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Zate%20Zewdneh%20Zana">Zate Zewdneh Zana</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Coffea arabica (Arabica coffee), a cornerstone of the global beverage industry, necessitates rigorous genetic conservation due to its economic significance and genetic complexity. In this study, we performed whole-genome resequencing of wild species collected from its birthplace, Ethiopia. Advanced Illumina sequencing technology facilitated the mapping of a high percentage of clean reads to the C. arabica reference genome, revealing a substantial number of genetic variants, predominantly SNPs. Our comprehensive analysis not only uncovered a notable distribution of genomic variants across the coffee genome but also identified distinct genetic groups through phylogenetic and population structure analyses. This genomic study provides invaluable insights into the genetic diversity of C. arabica, highlighting the potential of identified SNPs and InDels in enhancing our understanding of key agronomic traits. The findings contribute significantly to genetic studies and support strategic breeding and conservation efforts essential for sustaining the global coffee industry. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=population%20genetics" title="population genetics">population genetics</a>, <a href="https://publications.waset.org/abstracts/search?q=wild%20species" title=" wild species"> wild species</a>, <a href="https://publications.waset.org/abstracts/search?q=evolutionary%20study" title=" evolutionary study"> evolutionary study</a>, <a href="https://publications.waset.org/abstracts/search?q=coffee%20plant" title=" coffee plant"> coffee plant</a> </p> <a href="https://publications.waset.org/abstracts/187447/resequencing-and-genomic-study-of-wild-coffea-arabica-unveils-genetic-groups-at-its-origin-and-their-geographic-distribution" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/187447.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">40</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3822</span> Genome Sequencing, Assembly and Annotation of Gelidium Pristoides from Kenton-on-Sea, South Africa</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Sandisiwe%20Mangali">Sandisiwe Mangali</a>, <a href="https://publications.waset.org/abstracts/search?q=Graeme%20Bradley"> Graeme Bradley </a> </p> <p class="card-text"><strong>Abstract:</strong></p> Genome is complete set of the organism's hereditary information encoded as either deoxyribonucleic acid or ribonucleic acid in most viruses. The three different types of genomes are nuclear, mitochondrial and the plastid genome and their sequences which are uncovered by genome sequencing are known as an archive for all genetic information and enable researchers to understand the composition of a genome, regulation of gene expression and also provide information on how the whole genome works. These sequences enable researchers to explore the population structure, genetic variations, and recent demographic events in threatened species. Particularly, genome sequencing refers to a process of figuring out the exact arrangement of the basic nucleotide bases of a genome and the process through which all the afore-mentioned genomes are sequenced is referred to as whole or complete genome sequencing. Gelidium pristoides is South African endemic Rhodophyta species which has been harvested in the Eastern Cape since the 1950s for its high economic value which is one motivation for its sequencing. Its endemism further motivates its sequencing for conservation biology as endemic species are more vulnerable to anthropogenic activities endangering a species. As sequencing, mapping and annotating the Gelidium pristoides genome is the aim of this study. To accomplish this aim, the genomic DNA was extracted and quantified using the Nucleospin Plank Kit, Qubit 2.0 and Nanodrop. Thereafter, the Ion Plus Fragment Library was used for preparation of a 600bp library which was then sequenced through the Ion S5 sequencing platform for two runs. The produced reads were then quality-controlled and assembled through the SPAdes assembler with default parameters and the genome assembly was quality assessed through the QUAST software. From this assembly, the plastid and the mitochondrial genomes were then sampled out using Gelidiales organellar genomes as search queries and ordered according to them using the Geneious software. The Qubit and the Nanodrop instruments revealed an A260/A280 and A230/A260 values of 1.81 and 1.52 respectively. A total of 30792074 reads were obtained and produced a total of 94140 contigs with resulted into a sequence length of 217.06 Mbp with N50 value of 3072 bp and GC content of 41.72%. A total length of 179281bp and 25734 bp was obtained for plastid and mitochondrial respectively. Genomic data allows a clear understanding of the genomic constituent of an organism and is valuable as foundation information for studies of individual genes and resolving the evolutionary relationships between organisms including Rhodophytes and other seaweeds. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Gelidium%20pristoides" title="Gelidium pristoides">Gelidium pristoides</a>, <a href="https://publications.waset.org/abstracts/search?q=genome" title=" genome"> genome</a>, <a href="https://publications.waset.org/abstracts/search?q=genome%20sequencing%20and%20assembly" title=" genome sequencing and assembly"> genome sequencing and assembly</a>, <a href="https://publications.waset.org/abstracts/search?q=Ion%20S5%20sequencing%20platform" title=" Ion S5 sequencing platform"> Ion S5 sequencing platform</a> </p> <a href="https://publications.waset.org/abstracts/98685/genome-sequencing-assembly-and-annotation-of-gelidium-pristoides-from-kenton-on-sea-south-africa" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/98685.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">150</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3821</span> Genomic Adaptation to Local Climate Conditions in Native Cattle Using Whole Genome Sequencing Data</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Rugang%20Tian">Rugang Tian</a> </p> <p class="card-text"><strong>Abstract:</strong></p> In this study, we generated whole-genome sequence (WGS) data from110 native cattle. Together with whole-genome sequences from world-wide cattle populations, we estimated the genetic diversity and population genetic structure of different cattle populations. Our findings revealed clustering of cattle groups in line with their geographic locations. We identified noticeable genetic diversity between indigenous cattle breeds and commercial populations. Among all studied cattle groups, lower genetic diversity measures were found in commercial populations, however, high genetic diversity were detected in some local cattle, particularly in Rashoki and Mongolian breeds. Our search for potential genomic regions under selection in native cattle revealed several candidate genes related with immune response and cold shock protein on multiple chromosomes such as TRPM8, NMUR1, PRKAA2, SMTNL2 and OXR1 that are involved in energy metabolism and metabolic homeostasis. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=cattle" title="cattle">cattle</a>, <a href="https://publications.waset.org/abstracts/search?q=whole-genome" title=" whole-genome"> whole-genome</a>, <a href="https://publications.waset.org/abstracts/search?q=population%20structure" title=" population structure"> population structure</a>, <a href="https://publications.waset.org/abstracts/search?q=adaptation" title=" adaptation"> adaptation</a> </p> <a href="https://publications.waset.org/abstracts/184122/genomic-adaptation-to-local-climate-conditions-in-native-cattle-using-whole-genome-sequencing-data" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/184122.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">74</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3820</span> Genetic Diversity and Variation of Nigerian Pigeon (Columba livia domestica) Populations Based on the Mitochondrial Coi Gene</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Foluke%20E.%20Sola-Ojo">Foluke E. Sola-Ojo</a>, <a href="https://publications.waset.org/abstracts/search?q=Ibraheem%20A.%20Abubakar"> Ibraheem A. Abubakar</a>, <a href="https://publications.waset.org/abstracts/search?q=Semiu%20F.%20Bello"> Semiu F. Bello</a>, <a href="https://publications.waset.org/abstracts/search?q=Isiaka%20H.%20Fatima"> Isiaka H. Fatima</a>, <a href="https://publications.waset.org/abstracts/search?q=Sule%20Bisola"> Sule Bisola</a>, <a href="https://publications.waset.org/abstracts/search?q=Adesina%20M.%20Olusegun"> Adesina M. Olusegun</a>, <a href="https://publications.waset.org/abstracts/search?q=Adeniyi%20C.%20Adeola"> Adeniyi C. Adeola</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The domesticated pigeon, Columba livia domestica, has many valuable characteristics, including high nutritional value and fast growth rate. There is a lack of information on its genetic diversity in Nigeria; thus, the genetic variability in mitochondrial cytochrome oxidase subunit I (COI) sequences of 150 domestic pigeons from four different locations was examined. Three haplotypes (HT) were identified in Nigerian populations; the most common haplotype, HT1, was shared with wild and domestic pigeons from Europe, America, and Asia, while HT2 and HT3 were unique to Nigeria. The overall haplotype diversity was 0.052± 0.025, and nucleotide diversity was 0.026± 0.068 across the four investigated populations. The phylogenetic tree showed significant clustering and genetic relationship of Nigerian domestic pigeons with other global pigeons. The median-joining network showed a star-like pattern suggesting population expansion. AMOVA results indicated that genetic variations in Nigerian pigeons mainly occurred within populations (99.93%), while the Neutrality tests results suggested that the Nigerian domestic pigeons’ population experienced recent expansion. This study showed a low genetic diversity and population differentiation among Nigerian domestic pigeons consistent with a relatively conservative COI sequence with few polymorphic sites. Furthermore, the COI gene could serve as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species. The current data is insufficient for further conclusions; therefore, more research evidence from multiple molecular markers is required. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=Nigeria%20pigeon" title="Nigeria pigeon">Nigeria pigeon</a>, <a href="https://publications.waset.org/abstracts/search?q=COI" title=" COI"> COI</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20diversity" title=" genetic diversity"> genetic diversity</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic%20variation" title=" genetic variation"> genetic variation</a>, <a href="https://publications.waset.org/abstracts/search?q=conservation" title=" conservation"> conservation</a> </p> <a href="https://publications.waset.org/abstracts/153807/genetic-diversity-and-variation-of-nigerian-pigeon-columba-livia-domestica-populations-based-on-the-mitochondrial-coi-gene" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/153807.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">195</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3819</span> Molecular Characterization of Cysticercus tenuicolis of Slaughtered Livestock in Upper-Egypt Governorates</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Mosaab%20A.%20Omara">Mosaab A. Omara</a>, <a href="https://publications.waset.org/abstracts/search?q=Layla%20O.%20Elmajdoubb"> Layla O. Elmajdoubb</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohammad%20Saleh%20Al-Aboodyc"> Mohammad Saleh Al-Aboodyc</a>, <a href="https://publications.waset.org/abstracts/search?q=Ahmed%20ElSifyd"> Ahmed ElSifyd</a>, <a href="https://publications.waset.org/abstracts/search?q=Ahmed%20O.%20Elkhtamd"> Ahmed O. Elkhtamd</a> </p> <p class="card-text"><strong>Abstract:</strong></p> The aim of this study is to present the molecular characterization of cysticercus tenuicolis of Taenia hydatigena from livestock isolates in Egypt, using the amplification of sequencing of the mt-CO1 gene. We introduce a detailed image of the Cysticercus tenuicolis infection in ruminant animals in Upper Egypt. Cysticercus tenuicolis inhabits such organs in ruminants as the omentum, viscera, and liver. In the present study, the infection rate of Cysticercus tenuicolis was found to be 16% and 19% in sheep and goat sample respectively. Firstly we report one larval stage of Taenia hydatigena detected in the camel liver in Egypt. Cysticercus tenuicolis infection manifested a higher prevalence in females than in males. Those above 2 years of age manifested a higher infection rate than younger animals. The preferred site for the infection was the omentum: a 70% preference in sheep and a 68% preference in goat samples. The molecular characterization using the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene of isolates from sheep, goats and camels corresponded to T. hydatigena. For this study, molecular characterizations of T. hydatigena were done for the first time in Egypt. Molecular tools are of great assistance in characterizing the Cysticercus tenuicolis parasite especially when the morphological character cannot be detected because the metacestodes are frequently confused with infection by the Hydatid cyst, especially when these occur in the visceral organs. In the present study, Cysticercus tenuicolis manifested high identity in the goat and sheep samples, while differences were found more frequently in the camel samples (10 pairbase). Clearly molecular diagnosis for Cysticercus tenuicolis infection significantly helps to differentiate it from such other metacestodes. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=cysticercus%20tenuicolis" title="cysticercus tenuicolis">cysticercus tenuicolis</a>, <a href="https://publications.waset.org/abstracts/search?q=its2" title=" its2"> its2</a>, <a href="https://publications.waset.org/abstracts/search?q=genetic" title=" genetic"> genetic</a>, <a href="https://publications.waset.org/abstracts/search?q=qena" title=" qena"> qena</a>, <a href="https://publications.waset.org/abstracts/search?q=molecular%20and%20taenia%20hydatigena" title=" molecular and taenia hydatigena"> molecular and taenia hydatigena</a> </p> <a href="https://publications.waset.org/abstracts/30593/molecular-characterization-of-cysticercus-tenuicolis-of-slaughtered-livestock-in-upper-egypt-governorates" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/30593.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">523</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3818</span> Non-Invasive Pre-Implantation Genetic Assessment Using NGS in IVF Clinical Routine</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Katalin%20Gombos">Katalin Gombos</a>, <a href="https://publications.waset.org/abstracts/search?q=Bence%20G%C3%A1lik"> Bence Gálik</a>, <a href="https://publications.waset.org/abstracts/search?q=Krisztina%20Ildik%C3%B3%20Kal%C3%A1cs"> Krisztina Ildikó Kalács</a>, <a href="https://publications.waset.org/abstracts/search?q=Krisztina%20G%C3%B6d%C3%B6ny"> Krisztina Gödöny</a>, <a href="https://publications.waset.org/abstracts/search?q=%C3%81kos%20V%C3%A1rnagy"> Ákos Várnagy</a>, <a href="https://publications.waset.org/abstracts/search?q=J%C3%B3zsef%20B%C3%B3dis"> József Bódis</a>, <a href="https://publications.waset.org/abstracts/search?q=Attila%20Gyenesei"> Attila Gyenesei</a>, <a href="https://publications.waset.org/abstracts/search?q=G%C3%A1bor%20L.%20Kov%C3%A1cs"> Gábor L. Kovács</a> </p> <p class="card-text"><strong>Abstract:</strong></p> Although non-invasive pre-implantation genetic testing for aneuploidy (NIPGT-A) is potentially appropriate to assess chromosomal ploidy of the embryo, practical application of it in a routine IVF center has not been started in the absence of a recommendation. We developed a comprehensive workflow for a clinically applicable strategy for NIPGT-A based on next-generation sequencing (NGS) technology. We performed MALBAC whole genome amplification and NGS on spent blastocyst culture media of Day 3 embryos fertilized with intra-cytoplasmic sperm injection (ICSI). Spent embryonic culture media of morphologically good quality score embryos were enrolled in further analysis with the blank culture media as background control. Chromosomal abnormalities were identified by an optimized bioinformatics pipeline applying a copy number variation (CNV) detecting algorithm. We demonstrate a comprehensive workflow covering both wet- and dry-lab procedures supporting a clinically applicable strategy for NIPGT-A. It can be carried out within 48 h which is critical for the same-cycle blastocyst transfer, but also suitable for “freeze all” and “elective frozen embryo” strategies. The described integrated approach of non-invasive evaluation of embryonic DNA content of the culture media can potentially supplement existing pre-implantation genetic screening methods. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=next%20generation%20sequencing" title="next generation sequencing">next generation sequencing</a>, <a href="https://publications.waset.org/abstracts/search?q=in%20vitro%20fertilization" title=" in vitro fertilization"> in vitro fertilization</a>, <a href="https://publications.waset.org/abstracts/search?q=embryo%20assessment" title=" embryo assessment"> embryo assessment</a>, <a href="https://publications.waset.org/abstracts/search?q=non-invasive%20pre-implantation%20genetic%20testing" title=" non-invasive pre-implantation genetic testing"> non-invasive pre-implantation genetic testing</a> </p> <a href="https://publications.waset.org/abstracts/143714/non-invasive-pre-implantation-genetic-assessment-using-ngs-in-ivf-clinical-routine" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/143714.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">156</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3817</span> Whole Exome Sequencing Data Analysis of Rare Diseases: Non-Coding Variants and Copy Number Variations</h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=S.%20Fahiminiya">S. Fahiminiya</a>, <a href="https://publications.waset.org/abstracts/search?q=J.%20Nadaf"> J. Nadaf</a>, <a href="https://publications.waset.org/abstracts/search?q=F.%20Rauch"> F. Rauch</a>, <a href="https://publications.waset.org/abstracts/search?q=L.%20Jerome-Majewska"> L. Jerome-Majewska</a>, <a href="https://publications.waset.org/abstracts/search?q=J.%20Majewski"> J. Majewski </a> </p> <p class="card-text"><strong>Abstract:</strong></p> Background: Sequencing of protein coding regions of human genome (Whole Exome Sequencing; WES), has demonstrated a great success in the identification of causal mutations for several rare genetic disorders in human. Generally, most of WES studies have focused on rare variants in coding exons and splicing-sites where missense substitutions lead to the alternation of protein product. Although focusing on this category of variants has revealed the mystery behind many inherited genetic diseases in recent years, a subset of them remained still inconclusive. Here, we present the result of our WES studies where analyzing only rare variants in coding regions was not conclusive but further investigation revealed the involvement of non-coding variants and copy number variations (CNV) in etiology of the diseases. Methods: Whole exome sequencing was performed using our standard protocols at Genome Quebec Innovation Center, Montreal, Canada. All bioinformatics analyses were done using in-house WES pipeline. Results: To date, we successfully identified several disease causing mutations within gene coding regions (e.g. SCARF2: Van den Ende-Gupta syndrome and SNAP29: 22q11.2 deletion syndrome) by using WES. In addition, we showed that variants in non-coding regions and CNV have also important value and should not be ignored and/or filtered out along the way of bioinformatics analysis on WES data. For instance, in patients with osteogenesis imperfecta type V and in patients with glucocorticoid deficiency, we identified variants in 5'UTR, resulting in the production of longer or truncating non-functional proteins. Furthermore, CNVs were identified as the main cause of the diseases in patients with metaphyseal dysplasia with maxillary hypoplasia and brachydactyly and in patients with osteogenesis imperfecta type VII. Conclusions: Our study highlights the importance of considering non-coding variants and CNVs during interpretation of WES data, as they can be the only cause of disease under investigation. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=whole%20exome%20sequencing%20data" title="whole exome sequencing data">whole exome sequencing data</a>, <a href="https://publications.waset.org/abstracts/search?q=non-coding%20variants" title=" non-coding variants"> non-coding variants</a>, <a href="https://publications.waset.org/abstracts/search?q=copy%20number%20variations" title=" copy number variations"> copy number variations</a>, <a href="https://publications.waset.org/abstracts/search?q=rare%20diseases" title=" rare diseases"> rare diseases</a> </p> <a href="https://publications.waset.org/abstracts/24069/whole-exome-sequencing-data-analysis-of-rare-diseases-non-coding-variants-and-copy-number-variations" class="btn btn-primary btn-sm">Procedia</a> <a href="https://publications.waset.org/abstracts/24069.pdf" target="_blank" class="btn btn-primary btn-sm">PDF</a> <span class="bg-info text-light px-1 py-1 float-right rounded"> Downloads <span class="badge badge-light">419</span> </span> </div> </div> <div class="card paper-listing mb-3 mt-3"> <h5 class="card-header" style="font-size:.9rem"><span class="badge badge-info">3816</span> Isolate-Specific Variations among Clinical Isolates of Brucella Identified by Whole-Genome Sequencing, Bioinformatics and Comparative Genomics </h5> <div class="card-body"> <p class="card-text"><strong>Authors:</strong> <a href="https://publications.waset.org/abstracts/search?q=Abu%20S.%20Mustafa">Abu S. Mustafa</a>, <a href="https://publications.waset.org/abstracts/search?q=Mohammad%20W.%20Khan"> Mohammad W. Khan</a>, <a href="https://publications.waset.org/abstracts/search?q=Faraz%20Shaheed%20%20Khan"> Faraz Shaheed Khan</a>, <a href="https://publications.waset.org/abstracts/search?q=Nazima%20Habibi"> Nazima Habibi </a> </p> <p class="card-text"><strong>Abstract:</strong></p> Brucellosis is a zoonotic disease of worldwide prevalence. There are at least four species and several strains of Brucella that cause human disease. Brucella genomes have very limited variation across strains, which hinder strain identification using classical molecular techniques, including PCR and 16 S rDNA sequencing. The aim of this study was to perform whole genome sequencing of clinical isolates of Brucella and perform bioinformatics and comparative genomics analyses to determine the existence of genetic differences across the isolates of a single Brucella species and strain. The draft sequence data were generated from 15 clinical isolates of Brucella melitensis (biovar 2 strain 63/9) using MiSeq next generation sequencing platform. The generated reads were used for further assembly and analysis. All the analysis was performed using Bioinformatics work station (8 core i7 processor, 8GB RAM with Bio-Linux operating system). FastQC was used to determine the quality of reads and low quality reads were trimmed or eliminated using Fastx_trimmer. Assembly was done by using Velvet and ABySS softwares. The ordering of assembled contigs was performed by Mauve. An online server RAST was employed to annotate the contigs assembly. Annotated genomes were compared using Mauve and ACT tools. The QC score for DNA sequence data, generated by MiSeq, was higher than 30 for 80% of reads with more than 100x coverage, which suggested that data could be utilized for further analysis. However when analyzed by FastQC, quality of four reads was not good enough for creating a complete genome draft so remaining 11 samples were used for further analysis. The comparative genome analyses showed that despite sharing same gene sets, single nucleotide polymorphisms and insertions/deletions existed across different genomes, which provided a variable extent of diversity to these bacteria. In conclusion, the next generation sequencing, bioinformatics, and comparative genome analysis can be utilized to find variations (point mutations, insertions and deletions) across different genomes of Brucella within a single strain. This information could be useful in surveillance and epidemiological studies supported by Kuwait University Research Sector grants MI04/15 and SRUL02/13. <p class="card-text"><strong>Keywords:</strong> <a href="https://publications.waset.org/abstracts/search?q=brucella" title="brucella">brucella</a>, <a href="https://publications.waset.org/abstracts/search?q=bioinformatics" title=" bioinformatics"> bioinformatics</a>, <a href="https://publications.waset.org/abstracts/search?q=comparative%20genomics" title=" comparative genomics"> comparative genomics</a>, <a href="https://publications.waset.org/abstracts/search?q=whole%20genome%20sequencing" title=" whole genome sequencing"> whole genome sequencing</a> </p> <a href="https://publications.waset.org/abstracts/39774/isolate-specific-variations-among-clinical-isolates-of-brucella-identified-by-whole-genome-sequencing-bioinformatics-and-comparative-genomics" class="btn btn-primary btn-sm">Procedia</a> <a 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