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Utilizing Short Tandem repeats (STRs) as a Resolving Matrix in Parental Dispute DNA Analysis

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American Journal of Molecular Biology 2018年第3期8卷 156-165页

作者： George Gborienemi Simeon Alade Tolulope Olukemi Department of Medical Laboratory Science Niger Delta University Amassoma Nigeria

Interest in DNA analysis using short tandem repeats (STR) as finger printing tools in forensic medicine has gained tremendous application, as expression of these nuclear factors have enhanced forensic examination. Here we used this Biochemical characterization after conventional extraction process, polymerase chain reaction (PCR), gel electrophoresiss and a sequencer to distinguish and resolve parental dispute. The differential migration of labeled DNA fragments which attains excitation energy with a laser elicits fluorescent light of different wavelength depending on the dye used. A data collection software (Genemapper) collects raw data (spectrograph) and converts it to an electropherogram that is interpreted. By comparing the DNA profiles, inclusion and exclusion criteria were elucidated to resolve disputes. The inherent discriminating power of STRs used in analysis enhances resolution of cell mixtures, genetic aberration, substantiation of tissue origin and provides genetic distinction which is a robust and reliable approach in resolving parental disputes.

关键词： Short Tandem repeats Matrix Parental DNA Analysis

Analysis of Simple Sequence repeats Information from Floral Expressed Sequence Tags Resources of Papaya (<i>Carica papaya</i>L.)

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American Journal of Plant Sciences 2017年第9期8卷 2315-2331页

作者： Priyanka Priyanka Dileep Kumar Anurag Yadav Kusum Yadav U. N. Dwivedi Department of Biochemistry University of Lucknow Lucknow India College of Basic Sciences & Humanities Sardarkrushinagar Agricultural University Dantiwada Banaskantha India

Papaya (Carica papaya L.) is one of the most economically, medicinally and nutritionally important tropical fruit crops. Expressed sequence tags (ESTs) derived simple sequence repeat (SSR) markers are more valuable as they are derived from conserved genic portion. Development of EST-SSRs markers through in silico approach is cheaper, less time consuming and labour-intensive. In this study, we aimed to mine SSRs and developed EST-SSR primers from papaya floral ESTs. A total of 75,846 papaya floral ESTs were downloaded from public database National Centre for Biotechnology Information (NCBI). A total of 26,039 floral unigenes (7961 contigs and 18,078 singletons) were generated after assembly of these ESTs. From these floral unigenes, 433,782 perfect SSRs, 204,968 compound SSRs and 6061 imperfect SSRs were mined, respectively. In perfect SSRs, mononucleotide repeats were most abundant (94.7%) followed by tri- (3.1%) and di-nucleotide repeats (1.7%). The frequencies of tetra-, hexa- and penta-nucleotide repeats accounted for only (0.17%), (0.04%) and (0.03%), respectively. In mononucleotide repeats, the most abundant motif was A/T (69.3%) and in di- and tri-nucleotide repeats were AG/CT (61%) and AAG/CTT (31%), respectively. In imperfect SSRs, mononucleotide repeats (56.5%) were most abundant. 176 different types of motifs were identified. A total of 3807 primer pairs for floral papaya ESTs were successfully designed. These developed EST-SSR primers are being used for the genetic improvement of papaya such as study of cross-transferability across genera/species, evaluation of genetic diversity, and identification of sex-specific markers. These EST derived SSRs can also be used in filling gaps in existing linkage maps in papaya.

关键词： Papaya (Carica papaya L.) In Silico Simple Sequence repeats Expressed Sequence Tags (ESTs) SSR Mining EST-SSR SSR Motifs Primer Pairs

Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm(Phoenix dactylifera) and related species

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Plant Diversity 2019年第5期41卷 330-339页

作者： Srinivasa R.Chaluvadi Porter Young Kentrez Thompson Bochra Amina Bahri Bhavesh Gajera Subhash Narayanan Robert Krueger Jeffrey L.Bennetzen Department of Genetics University of GeorgiaAthensGAUSA Institute of Plant Breeding Genetics and Genomics(Department of Crop and Soil Sciences)and Department of Plant BiologyUniversity of GeorgiaAthensGA 30602USA Laboratory of Bioaggressors and Integrated Protection in Agriculture The National Agronomic Institute of TunisiaUniversity of Carthage43 Avenue Charles-NicolleTunis 1082Tunisia Anand Agricultural University AnandIndia USDA-ARS National Clonal Germplasm Repository for Citrus and Dates RiversideCAUSA

Date palm(Phoenix dactylifera),one of the most ancient crops,is grown commercially in>30 countries.Using whole plastome assemblies,phylogenetic analyses revealed that cultivated date palm accessions share the same clade with Phoenix sylvestris,Phoenix pusilla and Phoenix acaulis,which are native to the Indian subcontinent,and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia.Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci.Extensive genetic diversity was observed,with many accessions heterozygous for most markers in this clonally propagated crop.The average number of alleles per locus(42.1),expected heterozygosity(0.8),observed heterozygosity(0.47)and fixation indices(FST=0.42)demonstrated substantial genetic diversity and population structure.Iraqi accessions were found to have the richest allelic diversity,and the most private alleles.The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups,one group with predominantly African accessions and another predominantly Asian.Some germplasm,especially from Tunisia and Iraq,deviated from this generalization.Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures,with gene flow between Asian and African groups.Indian and Pakistani date palms were found to be most closely related to North African germplasm.

关键词： Date palm improvement Germplasm dissemination Plastome Simple sequence repeats

Differential expression of glial cell line-derived neurotrophic factor splice variants in the mouse brain

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Neural Regeneration Research 2020年第2期15卷 270-276页

作者： Xiao-He Gu Heng Li Lin Zhang Tao He Xiang Chai He Wei Dian-Shuai Gao Department of Anatomy and Neurobiology Xuzhou Medical UniversityXuzhouJiangsu ProvinceChina Department of Neurosurgery First Affiliated Hospital of Soochow UniversitySuzhouJiangsu ProvinceChina

Glial cell line-derived neurotrophic factor(GDNF) plays a critical role in neuronal survival and function. GDNF has two major splice variants in the brain,α-pro-GDNF and β-pro-GDNF, and both isoforms have strong neuroprotective effects on dopamine neurons. However, the expression of the GDNF splice variants in dopaminergic neurons in the brain remains unclear. Therefore, in this study, we investigated the mRNA and protein expression of α-and β-pro-GDNF in the mouse brain by real-time quantitative polymerase chain reaction, using splice variant-specific primers, and western blot analysis. At the mRNA level,β-pro-GDNF expression was significantly greater than that of α-pro-GDNF in the mouse brain. In contrast, at the protein level,α-pro-GDNF expression was markedly greater than that of β-pro-GDNF. To clarify the mechanism underlying this inverse relationship in mRNA and protein expression levels of the GDNF splice variants, we analyzed the expression of sorting protein-related receptor with A-type repeats(SorLA) by real-time quantitative polymerase chain reaction. At the mRNA level, SorLA was positively associated with β-pro-GDNF expression, but not with α-pro-GDNF expression. This suggests that the differential expression of α-and β-pro-GDNF in the mouse brain is related to SorLA expression. As a sorting protein, SorLA could contribute to the inverse relationship among the mRNA and protein levels of the GDNF isoforms. This study was approved by the Animal Ethics Committee of Xuzhou Medical University, China on July 14, 2016.

关键词： Δ78 locus brain region dopaminergic neurons glial cell line-derived neurotrophic factor mouse brain precursor protein α-pro-GDNF β-pro-GDNF sorting protein-related receptor with A-type repeats splice variants

Plastome characteristics of Cannabaceae

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Plant Diversity 2018年第3期40卷 127-137页

作者： Huanlei Zhang Jianjun Jin Michael J.Moore Tingshuang Yi Dezhu Li Germplasm Bank of Wild Species Kunming Institute of Botany Chinese Academy of Sciences Kunming College of Life Sciences University of Chinese Academy of Sciences Department of Biology Oberlin College

Cannabaceae is an economically important family that includes ten genera and ca. 117 accepted species.To explore the structure and size variation of their plastomes, we sequenced ten plastomes representing all ten genera of Cannabaceae. Each plastome possessed the typical angiosperm quadripartite structure and contained a total of 128 genes. The Inverted Repeat(IR) regions in five plastomes had experienced small expansions(330 e983 bp) into the Large Single-Copy(LSC) region. The plastome of Chaetachme aristata has experienced a 942-bp IR contraction and lost rpl22 and rps19 in its IRs. The substitution rates of rps19 and rpl22 decreased after they shifted from the LSC to IR. A 270-bp inversion was detected in the Parasponia rugosa plastome, which might have been mediated by 18-bp inverted repeats. Repeat sequences, simple sequence repeats, and nucleotide substitution rates varied among these plastomes.Molecular markers with more than 13% variable sites and 5% parsimony-informative sites were identified, which may be useful for further phylogenetic analysis and species identification. Our results show strong support for a sister relationship between Gironniera and Lozanell(BS ? 100). Celtis, CannabisHumulus, Chaetachme-Pteroceltis, and Trema-Parasponia formed a strongly supported clade, and their relationships were well resolved with strong support(BS ? 100). The availability of these ten plastomes provides valuable genetic information for accurately identifying species, clarifying taxonomy and reconstructing the intergeneric phylogeny of Cannabaceae.

关键词： Plastome IR expansion/contraction repeats SSR Sequence divergence Phylogenomics

High expression level of EDIL3 in HCC predicts poor prognosis of HCC patients

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World Journal of Gastroenterology 2010年第36期16卷 4611-4615页

作者： Jian-Cong Sun,Xiao-Ting Liang,Ke Pan,Hui Wang,Jing-Jing Zhao,Jian-Jun Li,Hai-Qing Ma,Yi-Bing Chen,Jian-Chuan Xia,State Key Laboratory of Oncology in South China,Cancer Center,Sun Yat-Sen University,Guangzhou 510060,Guangdong Province,China State Key Laboratory of Oncology in Southern China Cancer Center Sun Yat-Sen University Guangzhou 510060 Guangdong Province China.

AIM:To determine the role of epidermal growth factor-like repeats and discoidin I-like domains 3(EDIL3)in pathogenesis of hepatocellular carcinoma(HCC)by investigating the EDIL3 expression in HCC and its prognostic value for HCC.METHODS:EDIL3 expression was detected in 101 HCC surgical tissue samples with immunohistochemistry method,and its relation with clinicopathologic features and prognosis of HCC patients was analyzed.RESULTS:EDIL3 was highly expressed in 48.5%of the HCC patients.Although the EDIL3 expression level did not correlate with any clinicopathological parameters,KaplanMeier survival analysis showed that high expression level of EDIL3 resulted in a significantly poor prognosis of HCC patients(log-rank test,P=0.010).Multivariate Cox's analysis showed that the EDIL3 expression level was a significant and independent prognostic parameter for the overall survival rate of HCC patients(hazard ratio=1.978,95%confidence interval =1.139-3.435,P=0.015).CONCLUSION:High expression level of EDIL3 pre-dicts poor prognosis of HCC patients.EDIL3 may be a potential target of antiangiogenic therapy for HCC.

关键词： Epidermal growth factor-like repeats and discoidin I-like domains 3 Hepatocellular carcinoma Prognosis Angiogenesis

Harnessing the potential of gene editing technology using CRISPR in inflammatory bowel disease

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World Journal of Gastroenterology 2019年第18期25卷 2177-2187页

作者： Viktor Limanskiy Arpita Vyas Lakshmi Shankar Chaturvedi Dinesh Vyas Department of Surgery San Joaquin General Hospital College of Medicine CNSU College of Medicine and College of Pharmacy California Northstate University

The molecular scalpel of clustered regularly interspersed short palindromic repeats/CRISPR associated protein 9(CRISPR/Cas9) technology may be sharp enough to begin cutting the genes implicated in inflammatory bowel disease(IBD) and consequently decrease the 6.3 billion dollar annual financial healthcare burden in the treatment of IBD. For the past few years CRISPR technology has drastically revolutionized DNA engineering and biomedical research field. We are beginning to see its application in gene manipulation of sickle cell disease,human immunodeficiency virus resistant embryologic twin gene modification and IBD genes such as Gatm(Glycine amidinotransferase, mitochondrial),nucleotide-binding oligomerization domain-containing protein 2, KRT12 and other genes implicated in adaptive immune convergence pathways have been subjected to gene editing, however there are very few publications. Furthermore,since Crohn's disease and ulcerative colitis have shared disease susceptibility and share genetic gene profile, it is paramount and is more advantageous to use CRISPR technology to maximize impact. Although, currently CRISPR does have its limitations due to limited number of specific Cas enzymes, off-target activity,protospacer adjacent motifs and crossfire between different target sites. However,these limitations have given researchers further insight on how to augment and manipulate enzymes to enable precise gene excision and limit crossfire between target sites.

关键词： Clustered regularly interspersed short palindromic repeats Inflammatory bowel disease Crohn’s disease Ulcerative colitis Gene excision Gene editing Gene therapy Financial impact of inflammatory bowel disease on healthcare Clustered regularly interspersed short palindromic repeats crossfire

A novel RNA-guided RNA-targeting CRISPR tool

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Science China(Life Sciences) 2016年第8期59卷 854-856页

作者： Dandan Zhang Zhenxiang Li Bingyu Yan Jian-Feng Li Key Laboratory of Gene Engineering of the Ministry of Education State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources School of Life Sciences Sun Yat-sen University

Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein(Cas)technology has emerged as a programmable RNA-guided DNA-targeting tool for sequence-specific genome editing in diverse or... 详细信息

关键词： targeting RNA guided programmable editing diverse regularly repeats DNA visualization

Inflammation-associated microsatellite alterations:Mechanisms and significance in the prognosis of patients with colorectal cancer

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World Journal of Gastrointestinal Oncology 2018年第1期10卷 1-14页

作者： Minoru Koi Stephanie S Tseng-Rogenski John M Carethers Department of Internal Medicine and Comprehensive Cancer Center University of MichiganAnn ArborMI 48109-5368United States

Microsatellite alterations within genomic DNA frameshift as a result of defective DNA mismatch repair(MMR). About 15% of sporadic colorectal cancers(CRCs) manifest hypermethylation of the DNA MMR gene MLH1, resulting in mono-and di-nucleotide frameshifts to classify it as microsatellite instability-high(MSI-H) and hypermutated, and due to frameshifts at coding microsatellites generating neo-antigens, produce a robust protective immune response that can be enhanced with immune checkpoint blockade. More commonly, approximately 50% of sporadic nonMSI-H CRCs demonstrate frameshifts at di-and tetra-nucleotide microsatellites to classify it as MSIlow/elevated microsatellite alterations at selected tetranucleotide repeats(EMAST) as a result of functional somatic inactivation of the DNA MMR protein MSH3 via a nuclear-to-cytosolic displacement. The trigger for MSH3 displacement appears to be inflammation and/or oxidative stress, and unlike MSI-H CRC patients, patients with MSI-L/EMAST CRCs show poor prognosis. These inflammatory-associated microsatellite alterations are a consequence of the local tumor microenvironment, and in theory, if the microenvironment is manipulated to lower inflammation, the microsatellite alterations and MSH3 dysfunction should be corrected. Here we describe the mechanisms and significance of inflammatory-associated microsatellite alterations, and propose three areas to deeply explore the consequences and prevention of inflammation's effect upon the DNA MMR system.

关键词： Microsatellite instability Microsatellite stable Elevated microsatellite alterations at selected tetranucleotide repeats Colorectal cancer Mismatch repair Inflammation MSH3