scholarly journals Evolution of Old World monkeys and great apes links to massive and directional shrinkage of the dinucleotide short tandem repeat compartment

2021 ◽  
Author(s):  
M Arabfard ◽  
M Salesi ◽  
I Arabipour ◽  
M Ohadi
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Great Apes ◽  
Old World Monkeys ◽  
Evolutionary Trend ◽  
Random Evolution ◽  
Old World ◽  
Short Tandem

Abstract Background: The evolutionary trend of short tandem repeats (STRs) at the crossroads of speciation remains largely elusive and attributed to random evolution for the most part. To explore this trend, we selected nine species, which shared sequential chronological ancestors, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human, and collected three sets of data on the abundance of all classes of dinucleotide STRs (≥6-repeats) for three regions of every chromosome, each region spanning 10 Mb of DNA. Results: In all three datasets, we found directional shrinkage of the dinucleotide STR compartment as follows: rodents>Old World monkeys>great apes (P=0.000). The decremented gradient observed for the dinucleotide STRs was not detected for a number of other classes of STRs, such as mono and trinucleotide STRs. Conclusion: We report the first instance of massive and directional gradient of STRs, which may link with the evolution of Old World monkeys and great apes.

scholarly journals Primate Speciation Links to Massive and Directional Shrinkage of the Dinucleotide Short Tandem Repeat Compartment.

2021 ◽  
Author(s):  
Masoud Arabfard ◽  
Mahmood Salesi ◽  
Iman Arabipour ◽  
Reza Najafipour ◽  
Ahmad Delbari ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Great Apes ◽  
Primate Species ◽  
Evolutionary Trend ◽  
Random Evolution ◽  
Short Tandem

Abstract The evolutionary trend of short tandem repeats (STRs) at the crossroads of speciation remains largely elusive and attributed to random evolution for the most part. Here we investigated the dinucleotide STR compartment in primate speciation. We selected six species, which shared sequential chronological ancestors, including mouse, macaque, gorilla, chimpanzee, bonobo, and human, and collected three sets of data on the abundance of all classes of dinucleotide STRs (≥6-repeats) for three regions of every chromosome, each region spanning 10 Mb of DNA. In all three datasets, we found consistent directional shrinkage of the dinucleotide STR compartment in all the primate species selected vs. mouse, as follows: mouse>macaque>great apes. The >20-repeat STRs were the most significantly affected as a result of this shrinkage. We propose that massive and directional shrinkage of the dinucleotide STR compartment had a decisive link with primate speciation. This is a prime instane of massive directional STR trend in multiple speciation.

Contribution of ABO-Rhesus/Electrophoresis of hemoglobin methods and Short Tandem Repeats analysis in the determination of paternity in Burkina Faso, West Africa

2020 ◽  
Author(s):  
Missa Millogo ◽  
Serge Theophile Soubeiga ◽  
Bapio Valerie Jean Telesphore Bazie ◽  
Theodora Mahoukede Zohoncon ◽  
Albert Theophane Yonli ◽  
...  
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
High Performance ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Repeat Analysis ◽  
Paternity Index ◽  
Genetic Analyzer ◽  
Short Tandem

Abstract Background: the establishment of filiation by the current ABO, HLA, MNS, Kells and serum tests, pose a real reliability problem. It is then necessary to combine these methods with or to use high-performance methods such as microsatellite genetic analysis or short tandem repeats. This study aimed to compare the short tandem repeat technique with ABO/Rhesus system in combination with electrophoresis of hemoglobin. Methods: Fourteen (14) contested paternity trios were investigated. Blood samples were collected to determine blood groups using the Beth-Vincent method and the type of hemoglobin by electrophoresis. Blood spots on FTA paper were used for the analysis of 16 STR loci (D8S1179, D21S11, D7S820, CSF1PO, D3S1358, TH01, D13S317, D16S539, D2S1338, D19S433, vWA, TPOX, D18S51, D5S818, FGA, Amel) by capillary electrophoresis on the ABI 31310 Genetic Analyzer. The generated sequences were analyzed with GeneMapper® software version 3.2.1. The data were analyzed to determine the paternity index and the probability of paternity. Results: Of the fourteen (14) trios studied, ten (10) cases were probable inclusion, three (03) cases were exclusion and one (01) case was an undetermined paternity outcome with the ABO-Rhesus/ electrophoresis of hemoglobin system. While the analysis of genetic polymorphisms in DNA gave five (05) inclusions versus nine (09) exclusions of paternity. Of the 10 probable inclusion cases given by the ABO-Rhesus/Electrophoresis of hemoglobin system, only 05 cases (50%) were confirmed for inclusion by Short tandem repeat analysis. Conclusion: The analysis of short tandem repeat with sixteen genetic markers is more reliable in determining paternity than ABO-Rhesus/hemoglobin electrophoresis techniques.

scholarly journals Disputed paternity presumption in Burkina Faso: determination of the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays

2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Missa Millogo ◽  
Serge Theophile Soubeiga ◽  
Bapio Valerie Jean Telesphore Bazie ◽  
Theodora Mahoukede Zohoncon ◽  
Abdoul Karim Ouattara ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Str Analysis ◽  
Resource Limited ◽  
Biological Fathers ◽  
Short Tandem

Abstract Background In resource-limited countries, ABO, HLA, MNS, Kells, and hemoglobin electrophoresis are classic tests for the resolution of paternity disputes due to their affordable cost. The limitations of these tests in cases of disputed paternity require the use of Short Tandem Repeats (STR) for their certification. This study aimed to determine the biological fathers of children using ABO-rhesus/hemoglobin electrophoresis and STR assays in Burkina Faso, West Africa. Results Of the fourteen trios studied, the ABO-rhesus/hemoglobin electrophoresis analysis revealed ten probable inclusion cases, three exclusion cases, and one undetermined paternity. DNA STR analysis found five inclusions of paternity out of the ten probable inclusions with ABO-rhesus/hemoglobin electrophoresis assay versus nine exclusions of paternity. Conclusion This study showed that the implementation of the analysis of short tandem repeat is required to resolve increasing disputed filiation cases in Burkina Faso.

Y-Chromosome short tandem repeat (STR) haplotypes in a Campania population sample

2005 ◽  
Vol 43 (2) ◽  
Author(s):  
Giuseppe Calcagno ◽  
Giuseppe Labruna ◽  
Lucia Sacchetti
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Southern Italy ◽  
Population Sample ◽  
Lack Of Information ◽  
Pcr Multiplex ◽  
Y Haplotype ◽  
Short Tandem

AbstractGiven the lack of information about Y haplotypes for Campania (southern Italy), we analyzed eight Y short tandem repeats in a sample of males from this region with the aim of establishing a Y-haplotype database that can be used for forensic purposes. The eight Y short tandem repeats were amplified by two PCR multiplex reactions: multiplex A for loci

scholarly journals Global non-random abundance of short tandem repeats in rodents and primates.

2021 ◽  
Author(s):  
Masoud Arabfard ◽  
Mahmood Salesi ◽  
Yazdan Hassani Nourian ◽  
Iman Arabipour ◽  
Ali Mohammad Ali Maddi ◽  
...  
Keyword(s):  
Hierarchical Clustering ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Short Tandem Repeats ◽  
Tandem Repeats ◽  
Whole Genome ◽  
Random Coincidence ◽  
Olive Baboon ◽  
Model Study ◽  
Short Tandem

Background:  While of predominant abundance across vertebrate genomes and significant biological implications, the relevance of short tandem repeat (STR) abundance to speciation remains largely elusive and attributed to random coincidence for the most part.  In a model study, here we collected whole-genome abundance of mono-, di-, and trinucleotide STRs in nine species, encompassing rodents and primates, including rat, mouse, olive baboon, gelada, macaque, gorilla, chimpanzee, bonobo, and human.  The obtained unnormalized and normalized data were used to analyze hierarchical clustering of the STR abundances in the selected species.  Results:  We found massive differential abundances between the rodent and primate orders.  In addition, while numerous STRs had random abundance across the nine selected species, the global abundance conformed to three consistent <clusters>, as follows: <rat, mouse>, <gelada, macaque, olive baboon>, <gorilla, chimpanzee, bonobo, human>, which coincided with the phylogenetic distances of the selected species (p< 4E-05).  Exceptionally, in the trinucleotide STR compartment, human was significantly distant from all other species. Conclusion:   We propose that the global abundance of STRs is non-random in rodents and primates, and probably had a determining impact on the speciation of the two orders.  We also propose the STRs and STR lengths which specifically coincided with the phylogeny of the selected species.

scholarly journals Determining the Genetic Similarities and Variability of Javanese and Arab Ethnic Families with DNA Fingerprint in Malang East Java Indonesia

2017 ◽  
Vol 17 (1) ◽  
pp. 51
Author(s):  
Nila Kartika Sari
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Tandem Repeats ◽  
Pcr Amplification ◽  
Dna Fingerprint ◽  
Salting Out ◽  
Breeding Populations ◽  
Human White Blood Cell ◽  
And Migration ◽  
Short Tandem

PENENTUAN SIMILARITAS DAN VARIABILITAS GENETIK PADA KELUARGA ETNIS JAWA DAN ARAB DENGAN DNA FINGERPRINT DI MALANG, JAWA TIMUR, INDONESIA ABSTRAKLebih dari sepertiga genom manusia terdiri dari urutan daerah berulang (Repeat area) yang terdiri dari Minisatellite atau Variant Number Of Tandem Repeats (VNTR) dan Microsatellite atau Short Tandem Repeat (STR). STR sebagai daerah berulang dengan rentang alel yang pendek sering digunakan untuk tes paternitas, penelitian penyakit genetik dalam bidang kesehatan, arkeologi molekular, maupun kasus kriminalitas dalam bidang forensic. Tujuan dari penelitian ini adalah untuk mengidentifikasi DNA Fingerprint pada etnis Jawa – Arab dengan menentukan similaritas dan variabilitas genetiknya. Bahan dan metode yang digunakan untuk mengerjakan adalah menggunakan sel darah putih manusia yang berasal dari tiga generasi dalam tiga keluarga yang terdiri dari : (1) Nenek – Ibu, Ayah – anak perempuan, (2) Kakek – Ibu, Ayah – Anak perempuan, (3) Kakek, Nenek – Ibu, Ayah – Anak laki-laki. Isolasi DNA pada tiap sampel diperoleh dengan salting out, selanjutnya Amplifikasi PCR dengan menggunakan 13 CODIS yang meliputi TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 dan amelogenin yang dapat dilihat melalui hasil elektroforesis gel poliakrilamid 8% dengan Chemidoc Gel Imaging. Analisis profil pita pada tiap individu untuk menentukan similaritas dan variabilitas genetik serta pola alel dengan menggunakan software Quantity One. Variasi pola pita DNA dianalisis dengan menggunakan program software GENEPOP package versi 4.2 yang akan didapat frekuensi alel, heterozigositas, dan migrasi alel. Berdasarkan identifikasi yang dilakukan diperoleh bahwa nilai heterozigositas pada populasi III (93.8461%) memiliki nilai heterozigositas lebih tinggi dibandingkan dengan populasi I (88.4615%) dan II (76.9230%) dan telah terjadi migrasi alel 0.341373%.  Adanya persentase migrasi alel tersebut meskipun kecil menunjukkan telah terjadi Breeding diantara populasi Jawa dengan populasi Arab sehingga meningkatkan rata-rata nilai heterozigositas pada tiap populasi. Pola alel heterozigot dengan berdasarkan nilai heterozigositas, jumlah alel pada D21S11, VWA dan THO1 dapat direkomendasikan sebagai penanda molekular untuk identifikasi variasi genetik.Kata kunci: Etnis Jawa–Arab, DNA Fingerprint, 13 CODIS DETERMINING THE GENETIC SIMILARITIES AND VARIABILITY OF JAVANESE AND ARAB ETHNIC FAMILIES WITH DNA FINGERPRINT IN MALANG EAST JAVA INDONESIAABSTRACTMore than one-third of human genome consists of repetitive sequence region (Repeat Area) which consist of Minisatellite or Variant Number Of Tandem Repeats (VNTR) and Microsatellite or Short Tandem Repeat (STR). Based on its short allele range STR can be used for the paternity testing study of genetics disease, molecular archeology, as well as in forensic crime cases. The aim of this study is to identify Javanese – Arab Ethnic DNA fingerprint in determining the similarities and genetic variability. Materials and methods to accomplish this, we used human white blood cell from three generations of three family consists of: (1) grandmother-mother, father-daughter, (2) grandfather-mother, father-daughter, (3) grandfather, grandmother–mother, father-son. DNA blood samples were Isolated by salting out, furthermore PCR amplification used by applying 13 CODIS which consists of TPOX, D3S1358, FGA, D5S818, CSF1PO, D7S820, D8S1179, TH01, VWA, D13S317, D16S539, D18S51, D21S11 and amelogenin, and then it was visualized by 8% polyacrylamid gel. The Fingerprint profile was visualized by 8% polyacrylamide gel and took the picture by ChemiDoc gel Imaging and measure the intensity band pattern by Quantity One software. Variations in the pattern of DNA bands were analyzed using the program GENEPOP software package version 4.2 that will be obtained allele frequencies, heterozygosity, and allele migration. Based on identification, this result showed analysis heterozygosity values, population III (93.8461%) have higher heterozygosity values compared with the population I (88.4615%) and II (76.9230%) and migration of alleles 0.341373%. The percentage of the migration though minor allele had occurred Breeding populations between Java to the Patterns of heterozygous alleles with values based on heterozygosity, number of alleles at D21S11,VWA and THO1 can be recommended as a molecular marker for the identification of genetic variation.Keywords: Javanese – Arab Ethnics, DNA fingerprint, 13 CODIS

scholarly journals OSTRFPD: Multifunctional Tool for Genome-Wide Short Tandem Repeat Analysis for DNA, Transcripts, and Amino Acid Sequences with Integrated Primer Designer

2019 ◽  
Vol 15 ◽  
pp. 117693431984313
Author(s):  
Vivek Bhakta Mathema ◽  
Arjen M Dondorp ◽  
Mallika Imwong
Keyword(s):  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Tandem Repeats ◽  
Gc Content ◽  
Plasmodium Species ◽  
Single Step ◽  
Amino Acid Sequences ◽  
Practical Implementation ◽  
Genome Wide ◽  
Short Tandem

Microsatellite mining is a common outcome of the in silico approach to genomic studies. The resulting short tandemly repeated DNA could be used as molecular markers for studying polymorphism, genotyping and forensics. The omni short tandem repeat finder and primer designer (OSTRFPD) is among the few versatile, platform-independent open-source tools written in Python that enables researchers to identify and analyse genome-wide short tandem repeats in both nucleic acids and protein sequences. OSTRFPD is designed to run either in a user-friendly fully featured graphical interface or in a command line interface mode for advanced users. OSTRFPD can detect both perfect and imperfect repeats of low complexity with customisable scores. Moreover, the software has built-in architecture to simultaneously filter selection of flanking regions in DNA and generate microsatellite-targeted primers implementing the Primer3 platform. The software has built-in motif-sequence generator engines and an additional option to use the dictionary mode for custom motif searches. The software generates search results including general statistics containing motif categorisation, repeat frequencies, densities, coverage, guanine–cytosine (GC) content, and simple text-based imperfect alignment visualisation. Thus, OSTRFPD presents users with a quick single-step solution package to assist development of microsatellite markers and categorise tandemly repeated amino acids in proteome databases. Practical implementation of OSTRFPD was demonstrated using publicly available whole-genome sequences of selected Plasmodium species. OSTRFPD is freely available and open-sourced for improvement and user-specific adaptation.

scholarly journals Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic Groups

2009 ◽  
Vol 12 (1) ◽  
pp. 69-72
Author(s):  
A Ozkorkmaz ◽  
A Baransel Isir ◽  
S Pehlivan ◽  
E Özkorkmaz
Keyword(s):  
Ethnic Groups ◽  
Tandem Repeat ◽  
Short Tandem Repeat ◽  
Tandem Repeats ◽  
Unrelated Individual ◽  
Published Data ◽  
Short Tandem Repeat Loci ◽  
Hardy Weinberg Equilibrium ◽  
Forensic Value ◽  
Short Tandem

Forensic Value of Ten Short Tandem Repeat Loci in Turkey Compared to Other Ethnic GroupsAllele frequencies of the 10 short tandem repeats (STRs) loci (D16S539, D2S1338, D3S1358, vWA, D18S51, D21S11, D8S1179, D19S433, FGA, THO1) included in the AmpFISTR SGM Plus kit, were obtained from biological samples from 100 unrelated individual residing in different part of Turkey. The χ2 test showed that all these loci agreed with Hardy-Weinberg equilibrium, The results were compared with the previously published data from Turkish and other ethnic groups. Suggest that these loci with their high heterozygosity and combined power of discrimination (PD) values are useful for forensic identifications.

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