Forensic science international. Genetics, May 7, 2017
DNA is a powerful tool available for forensic investigations requiring identification of species.... more DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis. The exercise was organized during 2014 by a Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG), created in 2013. The 24 participating laboratories from 10 countries were asked to identify the species in 11 DNA samples from previous GHEP-ISFG profi...
ABSTRACT Compared to other domestic species, little is known about variability of genes related t... more ABSTRACT Compared to other domestic species, little is known about variability of genes related to energetic metabolism and growth in camelids. Here, we have analyzed leptin (LEP) and growth hormone (GH1) genes and characterized their variability in three local llama (Lama glama) populations from the Argentine Northwest. Eleven novel SNPs and one indel were identified in the Lep gene. In total, eight haplotypes were found for LEP and seven for GH1. Although geographical origin clustering was not observed, SNP and haplotype frequencies varied significantly among populations. Based on variation of both loci, we detected significant genetic differentiation measured through Fst values. Network analysis of LEP gene supported the well-documented history of hybridization in camelids previously identified by mtDNA analysis.
ATP synthase is an enzyme involved in oxidative phosphorylation from prokaryotic to eukaryotic ce... more ATP synthase is an enzyme involved in oxidative phosphorylation from prokaryotic to eukaryotic cells. In mammals it comprises at least 16 subunits from which the mitochondrial encoded ATP6 and ATP8 are essential. Mitochondrial genes variations have been suggested to allow rapid human and animal adaptation to new climates and dietary conditions (Mishmar et al. 2003). Camelidae taxa are uniquely adapted to extremely hot and dry climates of African-Asian territories and to cold and hypoxic environments of the South American Andean region. We sequenced and analyzed ATP6 and ATP8 genes in all camelid species. Based on the available structural data and evolutionary conservation of the deduced proteins we identified features proper of the group. In Old World camels the ATP8, important in the assembly of the F0 complex, showed a number of positively charged residues higher than in the other aligned species. In ATP6 we found the camelid specific substitutions Q47H and I106V that occur in sites highly conserved in other species. We speculate that these changes may have functional importance.
... ML Maté a , F. Di Rocco a , A. Zambelli a , b and L. Vidal-Rioja a , Corresponding Author Con... more ... ML Maté a , F. Di Rocco a , A. Zambelli a , b and L. Vidal-Rioja a , Corresponding Author Contact Information , E-mail The ... in bird species (Abbott et al., 2005), (2) nucleotide number variation at the homopolymer tract in human and cattle species ([Bendall and Sykes, 1995] and ...
South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), wh... more South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), which are wild species, and the domestic llama (Lama glama) and alpaca (Lama pacos). This paper presents the first complete mitochondrial (mt) genome of the guanaco and the mt coding sequence of the vicuña. The guanaco mtDNA is 16,649 nt long and its composition and organization are similar to the mitochondrial genome of other mammals. Excluding the control region, comparison of the complete guanaco and vicuña mtDNA showed 4.4% sequence divergence. Nucleotide differences in peptide coding genes varied from 1.9% in ATP6 to 6.4% in Cyt b. These values are compatible with the close relatedness of both species identified by other authors. Based on the differences between the control region sequence here reported and that previously described, we also discuss the occurrence of NUMTs in the genome of South American camelids.
Within cetartiodactyl species, both New and Old World camelids are uniquely adapted to the extrem... more Within cetartiodactyl species, both New and Old World camelids are uniquely adapted to the extremely hot and dry climates of African-Asian territories and to the high altitude cold and hypoxic environment of the whole Andean area. In order to investigate the potential association between these particular adaptations and mitochondrial aerobic energy production, we examined the camelid genes of cytochrome c oxidase subunits I, II, and III and the replacement of amino acids inferred. We found that all subunits had undergone a number of replacements in sites otherwise conserved in other cetartiodactyls. Changes of COXI and COXIII were mainly located in the transmembrane helices of proteins. For COXII, although most of the changes did not occur in sites directly involved in electron transfer, a shift of D by T at 115 position of Old World camelid might modify electrostatic interactions with cytochrome c. COXII also showed an increased relative evolutionary rate respect to other cetartiodactyls compared.
Forensic science international. Genetics, May 7, 2017
DNA is a powerful tool available for forensic investigations requiring identification of species.... more DNA is a powerful tool available for forensic investigations requiring identification of species. However, it is necessary to develop and validate methods able to produce results in degraded and or low quality DNA samples with the high standards obligatory in forensic research. Here, we describe a voluntary collaborative exercise to test the recently developed Species Identification by Insertions/Deletions (SPInDel) method. The SPInDel kit allows the identification of species by the generation of numeric profiles combining the lengths of six mitochondrial ribosomal RNA (rRNA) gene regions amplified in a single reaction followed by capillary electrophoresis. The exercise was organized during 2014 by a Working Commission of the Spanish and Portuguese-Speaking Working Group of the International Society for Forensic Genetics (GHEP-ISFG), created in 2013. The 24 participating laboratories from 10 countries were asked to identify the species in 11 DNA samples from previous GHEP-ISFG profi...
ABSTRACT Compared to other domestic species, little is known about variability of genes related t... more ABSTRACT Compared to other domestic species, little is known about variability of genes related to energetic metabolism and growth in camelids. Here, we have analyzed leptin (LEP) and growth hormone (GH1) genes and characterized their variability in three local llama (Lama glama) populations from the Argentine Northwest. Eleven novel SNPs and one indel were identified in the Lep gene. In total, eight haplotypes were found for LEP and seven for GH1. Although geographical origin clustering was not observed, SNP and haplotype frequencies varied significantly among populations. Based on variation of both loci, we detected significant genetic differentiation measured through Fst values. Network analysis of LEP gene supported the well-documented history of hybridization in camelids previously identified by mtDNA analysis.
ATP synthase is an enzyme involved in oxidative phosphorylation from prokaryotic to eukaryotic ce... more ATP synthase is an enzyme involved in oxidative phosphorylation from prokaryotic to eukaryotic cells. In mammals it comprises at least 16 subunits from which the mitochondrial encoded ATP6 and ATP8 are essential. Mitochondrial genes variations have been suggested to allow rapid human and animal adaptation to new climates and dietary conditions (Mishmar et al. 2003). Camelidae taxa are uniquely adapted to extremely hot and dry climates of African-Asian territories and to cold and hypoxic environments of the South American Andean region. We sequenced and analyzed ATP6 and ATP8 genes in all camelid species. Based on the available structural data and evolutionary conservation of the deduced proteins we identified features proper of the group. In Old World camels the ATP8, important in the assembly of the F0 complex, showed a number of positively charged residues higher than in the other aligned species. In ATP6 we found the camelid specific substitutions Q47H and I106V that occur in sites highly conserved in other species. We speculate that these changes may have functional importance.
... ML Maté a , F. Di Rocco a , A. Zambelli a , b and L. Vidal-Rioja a , Corresponding Author Con... more ... ML Maté a , F. Di Rocco a , A. Zambelli a , b and L. Vidal-Rioja a , Corresponding Author Contact Information , E-mail The ... in bird species (Abbott et al., 2005), (2) nucleotide number variation at the homopolymer tract in human and cattle species ([Bendall and Sykes, 1995] and ...
South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), wh... more South American camelids comprise the guanaco (Lama guanicoe) and the vicuña (Vicugna vicugna), which are wild species, and the domestic llama (Lama glama) and alpaca (Lama pacos). This paper presents the first complete mitochondrial (mt) genome of the guanaco and the mt coding sequence of the vicuña. The guanaco mtDNA is 16,649 nt long and its composition and organization are similar to the mitochondrial genome of other mammals. Excluding the control region, comparison of the complete guanaco and vicuña mtDNA showed 4.4% sequence divergence. Nucleotide differences in peptide coding genes varied from 1.9% in ATP6 to 6.4% in Cyt b. These values are compatible with the close relatedness of both species identified by other authors. Based on the differences between the control region sequence here reported and that previously described, we also discuss the occurrence of NUMTs in the genome of South American camelids.
Within cetartiodactyl species, both New and Old World camelids are uniquely adapted to the extrem... more Within cetartiodactyl species, both New and Old World camelids are uniquely adapted to the extremely hot and dry climates of African-Asian territories and to the high altitude cold and hypoxic environment of the whole Andean area. In order to investigate the potential association between these particular adaptations and mitochondrial aerobic energy production, we examined the camelid genes of cytochrome c oxidase subunits I, II, and III and the replacement of amino acids inferred. We found that all subunits had undergone a number of replacements in sites otherwise conserved in other cetartiodactyls. Changes of COXI and COXIII were mainly located in the transmembrane helices of proteins. For COXII, although most of the changes did not occur in sites directly involved in electron transfer, a shift of D by T at 115 position of Old World camelid might modify electrostatic interactions with cytochrome c. COXII also showed an increased relative evolutionary rate respect to other cetartiodactyls compared.
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