RESUMO
The Tlingit from Southeast Alaska belong to the Northwest Coast cultural tradition, which is defined by regionally shared sociocultural practices. A distinctive feature of Tlingit social organization is the matrilineal exogamous marriage system among clans from two opposite moieties: the Raven/Crow and Eagle/Wolf. Clan and moiety membership are determined by matrilineal descent, and previous genetic studies of Northwest Coast populations have shown a relationship between clan membership and genetic variation of matrilines and patrilines. To further understand this association, in this study mitochondrial DNA sequences from the Tlingit (n = 154) were examined. By comparing mitochondrial DNA with moiety membership information, the authors explore the impact of marriage traditions among the Tlingit with their observable genetic variation. At the genetic level, the results support cultural persistence of Tlingit maternal moiety identity despite the negative impacts of European colonization. This study additionally illustrates the relevance of data derived from Tlingit oral traditions to test hypotheses about population history on the Northwest Coast.
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The success in recovering genetic profiles from aged and degraded biological samples is diminished by fundamental aspects of DNA extraction, as well as its long-term preservation, that are not well understood. While numerous studies have been conducted to determine whether one extraction method was superior to others, nearly all of them were initiated with no knowledge of the actual starting DNA quantity in the samples prior to extraction, so they ultimately compared the outcome of all methods relative to the best. Using quantitative PCR to estimate the copy count of synthetic standards before (i.e., "copies in") and after (i.e., "copies out") purification by the Qiagen MinElute PCR Purification Kit, we documented DNA loss within a pool of 16 different-sized fragments ranging from 106 to 409 bp in length, corresponding to those targeted by the PowerPlex 16 System (Promega, Madison, WI). Across all standards from 10(4) to 10(7) copies/µL, loss averaged between 21.75% and 60.56% (mean, 39.03%), which is not congruent with Qiagen's claim that 80% of 70 bp to 4 kb fragments are retained using this product (i.e., 20% loss). Our study also found no clear relationship either between DNA strand length and retention or between starting copy number and retention. This suggests that there is no molecule bias across the MinElute column membrane and highlights the need for manufacturers to clearly and accurately describe on what their claims are based, and should also encourage researchers to document DNA retention efficiencies of their own methods and protocols. Understanding how and where to reduce loss of molecules during extraction and purification will serve to generate clearer and more accurate data, which will enhance the utility of ancient and low-copy-number DNA as a tool for closing forensic cases or in reconstructing the evolutionary history of humans and other organisms.
Assuntos
Impressões Digitais de DNA/instrumentação , Marcadores Genéticos/genética , Testes Genéticos , Repetições de Microssatélites/genética , Técnicas de Amplificação de Ácido Nucleico/métodos , Impressões Digitais de DNA/métodos , Genótipo , Humanos , Reação em Cadeia da Polimerase , Padrões de ReferênciaRESUMO
A recent study of mitochondrial DNA variation in Native American populations from the American Southwest detected signatures of a population expansion of subhaplogroup B2a, dated to 2,105 years before present (99.5% confidence interval, 1,273-3,773 YBP), following the introduction and intensification of maize agriculture in the region. Only one Yuman group and no Athapaskan speakers were analyzed in previous studies. Here we report mtDNA haplogroup and hypervariable region (HVR I, and II) sequence data from 263 extant Yuman speakers, representing the major branches of the Yuman language family, in addition to the Western Apache (Athapaskan) to further investigate the demographic context and geographic extent of this expansion. Data presented indicate that the expansion of B2a is only slightly older [2,410 YBP (99.5% CI: 1,458-4,320 YBP)] than previously estimated and not significantly. Despite large confidence intervals there are implications for the origin and expansion of the Yuman language family. Cultural transformations due to the inundation and draining of Lake Cahuilla may explain in part the frequencies of this lineage among the Kumeyaay and other Yuman and Takic groups in Southern California. This may have been the result of group fissions and fusions followed by migration and interaction that included expanded trade networks and intermarriage among Yuman speakers. In addition, a series of in-situ genetic bottlenecks is proposed to have occurred among the Western Apache leading to increasing homogeneity within haplogroup A, culminating in an admixture event with the Yavapai.
Assuntos
DNA Mitocondrial/genética , Variação Genética , Haplótipos/genética , Indígenas Norte-Americanos/genética , Antropologia Física , DNA Mitocondrial/sangue , Feminino , Humanos , Idioma , México , Mutação , Análise de Componente Principal , Sudoeste dos Estados UnidosRESUMO
In this study, we explore the geographic and temporal distribution of a unique variant of the O blood group allele called O1v(G542A) , which has been shown to be shared among Native Americans but is rare in other populations. O1v(G542A) was previously reported in Native American populations in Mesoamerica and South America, and has been proposed as an ancestry informative marker. We investigated whether this allele is also found in the Tlingit and Haida, two contemporary indigenous populations from Alaska, and a pre-Columbian population from California. If O1v(G542A) is present in Na-Dene speakers (i.e., Tlingits), it would indicate that Na-Dene speaking groups share close ancestry with other Native American groups and support a Beringian origin of the allele, consistent with the Beringian Incubation Model. If O1v(G542A) is found in pre-Columbian populations, it would further support a Beringian origin of the allele, rather than a more recent introduction of the allele into the Americas via gene flow from one or more populations which have admixed with Native Americans over the past five centuries. We identified this allele in one Na-Dene population at a frequency of 0.11, and one ancient California population at a frequency of 0.20. Our results support a Beringian origin of O1v(G542A) , which is distributed today among all Native American groups that have been genotyped in appreciable numbers at this locus. This result is consistent with the hypothesis that Na-Dene and other Native American populations primarily derive their ancestry from a single source population.
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Sistema ABO de Grupos Sanguíneos/genética , Alelos , Evolução Biológica , Fluxo Gênico/genética , Indígenas Norte-Americanos/genética , Alaska , Sequência de Bases , California , Primers do DNA/genética , DNA Mitocondrial/genética , Demografia , Genética Populacional , Haplótipos/genética , Humanos , Dados de Sequência Molecular , Análise de Sequência de DNARESUMO
Although the cultural and nutritive importance of the turkey (Meleagris gallopavo) to precontact Native Americans and contemporary people worldwide is clear, little is known about the domestication of this bird compared to other domesticates. Mitochondrial DNA analysis of 149 turkey bones and 29 coprolites from 38 archaeological sites (200 BC-AD 1800) reveals a unique domesticated breed in the precontact Southwestern United States. Phylogeographic analyses indicate that this domestic breed originated from outside the region, but rules out the South Mexican domestic turkey (Meleagris gallopavo gallopavo) as a progenitor. A strong genetic bottleneck within the Southwest turkeys also reflects intensive human selection and breeding. This study points to at least two occurrences of turkey domestication in precontact North America and illuminates the intensity and sophistication of New World animal breeding practices.
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Animais Domésticos/genética , Cruzamento/métodos , DNA Mitocondrial/genética , Fósseis , Filogenia , Perus/genética , Animais , Sequência de Bases , Osso e Ossos/química , Análise por Conglomerados , Primers do DNA/genética , Demografia , Fezes/química , Efeito Fundador , Geografia , Humanos , Dados de Sequência Molecular , Análise de Sequência de DNA , Sudoeste dos Estados Unidos , Especificidade da EspécieRESUMO
The Farming/Language Dispersal Hypothesis posits that prehistoric population expansions, precipitated by the innovation or early adoption of agriculture, played an important role in the uneven distribution of language families recorded across the world. In this case, the most widely spread language families today came to be distributed at the expense of those that have more restricted distributions. In the Americas, Uto-Aztecan is one such language family that may have been spread across Mesoamerica and the American Southwest by ancient farmers. We evaluated this hypothesis with a large-scale study of mitochondrial DNA (mtDNA) and Y-chromosomal DNA variation in indigenous populations from these regions. Partial correlation coefficients, determined with Mantel tests, show that Y-chromosome variation in indigenous populations from the American Southwest and Mesoamerica correlates significantly with linguistic distances (r = 0.33-0.384; P < 0.02), whereas mtDNA diversity correlates significantly with only geographic distance (r = 0.619; P = 0.002). The lack of correlation between mtDNA and Y-chromosome diversity is consistent with differing population histories of males and females in these regions. Although unlikely, if groups of Uto-Aztecan speakers were responsible for the northward spread of agriculture and their languages from Mesoamerica to the Southwest, this migration was possibly biased to males. However, a recent in situ population expansion within the American Southwest (2,105 years before present; 99.5% confidence interval = 1,273-3,773 YBP), one that probably followed the introduction and intensification of maize agriculture in the region, may have blurred ancient mtDNA patterns, which might otherwise have revealed a closer genetic relationship between females in the Southwest and Mesoamerica.
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Cromossomos Humanos Y/ultraestrutura , DNA Mitocondrial/ultraestrutura , Variação Genética , Indígenas Norte-Americanos/genética , Idioma , Agricultura/métodos , Evolução Biológica , América Central , Emigração e Imigração , Etnicidade/genética , Feminino , Genética Populacional , História Antiga , Humanos , Indígenas Norte-Americanos/história , Masculino , Dados de Sequência Molecular , Fatores Sexuais , Sudoeste dos Estados Unidos , Zea mays/metabolismoRESUMO
OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA. MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted. RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains. DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.
Assuntos
Indígena Americano ou Nativo do Alasca , Metagenoma , Boca , Humanos , Cálculos/genética , Chloroflexi/genética , DNA Bacteriano/análise , Metagenoma/genética , Periodontite/microbiologia , Treponema denticola/genética , Boca/microbiologiaRESUMO
BACKGROUND: Adenoid cystic carcinoma (AdCC) is an uncommon malignancy of the salivary gland characterized by slow growth, increased risk of recurrence and poor prognosis. The annual incidence in the United States is approximately 1200 cases per year and rarely involves the body cavities. CASE PRESENTATION: We present a case of a 48-year-old male diagnosed with AdCC of the left submandibular gland. He received his last chemotherapy in 2006 and presented with pleural metastasis. After undergoing pleurectomy and decortication procedure, pericardial fluid and biopsies from the chest wall, sixth rib, diaphragm, pleural cavity and pericardium were sent for pathologic evaluation. A diagnosis of metastatic adenoid cystic carcinoma was confirmed, including in the pericardium, pericardial fluid and diaphragm. CONCLUSION: AdCC of the submandibular gland is a malignant tumor with a high mortality rate. It is very rare for AdCC to metastasize to the pericardium and diaphragm. Metastasis to uncommon sites such as seen in our case with metastases to the pericardium and diaphragm shows the aggressive and unpredictable nature of this tumor, requiring close follow up, and indicating the need for molecular profile analysis and biomarker-stratified clinical trials.
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Carcinoma Adenoide Cístico/patologia , Metástase Neoplásica/patologia , Neoplasias da Glândula Submandibular/patologia , Biópsia , Diafragma/patologia , Humanos , Masculino , Pessoa de Meia-Idade , Recidiva Local de Neoplasia , Pericárdio/patologia , Glândulas Salivares/patologiaRESUMO
Though chickens (Gallus gallus domesticus) are globally ubiquitous today, the timing, location, and manner of their domestication is contentious. Until recently, archaeologists placed the origin of the domestic chicken in northern China, perhaps as early as 8,000 years ago. Such evidence however complicates our understanding of how the chicken was domesticated because its wild progenitor - the red jungle fowl (Gallus gallus) - lives in tropical ecosystems and does not exist in northern China today or in the recent past. Increasingly, multiple lines of evidence suggest that many of the archaeological bird remains underlying this northern origins hypothesis have been misidentified. Here we analyze the mitochondrial DNA of some of the earliest purported chickens from the Dadiwan site in northern China and conclude that they are pheasants (Phasianus colchicus). Curiously, stable isotope values from the same birds reveal that their diet was heavy in agricultural products (namely millet), meaning that they lived adjacent to or among some of the earliest farming communities in East Asia. We suggest that the exploitation of these baited birds was an important adaptation for early farmers in China's arid north, and that management practices like these likely played a role in the domestication of animals - including the chicken - in similar contexts throughout the region.
Assuntos
Arqueologia , DNA Mitocondrial/genética , Domesticação , Animais , Galinhas/genética , China , Fazendeiros , Humanos , Milhetes , Filogenia , Codorniz/genética , Codorniz/fisiologiaRESUMO
INTRODUCTION: Glomus tumors (GTs) are rare neoplasms that originate from the modified smooth muscle cells of glomus bodies and occasionally arise from visceral primary sites. All previously reported primary hepatic GTs were benign. Here we report the first malignant primary hepatic GT. PRESENTATION OF CASE: Our patient is a 60-year-old male who presented with weight loss, early satiety, night sweats, and abdominal distention. Imaging demonstrated a large mass abutting the stomach, duodenum, and head of the pancreas, exerting mass effect on the portal vein and inferior vena cava. Biopsy results were deemed nondiagnostic after extensive review at multiple academic institutions. We performed a caudate lobe resection, antrectomy, and Bilroth II gastrojejunostomy that required skeletonization of much of the periportal vascular anatomy and the repair of multiple venotomies due to the tumor's adherence to the inferior vena cava. Histopathologic evaluation revealed morphologic and immunohistochemical findings consistent with a malignant GT, and next-generation sequencing using a targeted panel revealed an inactivating TP53 mutation. DISCUSSION: This case presented both a surgical and histopathologic challenge, requiring meticulous operative technique for resection in conjunction with a combination of characteristic morphologic features and immunohistochemical staining for diagnosis. Sequencing results using a targeted panel add to the limited GT genomic literature. CONCLUSION: While rare, it is important to consider malignant GTs in the differential diagnosis for heterogeneous liver masses. Close follow-up will be essential to monitor our patient's clinical course and expeditiously pursue any further interventions.
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Human microbiome studies are increasingly incorporating macroecological approaches, such as community assembly, network analysis and functional redundancy to more fully characterize the microbiome. Such analyses have not been applied to ancient human microbiomes, preventing insights into human microbiome evolution. We address this issue by analysing published ancient microbiome datasets: coprolites from Rio Zape (n = 7; 700 CE Mexico) and historic dental calculus (n = 44; 1770-1855 CE, UK), as well as two novel dental calculus datasets: Maya (n = 7; 170 BCE-885 CE, Belize) and Nuragic Sardinians (n = 11; 1400-850 BCE, Italy). Periodontitis-associated bacteria (Treponema denticola, Fusobacterium nucleatum and Eubacterium saphenum) were identified as keystone taxa in the dental calculus datasets. Coprolite keystone taxa included known short-chain fatty acid producers (Eubacterium biforme, Phascolarctobacterium succinatutens) and potentially disease-associated bacteria (Escherichia, Brachyspira). Overlap in ecological profiles between ancient and modern microbiomes was indicated by similarity in functional response diversity profiles between contemporary hunter-gatherers and ancient coprolites, as well as parallels between ancient Maya, historic UK, and modern Spanish dental calculus; however, the ancient Nuragic dental calculus shows a distinct ecological structure. We detected key ecological signatures from ancient microbiome data, paving the way to expand understanding of human microbiome evolution. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
Assuntos
Bactérias/isolamento & purificação , DNA Antigo/análise , Cálculos Dentários/história , Fezes/microbiologia , Microbiota , Arqueologia , Belize , DNA Bacteriano/análise , Cálculos Dentários/microbiologia , Sequenciamento de Nucleotídeos em Larga Escala , História Antiga , História Medieval , Humanos , Itália , MéxicoRESUMO
In this study, we sought to document the efficiency of primer extension capture (PEC) as a method to enrich DNA eluates of targeted DNA molecules and remove nontarget molecules from pools containing both. Efficiency of the method was estimated by comparing number of "copies in" to "copies out" by quantitative polymerase chain reaction. PEC retention of DNA targets ranging 109-288 base pairs (bps) in length was 15.88-2.14% (i.e., loss of 84.12-97.86% of target molecules). Experimental modifications of the PEC method resulted in no significant improvements. However, the benefit of PEC was revealed in its ability to remove most nontarget DNA molecules (99.99%). We also discovered that many (56.69%) of the target molecules are "lost" prior to their immobilization on the streptavidin-coated beads. These estimates of methodological efficiency are directly comparable to previous ones observed following "fishing" for DNA, an alternative method for DNA enrichment.
Assuntos
Primers do DNA , DNA/isolamento & purificação , Análise de Sequência de DNA/métodos , Genética Forense/métodos , Humanos , Reação em Cadeia da Polimerase , Estreptavidina/químicaRESUMO
BACKGROUND: Oxidative stress largely contributes to early brain injury after subarachnoid hemorrhage (SAH). One of the major sources of reactive oxygen species is NADPH oxidase, upregulated after SAH. We hypothesized that NADPH oxidase-induced oxidative stress plays a major causative role in early brain injury after SAH. METHODS: Using gp91phox knockout (ko) and wild-type (wt) mice, we studied early brain injury in the endovascular perforation model of SAH. Mortality rate, cerebral edema, oxidative stress, and superoxide production were measured at 24 h after SAH. Neurological evaluation was done at 23 h after SAH surgery. RESULTS: Genotyping confirmed the existence of a nonfunctional gp91phox gene in the ko mice. CBF measurements did not show differences in SAH-induced acute ischemia between ko and wt mice. SAH caused a significant increase of water content in the ipsilateral hemisphere as well as an increase of Malondialdehyde (MDA) levels and superoxide production. There were no significant differences in post-SAH mortality rate, brain water content and the intensity of the oxidative stress between knockout and wild type groups of mice. CONCLUSIONS: Our results suggest that gp91phox is not critically important to the early brain injury after SAH. An adaptive compensatory mechanism for free radical production in knockout mice is discussed.
Assuntos
Dano Encefálico Crônico/genética , Glicoproteínas de Membrana/genética , NADPH Oxidases/genética , Degeneração Neural/genética , Estresse Oxidativo/genética , Hemorragia Subaracnóidea/complicações , Animais , Barreira Hematoencefálica/enzimologia , Barreira Hematoencefálica/fisiopatologia , Dano Encefálico Crônico/enzimologia , Dano Encefálico Crônico/fisiopatologia , Edema Encefálico/enzimologia , Edema Encefálico/genética , Edema Encefálico/fisiopatologia , Artérias Cerebrais/enzimologia , Artérias Cerebrais/fisiopatologia , Radicais Livres/metabolismo , Marcadores Genéticos/genética , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , NADPH Oxidase 2 , Degeneração Neural/enzimologia , Degeneração Neural/fisiopatologia , Hemorragia Subaracnóidea/enzimologia , Hemorragia Subaracnóidea/fisiopatologia , Superóxidos/metabolismoRESUMO
This study sought to document the efficiency of DNA bait capture (i.e., "fishing") methods by two measures: (1) its ability to retain targeted DNA molecules, and (2) its ability to remove non-target DNA molecules from a pool containing both. DNA bait capture uses synthetic biotinylated DNA primers to bind target DNA, which are then immobilized onto streptavidin coated magnetic beads and drawn to a magnet. Bound DNA should, therefore, be isolated from non-target DNA and impurities (e.g., PCR inhibitors) and can be later eluted from the beads for downstream applications. Efficiencies were estimated by comparing the number of "copies in" to "copies out" with quantitative polymerase chain reaction (qPCR). Retention of target DNA molecules, ranging from 109 to 288 base pairs (bps) in length, averaged just 9.06-3.53% (i.e., loss of 90.94-96.47%) using the fishing protocol as originally described. Some improvement was achieved by employing a modified protocol (i.e., with a shortened hybridization time, use of twice the amount of M-270 streptavidin-coated beads, and modified bead washing), resulting in average retention of 31.41-12.08% of the same set of targeted molecules. Noted was the lack of efficacy in removing non-target DNA molecules as opposed to targeted molecules. It was also observed that most of the molecules (61.35-69.49%) are "lost" during the essential hybridization step of the fishing protocol, suggesting its suitability for high copy number samples only. While the bait capture method may be useful in the study of polymerase chain reaction (PCR) inhibited DNA samples as previously suggested, it is necessary to carefully weigh this possible advantage against the degree of expected DNA loss and the non-selectivity of the method for targeted over non-targeted DNA.
Assuntos
DNA/isolamento & purificação , Hibridização de Ácido Nucleico/métodos , Degradação Necrótica do DNA , Primers do DNA , Humanos , Magnetismo , Reação em Cadeia da Polimerase , Estreptavidina/químicaRESUMO
The 13th century Puebloan depopulation of the Four Corners region of the US Southwest is an iconic episode in world prehistory. Studies of its causes, as well as its consequences, have a bearing not only on archaeological method and theory, but also social responses to climate change, the sociology of social movements, and contemporary patterns of cultural diversity. Previous research has debated the demographic scale, destinations, and impacts of Four Corners migrants. Much of this uncertainty stems from the substantial differences in material culture between the Four Corners vs. hypothesized destination areas. Comparable biological evidence has been difficult to obtain due to the complete departure of farmers from the Four Corners in the 13th century CE and restrictions on sampling human remains. As an alternative, patterns of genetic variation among domesticated species were used to address the role of migration in this collapse. We collected mitochondrial haplotypic data from dog (Canis lupus familiaris) and turkey (Meleagris gallopavo) remains from archaeological sites in the most densely-populated portion of the Four Corners region, and the most commonly proposed destination area for that population under migration scenarios. Results are consistent with a large-scale migration of humans, accompanied by their domestic turkeys, during the 13th century CE. These results support scenarios that suggest contemporary Pueblo peoples of the Northern Rio Grande are biological and cultural descendants of Four Corners populations.
Assuntos
DNA Mitocondrial/história , Fósseis , Migração Humana , Animais , Animais Domésticos , Arqueologia , Mudança Climática , DNA Antigo/química , DNA Mitocondrial/química , DNA Mitocondrial/genética , Cães , Variação Genética , Haplótipos , História Medieval , Humanos , Indígenas Norte-Americanos/história , Dinâmica Populacional , Análise de Sequência de DNA/métodos , Sudoeste dos Estados Unidos , PerusRESUMO
While cytosine methylation has been widely studied in extant populations, relatively few studies have analyzed methylation in ancient DNA. Most existing studies of epigenetic marks in ancient DNA have inferred patterns of methylation in highly degraded samples using post-mortem damage to cytosines as a proxy for cytosine methylation levels. However, this approach limits the inference of methylation compared with direct bisulfite sequencing, the current gold standard for analyzing cytosine methylation at single nucleotide resolution. In this study, we used direct bisulfite sequencing to assess cytosine methylation in ancient DNA from the skeletal remains of 30 Native Americans ranging in age from approximately 230 to 4500 years before present. Unmethylated cytosines were converted to uracils by treatment with sodium bisulfite, bisulfite products of a CpG-rich retrotransposon were pyrosequenced, and C-to-T ratios were quantified for a single CpG position. We found that cytosine methylation is readily recoverable from most samples, given adequate preservation of endogenous nuclear DNA. In addition, our results indicate that the precision of cytosine methylation estimates is inversely correlated with aDNA preservation, such that samples of low DNA concentration show higher variability in measures of percent methylation than samples of high DNA concentration. In particular, samples in this study with a DNA concentration above 0.015 ng/µL generated the most consistent measures of cytosine methylation. This study presents evidence of cytosine methylation in a large collection of ancient human remains, and indicates that it is possible to analyze epigenetic patterns in ancient populations using direct bisulfite sequencing approaches.
Assuntos
Citosina/metabolismo , Metilação de DNA/genética , Indígenas Norte-Americanos/genética , Sulfitos/química , Ilhas de CpG/genética , Metilação de DNA/fisiologia , Humanos , Retroelementos/genética , Análise de Sequência de DNARESUMO
While recent forensic research has focused on determining which skeletal elements are superior in their preservation of DNA over the long term, little focus has been placed on measuring intra-element variation. Moreover, there is a general belief that dense (cortical) bone material will contain better-preserved DNA than does spongy (cancellous) bone. To address these ideas, quantitative PCR was used to estimate the degree of mitochondrial DNA (mtDNA) preservation variance across sections of 19 northern fur seal ribs (Callorhinus ursinus) that date to â¼3000 years before present. Further, we developed a measure called the "density index" that was used to gauge the relative densities of the rib sections studied here to determine if density was an appropriate predictor of preservation. The average preservation among the samples was significantly different (ANOVA, p=1.9×10(-9)) with only 15% of the total variance observed within samples. However, 12 of the 19 specimens (â¼63.2%) exhibited at least an order of magnitude difference in mtDNA preservation across the whole. Regression of the amount of mtDNA extracted per gram of bone material against the density index of the bone from which it was extracted demonstrates no relationship between these variables (R(2)=0.03, p=0.28).
Assuntos
Densidade Óssea , DNA Mitocondrial/genética , DNA Mitocondrial/isolamento & purificação , Otárias/genética , Costelas/química , Animais , Antropologia Forense , Reação em Cadeia da PolimeraseRESUMO
PURPOSE: To evaluate the prevalence of parent-reported attention-deficit/hyperactivity disorder (ADHD) in two clinics in Alabama serving children with vision impairment. METHODS: The medical records of children 4-17 years of age attending the Alabama School for the Blind (ASB) during the 2010-2011 school year or seen at the University of Alabama at Birmingham (UAB) Center for Low Vision Rehabilitation between 2006 and 2010 were retrospectively reviewed. Sociodemographics, ocular characteristics, and parental report of ADHD diagnosis were obtained. The prevalence of ADHD was compared to national and state figures for age-similar children regardless of comorbidities. The prevalence of ADHD, sociodemographic, and ocular characteristics was also compared between clinical sites. RESULTS: A total of 264 children participated in the study (95 from ASB and 169 from UAB). The prevalence of ADHD among children with visual acuity better than hand motion (n = 245) was 22.9%, which is higher than reported state (14.3%) and national prevalence (9.5%) for children in this age range. The prevalence was similar at ASB (22.4%) and UAB (23.1%). Those with ADHD were similar to those without ADHD with respect to age, sex, and race. Children with ADHD were significantly less likely to have nystagmus and more likely to have better visual acuity (P < 0.05). The prevalence of ADHD among the 19 participants with total or near total vision loss (all from ASB) was 10.5%. CONCLUSIONS: Our analyses suggest that children with vision impairment may be more likely to be diagnosed with ADHD than children in the general population.
Assuntos
Transtorno do Deficit de Atenção com Hiperatividade/epidemiologia , Baixa Visão/epidemiologia , Pessoas com Deficiência Visual/estatística & dados numéricos , Adolescente , Criança , Pré-Escolar , Estudos Transversais , Feminino , Humanos , Masculino , Prevalência , Estados Unidos/epidemiologiaRESUMO
DNA from ancient and forensic specimens is often co-extracted with unknown amounts of unknown PCR inhibitors, which can lead to underestimated DNA concentrations, allelic drop-out, and/or false-negative results. It is not surprising, in this case, that numerous methods have been developed to remove PCR inhibitors or subdue their effects. One simple and cost effective approach could be the adoption of a polymerase that overcomes or is less affected by PCR inhibitors. In this study, nine different polymerases were evaluated for their efficacy against PCR inhibitors co-extracted with DNA from 63 ancient salmon vertebrae. These samples were excavated from two archeological sites located at the Dionisio Point locality on the northern end of Galiano Island in coastal southwestern British Columbia, Canada and date to 700-1000 and 1300-1500 years before present. Previously, DNA extracts from samples studied from this locality were determined to be largely inhibited to PCR amplification. In the present study, Omni Klentaq LA (DNA Polymerase Technology, Inc.) outperformed the other 8 polymerases in two measures: (1) its success in genetic species identification of these vertebrae, and (2) its ability to amplify an ancient DNA positive control when spiked with a volume of potentially inhibited extract from the vertebrae.