scholarly journals Adaptation to Extreme Environments in an Admixed Human Population from the Atacama Desert

2019 ◽  
Vol 11 (9) ◽  
pp. 2468-2479 ◽  
Author(s):  
Lucas Vicuña ◽  
Mario I Fernandez ◽  
Cecilia Vial ◽  
Patricio Valdebenito ◽  
Eduardo Chaparro ◽  
...  
Keyword(s):  
Native American ◽  
Ribosome Biogenesis ◽  
Coronary Thrombosis ◽  
Extreme Environments ◽  
Atacama Desert ◽  
Inorganic Arsenic ◽  
Urinary Bladder Cancer ◽  
Enrichment Test ◽  
Genome Wide ◽  
Before And After

Abstract Inorganic arsenic (As) is a toxic xenobiotic and carcinogen associated with severe health conditions. The urban population from the Atacama Desert in northern Chile was exposed to extremely high As levels (up to 600 µg/l) in drinking water between 1958 and 1971, leading to increased incidence of urinary bladder cancer (BC), skin cancer, kidney cancer, and coronary thrombosis decades later. Besides, the Andean Native-American ancestors of the Atacama population were previously exposed for millennia to elevated As levels in water (∼120 µg/l) for at least 5,000 years, suggesting adaptation to this selective pressure. Here, we performed two genome-wide selection tests—PBSn1 and an ancestry-enrichment test—in an admixed population from Atacama, to identify adaptation signatures to As exposure acquired before and after admixture with Europeans, respectively. The top second variant selected by PBSn1 was associated with LCE4A-C1orf68, a gene that may be involved in the immune barrier of the epithelium during BC. We performed association tests between the top PBSn1 hits and BC occurrence in our population. The strongest association (P = 0.012) was achieved by the LCE4A-C1orf68 variant. The ancestry-enrichment test detected highly significant signals (P = 1.3 × 10−9) mapping MAK16, a gene with important roles in ribosome biogenesis during the G1 phase of the cell cycle. Our results contribute to a better understanding of the genetic factors involved in adaptation to the pathophysiological consequences of As exposure.

scholarly journals Impact of the 2017 Child and Adult Care Food Program Meal Pattern Requirement Change on Menu Quality in Tribal Early Care Environments: The Food Resource Equity and Sustainability for Health Study

2019 ◽  
Vol 4 (Supplement_1) ◽  
pp. 12-22 ◽  
Author(s):  
Susan B Sisson ◽  
Kaysha Sleet ◽  
Rachel Rickman ◽  
Charlotte Love ◽  
Alexandria Bledsoe ◽  
...  
Keyword(s):  
Native American ◽  
Best Practice ◽  
Food Resource ◽  
Saturated Fat ◽  
Health Study ◽  
Healthy Weight ◽  
Early Care ◽  
Adult Care ◽  
Nutrient Analysis ◽  
Before And After

ABSTRACT Background Native American (NA) children have a high prevalence of obesity contributing to lifespan health disparities. Dietary intake is important to promote healthy weight gain, growth, and development. In 2017, the USDA enforced changes to the Child and Adult Care Food Program (CACFP). The CACFP provides reimbursement to qualifying Early Care and Education (ECE) programs that serve foods that uphold the program's nutrition requirements. Objective This study had the following 2 objectives: 1) Describe a novel index to evaluate ECE menus based on revised CACFP requirements (accounting for food substitutions) and best practices for 3- to-5-y-old children, and 2) analyze CACFP requirement and best practice compliance and nutrient changes in 9 NA ECE programs before and after enforcement of the revised CACFP requirements. Methods This longitudinal study is within a larger community-based participatory research study. Menus and meals served were evaluated for 1 wk at each of 9 programs before and after enforcement of the revised meal patterns. Nutrient analysis, CACFP requirement and best practice compliance, and substitution quality were evaluated. Differences were determined using a paired t-test or Wilcoxon matched test. This trial was registered at clinicaltrials.gov as NCT03251950. Results Total grams of fiber consumed increased (5.0 ± 1.2 compared with 5.9 ± 0.8 g, P = 0.04) and total grams of sugar consumed decreased (53.8 ± 12.6 compared with 48.4 ± 7.9 g, P = 0.024), although room for further improvement exists. Although total grams of fat remained unchanged, grams of saturated fat significantly increased (7.8 ± 1.4 compared with 10.5 ± 3.4, P = 0.041). Other nutrients remained unchanged. Overall CACFP requirement and best practice compliance scores improved, although this finding was not statistically significant. No significant changes in food quality associated with substitutions occurred. Conclusions This study provides early evidence to support the beneficial impact of the revised CACFP requirements. Understanding barriers to compliance within rural NA communities would be an important next step in enhancing the health of vulnerable children.

A Cultural Approach to Conducting HIV/AIDS and Hepatitis C Virus Education Among Native American Adolescents

2008 ◽  
Vol 24 (4) ◽  
pp. 229-238 ◽  
Author(s):  
John Lowe
Keyword(s):  
Native American ◽  
Hepatitis C Virus ◽  
Hepatitis C ◽  
Cultural Values ◽  
Prevention Program ◽  
Public High School ◽  
Convenience Sample ◽  
Self Reliance ◽  
Before And After ◽  
Hiv Aids

This pilot study tests the feasibility of using a Talking Circle approach and measures cultural values and beliefs within a HIV/AIDS and hepatitis C virus (HCV) prevention program conducted among a Native American (Cherokee) youth population. A descriptive correlation design was used to examine the relationship between Cherokee self-reliance and HIV/AIDS and HCV knowledge, attitudes, and behaviors. The study used three questionnaires that were administered before and after the prevention program to collect data from a convenience sample of 41 students at a public high school within the boundaries of the Cherokee Nation in Oklahoma. Statistical analysis revealed immediate differences between pretests and posttests related to knowledge, attitudes, and behavioral intentions concerning HIV/AIDS and HCV and the cultural dynamic of Cherokee self-reliance.

scholarly journals Novel water source for endolithic life in the hyperarid core of the Atacama Desert

2012 ◽  
Vol 9 (6) ◽  
pp. 2275-2286 ◽  
Author(s):  
J. Wierzchos ◽  
A. F. Davila ◽  
I. M. Sánchez-Almazo ◽  
M. Hajnos ◽  
R. Swieboda ◽  
...  
Keyword(s):  
Liquid Water ◽  
Capillary Condensation ◽  
Extreme Environments ◽  
Atacama Desert ◽  
Water Source ◽  
Life Forms ◽  
Alternative Source ◽  
Biological Adaptation ◽  
Salt Flats ◽  
Life On Earth

Abstract. The hyperarid core of the Atacama Desert, Chile, is possibly the driest and most life-limited place on Earth, yet endolithic microorganisms thrive inside halite pinnacles that are part of ancient salt flats. The existence of this microbial community in an environment that excludes any other life forms suggests biological adaptation to high salinity and desiccation stress, and indicates an alternative source of water for life other than rainfall, fog or dew. Here, we show that halite endoliths obtain liquid water through spontaneous capillary condensation at relative humidity (RH) much lower than the deliquescence RH of NaCl. We describe how this condensation could occur inside nano-pores smaller than 100 nm, in a newly characterized halite phase that is intimately associated with the endolithic aggregates. This nano-porous phase helps retain liquid water for long periods of time by preventing its evaporation even in conditions of utmost dryness. Our results explain how life has colonized and adapted to one of the most extreme environments on our planet, expanding the water activity envelope for life on Earth, and broadening the spectrum of possible habitats for life beyond our planet.

scholarly journals Ideas in Genomic Selection that Transformed Plant Molecular Breeding: A Review

2020 ◽  
Author(s):  
Matthew McGowan ◽  
Zhiwu Zhang ◽  
Jiabo Wang ◽  
Haixiao Dong ◽  
Xiaolei Liu ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Genetic Markers ◽  
Random Effects ◽  
Genome Wide Association Study ◽  
Single Step ◽  
Hybrid Breeding ◽  
Multiple Trait ◽  
Underlying Distribution ◽  
Genome Wide ◽  
Before And After

Estimation of breeding values through Best Linear Unbiased Prediction (BLUP) using pedigree-based kinship and Marker-Assisted Selection (MAS) are the two fundamental breeding methods used before and after the introduction of genetic markers, respectively. The emergence of high-density genome-wide markers has led to the development of two parallel series of approaches inspired by BLUP and MAS, which are collectively referred to as Genomic Selection (GS). The first series of GS methods alters pedigree-based BLUP by replacing pedigree-based kinship with marker-based kinship in a variety of ways, including weighting markers by their effects in genome-wide association study (GWAS), joining both pedigree and marker-based kinship together in a single-step BLUP, and substituting individuals with groups in a compressed BLUP. The second series of GS methods estimates the effects for all genetic markers simultaneously. For the second series methods, the marker effects are summed together regardless of their individual significance. Instead of fitting individuals as random effects like in the BLUP series, the second series fits markers as random effects. Differing assumptions regarding the underlying distribution of these marker effects have resulted in the development of many Bayesian-based GS methods. This review highlights critical concept developments for both of these series and explores ongoing GS developments in machine learning, multiple trait selection, and adaptation for hybrid breeding. Furthermore, considering the increasing use and variety of GS methods in plant breeding programs, this review addresses important concerns for future GS development and application, such as the use of GWAS-assisted GS, the long-term effectiveness of GS methods, and the valid assessment of prediction accuracy.

scholarly journals Dietary adaptation of FADS genes in Europe varied across time and geography

2017 ◽  
Author(s):  
Kaixiong Ye ◽  
Feng Gao ◽  
David Wang ◽  
Ofer Bar-Yosef ◽  
Alon Keinan
Keyword(s):  
Positive Selection ◽  
Association Studies ◽  
Fatty Acid Desaturase ◽  
Genome Wide Association Studies ◽  
Omega 3 ◽  
Dietary Adaptation ◽  
Genome Wide ◽  
Before And After ◽  
Omega 6 ◽  
Rate Limiting

AbstractFatty acid desaturase (FADS) genes encode rate-limiting enzymes for the biosynthesis of omega-6 and omega-3 long chain polyunsaturated fatty acids (LCPUFAs). This biosynthesis is essential for individuals subsisting on LCPUFAs-poor, plant-based diets. Positive selection on FADS genes has been reported in multiple populations, but its presence and pattern in Europeans remain elusive. Here, with analyses of ancient and modern DNA, we demonstrated that positive selection acted on the same FADS variants both before and after the advent of farming in Europe, but on opposite alleles. Selection in recent farmers also varied geographically, with the strongest signal in Southern Europe. These varying selection patterns concur with anthropological evidence of differences in diets, and with the association of recently-adaptive alleles with higher FADS1 expression and enhanced LCPUFAs biosynthesis. Genome-wide association studies revealed associations of recently-adaptive alleles with not only LCPUFAs, but also other lipids and decreased risk of several inflammation-related diseases.

scholarly journals Genome-wide Association Study of Non-syndromic Orofacial Clefts in a Multiethnic Sample of Families and Controls Identifies Novel Regions

2020 ◽  
Author(s):  
Nandita Mukhopadhyay ◽  
Eleanor Feingold ◽  
Lina Moreno-Uribe ◽  
George Wehby ◽  
Luz Consuelo Valencia-Ramirez ◽  
...  
Keyword(s):  
Native American ◽  
Cleft Lip ◽  
Genome Wide Association Study ◽  
Population Level ◽  
Allele Frequencies ◽  
Genome Wide Association ◽  
South American ◽  
Orofacial Clefts ◽  
Public Health Burden ◽  
Genome Wide

AbstractOrofacial clefts (OFCs) are among the most prevalent craniofacial birth defects worldwide and create a significant public health burden. The majority of OFCs are non-syndromic and vary in prevalence by ethnicity. Africans have the lowest prevalence of OFCs (∼ 1/2,500), Asians have the highest prevalence (∼1/500), European and Latin Americans lie somewhere in the middle (∼1/800 and 1/900 respectively). Thus, ethnicity appears to be a major determinant of the risk of developing OFC. The Pittsburgh Orofacial Clefts Multiethnic study was designed to explore this ethnic variance, comprising a large number of families and individuals (∼12,000 individuals) from multiple populations worldwide: US and Europe, Asians, mixed Native American/Caucasians, and Africans. In this current study, we analyzed 2,915 OFC cases, 6,044 unaffected individuals related to the OFC cases, and 2,685 controls with no personal or family history of OFC. Participants were grouped by their ancestry into African, Asian, European, and Central and South American subsets, and genome-wide association run on the combined sample as well as the four ancestry-based groups. We observed 22 associations to cleft lip with or without cleft palate at 18 distinct loci with p-values < 1e-06, including 10 with genome-wide significance (< 5e-08), in the combined sample and within ancestry groups. Three loci - 2p12 (rs62164740, p=6.27e-07), 10q22.2 (rs150952246, p=3.14e-07), and 10q24.32 (rs118107597, p=8.21e-07) are novel. Nine were in or near known OFC loci - PAX7, IRF6, FAM49A, DCAF4L2, 8q24.21, NTN1, WNT3-WNT9B, TANC2, and RHPN2. The majority of the associations were observed only in the combined sample, European, and Central and South American groups. We investigated whether the observed differences in association strength were a) purely due to sample sizes, b) due to systematic allele frequency difference at the population level, or (c) due to the fact certain OFC-causing variants confer different amounts of risk depending on ancestral origin, by comparing effect sizes to observed allele frequencies of the effect allele in our ancestry-based groups. While some of the associations differ due to systematic differences in allele frequencies between groups, others show variation in effect size despite similar frequencies across ancestry groups.

Effect of the FDA Safety and Innovation Act on racial and gender diversity in neurosurgical device trials

2021 ◽  
pp. 1-8
Author(s):  
Neha Siddiqui ◽  
Ryan G. Chiu ◽  
Ravi S. Nunna ◽  
Georgia Glastris ◽  
Ankit I. Mehta
Keyword(s):  
Clinical Trials ◽  
Native American ◽  
Gender Diversity ◽  
Chi Square ◽  
Clinical Patient ◽  
New Device ◽  
Before And After ◽  
Device Applications ◽  
Us Fda ◽  
And Gender

OBJECTIVE The US FDA uses evidence from clinical trials in its determination of safety and utility. However, these trials have often suffered from limited external validity and generalizability due to unrepresentative study populations with respect to clinical patient demographics. Section 907 of the FDA Safety and Innovation Act (FDASIA) of 2012 attempted to address this issue by mandating the reporting of certain study demographics in new device applications. However, no study has been performed on its effectiveness in the participant diversity of neurosurgical device trials. METHODS The FDA premarket approval (PMA) online database was queried for all original neurosurgical device submissions from January 1, 2006, to December 31, 2019. Endpoints of the study included racial and gender demographics of reported effectiveness trials, which were summated for each submission. Chi-square tests were performed on both endpoints for before and after years of FDASIA passage and implementation. RESULTS A total of 33 device approvals were analyzed, with 14 occurring before SIA implementation and 19 after. Most trials (96.97%) reported gender to the FDA, while 66.67% reported race and 63.64% reported ethnicity. Gender breakdown did not change significantly post-SIA (53.30% female, p = 0.884). Racial breakdown was significantly different from the 2010 US Census for all races (p < 0.001) both pre- and post-SIA. Only Native American race was significantly different in terms of representation post-SIA, increasing from 0% to 0.63% (p = 0.0187). There was no significant change in ethnicity. CONCLUSIONS The FDASIA, as currently written, does not appear to have had a significant impact on the racial or gender diversity of neurosurgical device clinical trial populations. This may be due to the noncompulsory nature of its guidance, or a lack of more stringent regulation on the composition of clinical trials themselves.

Epigenomic changes after acupuncture treatment in patients suffering from burnout

2021 ◽  
Author(s):  
Marc Petitpierre ◽  
Ludwig Stenz ◽  
Ariane Paoloni-Giacobino
Keyword(s):  
Acupuncture Treatment ◽  
Maslach Burnout Inventory ◽  
Personal Accomplishment ◽  
Steroid Synthesis ◽  
Genome Wide ◽  
A Genome ◽  
Before And After ◽  
High Level ◽  
The Brain

Introduction: The effects of acupuncture treatment in patients suffering from burnout may imply an epigenetic control mediated by DNA methylation changes. In this observational study, a genome-wide characterization of epigenetic changes in blood DNA, before and after acupuncture treatment, was performed in a cohort of 11 patients suffering from burnout. Methods: Burnout was assessed using the Maslach Burnout Inventory (MBI) and DNA was extracted from blood samples and analyzed by Illumina EPIC BeadChip. Results: Before acupuncture, all patients suffered of emotional exhaustion (EE) (MBI-EE score, 44±6), 81% suffered of depersonalization (DP) (MBI-DP score, 16±6), and 72% of low feelings of personal accomplishment (PA) (MBI-PA score, 29±9). After acupuncture, all MBI dimensions improved significantly (EE, 16±11 [p=1.5*10-4]; DP, 4±5 [p=5.3*10-4]; and PA, 40±6 [p=4.1*10-3]). For each patient, both methylomes obtained before and after acupuncture co-clustered in the multidimensional scaling plot, indicating a high level of similarity. Genes corresponding to the 10 most differentially methylated CpGs showed enrichment in the brain dopaminergic signalling, steroid synthesis and in the insulin sensitivity pathways. Conclusion: Acupuncture treatment was found to be highly effective on all burnout dimensions and the epigenetic targets identified were involved in some major disturbances of this syndrome.

scholarly journals PDTM-33. EUROPEAN GENETIC ANCESTRY ASSOCIATED WITH RISK OF CHILDHOOD EPENDYMOMA

2019 ◽  
Vol 21 (Supplement_6) ◽  
pp. vi194-vi194
Author(s):  
Chenan Zhang ◽  
Quinn Ostrom ◽  
Helen Hansen ◽  
Adam de Smith ◽  
Cassie Kline ◽  
...  
Keyword(s):  
African American ◽  
Native American ◽  
Large Scale ◽  
Genetic Ancestry ◽  
European Ancestry ◽  
Admixture Mapping ◽  
Myxopapillary Ependymoma ◽  
Central Nervous System Tumor ◽  
Molecular Subgroup ◽  
Genome Wide

Abstract BACKGROUND Ependymoma is a histologically-defined central nervous system tumor most commonly occurring in children. Incidence differs by race/ethnicity, with individuals of European ancestry at highest risk. No large-scale genomic analyses of ependymoma predisposition have been conducted to date. We aimed to determine whether extent of European genetic ancestry is associated with ependymoma risk. METHODS In a multi-ethnic study of Californian children (327 cases, 1970 controls), we estimated the proportions of European, African, and Native American ancestry among admixed Hispanic and African-American subjects and estimated European substructure among non-Hispanic white subjects using genome-wide data. We tested whether genome-wide ancestry differences were associated with ependymoma risk and performed admixture mapping to identify associations with local European ancestry. We also re-analyzed CBTRUS data to examine subtype-specific differences in ependymoma incidence across racial/ethnic groups. RESULTS Each 20% increase in European ancestry was associated with 1.31-fold greater odds of ependymoma among Hispanic and African-American subjects (95% CI: 1.08–1.59, Pmeta=6.7×10–3). Among non-Hispanic whites, European ancestral substructure was also significantly associated with ependymoma risk. Local admixture mapping revealed a peak at 20p13 associated with increased local European ancestry, and genotype association analysis in the region identified an association upstream of R-spondin 4 that survived Bonferroni correction (P=2.2x10-5) but was not validated in an independent set of posterior fossa type A (PF-EPN-A) patients. In complementary CBTRUS analyses, American Indian/Alaskan Natives were at reduced risk relative to non-Hispanic whites (RR=0.64, 95% CI:0.46–0.87), as were African-Americans (RR=0.67, 95% CI:0.60–0.74) and Asian/Pacific Islanders (RR=0.86, 95% CI:0.73–1.00). Although overall ependymoma rates were similar in U.S. Hispanics (RR=0.96, 95% CI:0.88–1.05), lower rates were observed for myxopapillary ependymoma and other spinal ependymoma. CONCLUSION Inter-ethnic differences in ependymoma risk vary by histopathologic and potentially molecular subgroup, and are recapitulated in the genomic ancestry of ependymoma patients.

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