Genetic and seasonal determinants of vitamin D status in Confederated Salish and Kootenai Tribes (CSKT) participants

Background: Vitamin D is a hormone produced in the skin upon ultraviolet B (UVB) radiation. Vitamin D is a crucial regulator of calcium and phosphate levels for bone mineralization and other physiological roles. Vitamin D levels vary globally in human populations due to genetics, geography, and other demographic factors. It is estimated that 20-85 % of the variability in vitamin D levels is driven by genetic variation. To improve our understanding of contributors to vitamin D levels, we conducted a candidate-gene study in partnership with the Confederated Salish and Kootenai Tribes (CSKT). Methods: We recruited 472 CSKT study participants on the Flathead Reservation in Montana. Demographic factors included age, BMI, and gender (185 male and 287 female; ≥ 18 years old). Genomic DNA and plasma were isolated from whole blood. We sequenced 14 vitamin D regulatory candidate genes: CASR, CUBN, CYP2R1, CYP3A4,CYP24A1, CYP27B1, DHCR7, GC, RXRA, RXRB, RXRG, SULT2A1, UGT1A4, and VDR. We also measured plasma levels of vitamin D and vitamin D metabolites by liquid chromatography/mass-spectrometry (LC/MS), including the clinical marker of vitamin D status, 25-hydroxyvitamin D3 [25(OH)D3]. We tested demographic factors as well as common and rare genetic variants for statistical associations with vitamin D levels using bioinformatics software and R statistical programming language code. Results: We identified 7,370 total genetic variants with 8% (n = 585) of them being novel. We identified 60 genetic variants that may be of clinical significance (disease associated or predicted to influence medication response). Vitamin D levels were below sufficiency [25(OH)D3 + 25(OH)D2 levels \u3c 20 ng/mL] in 56 % of CSKT participants across the year. We observed seasonal vitamin D and metabolite level fluctuations in a seasonal, sinusoidal statistical model with peak concentrations in June – August and trough concentrations in December – February. In linear regression analysis, we found that age, BMI, season, and 5 variants in CUBN and CYP3A4 were significantly associated with 25(OH)D3 concentration (p-value\u3c 0.05). In logistic regression, we found that 4 variants in CUBN, CYP3A4, and UGT1A4 were associated with 25(OH)D sufficiency status [25(OH)D3 + 25(OH)D2 levels of 20 ng/mL] (p-value\u3c 0.05). Multivariate linear regression analysis revealed that genetic variation alone explained ~13% of the variability in 25(OH)D3 concentration in CSKT participants. Genetic variation and environmental factors together explained ~23 % of the variability in 25(OH)D3 concentration in CSKT participants. It is likely that genetic variation in additional genes and other environmental factors (e.g., dietary vitamin D intake) that were not included in this study explain the remaining variability in 25(OH)D3 concentration. Conclusion: This research addresses the need for increased inclusion of American Indian and Alaska Natives in precision medicine health research. We are the first to describe the contribution of season and genetics to vitamin D levels in an American Indian population. Our next steps will be to use these findings to perform mechanistic studies and develop interventional strategies for the CSKT people

Functional stacking of three resistance genes against Phytophthora infestans in potato

Functional stacking of broad spectrum resistance (R) genes could potentially be an effective strategy for more durable disease resistance, for example, to potato late blight caused by Phytophthora infestans (Pi). For this reason, three broad spectrum potato R genes (Rpi), Rpi-sto1 (Solanum stoloniferum), Rpi-vnt1.1 (S. venturii) and Rpi-blb3 (S. bulbocastanum) were selected, combined into a single binary vector pBINPLUS and transformed into the susceptible cultivar Desiree. Among the 550 kanamycin resistant regenerants, 28 were further investigated by gene specific PCRs. All regenerants were positive for the nptII gene and 23 of them contained the three Rpi genes, referred to as triple Rpi gene transformants. Detached leaf assay and agro-infiltration of avirulence (Avr) genes showed that the 23 triple Rpi gene transformants were resistant to the selected isolates and showed HR with the three Avr effectors indicating functional stacking of all the three Rpi genes. It is concluded that Avr genes, corresponding to the R genes to be stacked, must be available in order to assay for functionality of each stack component. No indications were found for silencing or any other negative effects affecting the function of the inserted Rpi genes. The resistance spectrum of these 23 triple Rpi gene transformants was, as expected, a sum of the spectra from the three individual Rpi genes. This is the first example of a one-step approach for the simultaneous domestication of three natural R genes against a single disease by genetic transformation

Genetic and seasonal contributions to variability in vitamin D levels among American Indians

Purpose: Vitamin D is an essential hormone in maintenance of calcium and phosphate homeostasis for adequate bone mineralization with roles in the immune system as well. Sources of vitamin D include natural synthesis in the skin upon ultraviolet B (UVB) radiation, dietary intake from plant and animal sources, and supplementation. Vitamin D levels, measured by the primary circulating vitamin D metabolite, 25-hydroxyvitamin D (25(OH)D), are variable across individuals due to latitude, season, diet, gender, disease states, medication use, and genetics. Populations living at northern latitudes (~400N) such as American Indians of the Confederated Salish and Kootenai Tribes (CSKT) are at increased susceptibility of having lower vitamin D levels in the winter months because there is decreased UVB exposure. There are currently no published data that exist on the genetic and seasonal influence on vitamin D status in CSKT people. Methods: We recruited 472 research participants from the Confederated Salish and Kootenai Tribes (CSKT) (185 male and 287 female; 18 years or older) at various sites in the Flathead Reservation in western Montana. Demographic factors were collected (e.g., age, body mass index, and gender). Genomic DNA and plasma were isolated from whole blood. We sequenced 12 candidate genes: 7-dehydrocholesterol reductase (DHCR7), calcium-sensing receptor (CASR), cubulin (CUBN), cytochrome P450 enzymes (CYP2R1, CYP27B1, CYP24A1, and CYP3A4), retinoid X receptors (RXR alpha, beta, and gamma), sulfotransferase family 2A member 1 (SULT2A1), UDP-glucuronosyltransferase family 1A3 and 1A4 (UGT1A3 and UGT1A4), vitamin D binding protein (GC), and vitamin D receptor (VDR). We also measured circulating levels of vitamin D and metabolites: vitamin D3 and vitamin D2, 25-hydroxyvitamin D [25(OH)D3 and 25(OH)D2], 1,25-dihydroxyvitamin D3 and D2 [1,25(OH)2D3 and 1,25(OH)2D2], 24R,25-dihydroxyvitamin D3 [24R,25(OH)D3], and 4-b,25-dihydroxyvitamin D3 [4b,25(OH)2D3]. Candidate genes were resequenced with Illumina next generation sequencing technology and vitamin D and metabolites were quantitated with liquid chromatography mass spectrometry (LC-MS/MS). The data we collected was summarized using a pipeline state of the art bioinformatics software. Originality: This research addresses the need for increased inclusion of American Indian and Alaska Natives in precision medicine health research. We have characterized genetic variation in vitamin D endocrinology genes and seasonal variability in vitamin D and vitamin D metabolite levels for the first time in CSKT people. Significance: We observed known and novel genetic variation in the CSKT population based on the presence or absence of genetic variants in the National Center for Biotechnology Information (NCBI) Single Nucleotide Polymorphism Database (dbSNP). We observed clinically relevant genetic variants that are associated with disease and variability in response to medication based on presence in the NCBI ClinVar and Pharmacogenomics Knowledge Base (PharmGKB) databases. Vitamin D and metabolite levels varied in a seasonal, fluctuating way, as expected, with lowest levels in January, February, and March months and highest levels in June, July, and August months. A significant percentage of CSKT participants had measured vitamin D levels below sufficiency (~43%). We will use these data to design an interventional strategy to address the low vitamin D levels we observed in CSKT people

An Evaluation of Florida\u27s Zika Response Using the WHO Health Systems Framework: Can We Apply These Lessons to COVID-19?

OBJECTIVES: From 2016 to 2018 Florida documented 1471 cases of Zika virus, 299 of which were pregnant women (Florida Department of Health, https://www.floridahealth.gov/diseases-and-conditions/mosquito-bornediseases/surveillance.html , 2019a). Florida\u27s response required unprecedented rapid and continuous cross-sector communication, adaptation, and coordination. Zika tested public health systems in new ways, particularly for maternal child health populations. The systems are now being challenged again, as the Coronavirus COVID-19 pandemic spreads throughout Florida. This qualitative journey mapping evaluation of Florida\u27s response focused on care for pregnant women and families with infants exposed to Zika virus. METHODS: Fifteen focus groups and interviews were conducted with 33 public health and healthcare workers who managed outbreak response, case investigations, and patient care in south Florida. Data were thematically analyzed, and the results were framed by the World Health Organization\u27s (WHO) Healthcare Systems Framework of six building blocks: health service delivery, health workforce, health information systems, access to essential medicines, financing, and leadership and governance (World Health Organization, https://www.who.int/healthsystems/strategy/everybodys_business.pdf , 2007, https://www.who.int/healthinfo/systems/monitoring/en/ , 2010). RESULTS: Results highlighted coordination of resources, essential services and treatment, data collection, communication among public health and healthcare systems, and dissemination of information. Community education, testing accuracy and turnaround time, financing, and continuity of health services were areas of need, and there was room for improvement in all indicator areas. CONCLUSIONS: The WHO Framework encapsulated important infrastructure and process factors relevant to the Florida Zika response as well as future epidemics. In this context, similarities, differences, and implications for the Coronavirus COVID-19 pandemic response are discussed. SIGNIFICANCE: During infectious disease outbreaks, public health systems work in concert with multiple national, state, and local health, communication, and environmental systems to prevent spread and to mitigate morbidity and mortality. Much was learned from the 2015 Zika pandemic. These lessons should be applied to address the much larger COVID-19 pandemic. The WHO Building Blocks of Health Systems provides a framework for planning, action, and evaluation