Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces

Citation: Hu, Z., Mbacké, B., Perumal, R., Guèye, M. C., Sy, O., Bouchet, S., . . . Morris, G. P. (2015). Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. Bmc Genomics. doi:10.1186/s12864-015-2255-0Background: Pearl millet is a staple food for people in arid and semi-arid regions of Africa and South Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal. Results: We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (?), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage. Conclusions: We identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops. © 2015 Hu et al

Strengthening human genetics research in Africa: report of the 9th meeting of the African Society of Human Genetics in Dakar in May 2016.

The 9th meeting of the African Society of Human Genetics, in partnership with the Senegalese Cancer Research and Study Group and the Human Heredity and Health in Africa (H3Africa) Consortium, was held in Dakar, Senegal. The theme was Strengthening Human Genetics Research in Africa. The 210 delegates came from 21 African countries and from France, Switzerland, UK, UAE, Canada and the USA. The goal was to highlight genetic and genomic science across the African continent with the ultimate goal of improving the health of Africans and those across the globe, and to promote the careers of young African scientists in the field. A session on the sustainability of genomic research in Africa brought to light innovative and practical approaches to supporting research in resource-limited settings and the importance of promoting genetics in academic, research funding, governmental and private sectors. This meeting led to the formation of the Senegalese Society for Human Genetics

Production of highly-polarized positrons using polarized electrons at MeV energies

The Polarized Electrons for Polarized Positrons experiment at the injector of the Continuous Electron Beam Accelerator Facility has demonstrated for the first time the efficient transfer of polarization from electrons to positrons produced by the polarized bremsstrahlung radiation induced by a polarized electron beam in a high-$Z$ target. Positron polarization up to 82\% have been measured for an initial electron beam momentum of 8.19~MeV/$c$, limited only by the electron beam polarization. This technique extends polarized positron capabilities from GeV to MeV electron beams, and opens access to polarized positron beam physics to a wide community.Comment: 5 pages, 4 figure

Measurements of electron-proton elastic cross sections for 0.4<Q2<5.5(GeV/c)20.4 < Q^2 < 5.5 (GeV/c)^2

We report on precision measurements of the elastic cross section for electron-proton scattering performed in Hall C at Jefferson Lab. The measurements were made at 28 unique kinematic settings covering a range in momentum transfer of 0.4 $<$ $Q^2$ $<$ 5.5 $(\rm GeV/c)^2$. These measurements represent a significant contribution to the world's cross section data set in the $Q^2$ range where a large discrepancy currently exists between the ratio of electric to magnetic proton form factors extracted from previous cross section measurements and that recently measured via polarization transfer in Hall A at Jefferson Lab.Comment: 17 pages, 18 figures; text added, some figures replace

A Study of the Quasi-elastic (e,e'p) Reaction on 12^{12}C, 56^{56}Fe and 97^{97}Au

We report the results from a systematic study of the quasi-elastic (e,e'p) reaction on $^{12}$C, $^{56}$Fe and $^{197}$Au performed at Jefferson Lab. We have measured nuclear transparency and extracted spectral functions (corrected for radiation) over a Q$^2$ range of 0.64 - 3.25 (GeV/c)$^2$ for all three nuclei. In addition we have extracted separated longitudinal and transverse spectral functions at Q$^2$ of 0.64 and 1.8 (GeV/c)$^2$ for these three nuclei (except for $^{197}$Au at the higher Q$^2$). The spectral functions are compared to a number of theoretical calculations. The measured spectral functions differ in detail but not in overall shape from most of the theoretical models. In all three targets the measured spectral functions show considerable excess transverse strength at Q$^2$ = 0.64 (GeV/c)$^2$, which is much reduced at 1.8 (GeV/c)$^2$.Comment: For JLab E91013 Collaboration, 19 pages, 20 figures, 3 table

Nuclear transparency from quasielastic A(e,e'p) reactions uo to Q^2=8.1 (GeV/c)^2

The quasielastic (e,e$^\prime$p) reaction was studied on targets of deuterium, carbon, and iron up to a value of momentum transfer $Q^2$ of 8.1 (GeV/c)$^2$. A nuclear transparency was determined by comparing the data to calculations in the Plane-Wave Impulse Approximation. The dependence of the nuclear transparency on $Q^2$ and the mass number $A$ was investigated in a search for the onset of the Color Transparency phenomenon. We find no evidence for the onset of Color Transparency within our range of $Q^2$. A fit to the world's nuclear transparency data reflects the energy dependence of the free proton-nucleon cross section.Comment: 11 pages, 6 figure

Implementing a multisector public-private partnership to improve urban hypertension management in low-and middle- income countries

BACKGROUND: Cardiovascular disease presents an increasing health burden to low- and middle-income countries. Although ample therapeutic options and care improvement frameworks exist to address its prime risk factor, hypertension, blood pressure control rates remain poor. We describe the results of an effectiveness study of a multisector urban population health initiative that targets hypertension in a real-world implementation setting in cities across three continents. The initiative followed the "CARDIO4Cities" approach (quality of Care, early Access, policy Reform, Data and digital technology, Intersectoral collaboration, and local Ownership). METHOD: The approach was applied in Ulaanbaatar in Mongolia, Dakar in Senegal, and Sao Paulo in Brazil. In each city, a portfolio of evidence-based practices was implemented, tailored to local priorities and available data. Outcomes were measured by extracting hypertension diagnosis, treatment and control rates from primary health records. Data from 18,997 patients with hypertension in primary health facilities were analyzed. RESULTS: Over one to two years of implementation, blood pressure control rates among enrolled patients receiving medication tripled in Sao Paulo (from 12.3% to 31.2%) and Dakar (from 6.7% to 19.4%) and increased six-fold in Ulaanbaatar (from 3.1% to 19.7%). CONCLUSIONS: This study provides first evidence that a multisectoral population health approach to implement known best-practices, supported by data and digital technologies, and relying on local buy-in and ownership, can improve hypertension control in high-burden urban primary care settings in low-and middle-income countries

Incidence and determinants of new AIDS-defining illnesses after HAART initiation in a Senegalese cohort

<p>Abstract</p> <p>Background</p> <p>Although a dramatic decrease in AIDS progression has been observed after Highly Active Anti Retroviral Therapy (HAART) in both low- and high-resource settings, few data support that fact in low-resource settings.</p> <p>This study describes the incidence of AIDS-defining illnesses (ADI) after HAART initiation and analyzes their risk factors in a low-resource setting. A focus was put on CD4 cell counts and viral load measurements.</p> <p>Methods</p> <p>404 HIV-1-infected Senegalese adult patients were enrolled in a prospective observational cohort and data censored as of April 2008. A Poisson regression was used to model the incidence of ADIs over two periods and to assess its association with baseline variables, current CD4, current viral load, CD4 response, and virological response.</p> <p>Results</p> <p>ADI incidence declined from 20.5 ADIs per 100 person-years, 95% CI = [16.3;25.8] during the first year to 4.3, 95% CI = [2.3;8.1] during the fourth year but increased afterwards. Before 42 months, the decrease was greater in patients with clinical stage CDC-C at baseline and with a viral load remaining below 1000 cp/mL but was uniform across CD4 strata (p = 0.1). After 42 months, 293 patients were still at risk. The current CD4 and viral load were associated with ADI incidence (decrease of 21% per 50 CD4/mm³and of 61% for patients with a viral load < 1000 cp/mL).</p> <p>Conclusions</p> <p>During the first four years, a uniform decline of ADI incidence was observed even in patients with low CD4-cell counts at HAART initiation as long as the viral load remained undetectable. An increase was noted later in patients with immunologic and virological failures but also in patients with only virological failure.</p

Search for three-nucleon short-range correlations in light nuclei

We present new data probing short-range correlations (SRCs) in nuclei through the measurement of electron scattering off high-momentum nucleons in nuclei. The inclusive ^{4}He/^{3}He cross section ratio is observed to be both x and Q^{2} independent for 1.52, our data support the hypothesis that a previous claim of three-nucleon correlation dominance was an artifact caused by the limited resolution of the measurement. While 3N-SRCs appear to have an important contribution, our data show that isolating 3N-SRCs is significantly more complicated than for 2N-SRCs.United States. Department of Energy (Contract DE-AC05-06OR23177)United States. Department of Energy (Contract DE-AC02-06CH11357)United States. Department of Energy (Contract DE-FG02-96ER40950