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- Liti, Gianni, et al.
(author)
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Population genomics of domestic and wild yeasts.
- 2009
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In: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 458:7236, s. 337-41
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Journal article (peer-reviewed)abstract
- Since the completion of the genome sequence of Saccharomyces cerevisiae in 1996 (refs 1, 2), there has been a large increase in complete genome sequences, accompanied by great advances in our understanding of genome evolution. Although little is known about the natural and life histories of yeasts in the wild, there are an increasing number of studies looking at ecological and geographic distributions, population structure and sexual versus asexual reproduction. Less well understood at the whole genome level are the evolutionary processes acting within populations and species that lead to adaptation to different environments, phenotypic differences and reproductive isolation. Here we present one- to fourfold or more coverage of the genome sequences of over seventy isolates of the baker's yeast S. cerevisiae and its closest relative, Saccharomyces paradoxus. We examine variation in gene content, single nucleotide polymorphisms, nucleotide insertions and deletions, copy numbers and transposable elements. We find that phenotypic variation broadly correlates with global genome-wide phylogenetic relationships. S. paradoxus populations are well delineated along geographic boundaries, whereas the variation among worldwide S. cerevisiae isolates shows less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined, geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for cross-breeding and production of new combinations of pre-existing variations.
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- Jallow, Muminatou, et al.
(author)
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Genome-wide and fine-resolution association analysis of malaria in West Africa.
- 2009
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In: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; , s. 657-665
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Journal article (peer-reviewed)abstract
- We report a genome-wide association (GWA) study of severe malaria in The Gambia. The initial GWA scan included 2,500 children genotyped on the Affymetrix 500K GeneChip, and a replication study included 3,400 children. We used this to examine the performance of GWA methods in Africa. We found considerable population stratification, and also that signals of association at known malaria resistance loci were greatly attenuated owing to weak linkage disequilibrium (LD). To investigate possible solutions to the problem of low LD, we focused on the HbS locus, sequencing this region of the genome in 62 Gambian individuals and then using these data to conduct multipoint imputation in the GWA samples. This increased the signal of association, from P = 4 x 10(-7) to P = 4 x 10(-14), with the peak of the signal located precisely at the HbS causal variant. Our findings provide proof of principle that fine-resolution multipoint imputation, based on population-specific sequencing data, can substantially boost authentic GWA signals and enable fine mapping of causal variants in African populations.
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| 7. |
- Janhunen, P., et al.
(author)
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Statistics of a parallel Poynting vector in the auroral zone as a function of altitude using Polar EFI and MFE data and Astrid-2 EMMA data
- 2005
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In: Annales Geophysicae. - : Copernicus GmbH. - 0992-7689 .- 1432-0576. ; 23:5, s. 1797-1806
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Journal article (peer-reviewed)abstract
- We study the wave-related (AC) and static (DC) parallel Poynting vector (Poynting energy flux) as a function of altitude in auroral field lines using Polar EFI and MFE data. The study is statistical and contains 5 years of data in the altitude range 5000-30 000km. We verify the low altitude part of the results by comparison with earlier Astrid-2 EMMA Poynting vector statistics at 1000km altitude. The EMMA data are also used to statistically compensate the Polar results for the missing zonal electric field component. We compare the Poynting vector with previous statistical DMSP satellite data concerning the electron precipitation power. We find that the AC Poynting vector (Alfvenwave related Poynting vector) is statistically not sufficient to power auroral electron precipitation, although it may, for K-P> 2, power 25-50% of it. The statistical AC Poynting vector also has a stepwise transition at R=4 R-E, so that its amplitude increases with increasing altitude. We suggest that this corresponds to Alfven waves being in Landau resonance with electrons, so that wave-induced electron acceleration takes place at this altitude range, which was earlier named the Alfven Resonosphere (ARS). The DC Poynting vector is similar to 3 times larger than electron precipitation and corresponds mainly to ionospheric Joule heating. In the morning sector (02:00-06:00 MLT) we find that the DC Poynting vector has a nontrivial altitude profile such that it decreases by a factor of similar to 2 when moving upward from 3 to 4 RE radial distance. In other nightside MLT sectors the altitude profile is more uniform. The morning sector nontrivial altitude profile may be due to divergence
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| 8. |
- Moncuquet, M., et al.
(author)
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The radio waves and thermal electrostatic noise spectroscopy (SORBET) experiment on BEPICOLOMBO/MMO/PWI : Scientific objectives and performance
- 2006
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In: Advances in Space Research. - : Elsevier. - 0273-1177 .- 1879-1948. ; 38:4, s. 680-685
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Journal article (peer-reviewed)abstract
- SORBET (Spectroscopie des Ondes Radio and du Bruit Electrostatique Thermique) is a radio HF spectrometer designed for the radio and Plasma Waves Instrument onboard BepiColombo/Mercury Magnetospheric Orbiter (MMO), which performs remote and in situ measurements of waves (electromagnetic and electrostatic). Technically, SORBET includes a plasma wave spectrometer, with two E-field inputs from the two perpendicular electric antennas and one B-field input from a search coil, in the range 2.5-640 kHz. This frequency band includes the local gyrofrequency and plasma frequency expected on most part of the MMO orbits. SORBET also includes a higher frequency radio receiver for remote sensing in the range 500 kHz-10.2 MHz. Owing to its capabilities, SORBET will be able to address the following scientific objectives: High resolution mapping(similar to 30 km) of electron density and temperature in the solar wind and in the Hermean magnetosphere and exo-ionosphere, via the technique of Quasi-Thermal Noise (QTN) spectroscopy. These QTN measurements will be determinant for the dynamic modeling of the magnetosphere and will provide a fundamental input for the chemistry of cold ionized species (Na, K, O, . . .) in Mercury's environment. Detection and study of Hermean radio emissions, including possible cyclotron emissions (up to similar to 10-20 kHz) from mildly energetic electrons in most highly magnetized (polar?) regions, and possible synchrotron radiation (up to a few MHz?) from more energetic electrons. Monitoring of solar radio emissions up to similar to 10 MHz in order to create a solar activity index from the view point of Mercury, allowing to correlate it with the Hermean magnetospheric response. We especially discuss the capabilities of SORBET for performing the QTN spectroscopy in Mercury's magnetosphere, using the two electric dipole antennas equipping MMO, called MEFISTO and WPT.
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- Nasr, Amre, et al.
(author)
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Fc gamma receptor IIa (CD32) polymorphism and antibody responses to asexual blood-stage antigens of Plasmodium falciparum malaria in Sudanese patients
- 2007
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In: Scandinavian Journal of Immunology. - Oxford : Blackwell Science. - 0300-9475 .- 1365-3083. ; 66:1, s. 87-96
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Journal article (peer-reviewed)abstract
- In a prospective clinical study in New Halfa Teaching Hospital, the possible association between FcRIIa-R/H131 polymorphism and anti-malarial antibody responses with clinical outcome of Plasmodium falciparum malaria among Sudanese patients was investigated. A total of 256 individuals were consecutively enrolled, comprising 115 patients with severe malaria, 85 with mild malaria and 56 malaria-free controls. Genotyping of FcRIIa-R/H131 dimorphism was performed using gene-specific polymerase chain reaction (PCR) amplification with allele-specific restriction enzyme digestion of the PCR product. The antibody responses to asexual blood-stage antigens were assessed by an enzyme-linked immunosorbent assay. The frequency of the FcRIIa-R/R131 genotype was significantly higher in those with severe malaria when compared with patients with mild malaria, while the FcRIIa-H/H131 genotype showed a significant association with mild malaria. A reduced risk of severe malaria with IgG3 antibodies in combination with the H/H131 genotype was observed. Furthermore, low levels of IgG2 antibodies reactive with the Pf332-C231 antigen were also associated with lower risk of severe malaria in individuals carrying the H131 allele. The levels of IgG1 and IgG3 antibodies were statistically significantly higher in the mild malaria patients when compared with the severe malaria patients. Taken together, our study revealed that the FcRIIa-R/R131 genotype is associated with the development of severe malaria, while the H/H131 genotype is more likely to be associated with mild malaria. Our results also revealed that the natural acquisition of immunity against clinical malaria appeared to be more associated with IgG1 and IgG3 antibodies, signifying their roles in parasite-neutralizing immune mechanisms.
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