Population genetics of Glossina palpalis palpalis from central African sleeping sickness foci

<p>Abstract</p> <p>Background</p> <p><it>Glossina palpalis palpalis </it>(Diptera: Glossinidae) is widespread in west Africa, and is the main vector of sleeping sickness in Cameroon as well as in the Bas Congo Province of the Democratic Republic of Congo. However, little is known on the structure of its populations. We investigated <it>G. p. palpalis </it>population genetic structure in five sleeping sickness foci (four in Cameroon, one in Democratic Republic of Congo) using eight microsatellite DNA markers.</p> <p>Results</p> <p>A strong isolation by distance explains most of the population structure observed in our sampling sites of Cameroon and DRC. The populations here are composed of panmictic subpopulations occupying fairly wide zones with a very strong isolation by distance. Effective population sizes are probably between 20 and 300 individuals and if we assume densities between 120 and 2000 individuals per km², dispersal distance between reproducing adults and their parents extends between 60 and 300 meters.</p> <p>Conclusions</p> <p>This first investigation of population genetic structure of <it>G. p. palpalis </it>in Central Africa has evidenced random mating subpopulations over fairly large areas and is thus at variance with that found in West African populations of <it>G. p. palpalis</it>. This study brings new information on the isolation by distance at a macrogeographic scale which in turn brings useful information on how to organise regional tsetse control. Future investigations should be directed at temporal sampling to have more accurate measures of demographic parameters in order to help vector control decision.</p

Principles guiding embryo selection following genome-wide haplotyping of preimplantation embryos.

STUDY QUESTION How to select and prioritize embryos during PGD following genome-wide haplotyping? SUMMARY ANSWER In addition to genetic disease-specific information, the embryo selected for transfer is based on ranking criteria including the existence of mitotic and/or meiotic aneuploidies, but not carriership of mutations causing recessive disorders. WHAT IS KNOWN ALREADY Embryo selection for monogenic diseases has been mainly performed using targeted disease-specific assays. Recently, these targeted approaches are being complemented by generic genome-wide genetic analysis methods such as karyomapping or haplarithmisis, which are based on genomic haplotype reconstruction of cell(s) biopsied from embryos. This provides not only information about the inheritance of Mendelian disease alleles but also about numerical and structural chromosome anomalies and haplotypes genome-wide. Reflections on how to use this information in the diagnostic laboratory are lacking. STUDY DESIGN, SIZE, DURATION We present the results of the first 101 PGD cycles (373 embryos) using haplarithmisis, performed in the Centre for Human Genetics, UZ Leuven. The questions raised were addressed by a multidisciplinary team of clinical geneticist, fertility specialists and ethicists. PARTICIPANTS/MATERIALS, SETTING, METHODS Sixty-three couples enrolled in the genome-wide haplotyping-based PGD program. Families presented with either inherited genetic variants causing known disorders and/or chromosomal rearrangements that could lead to unbalanced translocations in the offspring. MAIN RESULTS AND THE ROLE OF CHANCE Embryos were selected based on the absence or presence of the disease allele, a trisomy or other chromosomal abnormality leading to known developmental disorders. In addition, morphologically normal Day 5 embryos were prioritized for transfer based on the presence of other chromosomal imbalances and/or carrier information. LIMITATIONS, REASONS FOR CAUTION Some of the choices made and principles put forward are specific for cleavage-stage-based genetic testing. The proposed guidelines are subject to continuous update based on the accumulating knowledge from the implementation of genome-wide methods for PGD in many different centers world-wide as well as the results of ongoing scientific research. WIDER IMPLICATIONS OF THE FINDINGS Our embryo selection principles have a profound impact on the organization of PGD operations and on the information that is transferred among the genetic unit, the fertility clinic and the patients. These principles are also important for the organization of pre- and post-counseling and influence the interpretation and reporting of preimplantation genotyping results. As novel genome-wide approaches for embryo selection are revolutionizing the field of reproductive genetics, national and international discussions to set general guidelines are warranted. STUDY FUNDING/COMPETING INTEREST(S) The European Union's Research and Innovation funding programs FP7-PEOPLE-2012-IAPP SARM: 324509 and Horizon 2020 WIDENLIFE: 692065 to J.R.V., T.V., E.D. and M.Z.E. J.R.V., T.V. and M.Z.E. have patents ZL910050-PCT/EP2011/060211-WO/2011/157846 (‘Methods for haplotyping single cells’) with royalties paid and ZL913096-PCT/EP2014/068315-WO/2015/028576 (‘Haplotyping and copy-number typing using polymorphic variant allelic frequencies’) with royalties paid, licensed to Cartagenia (Agilent technologies). J.R.V. also has a patent ZL91 2076-PCT/EP20 one 3/070858 (‘High throughout genotyping by sequencing’) with royalties paid

Circadian rhythms regulate the environmental responses of net CO2 exchange in bean and cotton canopies

Studies on the dependence of the rates of ecosystem gas exchange on environmental parameters often rely on the up-scaling of leaf-level response curves ('bottom-up' approach), and/or the down-scaling of ecosystem fluxes ('top-down' approach), where one takes advantage of the natural diurnal covariation between the parameter of interest and photosynthesis rates. Partly independent from environmental variation, molecular circadian clocks drive ∼24 h oscillations in leaf-level photosynthesis, stomatal conductance and other physiological processes in plants under controlled laboratory conditions. If present and of sufficient magnitude at ecosystem scales, circadian regulation could lead to different results when using the bottom-up approach (where circadian regulation exerts a negligible influence over fluxes because the environment is modified rapidly) relative to the top-down approach (where circadian regulation could affect fluxes as it requires the passage of a few hours). Here we dissected the drivers of diurnal net CO2 exchange in canopies of an annual herb (bean) and of a perennial shrub (cotton) through a set of experimental manipulations to test for the importance of circadian regulation of net canopy CO2 exchange, relative to that of temperature and vapor pressure deficit, and to understand whether circadian regulation could affect the derivation of environmental flux dependencies. Contrary to conventional wisdom, we observed how circadian regulation exerted controls over net CO2 exchange that were of similar magnitude to the controls exerted by direct physiological responses to temperature and vapor pressure deficit. Diurnal patterns of net CO2 exchange could only be explained by considering effects of environmental responses combined with circadian effects. Consequently, we observed significantly different results when inferring the dependence of photosynthesis over temperature and vapor pressure deficit when using the top-down and the bottom up approaches.We remain indebted to E. Gerardeau, D. Dessauw, J. Jean, P. Prudent (Aïda CIRAD), J.-J. Drevon, C. Pernot (Eco&Sol INRA), B. Buatois, A. Rocheteau (CEFE CNRS), A. Pra, A. Mokhtar and the full Ecotron team, in particular C. Escape, for outstanding technical assistance during experiment set-up, plant cultivation and measurements. Earlier versions of the manuscript benefitted from comments by M. Dietze, B. Medlyn, R. Duursma and Y.-S. Lin. This study benefited from the CNRS human and technical resources allocated to the ECOTRONS Research Infrastructures as well as from the state allocation ‘Investissement d'Avenir’ ANR-11-INBS-0001, ExpeER Transnational Access program, Ramón y Cajal fellowships (RYC-2012-10970 to VRD and RYC-2008-02050 to JPF), the Erasmus Mundus Master Course Mediterranean Forestry and Natural Resources Management (MEDfOR) and internal grants from UWS-HIE to VRD and ZALF to AG. We thank the Associate Editor T. Vesala and two anonymous reviewers for their help to improve this manuscript

A group-galaxy cross-correlation function analysis in zCOSMOS

We present a group-galaxy cross-correlation analysis using a group catalog produced from the 16,500 spectra from the optical zCOSMOS galaxy survey. Our aim is to perform a consistency test in the redshift range 0.2 < z < 0.8 between the clustering strength of the groups and mass estimates that are based on the richness of the groups. We measure the linear bias of the groups by means of a group-galaxy cross-correlation analysis and convert it into mass using the bias-mass relation for a given cosmology, checking the systematic errors using realistic group and galaxy mock catalogs. The measured bias for the zCOSMOS groups increases with group richness as expected by the theory of cosmic structure formation and yields masses that are reasonably consistent with the masses estimated from the richness directly, considering the scatter that is obtained from the 24 mock catalogs. An exception are the richest groups at high redshift (estimated to be more massive than 10^13.5 M_sun), for which the measured bias is significantly larger than for any of the 24 mock catalogs (corresponding to a 3-sigma effect), which is attributed to the extremely large structure that is present in the COSMOS field at z ~ 0.7. Our results are in general agreement with previous studies that reported unusually strong clustering in the COSMOS field.Comment: 13 pages, 9 figures, published in Ap

The majority of autosomal recessive nanophthalmos and posterior microphthalmia can be attributed to biallelic sequence and structural variants in MFRP and PRSS56

This study aimed to genetically and clinically characterize a unique cohort of 25 individuals from 21 unrelated families with autosomal recessive nanophthalmos (NNO) and posterior microphthalmia (MCOP) from diferent ethnicities. An ophthalmological assessment in all families was followed by targeted MFRP and PRSS56 testing in 20 families and whole-genome sequencing in one family. Three families underwent homozygosity mapping using SNP arrays. Eight distinct MFRP mutations were found in 10/21 families (47.6%), fve of which are novel including a deletion spanning the 5′ untranslated region and the frst coding part of exon 1. Most cases harbored homozygous mutations (8/10), while a compound heterozygous and a monoallelic genotype were identifed in the remaining ones (2/10). Six distinct PRSS56 mutations were found in 9/21 (42.9%) families, three of which are novel. Similarly, homozygous mutations were found in all but one, leaving 2/21 families (9.5%) without a molecular diagnosis. Clinically, all patients had reduced visual acuity, hyperopia, short axial length and crowded optic discs. Retinitis pigmentosa was observed in 5/10 (50%) of the MFRP group, papillomacular folds in 12/19 (63.2%) of MCOP and in 3/6 (50%) of NNO cases. A considerable phenotypic variability was observed, with no clear genotype-phenotype correlations. Overall, our study represents the largest NNO and MCOP cohort reported to date and provides a genetic diagnosis in 19/21 families (90.5%), including the frst MFRP genomic rearrangement, ofering opportunities for gene-based therapies in MFRP-associated disease. Finally, our study underscores the importance of sequence and copy number analysis of the MFRP and PRSS56 genes in MCOP and NNO

zCOSMOS 20k: Satellite galaxies are the main drivers of environmental effects in the galaxy population at least to z~0.7

We explore the role of environment in the evolution of galaxies over 0.1<z<0.7 using the final zCOSMOS-bright data set. Using the red fraction of galaxies as a proxy for the quenched population, we find that the fraction of red galaxies increases with the environmental overdensity and with the stellar mass, consistent with previous works. As at lower redshift, the red fraction appears to be separable in mass and environment, suggesting the action of two processes: mass and environmental quenching. The parameters describing these appear to be essentially the same at z~0.7 as locally. We explore the relation between red fraction, mass and environment also for the central and satellite galaxies separately, paying close attention to the effects of impurities in the central-satellite classification and using carefully constructed samples matched in stellar mass. There is little evidence for a dependence of the red fraction of centrals on overdensity. Satellites are consistently redder at all overdensities, and the satellite quenching efficiency increases with overdensity at 0.1<z<0.4. This is less marked at higher redshift, but both are nevertheless consistent with the equivalent local measurements. At a given stellar mass, the fraction of galaxies that are satellites also increases with the overdensity. At a given overdensity and mass, the obtained relation between the environmental quenching and the satellite fraction agrees well with the satellite quenching efficiency, demonstrating that the environmental quenching in the overall population is consistent with being entirely produced through the satellite quenching process at least up to z=0.7. However, despite the unprecedented size of our high redshift samples, the associated statistical uncertainties are still significant and our statements should be understood as approximations to physical reality, rather than physically exact formulae.Comment: 22 pages, 19 figures, submitted to MNRA

Extreme emission-line galaxies out to z∼\sim1 in zCOSMOS. I. Sample and characterization of global properties

We present a thorough characterization of a large sample of 183 extreme emission-line galaxies (EELGs) at redshift 0.11 < z < 0.93 selected from the 20k zCOSMOS Bright Survey because of their unusually large emission line equivalent widths. We use multiwavelength COSMOS photometry, HST-ACS I-band imaging and optical zCOSMOS spectroscopy to derive the main global properties of EELGs, such as sizes, masses, SFRs, reliable metallicities from both "direct" and "strong-line" methods. The EELGs are compact (R_50 ~ 1.3 kpc), low-mass (log(M*/Msol)~7-10) galaxies forming stars at unusually high specific SFR (log(sSFR/yr) up to ~ -7) compared to main sequence SFGs of the same stellar mass and redshift. At UV wavelengths, the EELGs are luminous and show high surface brightness and include strong Ly$\alpha$ emitters, as revealed by GALEX spectroscopy. We show that zCOSMOS EELGs are high-ionization, low-metallicity systems, with median 12+log(O/H)=8.16, including a handful of extremely metal-deficient galaxies (<10% solar). While ~80% of the EELGs show non-axisymmetric morphologies, including clumpy and tadpole galaxies, we find that ~29% of them show additional low surface-brightness features, which strongly suggest recent or ongoing interactions. As star-forming dwarfs in the local Universe, EELGs are most often found in relative isolation. While only very few EELGs belong to compact groups, almost one third of them are found in spectroscopically confirmed loose pairs or triplets. We conclude that EELGs are galaxies caught in a transient and probably early period of their evolution, where they are efficiently building-up a significant fraction of their present-day stellar mass in an ongoing galaxy-wide starburst. Therefore, the EELGs constitute an ideal benchmark for comparison studies between low- and high-redshift low-mass star-forming galaxies.Comment: Accepted in A&A. Final replacement to match the version in press. It includes a minor change in the title and a new figur

The VIMOS-VLT Deep Survey: Evolution in the Halo Occupation Number since z ∼\sim 1

We model the evolution of the mean galaxy occupation of dark-matter halos over the range $0.1<z<1.3$, using the data from the VIMOS-VLT Deep Survey (VVDS). The galaxy projected correlation function $w_p(r_p)$ was computed for a set of luminosity-limited subsamples and fits to its shape were obtained using two variants of Halo Occupation Distribution models. These provide us with a set of best-fitting parameters, from which we obtain the average mass of a halo and average number of galaxies per halo. We find that after accounting for the evolution in luminosity and assuming that we are largely following the same population, the underlying dark matter halo shows a growth in mass with decreasing redshift as expected in a hierarchical structure formation scenario. Using two different HOD models, we see that the halo mass grows by 90% over the redshift interval z=[0.5,1.0]. This is the first time the evolution in halo mass at high redshifts has been obtained from a single data survey and it follows the simple form seen in N-body simulations with $M(z) = M_0 e^{-\beta z}$, and $\beta = 1.3 \pm 0.30$. This provides evidence for a rapid accretion phase of massive halos having a present-day mass $M_0 \sim 10^{13.5} h^{-1} M_\odot$, with a $m > 0.1 M_0$ merger event occuring between redshifts of 0.5 and 1.0. Futhermore, we find that more luminous galaxies are found to occupy more massive halos irrespectively of the redshift. Finally, the average number of galaxies per halo shows little increase from redshift z$\sim$ 1.0 to z$\sim$ 0.5, with a sharp increase by a factor $\sim$3 from z$\sim$ 0.5 to z$\sim$ 0.1, likely due to the dynamical friction of subhalos within their host halos.Comment: 14 pages, 6 figures, 5 tables. MNRAS accepted