Genomic architecture of sickle cell disease clinical variation in children from West Africa : a case-control study design

Contexte : L’anémie falciforme ou drépanocytose est un problème de santé important, particulièrement pour les patients d’origine africaine. La variation phénotypique de l’anémie falciforme est problématique pour le suivi et le traitement des patients. L’architecture génomique responsable de cette variabilité est peu connue. Principe : Mieux saisir la contribution génétique de la variation clinique de cette maladie facilitera l’identification des patients à risque de développer des phénotypes sévères, ainsi que l’adaptation des soins. Objectifs : L’objectif général de cette thèse est de combler les lacunes relatives aux connaissances sur l’épidémiologie génomique de l’anémie falciforme à l’aide d’une cohorte issue au Bénin. Les objectifs spécifiques sont les suivants : 1) caractériser les profils d’expressions génomiques associés à la sévérité de l’anémie falciforme ; 2) identifier des biomarqueurs de la sévérité de l’anémie falciforme ; 3) identifier la régulation génétique des variations transcriptionelles ; 4) identifier des interactions statistiques entre le génotype et le niveau de sévérité associé à l’expression ; 5) identifier des cibles de médicaments pour améliorer l’état des patients atteints d’anémie falciforme. Méthode : Une étude cas-témoins de 250 patients et 61 frères et soeurs non-atteints a été menée au Centre de Prise en charge Médical Intégré du Nourrisson et de la Femme Enceinte atteints de Drépanocytose, au Bénin entre février et décembre 2010. Résultats : Notre analyse a montré que des profils d’expressions sont associés avec la sévérité de l’anémie falciforme. Ces profils sont enrichis de génes des voies biologiques qui contribuent à la progression de la maladie : l’activation plaquettaire, les lymphocytes B, le stress, l’inflammation et la prolifération cellulaire. Des biomarqueurs transcriptionnels ont permis de distinguer les patients ayant des niveaux de sévérité clinique différents. La régulation génétique de la variation de l’expression des gènes a été démontrée et des interactions ont été identifiées. Sur la base de ces résultats génétiques, des cibles de médicaments sont proposées. Conclusion: Ce travail de thèse permet de mieux comprendre l’impact de la génomique sur la sévérité de l’anémie falciforme et ouvre des perspectives de développement de traitements ciblés pour améliorer les soins offerts aux patients.

Studies on the Characteristics of Vertical Circulation and Equatorial Waves using Indian MST Radar

The aim of the present study is to understand the characteristics and properties of different wave modes and the vertical circulation pattern in the troposphere and lower stratosphere over Indian region using data obtained from the Indian Mesosphere-Stratosphere Troposphere (MST) radar, National Center for Environmental Prediction/National Centres of Atmospheric Research (NCEP/NCAR) reanalysed data and radiosonde observations.Studies on the vertical motion in monsoon Hadley circulation are carried out and the results are discussed . From the analysis of MST radar data, an overall picture of vertical motion of air over Indian region is explained and noted that there exists sinking motion both during winter and summer. Besides, the study shows that there is an anomalous northerly wind in the troposphere over the southern peninsular region during southwest monsoon season.The outcome of the study on intrusion of mid-latitude upper tropospheric trough and associated synoptic-scale vertical velocity over the tropical Indian latitudes are reported and discussed . It shows that there is interaction between north Indian latitudes and tropical easterly region, when there is an eastward movement of Western Disturbance across the country. It explains the strengthening of westerlies and a change of winter westerlies into easterlies in the tropical troposphere and lower stratosphere. The divergence field computed over the MST radar station shows intensification in the downward motion in association with the synoptic systems of the northwest Indian region.

Studies on equatorial undercurrent in the indian ocean

This thesis is an outcome of the studies, carried out by the author on the Equatorial Undercurrent and the Equatorial Jet, an interesting and unique phenomenon discovered, recently, in the Indian Ocean (wyrtxi, 1973). The main objective of the thesis is to carry out a detailed investigation of the seasonal, latitudinal and longitudinal variation of the Equatorial Undercurrent in the Indian Ocean and also the Equatorial Jet, through mapping the vertical distribution of the oceanographic properties across the equator along various longitudes for all the months of an year, between SON and SOS, utilising the oceanographic data collected during the International Indian Ocean Expedition and subsequently in the equatorial Indian Ocean. As the distribution of the hydrographic properties give only a qualitative identification of the Undercurrent, a novel technique of computing the zonal flux through bivariate distribution of salinity and thermosteric anomaly introduced by Montgomery and Stroup (1962), is adopted in order to have a quantitative variation of the Equatorial Undercurrent and the Equatorial Jet. Finally, an attempt is made to give a plausible explanation of the features observed.

Mass Transport In The Equatorial Indian Ocean

In the equatorial oceans, the meridional currents are far less energetic than their zonal counterparts. The response of the Equatorial Indian Ocean to the seasonal reversals in the zonal wind field. is quite interesting and unique. A modest attempt, considering the shortcomings in the hydrographic data availability and distribution, is made to evaluate the variability in the zonal transport of mass. in_ both space and time. The peculiarities in its hydrological regime imposed upon by the seasonally varying winds is best appreciated when compared with the quasi permanent circulation characteristics of the Pacific and Atlanti'c.The major features of the tequatorial mass transport is outlined in the introductory chapter of this thesis for the Pacific and Atlantic Mass transport studies in the Indian Ocean, as can be seen from the earlier studies, gis“ the least known and understood, though could have captured the attention of both the experimentalist and the theoretician alike. owing to its complexity. Since in the Indian Ocean, the studies on the zonal mass transport are limited and are confined to the equator only, an attempt has been made to compute the mass transport extending from 5 N to 20 S.

Root-induced increases in soil pH and nutrient availability to field-grown cereals and legumes on acid sandy soils of Sudano-Sahelian West Africa

A field experiment with millet (Pennisetum glaucum L.), sorghum [Sorghum bicolor (L.) Moench], cowpea (Vigna unguiculata L.) and groundnut (Arachnis hypogeae L.) was conducted on severely P-deficient acid sandy soils of Niger, Mali and Burkina Faso to measure changes in pH and nutrient availability as affected by distance from the root surface and by mineral fertiliser application. Treatments included three rates of phosphorus (P) and four levels of nitrogen (N) application. Bulk, rhizosphere and rhizoplane soils were sampled at 35, 45 and 75 DAS in 1997 and at 55 and 65 DAS in 1998. Regardless of the cropping system and level of mineral fertiliser applied, soil pH consistently increased between 0.7 and two units from the bulk soil to the rhizoplane of millet. Similar pH gradients were observed in cowpea, but pH changes were much smaller in sorghum with a difference of only 0.3 units. Shifts in pH led to large increases in nutrient availability close to the roots. Compared with the bulk soil, available P in the rhizoplane was between 190 and 270% higher for P-Bray and between 360 and 600% higher for P-water. Exchangeable calcium (Ca) and magnesium (Mg) levels were also higher in the millet rhizoplane than in the bulk soil, whereas exchangeable aluminium (Al) levels decreased with increasing pH close to the root surface. The results suggest an important role of root-induced pH increases for crops to cope with acidity-induced nutrient deficiency and Al stress of soils in the Sudano-Sahelian zone of West Africa.

Mechanisms of residue mulch-induced cereal growth increases in West Africa

The use of crop residues (CR) has been widely reported as a means of increasing crop yields across West Africa. However, little has been done to compare the magnitude and mechanisms of CR effects systematically in the different agro-ecological zones of the region. To this end, a series of field trials with millet (Pennisetum glaucum L.), sorghum [Sorghum bicolor (L.) Moench], and maize (Zea mays L.) was conducted over a 4-yr period in the Sahelian, Sudanian, and Guinean zones of West Africa. Soils ranged in pH from 4.1 to 5.4 along a rainfall gradient from 510 to 1300 mm. Treatments in the factorial experiments were three CR rates (0,500, and 2000 kg ha^-1)and several levels of phosphorus and nitrogen. The results showed CR-induced total dry matter (TDM) increases in cereals up to 73% for the Sahel compared with a maximum of 16% in the wetter Sudanian and Guinean zones. Residue effects on weakly buffered Sahelian soils were due to improved P availability and to a protection of seedlings against wind erosion. Additional effects of CR mulching on topsoil properties in the Sahel were a decrease in peak temperatures by 4°C and increased water availability. These mulch effects on soil chemical and physical properties strongly decreased from North to South. Likely explanations for this decrease are the decline of dust deposition and wind erosion hazards, the higher soil clay content, lower air temperature, and a faster decomposition rate of mulch material with increasing rainfall from the Sahel to the Sudanian and Guinean zones.

Decomposition of and nutrient release from ruminant manure on acid sandy soils in the Sahelian zone of Niger, West Africa

In ago-pastoral systems of the semi-arid West African Sahel, targeted applications of ruminant manure to the cropland is a widespread practice to maintain soil productivity. However, studies exploring the decomposition and mineralisation processes of manure under farmers' conditions are scarce. The present research in south-west Niger was undertaken to examine the role of micro-organisms and meso-fauna on in situ release rates of nitrogen (N), phosphorus (P) and potassium (K) from cattle and sheep-goat manure collected from village corrals during the rainy season. The results show tha (1) macro-organisms played a dominant role in the initial phase of manure decomposition; (2) manure decomposition was faster on crusted than on sandy soils; (3) throughout the study N and P release rates closely followed the dry matter decomposition; (4) during the first 6 weeks after application the K concentration in the manure declined much faster than N or P. At the applied dry matter rate of 18.8 Mg ha^-1, the quantities of N, P and K released from the manure during the rainy season were up to 10-fold larger than the annual nutrient uptake of pearl millet (Pennisetum glaucum L.), the dominant crop in the traditional agro-pastoral systems. The results indicate considerable nutrient losses with the scarce but heavy rainfalls which could be alleviated by smaller rates of manure application. Those, however, would require a more labour intensive system of corralling or manure distribution.

Efficient phosphorus application strategies for increased crop production in sub-Saharan West Africa

Comparable data are lacking from the range of environments found in sub-Saharan West Africa to draw more general conclusions about the relative merits of locally available rockphosphate (RockP) in alleviating phosphorus (P) constraints to crop growth. To fill this gap, a multi-factorial field experiment was conducted over 4 years at eight locations in Niger, Burkina Faso and Togo. These ranged in annual rainfall from 510 to 1300 mm. Crops grown were pearl millet (Pennisetum glaucum L.), sorghum (Sorghum bicolor (L.) Moench) and maize (Zea mays L.) either continuously or in rotation with cowpea (Vigna unguiculata Walp.) and groundnut (Arachis hypogaea L.). Crops were subjected to six P fertiliser treatments comprising RockP and soluble P at different rates and combined with 0 and 60 kg N ha^-1. For legumes, time trend analyses showed P-induced total dry matter (TDM) increases between 28 and 72% only with groundnut. Similarly, rotation-induced raises in cereal TDM compared to cereal monoculture were only observed with groundnut. For cereals, at the same rate of application, RockP was comparable to single superphosphate (SSP) only at two millet sites with topsoil pH-KCl <4.2 and annual average rainfall >600 mm. Across the eight sites NPK placement at 0.4 g P per hill raised average cereal yields between 26 and 220%. This was confirmed in 119 on-farm trials revealing P placement as a promising strategy to overcome P deficiency as the regionally most growth limiting nutrient constraint to cereals.

Causes of legume-rotation effects in increasing cereal yields across the Sudanian, Sahelian and Guinean zone of West Africa

On-farm experiments and pot trials were conducted on eight West African soils to explore the mechanisms governing the often reported legume rotation-induced cereal growth increases in this region. Crops comprised pearl millet (Pennisetum glaucum L.), sorghum (Sorghum bicolor Moench), maize (Zea mays L.), cowpea (Vigna unguiculata Walp.) and groundnut (Arachis hypogaea L.). In groundnut trials the observed 26 to 85% increases in total dry matter (TDM) of rotation cereals (RC) compared with continuous cereals (CC) in the 4th year appeared to be triggered by site- and crop-specific early season differences in nematode infestation (up to 6-fold lower in RC than in CC), enhanced Nmin and a 7% increase in mycorrhizal (AM) infection. In cowpea trials yield effects on millet and differences in nematode numbers, Nmin and AM were much smaller. Rhizosphere studies indicated effects on pH and acid phosphatase activity as secondary causes for the observed growth differences between RC and CC. In the study region legume-rotation effects on cereals seemed to depend on the capability of the legume to suppress nematodes and to enhance early N and P availability for the subsequent cereal.

Soil organic carbon management for sustainable land use in Sudano-Sahelian West Africa

Judged by their negative nutrient balances, low soil cover and low productivity, the predominant agro-pastoral farming systems in the Sudano-Sahelian zone of West Africa are highly unsustainable for crop production intensification. With kaolinite as the main clay type, the cation exchange capacity of the soils in this region, often less than 1 cmol_c kg^-1 soil, depends heavily on the organic carbon (Corg) content. However, due to low carbon sequestration and to the microbe, termite and temperature-induced rapid turnover rates of organic material in the present land-use systems, Corg contents of the topsoil are very low, ranging between 1 and 8 g kg^-1 in most soils. For sustainable food production, the availability of phosphorus (P) and nitrogen (N) has to be increased considerably in combination with an improvement in soil physical properties. Therefore, the adoption of innovative management options that help to stop or even reverse the decline in Corg typically observed after cultivating bush or rangeland is of utmost importance. To maintain food production for a rapidly growing population, targeted applications of mineral fertilisers and the effective recycling of organic amendments as crop residues and manure are essential. Any increase in soil cover has large effects in reducing topsoil erosion by wind and water and favours the accumulation of wind-blown dust high in bases which in turn improves P availability. In the future decision support systems, based on GIS, modelling and simulation should be used to combine (i) available fertiliser response data from on-station and on-farm research, (ii) results on soil productivity restoration with the application of mineral and organic amendments and (iii) our present understanding of the cause-effect relationships governing the prevailing soil degradation processes. This will help to predict the effectiveness of regionally differentiated soil fertility management approaches to maintain or even increase soil Corg levels.

Multi-site time-trend analysis of soil fertility management effects on crop production in sub-Saharan West Africa

Soil fertility constraints to crop production have been recognized widely as a major obstacle to food security and agro-ecosystem sustainability in sub-Saharan West Africa. As such, they have led to a multitude of research projects and policy debates on how best they should be overcome. Conclusions, based on long-term multi-site experiments, are lacking with respect to a regional assessment of phosphorus and nitrogen fertilizer effects, surface mulched crop residues, and legume rotations on total dry matter of cereals in this region. A mixed model time-trend analysis was used to investigate the effects of four nitrogen and phosphorus rates, annually applied crop residue dry matter at 500 and 2000 kg ha^-1, and cereal-legume rotation versus continuous cereal cropping on the total dry matter of cereals and legumes. The multi-factorial experiment was conducted over four years at eight locations, with annual rainfall ranging from 510 to 1300 mm, in Niger, Burkina Faso, and Togo. With the exception of phosphorus, treatment effects on legume growth were marginal. At most locations, except for typical Sudanian sites with very low base saturation and high rainfall, phosphorus effects on cereal total dry matter were much lower with rock phosphate than with soluble phosphorus, unless the rock phosphate was combined with an annual seed-placement of 4 kg ha^-1 phosphorus. Across all other treatments, nitrogen effects were negligible at 500 mm annual rainfall but at 900 mm, the highest nitrogen rate led to total dry matter increases of up to 77% and, at 1300 mm, to 183%. Mulch-induced increases in cereal total dry matter were larger with lower base saturation, reaching 45% on typical acid sandy Sahelian soils. Legume rotation effects tended to increase over time but were strongly species-dependent.

Identifying the component structure of job satisfaction by principal components analysis among extension officers in North West Province, South Africa

The component structure of a 34-item scale measuring different aspects of job satisfaction was investigated among extension officers in North West Province, South Africa. A simple random sampling technique was used to select 40 extension officers from which data were collected. A structured questionnaire consisting of 34 job satisfaction and 10 personal characteristic items was administered to the extension officers. Items on job satisfaction were measured at interval level and analyzedwith Principal ComponentAnalysis. Most of the respondents (82.5%) weremales, between 40 to 45 years, 85% were married and 87.5% had a diploma as their educational qualification. Furthermore, 54% of the households size between 4 to 6 persons, whereas 75% were Christians. The majority of the extension officers lived in their job area (82.5), while 80% covered at least 3 communities and 3 farmer groups. In terms of number of farmers covered, only 40% of the extension officers covered more than 500 farmers and 45% travelled more than 40 km to reach their farmers. From the job satisfaction items 9 components were extracted to show areas for job satisfaction among extension officers. These were in-service training, research policies, communicating recommended practices, financial support for self and family, quality of technical help, opportunity to advance education, management and control of operations, rewarding system and sanctions. The results have several implications for motivating extension officers for high job performance especially with large number of clients and small number of extension agents.