Concordance of gene genealogies reveals reproductive isolation in the pathogenic fungus Coccidioides immitis

Simple cladogenetic theory suggests that gene genealogies can be used to detect mixis in a population and delineate reproductively isolated groups within sexual taxa. We have taken this approach in a study of Coccidioides immitis, an ascomycete fungus responsible for a recent epidemic of coccidioidomycosis (Valley fever) in California. To test whether this fungus represents a single sexual species throughout its entire geographic range, we have compared genealogies from fragments of five nuclear genes. The five genealogies show multiple incompatibilities indicative of sex, but also share a branch that partitions the isolates into two reproductively isolated taxa, one centered in California and the other outside California. We conclude that coccidioidomycosis can be caused by two distinct noninterbreeding taxa. This result should aid the future study of the disease and illustrates the utility of the genealogical approach in population genetics.

Molecular markers reveal cryptic sex in the human pathogen Coccidioides immitis.

Coccidioides immitis, cause of a recent epidemic of "Valley fever" in California, is typical of many eukaryotic microbes in that mating and meiosis have yet to be reported, but it is not clear whether sex is truly absent or just cryptic. To find out, we have undertaken a population genetic study using PCR amplification, screening for single-strand conformation polymorphisms, and direct DNA sequencing to find molecular markers with nucleotide-level resolution. Both population genetic and phylogenetic analyses indicate that C. immitis is almost completely recombining. To our knowledge, this study is the first to find molecular evidence for recombination in a fungus for which no sexual stage has yet been described. These results motivate a directed search for mating and meiosis and illustrate the utility of single-strand conformation polymorphism and sequencing with arbitrary primer pairs in molecular population genetics.

Compositional and Geochemical Signatures for the Sedimentary Evolution of the Middle Triassic–Lower Jurassic Continental Redbeds from Western-Central Mediterranean Alpine Chains

Compositional and chemical analyses suggest that Middle Triassic–Lower Liassic continental redbeds (in the internal domains of the Betic, Maghrebian, and Apenninic chains) can be considered a regional lithosome marking the Triassic-Jurassic rift-valley stage of Tethyan rifting, which led to the Pangaea breakup and subsequent development of a mosaic of plates and microplates. Sandstones are quartzose to quartzolithic and represent a provenance of continental block and recycled orogen, made up mainly of Paleozoic metasedimentary rocks similar to those underlying the redbeds. Mudrocks display K enrichments; intense paleoweathering under a hot, episodically humid climate with a prolonged dry season; and sediment recycling. Redbeds experienced temperatures in the range of 100°–160°C and lithostatic/tectonic loading of more than 4 km. These redbeds represent an important stratigraphic signature to reconstruct a continental block (Mesomediterranean Microplate) that separated different realms of the western Tethys from Middle-Late Jurassic to Miocene, when it was completely involved in Alpine orogenesis.

Abandoned and forgotten: the sad story of Kenya's internally displaced persons

This documentary is about the internal displacement of ethnic minorities brought about by politically instigated post-election violence towards ethnic minorities in all eight provinces, namely, Coast, Rift Valley, Western, Eastern, North Eastern, Central Kenya, Nairobi, and Nyanza. During the years of 1991 to 1996, over 15,000 people died and almost 300,000 were displaced in the Rift Valley, Central, Nyanza and Western provinces. Before the 1997 elections, violence erupted. Again, following the disputed presidential elections in December 2007 politically and ethnically instigated displacements resulted in human rights violations against 600,000 people in 8 provinces of Kenya.

Chemistry of very young basalts from ODP Hole 106-648B

Basalts in Hole 648B, located in the rift valley of the Mid-Atlantic Ridge at 23°N in crust estimated to be less than 100,000 years old, are mainly fresh, but small amounts of secondary phases are found on fracture surfaces and in alteration halos within the rocks. The halos are defined by dark bands 1-4 mm thick that have developed parallel to fracture surfaces or pillow margins and which in some cases have migrated some centimeters into the rock. The dark bands are the principal locus of secondary phases. The secondary phases are olive-green and yellow protoceladonites, of composition and structure intermediate between celadonite and iron-rich saponite, red (Mn-poor) to opaque (Mn-rich) iron oxyhydroxides, mixtures of protoceladonite and iron oxyhydroxide, and rare manganese oxides. These phases occur mainly as linings or fillings of open spaces in the basalt within the dark bands. Sulfides and intersertal glass are the only primary phases that can be seen to have been altered. Where dark bands have migrated into the rock, the rock behind the advancing band is almost devoid of secondary phases, implying redissolution. The potassium and magnesium in the secondary phases could have been supplied from ambient seawater. The aluminum in the protoceladonites must have been derived from local reaction of intergranular glass. The source of iron and silica could have been intergranular glass or low temperature mineralizing solutions of the type responsible for the formation of deposits of manganese oxides and iron oxyhydroxides and silicates on the seafloor.

(Table 1) Distribution of planktic foraminifera in sediments from Core AMK4-410GC

Sediments in 36 cores recovered from the rift zone of the Reykjanes Ridge were dated on the basis of planktic foraminifera. Their ratios in samples were used to determine temperature of the water surface layer during the last glaciation. Benthic foraminifera were studied in 12 samples of surface sediments and in five cores, and conclusions made on changes in the bottom water layer from changes in composition of these benthic foraminifera.

Age of bottom sediments from the South Atlantic Rise as indicated by 14C data for stations of R/V Professor Shtokman

Sedimentation of pelagic biogenic coccolithic-foraminiferal sediments predominates in the section of the South Atlantic ridge between 20° and 30°S. Sedimentation rate and thickness of Late Quaternary sediments differ in the rift valley, the crestal section of the ridge, its flanks and transform faults. Holocene and layers representing the most recent and pen¬ultimate continental glaciations and the last interglacial are distinguishable in the late Quaternary profile. During their development, changes in the mean annual sea surface temperature in the tropical zone of the South Atlantic were minimal, i.e. 1-2°C.

The Political Economy of Climate Adaptation and Environmental Health: The Case of Ethiopia

The environment affects our health, livelihoods, and the social and political institutions within which we interact. Indeed, nearly a quarter of the global disease burden is attributed to environmental factors, and many of these factors are exacerbated by global climate change. Thus, the central research question of this dissertation is: How do people cope with and adapt to uncertainty, complexity, and change of environmental and health conditions? Specifically, I ask how institutional factors, risk aversion, and behaviors affect environmental health outcomes. I further assess the role of social capital in climate adaptation, and specifically compare individual and collective adaptation. I then analyze how policy develops accounting for both adaptation to the effects of climate and mitigation of climate-changing emissions. In order to empirically test the relationships between these variables at multiple levels, I combine multiple methods, including semi-structured interviews, surveys, and field experiments, along with health and water quality data. This dissertation uses the case of Ethiopia, Africa’s second-most populous nation, which has a large rural population and is considered very vulnerable to climate change. My fieldwork included interviews and institutional data collection at the national level, and a three-year study (2012-2014) of approximately 400 households in 20 villages in the Ethiopian Rift Valley. I evaluate the theoretical relationships between households, communities, and government in the process of adaptation to environmental stresses. Through my analyses, I demonstrate that water source choice varies by individual risk aversion and institutional context, which ultimately has implications for environmental health outcomes. I show that qualitative measures of trust predict cooperation in adaptation, consistent with social capital theory, but that measures of trust are negatively related with private adaptation by the individual. Finally, I describe how Ethiopia had some unique characteristics, significantly reinforced by international actors, that led to the development of an extensive climate policy, and yet with some challenges remaining for implementation. These results suggest a potential for adaptation through the interactions among individuals, communities, and government in the search for transformative processes when confronting environmental threats and climate change.

Geochemistry of ODP Hole 176-735B igneous and hydrothermal veins

During Legs 118 and 176, Ocean Drilling Program Hole 735B, located on Atlantis Bank on the Southwest Indian Ridge, was drilled to a total depth of 1508 meters below seafloor (mbsf) with nearly 87% recovery. The recovered core provides a unique section of oceanic Layer 3 produced at an ultraslow spreading ridge. Metamorphism and alteration are extensive in the section but decrease markedly downward. Both magmatic and hydrothermal veins are present in the core, and these were active conduits for melt and fluid in the crust. We have identified seven major types of veins in the core: felsic and plagioclase rich, plagioclase + amphibole, amphibole, diopside and diopside + plagioclase, smectite ± prehnite ± carbonate, zeolite ± prehnite ± carbonate, and carbonate. A few epidote and chlorite veins are also present but are volumetrically insignificant. Amphibole veins are most abundant in the upper 50 m of the core and disappear entirely below 520 mbsf. Felsic and plagioclase ± amphibole ± diopside veins dominate between ~50 and 800 mbsf, and low-temperature smectite, zeolite, and prehnite veins are present in the lower 500 m of the core. Carbonate veinlets are randomly present throughout the core but are most abundant in the lower portions. The amphibole veins are closely associated with zones of intense crystal plastic deformation formed at the brittle/ductile boundary at temperatures above 700°C. The felsic and plagioclase-rich veins were formed originally by late magmatic fluids at temperatures above 800°C, but nearly all of these have been overprinted by intense hydrothermal alteration at temperatures between 300° and 600°C. The zeolite, prehnite, and smectite veins formed at temperatures <100°C. The chemistry of the felsic veins closely reflects their dominant minerals, chiefly plagioclase and amphibole. The plagioclase is highly zoned with cores of calcic andesine and rims of sodic oligoclase or albite. In the felsic veins the amphibole ranges from magnesio-hornblende to actinolite or ferro-actinolite, whereas in the monomineralic amphibole veins it is largely edenite and magnesio-hornblende. Diopside has a very narrow range of composition but does exhibit some zoning in Fe and Mg. The felsic and plagioclase-rich veins were originally intruded during brittle fracture at the ridge crest. The monomineralic amphibole veins also formed near the ridge axis during detachment faulting at a time of low magmatic activity. The overprinting of the igneous veins and the formation of the hydrothermal veins occurred as the crustal section migrated across the floor of the rift valley over a period of ~500,000 yr. The late-stage, low-temperature veins were deposited as the section migrated out of the rift valley and into the transverse ridge along the margin of the fracture zone.

(Supplement Table1) Abundances of major elements from KH93-3_DR10 at the Southwest Indian Ridge near the Rodriguez Triple Junction

Petrographic and geochemical analyses of basaltic rocks dredged from the first segment of the Southwest Indian Ridge near the Rodriguez Triple Junction have been completed in order to investigate water-rock interaction processes during mid-ocean ridge (MOR) hydrothermal alteration in the Indian Ocean. In the study area, we have successfully recovered a serial section of upper oceanic crust exposed along a steep rift valley wall which was uplifted and emplaced along a low angle normal fault. On the basis of microscopic observation, dredged samples are classified into three types: fresh lavas, low-temperature altered rocks, and high-temperature altered rocks. The fresh lavas have essentially the same chemical composition as typical N-MORB, although LILE and Nb are slightly enriched and depleted, respectively. Low temperature alteration brought about the enrichment of K2O, Rb, and U due to the presence of K-rich celadonite and U-adsorption onto Fe-oxyhydroxide and clay minerals. On the other hand, chloritization, albitization, and addition of base metals by high temperature hydrothermal alteration result in enrichments of MnO, MgO, Na2O, Cu, and Zn and depletions of CaO, K2O, Cr, Co, Ni, Rb, Sr, and Ba. In addition, U-enrichment is also observable in the high temperature altered rocks probably due to the decrease of uranite solubility in the reducing high-temperature hydrothermal solution. These petrological and geochemical features are comparable to those of the volcanic zone to transition zone rocks in the DSDP/ODP Hole 504B, indicating that our samples were recovered from the upper ~1000 m section of the oceanic crust. Only the alteration minerals related to off-axis alteration are absent in our samples dredged from near the spreading axis. The similarity of alteration between our samples from the Indian Ocean and the Hole 504B rocks from the Pacific Ocean suggests that MOR hydrothermal systems are probably similar across all world oceans.

Lake Albert fisheries resources and their management strategy

Lake Albert/Mobutu lies along the Zaire-Uganda border in 43/57 per cent ratio in the faulted depression tending south-west to the north east. It is bounded by latitudes 1o0 n to 2o 20’ N and longitudes 30o 20’ to 31o 20’E. It has a width varying from 35 to 45 km (22 to 28 miles) as measured between the scarps at the lake level. It covers an area of 5600km2 and has a maximum depth of 48m. The major inflow is through the Semiliki, an outflow of Lake Edward, Muzizi and Victoria Nile draining lakes Victoria and Kyoga while the Albert Nile is the outflow. The physical, chemical and biological productivity parameters are summarized in Table 1. The scarp is steep but not sheer and there are at least 4 tracks leading down it to villages on the shore and scarp land scarp is a young one, formed as a result of earth movements of the Pleistocene times, and the numerous streams come down headlong down its thousand feet drop, more often than not in falls (Baker, 1954). Sometimes there appears to be a clean fault; and at other places there is the appearrence of step faulting, although this may be of only a superical nature .The escarpment’s composed of rocks belonging to the pre-Cambrian Basement complex of the content; but the floor of the depression is covered with young sedimentary rocks, known as kaiso beds. In their upper part these latter beds contains many pebbles; whilst low down the occurrence fossiliferous beds is sufficiently rare phenomenon in the interior plateau of Africa. The kaiso beds dated as possibly middle Pleistocene in age, are exposed in various flats on the shore, and they presumably extend under the relatively shallow waters of the lake. A feature of the shore is the development of sandpits and the enclosure of lagoons; and these can be observed in various stages of development at kaiso, Tonya, kibiro, Buhuka and above all, at Butiaba. On an island lake over 1100 km (700 miles) from the shores of the Indian Ocean one can thus study some of the shore-line phenomena usually associated with the sea- coast (Worthington, 1929). In the north, from Butiaba onwards, the flats become wider and from a continuous lowland as the lake shore curves away from the straight edge of the escarpment. At a height of just 610m (2000 feet) above sea-level, the rift valley floor at Butiaba has a mean annual temperature of 25.60c (780 f), from which there is virtually no seasonal variation; and and the mean daily range is only 6.50c (130f) (E.Afr. met. Dept.1953). With a mean annual rainfall of not much more than 762mm (309 inches) and only 92 rain days in ayear, again to judge from Butiaba, conditions in the rift valley are semi-arid; and the vegetation cover consists of grasses and scattered drought-resisting trees and bushes. Only near the stream courses does the vegetation thicken.

The Southeast Indian Ridge between 88°E and 118°E: Variations in crustal accretion at constant spreading rate

The temperature of the mantle and the rate of melt production are parameters which play important roles in controlling the style of crustal accretion along mid-ocean ridges. To investigate the variability in crustal accretion that develops in response to variations in mantle temperature, we have conducted a geophysical investigation of the Southeast Indian Ridge (SEIR) between the Amsterdam hotspot and the Australian-Antarctic Discordance (88 degrees E-118 degrees E). The spreading center deepens by 2100 m from west to east within the study area. Despite a uniform, intermediate spreading rate (69-75 mm yr-l), the SEIR exhibits the range in axial morphology displayed by the East Pacific Rise and the Mid-Atlantic Ridge (MAR) and usually associated with variations in spreading rate. The spreading center is characterized by an axial high west of 102 degrees 45'E, whereas an axial valley is prevalent east of this longitude. Both the deepening of the ridge axis and the general evolution of axial morphology from an axial high to a rift valley are not uniform. A region of intermediate morphology separates axial highs and MAR-like rift valleys. Local transitions in axial morphology occur in three areas along the ridge axis. The increase in axial depth toward the Australian-Antarctic Discordance may be explained by the thinning of the oceanic crust by similar to 4 km and the change in axial topography. The long-wavelength changes observed along the SEIR can be attributed to a gradient in mantle temperature between regions influenced by the Amsterdam and Kerguelen hot spots and the Australian-Antarctic Discordance. However, local processes, perhaps associated with an heterogeneous mantle or along-axis asthenospheric flow, may give rise to local transitions in axial topography and depth anomalies.

Hydrothermal-vent alvinellid polychaete dispersal in the eastern Pacific .1. Influence of vent site distribution, bottom currents, and biological patterns

Deep-sea hydrothermal-vent habitats are typically linear, discontinuous, and short-lived. Some of the vent fauna such as the endemic polychaete family Alvinellidae are thought to lack a planktotrophic larval stage and therefore not to broadcast-release their offspring. The genetic evidence points to exchanges on a scale that seems to contradict this type of reproductive pattern. However, the rift valley may topographically rectify the bottom currents, thereby facilitating the dispersal of propagules between active vent sites separated in some cases by 10s of kilometers or more along the ridge axis. A propagule flux model based on a matrix of intersite distances, long-term current-meter data, and information on the biology and ecology of Alvinellidae was developed to test this hypothesis. Calculations of the number of migrants exchanged between two populations per generation (N-m) allowed comparisons with estimates obtained from genetic studies. N, displays a logarithmic decrease with increasing dispersal duration and reaches the critical value of 1 after 8 d when the propagule Aux model was run in standard conditions. At most, propagule traveling time cannot reasonably exceed 15-30 d, according to the model, whereas reported distances between sites would require longer lasting dispersal abilities. Two nonexclusive explanations are proposed. First, some aspects of the biology of Alvinellidae have been overlooked and long-distance dispersal does occur. Second, such dispersal never occurs in Alvinellidae, but the spatial-temporal dynamics of vent sites over geological timescales allows short-range dispersal processes to maintain gene flow.

COMMUNITY KNOWLEDGE, ATTITUDE AND PRACTICES (KAP) ON FLUOROSIS AND ITS MITIGATION IN ENDEMIC AREAS OF ETHIOPIA

Optimum fluoride intake plays an essential role in the prevention of dental caries while fluoride consumption above recommended level interferes with the normal formation of tooth enamel and bones and may increase risk of dental and skeletal fluorosis. The knowledge and practices of endemic communities on etiology of fluorosis will help in its mitigation and prevention. The objective of this study was to investigate the knowledge, attitude and practices of endemic community on fluoride contamination, fluorosis and prevention practices in order to devise coordinated and targeted prevention mechanisms. Focus group discussions (FGD) and key-informant interview were conducted in three dietary areas to collect knowledge, attitude and practices (KAP) of the endemic community in July 2013.The results indicated that health consequences of fluoride contaminated water are fairly understood. None of the discussants mentioned the word “fluoride”. The knowledge and perception of the community on fluoride ingestion is poor. Health extension workers (HEWs) did not teach about fluoride and related health consequences. Dental fluorosis was reported to start at early ages and not commonly perceived as a major problem. However, adolescents worried and felt that they might be singled out when going to other areas. Older people have a skeletal fluorosis, which interferes with their day to day activities. In severely affected people, the teeth were weak and fragile and thus create difficulty in chewing hard foods like unfermented dry flat bread, sugar cane and toasted grains. People prefer rain water rather than water from borehole because of the inconvenient taste of the latter. The endemic communities have no sufficient knowledge and skills on potential sources of fluoride intake, the debilitating effect of high fluoride ingestion, and preventive and mitigatory measures to reduce fluoride intake. The effect of fluoride contamination and mitigatory methods should get sufficient attention by the community, health workers and concerned governmental bodies. The trend of harvesting and using rain water should be encouraged as it reduces fluoride intake. Future studies should focus on information communication on possible fluoride risks, intervention and evaluation studies on defluoridation, rain water harvesting and mitigatory techniques.