Sm-Nd, Rb-Sr, and He isotopic composition and hydrocarbon gases in rocks and minerals from the Markov Deep, Mid-Atlantic Ridge rift valley

The paper presents characteristics of the Nd and Sr isotopic systems of ultrabasic rocks, gabbroids, plagiogranites, and their minerals as well as data on helium and hydrocarbons in fluid inclusions of the same samples. Materials presented in this publication were obtained by studying samples dredged from the MAR crest zone at 5°-6°N (U/Pb zircon dating, geochemical and petrological-mineralogical studies). It was demonstrated that variations in the isotopic composition of He entrapped in rocks and minerals were controlled by variable degrees of mixing of juvenile He, which is typical of basaltic glass for MAR (DM source), and atmospheric He. Increase in the atmospheric He fraction in plutonic rocks and, to a lesser degree, in their minerals reflects involvement of seawater or hydrated material of the oceanic crust in magmatic and postmagmatic processes. This conclusion finds further support in positive correlation between the fraction of mantle He (R ratio) and 87Sr/86Sr ratio. High-temperature hydration of ultrabasic rocks (amphibolization) was associated with increase in the fraction of mantle He, while their low-temperature hydration (serpentinization) was accompanied by drastic decrease in this fraction and significant increase in 87Sr/86Sr ratio. Insignificant variations in 143Nd/144Nd (close to 0.5130) and 87Sr/86Sr (0.7035) in most of gabbroids and plagiogranites as well as the fraction of mantle He in these rocks, amphibolites, and their ore minerals indicate that the melts were derived from the depleted mantle. Similar e-Nd values of gabbroids, plagiogranites, and fresh harzburgites (6.77-8.39) suggest that these rocks were genetically related to a single mantle source. e-Nd value of serpentinized lherzolites (2.62) likely reflects relations of these relatively weakly depleted mantle residues to another source. Aforementioned characteristics of the rocks generally reflect various degrees of mixing of depleted mantle components with crustal components (seawater) during metamorphic and hydrothermal processes that accompanied formation of the oceanic crust.

Chemical and isotopic compositions of basaltic glasses and crusts from the Mid-Atlantic Ridge rift valley

Data presented in the paper suggest significant differences between thermodynamic conditions, under which magmatic complexes were formed in MAR at 29°-34°N and 12°-18°N. Melts occurring at 29°-34°N were derived by melting of a mantle source with homogeneous distribution of volatile components and arrived at the surface without significant fractionation, likely, due to their rapid ascent. The MAR segments between 12° and 18°N combine contrasting geodynamic environments of magmatism, which predetermined development of a large plume region with widespread mixing of melting products of geochemically distinct mantle sources. At the same time, this region is characterized by conditions favorable for origin of localized zones of anomalous plume magmatism. These sporadic magmatic sources were spatially restricted to MAR fragments with the Hess crust, whose compositional and mechanical properties were, perhaps, favorable for focusing and localization of plume magmatism. The plume source between 12° and 18°N beneath MAR may be geochemically heterogeneous.

The Uganda protectorate; an attempt to give some description of the physical geography, botany, zoology, anthropology, languages and history of the territories under British protection in East Central Africa, between the Congo Free State and the Rift Valley and between the first degree of south latitude and the fifth degree of north latitude,

Appendix to chapter XIII "Anthropology," and to chapter XIV "Pygmies and forest negroes," by Dr. F. Shrubsall.

Climate change adaptation strategies of maize producers of the Central Rift Valley of Ethiopia

The impacts of climate change are considered to be strong in countries located in tropical Africa that depend on agriculture for their food, income and livelihood. Therefore, a better understanding of the local dimensions of adaptation strategies is essential to develop appropriate measures that will mitigate adverse consequences. Hence, this study was conducted to identify the most commonly used adaptation strategies that farm households practice among a set of options to withstand the effects of climate change and to identify factors that affect the choice of climate change adaptation strategies in the Central Rift Valley of Ethiopia. To address this objective, Multivariate Probit model was used. The results of the model indicated that the likelihood of households to adapt improved varieties of crops, adjust planting date, crop diversification and soil conservation practices were 58.73%, 57.72%, 35.61% and 41.15%, respectively. The Simulated Maximum Likelihood estimation of the Multivariate Probit model results suggested that there was positive and significant interdependence between household decisions to adapt crop diversification and using improved varieties of crops; and between adjusting planting date and using improved varieties of crops. The results also showed that there was a negative and significant relationship between household decisions to adapt crop diversification and soil conservation practices. The paper also recommended household, socioeconomic, institutional and plot characteristics that facilitate and impede the probability of choosing those adaptation strategies.

FAULT MORPHOLOGY WITHIN THE SOUTHERN KENYAN PORTION OF THE EAST AFRICAN RIFT VALLEY

Faults form quickly, geologically speaking, with sharp, crisp step-like profiles. Logic dictates that erosion wears away this "sharpness" or angularity creating more rounded features. As erosion occurs, debris accumulates at the base of the scarp slope. The stable end point of this process is when the scarp slope approaches an ideal sigmoid shape. This theory of fault end process, in combination with a new method developed in this report for fault profile delineation, has the potential to enable observation and categorization of fault profiles over large, diverse swaths of fault formation-- in remote areas such as the Southern Kenyan Rift Valley. This up-to date method uses remote sensing data and the digitizer tool in Global Mapper to create shape files of fault segments. This method can provide further evidence to support the notion that sigmoidal- shaped profiles represent a natural endpoint of the erosional process of fault scarps. Over time, faults of many different ages would exist in this similar shape over a wide region. However, keeping in mind that other processes can be at work on scarps-- most notably drainage patterns, when anomalies in profiles are observed, reactivation in some form possibly has occurred.

Panzootics and the poor: devising a global livestock disease prioritisation framework for poverty alleviation

Panzootics such as highly pathogenic avian influenza and Rift Valley fever have originated from the South, largely among poor communities. On a global level, approximately two-thirds of those individuals living on less than US$2 per day keep livestock. Consequently, there is a need to better target animal health interventions for poverty reduction using an evidence-based approach. Therefore, the paper offers a three-step prioritisation framework using calculations derived from standard poverty measures: the poverty gap and the head count ratio. Data from 265 poor livestock-keeping households in Kenya informed the study. The results demonstrate that, across a spectrum of producers, the dependence upon particular species varies. Furthermore, the same livestock disease has differing impacts on the depth and severity of poverty. Consequently, animal health interventions need to

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Stress field control of eruption dynamics at a rift volcano: Nyamuragira, D.R.Congo

Using the record of 30 flank eruptions over the last 110 years at Nyamuragira, we have tested the relationship between the eruption dynamics and the local stress field. There are two groups of eruptions based on their duration (< 80days >) that are also clustered in space and time. We find that the eruptions fed by dykes parallel to the East African Rift Valley have longer durations (and larger volumes) than those eruptions fed by dykes with other orientations. This is compatible with a model for compressible magma transported through an elastic-walled dyke in a differential stress field from an over-pressured reservoir (Woods et al., 2006). The observed pattern of eruptive fissures is consistent with a local stress field modified by a northwest-trending, right lateral slip fault that is part of the northern transfer zone of the Kivu Basin rift segment. We have also re-tested with new data the stochastic eruption models for Nyamuragira of Burt et al. (1994). The time-predictable, pressure-threshold model remains the best fit and is consistent with the typically observed declining rate of sulphur dioxide emission during the first few days of eruption with lava emission from a depressurising, closed, crustal reservoir. The 2.4-fold increase in long-term eruption rate that occurred after 1977 is confirmed in the new analysis. Since that change, the record has been dominated by short-duration eruptions fed by dykes perpendicular to the Rift. We suggest that the intrusion of a major dyke during the 1977 volcano-tectonic event at neighbouring Nyiragongo volcano inhibited subsequent dyke formation on the southern flanks of Nyamuragira and this may also have resulted in more dykes reaching the surface elsewhere. Thus that sudden change in output was a result of a changed stress field that forced more of the deep magma supply to the surface. Another volcano-tectonic event in 2002 may also have changed the magma output rate at Nyamuragira.