Structure determination of Split-soret Cytochrome from a Desulfovibrio species isolated from a human abdominal abcess

The determined structure of the split-soret cytochrome (SSC) isolated from Desulfovibrio desulfuricans ATCC 27774 (D.d.) revealed a new Heme arrangement, which suggests that this protein constitutes a new cytochrome class.. SSC is a 52.6kDa homodimer containing four hemes at one end of the molecule. In each monomer the two hemes have their edges overlapped within van der Waals contacts. The polypeptide chain of each monomer supplies the sixth ligand to the heme-iron of the other monomer. A similar protein was recently purified from a homologous Desulfovibrio clinical strain isolated from an abdominal wall abscess in human patient2. Crystals of this SSC were grown using vapour diffusion method in the presence of agarose gel. Diffraction data were collected using X-ray synchrotron radiation at the ESRF, beamline, ID 14-1. The structure will be solved by molecular replacement using the structure of the D.d. as a starting model

Field Evidence for Geophysical Detection of Subsurface Zones of Enhanced Microbial Activity

Geochemical data from closely spaced vertical intervals in a hydrocarbon-impacted aquifer were used to assess the relationship between bulk conductivity and zones of enhanced microbial activity. The bulk conductivity was measured using in situ vertical resistivity probes. Microbial activity was verified using terminal electron acceptors (nitrate, sulfate, iron, and manganese), dissolved inorganic carbon (DIC), and major ion chemistry. Peaks in bulk conductivity in the aquifer overlapped with zones where nitrates and sulfates were depleted, total petroleum hydrocarbon, iron, manganese, dissolved ions, and DIC were elevated, suggesting a link between higher electrical conductivity and zones of enhanced microbial activity stimulated by the presence of hydrocarbon. Thus the subsurface expression of microbial activity is apparently recorded in the bulk conductivity measurements. Our results argue for combining geophysics with biogeochemistry studies to delineate subsurface zones of enhanced microbial activity

Basement control on dyke distribution in Large Igneous Provinces: Case study of the Karoo triple junction.

Continental flood basalts consist of vast quantities of lava, sills and giant dyke swarms that are associated with continental break-up. The commonly radiating geometry of dyke swarms in these provinces is generally interpreted as the result of the stress regime that affected the lithosphere during the initial stage of continental break-up or as the result of plume impact. On the other hand, structures in the basement may also control dyke orientations, though such control has not previously been documented. In order to test the role of pre-dyke structures, we investigated four major putative Karoo-aged dyke swarms that taken together represent a giant radiating dyke swarm (the so-called "triple-junction") ascribed to the Jurassic Karoo continental flood basalt (> 3x10 6 km2; southern Africa). One of the best tests to discriminate between neoformed and inherited dyke orientation is to detect Precambrian dykes in the Jurassic swarms. Accordingly, we efficiently distinguished between Jurassic and Precambrian dykes using abbreviated low resolution, 40Ar/39Ar incremental heating schedules. Save-Limpopo dyke swarm samples (n = 19) yield either apparent Proterozoic (728-1683 Ma) or Mesozoic (131-179 Ma) integrated ages; the Olifants River swarm (n = 20) includes only Proterozoic (851-1731 Ma) and Archaean (2470-2872 Ma) dykes. The single age obtained on one N-S striking dyke (1464 Ma) suggests that the Lebombo dyke swarm includes Proterozoic dykes in the basement as well. These dates demonstrate the existence of pre-Karoo dykes in these swarms as previously hypothesized without supporting age data.In addition, aeromagnetic and air-photo interpretations indicate that: (1) dyke emplacement was largely controlled by major discontinuities such as the Zimbabwe and Kaapvaal craton boundaries, the orientation of the Limpopo mobile belt, and other pre-dyke structures including shear zones and (2) considering its polygenetic, pre-Mesozoic origin, the Olif ants River dyke swarm cannot be considered part of the Karoo magmatic event.This study, along with previous results obtained on the Okavango dyke swarm, shows that the apparent "triple junction" formed by radiating dyke swarms is not a Jurassic structure; rather, it reflects weakened lithospheric pathways that have controlled dyke orientations over hundreds of millions of years. One consequence is that the "triple-junction" geometry can no longer be unambiguously used as a mantle plume marker as previously proposed, although it does not preclude the possible existence of a mantle plume. More generally, we suggest that most Phanerozoic dyke swarms (including triple junctions) related to continental flood basalts were probably controlled in part by pre-existing lithospheric discontinuities

The Karoo triple junction questioned : evidence from Jurassic and Proterozoc 40Ar/39Ar ages and geochemistry of the giant Okavango dyke swarm (Botswana).

The lower Jurassic Karoo-Ferrar magmatism represents one of the most important Phanerozoic continental flood basalt (CFB) provinces. The Karoo CFB province is dominated by tholeiitic traps and apparently radiating giant dyke swarms covering altogether ca. 3 106 km2. This study focuses on the giant N110j-trending Okavango dyke swarm (ODS) stretching over 1500 km across Botswana. This dyke swarm represents the main (failed) arm of the so-called Karoo triple junction that is generally considered as a key marker of the impingement of the Karoo starting mantle plume head. ODS dolerites yield six new plagioclase 40Ar/39Ar plateau (and miniplateau) ages ranging from 178.7F0.7 and 180.9F1.3 Ma. The distribution of the ages along a narrow Gaussian curve suggests a short period of magmatic activity centered around 179 Ma, i.e., f5 Ma younger than the emplacement age of Karoo mafic magmas in the southern part of the Karoo CFB province (f184). This age difference indicates that Karoo magmatism does not represent a short-lived event as is generally the case for most CFB but lasted at least 5Ma over the whole province. In addition, small clusters of plagioclase separated from 28 other dykes and measured by "speedy" step-heating experiments (with mostly two to three steps), gave either "Karoo" or Proterozoic ages.Integrated ages of the Proterozoic rocks range from 851 6 to 1672 7 Ma, and one plateau age (959.1 4.6 Ma) and one possibly geologically significant weighted mean age (982.7 4.0 Ma) were obtained. Proterozoic and Karoo mafic rocks are petrographically similar, but Proterozoic dykes display clear geochemical differences (e.g., TiO 22.1%). Geochemical data combined with available Ar/Ar dates allow the identification of the two groups within a total set of 77 dykes investigated: f10% of the bulk ODS dykes are Proterozoic. Thus, the Jurassic Karoo ODS dykes were emplaced along reactivated Proterozoic structures and there is no pristine Jurassic Nuanetsi triple junction as commonly proposed. This throws into doubt the validity of the "active plume head" Karoo CFB rift models as being responsible for the observed "triple junction" dyke geometr

Survey of Water Bugs in Bankim, a New Buruli Ulcer Endemic Area in Cameroon

Buruli ulcer is a debitliating human skin disease with an unknown transmission mode although epidemiological data link it with swampy areas. Data available suggest that aquatic insects play a role in the dissemination and/or transmission of this disease. However, their biodiversity and biology remain poorly documented. We conducted an entomological survey in Bankim, Cameroon, an area recently described as endemic for Buruli ulcer in order to identify the commonly occurring aquatic bugs and document their relative abundance, diversity, and spatial distribution. Collection of aquatic bugs was realized over a period of one month by daily direct capture in different aquatic environments (streams, ponds, and rivers) and through light traps at night. Globally, the data obtained showed the presence of five families (Belostomatidae, Naucoridae, Nepidae, Notonectidae, and Gerridae), their abundance, distribution and diversity varying according to the type of aquatic environments and light attraction

The Okavango giant mafic dyke swarm (NE Botswana): its structural significance within the Karoo Large Igneous Province

The structural organization of a giant mafic dyke swarm, the Okavango complex, in the northern Karoo Large Igneous Province (LIP) of NE Botswana is detailed. This N110E-oriented dyke swarm extends for 1500 km with a maximum width of 100 km through Archaean basement terranes and Permo-Jurassic sedimentary sequences. The cornerstone of the study is the quantitative analysis of N>170 (exposed) and N>420 (detected by ground magnetics) dykes evidenced on a ca. 80-km-long section lying in crystalline host-rocks, at high-angle to the densest zone of the swarm (Shashe area). Individual dykes are generally sub-vertical and parallel to the entire swarm. Statistical analysis of width data indicates anomalous dyke frequency (few data <5.0 m) and mean dyke thickness (high value of 17 m) with respect to values classically obtained from other giant swarms. Variations of mean dyke thicknesses from 17 (N110E swarm) to 27 m (adjoining and coeval N70E giant swarm) are assigned to the conditions hosting fracture networks dilated as either shear or pure extensional structures, respectively, in response to an inferred NNW?SSE extension. Both fracture patterns are regarded as inherited brittle basement fabrics associated with a previous (Proterozoic) dyking event. The Okavango N110E dyke swarm is thus a polyphase intrusive system in which total dilation caused by Karoo dykes (estimated frequency of 87%) is 12.2% (6315 m of cumulative dyke width) throughout the 52-km-long projected Shashe section. Assuming that Karoo mafic dyke swarms in NE Botswana follow inherited Proterozoic fractures, as similarly applied for most of the nearly synchronous giant dyke complexes converging towards the Nuanetsi area, leads us to consider that the resulting triple junction-like dyke/fracture pattern is not a definitive proof for a deep mantle plume in the Karoo LIP

In-situ Apparent Conductivity Measurements and Microbial Population Distribution at a Hydrocarbon-Contaminated Site

We investigated the bulk electrical conductivity and microbial population distribution in sediments at a site contaminated with light nonaqueous-phase liquid (LNAPL). The bulk conductivity was measured using in-situ vertical resistivity probes; the most probable number method was used to characterize the spatial distribution of aerobic heterotrophic and oil-degrading microbial populations. The purpose of this study was to assess if high conductivity observed at aged LNAPL-impacted sites may be related to microbial degradation of LNAPL. The results show higher bulk conductivity coincident with LNAPL-impacted zones, in contrast to geoelectrical models that predict lower conductivity in such zones. The highest bulk conductivity was observed to be associated with zones impacted by residual and free LNAPL. Data from bacteria enumeration from sediments close to the resistivity probes show that oil-degrading microbes make up a larger percentage (5-55&percnt;) of the heterotrophic microbial community at depths coincident with the higher conductivity compared to ∼5&percnt; at the uncontaminated location. The coincidence of a higher percentage of oil-degrading microbial populations in zones of higher bulk conductivity suggests that the higher conductivity in these zones may result from increased fluid conductivity related to microbial degradation of LNAPL, consistent with geochemical studies that suggest that intrinsic biodegradation is occurring at the site. The findings from this study point to the fact that biogeochemical processes accompanying biodegradation of contaminants can potentially alter geoelectrical properties of the subsurface impacted media

DisProt: the Database of Disordered Proteins

The Database of Protein Disorder (DisProt) links structure and function information for intrinsically disordered proteins (IDPs). Intrinsically disordered proteins do not form a fixed three-dimensional structure under physiological conditions, either in their entireties or in segments or regions. We define IDP as a protein that contains at least one experimentally determined disordered region. Although lacking fixed structure, IDPs and regions carry out important biological functions, being typically involved in regulation, signaling and control. Such functions can involve high-specificity low-affinity interactions, the multiple binding of one protein to many partners and the multiple binding of many proteins to one partner. These three features are all enabled and enhanced by protein intrinsic disorder. One of the major hindrances in the study of IDPs has been the lack of organized information. DisProt was developed to enable IDP research by collecting and organizing knowledge regarding the experimental characterization and the functional associations of IDPs. In addition to being a unique source of biological information, DisProt opens doors for a plethora of bioinformatics studies. DisProt is openly available at

Amino acid sequence of rubredoxin from Desulfovibrio desulfuricans strain 27774

AbstractThe amino acid sequence of a rubredoxin from Desulfovibrio desulfuricans (strain 27774) has been determined. Comparison with rubredoxins from other species reveals pervasive homology, including the regions known to provide the cysteine ligands to the iron atom in several rubredoxins. Neither an extra cysteinyl residue nor a unique histidyl residue in the new sequence is located in the sequence in such a way that, by homology, a functional role in the structure is suggested