ALBERT

Description: Enterohemorrhagic Escherichia coli (EHEC) O26:H11/H – is the predominant non-O157 EHEC serotype among patients with diarrhea, bloody diarrhea, and hemolytic uremic syndrome (HUS) worldwide. To elucidate their phylogeny and association between their phylogenetic background and clinical outcome of the infection, we investigated 120 EHEC O26:H11/H – strains isolated between 1965 and 2012 from asymptomatic carriers and patients with diarrhea or HUS. Whole-genome shotgun sequencing (WGS) was applied to ten representative EHEC O26 isolates to determine single nucleotide polymorphism (SNP) localizations within a predefined set of core genes. A multiplex SNP assay, comprising a randomly distributed subset of 48 SNPs, was established to detect SNPs in 110 additional EHEC O26 strains. Within approximately 1 Mb of core genes, WGS resulted in 476 high-quality bi-allelic SNP localizations. Forty-eight of these were subsequently investigated in 110 EHEC O26 and four different SNP clonal complexes (SNP-CC) were identified. SNP-CC2 was significantly associated with the development of HUS. Within the subsequently established evolutionary model of EHEC O26, we dated the emergence of human EHEC O26 to approximately 19,700 years ago and demonstrated a recent evolution within humans into the 4 SNP-CCs over the past 1,650 years. WGS and subsequent SNP typing enabled us to gain new insights into the evolution of EHEC O26 suggesting a common theme in this EHEC group with analogies to EHEC O157. In addition, the SNP-CC analysis may help to assess a risk in infected individuals for the progression to HUS and to implement more specific infection control measures.

Description: Ectomycorrhiza (EM) formation improves tree growth and nutrient acquisition, particularly that of nitrogen (N). Few studies have coupled the effects of naturally occurring EM morphotypes to the nutrition of host trees. To investigate this, pine seedlings were grown on raw humus substrates collected at two forest sites, R2 and R3. Ectomycorrhiza morphotypes were identified, and their respective N uptake rates from organic (2- 13 C, 15 N-glycine) and inorganic ( 15 NH 4 Cl, Na 15 NO 3 , 15 NH 4 NO 3 , NH 4 15 NO 3 ) sources as well as their phosphate uptake rates were determined. Subsequently, the growth and nutritional status of the seedlings were analyzed. Two dominant EM morphotypes displayed significantly different mycorrhization rates in the two substrates. Rhizopogon luteolus Fr. (RL) was dominant in R2 and Suillus bovinus (Pers.) Kuntze (SB) was dominant in R3. 15 N uptake of RL EM was at all times higher than that of SB EM. Phosphate uptake rates by the EM morphotypes did not differ significantly. The number of RL EM correlated negatively and the number of SB EM correlated positively with pine growth rate. Increased arginine concentrations and critical P/N ratios in needles indicated nutrient imbalances of pine seedlings from humus R2, predominantly mycorrhizal with RL. We conclude that different N supply in raw humus under Scots pine stands can induce shifts in the EM frequency of pine seedlings, and this may lead to EM formation by fungal strains with different ability to support tree growth.

Description: The reconstruction of thermal history is essential for evaluating the potential for hydrocarbon generation within sedimentary basins. Magnetic techniques provide an alternative to more traditional methods to study the geothermal history of sedimentary basins (such as illite crystallinity and vitrinite reflectance), which are often associated with significant uncertainty. In this paper the application of various magnetic geothermometers to the western Karoo Basin of South Africa are evaluated. Three magnetic experiments were conducted on samples from stratigraphic borehole G39977 to determine the thermal effect of large scale dolerite intrusions on the sedimentary strata of the Karoo Supergroup in western South Africa. Alteration index (A 40 ) data indicate maximum acquired temperatures for the sedimentary units ranging between 200°C and 650°C, with the highest temperatures restricted to short distances (less than half the sill thicknesses) within the contact aureoles. Both magnetostratigraphy and anisotropy of low field magnetic susceptibility (AMS) data confirm that re-magnetization of magnetic fabric does not exceed distances more than half the sill thicknesses. Our results indicate the general elevation of the palaeotemperatures of the organic-rich sedimentary rocks of the Ecca Group to temperatures where hydrocarbons are normally converted into gas. Importantly, it is clear from this study that the greatest thermal effects of the sill intrusions on the sedimentary strata are limited to the contact aureoles, suggesting that there is an, as yet unquantified, potential for hydrocarbon resources remaining between these intrusions.

Description: 〈span〉〈div〉Abstract〈/div〉The ultramafic-mafic layered igneous Molopo Farms Complex straddles the border between South Africa and Botswana. Younger cover obscures this igneous complex and its country rocks, which are generally assigned to the Paleoproterozoic Transvaal Supergroup. The area intruded by the complex is characterized by abutting and contrasting successions of the upper Transvaal Supergroup (i.e., the Pretoria and Postmasburg groups), the correlation of which is critical to understanding the first significant build-up in atmospheric oxygen, also known as the Great Oxidation Event. Recent dating of the Postmasburg Group necessitates a reinterpretation of Transvaal Supergroup stratigraphy involving a 200 million year downward revision of the Postmasburg Group relative to the Pretoria Group. The geology of the area intruded by the Molopo Farms Complex may provide important insights into this correlation model. Here we report a 〈sup〉207〈/sup〉Pb/〈sup〉206〈/sup〉Pb ID-TIMS baddeleyite date of 2054 ± 5 Ma from a gabbroic sample from the Molopo Farms Complex in South Africa, and an U-Pb zircon date of 2056 ± 10 Ma from a highly altered and metamorphosed quartzite in direct contact with ultramafic rocks of the complex in Botswana. We interpret these as crystallization ages of the Complex, which are within error of the 2056 to 2055 Ma age of the Bushveld Complex. Also reported from drill core intersections are U-Pb LA-ICP-MS detrital zircon age data from quartzite samples of both the floor and roof country rock. The roof rock detrital zircon age populations are comparable to those of the Paleoproterozoic Waterberg Group. Age populations in floor rocks are generally similar to those of the Pretoria Group, with the addition of ~2050 Ma populations, which likely reflect the metamorphic aureole of the complex on distinctly recrystallized country rock. A revised pre-Kalahari regional geology of the Molopo Farms Complex in South Africa, that incorporates the Pretoria Group in the area, implies an unconformable relationship with the Potsmasburg Group. Future recognition of such an unconformable relationship in drill core will ultimately resolve the problem of Transvaal strata correlation.〈/span〉

Description: 〈span〉〈div〉Abstract〈/div〉The ultramafic-mafic layered igneous Molopo Farms Complex straddles the border between South Africa and Botswana. Younger cover obscures this igneous complex and its country rocks, which are generally assigned to the Paleoproterozoic Transvaal Supergroup. The area intruded by the complex is characterized by abutting and contrasting successions of the upper Transvaal Supergroup (i.e., the Pretoria and Postmasburg groups), the correlation of which is critical to understanding the first significant build-up in atmospheric oxygen, also known as the Great Oxidation Event. Recent dating of the Postmasburg Group necessitates a reinterpretation of Transvaal Supergroup stratigraphy involving a 200 million year downward revision of the Postmasburg Group relative to the Pretoria Group. The geology of the area intruded by the Molopo Farms Complex may provide important insights into this correlation model. Here we report a 〈sup〉207〈/sup〉Pb/〈sup〉206〈/sup〉Pb ID-TIMS baddeleyite date of 2054 ± 5 Ma from a gabbroic sample from the Molopo Farms Complex in South Africa, and an U-Pb zircon date of 2056 ± 10 Ma from a highly altered and metamorphosed quartzite in direct contact with ultramafic rocks of the complex in Botswana. We interpret these as crystallization ages of the Complex, which are within error of the 2056 to 2055 Ma age of the Bushveld Complex. Also reported from drill core intersections are U-Pb LA-ICP-MS detrital zircon age data from quartzite samples of both the floor and roof country rock. The roof rock detrital zircon age populations are comparable to those of the Paleoproterozoic Waterberg Group. Age populations in floor rocks are generally similar to those of the Pretoria Group, with the addition of ~2050 Ma populations, which likely reflect the metamorphic aureole of the complex on distinctly recrystallized country rock. A revised pre-Kalahari regional geology of the Molopo Farms Complex in South Africa, that incorporates the Pretoria Group in the area, implies an unconformable relationship with the Potsmasburg Group. Future recognition of such an unconformable relationship in drill core will ultimately resolve the problem of Transvaal strata correlation.〈/span〉

Description: The Karoo Basin of South Africa is of economic importance for its large coal reserves but has in recent years also been in the spotlight due to the possibility of extensive shale gas reserves. Reconstruction of the thermal history of the Karoo Basin is essential for evaluating the potential hydrocarbon generation within this Late Carboniferous – Middle Jurassic sedimentary basin. Magnetic techniques provide an alternative approach in comparison to more traditional methods to study the geothermal history of sedimentary basins (such as illite crystallinity and vitrinite reflectance), which are often associated with significant uncertainty. In this paper variations in the thermal history across the Karoo Basin as a result of heating by the Karoo LIP are evaluated using different magnetic "geothermometers". These include palaeomagnetism (baked contact test), thermomagnetic analysis (alteration index method) and anisotropy of magnetic susceptibility (AMS). Although these techniques were successful in identifying a variation in metamorphic effects adjacent to contact aureoles, only the alternating index (A 40 ) provides a means of estimating peak temperatures. Our results indicate a regional elevation of palaeotemperatures of the organic-rich sedimentary rocks of the Ecca Group to temperatures where hydrocarbons are normally converted into gas. This study shows that the greatest thermal effects of the sill intrusions on the sedimentary strata are limited to the contact aureoles, suggesting that there is an, as yet unquantified, potential for hydrocarbon resources remaining in strata between these intrusions. An increase in the paleotemperatures from 200°C in the southwest to 400°C in the northeast of the basin is observed. We hypothesize that this trend is mainly due to differences in thermal conductivity of the different sedimentary rock types across the basin as the Karoo Basin transgresses from tight low porosity marine shales in the south and southwest towards more lacustrine mudstone and porous sandstone towards the northeast.

Description: 〈span class="paragraphSection"〉〈div class="boxTitle"〉Abstract〈/div〉The Kaapvaal craton (South Africa) was the host of several major magmatic events during the Palaeoproterozoic, including the volcanic Hekpoort and Ongeluk Formations. Their possible comagmatic origin is the subject of a long debate. We performed a palaeomagnetic study of the Hekpoort Formation to be compared with the available palaeopole of the Ongeluk Formation, but also to contribute to the apparent polar wander path of the Kaapvaal craton. Characterization of magnetic mineralogy by three-axis thermal demagnetization of isothermal remanent magnetization and magnetic susceptibility versus temperature points out magnetite as the main remanence carrier in most samples.Five magnetic components were identified in total, of which the least stable (HKE) near parallels the present geomagnetic field. At higher levels of demagnetization (above 400 °C), two components (HKD and HKC) are identified as thermoviscous overprints likely related to the Karoo large igneous province (LIP) and a magmatic event which occurred between the emplacement of the ∼2055 Ma Bushveld Complex and HKD (possibly linked to the Umkondo LIP), respectively. This LIP is known to be associated with extensive remagnetization. The second most stable component HKB was also revealed at higher steps of thermal and alternative-field treatment. The HKB palaeopole (latitude = 28.4°N and longitude = 54°E) is similar to those reported from the Bushveld Complex (∼2055 Ma) and the Vredefort impact structure (∼2023 Ma). A potentially primary remanence direction (HKA; declination = 337°, inclination = 80° and α = 6.2°) was identified in most sites during the highest levels of thermal demagnetization. Note that the HKA pole position (latitude = −44°N and longitude = 40°E) is significantly different from the palaeopole for the Ongeluk Formation (latitude = −0.5°N and longitude = 107°E). Although, the primary nature of HKA is supported by positive fold and reversal tests, we cannot exclude the possibility that this component represents an overprint. HKA is, however, most likely older than ∼2.0 Ga given its anteriority to HKB components.〈/span〉

Description: Mirtrons are introns that form pre-miRNA hairpins after splicing to produce RNA interference (RNAi) effectors distinct from Drosha-dependent intronic miRNAs, and will be especially useful for co-delivery of coding genes and RNAi. A specific family of mirtrons – 3'-tailed mirtrons – has hairpins precisely defined on the 5' end by the 5' splice site and 3' end by the branch point. Here, we present design principles for artificial 3'-tailed mirtrons and demonstrate, for the first time, efficient gene knockdown with tailed mirtrons within eGFP coding region. These artificial tailed mirtrons, unlike canonical mirtrons, have very few sequence design restrictions. Tailed mirtrons targeted against VEGFA mRNA, the misregulation of which is causative of several disorders including cancer, achieved significant levels of gene knockdown. Tailed mirtron-mediated knockdown was further shown to be splicing-dependent, and at least as effective as equivalent artificial intronic miRNAs, with the added advantage of very defined cleavage sites for generation of mature miRNA guide strands. Further development and exploitation of this unique mirtron biogenesis pathway for therapeutic RNAi coupled into protein-expressing genes can potentially enable the development of precisely controlled combinatorial gene therapy.