Exploration of Natural and Artificial Sequence Spaces: Towards a Functional Remodeling of Membrane-bound Cytochrome P450

Abstract

Two complementary methods are described that associate in vitro and in vivo steps to generate sequence diversity by segment directed saturated mutagenesis and family shuffling. A high-throughput DNA chip-based procedure for the characterization and potentially the equalization of combinatorial libraries is also presented. Using these approaches, two combinatorial libraries of cytochrome P450 variants derived from the CYP1A subfamily were constructed and their sequence diversity characterized. The results of functional screening using high-throughput tools for the characterization of membrane P450-catalyzed activities, suggest that the 204–214 sequence segment of human CYP1A1 is not critical for polycyclic aromatic hydrocarbon recognition, as was hypothesized from previous data. Moreover, mutations in this segment do not alter the discrimination between alkoxyresorufins, which, for all tested mutants, remained similar to that of wild-type CYP1A1. In contrast, the constructed CYP1A1–CYP1A2 mosaic structures, containing multiple crossovers, exhibit a wide range of substrate preference and regioselectivity. These mosaic structures also discriminate between closely related alkoxyresorufin substrates. These results open the way to global high-throughput analysis of structure–function relationships using combinatorial libraries of enzymes together with libraries of structurally related substrates.     

Incorporating trnH-psbA to the core DNA barcodes improves significantly species discrimination within?southern African Combretaceae

Recent studies indicate that the discriminatory power of the core DNA barcodes (rbcLa + matK) for land plants may have been overestimated since their performance have been tested only on few closely related species. In this study we focused mainly on how the addition of complementary barcodes (nrITS and trnH-psbA) to the core barcodes will affect the performance of the core barcodes in discriminating closely related species from family to section levels. In general, we found that the core barcodes performed poorly compared to the various combinations tested. Using multiple criteria, we finally advocated for the use of the core + trnH-psbA as potential DNA barcode for the family Combretaceae at least in southern Africa. Our results also indicate that the success of DNA barcoding in discriminating closely related species may be related to evolutionary and possibly the biogeographic histories of the taxonomic group tested.     

A Global Trend towards the Loss of Evolutionarily Unique Species in Mangrove Ecosystems

The mangrove biome stands out as a distinct forest type at the interface between terrestrial, estuarine, and near-shore marine ecosystems. However, mangrove species are increasingly threatened and experiencing range contraction across the globe that requires urgent conservation action. Here, we assess the spatial distribution of mangrove species richness and evolutionary diversity, and evaluate potential predictors of global declines and risk of extinction. We found that human pressure, measured as the number of different uses associated with mangroves, correlated strongly, but negatively, with extinction probability, whereas species ages were the best predictor of global decline, explaining 15% of variation in extinction risk. Although the majority of mangrove species are categorised by the IUCN as Least Concern, our finding that the more threatened species also tend to be those that are more evolutionarily unique is of concern because their extinction would result in a greater loss of phylogenetic diversity. Finally, we identified biogeographic regions that are relatively species-poor but rich in evolutionary history, and suggest these regions deserve greater conservation priority. Our study provides phylogenetic information that is important for developing a unified management plan for mangrove ecosystems worldwide.     

Estimation of the mean distance of closest approach of some heavy metal ions in aqueous solutions: some experimental and theoretical calculations

The estimation of numerical values of the mean distance of closest approach of ions, a, of heavy metal ion salts in aqueous solutions, determined from activity coefficients, as well as from different theoretical approaches, is presented and discussed.     

Picking at the Paint: Viewing Contemporary Bushman Art as Art

In most writing on contemporary Bushman art the art is discussed as a tool of development, a tourism endeavor and an income generator. While these are aims both legitimate and beneficial to the communities involved, they also work (implicitly yet effectively) to separate the art, artist and subsequently the community out of which the art is produced from “the rest of us,” defining these communities as “other.” This article attempts to engage with contemporary Bushman art as art objects. Using criteria of judgment based on a functional semiotics of art, two works will be analyzed to prove that the works may be discussed as Art. The premise is that once people recognize the aesthetic intelligence imbued in these artworks they will be able to engage with the work in a way that is similarly intelligent and contemporary. The art and its people will then stand a better chance of being accepted into the realm of the everyday as opposed to being relegated to the sarcophagi of history. Once taken from this starting position, goals of community development and tourism endeavors linked to indigenous art can become that much more beneficial and life-changing for the communities concerned.     

Understanding the Potential Impact of a Combination HIV Prevention Intervention in a Hyper-Endemic Community

Objectives

Despite demonstrating only partial efficacy in preventing new infections, available HIV prevention interventions could offer a powerful strategy when combined. In anticipation of combination HIV prevention programs and research studies we estimated the population-level impact of combining effective scalable interventions at high population coverage, determined the factors that influence this impact, and estimated the synergy between the components.

Methods

We used a mathematical model to investigate the effect on HIV incidence of a combination HIV prevention intervention comprised of high coverage of HIV testing and counselling, risk reduction following HIV diagnosis, male circumcision for HIV-uninfected men, and antiretroviral therapy (ART) for HIV-infected persons. The model was calibrated to data for KwaZulu-Natal, South Africa, where adult HIV prevalence is approximately 23%.

Results

Compared to current levels of HIV testing, circumcision, and ART, the combined intervention with ART initiation according to current guidelines could reduce HIV incidence by 47%, from 2.3 new infections per 100 person-years (pyar) to 1.2 per 100 pyar within 4 years and by almost 60%, to 1 per 100 pyar, after 25 years. Short-term impact is driven primarily by uptake of testing and reductions in risk behaviour following testing while long-term effects are driven by periodic HIV testing and retention in ART programs. If the combination prevention program incorporated HIV treatment upon diagnosis, incidence could be reduced by 63% after 4 years and by 76% (to about 0.5 per 100 pyar) after 15 years. The full impact of the combination interventions accrues over 10–15 years. Synergy is demonstrated between the intervention components.

Conclusion

High coverage combination of evidence-based strategies could generate substantial reductions in population HIV incidence in an African generalized HIV epidemic setting. The full impact could be underestimated by the short assessment duration of typical evaluations.     

Dynamics of Cattle Production in Brazil

Movement of livestock production within a country or region has implications for genetics, adaptation, well-being, nutrition, and production logistics, particularly in continental-sized countries, such as Brazil. Cattle production in Brazil from 1977 to 2011 was spatialized, and the annual midpoint of production was calculated. Changes in the relative production and acceleration of production were calculated and spatialized using ARCGIS®. Cluster and canonical discriminant analyses were performed to further highlight differences between regions in terms of cattle production. The mean production point has moved from the Center of Minas Gerais State (in the southeast region) to the North of Goiás State (in the Midwest region). This reflects changes in environmental factors, such as pasture type, temperature and humidity. Acceleration in production in the northern region of Brazil has remained strong over the years. More recently, “traditional” cattle-rearing regions, such as the south and southeast, showed a reduction in growth rates as well as a reduction in herd size or internal migration over the period studied. These maps showed that this movement tends to be gradual, with few regions showing high acceleration or deceleration rates.     

Phylogenetic taxonomy of the marine mite genus Rhombognathides (Acari: Halacaridae: Rhombognathinae)

This study examined the impacts of the alien waterweed, water hyacinth, on the abundance and diversity of aquatic macroinvertebrates in the littoral areas of northern Lake Victoria in Uganda. The weed had undergone explosive growth on the lake causing serious disruption to people, the economy and the ecosystem. This study was confined to impact of the weed in the littoral zone, not to the large floating mats of vegetation which float across the lake and clog large areas of shoreline.The littoral area studied comprised of fringing mats of Eichhornia crassipes (Mart) Solms (water hyacinth) to the lakeward of Cyperus papyrus; water hyacinth mats undergoing colonisation by Vossia cuspidata (Roxb.) Griff.; and a typical Cyperus papyrus L shore with no outer floating mat of water hyacinth. Numerical abundance (Nos. m^–2) and diversity (No. of taxa) of macroinvertebrates recovered from pure Eichhornia crassipes and the Eichhornia-Vossia succession increased from the fringe of the Cyperus papyrus towards the open water. In the typical Cyperus papyrus fringe, in the absence of water hyacinth, abundance was highest at the papyrus/open water interface and dropped off sharply towards open water. The Shannon–Weaver diversity index (H) of macroinvertebrates decreased progressively from pure Eichhornia crassipes stands, to Vossia/Eichhornia beds and Cyperus papyrus stands (H=0.56, 0.54 and 0.34, respectively) but were not significantly different. Dissolved oxygen decreased from open water into vegetation where it approached anoxia. Water hyacinth appeared to enhance the abundance and diversity of aquatic macroinvertebrates at the interface with the open water. The impoverished abundance and diversity of the macroinvertebrates deeper into the vegetation mats suggested negative environmental impacts of the water hyacinth when the fringe is too wide. Further research is recommended to establish the optimum width of the fringe of stationery water hyacinth that promotes maximum abundance and diversity of aquatic macroinvertebrates and, possibly, of other aquatic life. Since this study in 1997, there has been a dramatic decrease in Eichhornia infestations and by June 2000 it appeared largely to exist only as fringing vegetation in bays and inlets.     

Endocrine correlates of sexual behavior in the Mohor gazelle (Gazella dama mhorr)

In this study, we quantitatively examined male sexual behavior in relation to fecal estrogen and progesterone concentrations in female Mohor gazelles. We investigated the hypothesis that, during natural mating, males detect cues relating to the potential for successful conception and pregnancy. Time series analysis revealed that males could detect the approach of estrus 2-3 days before female fecal estrogens and estrogen/progestagen (E/P) ratio reached their peak values. Males also paid closer attention to those females excreting higher fecal estrogen concentrations. Mounting and copulation frequencies were positively correlated with both peri-ovulatory fecal estrogen concentrations, and the frequency of pre-copulatory courtship behaviors. These data suggested that males invest their reproductive effort selectively by mating the most fertile females, assuming that estrogen is a valid index of fertility. This assumption was investigated by examining sequential phases of the reproductive cycle for evidence that oocytes and follicles produced in a more estrogenic environment would lead to the formation of the most competent corpora lutea, thereby maximizing the chance of sustaining pregnancy. Associations between sexual behavior and hormone excretion support the hypothesis that males may use this mechanism to assess female fertility.