Use of Geographic Information Systems in the development of prediction models for onchocerciasis control in Ethiopia

A risk assessment model was developed for onchocerciasis distribution and its control in Ethiopia using Geographic Information System (GIS) methods. GIS data analysis was done to generate 3 separate risk models using selected environmental features of (1) earth observing satellite data on Normalized Difference Vegetation Index (NDVI) and midday Land Surface Temperature (LST) prepared from AVHRR sensor data of the Global land 1-km project for the years 1992 and 1995, (2) FAO agroclimatic databases from the Crop Production System Zone (CPSZ) of the Intergovernmental Authority on Development (IGAD) sub-region of East Africa, and (3) a climate-based forecast index based on the growing degree days (GDD) and water budget concepts. Parasitological data used for the analysis were published and unpublished reports of onchocerciasis surveillance made between 1969 and 2000 in various parts of the country. Analysis of queries based on 1992 and 1995 annual wet and dry season data of the Global land 1-km project resulted in a predictive value of 95.1%, 94.0% and 96.3%, respectively, using data values extracted from buffers centered on sites above 5% prevalence. The model based on CPSZ data predicted an endemic area that best fit the distribution of sites over 5% prevalence; the query was based on CPSZ values of average altitude (442-2134 m), annual mean temperature (18-28 degrees C), annual rainfall (822-1980 mm), annual potential evapotranspiration (1264-1938 mm), rain minus potential evapotranspiration (-124 - 792 mm), average NDVI x 100 (2000-5000) and average terrain percent slope (9-34). The climate-based model based on GDD and water-budget predicted high risk to severe risk areas in the western and southwestern parts of the country. All three of the models predicted suitable areas for the transmission of onchocerciasis outside known endemic areas, suggesting the need for ground-based validation and potential application to current community-directed treatment programs with ivermectin (CDTI) for control of onchocerciasis in Ethiopia.     

Geographical Information Systems risk assessment models for zoonotic fascioliasis in the South American Andes region

The WHO recognises Fasciola hepatica to be an important human health problem. The Andean countries of Peru, Bolivia and Chile are those most severely affected by this distomatosis, though areas of Ecuador, Colombia and Venezuela are also affected. As part of a multidisciplinary project, we present results of use of a Geographical Information Systems (GIS) forecast model to conduct an epidemiological analysis of human and animal fasciolosis in the central part of the Andes mountains. The GIS approach enabled us to develop a spatial and temporal epidemiological model to map the disease in the areas studied and to classify transmission risk into low, moderate and high risk areas so that areas requiring the implementation of control activities can be identified. Current results are available on a local scale for: (1) the northern Bolivian Altiplano, (2) Puno in the Peruvian Altiplano, (3) the Cajamarca and Mantaro Peruvian valleys, and (4) the Ecuadorian provinces of Azuay, Cotopaxi and Imbabura. Analysis of results demonstrated the validity of a forecast model that combines use of climatic data to calculate of forecast indices with remote sensing data, through the classification of Normalized Difference Vegetation Index (NDVI) maps.     

A novel approach to determine water content in DMSO for a compound collection repository

The quality of a corporate compound collection can be significantly affected by a complex combination of storage and operational processing factors. Water content in DMSO solutions is one factor that is of great interest as it can affect solubility, degradation, and freeze-thaw cycle parameters. To the authors' knowledge, this is the first report of using near-infrared (NIR) spectroscopy to assess water content in DMSO compound stock solutions within the common storage vessel format of polypropylene microtubes. The precision and accuracy of the NIR technique was benchmarked against a Karl Fisher titration method, and a correlation coefficient was determined to be 0.985 over a range of 1% to 10% water in DMSO by weight. The advantages of the NIR technique include accuracy, precision, speed, nondestructiveness, and the capability of assessing compounds under in situ storage conditions within microtubes. In this report, the authors demonstrate the accuracy and precision of using NIR to assess water content in DMSO solutions and present a case study to demonstrate the utility of the technique to aid in assessing a pharmaceutical compound collection.     

Structure and assembly of the heterotrimeric and homotrimeric C-propeptides of type I collagen: significance of the alpha2(I) chain

Assembly of the type I procollagen molecule begins with interactions among the C-pro alpha1(I) and C-pro alpha2(I) domains. The C-propeptide domains themselves have subdomains of distinct structures. The important questions are where chain association begins and the basis of the chain selectivity which leads to the preferential formation of the [C-pro alpha1(I)]2[C-pro alpha2(I)] heterotrimer. These questions are addressed by energy minimization modeling of the individual C-propeptide structures, study of their docking interactions, and comparison of the heterotrimeric and homotrimeric C-pro structures and stability. The comparisons show the remarkable impact of the C-pro alpha2 chain on the structure of the assembled trimeric C-propeptide. In the modeling, the three chains were anchored and registered by a short C-terminal collagen triple-helical segment followed by the C-telopeptides in their docked conformation, and then the remaining C-propeptide chains were allowed to interact and dock. Surprisingly, propeptide trimerization did not proceed through the previously proposed N-terminal "oligomerization domain" of the C-propeptide [McAlinden et al. (2003) J. Biol. Chem. 278, 42200] but rather in the most C-terminal domains of type I procollagen chains. Molecular dynamics showed heterotrimer assembly to begin with dimer formation between globular G2alpha2 and the G2alpha1(2) domains followed by trimerization at the G1 domains. Assembly initiation in the putative oligomerization coiled-coil domain is not possible because of the Pro residues at positions 3, 7, and 11 at the N-terminus of the alpha2 C-propeptide chain. To confirm the computations and proposed assembly pathway, the G2alpha1 and G2alpha2 domains were prepared recombinantly as the maltose binding protein constructs, and their interactions were studied by dynamic light scattering and gel filtration chromatography. Under the conditions examined MBP remained as monomer, MBP-G2alpha1 and MBP-G2alpha2 alone formed dimers, but a 2:1 mixture of MBP-G2alpha1 and MBP-G2alpha2 favored trimer formation. Thus, the C-terminal globular domains (G2) of the type I collagen C-propeptides play a crucial role in the initiation of intermolecular assembly and heterotrimer selectivity.     

A surface plasmon resonance-based assay for small molecule inhibitors of human cyclophilin A

A simple protocol for generating a highly stable and active surface plasmon resonance (SPR) sensor surface of recombinant human hexahistidine cyclophilin A (His-CypA) is described. The sensor surface was sensitive and stable enough to allow, for the first time, the screening and ranking of several novel small-molecule (Mr approximately 250-500 Da) ligands in a competition binding assay with cyclosporin A (CsA). It also allowed us to accurately determine the kinetic rate constants for the interaction between His-CypA and CsA. His-CypA was first captured on a Ni2+-nitrilotriacetic acid (NTA) sensor chip and was then briefly covalently stabilized, coupling via primary amines. The significant baseline drift observed due to dissociation of weakly bound His-CypA from the Ni2+-NTA moiety was eliminated, resulting in a surface that was stable for at least 36 h. In addition, immobilized protein activity levels were high, typically between 85 and 95%, assayed by the interaction between His-CypA and CsA. The mean equilibrium dissociation constant for CsA (K(dCsA)) binding to the immobilized His-CypA was 23+/-6 nM, with on and off rates of 0.53+/-0.1 microM(-1) s(-1) and 1.2+/-0.1 (x 10(-2)) s(-1), respectively. These values agree well with the values for the corresponding binding constants determined from steady-state and kinetic fluorescence titrations in solution.     

Heterotrimeric type I collagen C-telopeptide conformation as docked to its helix receptor

The amino (N-telo) and carboxyl (C-telo) telopeptides of type I collagen play crucial roles, in vivo and in vitro, in the assembly of collagen fibrils, regulating the axial alignment of the molecules within a fibril, azimuthal orientations of neighboring molecules, and cross-link formation. High-resolution structures of the telopeptides are not available from X-ray diffraction studies, but computational methods permitted prediction of the N-telo structure within a fibril. Here, using a suite of molecular modeling software, the more complex heterotrimeric C-telo of human type I collagen has been built from the correct sequences and energy minimized and the energy minimum confirmed by molecular dynamics. The receptor triple helix was modeled on the basis of the Protein Data Bank coordinates of a collagen-like sequence. Docking of the heterotrimeric C-telopeptide to its receptor showed that hydrophobic interactions involving the short alpha2 C-telopeptide are crucial determinants of its azimuthal orientation within the docked structure. A docked C-telo can interact with only one neighboring helix. The two alpha1(I) C-telo chains in the alpha1(Alpha)-alpha2-alpha1(B) chain stagger do not have identical docked conformations, and one of the alpha1(I) C-telo chains appears to be favored for formation of a cross-link between its K(16C) and a helix K87. Prior studies showed that a docked N-telopeptide can interact with two adjacent collagen monomers, forming a tightly packed region. A recent X-ray analysis showed the N- and C-telo regions pack differently, with the C-telo region being less densely packed than N-telo regions. This difference between N- and C-telopeptide docked structures demonstrates how unique and specific packing can occur in the fibril at each boundary of the type I collagen gap region.     

Homogeneity of the 16S rDNA sequence among geographically disparate isolates of Taylorella equigenitalis

Background

At present, six accessible sequences of 16S rDNA from Taylorella equigenitalis (T. equigenitalis) are available, whose sequence differences occur at a few nucleotide positions. Thus it is important to determine these sequences from additional strains in other countries, if possible, in order to clarify any anomalies regarding 16S rDNA sequence heterogeneity. Here, we clone and sequence the approximate full-length 16S rDNA from additional strains of T. equigenitalis isolated in Japan, Australia and France and compare these sequences to the existing published sequences.

Results

Clarification of any anomalies regarding 16S rDNA sequence heterogeneity of T. equigenitalis was carried out. When cloning, sequencing and comparison of the approximate full-length 16S rDNA from 17 strains of T. equigenitalis isolated in Japan, Australia and France, nucleotide sequence differences were demonstrated at the six loci in the 1,469 nucleotide sequence. Moreover, 12 polymorphic sites occurred among 23 sequences of the 16S rDNA, including the six reference sequences.

Conclusion

High sequence similarity (99.5% or more) was observed throughout, except from nucleotide positions 138 to 501 where substitutions and deletions were noted.     

Adaptive divergence in experimental populations of Pseudomonas fluorescens. II. Role of the GGDEF regulator WspR in evolution and development of the wrinkly spreader phenotype

Wrinkly spreader (WS) genotypes evolve repeatedly in model Pseudomonas populations undergoing adaptive radiation. Previous work identified genes contributing to the evolutionary success of WS. Here we scrutinize the GGDEF response regulator protein WspR and show that it is both necessary and sufficient for WS. Activation of WspR occurs by phosphorylation and different levels of activation generate phenotypic differences among WS genotypes. Five alleles of wspR, each encoding a protein with a single amino acid substitution, were generated by mutagenesis. Two alleles are constitutively active and cause the ancestral genotype to develop a WS phenotype; the phenotypic effects are allele specific and independent of phosphorylation. Three alleles contain changes in the GGDEF domain and when overexpressed in WS cause reversion to the ancestral phenotype. Ability to mimic this effect by overexpression of a liberated N-terminal domain shows that in WS, regulatory components upstream of WspR are overactive. To connect changes at the nucleotide level with fitness, the effects of variant alleles were examined in both structured and unstructured environments: alleles had adaptive and deleterious effects with trade-offs evident across environments. Despite the proclivity of mutations within wspR to generate WS, sequence analysis of wspR from 53 independently obtained WS showed no evidence of sequence change in this gene.     

In situ adaptation and ecological release facilitate the occupied niche expansion of a non‐native Madagascan day gecko in Florida

AimTo investigate whether the frequently advocated climate‐matching species distribution modeling approach could predict the well‐characterized colonization of Florida by the Madagascar giant day gecko Phelsuma grandis.LocationMadagascar and Florida, USA.MethodsTo determine the climatic conditions associated with the native range of P. grandis, we used native‐range presence‐only records and Bioclim climatic data to build a Maxent species distribution model and projected the climatic thresholds of the native range onto Florida. We then built an analogous model using Florida presence‐only data and projected it onto Madagascar. We constructed a third model using native‐range presences for both P. grandis and the closely related parapatric species P. kochi.ResultsDespite performing well within the native range, our Madagascar Bioclim model failed to identify suitable climatic habitat currently occupied by P. grandis in Florida. The model constructed using Florida presences also failed to reflect the distribution in Madagascar by overpredicting distribution, especially in western areas occupied by P. kochi. The model built using the combined P. kochi/P. grandis dataset modestly improved the prediction of the range of P. grandis in Florida, thereby implying competitive exclusion of P. grandis by P. kochi from habitat within the former''s fundamental niche. These findings thus suggest ecological release of P. grandis in Florida. However, because ecological release cannot fully explain the divergent occupied niches of P. grandis in Madagascar versus Florida, our findings also demonstrate some degree of in situ adaptation in Florida.Main conclusionsOur models suggest that the discrepancy between the predicted and observed range of P. grandis in Florida is attributable to either in situ adaptation by P. grandis within Florida, or a combination of such in situ adaptation and competition with P. kochi in Madagascar. Our study demonstrates that climate‐matching species distribution models can severely underpredict the establishment risk posed by non‐native herpetofauna.     

Impact of neonicotinoid seed treatments on thrips (Thysanoptera: Thripidae) and soybean yield in Virginia and North Carolina

Currently there are several neonicotinoid insecticide seed treatments registered for use on soybean (Glycine max L.), with disparity in adoption rates in the eastern United States. A complex of seedling insect pests is found in mid-south soybean, but thrips are the primary early season pest of soybean in Virginia and North Carolina. Published knowledge regarding their impact on soybean yield is minimal, as is the impact of thrips on soybean yield; thrips species composition is also understudied. In 2008 through 2010, nine field experiments in Virginia and North Carolina were conducted to evaluate the impact on thrips population dynamics; the influence on yield of neonicotinoid seed treatments, imidacloprid and thiamethoxam, was reported from nine of these experiments. Moreover, thrips species abundance was recorded in three of these experiments. Both imidacloprid and thiamethoxam reduced thrips densities compared with untreated soybean. Thiamethoxam was more effective than imidacloprid in reducing adult thrips densities at 5 wk after planting. Adult densities peaked at 3 wk after planting, followed by larval densities, which peaked at 4 wk after planting. The most abundant thrips species was Frankliniella fusca (Hinds), followed by Neohydatothrips variabilis (Beach). Other common species included F. occidentalis (Pergande) and F. tritici (Fitch). In general, F. fusca was more common earlier in the season, while N. variabilis was more common later in the season. There were no significant differences in yield among any of the treatments or in the untreated controls. Although neonicotinoid insecticides reduced thrips abundance, data collected in these studies demonstrated that there was no positive yield response.