Targeting metabolic pathways proteins of Orientia tsutsugamushi using combined hierarchical approach to combat scrub typhus

Orientia tsutsugamushi (Ott) is a causative agent of chigger‐borne zoonosis, scrub typhus which is life threatening and highly pervasive illness in humans. In this report, we have mined and classified the proteins involved in pathways unique to Ott by using high‐throughput computational techniques. The 12 metabolic pathways were found to be unique to the pathogen. Forty‐six proteins were reported to be essential for the pathogen's survival and non‐homologous to the humans. The proteins were categorized into different classes, ie, enzymes, transporters, DNA‐binding, secretory, and outer membrane proteins. Further, in silico analysis of 46 proteins showed that 25 proteins were suitable therapeutic targets with known druggable properties. The structural modeling of B3CSG3 (MurA) protein was carried out and catalytic site essential for its functioning was analyzed. Virtual screening of chemical compounds was performed against modeled structure. The docking study by AutodockVina reported compound from PubChem with CID: 16036947 as best and potential inhibitor by means of docking score and binding affinity. The reliability and stability of the MurA‐16036947 complex were confirmed with molecular dynamics simulation. The report will provide insight to understand the mechanism of pathogenesis of Ott and instigate the development of effective treatment strategies against this disease.     

Elevated CO2 increases nitrogen fixation and decreases soil nitrogen mineralization in Florida scrub oak

We report changes in nitrogen cycling in Florida scrub oak in response to elevated atmospheric CO₂ during the first 14 months of experimental treatment. Elevated CO₂ stimulated above-ground growth, nitrogen mass, and root nodule production of the nitrogen-fixing vine, Galactia elliottii Nuttall. During this period, elevated CO₂ reduced rates of gross nitrogen mineralization in soil, and resulted in lower recovery of nitrate on resin lysimeters. Elevated CO₂ did not alter nitrogen in the soil microbial biomass, but increased the specific rate of ammonium immobilization (NH₄⁺ immobilized per unit microbial N) measured over a 24-h period. Increased carbon input to soil through greater root growth combined with a decrease in the quality of that carbon in elevated CO₂ best explains these changes. These results demonstrate that atmospheric CO₂ concentration influences both the internal cycling of nitrogen (mineralization, immobilization, and nitrification) as well as the processes that regulate total ecosystem nitrogen mass (nitrogen fixation and nitrate leaching) in Florida coastal scrub oak. If these changes in nitrogen cycling are sustained, they could cause long-term feedbacks to the growth responses of plants to elevated CO₂. Greater nitrogen fixation and reduced leaching could stimulate nitrogen-limited plant growth by increasing the mass of labile nitrogen in the ecosystem. By contrast, reduced nitrogen mineralization and increased immobilization will restrict the supply rate of plant-available nitrogen, potentially reducing plant growth. Thus, the net feedback to plant growth will depend on the balance of these effects through time.     

Monthly Occurrence of Vectors and Reservoir Rodents of Scrub Typhus in an Endemic Area of Jeollanam-do, Korea

Monthly surveys were conducted to investigate the occurrence of chigger mites and seroprevalence of scrub typhus among small mammals in Jeollanam-do, the southwestern part of Korea, from November 2006 through October 2007. Fifty-eight small mammals, including 57 Apodemus agrarius (98.3%) and 1 Crocidura lasiura (1.7%), were captured, and a total of 4,675 chigger mites representing 4 genera and 8 species were collected from them. The chigger infestation rate among small mammals was 69.0%. The most predominant species in A. agrarius was Leptotrombidium scutellare (54.0%), followed by Leptotrombidium pallidum (39.4%), Leptotrombidium orientale (4.4%), Leptotrombidium palpale (1.1%), Neotrombicula tamiyai (0.6%), Eushoengastia koreaensis (0.3%), Neotrombicula gardellai (0.3%), and Cheladonta ikaoensis (<0.1%). The chigger index of A. agrarius was the highest in October (740.0), followed by November (242.0), September (134.6), March (98.3), February (38.2), January (35.3), December (34.5), April (30.8), and May (1.7). The average antibody positive rate of scrub typhus in wild rodents was 50.0%. The seropositive rates were high in October (100.0%) and November (83.3%), whereas those in other months were relatively low (28.6-57.1%). The chigger index of L. scutellare rapidly increased in September to form an acuminate peak in October, followed by a gradual decline. These results suggest that the outbreak of scrub typhus in the southwestern part of Korean peninsula is mostly due to L. scutellare.     

Mating systems and limits to seed production in two Dicerandra mints endemic to Florida scrub

We used hand-pollination experiments to test the mating systems of and evaluate limits to seed production in two federally listed endangered plants endemic to the Lake Wales Ridge in Florida, USA: Dicerandra frutescens Shinners ssp. frutescens Huck and D. christmanii Huck and Judd (Lamiaceae). Both are nonclonal, short-lived perennials found in gaps created by disturbance (e.g., fire, roads) in Florida scrub. We found that both species require pollen and insect visitation to produce seeds. We detected pollinator limitation of seed production in D. christmanii but not D. frutescens ssp. frutescens, which we suggest is a function of time-since-disturbance or gap size rather than intrinsic differences between the two species. Both species are self-compatible. Inbreeding depression reduced seed set by 60% in D. frutescens ssp. frutescens but did not occur in D. christmanii. We conclude that pollinator limitation (in fire-suppressed populations of both species) and inbreeding depression (in D. frutescens ssp. frutescens) have the potential to limit seed production in these seed-dependent, rare species. Appropriate fire management should mitigate both of these risks, by maintaining large populations and conditions attractive to pollinators. Although these two species are very similar in reproductive biology, comparisons with other Florida scrub endemics and with rare plants in general suggest that potential threats to conservation via reproductive biology are difficult to predict, depending on combinations of ecology, life-history, and phylogenetic history.     

Woody vegetation composition and diversity in woodlands inside and outside a Forest Reserve in Jos,Nigeria

Protected areas such as forest reserves are often assumed to be best ways to conserve biodiversity and maintain intact ecosystems. We examined woody plant composition and diversity in the gallery forest and savannah woodland habitats of Amurum Forest Reserve and areas immediately surrounding it in Jos, Nigeria. A total of 100 10 × 10 m sample plots were established inside and outside the reserve. All woody plants ≥1 cm diameter at breast height (dbh) were identified and measured. A total of 7,564 individual plants categorized as 134 species from 44 families were recorded. Overall species diversity was significantly higher in the Forest Reserve than outside the reserve, although more species were encountered outside the reserve. Our findings suggest that, protected areas and the areas surrounding them are important for the conservation of biodiversity as the areas outside protected areas also contain species of conservation value. The continuous degrading areas outside protected areas isolates them and poses a serious threat to the long‐term viability of wildlife populations, so it is important that biodiversity in protected areas and their surrounding areas be conserved.     

New breeding localities of Worthen's Sparrows in northeastern Mexico

ABSTRACT.   Worthen's Sparrows ( Spizella wortheni ) are endemic to the Mexican Plateau and have been listed as globally endangered. The breeding biology of these sparrows is poorly understood, and nesting is only known to occur at three locations (Las Esperanzas, Nuevo León, and La India and Tanque de Emergencia, Coahuila). In June and July 2006, we searched for nests of  Worthen's Sparrows and located three new breeding localities: La Carbonera and San Rafael in the state of Nuevo León, and San José del Alamito in the state of Coahuila. We subsequently sampled vegetation where nests were located and, on 26 August 2006, conducted surveys along 1-km transects at the three new breeding locations as well as at El Erial-La Casita, Nuevo León. We recorded the most Worthen's Sparrows at El Erial-La Casita ( N = 33), followed by San José del Alamito ( N = 9), San Rafael ( N = 6), and La Carbonera ( N = 3). No nests were located at El Erial-La Casita, but small groups of sparrows that included juveniles were observed. At the three breeding locations, shrub strata were dominated by tarbush ( Flourensia cernua ; San José del Alamito and La Carbonera) and Berlandier's wolfberry ( Lycium berlandieri ; San Rafael). Most (68%) recently recorded nests for this species have been found in tarbush. Historical and recent data (including our study) suggest that Worthen's Sparrows typically breed in grassland habitat where shrubs of some type are also present. Because conversion of land to agriculture continues to be a major threat to grasslands in northeastern Mexico, we recommend that conservation efforts be implemented to protect the known breeding areas of Worthen's Sparrow.     

Water and carbon storage capacity in Isolatocereus dumortieri (Cactaceae) in an intertropical semiarid zone in Mexico

In the biosphere reserve Barranca de Metztitlán in Mexico, there is an extensive area with a semiarid scrub. The dominant species is the cactus Isolatocereus dumortieri. This is a key species in the ecosystem, because many species of birds, bats and insects are feeding from its nectar, pollen and fruits during the dry season thanks to their capacity to store water and carbon. However, there is no information about their potential to store water and carbon. The purpose of this study was to estimate the ability of I. dumortieri to store water and carbon. Water content per plant was estimated as 537.64 ± 71.59 L during the dry season and 692.24 ± 92.18 L during the wet season. In the same way the carbon stored per cactus was 16.75 kg ± 7.07 corresponding to 1.25 kg C m². The results shows the importance of I. dumortieri in maintaining the ecosystem services of the scrub vegetation.     

Functional groups based on leaf physiology: are they spatially and temporally robust?

The functional grouping concept, which suggests that complexity in ecosystem function can be simplified by grouping species with similar responses, was tested in the Florida scrub habitat. Functional groups were identified based on how species regulate exchange of carbon and water with the atmosphere as indicated by both instantaneous gas exchange measurements and integrated measures of function (%N, δ¹³C, δ¹⁵N, C:N ratio) in fire-maintained Florida scrub, which was considered the natural state for scrub habitat. Using cluster analysis, five distinct physiologically based functional groups were identified in the fire-maintained scrub and were determined to be distinct clusters and not just arbitrary divisions in a continuous distribution by the non-parametric multivariate analysis of similarities (ANOSIM; R=0.649, P=0.005). These functional groups were tested for robustness spatially, temporally, and with management regime using ANOSIM. The physiological functional groups remained distinct clusters in this broader array of sites (R=0.794, P=0.001) and were not altered by plot differences, primarily, water table depth (R=−0.115, P=0.893) or by the three different management regimes: prescribed burn, mechanically treated and burned, and fire-suppressed (R=0.018, P=0.349). The physiological groupings also remained robust between the two climatically different years, with 1999 being a much wetter year than 2000 (R=−0.027, P=0.725). Easy-to-measure morphological characteristics, if they indicate the same functional groups, would be more practical for scaling and modeling ecosystem processes than detailed gas exchange measurements; therefore, we tested a variety of morphological characteristics as functional indicators. A combination of non-parametric multivariate techniques were used to compare the ability of life form, leaf thickness (LT), and specific leaf area (SLA) classifications to identify the physiologically based functional groups. Life form classifications (ANOSIM; R=0.629, P=0.001) were able to depict the physiological groupings more adequately than either SLA (ANOSIM; R=0.426, P=0.001) or LT (ANOSIM; R=0.344, P=0.001). The ability of life forms to depict the physiological groupings was improved by separating the parasitic Ximenia americana from the shrub category (ANOSIM; R=0.794, P=0.001). Therefore, a life form classification including parasites was determined to be a good indicator of the physiological processes of scrub species and would be a useful method of grouping species for scaling physiological processes to the ecosystem level.     

Composition and ecological drivers of the kwongan scrub and woodlands in the northern Swan Coastal Plain,Western Australia

The nature of community patterns and environmental drivers in kwongan mediterranean‐type shrubland on nutrient‐poor soils occurring in Western Australia remain poorly examined. We aimed to determine whether (i) classification of the kwongan vegetation of the northern Swan Coastal Plain would be ecologically informative and (ii) which environmental drivers underpin the plant community patterns. The study area was positioned on the northern Swan Coastal Plain, locality of Cooljarloo (30°39′ S, 115°22′ E), situated 170 km north of Perth, Western Australia. Compositional (518 species × 337 relevés) and environmental data set (29 variables × 87 relevés) describing time since last fire, soil chemical and physical properties, and terrain characteristics were analysed using classification and ordination techniques. OptimClass assisted in the selection of a robust data transformation, resemblance function and clustering algorithm to identify the vegetation patterns. Major ecological drivers of the vegetation patterns were detected using distance‐based redundancy analysis (db‐RDA). Classification revealed major groupings of Wet Heath and Banksia Woodland distinguishable by the high prevalence of myrtyoid and proteoid taxa, respectively. On floristic‐sociological grounds, we recognised four Wet Heath and two Banksia Woodland communities. The Wet Heath was constrained to areas of higher litter depth (db‐RDA axis 1: 9%). Soil chemical and physical properties explained the highest proportion (17%) of the compositional variance, while the terrain‐ and fire‐related variables explained 2% and <0.001%, respectively. While fire explained little compositional variance overall, a separate db‐RDA analysis found that it may play an important pattern‐structuring role within Banksia Woodlands. Fine‐scale compositional patterns correspond only to a small extent to environmental data; the substantial unexplained variance may be due to slow‐acting neutral and stochastic processes.