Importing statistical measures into Artemis enhances gene identification in the Leishmania genome project

BACKGROUND: Seattle Biomedical Research Institute (SBRI) as part of the Leishmania Genome Network (LGN) is sequencing chromosomes of the trypanosomatid protozoan species Leishmania major. At SBRI, chromosomal sequence is annotated using a combination of trained and untrained non-consensus gene-prediction algorithms with ARTEMIS, an annotation platform with rich and user-friendly interfaces. RESULTS: Here we describe a methodology used to import results from three different protein-coding gene-prediction algorithms (GLIMMER, TESTCODE and GENESCAN) into the ARTEMIS sequence viewer and annotation tool. Comparison of these methods, along with the CODONUSAGE algorithm built into ARTEMIS, shows the importance of combining methods to more accurately annotate the L. major genomic sequence. CONCLUSION: An improvised and powerful tool for gene prediction has been developed by importing data from widely-used algorithms into an existing annotation platform. This approach is especially fruitful in the Leishmania genome project where there is large proportion of novel genes requiring manual annotation

Effects of elevated [CO2 ] on maize defence against mycotoxigenic Fusarium verticillioides.

Maize is by quantity the most important C4 cereal crop; however, future climate changes are expected to increase maize susceptibility to mycotoxigenic fungal pathogens and reduce productivity. While rising atmospheric [CO2 ] is a driving force behind the warmer temperatures and drought, which aggravate fungal disease and mycotoxin accumulation, our understanding of how elevated [CO2 ] will effect maize defences against such pathogens is limited. Here we report that elevated [CO2 ] increases maize susceptibility to Fusarium verticillioides proliferation, while mycotoxin levels are unaltered. Fumonisin production is not proportional to the increase in F. verticillioides biomass, and the amount of fumonisin produced per unit pathogen is reduced at elevated [CO2 ]. Following F. verticillioides stalk inoculation, the accumulation of sugars, free fatty acids, lipoxygenase (LOX) transcripts, phytohormones and downstream phytoalexins is dampened in maize grown at elevated [CO2 ]. The attenuation of maize 13-LOXs and jasmonic acid production correlates with reduced terpenoid phytoalexins and increased susceptibility. Furthermore, the attenuated induction of 9-LOXs, which have been suggested to stimulate mycotoxin biosynthesis, is consistent with reduced fumonisin per unit fungal biomass at elevated [CO2 ]. Our findings suggest that elevated [CO2 ] will compromise maize LOX-dependent signalling, which will influence the interactions between maize and mycotoxigenic fungi

Full coherent control of nuclear spins in an optically pumped single quantum dot

Highly polarized nuclear spins within a semiconductor quantum dot (QD) induce effective magnetic (Overhauser) fields of up to several Tesla acting on the electron spin or up to a few hundred mT for the hole spin. Recently this has been recognized as a resource for intrinsic control of QD-based spin quantum bits. However, only static long-lived Overhauser fields could be used. Here we demonstrate fast redirection on the microsecond time-scale of Overhauser fields of the order of 0.5 T experienced by a single electron spin in an optically pumped GaAs quantum dot. This has been achieved using full coherent control of an ensemble of 10^3-10^4 optically polarized nuclear spins by sequences of short radio-frequency (rf) pulses. These results open the way to a new class of experiments using rf techniques to achieve highly-correlated nuclear spins in quantum dots, such as adiabatic demagnetization in the rotating frame leading to sub-micro K nuclear spin temperatures, rapid adiabatic passage, and spin squeezing

Comparative description of land use and characteristics of belowground biodiversity benchmark sites in Kenya = Descripción comparativa de usos del suelo y características de la diversidad del subsuelo en sitios empleados como referencia en Kenia

In Kenya, the below-ground biodiversity (BGBD) project selected two benchmark sites for the inventory of soil biota; these included the Irangi and Ngangao forest sites in the Mount Kenya region of Embu District and the Taita Hills area of Taita Taveta District. The areas selected by the project were located in biodiversity hotspots that are supporting rare and endemic plant and animal species. For more in-depth studies and analysis, the broader Embu and Taita benchmark areas were further sub-sampled into smaller areas that we refer to as study areas, designated by the symbols E1 and E2 for Embu and T1 and T2 for Taita benchmark. Within the study areas, we plotted and sampled 200x200 square grids for collecting soil as well as socio-economic data. Site characterization was carried out using the method provided by FAO-UNESCO for characterizing and classifying soils. Further to this, attempts were made to establish land use intensity (LUI) and land productivity (PI) indices that provided land condition indicators. The indicators offered insights into the quantitative relationship between the environmental conditions and land use. Parameters used in the computation of the land use intensity were; total quantity of inputs per ha, the frequency of input application, cropping intensity and cultivation frequency. The soils in Taita Taveta benchmark site were classified as Plinthic Lixisols, Plinthic Acrisols, Dystric Cambisols and Chromic Luvisols, while those from Embu ones were Rhodic Nitisols, Humic Nitisols, Humic Acrisols, Haplic Acrisols and Umbric Andosols. The highest level of soil organic carbon recorded was 7.6% in the forest and the lowest value of 1.6% in intensely cultivated maize-based and horticultural systems. Low land use intensity gradients were observed in the forests (LUI40%). The productivity index (PI) followed a similar trend, being highest in the natural forest and grassland (40-50%) and lowest in horticultural and maize-based systems (15-20%) It was concluded that the decline in soil quality and productivity was linked to increased land use intensification and lack of knowledge of the appropriate management practices for sustainable ecosystem functions and services

Ectoparasitic fauna of poultry species in Maiduguri, Borno State, Nigeria

Ectoparasitic fauna of 397 conveniently sampled domestic birds consisting of 213 chickens, 128 turkeys, 21 ducks, 19 guinea fowls, 8 pigeons and 8 geese were investigated in Maiduguri, Borno State. A total of one hundred and fifty-two 152 (38.29%) birds were infested with one ectoparasitic species or the other comprising of 115 (54.00%) chickens, 33 (25.78%) turkeys, 1 (5.26%) guinea fowl and 3 (37.50%) pigeons. No infestation was encountered among geese and ducks examined. The infestation rate differed significantly based on sex and age (p<0.05), but not the management system. Similarly, the occurrence varied significantly (p<0.05) based on locations of sampling (p<0.00001) and species of poultry examined (p<0.000049). Furthermore, 116 (29.21%) of the total birds examined had a single infestation with either louse, tick or mite species, while 36(9.06%) birds had mixed infestation with species from two or more of these ectoparasitic groups. Among the parasites encountered, lice present on 146 (36.77%) birds were the most prevalent, followed by mites 28(7.05%) and ticks 15(3.78%). Nine different species of ectoparasites belonging to the orders Mallophaga and Acarina were identified in the study. Menopon gallinae, Lipeurus caponis, Menacanthus stramineus, Goniodes gigas, Goniocotes gallinae and Columbicola columbae were the lice identified, while Cnemidocoptes mutans and Ornithonyssus bursa were the only species of mite identified. The poultry tick, Argas persicus was the only tick species found. Conclusively, the study revealed a high but variable burden of ectoparasitic infestation among poultry species examined, and that ectoparasites are common in minor poultry species as they do occur in chickens under different management systems in the study area. The need to investigate the diverse effects of ectoparasitism on the different poultry species is suggested here

The high correlation between counts and area fractions of lipofuscin granules, a biomarker of oxidative stress in muscular dystrophies

Images of cryostat unstained sections of two skeletal muscles, diaphragm and extensor digitorum longus (EDL), from wild-type normal and dystrophic mdx mice were captured with a fluorescence microscope, binarised and analysed by an automated procedure using ImageJ free software. The numbers, Feret diameters and areas of autofluorescent lipofuscin (LF)-like granules in the sections were determined from the binary images. The mean numbers of counted LF granules per mm(3) muscle tissue correlated highly (r ≥ 0.9) with the area fractions of the granules in sections of both normal and mdx muscles. The similar distribution patterns of granule sizes in sections of diaphragm and EDL muscles are consistent with the high correlations

Microcavity controlled coupling of excitonic qubits

Controlled non-local energy and coherence transfer enables light harvesting in photosynthesis and non-local logical operations in quantum computing. The most relevant mechanism of coherent coupling of distant qubits is coupling via the electromagnetic field. Here, we demonstrate the controlled coherent coupling of spatially separated excitonic qubits via the photon mode of a solid state microresonator. This is revealed by two-dimensional spectroscopy of the sample's coherent response, a sensitive and selective probe of the coherent coupling. The experimental results are quantitatively described by a rigorous theory of the cavity mediated coupling within a cluster of quantum dots excitons. Having demonstrated this mechanism, it can be used in extended coupling channels - sculptured, for instance, in photonic crystal cavities - to enable a long-range, non-local wiring up of individual emitters in solids

Hospitalization for heart disease, stroke, and diabetes mellitus among Indian-born persons: a small area analysis

BACKGROUND: We set out to describe the risk of hospitalization from heart disease, stroke, and diabetes among persons born in India, all foreign-born persons, and U.S.-born persons residing in New York City. METHODS: We examined billing records of 1,083,817 persons hospitalized in New York City during the year 2000. The zip code of each patient's residence was linked to corresponding data from the 2000 U.S. Census to obtain covariates not present in the billing records. Using logistic models, we evaluated the risk of hospitalization for heart disease, stroke and diabetes by country of origin. RESULTS: After controlling for covariates, Indian-born persons are at similar risk of hospitalization for heart disease (RR = 1.02, 95% confidence interval 1.02, 1.03), stroke (RR = 1.00, 95% confidence interval, 0.99, 1.01), and diabetes mellitus (RR = 0.96 95% confidence interval 0.94, 0.97) as native-born persons. However, Indian-born persons are more likely to be hospitalized for these diseases than other foreign-born persons. For instance, the risk of hospitalization for heart disease among foreign-born persons is 0.70 (95% confidence interval 0.67, 0.72) and the risk of hospitalization for diabetes is 0.39 (95% confidence interval 0.37, 0.42) relative to native-born persons. CONCLUSIONS: South Asians have considerably lower rates of hospitalization in New York than reported in countries with national health systems. Access may play a role. Clinicians working in immigrant settings should nonetheless maintain a higher vigilance for these conditions among Indian-born persons than among other foreign-born populations