Research Design, Soil and Biodiversity Baseline for Long-term Farming Systems Comparison of Full Sun and Shaded Agroforestry Cocoa Production under Conventional and Organic Management in Alto Beni, Bolivia

Cocoa, mainly produced by 5 to 6 millions of smallholder farmers, is considered as one of the most sustainable production system in the humid tropics. Little is known about the sustainability of different cocoa production systems. A long-term experiment is set up in Alto Beni at 400m above sea level with a humid winter dry climate, 1’540 mm annual rainfall. The trial assesses the sustainability of five cocoa (Theobroma cacao) production systems with the parameters of yield and yield stability, input-output efficiency of nutrients and energy, soil fertility, biodiversity, economic result, climate change mitigation and adaptation. The two-factorial experiment is arranged in an completely randomised block design; the five cocoa treatments, based on local and international practices, are four times repeated. The production systems are differentiated by the diversity of shade canopy and by crops, from mono culture full sun cocoa to a agroforestry cocoa with leguminous species (Inga edulis, Erythrina poeppigiana) shade canopy, including fruits (e.g. Euterpe precatoria, Theobroma grandiflorum) and timber (e.g. Centrolobium ochroxylum, Swietenia macrophylla) species, and a higher diversified agroforestry system based on the natural successions of species. The management of the cocoa is conventional and organic. The five treatments are: mono culture full sun cocoa conventional, mono culture full sun organic, agroforestry conventional, agroforestry organic and successional agroforestry organic. Fallow plots and nearby forests plots are monitored for soil fertility and biodiversity. Field clearing started in 2007 followed by maize (Zea mays) crop and end of 2008 the cocoa plots (48m×48 m) were established. The results of the baseline studies concerning soil fertility show good nutrient level for cocoa production; the variance of soil parameters is documented in a soil map. According the FAO soil classification (2006) the soils are Lixisole and Luvisole with high base saturation

Transformation and regeneration of the holoparasitic plant Phelipanche aegyptiaca

<p>Abstract</p> <p>Background</p> <p>Transformation and subsequent regeneration of holoparasitic plants has never been reported, in part due to challenges in developing transformation protocols, but also because regeneration of obligate parasites is difficult since their survival depends completely on successful haustorium penetration of a host and the formation of vascular connections. The recent completion of a massive transcriptome sequencing project (the Parasitic Plant Genome Project) will fuel the use of genomic tools for studies on parasitic plants. A reliable system for holoparasite transformation is needed to realize the full value of this resource for reverse genetics and functional genomics studies.</p> <p>Results</p> <p>Here we demonstrate that transformation of <it>Phelipanche aegyptiaca </it>is achieved by infection of 3 month-old <it>in vitro </it>grown <it>P. aegyptiaca </it>calli with <it>Agrobacterium rhizogenes </it>harboring the yellow fluorescent protein (YFP). Four months later, YFP-positive regenerated calli were inoculated onto tomato plants growing in a minirhizotron system. Eight days after inoculation, transgenic parasite tissue formed lateral haustoria that penetrated the host and could be visualized under UV illumination through intact host root tissue. YFP-positive shoot buds were observed one month after inoculation.</p> <p>Conclusions</p> <p>This work constitutes a breakthrough in holoparasitic plant research methods. The method described here is a robust system for transformation and regeneration of a holoparasitic plant and will facilitate research on unique parasitic plant capabilities such as host plant recognition, haustorial formation, penetration and vascular connection.</p

Improving Phrap-Based Assembly of the Rat Using “Reliable” Overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of “reliable” overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our “reliable-overlap” algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps

Ampliación de la distribución geográfica de Liolaemus variegatus Laurent 1984 (Iguania: Liolaemidae) en Bolivia

Según el modelo de distribución potencial para Liolaemus variegatus desarrollado por Embert (2007), la especie se encontraría únicamente en el departamento de Cochabamba, con una distribución restringida a nivel nacional, razón por la cual, está considerada como especie vulnerable en el libro rojo de los vertebrados de Bolivia. Sin embargo, una revisión rigurosa de varios ejemplares depositados en la Colección Boliviana de Fauna, muestra que Liolaemus variegatus se distribuye hasta el departamento de Tarija al sur de Bolivia, ampliando su distribución conocida a 517 km aproximadamente de la localidad tipo (Tiraque, Cochabamba).Asociación Herpetológica Argentin

A consensus prognostic gene expression classifier for ER positive breast cancer.

BACKGROUND: A consensus prognostic gene expression classifier is still elusive in heterogeneous diseases such as breast cancer. RESULTS: Here we perform a combined analysis of three major breast cancer microarray data sets to hone in on a universally valid prognostic molecular classifier in estrogen receptor (ER) positive tumors. Using a recently developed robust measure of prognostic separation, we further validate the prognostic classifier in three external independent cohorts, confirming the validity of our molecular classifier in a total of 877 ER positive samples. Furthermore, we find that molecular classifiers may not outperform classical prognostic indices but that they can be used in hybrid molecular-pathological classification schemes to improve prognostic separation. CONCLUSION: The prognostic molecular classifier presented here is the first to be valid in over 877 ER positive breast cancer samples and across three different microarray platforms. Larger multi-institutional studies will be needed to fully determine the added prognostic value of molecular classifiers when combined with standard prognostic factors

Primer registro de <i>Liolaemus pleopholis</i> Laurent, 1998 para Bolivia (Reptilia, Squamata, Liolaemidae)

La revisión exhaustiva en los ejemplares del grupo Liolaemus montanus depositados en la Colección Boliviana de Fauna permite ampliar la distribución geográfica de la especie Liolaemus pleopholis de oeste a este llegando a territorio boliviano y considerarla como un primer registro para el país.Asociación Herpetológica Argentina (AHA

A Computational study of NaVOPO4 polymorphs as cathode materials for Na-Ion batteries: Diffusion, electronic properties and cation doping behavior

Rechargeable sodium-ion batteries have gained interest as potential alternatives to lithium-ion batteries, owing to their low cost and the wide abundance of sodium. Phosphate compounds are promising materials for sodium-ion batteries because of their high structural stability. Vanadium phosphates have shown high energy densities as cathode materials, but their Na-ion transport and cation doping properties are not as yet fully understood. Here, we have combined density functional theory calculations and molecular dynamics techniques to study the diffusion, electronic properties and cation doping of the α-, β- and αI-NaVOPO4 polymorphs. The calculated Na-ion activation energies of these compounds (0.3–0.5 eV) are typical for Na-based cathode materials and the simulations predict Na-ion diffusion coefficients of 10-11–10-12 cm2 s-1. The cell voltage trends show an operating range of 3.1–3.3 V vs. Na/Na+, with the partial substitution of vanadium by other metals (Al3+, Co2+, Fe3+, Mn4+, Ni2+ or Ti4+) increasing the cell voltage by up to 0.2–1.0 V vs. Na/Na+. Our study provides new quantitative insights into the electrochemical behavior of a potentially important class of phosphate cathode materials for sodium-ion batteries