Structural variant calling: the long and the short of it.

Recent research into structural variants (SVs) has established their importance to medicine and molecular biology, elucidating their role in various diseases, regulation of gene expression, ethnic diversity, and large-scale chromosome evolution-giving rise to the differences within populations and among species. Nevertheless, characterizing SVs and determining the optimal approach for a given experimental design remains a computational and scientific challenge. Multiple approaches have emerged to target various SV classes, zygosities, and size ranges. Here, we review these approaches with respect to their ability to infer SVs across the full spectrum of large, complex variations and present computational methods for each approach

Designing Spiral Plate Heat Exchangers to Extend Its Service and Enhance the Thermal and Hydraulic Performance

Spiral plate heat exchangers are well suitable for handling fluids with features linked to fouling, high viscosities, fluids with suspended fragments of solids and process streams with tough heat transfer targets. Correlations to describe the thermal and hydraulic performance are a function of the geometrical configuration of the equipment. The present work shows procedures to design spiral plate heat exchangers as a function of the fluid arrangements, government flow, as well whether the thermal equipment is for condensing, cooling or heating duty. An additional study looking for determining the geometrical variables that allow to enhance and improve the thermal and hydraulic performance is presented. Moreover, computational fluid dynamics to validate the thermal and hydraulic method is performed

In-solution Y-chromosome capture-enrichment on ancient DNA libraries.

As most ancient biological samples have low levels of endogenous DNA, it is advantageous to enrich for specific genomic regions prior to sequencing. One approach-in-solution capture-enrichment-retrieves sequences of interest and reduces the fraction of microbial DNA. In this work, we implement a capture-enrichment approach targeting informative regions of the Y chromosome in six human archaeological remains excavated in the Caribbean and dated between 200 and 3000 years BP. We compare the recovery rate of Y-chromosome capture (YCC) alone, whole-genome capture followed by YCC (WGC + YCC) versus non-enriched (pre-capture) libraries. The six samples show different levels of initial endogenous content, with very low (< 0.05%, 4 samples) or low (0.1-1.54%, 2 samples) percentages of sequenced reads mapping to the human genome. We recover 12-9549 times more targeted unique Y-chromosome sequences after capture, where 0.0-6.2% (WGC + YCC) and 0.0-23.5% (YCC) of the sequence reads were on-target, compared to 0.0-0.00003% pre-capture. In samples with endogenous DNA content greater than 0.1%, we found that WGC followed by YCC (WGC + YCC) yields lower enrichment due to the loss of complexity in consecutive capture experiments, whereas in samples with lower endogenous content, the libraries' initial low complexity leads to minor proportions of Y-chromosome reads. Finally, increasing recovery of informative sites enabled us to assign Y-chromosome haplogroups to some of the archeological remains and gain insights about their paternal lineages and origins. We present to our knowledge the first in-solution capture-enrichment method targeting the human Y-chromosome in aDNA sequencing libraries. YCC and WGC + YCC enrichments lead to an increase in the amount of Y-DNA sequences, as compared to libraries not enriched for the Y-chromosome. Our probe design effectively recovers regions of the Y-chromosome bearing phylogenetically informative sites, allowing us to identify paternal lineages with less sequencing than needed for pre-capture libraries. Finally, we recommend considering the endogenous content in the experimental design and avoiding consecutive rounds of capture, as clonality increases considerably with each round

Desempeño profesional del personal de los establecimientos de salud con funciones obstétricas-neonatales de Lima y Provincia del 2015

Objective: To compare the professional performance of the health establishments with essential obstetric and neonatal functions from Lima with respect provincie during September-October of 2015. Materials and methods: It´s a cross- sectional analytical investigation conducted in 350 health establishments with essential obstetric-neonatal functions I-II (FONE I-II) database based on national surveys conducted by the National Institute of Statistics and Informatics (INEI) during 2015. New variables were created from the databases to determinate the gynecology staff´s professional performance and analyzed the data with the R statistical software and the IBM SPSS Statistics 25 using the chi-square test. Results: The investigation showed that midwifes were the healthl staff who most frequently attended vaginal births, both in Lima (62.9%) and in provinces (91.4%). With respect to the partogram, only 5% of the establishments in Lima and 4% of the establishments in the provinces fully registered the partogram. Significant difference in professional performance was found during the vaginal delivery (p= 0.008) and the third stage of labor (p= 0.014). Similarly, we found significant differences in the late cord clamping (p = 0.002) between Lima and provinces. The average clamping time was 2 minutes 30 seconds in both cases and on skin-to-skin contact; it was 13 minutes for Lima and 10 minutes for provinces. Conclusions: There is a gap in professional performance during vaginal delivery care between the FONE I-II establishments in Lima and provinces. Nationally there are still deficits in compliance with the indicators to achieve adequate attention.Objetivo: Comparar el desempeño profesional del personal de los establecimientos de salud con funciones obstétricas-neonatales esenciales I-II entre Lima y Provincias durante el periodo setiembre-octubre del 2015. Materiales y métodos: Es una investigación analítica transversal realizada a 350 establecimientos de salud con funciones obstétricas-neonatales esenciales I-II, basada en las encuestas nacionales realizadas por el Instituto Nacional de Estadística e Informática durante el 2015. Se fusionó 2 bases de datos y se generó nuevas variables para determinar el desempeño laboral y se analizaron los datos con el software estadístico R y el IBM SPSS Statistics 25 usando la prueba chi cuadrado. Resultados: El estudio mostró que el licenciado de obstetricia fue el personal de salud que con más frecuencia atendió partos vaginales, tanto en Lima (62.9%) como en provincias (91.4%). Respecto al partograma, solo un 5% de establecimientos de Lima y un 4% de establecimientos de provincias llenaban de forma completa el partograma. Se encontró diferencia significativa en el desempeño laboral durante el manejo del parto expulsivo (p=0.008) y el alumbramiento (p=0.014). Igualmente, se encontró diferencias significativas en el retraso del clampaje del cordón umbilical (p=0.002) de Lima respecto a provincias. El tiempo promedio del clampaje fue de 2 minutos 30 segundos en ambos casos y sobre el contacto piel a piel, fue de 13 minutos para Lima y 10 minutos para provincias. Conclusiones: Existe una brecha en el desempeño profesional durante la atención del parto vaginal entre los establecimientos FONE I-II de Lima y provincias. Nacionalmente aún existen déficits de cumplimiento de los indicadores para lograr una adecuada atención

The O-mannosylation and production of recombinant APA (45/47 KDa) protein from Mycobacterium tuberculosis in Streptomyces lividans is affected by culture conditions in shake flasks

<p>Abstract</p> <p>Background</p> <p>The Ala-Pro-rich <it>O</it>-glycoprotein known as the 45/47 kDa or APA antigen from <it>Mycobacterium tuberculosis </it>is an immunodominant adhesin restricted to mycobacterium genus and has been proposed as an alternative candidate to generate a new vaccine against tuberculosis or for diagnosis kits. In this work, the recombinant <it>O</it>-glycoprotein APA was produced by the non-pathogenic filamentous bacteria <it>Streptomyces lividans</it>, evaluating three different culture conditions. This strain is known for its ability to produce heterologous proteins in a shorter time compared to <it>M. tuberculosis</it>.</p> <p>Results</p> <p>Three different shake flask geometries were used to provide different shear and oxygenation conditions; and the impact of those conditions on the morphology of <it>S. lividans </it>and the production of rAPA was characterized and evaluated. Small unbranched free filaments and mycelial clumps were found in baffled and coiled shake flasks, but one order of magnitude larger pellets were found in conventional shake flasks. The production of rAPA is around 3 times higher in small mycelia than in larger pellets, most probably due to difficulties in mass transfer inside pellets. Moreover, there are four putative sites of <it>O</it>-mannosylation in native APA, one of which is located at the carboxy-terminal region. The carbohydrate composition of this site was determined for rAPA by mass spectrometry analysis, and was found to contain different glycoforms depending on culture conditions. Up to two mannoses residues were found in cultures carried out in conventional shake flasks, and up to five mannoses residues were determined in coiled and baffled shake flasks.</p> <p>Conclusions</p> <p>The shear and/or oxygenation parameters determine the bacterial morphology, the productivity, and the <it>O</it>-mannosylation of rAPA in <it>S. lividans</it>. As demonstrated here, culture conditions have to be carefully controlled in order to obtain recombinant <it>O</it>-glycosylated proteins with similar "quality" in bacteria, particularly, if the protein activity depends on the glycosylation pattern. Furthermore, it will be an interesting exercise to determine the effect of shear and oxygen in shake flasks, to obtain evidences that may be useful in scaling-up these processes to bioreactors. Another approach will be using lab-scale bioreactors under well-controlled conditions, and study the impact of those on rAPA productivity and quality.</p

Uso de coberturas vegetales en el manejo sostenible del suelo asociado al cultivo de maíz amiláceo (Zea mays L.)

Soil is a living, dynamic entity and at the same time vulnerable to degradation, if it is not managed with sustainable practices, causing low crop yields. The objective of this research was to determine the effects of plant cover associated with the cultivation of corn on soil properties: bulk density, gravimetric moisture, soil pH and electrical conductivity, organic matter, estimation of nitrogen supply when leaf biomass is incorporated, and finally corn yield. The study was conducted under a randomized complete block experimental design with five treatments: corn without cover crop (control), corn with clover cover crop; corn with vetch cover crop; corn with vetch + oats cover crop and corn with dead cover crop (mulch). The results showed that corn associated with clover, vetch and mulch (dead cover) increased grain yield (kg.ha-1) of corn by 44%, 37% and 38%, respectively, compared to planting corn without any type of cover. Likewise, the use of clover, vetch and vetch cover crops associated with oats increased soil organic matter and soil input by 253, 163 and 149 kg ha-1 of nitrogen if the leaf biomass of the cover crops was incorporated into the soil. Therefore, the corn-clover association is the one that presents the best results to increase yields under sustainable soil management and agroecological principles.El suelo es un ente vivo, dinámico y a la vez vulnerable a la degradación, siempre y cuando no se maneje de manera sostenible ocasionando bajos rendimientos de los cultivos. El objetivo de la presente investigación fue determinar los efectos de las coberturas vegetales asociado al cultivo de maíz amiláceo en las propiedades del suelo: densidad aparente, humedad gravimétrica, pH y conductividad eléctrica del suelo, materia orgánica, estimación del aporte de nitrógeno cuando se incorpora la biomasa foliar y finalmente el rendimiento de maíz. El estudio se realizó bajo un diseño experimental de bloques completos al azar con cinco tratamientos: maíz sin cobertura (testigo), maíz con cobertura de trébol; maíz con cobertura de vicia; maíz con cobertura de vicia + avena y maíz con cobertura muerta-mulch. Los resultados demostraron que, el maíz asociado con coberturas de trébol, vicia y mulch (cobertura muerta) aumentó en 44%, 37% y 38% respectivamente el rendimiento (kg.ha-1) de grano de maíz amiláceo, comparados a la siembra de maíz sin ningún tipo de cobertura. Asimismo, el uso de coberturas de trébol, vicia y avena + vicia incrementan la materia orgánica del suelo y aporta al suelo 253; 163 y 149 kg.ha-1 de nitrógeno siempre y cuando la biomasa foliar de las coberturas se incorpora al suelo. Por lo tanto, la asociación maíz – trébol es la que presenta mejores resultados para incrementar los rendimientos bajo un manejo sostenible del suelo y bajo los principios de la agroecología

Arabica‑cofee and teobroma‑cocoa agro‑industrial waste biosorbents, for Pb(II) removal in aqueous solutions

Agro-industrial waste biosorbents of arabica–cofee (WCA) and theobroma–cocoa (WCT) have been characterized and tested to remove Pb(II) from aqueous media. The maximum adsorption capacity of WCA and WCT (qmax = 158.7 and 123.5 mg·g−1, respectively) is comparable or even higher than for several other similar agro-industrial waste biosorbents reported in the literature. Structural and morphological characterization were performed by infrared spectrometry with Fourier transform (FT-IR), scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDS), and charge measurements at the zero point charge (pHPZC). Both biosorbents, WCA and WCT, show cracked surfaces with heterogeneous plates which ones include functional adsorption groups such as OH, C = O and C-O-C. Optimal Pb(II) adsorption occurs for a pH between 4 and 5 at [WCA] and [WCT] dose concentrations of 2 g·L−1. We found that the adsorption process follows pseudo-second order kinetics with a rapid growth rate (almost six times larger for WCA than for WCT), basically controlled by the chemisorption process. The regeneration of both biosorbents was carried out in an eluent of 0.1M HNO3 and they can be eficiently reused up to 5 times.Campus Lima Centr

Protocolo para obtener células en suspensión de Artemia franciscana para realizar electroforesis unicelular alcalina

Unicellular electrophoresis is a highly sensitive assay to detect DNA damage caused by various physical, chemical and biological agents. Despite Artemia franciscana is an important experimental model in different areas, there are no studies that refer to genotoxicity in Artemia through this assay. The aim of this study was to establish the protocol to obtain a cell suspension of A. franciscana appropriate in quality and quantity to assess single DNA strand breaks through the comet assay in the future studies.La electroforesis unicelular es un ensayo muy sensible para detectar el daño en el ADN provocado por diferentes agentes físicos, químicos y biológicos. A pesar de que Artemia franciscana es un modelo experimental muy importante en diferentes áreas, en la literatura no se encuentran estudios en los que se lleve a cabo esa prueba de genotoxicidad con células de esta especie. El objetivo de este trabajo fue desarrollar el protocolo para obtener una suspensión celular de A. franciscana apropiada en calidad y cantidad para detectar posteriormente rompimientos sencillos en las cadenas de ADN mediante el ensayo cometa

Uso de coberturas vivas en un sistema de secano para conservar la humedad del suelo e incrementar el rendimiento de la quinua

El uso de coberturas puede traer múltiples ventajas a los sistemas de producción agrícola y a las propiedades de los suelos. El objetivo de este trabajo fue evaluar en un sistema con agricultura de secano, el efecto a corto plazo del trébol (Medicago hispida G.) y la arveja (Psium sativum L.) como coberturas vivas en la humedad del suelo y el rendimiento de la quinua, en las localidades de Patasucro, Qaqas, y Ccanis de Ayacucho, Perú. El experimento se condujo bajo un diseño de bloques completos al azar, se empleó como tratamientos al trébol, la arveja y un testigo sin cobertura. La comparación de medias se realizó mediante la prueba de Tukey (α 0,05). Con respecto al rendimiento, solo existieron diferencias significativas en la localidad de Qaqas, donde las coberturas superaron al control por 0,4 t ha-1 (trébol) y 0,29 t ha-1 (arveja). La humedad del suelo fue significativamente mayor en el trébol en las localidades de Qaqas y Patasucro, superando al control por 3,97% y 1,02%, respectivamente; la arveja y el control no presentaron diferencias estadísticas. Se sostiene que las mejoras en el rendimiento ocurrieron debido a la conservación de la humedad del suelo generada por el efecto de sombreamiento de las coberturas.