Caracterización Molecular de la Diversidad Fúngica de los Bosques Llucud y Palictahua: Potencialidades en Control Biológico/Molecular Characterization of Diversity Fungic of the Llucud and Palictahua Forests: Potential in Biological Control

Dentro de los microorganismos más abundantes que se pueden encontrar en formaciones ecosistémicas naturales como los bosques andinos del Ecuador se encuentran los hongos microscópicos, los cuales desempeñan funciones cruciales en dichos ecosistemas. Por lo cual el objetivo de esta investigación fue caracterizar molecularmente la diversidad de hongos presentes en los bosques nativos Llucud y Palictahua, estableciendo sus potencialidades de uso en el control biológico de plagas y enfermedades que afectan a los cultivos agrícolas y cuyo control en su mayoría se lo realiza con plaguicidas químicos. Mediante secuenciación de próxima generación (NGS por sus siglas en inglés) de las muestras compuestas de suelo tomadas del horizonte “A” (rizósfera) de cada bosque, se identificaron 56 especies de hongos en Palictahua y 38 en Llucud, presentándose en ambos bosques un total de 6 hongos con importantes potencialidades para su uso en el control biológico, dentro de las cuales se encontraron: Brachyphoris oviparasitica (nematófago), Simplicillium (entomopatógeno y micoparásito), Hamamotoa lignophila (levadura con actividad Killer) en Llucud, y Metarhizium robertsii (entomopatógeno), Brachyphoris oviparasitica (nematófago) y Paraphaeosphaeria parmeliae (micoparásito) en Palictahua. El Bosque Palictahua presentó mayor diversidad de hongos que el bosque Llucud, sin embargo es importante cuidar ambos bosques, pues poseen una gran riqueza microbiana con un sinnúmero de posibilidades de uso en la medicina, industria, biotecnología y otros campos. Among the most abundant microorganisms that can be found in natural ecosystem formations such as the Andean forests of Ecuador are microscopic fungi, which play crucial roles in these ecosystems. So that the objective of this research was to molecularly characterize the diversity of fungi present in the native forests Llucud and Palictahua, establishing their potential for use in the biological control of pests and diseases that affect agricultural crops and whose control is mostly carried out with chemical pesticides. Through next-generation sequencing (NGS for its acronym in English) of compound samples of soil took from “A” horizon (rhizosphere). 56 species of fungi were identified in Palictahua and 38 in Llucud, presenting in both forests a total of 6 fungi with significant potential for use in biological control, among which were found: Brachyphoris oviparasitica (nematophagous), Simplicillium sp. (entomopathogen and mycoparasite), Hamamotoa lignophila (yeast with Killer activity) in Llucud, and Metarhizium robertsii (entomopathogen), Brachyphoris oviparasitica (nematophagous) and Paraphaeosphaeria parmeliae (mycoparasite) in Palictahua. The Palictahua forest presented greater diversity of fungi than the Llucud forest, however it is important to take care of both forests, since they have a great microbial richness with a myriad of possibilities of use in medicine, industry, biotechnology and other fields. Palabras clave: Biodiversidad, Microbiota, Plaguicidas. Keywords: Biodiversity, Microbiota, Pesticides

BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

Magnetothermal Conductivity of Highly Oriented Pyrolytic Graphite in the Quantum Limit

We report on the magnetic field (0T$\le B \le 9$T) dependence of the longitudinal thermal conductivity $\kappa(T,B)$ of highly oriented pyrolytic graphite in the temperature range 5 K $\le T\le$ 20 K for fields parallel to the $c-$axis. We show that $\kappa(T,B)$ shows large oscillations in the high-field region (B > 2 T) where clear signs of the Quantum-Hall effect are observed in the Hall resistance. With the measured longitudinal electrical resistivity we show that the Wiedemann-Franz law is violated in the high-field regime.Comment: 4 Figures, to be published in Physical Review B (2003

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador

Background: Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses. Methodology/Principal findings: The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area. Conclusions/Significance: Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment. Author summary: Understanding Chagas disease vector (triatomine) population dispersal is key for the design of control measures tailored for the epidemiological situation of a particular region. In Ecuador, Rhodnius ecuadoriensis is a cause of concern for Chagas disease transmission, since it is widely distributed from the central coast to southern Ecuador. Here, a genome-wide sequencing (2b-RAD) approach was performed in 20 specimens from four communities from Manabí (central coast) and Loja (southern) provinces of Ecuador, and the effectiveness of three type IIB restriction enzymes was assessed. The findings of this study show that this genotyping methodology is cost effective in R. ecuadoriensis and likely in other triatomine species. In addition, preliminary population genomic analysis results detected a signal of population structure among geographically distinct communities and genetic variability within communities. As such, 2b-RAD shows significant promise as a relatively low-tech solution for determination of vector population genomics, dynamics, and spread

Thermoelectric assessment of laser peening induced effects on a metallic biomedical Ti6Al4V

Laser peening has recently emerged as a useful technique to overcome detrimental effects associated to another well-known surface modification processes such as shot peening or grit blasting used in the biomedical field. It is worth to notice that besides the primary residual stress effect, thermally induced effects might also cause subtle surface and subsurface microstructural changes that might influence corrosion resistance. Moreover, since maximum loads use to occur at the surface, they could also play a critical role in the fatigue strength. In this work, plates of Ti-6Al-4V alloy of 7 mm in thickness were modified by laser peening without using a sacrificial outer layer. Irradiation by a Q-switched Nd-YAG laser (9.4 ns pulse length) working in fundamental harmonic at 2.8 J/pulse and with water as confining medium was used. Laser pulses with a 1.5 mm diameter at an equivalent overlapping density (EOD) of 5000 cm-2 were applied. Attempts to analyze the global induced effects after laser peening were addressed by using the contacting and non-contacting thermoelectric power (TEP) techniques. It was demonstrated that the thermoelectric method is entirely insensitive to surface topography while it is uniquely sensitive to subtle variations in thermoelectric properties, which are associated with the different material effects induced by different surface modification treatments. These results indicate that the stress-dependence of the thermoelectric power in metals produces sufficient contrast to detect and quantitatively characterize regions under compressive residual stress based on their thermoelectric power contrast with respect to the surrounding intact material. However, further research is needed to better separate residual stress effects from secondary material effects, especially in the case of low-conductivity engineering materials like titanium alloys

Metal coordination and peripheral substitution modulate the activity of cyclic tetrapyrroles on αS aggregation: A structural and cell-based study.

The discovery of aggregation inhibitors and the elucidation of their mechanism of action are key in the quest to mitigate the toxic consequences of amyloid formation. We have previously characterized the antiamyloidogenic mechanism of action of sodium phtalocyanine tetrasulfonate ([Na4(H2PcTS)]) on α-Synuclein (αS), demonstrating that specific aromatic interactions are fundamental for the inhibition of amyloid assembly. Here we studied the influence that metal preferential affinity and peripheral substituents may have on the activity of tetrapyrrolic compounds on αS aggregation. For the first time, our laboratory has extended the studies in the field of the bioinorganic chemistry and biophysics to cellular biology, using a well-established cell-based model to study αS aggregation. The interaction scenario described in our work revealed that both N- and C-terminal regions of αS represent binding interfaces for the studied compounds, a behavior that is mainly driven by the presence of negatively or positively charged substituents located at the periphery of the macrocycle. Binding modes of the tetrapyrrole ligands to αS are determined by the planarity and hydrophobicity of the aromatic ring system in the tetrapyrrolic molecule and/or the preferential affinity of the metal ion conjugated at the center of the macrocyclic ring. The different capability of phthalocyanines and meso-tetra (N-methyl-4-pyridyl) porphine tetrachloride ([H2PrTPCl4]) to modulate αS aggregation in vitro was reproduced in cell-based models of αS aggregation, demonstrating unequivocally that the modulation exerted by these compounds on amyloid assembly is a direct consequence of their interaction with the target protein

HCN(1-0) enhancement in the bar of NGC 2903

We have mapped the \hcn emission from two spiral galaxies, NGC2903 and NGC3504 to study the gas properties in the bars. The HCN(1-0) emission is detected in the center and along the bar of NGC2903. The line ratio HCN(1-0)/CO(1-0) ranges from 0.07 to 0.12 with the lowest value in the center. The enhancement of HCN(1-0) emission along the bar indicates a higher fraction of dense molecular gas in the bar than at the center. The mass of dense molecular gas in the center (2.2x 10^7 Msun) is about 6 times lower than that in the bar (1.2x 10^8 Msun). The total star formation rate (SFR) is estimated to be 1.4 Msun/yr, where the SFR at the center is 1.9 times higher than that in the bar. The time scale of consumption of the dense molecular gas in the center is about 3x 10^7 yr which is much shorter than that in the bar of about 2 to 10 x 10^8 yr. The dynamical time scale of inflow of the gas from the bar to the center is shorter than the consumption time scale in the bar, which suggests that the star formation (SF) activity at the center is not deprived of fuel. In the bar, the fraction of dense molecular gas mass relative to the total molecular gas mass is twice as high along the leading edge than along the central axis of the bar. The \hcn emission has a large velocity dispersion in the bar, which can be attributed partially to the streaming motions indicative of shocks along the bar. In NGC3504, the HCN(2-0) emission is detected only at the center. The fraction of dense molecular gas mass in the center is about 15%. Comparison of the SFR with the predictions from numerical simulations suggest that NGC2903 harbors a young type B bar with a strong inflow of gas toward the center whereas NGC3504 has an older bar and has already passed the phase of inflow of gas toward the center.Comment: Acceoted for publication in A&A, 12 figure

Inflammatory stress of pancreatic beta cells drives release of extracellular heat-shock protein 90α

A major obstacle in predicting and preventing the development of autoimmune type 1 diabetes (T1D) in at-risk individuals is the lack of well-established early biomarkers indicative of ongoing beta cell stress during the pre-clinical phase of disease. Recently, serum levels of the α cytoplasmic isoform of heat-shock protein 90 (hsp90) were shown to be elevated in individuals with new-onset T1D. We therefore hypothesized that hsp90α could be released from beta cells in response to cellular stress and inflammation associated with the earliest stages of T1D. Here, human beta cell lines and cadaveric islets released hsp90α in response to stress induced by treatment with a combination of pro-inflammatory cytokines including interleukin-1β, tumour necrosis factor-α and interferon-γ. Mechanistically, hsp90α release was found to be driven by cytokine-induced endoplasmic reticulum stress mediated by c-Jun N-terminal kinase (JNK), a pathway that can eventually lead to beta cell apoptosis. Cytokine-induced beta cell hsp90α release and JNK activation were significantly reduced by pre-treating cells with the endoplasmic reticulum stress-mitigating chemical chaperone tauroursodeoxycholic acid. The hsp90α release by cells may therefore be a sensitive indicator of stress during inflammation and a useful tool in assessing therapeutic mitigation of cytokine-induced cell damage linked to autoimmunity