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Reyes-Herrera P.H.,Colombian Corporation for Agricultural Research CORPOICA | Speck-Hernandez C.A.,Antonio Narino University | Sierra C.A.,Antonio Narino University | Herrera S.,Woods Hole Oceanographic Institution | Herrera S.,Massachusetts Institute of Technology
Bioinformatics | Year: 2015

Motivation: PAR-CLIP, a CLIP-seq protocol, derives a transcriptome wide set of binding sites for RNA-binding proteins. Even though the protocol uses stringent washing to remove experimental noise, some of it remains. A recent study measured three sets of non-specific RNA backgrounds which are present in several PAR-CLIP datasets. However, a tool to identify the presence of common background in PAR-CLIP datasets is not yet available. Results: We used the measured sets of non-specific RNA backgrounds to build a common background set. Each element from the common background set has a score that reflects its presence in several PAR-CLIP datasets. We present a tool that uses this score to identify the amount of common backgrounds present in a PAR-CLIP dataset, and we provide the user the option to use or remove it. We used the proposed strategy in 30 PAR-CLIP datasets from nine proteins. It is possible to identify the presence of common backgrounds in a dataset and identify differences in datasets for the same protein. This method is the first step in the process of completely removing such backgrounds. Availability: The tool was implemented in python. The common background set and the supplementary data are available at https://github.com/phrh/BackCLIP. © The Author 2015. Published by Oxford University Press. All rights reserved. Source


Cristancho J.A.R.,University Putra Malaysia | Hanafi M.M.,University Putra Malaysia | Omar S.R.S.,University Putra Malaysia | Rafii Y.M.,University Putra Malaysia | And 2 more authors.
Journal of Plant Nutrition | Year: 2011

Aluminum (Al) toxicity is an important factor in limiting crop production. The present study examined the Al alleviation effects on the growth of hybrid (breeding) and clonal (tissue culture) of D × P oil palm seedlings. The experiment was performed using calcium carbonate (CaCO3), and ground magnesium limestone (GML) and magnesium carbonate (MgCO3) as soil-amendments at different rates in Colombia and Malaysia, respectively. The effects of the treatments were evaluated monthly on vegetative variables and visual symptoms. Chlorophyll concentrations were recorded in Malaysia at the fifth month growing stage. The different amendments improved the soil fertility and it was reflected on better performance of shoot and root growth. The chlorophyll content in the frond number 3 for both materials enhanced significantly when Al saturation was low (0-30%). The results from the experiment revealed the importance of neutralization of Al in reducing its toxicity in oil palm. © Taylor & Francis Group. Source


Cotes A.M.,Colombian Corporation for Agricultural Research CORPOICA
Acta Horticulturae | Year: 2011

The use of biological control agents as an integral component of biologicallybased pest management strategies has had increased awareness during the last decades. Microbial pesticides have been successfully promoted to farmers in many countries of South America, mainly in systems where not chemical pesticides are available or when pest/disease resistance has made chemical alternatives increasingly expensive and or unreliable. Although farmers in general show a high level of satisfaction with the microbial pesticides they also recognize technical shortcomings with the current generation of biopesticides that will require further technical development to overcome. Faster and reliable action, good storage characteristics and technologies to apply are the main constrains considered. Brazil, Chile and Colombia have 17, 36 and 48 biocontrol products registered in 2010, respectively. However, regulation is critical for the development of biological control; there are differences in time and expenses involved in registration where there is a regulatory system. In some countries there is not regulation for biopesticides, in others as in Brazil and Chile the legislation is the same for chemical pesticides, although in Brazil, a decree establishing the criteria for registration of BCAs for organic agriculture was approved in July 2009, and in others as in Colombia, since 1994 there is a specific regulation, which was updated in 2004. Thus, the low quality of some products and the regulatory and bureaucratic problems related to registration process are responsible for the increased number of illegal biocontrol products in South America. Source


McCormick A.L.C.,Colombian Corporation for Agricultural Research CORPOICA | Karlsson M.,Swedish University of Agricultural Sciences | Ochoa C.F.B.,Colombian Corporation for Agricultural Research CORPOICA | Proffit M.,Swedish University of Agricultural Sciences | And 6 more authors.
Journal of Chemical Ecology | Year: 2012

The behavioral mechanisms of mating disruption in Guatemalan potato moth Tecia solanivora were studied using the sex pheromone components, (E)-3-dodecenyl acetate, (Z)-3-dodecenyl acetate, and dodecyl acetate, formulated in a 100:1:20-ratio mimicking the female-produced blend, and in a 100:56:100 off-blend ratio. The mode of action of these two blends was tested in mating disruption experiments in the field and in a greenhouse, as well as in a laboratory wind tunnel. Field treatments with both blends at 80 g pheromone per ha reduced male attraction to trap lures baited with 100 μg of female sex pheromone. In mesh-house treatments, these two blends were equally effective at reducing male attraction to traps baited with live females and mating of caged females. Subsequent flight tunnel tests corroborated that both blends reduced attraction of naive males to calling females, and pre-exposure of males with either dispenser blend for 24 hr resulted in a strongly reduced response to calling females. The pre-exposure effect was reversible, with males again responsive after 24 hr in clean air. The two dispenser formulations produced a similar effect on male behavior, despite the differences in blend composition. One mating disruption dispenser formulated with either the female-blend or off-blend elicited the same rate of male upwind attraction in a wind-tunnel bioassay. Sensory overload and camouflage, therefore, are contributing mechanisms to mating disruption using either blend. The off-blend, which is more economical to synthesize, is a valuable tool for further development of mating disruption against this major pest of potatoes in Latin America. © 2011 Springer Science+Business Media, LLC. Source


Simbaqueba J.,Colombian Corporation for Agricultural Research CORPOICA | Sanchez P.,National University of Colombia | Sanchez E.,Colombian Corporation for Agricultural Research CORPOICA | Nunez Zarantes V.M.,Colombian Corporation for Agricultural Research CORPOICA | And 6 more authors.
PLoS ONE | Year: 2011

Physalis peruviana, commonly known as Cape gooseberry, is an Andean Solanaceae fruit with high nutritional value and interesting medicinal properties. In the present study we report the development and characterization of microsatellite loci from a P. peruviana commercial Colombian genotype. We identified 932 imperfect and 201 perfect Simple Sequence Repeats (SSR) loci in untranslated regions (UTRs) and 304 imperfect and 83 perfect SSR loci in coding regions from the assembled Physalis peruviana leaf transcriptome. The UTR SSR loci were used for the development of 162 primers for amplification. The efficiency of these primers was tested via PCR in a panel of seven P. peruviana accessions including Colombia, Kenya and Ecuador ecotypes and one closely related species Physalis floridana. We obtained an amplification rate of 83% and a polymorphic rate of 22%. Here we report the first P. peruviana specific microsatellite set, a valuable tool for a wide variety of applications, including functional diversity, conservation and improvement of the species. Source

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