Low density DNA microarray for detection of most frequent TP53 missense point mutations

BACKGROUND: We have developed an oligonucleotide microarray (genosensor) utilizing a double tandem hybridization technique to search for 9 point mutations located in the most frequently altered codons of the TP53 gene. Isolated and multiplexed PCR products, 108 and 92 bp long, from exons 7 and 8, respectively, were obtained from 24 different samples. Single-stranded target DNA was then prepared from isolated or multiplexed PCR products, through cyclic DNA synthesis. Independent ssDNA's were annealed with the corresponding pairs of labeled stacking oligonucleotides to create partially duplex DNA having a 7-nt gap, which contains the sequence that will be interrogated by the capture probes forming double tandem hybridization. In the case of multiplexed ssPCR products, only two stacking oligonucleotides were added per target, therefore the gap for the PCR products having two consecutive codons to be interrogated in exon 7 was 12 nt long, so only single tandem hybridization was produced with these respective probes. RESULTS: 18 codon substitutions were found by DNA sequencing. In 13 of them a perfect correlation with the pattern of hybridization was seen (In 5 no signal was seen with the wt probe while a new signal was seen with the appropriate mutant probe, and in 8 more, as expected, no signal was seen with any probe due to the absence of the corresponding probe in the array). In 3 other cases a mutation was falsely suggested by the combination of the absence of the wild type signal along with a false signal in the other probe. In the other 2 cases the presence of the mutation was not detected due to the production of a false hybridization signal with the wild type probe. In both cases (false mutation or no mutation detected) relatively stable mismatched target/probe duplexes should be formed. These problems could be avoided by the addition of probes to improve the performance of the array. CONCLUSION: Our results demonstrate that a simple TP53 microarray employing short (7-mer) probes, used in combination with single or double tandem hybridization approach and a simple or multiplex target preparation method, can identify common TP53 missense mutations from a variety of DNA sources with good specificity

Pasado, presente y futuro del búfalo en Argentina

El búfalo comenzó a ser introducido en Argentina a comienzos del siglo XX, mediante la importación de razas Mediterránea, Murrah y Jafarabadi. En la actualidad la población bubalina es de 87.711 cabezas, distribuidas en 20 de las 23 provincias que componen el territorio nacional. El 80% de la población de búfalos se encuentra en el nordeste argentino, siendo las provincias de Formosa y Corrientes las que cuentan con las mayores densidades poblacionales. En el país existen 8 millones de hectáreas aptas para soportar una carga de 4 millones de búfalos

Investigating mutations in the genes GDF9 and BMP15 in Pelibuey sheep through the amplification-refractory mutation system with tetra-primers

Single Nucleotide Polymorphisms (SNP) or mutations are variations with a broad distribution in the genome and, as part of genetic studies, SNP allow the identification of allelic variants related to characteristics of economic importance in sheep production. However, the identification of SNP and their genotypes through sequencing is expensive, as it requires specialized materials and equipment. The objective of this study was to identify polymorphisms and their genotypes in the growth differentiation factor 9 (GDF9) and bone morphogenetic protein 15 (BMP15) genes in Pelibuey sheep using the tetra-primer amplification-refractory mutation system through polymerase chain reaction (T-ARMS-PCR). DNA extraction and amplification of BMP15 and GDF9 were conducted from blood samples contained in WhatmanTM FTATM cards from 60 multiparous Pelibuey ewes with reproductive records. The T-ARMS-PCR methodology allowed the identification of wild-type genotypes and mutated homozygous genotypes in polymorphisms G4 and G6 of GDF9, whereas mutations in the BMP15 gene were not found. These results were confirmed by sequencing. In conclusion, the T-ARMS-PCR methodology allowed the identification of mutated and wild-type genotypes in SNP G4 and G6 of GDF9, although no mutations were found in BMP15 in Pelibuey sheep. This technique was found to be reliable, rapid, and easily applied to identify polymorphic genotypes

Conscious mobility for urban spaces: case studies review and indicator framework design

A lack of data collection on conscious mobility behaviors has been identified in current sustainable and smart mobility planning, development and implementation strategies. This leads to technocentric solutions that do not place people and their behavior at the center of new mobility solutions in urban centers around the globe. This paper introduces the concept of conscious mobility to link techno-economic analyses with user awareness on the impact of their travel decisions on other people, local urban infrastructure and the environment through systematic big data collection. A preliminary conscious mobility indicator framework is presented to leverage behavioral considerations to enhance urban-community mobility systems. Key factors for conscious mobility analysis have been derived from five case studies. The sample offers regional diversity (i.e., local, regional and the global urban contexts), as well as different goals in the transformation of conventional urban transport systems, from improving public transport efficiency and equipment electrification to mitigate pollution and climate risks, to focusing on equity, access and people safety. The case studies selected provide useful metrics on the adoption of cleaner, smarter, safer and more autonomous mobility technologies, along with novel people-centric program designs to build an initial set of conscious mobility indicators frameworks. The parameters were applied to the city of Monterrey, Nuevo Leon in Mexico focusing on the needs of the communities that work, study and live around the local urban campus of the Tecnologico de Monterrey’s Distrito Tec. This case study, served as an example of how conscious mobility indicators could be applied and customized to a community and region of interest. This paper introduces the first application of the conscious mobility framework for urban communities’ mobility system analysis. This more holistic assessment approach includes dimensions such as society and culture, infrastructure and urban spaces, technology, government, normativity, economy and politics, and the environment. The expectation is that the conscious mobility framework of analysis will become a useful tool for smarter and sustainable urban and mobility problem solving and decision making to enhance the quality of life all living in urban communities

MEGARA detector test bench at LICA-UCM

LICA (Laboratorio de Instrumentaci´on Cient´ıfica Avanzada) is an initiative of the Campus de Excelencia Internacional of UCM. Among the facilities within LICA, a new laboratory has been assigned to MEGARA project for subsystem tests and AIV. This paper presents the current facilities installed at LICA for detector characterization, which will be used to test and characterize MEGARA detectors

Genetic Characterization of Jaguars (Panthera onca) in Captivity in Zoological Parks of Colombia

The construction of the pedigree of captive jaguars (Panthera onca) in zoological parks of Colombia was done using the analysis of the Regional Studbook for Jaguars and DNA analysis of 9 microsatellites of 20 Jaguars (n=20). The assignments for paternities and maternities were done with for the program CERVUS and the relationship between animals were established with the KINSHIP program. The analysis of the Studbook was done with SPARKS and PM2000 software generating the following values: genetic diversity for the population (GD=0.7832), potential genetic diversity (GD=0.9113), genic value (GV=0.7846), mean coefficient of inbreeding (F=0.0179), and the Mean KINSHIP (MK) for each individual. The averages of the observed and expected heterozygosity were 0.687 and 0.684 respectively. Nevertheless, a wild jaguar sample of 156 individuals obtained in Colombia substantially showed a higher degree of gene diversity (H = 0.87) than the Colombian captive jaguar population. Thus, the captive jaguar population retained 78 % of the gene diversity of the Colombian wild jaguar population. With this study the pedigree of the captive population of jaguars was built in order to develop an ex situ conservation plan for the species in the Colombian zoological parks

Charge separation relative to the reaction plane in Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}}= 2.76 TeV

Measurements of charge dependent azimuthal correlations with the ALICE detector at the LHC are reported for Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV. Two- and three-particle charge-dependent azimuthal correlations in the pseudo-rapidity range $|\eta| < 0.8$ are presented as a function of the collision centrality, particle separation in pseudo-rapidity, and transverse momentum. A clear signal compatible with a charge-dependent separation relative to the reaction plane is observed, which shows little or no collision energy dependence when compared to measurements at RHIC energies. This provides a new insight for understanding the nature of the charge dependent azimuthal correlations observed at RHIC and LHC energies.Comment: 12 pages, 3 captioned figures, authors from page 2 to 6, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/286

A note on comonotonicity and positivity of the control components of decoupled quadratic FBSDE

In this small note we are concerned with the solution of Forward-Backward Stochastic Differential Equations (FBSDE) with drivers that grow quadratically in the control component (quadratic growth FBSDE or qgFBSDE). The main theorem is a comparison result that allows comparing componentwise the signs of the control processes of two different qgFBSDE. As a byproduct one obtains conditions that allow establishing the positivity of the control process.Comment: accepted for publicatio

Transverse sphericity of primary charged particles in minimum bias proton-proton collisions at s=0.9\sqrt{s}=0.9, 2.76 and 7 TeV

Measurements of the sphericity of primary charged particles in minimum bias proton--proton collisions at $\sqrt{s}=0.9$, 2.76 and 7 TeV with the ALICE detector at the LHC are presented. The observable is linearized to be collinear safe and is measured in the plane perpendicular to the beam direction using primary charged tracks with $p_{\rm T}\geq0.5$ GeV/c in $|\eta|\leq0.8$. The mean sphericity as a function of the charged particle multiplicity at mid-rapidity ($N_{\rm ch}$) is reported for events with different $p_{\rm T}$ scales ("soft" and "hard") defined by the transverse momentum of the leading particle. In addition, the mean charged particle transverse momentum versus multiplicity is presented for the different event classes, and the sphericity distributions in bins of multiplicity are presented. The data are compared with calculations of standard Monte Carlo event generators. The transverse sphericity is found to grow with multiplicity at all collision energies, with a steeper rise at low $N_{\rm ch}$, whereas the event generators show the opposite tendency. The combined study of the sphericity and the mean $p_{\rm T}$ with multiplicity indicates that most of the tested event generators produce events with higher multiplicity by generating more back-to-back jets resulting in decreased sphericity (and isotropy). The PYTHIA6 generator with tune PERUGIA-2011 exhibits a noticeable improvement in describing the data, compared to the other tested generators.Comment: 21 pages, 9 captioned figures, 3 tables, authors from page 16, published version, figures from http://aliceinfo.cern.ch/ArtSubmission/node/308