Human Endogenous Retrovirus (HERV) Insertional Polymorphisms

Human endogenous retroviruses (HERVs) are the result of ancient germ cell infections of human germ cells by exogenous retroviruses. HERVs belong to the long terminal repeat (LTR) group of retrotransposons that comprise ~8% of the human genome. The majority of the HERVs documented have been truncated and/or incurred lethal mutations and no longer encode functional genes; however a very small number of HERVs seem to maintain functional in making new copies by retrotranspositon as suggested by the identification of a handful of polymorphic HERV insertions in human populations. The objectives of this study were to identify novel insertion of HERVs via analysis of personal genomic data and survey the polymorphism levels of new and known HERV insertions in the human genome. Specifically, this study involves the experimental validation of polymorphic HERV insertion candidates predicted by personal genome-based computation prediction and survey the polymorphism level within the human population based on a set of 30 diverse human DNA samples. Based on computational analysis of a limited number of personal genome sequences, PCR genotyping aided in the identification of 15 dimorphic, 2 trimorphic and 5 fixed full-length HERV-K insertions not previously investigated. These results suggest that the proliferation rate of HERVKs, perhaps also other ERVs, in the human genome may be much higher than we previously appreciated and the recently inserted HERVs exhibit a high level of instability. Throughout this study we have observed the frequent presence of additional forms of genotypes for these HERV insertions, and we propose for the first time the establishment of new genotype reporting nomenclature to reflect all possible combinations of the pre-integration site, solo-LTR and full-length HERV alleles.

MiR-16, un nouveau régulateur du transporteur de glucose dépendant de l’insuline GLUT-4

Les microARNs sont des petits ARNs non codants d'environ 22 nucléotides qui régulent négativement la traduction de l'ARN messager cible (ARNm) et ont donc des fonctions cellulaires. Le microARN-16 (miR-16) est connu pour ses effets antiprolifératifs. Nous avons observé que l’expression de miR-16 est diminuée dans les cellules endothéliales humaines sénescentes et quiescentes en comparaison à des cellules prolifératives. Une analyse informatique des sites potentiels de liaison de miR-16 prévoit que GLUT-4, un transporteur du glucose insulinodépendant, pourrait être une cible potentielle du miR-16. Nous avons donc testé l'hypothèse que miR-16 régule négativement le métabolisme du glucose cellulaire. Dans des HUVEC, l'inhibition de miR-16 endogène avec des anti-miRNA oligonucléotides (AMO) augmente les niveaux protéiques de GLUT-4 de 1,7 ± 0,4 fois (p=0,0037 ; n=9). Dans des souris nourries avec un régime alimentaire normal ou riche en graisse et en sucre, l’expression de GLUT-4 dans le muscle squelettique a tendance à corréler négativement avec les niveaux de miR-16 (p=0,0998, r2=0,3866, n=4). Ces résultats suggèrent que miR-16 est un régulateur négatif de GLUT-4 et qu’il pourrait être impliqué dans la régulation du métabolisme cellulaire du glucose.

An exploratory assessment of the potential impact of the free trade area of the americas on the andean community

A través de una simulación llevada a cabo con GTAP, este documento presenta una evaluación preliminar del impacto potencial que el Área de Libre Comercio de las Américas tendría sobre la Comunidad Andina de Naciones. Mantenido por la Universidad de Purdue, el GTAP es un modelo multiregional de equilibrio general, ampliamente usado para el análisis de temas de economía internacional. El experimento llevado a cabo tiene lugar en un ambiente de competencia perfecta y rendimientos constantes a escala y consiste en la completa eliminación de aranceles a las importaciones de bienes entre los países del Hemisferio Occidental. Los resultados muestran la presencia de modestas pero positivas ganancias netas de bienestar para la Comunidad Andina, generadas fundamentalmente por mejoras en la asignación de recursos. Movimientos desfavorables en los términos de intercambio y el efecto de la desviación de comercio con respecto a terceros países, reducen considerablemente las ganancias potenciales de bienestar. De la misma forma, la existencia de distorsiones económicas al interior de la Comunidad Andina tiene un efecto negativo sobre el bienestar. El patrón de comercio aumenta su grado de concentración en el comercio bilateral con los Estados Unidos y la remuneración real a los factores productivos presenta mejoras con la implementación de la zona de libre comercio.

Detection of unusual mutation within the VP1 region of different re-isolates of poliovirus Sabin vaccine

In the present study, a genomic analysis of full VP1 sequence region of 15 clinical re-isolates (14 healthy vaccinees and one bone marrow tumor patient) was conducted, aiming to the identification of mutations and to the assessment of their impact on virus fitness, providing also insights relevant with the natural evolution of Sabin strains. Clinical re-isolates were analyzed by RT-PCR, sequencing and computational analysis. Some re-isolates were characterized by an unusual mutational pattern in which non-synonymous mutations outnumbered the synonymous ones. Furthermore, the majority of amino-acid substitutions were located in the capsid exterior, specifically in N-Ags, near N-Ags and in the north rim of the canyon. Also mutations, which are well-known determinants of attenuation, were identified. The results of this study propose that some re-isolates are characterized by an evolutionary pattern in which non-synonymous mutations with a direct phenotypic impact on viral fitness are fixed in viral genomes, in spite of synonymous ones with no phenotypic impact on viral fitness. Results of the present retrospective characterization of Sabin clinical re-isolates, based on the full VP1 sequence, suggest that vaccine-derived viruses may make their way through narrow breaches and may evolve into transmissible pathogens even in adequately immunized populations. For this reason increased poliovirus laboratory surveillance should be permanent and full VP1 sequence analysis should be conducted even in isolates originating from healthy vaccinees.

Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis

Type XVIII collagen is a component of basement membranes, and expressed prominently in the eye, blood vessels, liver, and the central nervous system. Homozygous mutations in COL18A1 lead to Knobloch Syndrome, characterized by ocular defects and occipital encephalocele. However, relatively little has been described on the role of type XVIII collagen in development, and nothing is known about the regulation of its tissue-specific expression pattern. We have used zebrafish transgenesis to identify and characterize cis-regulatory sequences controlling expression of the human gene. Candidate enhancers were selected from non-coding sequence associated with COL18A1 based on sequence conservation among mammals. Although these displayed no overt conservation with orthologous zebrafish sequences, four regions nonetheless acted as tissue-specific transcriptional enhancers in the zebrafish embryo, and together recapitulated the major aspects of col18a1 expression. Additional post-hoc computational analysis on positive enhancer sequences revealed alignments between mammalian and teleost sequences, which we hypothesize predict the corresponding zebrafish enhancers; for one of these, we demonstrate functional overlap with the orthologous human enhancer sequence. Our results provide important insight into the biological function and regulation of COL18A1, and point to additional sequences that may contribute to complex diseases involving COL18A1. More generally, we show that combining functional data with targeted analyses for phylogenetic conservation can reveal conserved cis-regulatory elements in the large number of cases where computational alignment alone falls short. (C) 2009 Elsevier Inc. All rights reserved.

A statistical evaluation of the field emission for copper oxide nanostructures

A statistical data analysis methodology was developed to evaluate the field emission properties of many samples of copper oxide nanostructured field emitters. This analysis was largely done in terms of Seppen-Katamuki (SK) charts, field strength and emission current. Some physical and mathematical models were derived to describe the effect of small electric field perturbations in the Fowler-Nordheim (F-N) equation, and then to explain the trend of the data represented in the SK charts. The field enhancement factor and the emission area parameters showed to be very sensitive to variations in the electric field for most of the samples. We have found that the anode-cathode distance is critical in the field emission characterization of samples having a non-rigid nanostructure. (C) 2007 Elsevier B.V. All rights reserved.

Molecular characterization of Arabidopsis thaliana PUF proteins - binding specificity and target candidates

PUF proteins regulate both stability and translation through sequence-specific binding to the 3` UTR of target mRNA transcripts. Binding is mediated by a conserved PUF domain, which contains eight repeats of approximately 36 amino acids each. Found in all eukaryotes, they have been related to several developmental processes. Analysis of the 25 Arabidopsis Pumilio (APUM) proteins presenting PUF repeats reveals that 12 (APUM-1 to APUM-12) have a PUF domain with 50-75% similarity to the Drosophila PUF domain. Through three-hybrid assays, we show that APUM-1 to APUM-6 can bind specifically to the Nanos response element sequence recognized by Drosophila Pumilio. Using an Arabidopsis RNA library in a three-hybrid screening, we were able to identify an APUM-binding consensus sequence. Computational analysis allowed us to identify the APUM-binding element within the 3` UTR in many Arabidopsis transcripts, even in important mRNAs related to shoot stem cell maintenance. We demonstrate that APUM-1 to APUM-6 are able to bind specifically to APUM-binding elements in the 3` UTR of WUSCHEL, CLAVATA-1, PINHEAD/ZWILLE and FASCIATA-2 transcripts. The results obtained in the present study indicate that the APUM proteins may act as regulators in Arabidopsis through an evolutionarily conserved mechanism, which may open up a new approach for investigating mRNA regulation in plants.

Dispositivos planares integrados utilizando método dinâmico com metamateriais e PBG

This work presents a theoretical, numerical and computation analysis of parameters of a rectangular microstrip antenna with metamaterial substrate, fin line as a coupler and also integrated devices like integrated filter antenna. It is applied theory to full-wave of Transverse Transmission Line - TTL method, to characterize the magnitude of the substrate and obtain the general equations of the electromagnetic fields. About the metamaterial, they are characterized by permittivity and permeability tensor, reaching to the general equations for the electromagnetic fields of the antenna. It is presented a study about main representation of PBG(Photonic Band Gap) material and its applied for a specific configuration. A few parameters are simulated some structures in order to reduce the physical dimensions and increase the bandwidth. The results are presented through graphs. The theoretical and computational analysis of this work have shown accurate and relatively concise. Conclusions are drawn and suggestions for future work

Antena de microfita com substrato metamaterial

This paper presents a theoretical and numerical analysis of the parameters of a rectangular microstrip antenna with metamaterial substrate. The metamaterial (MTM) theory was applied along with Transverse Transmission Line (LTT) method to characterize substrate quantities and obtain the general equations of the electromagnetic fields. A study on metamaterial theory was conducted to obtain the constructive parameters, which were characterized through permittivity and permeability tensors to arrive at a set of electromagnetic equations. Electromagnetic principes are used to obtained parameters such as complex resonance frequency, bandwidth and radiation pattern were then obtained. Different metamaterial and antenna configurations were simulated to miniaturize them physically and increase their bandwidth, the results of which are shown through graphics. The theoretical computational analysis of this work proved to be accurate when compared to other studies, and may be used for other metamaterial devices. Conclusions and suggestions for future work are also proposed

Bianisotropia uniaxial em estruturas irradiantes com multicamadas e supercondutores

This work presents a theoretical and numerical analysis of parameters of a rectangular microstrip antenna with bianisotropic substrate, and including simultaneously the superconducting patch. The full-wave Transverse Transmission Line - TTL method, is used to characterize these antennas. The bianisotropic substrate is characterized by the permittivity and permeability tensors, and the TTL gives the general equations of the electromagnetic fields of the antennas. The BCS theory and the two fluids model are applied to superconductors in these antennas with bianisotropic for first time. The inclusion of superconducting patch is made using the complex resistive boundary condition. The resonance complex frequency is then obtained. Are simulated some parameters of antennas in order to reduce the physical size, and increase the its bandwidth. The numerical results are presented through of graphs. The theoretical and computational analysis these works are precise and concise. Conclusions and suggestions for future works are presented

Performance comparativa entre R290/R600a (50:50) e R134a para drop-in em refrigerador doméstico

This research this based on the seminar on Use of Natural Fluids in Refrigeration and Air-Conditioning Systems conducted in 2007 in Sao Paulo. The event was inserted in the National Plan for Elimination of CFCs, coordinated by the Ministry of Environment and implemented by the United Nations Development Programme (UNDP). The objective of this research is analyze the performance of the hydrocarbons application as zeotropic mixtures in domestic refrigerator and validate the application of technical standards for pull down and cycling (on-off) tests to the mixture R290/R600a (50:50) in domestic refrigerator. It was first developed an computational analysis of R290/R600a (50:50) compared to R134a and other mass fractions of the hydrocarbons mixtures in the standard ASHRAE refrigeration cycle in order to compare the operational characteristics and thermodynamic properties of fluids based on the software REFPROP 6.0. The characteristics of the Lorenz cycle is presented as an application directed to zeotropic mixtures. Standardized pull down and cycling (on-off) tests were conducted to evaluate the performance of the hydrocarbons mixture R290/R600a (50:50) as a drop-in alternative to R134a in domestic refrigerator of 219 L. The results showed that the use of R290/R600a (50:50) with a charge of refrigerant reduced at 53% compared to R134a presents reduced energy performance than R134a. The COP obtained with hydrocarbon mixture was about 13% lower compared to R134a. Pull down times in the refrigerator compartments for fluids analyzed were quite close, having been found a 4,7% reduction in pull down time for the R290/R600a compared to R134a, in the freezer compartment. The data indicated a higher consumption of electric current from the refrigerator when operating with the R290/R600a. The values were higher than about 3% compared to R134a. The charge of 40 g of R290/R600a proved very low for the equipment analyzed

Neighborhood Interactions and Larval Dispersal Behavior in Blowflies

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Crotacetin, a novel snake venom C-type lectin homolog of convulxin, exhibits an unpredictable antimicrobial activity

Snake venom (sv) C-type lectins encompass a group of hemorrhagic toxins that are capable of interfering with blood stasis. A very well-studied svC-type lectin is the heterodimeric toxin, convulxin (CVX), from the venom of South American rattlesnake Crotalus durissus terrificus. CVX is able to activate platelets and induce their aggregation by acting via p62/GPVI collagen receptor. By using polymerase chain reaction homology screening, we have cloned several cDNA precursors of CVX subunit homologs. One of them, named crotacetin (CTC) beta-subunit, predicts a polypeptide with a topology very similar to the tridimensional conformations of other subunits of CVX-like snake toxins, as determined by computational analysis. Using gel permeation and reverse-phase high-performance liquid chromatography, CTC was purified from C. durissus venoms. CTC can be isolated from the venom of several C. durissus subspecies, but its quantitative predominance is in the venom of C. durissus cascavella. Functional analysis indicates that CTC induces platelet aggregation, and, importantly, exhibits an antimicrobial activity against Gram-positive and -negative bacteria, comparable with CVX.

Algorithms for network piecewise-linear programs: A comparative study

Piecewise-Linear Programming (PLP) is an important area of Mathematical Programming and concerns the minimisation of a convex separable piecewise-linear objective function, subject to linear constraints. In this paper a subarea of PLP called Network Piecewise-Linear Programming (NPLP) is explored. The paper presents four specialised algorithms for NPLP: (Strongly Feasible) Primal Simplex, Dual Method, Out-of-Kilter and (Strongly Polynomial) Cost-Scaling and their relative efficiency is studied. A statistically designed experiment is used to perform a computational comparison of the algorithms. The response variable observed in the experiment is the CPU time to solve randomly generated network piecewise-linear problems classified according to problem class (Transportation, Transshipment and Circulation), problem size, extent of capacitation, and number of breakpoints per arc. Results and conclusions on performance of the algorithms are reported.

A computer vision approach to quantify leaf anatomical plasticity: A case study on gochnatia polymorpha (less.) cabrera

Inferences about leaf anatomical characteristics had largely been made by manually measuring diverse leaf regions, such as cuticle, epidermis and parenchyma to evaluate differences caused by environmental variables. Here we tested an approach for data acquisition and analysis in ecological quantitative leaf anatomy studies based on computer vision and pattern recognition methods. A case study was conducted on Gochnatia polymorpha (Less.) Cabrera (Asteraceae), a Neotropical savanna tree species that has high phenotypic plasticity. We obtained digital images of cross-sections of its leaves developed under different light conditions (sun vs. shade), different seasons (dry vs. wet) and in different soil types (oxysoil vs. hydromorphic soil), and analyzed several visual attributes, such as color, texture and tissues thickness in a perpendicular plane from microscopic images. The experimental results demonstrated that computational analysis is capable of distinguishing anatomical alterations in microscope images obtained from individuals growing in different environmental conditions. The methods presented here offer an alternative way to determine leaf anatomical differences. © 2013 Elsevier B.V.