LTR point mutations in the Tax-responsive elements of HTLV-1 isolates from HIV/HTLV-1-coinfected patients

Background: In Virology Journal 2011, 8: 535, Neto et al. described point mutations into Tax-responsive elements (TRE) of the LTR region of HTLV-1 isolates from asymptomatic carriers from Sao Paulo, Brazil, and hypothesized that the presence of the G232A mutation in the TRE-1 increase viral proliferation and consequently the proviral load (PvL), while the A184G mutation in the TRE-2 do not have such effect. Findings: We performed the real-time PCR assay (pol) and sequenced LTR region of HTLV-1 isolates from 24 HIV/HTLV-1-coinfected patients without HTLV-1-associated diseases from the same geographic area. These sequences were classified as belonging to the transcontinental subgroup A of the Cosmopolitan subtype a. The frequency of G232A mutation (16/24, 66.7%) was high as much as 61.8% reported by Neto's in HTLV-1 asymptomatic carriers with high PvL. High frequency (13/24, 54.2%) of double mutations G232A and A184G was also detected in HIV/HTLV-1-coinfected patients. We did not quantify PvL, but comparative analyses of the cycle threshold (Ct) median values of the group of isolates presenting the mutated-types sequences (Ct 33.5, n = 16) versus the group of isolates with the wild-type sequences (Ct 32, n = 8) showed no statistical difference (p = 0.4220). Conclusion: The frequencies of mutated-type sequences in the TRE-1 and TRE-2 motifs were high in HIV/HTLV-1-coinfected patients from Sao Paulo, Brazil. If these LTR point mutations have predictive value for the development of HTLV-1-associated diseases or they correspond to the subtype of virus that circulate in this geographic area has to be determined.

Structural synaptic elements are differentially regulated in superior temporal cortex of schizophrenia patients

Inaccurate wiring and synaptic pathology appear to be major hallmarks of schizophrenia. A variety of gene products involved in synaptic neurotransmission and receptor signaling are differentially expressed in brains of schizophrenia patients. However, synaptic pathology may also develop by improper expression of intra- and extra-cellular structural elements weakening synaptic stability. Therefore, we have investigated transcription of these elements in the left superior temporal gyrus of 10 schizophrenia patients and 10 healthy controls by genome-wide microarrays (Illumina). Fourteen up-regulated and 22 downregulated genes encoding structural elements were chosen from the lists of differentially regulated genes for further qRT-PCR analysis. Almost all genes confirmed by this method were downregulated. Their gene products belonged to vesicle-associated proteins, that is, synaptotagmin 6 and syntaxin 12, to cytoskeletal proteins, like myosin 6, pleckstrin, or to proteins of the extracellular matrix, such as collagens, or laminin C3. Our results underline the pivotal roles of structural genes that control formation and stabilization of pre- and post-synaptic elements or influence axon guidance in schizophrenia. The glial origin of collagen or laminin highlights the close interrelationship between neurons and glial cells in establishment and maintenance of synaptic strength and plasticity. It is hypothesized that abnormal expression of these and related genes has a major impact on the pathophysiology of schizophrenia.

In silico identification of conserved intercoding sequences in Leishmania genomes: Unraveling putative cis-regulatory elements

In silico analyses of Leishmania spp. genome data are a powerful resource to improve the understanding of these pathogens' biology. Trypanosomatids such as Leishmania spp. have their protein-coding genes grouped in long polycistronic units of functionally unrelated genes. The control of gene expression happens by a variety of posttranscriptional mechanisms. The high degree of synteny among Leishmania species is accompanied by highly conserved coding sequences (CDS) and poorly conserved intercoding untranslated sequences. To identify the elements involved in the control of gene expression, we conducted an in silico investigation to find conserved intercoding sequences (CICS) in the genomes of L major, L infantum, and L braziliensis. We used a combination of computational tools, such as Linux-Shell, PERL and R languages, BLAST, MSPcrunch, SSAKE, and Pred-A-Term algorithms to construct a pipeline which was able to: (i) search for conservation in target-regions, (ii) eliminate CICS redundancy and mask repeat elements, (iii) predict the mRNA's extremities, (iv) analyze the distribution of orthologous genes within the generated LeishCICS-clusters, (v) assign GO terms to the LeishCICS-clusters. and (vi) provide statistical support for the gene-enrichment annotation. We associated the LeishCICS-cluster data, generated at the end of the pipeline, with the expression profile oft. donovani genes during promastigote-amastigote differentiation, as previously evaluated by others (GEO accession: GSE21936). A Pearson's correlation coefficient greater than 0.5 was observed for 730 LeishCICS-clusters containing from 2 to 17 genes. The designed computational pipeline is a useful tool and its application identified potential regulatory cis elements and putative regulons in Leishmania. (C) 2012 Elsevier B.V. All rights reserved.

The Effects of Processing Non-Timber Forest Products and Trade Partnerships on People's Well-Being and Forest Conservation in Amazonian Societies

This study evaluated whether processing non-timber forest products (NTFPs) and establishing trade partnerships between forest communities and companies enhance the outcomes of NTFP commercialization. In particular, we evaluated whether product processing, partnerships, or their combination was associated with a number of outcomes related to the well-being of forest inhabitants and forest conservation. We based our analyses on ethnographic and quantitative data (i.e., survey and systematic observations) gathered at seven communities from five societies of the Brazilian and Bolivian Amazon. Our results indicated that product processing and partnerships do not represent a silver bullet able to improve the results of NTFP commercialization in terms of well-being and conservation indicators. Compared with cases without interventions, households adopting partnerships but not product processing were most often associated with improved economic proxies of well-being (total income, NTFP income, food consumption and gender equality in income). In comparison, the combination of product processing and partnerships was associated with similar outcomes. Unexpectedly, product processing alone was associated with negative outcomes in the economic indicators of well-being. All of the investigated strategies were associated with less time spent in social and cultural activities. With respect to forest conservation, the strategies that included a partnership with or without processing produced similar results: while household deforestation tended to decrease, the hunting impact increased. Processing alone was also associated with higher levels of hunting, though it did not reduce deforestation. Our results indicate that establishing partnerships may enhance the outcomes of NTFP trade in terms of the financial outcomes of local communities, but practitioners need to use caution when adopting the processing strategy and they need to evaluate potential negative results for indicators of social and cultural activities. With respect to conservation, the three strategies are promising for reducing deforestation, but more pervasive impacts, such as hunting, might increase.

Risk factors for magnetic resonance imaging-detected patellofemoral and tibiofemoral cartilage loss during a six-month period: The Joints On Glucosamine study

Objective To assess several baseline risk factors that may predict patellofemoral and tibiofemoral cartilage loss during a 6-month period. Methods For 177 subjects with chronic knee pain, 3T magnetic resonance imaging (MRI) of both knees was performed at baseline and followup. Knees were semiquantitatively assessed, evaluating cartilage morphology, subchondral bone marrow lesions, meniscal morphology/extrusion, synovitis, and effusion. Age, sex, and body mass index (BMI), bone marrow lesions, meniscal damage/extrusion, synovitis, effusion, and prevalent cartilage damage in the same subregion were evaluated as possible risk factors for cartilage loss. Logistic regression models were applied to predict cartilage loss. Models were adjusted for age, sex, treatment, and BMI. Results Seventy-nine subregions (1.6%) showed incident or worsening cartilage damage at followup. None of the demographic risk factors was predictive of future cartilage loss. Predictors of patellofemoral cartilage loss were effusion, with an adjusted odds ratio (OR) of 3.5 (95% confidence interval [95% CI] 1.39.4), and prevalent cartilage damage in the same subregion with an adjusted OR of 4.3 (95% CI 1.314.1). Risk factors for tibiofemoral cartilage loss were baseline meniscal extrusion (adjusted OR 3.6 [95% CI 1.310.1]), prevalent bone marrow lesions (adjusted OR 4.7 [95% CI 1.119.5]), and prevalent cartilage damage (adjusted OR 15.3 [95% CI 4.947.4]). Conclusion Cartilage loss over 6 months is rare, but may be detected semiquantitatively by 3T MRI and is most commonly observed in knees with Kellgren/Lawrence grade 3. Predictors of patellofemoral cartilage loss were effusion and prevalent cartilage damage in the same subregion. Predictors of tibiofemoral cartilage loss were prevalent cartilage damage, bone marrow lesions, and meniscal extrusion.

Analysis of elastic functionally graded materials under large displacements via high-order tetrahedral elements

The purpose of this study is to present a position based tetrahedral finite element method of any order to accurately predict the mechanical behavior of solids constituted by functionally graded elastic materials and subjected to large displacements. The application of high-order elements makes it possible to overcome the volumetric and shear locking that appears in usual homogeneous isotropic situations or even in non-homogeneous cases developing small or large displacements. The use of parallel processing to improve the computational efficiency, allows employing high-order elements instead of low-order ones with reduced integration techniques or strain enhancements. The Green-Lagrange strain is adopted and the constitutive relation is the functionally graded Saint Venant-Kirchhoff law. The equilibrium is achieved by the minimum total potential energy principle. Examples of large displacement problems are presented and results confirm the locking free behavior of high-order elements for non-homogeneous materials. (C) 2011 Elsevier B.V. All rights reserved.

Determination of trace elements in bovine semen samples by inductively coupled plasma mass spectrometry and data mining techniques for identification of bovine class

The reproductive performance of cattle may be influenced by several factors, but mineral imbalances are crucial in terms of direct effects on reproduction. Several studies have shown that elements such as calcium, copper, iron, magnesium, selenium, and zinc are essential for reproduction and can prevent oxidative stress. However, toxic elements such as lead, nickel, and arsenic can have adverse effects on reproduction. In this paper, we applied a simple and fast method of multi-element analysis to bovine semen samples from Zebu and European classes used in reproduction programs and artificial insemination. Samples were analyzed by inductively coupled plasma spectrometry (ICP-MS) using aqueous medium calibration and the samples were diluted in a proportion of 1:50 in a solution containing 0.01% (vol/vol) Triton X-100 and 0.5% (vol/vol) nitric acid. Rhodium, iridium, and yttrium were used as the internal standards for ICP-MS analysis. To develop a reliable method of tracing the class of bovine semen, we used data mining techniques that make it possible to classify unknown samples after checking the differentiation of known-class samples. Based on the determination of 15 elements in 41 samples of bovine semen, 3 machine-learning tools for classification were applied to determine cattle class. Our results demonstrate the potential of support vector machine (SVM), multilayer perceptron (MLP), and random forest (RF) chemometric tools to identify cattle class. Moreover, the selection tools made it possible to reduce the number of chemical elements needed from 15 to just 8.

Seasonal Distribution of Airborne Trace Elements and Water-Soluble Ions in Sao Paulo Megacity, Brazil

This study deals with the seasonal distribution of Al, Ca, Cu, Fe, K, Mg, Na, Pb and Zn and water soluble ions (Cl-, PO43-, NO3-, SO42-, HCOO-, CH3COO-, oxalate, succinate, Na+, NH4+, K+, Mg2+ and Ca2+) found in PM10 samples (particulate matter less than 10 mu m in diameter) Sao Paulo City, Brazil, (April 2003-May 2004). Higher atmospheric levels were found for SO42-, NO3-, Cl- and PO43- while the main organic anions were oxalate and formate. Atmospheric levels for elements were: Fe > Al > Ca > K > Na > Mg > Zn > Cu > Pb. Some sources were predominant for some species: (i) fuel burning and/or biomass burning (NO3-, HCOO-, C2O42-, K+, Mg2+, Ca2+, Fe, Pb, Zn, Al, Ca, K and Mg), (ii) gas-to-particle conversion (SO42- and NH4+) and (iii) sea salt spray (Cl-, Na+ and Na).

Analysis of energetically biased transcripts of viruses and transposable elements

RNA interference (RNAi) is a natural endogenous process by which double-stranded RNA molecules trigger potent and specific gene silencing in eukaryotic cells and is characterized by target RNA cleavage. In mammals, small interfering RNAs (siRNAs) are the trigger molecules of choice and constitute a new class of RNA-based antiviral agents. In an efficient RNAi response, the antisense strand of siRNAs must enter the RNA-induced silencing complex (RISC) in a process mediated by thermodynamic features. In this report, we hypothesize that silent mutations capable of inverting thermodynamic properties can promote resistance to siRNAs. Extensive computational analyses were used to assess whether continuous selective pressure that promotes such mutations could lead to the emergence of viral strains completely resistant to RNAi (i.e., prone to transfer only the sense strands to RISC). Based on our findings, we propose that, although synonymous mutations may produce functional resistance, this strategy cannot be systematically adopted by viruses since the longest RNAi-refractory sequence is only 10 nt long. This finding also suggests that all mRNAs display fluctuating thermodynamic landscapes and that, in terms of thermodynamic features, RNAi is a very efficient antiviral system since there will always be sites susceptible to siRNAs.

Nutrients and Nonessential Elements in Soil after 11 Years of Wastewater Irrigation

Irrigation of citrus (Citrus aurantium L. x Citrus paradise Macf.) with urban reclaimed wastewater (RWW) can be economical and conserve fresh water. However, concerns remain regarding its deleterious effects on soil quality. We investigated the ionic speciation (ISP) of RWW and potential impacts of 11 yr of irrigation with RWW on soil quality, compared with well-water (WW) irrigation. Most of nutrients (similar to 53-99%) in RWW are free ionic species and readily available for plant uptake, such as: NH4+, NO3-, K+, Ca2+, Mg2+, SO42-, H3BO3, Cl-, Fe2+, Mn2+, Zn2+, Co2+, and Ni2+, whereas more than about 80% of Cu, Cr, Pb, and Al are complexed with CO3-, OH-, and/or organic matter. The RWW irrigation increased the availability and total concentrations of nutrients and nonessential elements, and soil salinity and sodicity by two to three times compared with WW-irrigated soils. Although RWW irrigation changed many soil parameters, no difference in citrus yield was observed. The risk of negative impacts from RWW irrigation on soil quality appears to be minimal because of: (i) adequate quality of RWW, according to USEPA limits; (ii) low concentrations of metals in soil after 11 yr of irrigation with RWW; and (iii) rapid leaching of salts in RWW-irrigated soil during the rainy season.

Distribution of major elements in Atlantic surface sediments (36 degrees N-49 degrees S): Imprint of terrigenous input and continental weathering

Numerous studies use major element concentrations measured on continental margin sediments to reconstruct terrestrial climate variations. The choice and interpretation of climate proxies however differ from site to site. Here we map the concentrations of major elements (Ca, Fe, Al, Si, Ti, K) in Atlantic surface sediments (36 degrees N-49 degrees S) to assess the factors influencing the geochemistry of Atlantic hemipelagic sediments and the potential of elemental ratios to reconstruct different terrestrial climate regimes. High concentrations of terrigenous elements and low Ca concentrations along the African and South American margins reflect the dominance of terrigenous input in these regions. Single element concentrations and elemental ratios including Ca (e. g., Fe/Ca) are too sensitive to dilution effects (enhanced biological productivity, carbonate dissolution) to allow reliable reconstructions of terrestrial climate. Other elemental ratios reflect the composition of terrigenous material and mirror the climatic conditions within the continental catchment areas. The Atlantic distribution of Ti/Al supports its use as a proxy for eolian versus fluvial input in regions of dust deposition that are not affected by the input of mafic rock material. The spatial distributions of Al/Si and Fe/K reflect the relative input of intensively weathered material from humid regions versus slightly weathered particles from drier areas. High biogenic opal input however influences the Al/Si ratio. Fe/K is sensitive to the input of mafic material and the topography of Andean river drainage basins. Both ratios are suitable to reconstruct African and South American climatic zones characterized by different intensities of chemical weathering in well-understood environmental settings.

Impacts of Trade in Non-timber Forest Products on Cooperation among Caboclo Households of the Brazilian Amazon

Trade in non-timber forest products (NTFPs) has been touted as promoting forest conservation and enhancing the well-being of local residents through increased cash income, which is considered a positive outcome. However, research on cooperation has demonstrated that increased market access and income may strengthen or weaken cooperation. Because cooperation is essential for community resilience in small-scale societies, negative effects on people's well-being can be expected if increased NTFP trade reduces cooperation. To evaluate whether NTFP trade affected cooperation, we used household data (survey and systematic observations) to compare the frequency of cooperation in two communities of Brazilian Amazon Caboclos, one of which engaged in NTFP trade, while the other did not. Cooperation was less frequent in the community trading NTFPs, but neither household cash income nor household participation in NTFP exploitation was associated with cooperative behavior. Decreased frequency most likely derived from indirect effects of NTFP trade, such as less time to fish or socialize, or other outcomes observable only at the community level, such as income inequality, the influx of new residents and consequent population growth. Our results indicate that conservation and development projects based on NTFP trade may negatively impact social and economic well-being of local communities.

Evaluation of the Concentration of Nonessential and Essential Elements in Chicken, Pork, and Beef Samples Produced in Brazil

Food safety is a global concern. Meat represents the most important protein source for humans. Thus, contamination of meat products by nonessential elements is a ready source of human exposure. In addition, knowledge of the concentration of essential elements is also relevant with respect to human nutrition. The aim of the present study was to determine the concentration of 17 elements in pork, beef, and chicken produced in Brazil. Meat samples were analyzed by inductively coupled plasma mass spectrometry. The estimated daily intake for nonessential elements including arsenic (As), cadmium (Cd), lead (Pb), mercury (Hg), and antimony (Sb) through meat consumption is below the toxicological reference values. However, high levels were detected for the nonessential element cesium (Cs), mainly in beef samples, an observation that deserves future studies to identify the source of contamination and potential adverse consequences.

Six new species of Paraleia Tonnoir (Diptera, Mycetophilidae): amphinotic elements at the northern range of the Andes

Paraleia was originally described by Tonnoir for P. fulvescens, known from Australia. More recently, eleven Neotropical species were added to the genus-nine of which are from Chile and southern Argentina, one from Bolivia, and one from Peru. This distribution pattern is typical of many mycetophilid genera. Six new Neotropical species of Paraleia from the Andean Colombia and Ecuador are herein described. Male terminalia of P. bolivari sp. n., P. denticulata sp. n., P. fumosa sp. n., and P. tonnoiri sp. n., as well as female terminalia of P. bolivari sp. n., P. denticulata sp. n., P. fumosa sp. n., P. nidorosa sp. n., P. sharkeyi sp. n., and Paraleia sp. are illustrated. High-resolution photos of wings for all species are presented. An identification key for world species of Paraleia is provided.

Origin of the heavy elements in HD 140283 Measurement of europium abundance

Context. HD 140283 is a nearby (V = 7.7) subgiant metal-poor star, extensively analysed in the literature. Although many spectra have been obtained for this star, none showed a signal-to-noise (S/N) ratio high enough to enable a very accurate derivation of abundances from weak lines. Aims. The detection of europium proves that the neutron-capture elements in this star originate in the r-process, and not in the s-process, as recently claimed in the literature. Methods. Based on the OSMARCS 1D LTE atmospheric model and with a consistent approach based on the spectrum synthesis code Turbospectrum, we measured the europium lines at 4129 angstrom and 4205 angstrom, taking into account the hyperfine structure of the transitions. The spectrum, obtained with a long exposure time of seven hours at the Canada-France-Hawaii Telescope (CFHT), has a resolving power of 81 000 and a S/N ratio of 800 at 4100 angstrom. Results. We were able to determine the abundance A(Eu) = -2.35 +/- 0.07 dex, compatible with the value predicted for the europium from the r-process. The abundance ratio [Eu/Ba] = +0.58 +/- 0.15 dex agrees with the trend observed in metal-poor stars and is also compatible with a strong r-process contribution to the origin of the neutron-capture elements in HD 140283.