Development of twenty-one polymorphic microsatellite markers for the fungus-growing ant, Mycocepurus goeldii (Formicidae: Attini), using Illumina paired-end genomic sequencing

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

Recanalization Rates after Acute Deep Vein Thrombosis: A Single-center Experience Using a Newly Proposed Vein Diameter Variation Index

Background: Duplex ultrasound scanning (DUS) is the method of choice for diagnosis of deep vein thrombosis (DVT). However, only a few studies have performed prospective serial DUS after an acute episode of DVT to assess its evolution. This study aimed to report our experience using DUS combined with a thrombosis score (TS) and a newly proposed vein diameter variation index (VDVI) to evaluate the rate of resolution of DVT by assessing and quantifying the early stages of vein recanalization in proximal vein segments within 6 months after an episode of acute lower extremity DVT.Methods: Twelve patients with first episode of acute lower extremity DVT confirmed by DUS as occurring in <= 10 days after the onset of venous thrombosis symptoms were followed up prospectively for 6 months. TS and VDVI were calculated at 1, 3, and 6 months to assess vein recanalization. Intra-thrombus arteriovenous fistula formation was also investigated and related to the recanalization process.Results: Seven (58%) women were included, with a total cohort median age of 53.5 +/- 19 years. The left lower extremity was affected in 7 (58%) patients. DVT was diagnosed in 55 proximal vein segments. All patients had proximal DVT, with involvement of the external iliac, femoral, and popliteal veins. After 6 months, there was a significant decrease in TS and increase in VDVI (P < 0.001) in all proximal vein segments assessed, indicating thrombus regression. The more distal the DVT was, the faster was the VDVI increase, with most popliteal veins being recanalized at 3 months (P < 0.001). Intra-thrombus arteriovenous fistula was identified in 50% of patients at 1 month while on anticoagulation.Conclusions: The combined use of two different DUS-based assessment tools, TS and the proposed VDVI, provided an effective method to prospectively assess vein recanalization rates after an episode of acute lower extremity DVT in this series of patients and may allow a correct evaluation of DVT and its resolution or progression.

Isolation and characterization of microsatellites markers for two South American frogs (Leptodactylus bufonius and L. chaquensis) using next generation sequencing

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Next-generation sequencing reveals large connected networks of intra-host HCV variants

Background: Next-generation sequencing (NGS) allows for sampling numerous viral variants from infected patients. This provides a novel opportunity to represent and study the mutational landscape of Hepatitis C Virus (HCV) within a single host.Results: Intra-host variants of the HCV E1/E2 region were extensively sampled from 58 chronically infected patients. After NGS error correction, the average number of reads and variants obtained from each sample were 3202 and 464, respectively. The distance between each pair of variants was calculated and networks were created for each patient, where each node is a variant and two nodes are connected by a link if the nucleotide distance between them is 1. The work focused on large components having > 5% of all reads, which in average account for 93.7% of all reads found in a patient. The distance between any two variants calculated over the component correlated strongly with nucleotide distances (r = 0.9499; p = 0.0001), a better correlation than the one obtained with Neighbour-Joining trees (r = 0.7624; p = 0.0001). In each patient, components were well separated, with the average distance between (6.53%) being 10 times greater than within each component (0.68%). The ratio of nonsynonymous to synonymous changes was calculated and some patients (6.9%) showed a mixture of networks under strong negative and positive selection. All components were robust to in silico stochastic sampling; even after randomly removing 85% of all reads, the largest connected component in the new subsample still involved 82.4% of remaining nodes. In vitro sampling showed that 93.02% of components present in the original sample were also found in experimental replicas, with 81.6% of reads found in both. When syringe-sharing transmission events were simulated, 91.2% of all simulated transmission events seeded all components present in the source.Conclusions: Most intra-host variants are organized into distinct single-mutation components that are: well separated from each other, represent genetic distances between viral variants, robust to sampling, reproducible and likely seeded during transmission events. Facilitated by NGS, large components offer a novel evolutionary framework for genetic analysis of intra-host viral populations and understanding transmission, immune escape and drug resistance.

Pirossequenciamento de alta cobertura da região hipervariável 1 do Vírus da Hepatite C

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Characterization of immobilized biomass by amplified rDNA restriction analysis (ARDRA) in an anaerobic sequencing-batch biofilm reactor (ASBBR) for the treatment of industrial wastewater

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

Relationship between therapeutic alliance and deep abdominal muscle recruitment in nonspecific low back pain sufferers

Chronic low back pain is a difficult condition to be treated. As some patients respond positively to treatment and others do not present any improvements, one can think there are others conditional factors that need to be elucidated. By means of this study, we sought to investigate the association between the occurrence of the formation of a positive relationship between patient and therapist, assessed by the therapeutic alliance inventory, and the adequate recruitment of the deep abdominal muscles, as well as to verify the effect of a protocol intervention based on motor control exercises on levels of pain and disability. The recruitment of the transverse abdominal and internal oblique muscles was examined by ultrasound imaging in 12 subjects with nonspecific chronic low back pain before and after implementation of a protocol for motor control exercises, with subsequent application of the therapeutic alliance inventory questionnaire. No association was found between the level of therapist/patient alliance and muscle recruitment. The proposed protocol was effective in reducing the levels of pain and disability; however, recruitment of transverse abdominal and internal oblique muscles showed no significant changes in the end of the intervention. Based on these findings, we verified that the therapeutic alliance has no association with muscle recruitment in the short term. However, although there were no changes in muscle recruitment after the intervention program, the level of pain and disability was reduced.

Flow sorting and exome sequencing reveal the oncogenome of primary Hodgkin and Reed-Sternberg cells

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Continental degassing of He-4 by surficial discharge of deep groundwater

Radiogenic He-4 is produced by the decay of uranium and thorium in the Earths mantle and crust. From here, it is degassed to the atmosphere(1-5) and eventually escapes to space(1,5,6). Assuming that all of the He-4 produced is degassed, about 70% of the total He-4 degassed from Earth comes from the continental crust(2,-5,7). However, the outgoing flux of crustal He-4 has not been directly measured at the Earths surface(2) and the migration pathways are poorly understood(2-4,7,8). Here we present measurements of helium isotopes and the long-lived cosmogenic radio-isotope Kr-81 in the deep, continental-scale Guarani aquifer in Brazil and show that crustal He-4 reaches the atmosphere primarily by the surficial discharge of deep groundwater. We estimate that He-4 in Guarani groundwater discharge accounts for about 20% of the assumed global flux from continental crust, and that other large aquifers may account for about 33%. Old groundwater ages suggest that He-4 in the Guarani aquifer accumulates over half- to one-million-year timescales. We conclude that He-4 degassing from the continents is regulated by groundwater discharge, rather than episodic tectonic events, and suggest that the assumed steady state between crustal production and degassing of He-4, and its resulting atmospheric residence time, should be re-examined.

Hydrochemical and stable isotopes (H, O, S) signatures in deep groundwaters of Parana basin, Brazil

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

Problem of the statistical model in deep inelastic scattering phenomenology

Recent deep inelastic data leads to an up-down quark asymmetry of the nucleon sea. Explanations of the flavour asymmetry and the di-lepton production in proton-nucleus collisions call for a temperature T ≈ 100 MeV in a statistical model. This T may be conjectured as being due to the Fulling-Davies-Unruh effect. But it is not possible to fit the structure function itself.

HLA-E coding and 3' untranslated region variability determined by next-generation sequencing in two West-African population samples

HLA-E is a non-classical Human Leucocyte Antigen class I gene with immunomodulatory properties. Whereas HLA-E expression usually occurs at low levels, it is widely distributed amongst human tissues, has the ability to bind self and non-self antigens and to interact with NK cells and T lymphocytes, being important for immunosurveillance and also for fighting against infections. HLA-E is usually the most conserved locus among all class I genes. However, most of the previous studies evaluating HLA-E variability sequenced only a few exons or genotyped known polymorphisms. Here we report a strategy to evaluate HLA-E variability by next-generation sequencing (NGS) that might be used to other HLA loci and present the HLA-E haplotype diversity considering the segment encoding the entire HLA-E mRNA (including 5'UTR, introns and the 3'UTR) in two African population samples, Susu from Guinea-Conakry and Lobi from Burkina Faso. Our results indicate that (a) the HLA-E gene is indeed conserved, encoding mainly two different protein molecules; (b) Africans do present several unknown HLA-E alleles presenting synonymous mutations; (c) the HLA-E 3'UTR is quite polymorphic and (d) haplotypes in the HLA-E 3'UTR are in close association with HLA-E coding alleles. NGS has proved to be an important tool on data generation for future studies evaluating variability in non-classical MHC genes.

ROBO1 deletion as a novel germline alteration in breast and colorectal cancer patients

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

The genome sequence of the plant pathogen Xylella fastidiosa: The Xylella fastidiosa consortium of the organization for nucleotide sequencing and analysis, Sao Paulo, Brazil

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes a range of economically important plant diseases. Here we report the complete genome sequence of X. fastidiosa clone 9a5c, which causes citrus variegated chlorosis - a serious disease of orange trees. The genome comprises a 52.7% GC-rich 2,679,305-base-pair (bp) circular chromosome and 'two plasmids of 51,158 bp and 1,285 bp. We can assign putative functions to47% of the 2,904 predicted coding regions. Efficient metabolic functions are predicted, with sugars as the principal energy and carbon source, supporting existence in the nutrient-poor xylem sap. The mechanisms associated with pathogenicity and virulence involve toxins, antibiotics and ion sequestration systems, as well as bacterium-bacterium and bacterium-host interactions mediated by a range of proteins. Orthologues of some of these proteins have only been identified in animal and human pathogens; their presence in X. fastidiosa indicates that the molecular basis for bacterial pathogenicity is both conserved and independent of host. At least 83 genes are bacteriophage-derived and include virulence-associated genes from other bacteria, providing direct evidence of phage-mediated horizontal gene transfer.