Identification of tRNAs incorporated into wild-type and mutant human immunodeficiency virus type 1

We have identified the tRNAs which are incorporated into both wild-type human immunodeficiency virus type 1 strain IIIB (HIV-1IIIB) produced in COS-7 cells transfected with HIV-1 proviral DNA and mutant, noninfectious HIV-1Lai particles produced in a genetically engineered Vero cell line. The mutant proviral DNA contains nucleotides 678 to 8944; i.e., both long terminal repeats and the primer binding site are absent. As analyzed by two-dimensional polyacrylamide gel electrophoresis, both mutant and wild-type HIV-1 contain four major-abundance tRNA species, which include tRNA(1,2Lys), tRNA(3Lys) (the putative primer for HIV-1 reverse transcriptase) and tRNA(Ile). Identification was accomplished by comparing the electrophoretic mobilities and RNase T1 digests with those of tRNA(3Lys) and tRNA(1,2Lys) purified from human placenta and comparing the partial nucleotide sequence at the 3' end of each viral tRNA species with published tRNA sequences. Thus, the absence of the primer binding site in the mutant virus does not affect tRNA(Lys) incorporation into HIV-1. However, only the wild-type virus contains tRNA(3Lys) tightly associated with the viral RNA genome. The identification of the tightly associated tRNA as tRNA(3Lys) is based upon an electrophoretic mobility identical to that of tRNA(3Lys) and the ability of this RNA to hybridize with a tRNA(3Lys)-specific DNA probe. In addition to the four wild-type tRNA species, the mutant HIV-1-like particle contains two tRNA(His) species and three tRNA-sized species that we have been unable to identify. Their absence in wild-type virus makes it unlikely that they are required for viral infectivity.

Integrated DNA extraction and amplification using electrokinetic pumping in a microfluidic device

An integrated system employing anion exchange for the extraction of DNA from biological samples prior to polymerase chain reaction DNA amplification has been developed, based on microfluidic methodology utilising electrokinetic pumping. In this system, the biological samples were added directly to chitosan-coated silica beads to facilitate DNA immobilisation. The purified, pre-concentrated DNA was then eluted using a combination of electro-osmotic flow enhanced with electrophoretic mobility, which enable DNA to be transported by both mechanisms into the DNA amplification chamber. Through optimisation of the DNA elution conditions, average DNA extraction efficiencies of 69.1% were achievable. Subsequent DNA amplification performed on the microfluidic system demonstrated not only the ability to use electrokinetic movement to integrate the two processes on a single device, but also that the quality and quantity of DNA eluted was suitable for downstream analysis. This work offers an attractive real-world to chip interface and a route to simpler Lab-on-a-Chip technology which eliminates the need for moving parts.

Complex coacervation between flaxseed protein isolate and flaxseed gum

Flaxseed protein isolate (FPI) and flaxseed gum (FG) were extracted, and the electrostatic complexation between these two biopolymers was studied as a function of pH and FPI-to-FG ratio using turbidimetric and electrophoretic mobility (zeta potential) tests. The zeta potential values of FPI, FG, and their mixtures at the FPI-to-FG ratios of 1:1, 3:1, 5:1, 10:1, 15:1 were measured over a pH range 8.0-1.5. The alteration of the secondary structure of FPI as a function of pH was studied using circular dichroism. The proportion of a-helical structure decreased, whereas both β-sheet structure and random coil structure increased with the lowering of pH from 8.0 to 3.0. The acidic pH affected the secondary structure of FPI and the unfolding of helix conformation facilitated the complexation of FPI with FG. The optimum FPI-to-FG ratio for complex coacervation was found to be 3:1. The critical pH values associated with the formation of soluble (pHc) and insoluble (pHΦ1) complexes at the optimum FPI-to-FG ratio were found to be 6.0 and 4.5, respectively. The optimum pH (pHopt) for the optimum complex coacervation was 3.1. The instability and dissolution of FPI-FG complex coacervates started (pHΦ2) at pH2.1. These findings contribute to the development of FPI-FG complex coacervates as delivery vehicles for unstable albeit valuable nutrients such as omega-3 fatty acids.

Evaluation of curcumin and cisplatin-induced DNA damage in PC12 cells by the alkaline comet assay

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Caracterização de hemoglobina N-Baltimore em doador de sangue de São José do Rio Preto, SP

As alterações que envolvem as globinas devem-se a modificações em genes responsáveis pela seqüência e estrutura das cadeias polipeptídicas, bem como aos genes reguladores da síntese destas cadeias. Hemoglobinas variantes apresentam estrutura química diferente da hemoglobina normal correspondente, resultante de mutações em uma ou mais bases nitrogenadas, ocasionando a troca de aminoácidos nas globinas alfa, beta, delta ou gama. A hemoglobina N-Baltimore é uma variante de globina beta, com substituição da lisina, na posição 95, por ácido glutâmico, apresentando mobilidade eletroforética mais rápida que a hemoglobina A em pH alcalino. Nas análises eletroforéticas em pH alcalino realizadas em doadores de sangue do Hemocentro de São José do Rio Preto (SP) identificamos a presença de portador de hemoglobina rápida em heterozigose, posteriormente confirmada por focalização isoelétrica e cromatografia líquida de alta pressão (HPLC). Os estudos de hemoglobinas anormais em doadores de sangue permitem a identificação de variantes raras e possibilitam o aconselhamento genético adequado a cada caso com estudo familial.

Association of matrix metalloproteinase-8 gene variation with breast cancer prognosis

Animal and cell studies indicate an inhibitory effect of matrix metalloproteinase-8 (MMP8) on tumorigenesis and metastasis. We investigated whether MMP8 gene variation was associated with breast cancer metastasis and prognosis in humans. We first studied nine tagging single nucleotide polymorphisms (SNP) in the MMP8 gene in 140 clinically and pathologically well-characterized breast cancer patients. Four of the SNPs were found to be associated with lymph node metastasis, the most pronounced being a promoter SNP (rs11225395) with its minor allele (T) associating with reduced susceptibility to lymph node metastasis (P = 0.02). This SNP was further evaluated for association with cancer relapse and survival among a cohort of similar to 1,100 breast cancer patients who had been followed for cancer recurrence and mortality for a median of 7.1 years. The T allele was associated with reduced cancer relapse and greater survival, particularly among patients with earlier stage cancer. Among patients of tumor-node-metastasis stage 0 to 11, the adjusted hazard ratio of disease-free survival was 0.7 [95% confidence interval (95% CI), 0.5-0.9] for patients carrying T allele compared with those homozygous for the C allele (P = 0.02). In vitro experiments showed that the T allele had higher promoter activity than the C allele in breast cancer cells. Electrophoretic mobility shift assays showed binding of nuclear proteins to the DNA sequence at the SNP site of the T allele but not that of the C allele. The data suggest that MMP8 gene variation may influence breast cancer prognosis and support the notion that MMP8 has an inhibitory effect on cancer metastasis.

A systematic approach to identify STRE-binding proteins of the gsn glycogen synthase gene promoter in Neurospora crassa

The gene encoding glycogen synthase in Neurospora crassa (gsn) is transcriptionally down-regulated when mycelium is exposed to a heat shock from 30 to 45 degrees C. The gsn promoter has one stress response element (STRE) motif that is specifically bound by heat shock activated nuclear proteins. In this work, we used biochemical approaches together with mass spectrometric analysis to identify the proteins that bind to the STRE motif and could participate in the gsn transcription regulation during heat shock. Crude nuclear extract of heat-shocked mycelium was prepared and fractionated by affinity chromatography. The fractions exhibiting DNA-binding activity were identified by electrophoretic mobility shift assay (EMSA) using as probe a DNA fragment containing the STRE motif DNA-protein binding activity was confirmed by Southwestern analysis. The molecular mass (MM) of proteins was estimated by fractionating the crude nuclear extract by SDS-PAGE followed by EMSA analysis of the proteins corresponding to different MM intervals. Binding activity was detected at the 30-50 MM kDa interval. Fractionation of the crude nuclear proteins by IEF followed by EMSA analysis led to the identification of two active fractions belonging to the pIs intervals 3.54-4.08 and 6.77-7.31. The proteins comprising the MM and pI intervals previously identified were excised from a 2-DE gel, and subjected to mass spectrometric analysis (MALDI-TOF/TOF) after tryptic digestion. The proteins were identified by search against the MIPS and MIT N. crassa databases and five promising candidates were identified. Their structural characteristics and putative roles in the gsn transcription regulation are discussed.

Ferric iron uptake genes are differentially expressed in the presence of copper sulfides in Acidithiobacillus ferrooxidans strain LR

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

A Genome-wide Screen for Neurospora crassa Transcription Factors Regulating Glycogen Metabolism

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

Colloidal particles: Spherical yttrium iron garnet

The purpose of this work is to obtain spherical particles YIG from micrometric to nanometric scales. The spherical particles were obtained from cation hydrolysis in acid medium by adding urea or ammonia in order to carry out a homogeneous nucleation process up to 90 degrees C. Different composition and morphology were achieved by changing reactant concentrations, precipitation agent and stabilizing agent. X-ray diffractometry, electrophoretic mobility, transmission and scanning electron microscopies were carried out on these particles to investigate the phase identification, mobility, morphology and particle size. Crystalline YIG, with spherical characteristics, was obtained. The surface potential presented different characteristics for different dispersion media.

Partículas nanométricas de ferritas de ítrio

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

Investigation of the systems silica and silica containing chromium in alcohol medium

The purpose of this work is to obtain micrometer sized spherical particles of silica and silica-chromium from sodium silicate. Spherical particles were prepared by sol-gel method from hydrolysis to polycondensation of aqueous sodium silicate in alcohol medium. Chromium was added to the system for some samples. Compositions and morphologies were achieved by changing the precipitation agent. X-ray diffractometry, electrophoretic mobility, infrared spectroscopy and scanning electron microscopies were carried out on these particles to identify phases, determine particle mobility, morphology, particle sizes, shapes and order at short distance. Non-crystalline silica particles with spherical shapes and micrometric size were obtained. The surface potentials of the silica particles differed from that of the silica-chromium particles. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Genomic organization of the Neurospora crassa gsn gene: possible involvement of the STRE and HSE elements in the modulation of transcription during heat shock

Glycogen synthase, an enzyme involved in glycogen biosynthesis, is regulated by phosphorylation and by the allosteric ligand glucose-6-phosphate (G6P). In addition, enzyme levels can be regulated by changes in gene expression. We recently cloned a cDNA for glycogen synthase (gsn) from Neurospora crassa, and showed that gsn transcription decreased when cells were exposed to heat shock (shifted from 30degreesC to 45degreesC). In order to understand the mechanisms that control gsn expression, we isolated the gene, including its 5' and 3' flanking regions, from the genome of N. crassa. An ORF of approximately 2.4 kb was identified, which is interrupted by four small introns (II-V). Intron I (482 bp) is located in the 5'UTR region. Three putative Transcription Initiation Sites (TISs) were mapped, one of which lies downstream of a canonical TATA-box sequence (5'-TGTATAAA-3'). Analysis of the 5'-flanking region revealed the presence of putative transcription factor-binding sites, including Heat Shock Elements (HSEs) and STress Responsive Elements (STREs). The possible involvement of these motifs in the negative regulation of gsn transcription was investigated using Electrophoretic Mobility Shift Assays (EMSA) with nuclear extracts of N. crassa mycelium obtained before and after heat shock, and DNA fragments encompassing HSE and STRE elements from the 5'-flanking region. While elements within the promoter region are involved in transcription under heat shock, elements in the 5'UTR intron may participate in transcription during vegetative growth. The results thus suggest that N. crassa possesses trans-acting elements that interact with the 5'-flanking region to regulate gsn transcription during heat shock and vegetative growth.

Preparation of ceramic membranes from surface modified tin oxide nanoparticles

The preparation of crack-free SnO2 supported membranes requires the development of new strategies of synthesis capable to allow controlled changes of surface chemistry and to improve the processability of supported layers. In this way, the controlled modification of the SnO2 nanoparticle surface by adding capping molecules like Tiron(R) ((OH)(2)C6H2(SO3Na)(2)) during the sol-gel process was studied, aiming to obtain high performance membranes. Colloidal suspensions were prepared by hydrolyzing SnCl4.5H(2)O aqueous solution with NH4OH in presence of Tiron(R). The effect of the amount of Tiro(R) (from I to 20 wt.%) on the structural features of nanoparticles, powder redispersability and particle-solution interface properties was investigated by X-ray powder diffraction (XRPD), extended X-ray absorption fine structure (EXAFS), quasi-elastic light scattering and electrophoretic mobility measurements. XRPD and EXAFS results showed that the addition of Tiron(R) up to 20 wt.% to colloidal suspensions does not affect the crystallite size of SnO2 primary particles, determined around 2-3 nm. This value is comparable to the hydrodynamic size measured after redispersion of powder prepared with amount of Tiro(R) higher than 7.5 wt.%, indicating the absence of condensation reactions between primary particles after the initial precipitation step. As a consequence the powder with amount of Tiron(R) > 7.5 wt.%, can be fully redispersed in aqueous solution at pH greater than or equal to I I until a nanoparticle concentration of 6 vol.%. The electrophoresis measurements showed a decrease of the isoelectric point by increasing the amount of grafted Tiron(R) at the SnO2 nanoparticle surface, resulting in negatively charged particle-solution interface in all the studied pH range (2-11). These features govern the gelation process favoring the preparation of crack-free SnO2 supported membranes. The control exercised by Tiron(R) modifying agent in the aggregation process allows the fine-tuning of the porosity, from 0.124 to 0.065 cm(3) g(-1), and mean pore size, from 6.4 to 1.9 nm, as the amount of grafted molecules increases from 0 to 10 wt.%. In consequence, the membrane cut-off determined by filtration of polyethylene glycol standard solutions can be screened from 1500 to 3500 g mol(-1). (C) 2002 Elsevier B.V. B.V. All rights reserved.

Zeta potential and doping in polyaniline dispersions

Polyaniline (PAni) has been classified as an intractable polymer, particularly in its conducting form, the emeraldine salt (ES). Therefore one can consider the mixture of water and PAni as a suspension. The conducting form of PAni can be obtained by a doping process known as acid doping, in which a strong acid turns PAni from its insulating form, the emeraldine base (EB), into the conducting form, the emeraldine salt. With the objective of establishing a correlation between the doping level and the zeta potential of polyaniline dispersions, polyaniline + HCl aqueous suspensions were prepared. Positive zeta potential values for the various suspensions of PAni showed that it acquired positive charges after the doping process. It was also observed an increase in zeta potential values as HCl concentration increased, which could be correlated to UV-visible spectra of PAni suspensions.