Poly(rC) binding protein 2 binds to stem-loop IV of the poliovirus RNA 5' noncoding region: identification by automated liquid chromatography-tandem mass spectrometry.

The 5' noncoding region of poliovirus RNA contains an internal ribosome entry site (IRES) for cap-independent initiation of translation. Utilization of the IRES requires the participation of one or more cellular proteins that mediate events in the translation initiation reaction, but whose biochemical roles have not been defined. In this report, we identify a cellular RNA binding protein isolated from the ribosomal salt wash of uninfected HeLa cells that specifically binds to stem-loop IV, a domain located in the central part of the poliovirus IRES. The protein was isolated by specific RNA affinity chromatography, and 55% of its sequence was determined by automated liquid chromatography-tandem mass spectrometry. The sequence obtained matched that of poly(rC) binding protein 2 (PCBP2), previously identified as an RNA binding protein from human cells. PCBP2, as well as a related protein, PCBP1, was over-expressed in Escherichia coli after cloning the cDNAs into an expression plasmid to produce a histidine-tagged fusion protein. Specific interaction between recombinant PCBP2 and poliovirus stem-loop IV was demonstrated by RNA mobility shift analysis. The closely related PCBP1 showed no stable interaction with the RNA. Stem-loop IV RNA containing a three nucleotide insertion that abrogates translation activity and virus viability was unable to bind PCBP2.

Simultaneous assessment of loss of heterozygosity at multiple microsatellite loci using semi-automated fluorescence-based detection: subregional mapping of chromosome 4 in cervical carcinoma.

Detection of loss of heterozygosity (LOH) by comparison of normal and tumor genotypes using PCR-based microsatellite loci provides considerable advantages over traditional Southern blotting-based approaches. However, current methodologies are limited by several factors, including the numbers of loci that can be evaluated for LOH in a single experiment, the discrimination of true alleles versus "stutter bands," and the use of radionucleotides in detecting PCR products. Here we describe methods for high throughput simultaneous assessment of LOH at multiple loci in human tumors; these methods rely on the detection of amplified microsatellite loci by fluorescence-based DNA sequencing technology. Data generated by this approach are processed by several computer software programs that enable the automated linear quantitation and calculation of allelic ratios, allowing rapid ascertainment of LOH. As a test of this approach, genotypes at a series of loci on chromosome 4 were determined for 58 carcinomas of the uterine cervix. The results underscore the efficacy, sensitivity, and remarkable reproducibility of this approach to LOH detection and provide subchromosomal localization of two regions of chromosome 4 commonly altered in cervical tumors.

Major histocompatibility complex class II DR alleles DRB1*1501 and those encoding HLA-DR13 are preferentially associated with a diminution in maternally transmitted human immunodeficiency virus 1 infection in different ethnic groups: determination by an automated sequence-based typing method.

Transmission of human immunodeficiency virus 1 (HIV-1) from an infected women to her offspring during gestation and delivery was found to be influenced by the infant's major histocompatibility complex class II DRB1 alleles. Forty-six HIV-infected infants and 63 seroreverting infants, born with passively acquired anti-HIV antibodies but not becoming detectably infected, were typed by an automated nucleotide-sequence-based technique that uses low-resolution PCR to select either the simpler Taq or the more demanding T7 sequencing chemistry. One or more DR13 alleles, including DRB1*1301, 1302, and 1303, were found in 31.7% of seroreverting infants and 15.2% of those becoming HIV-infected [OR (odds ratio) = 2.6 (95% confidence interval 1.0-6.8); P = 0.048]. This association was influenced by ethnicity, being seen more strongly among the 80 Black and Hispanic children [OR = 4.3 (1.2-16.4); P = 0.023], with the most pronounced effect among Black infants where 7 of 24 seroreverters inherited these alleles with none among 12 HIV-infected infants (Haldane OR = 12.3; P = 0.037). The previously recognized association of DR13 alleles with some situations of long-term nonprogression of HIV suggests that similar mechanisms may regulate both the occurrence of infection and disease progression after infection. Upon examining for residual associations, only only the DR2 allele DRB1*1501 was associated with seroreversion in Caucasoid infants (OR = 24; P = 0.004). Among Caucasoids the DRB1*03011 allele was positively associated with the occurrence of HIV infection (P = 0.03).

An automated multiplex oligonucleotide synthesizer: development of high-throughput, low-cost DNA synthesis.

An automated oligonucleotide synthesizer has been developed that can simultaneously and rapidly synthesize up to 96 different oligonucleotides in a 96-well microtiter format using phosphoramidite synthesis chemistry. A modified 96-well plate is positioned under reagent valve banks, and appropriate reagents are delivered into individual wells containing the growing oligonucleotide chain, which is bound to a solid support. Each well has a filter bottom that enables the removal of spent reagents while retaining the solid support matrix. A seal design is employed to control synthesis environment and the entire instrument is automated via computer control. Synthesis cycle times for 96 couplings are < 11 min, allowing a plate of 96 20-mers to be synthesized in < 5 hr. Oligonucleotide synthesis quality is comparable to commercial machines, with average coupling efficiencies routinely > 98% across the entire 96-well plate. No significant well-to-well variations in synthesis quality have been observed in > 6000 oligonucleotides synthesized to date. The reduced reagent usage and increased capacity allow the overall synthesis cost to drop by at least a factor of 10. With the development of this instrument, it is now practical and cost-effective to synthesize thousands to tens of thousands of oligonucleotides.

Development of data reduction pipelines for GTC instruments at the UCM

The UCM Instrumentation Group (GUAIX) is developing currently Data Reduction Pipelines (DRP) for four instruments of the GTC: EMIR, FRIDA, MEGARA and MIRADAS. The purpose of the DRPs is to provide astronomers scientific quality data, removing instrumental biases, calibrating the images in physical units and providing a estimation of the associated uncertainties.

Análise de incerteza de um sistema automatizado para ensaios de aspersores de irrigação

Ensaios de distribuição de água de aspersores são convencionalmente realizados manualmente, requerendo tempo e mão de obra treinada. A automação desses ensaios proporciona redução da demanda por esses recursos e apresenta potencial para minimizar falhas e/ou desvios de procedimento. Atualmente, laboratórios de ensaio e calibração acreditados junto a organismos legais devem apresentar em seus relatórios a incerteza de medição de seus instrumentos e sistemas de medição. Além disso, normas de ensaio e calibração apresentam especificação de incerteza aceitável, como a norma de ensaios de distribuição de água por aspersores, ISO 15886-3 (2012), a qual exige uma incerteza expandida de até 3% em 80% dos coletores. Os objetivos deste trabalho foram desenvolver um sistema automatizado para os ensaios de aspersores em laboratório e realizar a análise de incerteza de medição, para sua quantificação nos resultados de ensaio e para dar suporte ao dimensionamento dos tubos de coleta. O sistema automático foi constituído por um subsistema de gerenciamento, por meio de um aplicativo supervisório, um de pressurização e um de coleta, por meio de módulos eletrônicos microprocessados desenvolvidos. De acordo com instruções do sistema de gerenciamento o sistema de pressurização ajustava a pressão no aspersor por meio do controle da rotação da motobomba, e o sistema de coleta realizava a medição da intensidade de precipitação de água ao longo do raio de alcance do aspersor. A água captada por cada coletor drenava para um tubo de coleta, que estava conectado a uma das válvulas solenoides de um conjunto, onde havia um transmissor de pressão. Cada válvula era acionada individualmente numa sequência para a medição do nível de água em cada tubo de coleta, por meio do transmissor. Por meio das análises realizadas, as menores incertezas foram obtidas para os menores diâmetros de tubo de coleta, sendo que se deve utilizar o menor diâmetro possível. Quanto ao tempo de coleta, houve redução da incerteza de medição ao se aumentar a duração, devendo haver um tempo mínimo para se atingir a incerteza-alvo. Apesar de cada intensidade requer um tempo mínimo para garantir a incerteza, a diferença mínima de nível a ser medida foi a mesma. Portanto, para os ensaios visando atender a incerteza, realizou-se o monitoramento da diferença de nível nos tubos, ou diferença de nível, facilitando a realização do ensaio. Outra condição de ensaio considerou um tempo de coleta para 30 voltas do aspersor, também exigido pela norma ISO 15886-3 (2012). A terceira condição considerou 1 h de coleta, como tradicionalmente realizado. As curvas de distribuição de água obtidas por meio do sistema desenvolvido foram semelhantes às obtidas em ensaios convencionais, para as três situações avaliadas. Para tempos de coleta de 1 h ou 30 voltas do aspersor o sistema automático requereu menos tempo total de ensaio que o ensaio convencional. Entretanto, o sistema desenvolvido demandou mais tempo para atingir a incerteza-alvo, o que é uma limitação, mesmo sendo automatizado. De qualquer forma, o sistema necessitava apenas que um técnico informasse os parâmetros de ensaio e o acionasse, possibilitando que o mesmo alocasse seu tempo em outras atividades.

Do Things Change in Therapy That Are Not Measured By Self-report Instruments?

This study investigates a new way of assessing change in psychotherapy, with the goal of decreasing the schism in the field of psychology between research and clinical practice. Change in psychotherapy was assessed in clients presenting with depressive symptoms who were seeking therapy at the Professional Psychology Center (PPC) at the University of Denver. Prior to beginning treatment, the subjects completed the Beck Depression Inventory- II (BDI-II) and the Symptom Checklist-90-R (SCL-90), and were also assessed by independent clinicians using the Shedler-Westen Assessment Procedure II (SWAP-II). Six to nine months later, after completing at least 12 psychotherapy sessions (range 12-21 sessions), the assessment procedure was repeated.There were no significant differences pre- to post-treatment on any measure. However, two subjects in the sample appeared to benefit from treatment, as assessed by both the self-report measures and the SWAP-II. The findings for these two subjects suggest that the SWAP-II can provide a greater depth of understanding about what can change in therapy than self-report measures alone. Possible reasons for the lack of treatment effects in the larger sample are discussed.

Els instruments científics dels instituts d'ensenyament mitjà: un extraordinari patrimoni cultural que hem de preservar i estudiar

Several important collections of scientific instruments are preserved in secondary schools but just a small group have been properly catalogued and studied. Unfortunately, they are not commonly regarded as a relevant part of the cultural heritage. However, recent trends in history of science offer new perspectives to study these objects from new points of view. We review some recent studies about collections of scientific instruments in secondary schools and we offer preliminary conclusions of our current work on this topic.