Manipulating the mammalian genome by homologous recombination

Gene targeting in mammalian cells has proven invaluable in biotechnology, in studies of gene structure and function, and in understanding chromosome dynamics. It also offers a potential tool for gene-therapeutic applications. Two limitations constrain the current technology: the low rate of homologous recombination in mammalian cells and the high rate of random (nontargeted) integration of the vector DNA. Here we consider possible ways to overcome these limitations within the framework of our present understanding of recombination mechanisms and machinery. Several studies suggest that transient alteration of the levels of recombination proteins, by overexpression or interference with expression, may be able to increase homologous recombination or decrease random integration, and we present a list of candidate genes. We consider potentially beneficial modifications to the vector DNA and discuss the effects of methods of DNA delivery on targeting efficiency. Finally, we present work showing that gene-specific DNA damage can stimulate local homologous recombination, and we discuss recent results with two general methodologies—chimeric nucleases and triplex-forming oligonucleotides—for stimulating recombination in cells.

Internal ribosomal entry site substitution eliminates neurovirulence in intergeneric poliovirus recombinants.

Neuropathogenicity of poliovirus can be attenuated by mutations in the internal ribosomal entry site (IRES) within the 5' nontranslated region of its genome. The Sabin vaccine strains used in prevention of poliomyelitis carry such mutations in their IRES elements. In addition, mutations within the structural and nonstructural proteins of Sabin strains may equally contribute to the attenuation phenotype. Despite their effectiveness as vaccines, the Sabin strains retain a neuropathogenic potential in animal models for poliomyelitis and, at a very low rate, they can cause poliomyelitis in vaccine recipients. The elimination of the neurocytopathic phenotype was achieved through the exchange of the entire poliovirus IRES with its counterpart from human rhinovirus type 2 without affecting growth properties in nonneuronal cells. The attenuating effect of the human rhinovirus type 2 IRES within the context of a poliovirus genome has been mapped to the 3' portion of this genetic element.

An ATP-dependent As(III)-glutathione transport system in membrane vesicles of Leishmania tarentolae.

Membrane preparations enriched in plasma membrane vesicles prepared from promastigotes of Leishmania tarentolae were shown to accumulate thiolate derivatives of 73As(III). Free arsenite was transported at a low rate, but rapid accumulation was observed after reaction with reduced glutathione (GSH) conditions that favor the formation of As(GS)3. Accumulation required ATP but not electrochemical energy, indicating that As(GS)3 is transported by an ATP-coupled pump. Pentostam, a Sb(V)-containing drug that is one of the first-line therapeutic agents for treatment of leishmaniasis, inhibited uptake after reaction with GSH. Vesicles prepared from a strain in which both copies of the pgpA genes were disrupted accumulated As(GS)3 at wild-type levels, demonstrating that the PgpA protein is not the As(GS)3 pump. These results have important implications for the mechanism of drug resistance in the trypanosomatidae, suggesting that a plasma membrane As(GS)3 pump catalyzes active extrusion of metal thiolates, including the Pentostam-glutathione conjugate.

Voice-processing technologies--their application in telecommunications.

As the telecommunications industry evolves over the next decade to provide the products and services that people will desire, several key technologies will become commonplace. Two of these, automatic speech recognition and text-to-speech synthesis, will provide users with more freedom on when, where, and how they access information. While these technologies are currently in their infancy, their capabilities are rapidly increasing and their deployment in today's telephone network is expanding. The economic impact of just one application, the automation of operator services, is well over $100 million per year. Yet there still are many technical challenges that must be resolved before these technologies can be deployed ubiquitously in products and services throughout the worldwide telephone network. These challenges include: (i) High level of accuracy. The technology must be perceived by the user as highly accurate, robust, and reliable. (ii) Easy to use. Speech is only one of several possible input/output modalities for conveying information between a human and a machine, much like a computer terminal or Touch-Tone pad on a telephone. It is not the final product. Therefore, speech technologies must be hidden from the user. That is, the burden of using the technology must be on the technology itself. (iii) Quick prototyping and development of new products and services. The technology must support the creation of new products and services based on speech in an efficient and timely fashion. In this paper I present a vision of the voice-processing industry with a focus on the areas with the broadest base of user penetration: speech recognition, text-to-speech synthesis, natural language processing, and speaker recognition technologies. The current and future applications of these technologies in the telecommunications industry will be examined in terms of their strengths, limitations, and the degree to which user needs have been or have yet to be met. Although noteworthy gains have been made in areas with potentially small user bases and in the more mature speech-coding technologies, these subjects are outside the scope of this paper.

The folding of GroEL-bound barnase as a model for chaperonin-mediated protein folding.

We have analyzed the pathway of folding of barnase bound to GroEL to resolve the controversy of whether proteins can fold while bound to chaperonins (GroEL or Cpn60) or fold only after their release into solution. Four phases in the folding were detected by rapid-reaction kinetic measurements of the intrinsic fluorescence of both wild type and barnase mutants. The phases were assigned from their rate laws, sensitivity to mutations, and correspondence to regain of catalytic activity. At high ratios of denatured barnase to GroEL, 4 mol of barnase rapidly bind per 14-mer of GroEL. At high ratios of GroEL to barnase, 1 mol of barnase binds with a rate constant of 3.5 x 10(7) s-1.M-1. This molecule then refolds with a low rate constant that changes on mutation in parallel with the rate constant for the folding in solution. This rate constant corresponds to the regain of the overall catalytic activity of barnase and increases 15-fold on the addition of ATP to a physiologically relevant value of approximately 0.4 s-1. The multiply bound molecules of barnase that are present at high ratios of GroEL to barnase fold with a rate constant that is also sensitive to mutation but is 10 times higher. If the 110-residue barnase can fold when bound to GroEL and many moles can bind simultaneously, then smaller parts of large proteins should be able to fold while bound.

Investigação do mecanismo cinético da reação de redução de oxigênio em solventes não aquosos

O aumento no consumo energético e a crescente preocupação ambiental frente à emissão de gases poluentes criam um apelo mundial favorável para pesquisas de novas tecnologias não poluentes de fontes de energia. Baterias recarregáveis de lítio-ar em solventes não aquosos possuem uma alta densidade de energia teórica (5200 Wh kg-1), o que as tornam promissoras para aplicação em dispositivos estacionários e em veículos elétricos. Entretanto, muitos problemas relacionados ao cátodo necessitam ser contornados para permitir a aplicação desta tecnologia, por exemplo, a baixa reversibilidade das reações, baixa potência e instabilidades dos materiais empregados nos eletrodos e dos solventes eletrolíticos. Assim, neste trabalho um modelo cinético foi empregado para os dados experimentais de espectroscopia de impedância eletroquímica, para a obtenção das constantes cinéticas das etapas elementares do mecanismo da reação de redução de oxigênio (RRO), o que permitiu investigar a influência de parâmetros como o tipo e tamanho de partícula do eletrocatalisador, o papel do solvente utilizado na RRO e compreender melhor as reações ocorridas no cátodo dessa bateria. A investigação inicial se deu com a utilização de sistemas menos complexos como uma folha de platina ou eletrodo de carbono vítreo como eletrodos de trabalho em 1,2-dimetoxietano (DME)/perclorato de lítio (LiClO4). A seguir, sistemas complexos com a presença de nanopartículas de carbono favoreceu o processo de adsorção das moléculas de oxigênio e aumentou ligeiramente (uma ordem de magnitude) a etapa de formação de superóxido de lítio (etapa determinante de reação) quando comparada com os eletrodos de platina e carbono vítreo, atribuída à presença dos grupos laterais mediando à transferência eletrônica para as moléculas de oxigênio. No entanto, foi observada uma rápida passivação da superfície eletrocatalítica através da formação de filmes finos de Li2O2 e Li2CO3 aumentando o sobrepotencial da bateria durante a carga (diferença de potencial entre a carga e descarga > 1 V). Adicionalmente, a incorporação das nanopartículas de platina (Ptnp), ao invés da folha de platina, resultou no aumento da constante cinética da etapa determinante da reação em duas ordens de magnitude, o qual pode ser atribuído a uma mudança das propriedades eletrônicas na banda d metálica em função do tamanho nanométrico das partículas, e estas modificações contribuíram para uma melhor eficiência energética quando comparado ao sistema sem a presença de eletrocatalisador. Entretanto, as Ptnp se mostraram não específicas para a RRO, catalisando as reações de degradação do solvente eletrolítico e diminuindo rapidamente a eficiência energética do dispositivo prático, devido ao acúmulo de material no eletrodo. O emprego de líquido iônico como solvente eletrolítico, ao invés de DME, promoveu uma maior estabilização do intermediário superóxido formado na primeira etapa de transferência eletrônica, devido à interação com os cátions do líquido iônico em solução, o qual resultou em um valor de constante cinética da formação do superóxido de três ordens de magnitude maior que o obtido com o mesmo eletrodo de carbono vítreo em DME, além de diminuir as reações de degradação do solvente. Estes fatores podem contribuir para uma maior potência e ciclabilidade da bateria de lítio-ar operando com líquidos iônicos.

Recovery from Pediatric Brain Injury: A Preliminary Comparison of Longitudinal Data on Psychological Symptomology and Mental Health Treatment

Objective: To document the course of psychological symptomology, mental health treatment, and unmet psychological needs using caregiver reports in the first 18 months following pediatric brain injury (BI). Method: Participants included 28 children (aged 1-18 years) who were hospitalized at a children's hospital's rehabilitation unit. Caregiver reports of children's psychological symptoms, receipt of mental health treatment, and unmet psychological needs were assessed at one month, six months, 12 months, and 18 months post-BI. Results: Caregivers reported a general increase in psychological symptoms and receipt of mental health treatment over the 18 months following BI; however, there was a substantial gap between the high rate of reported symptoms and low rate of reported treatment. Across all four follow-up time points there were substantial unmet psychological needs (at least 60% of sample). Conclusions: Findings suggest that there are substantial unmet psychological needs among children during the first 18 months after BI. Barriers to mental health treatment for this population need to be addressed.

The Crowding-out Effect of Mandatory Labour Market Pension Schemes on Private Savings. Evidence from renters in Denmark. CEPS Working Document No. 389, February 2014

This paper aims to estimate the crowding-out effect of the Danish mandatory labour market pension reforms begun in 1993 on the level of total household savings for renters. The effect is identified via a large panel of individual administrative records utilising the differences in speed, timing and sectoral coverage of the implementation of the reform in the period 1997 to 2005. Little substitutability was found between current mandatory labour market pension savings and private voluntary savings. Each euro paid into mandatory labour market pension accounts results in a reduction in private savings of approximately 0 to 30 cents, depending on age. This low rate of substitution is only, to a minor extent, explained by liquidity constraints. The results point to mandatory pension savings having a large effect on total household savings. Thus, pension reforms that introduce mandatory savings have macroeconomic implications.

Age determinations for ODP Sites in the Norwegian-Greenland Sea

Records of biogenic and terrigenous components have been obtained from the interval corresponding to the last 2.6 m.y. of ODP Sites 643 and 644 in order to reconstruct surface and deep water regimes in the Norwegian Sea. Surface water regimes record long lasting moderate glacial conditions during the interval 2.6 1.0 Ma. Small intrusions of Atlantic water episodically penetrated into the Norwegian Sea forming a narrow tongue along the eastern margin, which is documented at Site 644. The polar front was most probably situated between the Site 644 and 643 locations on the outer Voring Plateau during these time intervals. Deep water regimes reflect long-term persistent corrosive bottom waters, most probably due to a weakly undersaturated water column and a low rate of carbonate shell production in surface waters. Deep water production in the Norwegian-Greenland Sea may have operated in a different way, e.g. brine formation during winter sea ice growth. Bottom waters were oxygenated throughout the entire period, and deep water was exchanged persistently with the North Atlantic. Increased glacial/interglacial enviromental contrasts are documented, reflecting a strengthening of the Norwegian Current and intensified glaciations on the surrounding land masses during the interval 1.0 0.6 Ma. During this time a major shift in the mode of deep water production occurred. Tile onset of large amplitudes in glacial/interglacial environmental conditions with maximum contrasts in surface water regimes, different modes of deep water production, and intensified exchange with the North Atlantic marks the last 0.6 Ma. A broad development of the Norwegian Current is observed during peak interglacials, while during glacials seasonally variable sea ice cover and iceberg drift dominate surface water conditions.

(Table 2) Age determination of sediments from lake basins near Polyarny, Russia

A relative sea-level curve for the Holocene is constructed for Polyarny on the Kola Peninsula, northwest Russia. The curve is based on 18 radiocarbon dates of isolation contacts, identified from lithological and diatomological criteria, in nine lake basins situated between 12 and 57 m a.s.l. Most of the lakes show a conformable, regressive I-II-III (marine-transitional-freshwater) facies succession, indicating a postglacial history comprising an early (10,000-9000 radiocarbon years BP) phase of rapid, glacio-isostatically induced emergence (~5 cm/year) and a later phase (after 7000 years BP,) having a moderate rate of emergence (<0.5 cm/year). Three lakes together record a phase of very low rate of emergence or slight sea-level rise at a level of ~27 m a.s.l., between 8500 and 7000 years BP, which correlates with the regional Tapes transgression. Pollen stratigraphy in the highest lake shows that the area was deglaciated before the Younger Dryas and that previously reconstructed Younger Dryas glacier margins along the north Kola coast lie too far north

Development and evaluation of an automated annotation pipeline and cDNA annotation system

Manual curation has long been held to be the gold standard for functional annotation of DNA sequence. Our experience with the annotation of more than 20,000 full-length cDNA sequences revealed problems with this approach, including inaccurate and inconsistent assignment of gene names, as well as many good assignments that were difficult to reproduce using only computational methods. For the FANTOM2 annotation of more than 60,000 cDNA clones, we developed a number of methods and tools to circumvent some of these problems, including an automated annotation pipeline that provides high-quality preliminary annotation for each sequence by introducing an uninformative filter that eliminates uninformative annotations, controlled vocabularies to accurately reflect both the functional assignments and the evidence supporting them, and a highly refined, Web-based manual annotation tool that allows users to view a wide array of sequence analyses and to assign gene names and putative functions using a consistent nomenclature. The ultimate utility of our approach is reflected in the low rate of reassignment of automated assignments by manual curation. Based on these results, we propose a new standard for large-scale annotation, in which the initial automated annotations are manually investigated and then computational methods are iteratively modified and improved based on the results of manual curation.

Friction factors and rheological behavior of Australian honey in a straight pipe

The pumping characteristics of four Australian honey samples were investigated in a straight pipe. Six flow rates (100-500 kg h(-1)) were studied at three temperatures (35-50degreesC). The pressure loss increased with an increase in the length of the pipe, as the low rate was increased and as the temperature was reduced. In the 25.4 mm-pipe, the Reynolds number ranged from 0.2-32.0 and are substantially less than the critica value (2040-2180) for laminar condition in the system. The relationship between the wall shear stress and shear rate approximated power-law behaviour, and the power-law index was not significantly (p>0.05) different from 1.0. The honey samples exhibited Newtonian behaviour at all the temperatures and this was confirmed by rheometric studies using Couette geometry. A friction chart was generated independent of temperature and the type of honey. An equation was developed to predict the pressure loss of the honey in a typical pipeline at any temperature once the viscosity-temperature relationship had been established.

Multivariate quantitative genetics and the Lek Paradox: Genetic variance in male sexually selected traits of Drosophila serrata under field control

Single male sexually selected traits have been found to exhibit substantial genetic variance, even though natural and sexual selection are predicted to deplete genetic variance in these traits. We tested whether genetic variance in multiple male display traits of Drosophila serrata was maintained under field conditions. A breeding design involving 300 field-reared males and their laboratory-reared offspring allowed the estimation of the genetic variance-covariance matrix for six male cuticular hydrocarbons (CHCs) under field conditions. Despite individual CHCs displaying substantial genetic variance under field conditions, the vast majority of genetic variance in CHCs was not closely associated with the direction of sexual selection measured on field phenotypes. Relative concentrations of three CHCs correlated positively with body size in the field, but not under laboratory conditions, suggesting condition-dependent expression of CHCs under field conditions. Therefore condition dependence may not maintain genetic variance in preferred combinations of male CHCs under field conditions, suggesting that the large mutational target supplied by the evolution of condition dependence may not provide a solution to the lek paradox in this species. Sustained sexual selection may be adequate to deplete genetic variance in the direction of selection, perhaps as a consequence of the low rate of favorable mutations expected in multiple trait systems.

Cyclopropane-1,1-dicarboxylate is a slow-, tight-binding inhibitor of rice ketol-acid reductoisomerase

Ketol-acid reductoisomerase (EC 1.1.1.86) catalyses the second reaction in the biosynthesis of the branched-chain amino acids. The reaction catalyzed consists of two stages, the first of which is an alkyl migration from one carbon atom to its neighbour. The likely transition state is therefore a cyclopropane derivative, and cyclopropane-1,1-dicarboxylate(CPD) has been reported to inhibit the Escherichia coli enzyme. In addition, this compound causes the accumulation of the substrate of ketol-acid reductoisomerase in plants. Here, we investigate the inhibition of the purified rice enzyme. The cDNA was cloned, and the recombinant protein was expressed in E. coli, purified and characterized kinetically. The purified enzyme is strongly inhibited by cyclopropane-1,1-dicarboxylate, with an inhibition constant of 90 nM. The inhibition is time-dependent and this is due to the low rate constants for formation (2.63 X 10(5) M-1 min(-1)) and dissociation (2.37 x 10(-2) min(-1)) of the enzyme-inhibitor complex. Other cyclopropane derivatives are much weaker inhibitors while dimethylmalonate is moderately effective. (c) 2004 Elsevier Ireland Ltd. All rights reserved.

Hydrogels for dermal applications

This thesis is concerned with the development of hydrogels that adhere to skin and can be used for topical or trans dermal release of active compounds for therapeutic or cosmetic use. The suitability of a range of monomers and initiator systems for the production of skin adhesive hydro gels by photopolymerisation was explored and an approximate order of monomer reactivity in aqueous solution was determined. Most notably, the increased reactivity of N-vinyl pyrrolidone within an aqueous system, as compared to its low rate of polymerisation in organic solvents, was observed. The efficacy of a series of photoinitiator systems for the preparation of sheet hydrogels was investigated. Supplementary redox and thermal initiators were also examined. The most successful initiator system was found to be Irgacure 184, which is commonly used in commercial moving web production systems that employ photopolymerisation. The influence of ionic and non-ionic monomers, crosslinking systems, water and glycerol on the adhesive and dynamic mechanical behaviour of partially hydrated hydrogel systems was examined. The aim was to manipulate hydrogel behaviour to modify topical and transdermal delivery capability and investigated the possibility of using monomer combinations that would influence the release characteristics of gels by modifying their hydrophobic and ionic nature. The copolymerisation of neutral monomers (N-vinyl pyrrolidone, N,N-dimethyl acrylamide and N-acryloyl morpholine) with ionic monomers (2-acrylamido-2-methylpropane sulphonic acid; sodium salt, and the potassium salt of 3-sulphopropyl acrylate) formed the basis of the study. Release from fully and partially hydrated hydrogels was studied, using model compounds and a non-steroidal anti-inflammatory drug, Ibuprofen. Release followed a common 3-stage kinetic profile that includes an initial burst phase, a secondary phase of approximate first order release and a final stage of infinitesimally slow release such that the compound is effectively retained within the hydrogel. Use of partition coefficients, the pKa of the active and a knowledge of charge-based and polar interactions of polymer and drug were complementary in interpreting experimental results. In summary, drug ionisation, hydrogel composition and external release medium characteristics interact to influence release behaviour. The information generated provides the basis for the optimal design of hydrogels for specific dermal release applications and some understanding of the limitations of these systems for controlled release applications.