One-sided Tests for Comparing Treatment Effects for Qualitative Data

Various one-sided tests for the comparison of differential treatment effects in two independent groups are developed for qualitative data. This is done for matched and for independent samples, in the case of identical and of different initial distributions. Tests for various kinds of treatment effects are considered. In each case the two observed contingency tables are collapsed into two independent fourfold tables. It is described in which way to select the appropriate procedure for practical problems, and most methods are illustrated in detail by means of a numerical example from clinical psychology.     

A novel method for preparing single-stranded DNA for pyrosequencing

Pyrosequencing technology is a powerful genotyping tool that requires the generation of single stranded DNA. Currently, two simple, solid-phase-based methods are available for this, but they require special equipment, they are not automated, and they are relatively expensive because of the need for biotinylated polymerase chain reaction primers. In this article, an enzymatic liquid-phase method for the generation of high-quality, single-stranded DNA, and its novel use for Pyrosequencing are described. The method has also been fully automated.     

Improved methods for calculating formation constants for nucleotide-cation complexes

Two data reduction methods that can be used to calculate formation constants for nucleotidecation complexes are described. Both methods are used to analyze data obtained by an anion-exchange resin method, and either method can improve the accuracy of the calculated formation constants by more than 50%. The key to this significant improvement in accuracy is the realization that the equation for the mathematical model describing such systems is always nonlinear in terms of the formation constants and, in the general case, is higher order in the cation concentration. There are two major reasons for the improved quality of the results associated with the new model. First, successive linear extrapolations are eliminated, and error propagation is reduced. Second, all of the data are used for the simultaneous calculation of all formation constants, and the uncertainty due to random experimental errors is minimized.     

Current strategies for identifying and validating targets for new treatment-shortening drugs for TB

There is an urgent need for new drugs to treat tuberculosis. During the last forty years the only drugs to have been developed are variations on existing ones, but new drug candidates must offer improvements over existing agents. In particular, we require new drugs having novel mechanisms of action that are active against drug-resistant strains and also kill persistent bacilli, thus shortening the length of chemotherapy. Recent advances in our understanding of the biology of Mycobacterium tuberculosis, in particularly the availability of the genome sequence coupled with development of new genetic tools, have greatly contributed to the discovery of potential drug targets for new antituberculars. However, although many potential new drug targets have been identified, greater effort is required in target validation to show properly that they are essential for bacterial growth and survival. In this review, the current drug development pipeline and the strategies employed to identify and validate novel tuberculosis drug targets are presented.     

Searching for a function for nuclear actin

The abundant cytoskeletal protein actin has numerous cytoplasmic roles. Although there are many reports of the presence of actin in the nucleus, in general they have been discounted as artifactual. However, recent work has begun to provide evidence for important roles for actin in nuclear processes ranging from chromatin remodelling to splicing. In addition, several regulators of actin polymerization are localized to the nucleus or translocate to the nucleus in a regulated manner, suggesting that there is some function of actin in the nucleus that is subject to regulation. This review discusses the evidence for actin in the nucleus and summarizes recent work suggesting that actin or actin-related proteins are involved in the regulation of nuclear processes such as chromatin remodelling.     

Wood for sound

The unique mechanical and acoustical properties of wood and its aesthetic appeal still make it the material of choice for musical instruments and the interior of concert halls. Worldwide, several hundred wood species are available for making wind, string, or percussion instruments. Over generations, first by trial and error and more recently by scientific approach, the most appropriate species were found for each instrument and application. Using material property charts on which acoustic properties such as the speed of sound, the characteristic impedance, the sound radiation coefficient, and the loss coefficient are plotted against one another for woods. We analyze and explain why spruce is the preferred choice for soundboards, why tropical species are favored for xylophone bars and woodwind instruments, why violinists still prefer pernambuco over other species as a bow material, and why hornbeam and birch are used in piano actions.     

Experimental designs for estimating the kinetic parameters for enzyme-catalysed reactions

The problem of evaluating the kinetic parameters associated with an enzyme-catalysed reaction is examined. If the errors associated with velocity measurements are unknown, or are known to deviate from a normal distribution, then methods based on the minimization of the sum of squares are inappropriate. It is shown that by using a proper experimental design then the kinetic parameters may be estimated unambiguously while making only minimal assumptions regarding the error structure of the data. The design consists of several replicate measurements of the velocity at as many experimental conditions as there are parameters to be estimated. Formulae are presented for choosing the experimental conditions for selected kinetic equations and a computer program is described for designing experiments for any kinetic model. The designs formulated are optimal in the sense that they minimize the overall variance of the parameter estimates.     

Bioprospecting for hyper-lipid producing microalgal strains for sustainable biofuel production

Global petroleum reserves are shrinking at a fast pace, increasing the demand for alternate fuels. Microalgae have the ability to grow rapidly, and synthesize and accumulate large amounts (approximately 20-50% of dry weight) of neutral lipid stored in cytosolic lipid bodies. A successful and economically viable algae based biofuel industry mainly depends on the selection of appropriate algal strains. The main focus of bioprospecting for microalgae is to identify unique high lipid producing microalgae from different habitats. Indigenous species of microalgae with high lipid yields are especially valuable in the biofuel industry. Isolation, purification and identification of natural microalgal assemblages using conventional techniques is generally time consuming. However, the recent use of micromanipulation as a rapid isolating tool allows for a higher screening throughput. The appropriate media and growth conditions are also important for successful microalgal proliferation. Environmental parameters recorded at the sampling site are necessary to optimize in vitro growth. Identification of species generally requires a combination of morphological and genetic characterization. The selected microalgal strains are grown in upscale systems such as raceway ponds or photobireactors for biomass and lipid production. This paper reviews the recent methodologies adopted for site selection, sampling, strain selection and identification, optimization of cultural conditions for superior lipid yield for biofuel production. Energy generation routes of microalgal lipids and biomass are discussed in detail.     

Strategies for computer modeling

Modeling is a ubiquitous and often misunderstood enterprise in which data from diverse disciplines are analyzed by techniques from other diverse disciplines in an attempt to confirm or falsify a set of hypotheses about the real world. Guidelines are offered for designing models to match the goals of modeling biological systems. Techniques for the construction and interpretation of models are discussed. The requirements for credibility of models are detailed, and tests are suggested for their validation.     

Carbohydrates for fermentation

Biomass accumulated by the photosynthetic fixation of carbon dioxide is the only renewable carbon source, and hence, the only renewable raw material for the chemical industry. Carbohydrates are the main constituents of biomass and occur as cell wall and storage carbohydrates, transportation carbohydrates and glycoconjugates. Cellulose, hemicelluloses and starch in particular as well as pectin, inulin and saccharose to a smaller extent are the most abundant carbohydrates. Glucose is the most important monosaccharide and monomer of polysaccharides in natural carbohydrates. Thus, it is the most abundant organic compound on earth. Production of pulp from wood cellulose, applications of starch for paper making as well as uses of glucose and saccharose for fermentation are the most important chemical and technical uses of carbohydrates. Carbohydrates used as fermentation feedstock are essential for the chemical industry. Their importance is steadily growing due to the increasing implementation of biotechnological processes.     

Recommendations for terminology and databases for biochemical thermodynamics

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K' for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ(r)G'°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ(f)G(i)'° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ(f)G(j)° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ(r)G'° of reactions and Δ(f)G(i)'° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K' can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature.     

Searching for a model for use in vegetation analysis

Summary Indirect gradient analysis methods require an explicit vegetation model which must be based on direct gradient analysis studies. Various vegetation models are reviewed. Field evidence for the models is discussed. Experimental studies of species response to environmental gradients are reviewed and discussed. Three types of gradient are recognized as important for development of models: indirect environmental gradients where the environmental factor has no direct physiological influence on plant growth e.g. elevation; direct environmental gradients where the factor has a direct physiological effect on growth but is not an essential resource, e.g. pH; resource gradients where the factor is an essential resource for plant growth. The behaviour of the ecological carrying capacity and the role of competition along such gradients are shown to be important for developing vegetation models.     

Mouse models for human deafness: current tools for new fashions

Mouse models are one of the major tools used for discovery and characterization of genes for non-syndromic deafness in humans. The similarities between the mouse and human genomes, and between the physiology and morphology of their auditory systems, are striking. This article describes the latest mouse models, including spontaneous, 'knockout' and ENU (N-ethyl-N-nitrosourea)-induced mutants, and the recent discovery of modifier genes that are involved in mouse deafness; this discovery is leading the search for genetic modifiers for human disorders.     

Biostatistical methods for the validation of alternative methods for in vitro toxicity testing

Statistical methods for the validation of toxicological in vitro test assays are developed and applied. Validation is performed either in comparison with in vivo assays or in comparison with other in vitro assays of established validity. Biostatistical methods are presented which are of potential use and benefit for the validation of alternative methods for the risk assessment of chemicals, providing at least an equivalent level of protection through in vitro toxicity testing to that obtained through the use of current in vivo methods. Characteristic indices are developed and determined. Qualitative outcomes are characterised by the rates of false-positive and false-negative predictions, sensitivity and specificity, and predictive values. Quantitative outcomes are characterised by regression coefficients derived from predictive models. The receiver operating characteristics (ROC) technique, applicable when a continuum of cut-off values is considered, is discussed in detail, in relation to its use for statistical modelling and statistical inference. The methods presented are examined for their use for the proof of safety and for toxicity detection and testing. We emphasise that the final validation of toxicity testing is human toxicity, and that the in vivo test itself is only a predictor with an inherent uncertainty. Therefore, the validation of the in vitro test has to account for the vagueness and uncertainty of the "gold standard" in vivo test. We address model selection and model validation, and a four-step scheme is proposed for the conduct of validation studies. Gaps and research needs are formulated to improve the validation of alternative methods for in vitro toxicity testing.     

Derivatives suitable for GC-MS

The preparation of derivatives is often advantageous or necessary for GC-MS, for a variety of reasons. In respect of GC, these include the need for conferring volatility or stability; the improvement of chromatographic behaviour or separation; information on functional groups; and provision for selective detection. In MS, derivatives are important for producing characteristic mass shifts and for directing particular modes of fragmentation under electron impact or chemical ionisation. Reagents used for derivative formation may be general or selective: among the latter class, reagents that yield cyclic derivatives from bifunctional substrates are of special value. Typical examples are given of the applications of derivatives in the analysis, by GC-MS, of long-chain fatty acids, prostaglandins, mono- and diglycerides, sphingolipids, and sterols. Recent developments in instrumentation and in the use of computer data systems are outlined.     

Pseudo-Likelihood for Combined Selection and Pattern-Mixture Models for Incomplete Data

In this paper we develop pseudo-likelihood methods for the estimation of parameters in a model that is specified in terms of both selection modelling and pattern-mixture modelling quantities. Two cases are considered: (1) the model is specified directly from a joint model for the measurement and dropout processes; (2) conditional models for the measurement process given dropout and vice versa are specified directly. In the latter case, compatibility constraints to ensure the existence of a joint density are derived. The method is applied to data from a psychiatric study, where a bivariate therapeutic outcome is supplemented with covariate information.     

Breeding for abiotic stresses for sustainable agriculture

Using cereal crops as examples, we review the breeding for tolerance to the abiotic stresses of low nitrogen, drought, salinity and aluminium toxicity. All are already important abiotic stress factors that cause large and widespread yield reductions. Drought will increase in importance with climate change, the area of irrigated land that is salinized continues to increase, and the cost of inorganic N is set to rise. There is good potential for directly breeding for adaptation to low N while retaining an ability to respond to high N conditions. Breeding for drought and salinity tolerance have proven to be difficult, and the complex mechanisms of tolerance are reviewed. Marker-assisted selection for component traits of drought in rice and pearl millet and salinity tolerance in wheat has produced some positive results and the pyramiding of stable quantitative trait locuses controlling component traits may provide a solution. New genomic technologies promise to make progress for breeding tolerance to these two stresses through a more fundamental understanding of underlying processes and identification of the genes responsible. In wheat, there is a great potential of breeding genetic resistance for salinity and aluminium tolerance through the contributions of wild relatives.     

Immunizations for foreign travel.

One of the most important aspects of preparing travelers for destinations throughout the world is providing them with immunizations. Before administering any vaccines, however, a careful health and immunization history and travel itinerary should be obtained in order to determine vaccine indications and contraindications. There are three categories of immunizations for foreign travel. The first category includes immunizations which are routinely recommended whether or not the individual is traveling. Many travelers are due for primary vaccination or boosting against tetanus-diphtheria, measles-mumps-rubella, pneumococcal pneumonia, and influenza, for example, and the pre-travel visit is an ideal time to administer these. The second category are immunizations which might be required by a country as a condition for entry; these are yellow fever and cholera. The final category contains immunizations which are recommended because there is a risk of acquiring a particular disease during travel. Typhoid fever, meningococcal disease, rabies, and hepatitis are some examples. Travelers who are pregnant or who are infected with the human immunodeficiency virus require special consideration. Provision of appropriate immunizations for foreign travel is an important aspect of preventing illness in travelers.     

Strategies for accessing soil metagenome for desired applications

Most of the microorganisms in nature are inaccessible as they are uncultivable in the laboratory. Metagenomic approaches promise the accessibility of the genetic resources and their potential applications. Genetic resources from terrestrial environments can be accessed by exploring the soil metagenome. Soil metagenomic analyses are usually initiated by the isolation of environmental DNAs. Several methods have been described for the direct isolation of environmental DNAs from soil and sediments. Application of metagenomics largely depends on the construction of genomic DNA libraries and subsequent high-throughput sequencing or library screening. Thus, obtaining large quantities of pure cloneable DNA from the environment is a prerequisite. This review discusses the recent developments related to efficient extraction and purification of soil metagenome highlighting the considerations for various metagenomic applications.