Science for medicine--time for another reappraisal.

The Amendments to the National Cancer Act of 1974 included a provision for a comprehensive review of the Federal policies and programs for medical research. This would appear to be a particularly timely review since many of the fundamental issues concerning the Government's role in biomedical research are presently in question. These issues include the rationale for public support for basic medical research, public expectations for returns on these investments, establishment of priorities among various research avenues, and a number of derivative as well as ethical questions. Since the professional and scientific communities have been historically successful in gaining public funds for research, a periodic opportunity for public review and consideration would appear to be highly desirable.     

Approaches for calculating power for case-cohort studies

An approach for determining the power of a case-cohort study for a single binary exposure variable and a low failure rate was recently proposed by Cai and Zeng (2004, Biometrics 60, 1015-1024). In this article, we show that computing power for a case-cohort study using a standard case-control method yields nearly identical levels of power. An advantage of the case-control approach is that existing sample size software can be used for the calculations. We also propose an additional formula for computing the power of a case-cohort study for the situation when the event is not rare.     

Risk factors for rejection for morphological reasons of heart valves for transplantation

The study aim was to identify risk factors for morphological rejection of aortic and pulmonary valves for transplantation that could be used to optimize donor selection. The files of all Dutch heart valve donors, donating in a 2.5 years period, whose hearts were processed at Heart Valve Bank Rotterdam, were reviewed for all factors that could be relevant for valve rejection and related to outcome of morphological assessment of the valves. Valves were retrieved from 813 deceased Dutch donors, 24.1% also donating organs. For 797 aortic and 767 pulmonary valves, who met retrieval criteria, morphological assessment was done. 69.5% of aortic and 37.5% of pulmonary valves were considered unsuitable for transplantation at morphological assessment. Backward stepwise multivariate logistic regression analysis, showed age, cardiac cause of death, cerebrovascular accident as cause of death or in medical history, and number of cardiovascular risk factors in a donor to be independent risk factors for morphological rejection of aortic valves. Age, sex, weight >100 kg and ruptured aortic aneurysm as cause of death were independent risk factors for morphological rejection of pulmonary valves. Being an organ donor was an independent predictor of morphological approval of aortic and pulmonary valves, while hypertension was an independent predictor for morphological approval of aortic valves. Thus, independent factors were identified that are associated with morphological rejection of aortic and pulmonary valves for transplantation, and that could be used to optimize donor selection by preventing unnecessary retrievals, limiting costs, while improving yield per donor with minimal compromise for availability.     

Biofortification for combating 'hidden hunger' for iron

Micronutrient deficiencies are responsible for so-called 'hidden undernutrition'. In particular, iron (Fe) deficiency adversely affects growth, immune function and can cause anaemia. However, supplementation of iron can exacerbate infectious diseases and current policies of iron therapy carefully evaluate the risks and benefits of these interventions. Here we review the approaches of biofortification of valuable crops for reducing 'hidden undernutrition' of iron in the light of the latest nutritional and medical advances. The increase of iron and prebiotics in edible parts of plants is expected to improve health, whereas the reduction of phytic acid concentration, in crops valuable for human diet, might be less beneficial for the developed countries, or for the developing countries exposed to endemic infections.     

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.     

Training for best practices for agricultural programs

As with other areas of animal research, ensuring the proper training and qualifications of the individuals working with agricultural animals for use in research, teaching, and testing is critical to both animal welfare and the successful outcome of the study or teaching exercise. The author provides guidance for the development of appropriate training programs for organizations that use agricultural animals in research.     

Imputation methods for missing data for polygenic models

Methods to handle missing data have been an area of statistical research for many years. Little has been done within the context of pedigree analysis. In this paper we present two methods for imputing missing data for polygenic models using family data. The imputation schemes take into account familial relationships and use the observed familial information for the imputation. A traditional multiple imputation approach and multiple imputation or data augmentation approach within a Gibbs sampler for the handling of missing data for a polygenic model are presented.We used both the Genetic Analysis Workshop 13 simulated missing phenotype and the complete phenotype data sets as the means to illustrate the two methods. We looked at the phenotypic trait systolic blood pressure and the covariate gender at time point 11 (1970) for Cohort 1 and time point 1 (1971) for Cohort 2. Comparing the results for three replicates of complete and missing data incorporating multiple imputation, we find that multiple imputation via a Gibbs sampler produces more accurate results. Thus, we recommend the Gibbs sampler for imputation purposes because of the ease with which it can be extended to more complicated models, the consistency of the results, and the accountability of the variation due to imputation.     

Testing for density dependence allowing for weather effects

A test for density dependence in time-series data allowing for weather effects is presented. The test is based on a discrete time autoregressive model for changes in population density with a covariate for the effects of weather. The distribution of the test statistic on the null hypothesis of density independence is obtained by parametric bootstrapping. A computer simulation exercise is used to demonstrate the gain in statistical power by allowing for weather effects. Application of the method to time-series data on three species of butterflies and two species of songbirds showed stronger evidence of density dependence than two standard tests. Received: 4 October 1996 / Accepted: 4 August 1997     

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.     

Relationship Between Competence for Transfection and for Transformation

Deoxyribonucleic acid (DNA) extracted from phage SPP1 is highly infectious on Bacillus subtilis competent cells; the efficiency of infection is 5 x 10(3) to 6 x 10(3) phage equivalents per plaque-forming unit. This DNA was used to study the relationship between competence for transfection and for transformation. The experiments were concerned with the frequency of infection and transformation in mutants exhibiting different levels of competence, the effect of periodate on competence for infection and for transformation, the competition between phage and bacterial DNA, the transformation of cells preinfected with phage DNA, and the infection of cells pretreated with bacterial DNA. The data show that B. subtilis cells competent for transformation are also competent for transfection and vice versa; transfection with phage DNA represents, therefore, a simple way to measure the total number of competent cells in a culture. The fraction of competent cells, determined by SPP1 DNA infection, varied from 10(-2) to 7 x 10(-2).     

Rationale for Leptin-Replacement Therapy for Severe Lipodystrophy

ObjectiveTo review evidence supporting the hypothesis that metabolic manifestations of lipodystrophy result from leptin deficiency and that leptin replacement may be a viable treatment for generalized lipodystrophy.MethodsThis review results from the authors’ collective clinical experience and a comprehensive MEDLINE search of the English-language literature (1998 to 2009) on “leptin and lipodystrophy.”ResultsSevere lipodystrophy syndromes are characterized by loss of subcutaneous adipose tissue and thus a relative deficiency of the adipocyte-secreted hormone leptin. Several small, nonrandomized, open-label trials in a composite total of more than 100 patients with severe lipodystrophy not related to human immunodeficiency virus infection have evaluated the efficacy and safety of recombinant human methionyl leptin (metreleptin) therapy. Variables observed to improve after treatment with metreleptin include glycemic control, insulin sensitivity, plasma triglycerides, caloric intake, liver volume and lipid content, intramyocellular lipid content, and neuroendocrine and immunologic end points. In these studies, metreleptin treatment was well tolerated. Typical daily replacement doses for metreleptin were 0.06 to 0.08 mg/kg for female patients and 0.04 mg/kg for male patients, administered by subcutaneous injection twice daily. Although metreleptin is not yet approved for routine clinical use, it is available by means of expanded access provisions for patients with severe lipodystrophy and associated metabolic abnormalities.ConclusionEvidence published in the medical literature indicates that treating severe lipodystrophy as a leptin deficiency syndrome can improve the metabolic outcomes in affected patients. (Endocr Pract. 2010;16:324-333)     

Dissociation constants for dihydrofolic acid and dihydrobiopterin and implications for mechanistic models for dihydrofolate reductase

The dissociation constants (pKa) for the pteridine ring system of dihydrofolate (H2folate) have been redetermined, and those for dihydrobiopterin (H2biopterin) have been determined. Determination of the pKa for N5 of H2folate is complicated by the low solubility and instability of H2folate at pH 2-4, and other complicating factors. The initial rate of absorbance change due to degradation is a maximum at pH 2.5, and the products depend on the oxygen concentration: under aerobic conditions, (p-aminobenzoyl)glutamic acid and 7,8-dihydropterin-6-carboxaldehyde are major products. H2Biopterin is much more soluble and more stable at low pH. For protonation of N5, the pKa is 2.56 +/- 0.01 for H2biopterin and 2.59 +/- 0.03 for H2folic acid. Spectrophotometric determination of the pKa for the N3-O4 amide group of H2folate is subject to serious errors when a wavelength between 220 and 235 nm is used. These errors arise from the pH-dependent absorbance of mercaptoethanol often present in the preparation. The amide group has a pKa of 10.41 +/- 0.04 in H2biopterin and 10.85 +/- 0.04 in H2folate. The redetermined value for the pKa of N5 of H2folate has implications for mechanistic models for dihydrofolate reductase, and revised kinetic constants have been calculated for one model.     

Evidence for a susceptibility gene for autism on chromosome 2 and for genetic heterogeneity

Although there is considerable evidence for a strong genetic component to idiopathic autism, several genomewide screens for susceptibility genes have been performed with limited concordance of linked loci, reflecting either numerous genes of weak effect and/or sample heterogeneity. Because decreasing sample heterogeneity would increase the power to identify genes, the effect on evidence for linkage of restricting a sample of autism-affected relative pairs to those with delayed onset (at age >36 mo) of phrase speech (PSD, for phrase speech delay) was studied. In the second stage of a two-stage genome screen for susceptibility loci involving 95 families with two or more individuals with autism or related disorders, a maximal multipoint heterogeneity LOD score (HLOD) of 1.96 and a maximal multipoint nonparametric linkage (NPL) score of 2.39 was seen on chromosome 2q. Restricting the analysis to the subset of families (n=49) with two or more individuals having a narrow diagnosis of autism and PSD generated a maximal multipoint HLOD score of 2.99 and an NPL score of 3.32. The increased scores in the restricted sample, together with evidence for heterogeneity in the entire sample, indicate that the restricted sample comprises a population that is more genetically homogeneous, which could therefore increase the likelihood of positional cloning of susceptibility loci.     

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.     

Prospects for biopesticides for aphid control

Diseases form an important component of the natural enemy complex of aphids. The most common and obvious of these diseases are entomophthoran fungi such asErynia neoaphidis Remaudiere & Herbert,Entomophthora planchoniana Cornu,Zoophthora radicans (Brefeld) Batko andConidiobolus obscurus (Hall & Dunn) Remaudiere & Keller. The pest status of some aphids such as the pea aphid,Acyrthosiphon pisum (Harris), is considerably reduced by natural epizootics of fungal disease. However, disease may contribute little to practical control as it is mainly effective in high density populations when weather conditions are suitable. Introduction of exotic diseases for classical biological control is only rarely possible since most diseases, like their aphid hosts, are distributed world-wide. One exception was the successful introduction into Australia of a strain ofZ. radicans for control of spotted alfalfa aphid,Therioaphis trifolii (Monell) f.maculata in 1979. Attempts to manipulate entomophthoran fungi have had limited success because of problems with mass production, the fragility of the conidia and the need for suitably moist conditions. Hyphomycete fungi such asVerticillium lecanii (Zimm.) Viegas,Metarhizium anisopliae (Metsch.) Sorokin,Beauveria bassiana (Bals.) Vuill. andPaecilomyces spp. are more suitable for development as mycoinsecticides as they are cheap to mass produce and form stable conidia. “Vertalec?”, a formulation ofV. lecanii, has been sold in small quantities commercially in Britain and parts of Europe for many years and used mainly in glasshouses. Recently promising results have been obtained with use ofM. anisopliae for control of lettuce root aphid,Pemphigus bursarius (L.) in the UK. Laboratory studies on selected isolates ofB. bassiana andPaecilomyces spp. show a promising level of activity. Problems may occur with these species as they can kill aphid predators such as coccinelids. In addition, more research is needed on developing improved formulations which enable control to be achieved under low humidity conditions.     

A new approach for anthelmintic discovery for humans

Natural product-based drug discovery has been deemphasized by the pharmaceutical industry. This situation is discordant with the fact that most people in developing countries rely on traditional medicines derived from local biodiversity for healthcare. Despite economic growth in the past 10 years, Africa remains plagued by parasitic infections, out of reach of eradication. Limited regional funding for drug discovery complicates the situation. Novel models are needed to bring sustainability to local drug discovery programs. This Opinion describes an innovative partnership that promotes local leadership to harness a recombinant yeast-based assay to screen for novel anthelmintic candidates in collections of African natural products. Implementation of this strategy in biodiversity-rich but resource-constrained settings can help build sustainable local capacity for drug discovery.     

Approaches for Calculating Power for Case–Cohort Studies

Summary .   An approach for determining the power of a case–cohort study for a single binary exposure variable and a low failure rate was recently proposed by Cai and Zeng (2004, Biometrics 60, 1015–1024). In this article, we show that computing power for a case–cohort study using a standard case–control method yields nearly identical levels of power. An advantage of the case–control approach is that existing sample size software can be used for the calculations. We also propose an additional formula for computing the power of a case–cohort study for the situation when the event is not rare.     

Method for electroporation for the early chick embryo

In vitro whole-embryo culture of chick embryos, originally invented by New, has been widely used for studies of early embryogenesis. Here, a method for electroporation using the New culture and its derivatives is described, to achieve misexpression of exogenous gene in a temporally and spatially controlled manner in gastrulating chick embryos. Detailed information for the devices and procedures, and some experimental examples are presented.     

Challenges in breeding for yield increase for drought

Crop genetic improvement for environmental stress at the molecular and physiological level is very complex and challenging. Unlike the example of the current major commercial transgenic crops for which biotic stress tolerance is based on chemicals alien to plants, the complex, redundant and homeostatic molecular and physiological systems existing in plants must be altered for drought tolerance improvement. Sophisticated tools must be developed to monitor phenotype expression at the crop level to characterize variation among genotypes across a range of environments. Once stress-tolerant cultivars are developed, regional probability distributions describing yield response across years will be necessary. This information can then aid in identifying environmental conditions for positive and negative responses to genetic modification to guide farmer selection of stress-tolerant cultivars.