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.     

Autophagy: for better or for worse

Autophagy is a lysosomal degradation pathway that degrades damaged or superfluous cell components into basic biomolecules, which are then recycled back into the cytosol. In this respect, autophagy drives a flow of biomolecules in a continuous degradation-regeneration cycle. Autophagy is generally considered a pro-survival mechanism protecting cells under stress or poor nutrient conditions. Current research clearly shows that autophagy fulfills numerous functions in vital biological processes. It is implicated in development, differentiation, innate and adaptive immunity, ageing and cell death. In addition, accumulating evidence demonstrates interesting links between autophagy and several human diseases and tumor development. Therefore, autophagy seems to be an important player in the life and death of cells and organisms. Despite the mounting knowledge about autophagy, the mechanisms through which the autophagic machinery regulates these diverse processes are not entirely understood. In this review, we give a comprehensive overview of the autophagic signaling pathway, its role in general cellular processes and its connection to cell death. In addition, we present a brief overview of the possible contribution of defective autophagic signaling to disease.     

T-Pile--a package for thermodynamic calculations for biomolecules

Molecular dynamics and Monte Carlo, usually conducted in canonical ensemble, deliver a plethora of biomolecular conformations. Proper analysis of the simulation data is a crucial part of biophysical and bioinformatics studies. Sequence alignment problem can be also formulated in terms of Boltzmann distribution. Therefore tools for efficient analysis of canonical ensemble data become extremely valuable. T-Pile package, presented here provides a user-friendly implementation of most important algorithms such as multihistogram analysis and reweighting technique. The package can be used in studies of virtually any system governed by Boltzmann distribution. AVAILABILITY: T-Pile can be downloaded from: http://biocomp.chem.uw.edu.pl/services/tpile. These pages provide a comprehensive tutorial and documentation with illustrative examples of applications. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

Protocols for data generation for predictive modeling

Summary Essential to the development of useful predictive models for foods is the collection of appropriate data. Within the UK Predictive Food Microbiology Program, a series of documents have been produced to aid the standardization of data collection by a number of laboratories. Documents include a protocols form, notes on experimental design, notes on the accuracy of counts by plating, the preferred method of calculating a plate count value, preferred MPN tables and the preferred methods of recording data values. These documents have proven useful in aiding collaboration between laboratories.     

Bioethics for human geneticists: models for reasoning and methods for teaching.

The ethical issues raised by the Human Genome Project (HGP) and by human genetics in general are not entirely novel. In fact, the ethical issues surrounding genetic research and the provision of genetic services fit into the evolution of bioethics, a field of inquiry which has its roots in concerns of the 1970s, concerns about the dignity and self-determination of individuals and about the development of medical technologies. Although bioethics has been largely occupied with patient-centered concerns, attention is currently shifting toward socially oriented issues, such as the justice of the existing health-care system. Genetic counseling has already incorporated many of the lessons of early bioethics and, as a profession, adheres to a consultand-centered ethic which reflects the values incorporated into the doctrine of informed consent, which is a cornerstone of bioethics. The mandate of the Ethical, Legal, and Social Implications Program of the HGP--to anticipate ethical problems arising from advances in genetics and to educate the public about genetics--reflects not only the nonpaternalistic approach of early bioethics but also bioethics' increasing attention to the ethical import of systemic and institutional factors, as well as an anticipatory and preventive approach to dealing with ethical concerns. Because bioethics has so much to contribute to current consideration of ethical issues in human genetics, it is important to provide training in ethics to those working in the field. Guidelines for using a case-oriented approach are suggested.     

Quantitative proteomics for identifying biomarkers for Rabies

Introduction

Rabies is a fatal acute viral disease of the central nervous system, which is a serious public health problem in Asian and African countries. Based on the clinical presentation, rabies can be classified into encephalitic (furious) or paralytic (numb) rabies. Early diagnosis of this disease is particularly important as rabies is invariably fatal if adequate post exposure prophylaxis is not administered immediately following the bite.

Methods

In this study, we carried out a quantitative proteomic analysis of the human brain tissue from cases of encephalitic and paralytic rabies along with normal human brain tissues using an 8-plex isobaric tags for relative and absolute quantification (iTRAQ) strategy.

Results and conclusion

We identified 402 proteins, of which a number of proteins were differentially expressed between encephalitic and paralytic rabies, including several novel proteins. The differentially expressed molecules included karyopherin alpha 4 (KPNA4), which was overexpressed only in paralytic rabies, calcium calmodulin dependent kinase 2 alpha (CAMK2A), which was upregulated in paralytic rabies group and glutamate ammonia ligase (GLUL), which was overexpressed in paralytic as well as encephalitic rabies. We validated two of the upregulated molecules, GLUL and CAMK2A, by dot blot assays and further validated CAMK2A by immunohistochemistry. These molecules need to be further investigated in body fluids such as cerebrospinal fluid in a larger cohort of rabies cases to determine their potential use as antemortem diagnostic biomarkers in rabies. This is the first study to systematically profile clinical subtypes of human rabies using an iTRAQ quantitative proteomics approach.     

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.     

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)     

Methods for Precisely Trimming Block Faces for Ultramicrotomy

Two devices are described to aid in trimming block faces of embedded tissue for ultramicrotomy. The first, a reticle to fit the ocular of a stereomicroscope, can be manufactured by the ultramicrotomist and is designed to outline the edges of the block face so that it can be trimmed to a standard size and shape with the area of interest centered in it. The second, a rectangular “trim-align” block mounted in the knife holder of the uitramicrotome, is, with the block face, aligned to the plane of sectioning, and aids in retrimming the top and bottom edges of the block face. This is the simplest trimming device yet described and the first which will, from any sort of embedded material, produce a block face with parallel top and bottom edges even if the block face is not perpendicular to the axis of the specimen holder. If the edge of the diamond knife used for sectioning is parallel to the axis of rotation of the knife holder, the block face has also been automatically aligned to the knife as a consequence of this aligning and trimming procedure. As a result, sectioning can begin immediately without further adjustments.     

Biobanks for genomics and genomics for biobanks

Biobanks include biological samples and attached databases. Human biobanks occur in research, technological development and medical activities. Population genomics is highly dependent on the availability of large biobanks. Ethical issues must be considered: protecting the rights of those people whose samples or data are in biobanks (information, autonomy, confidentiality, protection of private life), assuring the non-commercial use of human body elements and the optimal use of samples and data. They balance other issues, such as protecting the rights of researchers and companies, allowing long-term use of biobanks while detailed information on future uses is not available. At the level of populations, the traditional form of informed consent is challenged. Other dimensions relate to the rights of a group as such, in addition to individual rights. Conditions of return of results and/or benefit to a population need to be defined. With 'large-scale biobanking' a marked trend in genomics, new societal dimensions appear, regarding communication, debate, regulation, societal control and valorization of such large biobanks. Exploring how genomics can help health sector biobanks to become more rationally constituted and exploited is an interesting perspective. For example, evaluating how genomic approaches can help in optimizing haematopoietic stem cell donor registries using new markers and high-throughput techniques to increase immunogenetic variability in such registries is a challenge currently being addressed. Ethical issues in such contexts are important, as not only individual decisions or projects are concerned, but also national policies in the international arena and organization of democratic debate about science, medicine and society.     

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.     

Protocol for sampling environmental sites for legionellae

A protocol for sampling environmental sites was developed and used to identify possible sources of Legionella species in support of epidemiologic investigations at two hospitals. In hospital A, legionellae were isolated from 43 of 106 (40%) different sites. Three separate Legionella pneumophila serotypes and a previously unrecognized species were present in different combinations in the positive samples. Two of five cooling towers contained the same L. pneumophila serogroup 1 monoclonal type (1,2,4,5) as was isolated from patients. The same monoclonal type was also isolated from make-up water for the two cooling towers, a hot water tank, water separators in four main air compressor systems for respiratory therapy, and cold and hot water faucets. In hospital B, 13 of 37 (38%) sample sites contained legionellae, all of which were L. pneumophila serogroup 1. The monoclonal type matching isolates from patients (1,2,4,5) was found at the highest concentration in a hot water tank, but it was also present at four other sample sites. Since legionellae not related to disease may be found in many of the sites sampled, an epidemiologic association with the probable source should be established before intervention methods, such as disinfection, are undertaken.     

Method for Testing Virus Stocks for Viral Contaminants

A practical method for testing the purity of virus stocks has been developed and applied to reference stocks of enteroviruses. The method requires the use of a reference antiserum that is substantially free from heterotypic antibody. When selected dilutions of this antiserum are reacted with high concentrations of virus, virus intentionally allowed to escape neutralization is recovered and then identified. A contaminating virus present as a minor component of the population has a far greater probability of being revealed under the conditions of this "breakthrough" test than under the commonly used virus identity tests which customarily employ approximately 100 TCD(50) of virus and, therefore, only identify the major component of the virus population. The breakthrough test described has been used for tests of 104 reference stocks of all the enteroviruses that propagate in monkey kidney cells and human amnion cells. Although all the materials had been previously tested and approved by the commonly employed virus identity test, the breakthrough test in two instances revealed contaminating heterotypic enteroviruses present at a very low titer in the stocks. Without resorting to the stringent, elaborate, and expensive tests for absolute purity, such as those that are required to assure safety of vaccines, the use of the breakthrough test described provides reasonable assurance of purity for stock viruses to be employed as diagnostic reagents or for general laboratory research purposes where a multiplicity of viral agents and antisera are required.     

Prospects for using pyroproxyfen-treated targets for tsetse control

Using¹⁴C cholesterol as a marker a positive correlation was established between the amount of oil (a chlorinated n-alkane containing 43–46% chlorine, ‘cereclor S45’) picked up by an adult tsetse fly exposed by tarsal contact to a treated surface and the duration of such exposure. Only a poor uptake was achieved from netting surfaces treated with less than 50% oil in acetone. Terylene netting treated with radioactive pyriproxyfen, [1-methyl-2-(4-phenoxyphenoxy)ethoxy] pyridine, dissolved in cereclor, was exposed in the field for a year. After 9 months 20% of the original radioactivity remained and was shown to be 95% authentic pyriproxyfen. Brief tarsal contact (up to 5 seconds) with such netting, by adult females ofGlossina morsitans morsitans Westwood, reduced the viability of their offspring to 28–43% of untreated control values. The effect was greatest in the reproductive cycle immediately following contact. Between 10 and 12 months after treatment of the fabric the radioactivity fell to only 7% of the original level but was associated mainly (>80%) with intact pyriproxyfen. Exposure of female flies to this netting resulted in a positive correlation between the duration of exposure and the extent of suppression of offspring viability, such that 2 min was sufficient to reduce offspring viability to zero for the life of the female. Traps or targets impregnated with conventional formulations of pyrethroids to kill tsetse would have lost all their activity by this time. Results are discussed in terms of the prospects for using pyriproxyfen-treated targets to sterilize female tsetse directly and also indirectly through the contamination of males prior to mating through contact with such targets.     

An analytical model for a short-term advantage for sex

An analytical treatment is given for a model of Maynard Smith in which a short-term advantage for sex and recombination is provided by the mechanism of sib-competition. Suppose the next generation is formed by the winners of a large number of contests. Suppose a number of parents each contribute M offspring to a given contest, but the offspring of an asexual parent are identical whereas those of a sexual parent are distributed with some variance. If M is large there is a high probability that a sexual offspring will have a high enough fitness to win the contest. Calculations show that values of M around 3 and 4 are generally enough for sexual behaviour to overcome its two-fold disadvantage.     

The Need for a Kinetics for Biological Transport

The traditional theory of transport across capillary membranes via a laminar Poiseuille flow is shown to be invalid. It is demonstrated that the random, diffusive nature of the molecular flow and interactions with the “pore” walls play an important role in the transport process. Neither the continuum Navier-Stokes theory nor the equivalent theory of irreversible thermodynamics is adequate to treat the problem. Combination of near-continuum hydrodynamic theory, noncontinuum kinetic theory, and the theory of fluctuations provides a first step toward modeling both liquid processes in general and membrane transport processes as a specific application.     

Newborn screening for adrenoleukodystrophy: implications for therapy

X-Linked adrenoleukodystrophy (X-ALD) is a progressive metabolic condition affecting the adrenal glands and nervous system of males. Although variable in the age of onset and presentation in families, X-ALD does present in characteristic phenotypes including a devastating childhood form that affects 35% of boys with this genetic condition. The majority of males with X-ALD will also develop adrenal insufficiency, which may result in crisis. Early detection is desirable in order to prevent morbidity from this condition. We have recently developed a tandem mass spectroscopy method that allows this to be done during newborn screening for other genetic disorder. In this review, we discuss the rationale for early detection, its effect on treatment, and some of the uncertainties.     

AutoFAIR-A portal for automating FAIR assessments for bioinformatics resources

BackgroundResearch in Bioinformatics generates tools and datasets in Bioinformatics at a very fast rate. Meanwhile, a lot of effort is going into making these resources findable and reusable to improve resource discovery by researchers in the course of their work.PurposeThis paper proposes a semi-automated tool to assess a resource according to the Findability, Accessibility, Interoperability and Reusability (FAIR) criteria. The aim is to create a portal that presents the assessment score together with a report that researchers can use to gauge a resource.MethodOur system uses internet searches to automate the process of generating FAIR scores. The process is semi-automated in that if a particular property of the FAIR scores has not been captured by AutoFAIR, a user is able to amend and supply the information to complete the assessment.ResultsWe compare our results against FAIRshake that was used as the benchmark tool for comparing the assessments. The results show that AutoFAIR was able to match the FAIR criteria in FAIRshake with minimal intervention from the user.ConclusionsWe show that AutoFAIR can be a good repository for storing metadata about tools and datasets, together with comprehensive reports detailing the assessments of the resources. Moreover, AutoFAIR is also able to score workflows, giving an overall indication of the FAIRness of the resources used in a scientific study.