Diagnostics of thyroid cancer: Limitations of the existing methods and perspectives for future developments

A novel approach to the development of a precise method of intraoperative diagnostics of thyroid cancer has been proposed on the basis of fundamental study of proteasomes in malignant tumors of mammals and human. The method is based on estimation of proteasome activity in small fragments of the tumor and adjacent tissues.     

Haplotype mapping of a diploid non-meiotic organism using existing and induced aneuploidies

Haplotype maps (HapMaps) reveal underlying sequence variation and facilitate the study of recombination and genetic diversity. In general, HapMaps are produced by analysis of Single-Nucleotide Polymorphism (SNP) segregation in large numbers of meiotic progeny. Candida albicans, the most common human fungal pathogen, is an obligate diploid that does not appear to undergo meiosis. Thus, standard methods for haplotype mapping cannot be used. We exploited naturally occurring aneuploid strains to determine the haplotypes of the eight chromosome pairs in the C. albicans laboratory strain SC5314 and in a clinical isolate. Comparison of the maps revealed that the clinical strain had undergone a significant amount of genome rearrangement, consisting primarily of crossover or gene conversion recombination events. SNP map haplotyping revealed that insertion and activation of the UAU1 cassette in essential and non-essential genes can result in whole chromosome aneuploidy. UAU1 is often used to construct homozygous deletions of targeted genes in C. albicans; the exact mechanism (trisomy followed by chromosome loss versus gene conversion) has not been determined. UAU1 insertion into the essential ORC1 gene resulted in a large proportion of trisomic strains, while gene conversion events predominated when UAU1 was inserted into the non-essential LRO1 gene. Therefore, induced aneuploidies can be used to generate HapMaps, which are essential for analyzing genome alterations and mitotic recombination events in this clonal organism.     

Helicobacter pylori: new developments and treatments

The authors highlight new developments in research on Helicobacter pylori. There is now consensus that all patients with newly diagnosed or recurrent duodenal or gastric ulcers who have a positive test result for H. pylori should be treated for the infection. Patients presenting with complications of ulcers, such as bleeding, should also be treated. H. pylori has recently been classified as a definite human carcinogen by the International Agency for Research on Cancer. In treatment, new combination regimens, consisting of 3 or 4 different drugs, cure the infection in more than 80% of patients. Currently, the best combinations are: (1) omeprazole (or another proton-pump inhibitor), clarithromycin and metronidazole, (2) omeprazole (or another proton-pump inhibitor), clarithromycin and amoxicillin, (3) bismuth subsalicylate, tetracycline and metronidazole, and (4) omeprazole, bismuth subsalicylate, tetracycline and metronidazole.     

Marine algal lectins: new developments

Lectins can be extracted more readily from marine algae if the plant material is freeze-dried or frozen in liquid nitrogen prior to homogenisation. The addition of detergents, such as Tween 80, to the extraction medium and diluents, enhances extraction and detection of the lectins. Marine algal lectins can be isolated by affinity chromatography using a general affinity complex such as yeast mannan-Cellulofine which facilitates the isolation of purified lectin for biochemical characterisation. Red algal lectins exist as three types: low molecular weight molecules which bind glycoproteins, but not monosaccharides and have no requirement for divalent cations; lectins which bind monosaccharides and related small molecules, but have no divalent cation requirements; larger lectins (M.W. > 64000) which bind monosaccharides in the presence of divalent cations. No green algal lectin characterised so far requires divalent cations for haemagglutination. Possibly, only green algal lectins capable of forming oligomers have the capacity to bind monosaccharides.     

Evaluation of the ability of antioxidants to counteract lipid oxidation: existing methods, new trends and challenges

Oxidative degradation of lipids, especially that induced by reactive oxygen species (ROS), leads to quality deterioration of foods and cosmetics and could have harmful effects on health. Currently, a very promising way to overcome this is to use vegetable antioxidants for nutritional, therapeutic or food quality preservation purposes. A major challenge is to develop tools to assess the antioxidant capacity and real efficacy of these molecules. Many rapid in vitro tests are now available, but they are often performed in dissimilar conditions and different properties are thus frequently measured. The so-called 'direct' methods, which use oxidizable substrates, seem to be the only ones capable of measuring real antioxidant power. Some oxidizable substrates correspond to molecules or natural extracts exhibiting biological activity, such as lipids, proteins or nucleic acids, while others are model substrates that are not encountered in biological systems or foods. Only lipid oxidation and direct methods using lipid-like substrates will be discussed in this review. The main mechanisms of autoxidation and antioxidation are recapitulated, then the four components of a standard test (oxidizable substrate, medium, oxidation conditions and antioxidant) applied to a single antioxidant or complex mixtures are dealt with successively. The study is focused particularly on model lipids, but also on dietary and biological lipids isolated from their natural environment, including lipoproteins and phospholipidic membranes. Then the advantages and drawbacks of existing methods and new approaches are compared according to the context. Finally, recent trends based on the chemometric strategy are introduced as a highly promising prospect for harmonizing in vitro methods.     

Influenza A viruses: new research developments

Influenza A viruses are zoonotic pathogens that continuously circulate and change in several animal hosts, including birds, pigs, horses and humans. The emergence of novel virus strains that are capable of causing human epidemics or pandemics is a serious possibility. Here, we discuss the value of surveillance and characterization of naturally occurring influenza viruses, and review the impact that new developments in the laboratory have had on our understanding of the host tropism and virulence of viruses. We also revise the lessons that have been learnt from the pandemic viruses of the past 100 years.     

Detecting Local Haplotype Sharing and Haplotype Association

A novel haplotype association method is presented, and its power is demonstrated. Relying on a statistical model for linkage disequilibrium (LD), the method first infers ancestral haplotypes and their loadings at each marker for each individual. The loadings are then used to quantify local haplotype sharing between individuals at each marker. A statistical model was developed to link the local haplotype sharing and phenotypes to test for association. We devised a novel method to fit the LD model, reducing the complexity from putatively quadratic to linear (in the number of ancestral haplotypes). Therefore, the LD model can be fitted to all study samples simultaneously, and, consequently, our method is applicable to big data sets. Compared to existing haplotype association methods, our method integrated out phase uncertainty, avoided arbitrariness in specifying haplotypes, and had the same number of tests as the single-SNP analysis. We applied our method to data from the Wellcome Trust Case Control Consortium and discovered eight novel associations between seven gene regions and five disease phenotypes. Among these, GRIK4, which encodes a protein that belongs to the glutamate-gated ionic channel family, is strongly associated with both coronary artery disease and rheumatoid arthritis. A software package implementing methods described in this article is freely available at http://www.haplotype.org.     

Breaking new ground: challenging existing asthma guidelines

Background

While we have international guidelines and various national guidelines for asthma diagnosis and management, asthma remains poorly controlled in many children and adults. In this paper we review the limitations of current asthma guidelines and describe important issues and remaining questions regarding asthma guidelines for use, particularly in primary care.

Discussion

Clinical practice guidelines based on evidence from randomized controlled trials are considered the most rigorous and accurate. Current evidence-based guidelines are written predominantly from the perspective of the patient with a clear-cut asthma diagnosis, however, and tend not to consider the heterogeneity of asthma or to accommodate individual patient variations in response to treatment or their needs, differences in practice settings, or local differences in availability and cost of therapies. The results of randomized controlled trials, which are designed to establish efficacy of treatment under ideal conditions, may not apply to 'real-world' clinical practice, where patients are unselected, monitoring is less frequent, and effectiveness – the benefit of treatment in routine clinical practice – is the most relevant outcome. Moreover, most guidelines see asthma in isolation rather than considering other factors that may impact on asthma and response to asthma therapy, particularly age, allergic rhinitis, cigarette smoking, adherence, and genetic factors. When these links are recognized, guidelines rarely provide practical recommendations for treatment in these scenarios. Finally, there is some evidence that general practitioners are not convinced of the applicability of asthma guidelines to their practice settings, especially when those writing the guidelines principally work in specialist practice.

Conclusion

Developing country-specific guidelines or, ideally, local guidelines could provide more practical solutions for asthma care and could account for regional factors that influence patient choice and adherence to therapy. Pragmatic clinical trials and well-designed observational trials are needed in addition to randomized controlled trials to assess real-world effectiveness of therapies, and such evidence needs also to be considered by guideline writers. Finally, practical tools to facilitate the diagnosis and assessment of asthma and factors responsible for poor control, such as associated allergic rhinitis, limited adherence, and smoking behavior, are needed to supplement treatment information provided in clinical practice guidelines for asthma.

     

Chitin synthesis inhibitors: old molecules and new developments

Abstract Chitin is the most abundant natural aminopolysaccharide and serves as a structural component of extracellular matrices. It is found in fungal septa, spores, and cell walls, and in arthropod cuticles and peritrophic matrices, squid pens, mollusk shells, nematode egg shells, and some protozoan cyst walls. As prokaryotes, plants and vertebrates including humans do not produce chitin, its synthesis is considered as an attractive target site for fungicides, insecticides, and acaricides. Although no chitin synthesis inhibitor has been developed into a therapeutic drug to treat fungal infections in humans, a larger number of compounds have been successfully launched worldwide to combat arthropod pests in agriculture and forestry. This review summarizes the latest advances on the mode of action of chitin synthesis inhibitors with a special focus on those molecules that act on a postcatalytic step of chitin synthesis.     

Extending long-range phasing and haplotype library imputation methods to impute genotypes on sex chromosomes

AlphaImpute is a flexible and accurate genotype imputation tool that was originally designed for the imputation of genotypes on autosomal chromosomes. In some species, sex chromosomes comprise a large portion of the genome. For example, chromosome Z represents approximately 8% of the chicken genome and therefore is likely to be important in determining genetic variation in a population. When breeding programs make selection decisions based on genomic information, chromosomes that are not represented on the genotyping platform will not be subject to selection. Therefore imputation algorithms should be able to impute genotypes for all chromosomes. The objective of this research was to extend AlphaImpute so that it could impute genotypes on sex chromosomes. The accuracy of imputation was assessed using different genotyping strategies in a real commercial chicken population. The correlation between true and imputed genotypes was high in all the scenarios and was 0.96 for the most favourable scenario. Overall, the accuracy of imputation of the sex chromosome was slightly lower than that of autosomes for all scenarios considered.     

Plant hormones and signaling: common themes and new developments

About 200 plant biologists convened in Keystone, Colorado, for the "Plant Hormones and Signaling" symposium, which was organized by Joanne Chory, Joe Ecker, and Mark Estelle. The meeting was run concurrently with the "Plant Innate Immunity" symposium organized by Jonathan Jones and Jane Glazebrook. In this report, we summarize the progress in plant hormones and signaling.