A Nonparametric Mean-Variance Smoothing Method to Assess Arabidopsis Cold Stress Transcriptional Regulator CBF2 Overexpression Microarray Data

Microarray is a powerful tool for genome-wide gene expression analysis. In microarray expression data, often mean and variance have certain relationships. We present a non-parametric mean-variance smoothing method (NPMVS) to analyze differentially expressed genes. In this method, a nonlinear smoothing curve is fitted to estimate the relationship between mean and variance. Inference is then made upon shrinkage estimation of posterior means assuming variances are known. Different methods have been applied to simulated datasets, in which a variety of mean and variance relationships were imposed. The simulation study showed that NPMVS outperformed the other two popular shrinkage estimation methods in some mean-variance relationships; and NPMVS was competitive with the two methods in other relationships. A real biological dataset, in which a cold stress transcription factor gene, CBF2, was overexpressed, has also been analyzed with the three methods. Gene ontology and cis-element analysis showed that NPMVS identified more cold and stress responsive genes than the other two methods did. The good performance of NPMVS is mainly due to its shrinkage estimation for both means and variances. In addition, NPMVS exploits a non-parametric regression between mean and variance, instead of assuming a specific parametric relationship between mean and variance. The source code written in R is available from the authors on request

Variation at the Calpain 3 gene is associated with meat tenderness in zebu and composite breeds of cattle

<p>Abstract</p> <p>Background</p> <p>Quantitative Trait Loci (QTL) affecting meat tenderness have been reported on Bovine chromosome 10. Here we examine variation at the Calpain 3 (<it>CAPN3</it>) gene in cattle, a gene located within the confidence interval of the QTL, and which is a positional candidate gene based on the biochemical activity of the protein.</p> <p>Results</p> <p>We identified single nucleotide polymorphisms (SNP) in the genomic sequence of the <it>CAPN3 </it>gene and tested three of these in a sample of 2189 cattle. Of the three SNP genotyped, the <it>CAPN3:c.1538+225G>T </it>had the largest significant additive effect, with an allele substitution effect in the Brahman of <it>α </it>= -0.144 kg, SE = 0.060, <it>P </it>= 0.016, and the polymorphism explained 1.7% of the residual phenotypic variance in that sample of the breed. Significant haplotype substitution effects were found for all three breeds, the Brahman, the Belmont Red, and the Santa Gertrudis. For the common haplotype, the haplotype substitution effect in the Brahman was <it>α </it>= 0.169 kg, SE = 0.056, <it>P </it>= 0.003. The effect of this gene was compared to Calpastatin in the same sample. The SNP show negligible frequencies in taurine breeds and low to moderate minor allele frequencies in zebu or composite animals.</p> <p>Conclusion</p> <p>These associations confirm the location of a QTL for meat tenderness in this region of bovine chromosome 10. SNP in or near this gene may be responsible for part of the overall difference between taurine and zebu breeds in meat tenderness, and the greater variability in meat tenderness found in zebu and composite breeds. The evidence provided so far suggests that none of these tested SNP are causative mutations.</p

Hv-CBF2A overexpression in barley accelerates COR gene transcript accumulation and acquisition of freezing tolerance during cold acclimation

Abstract C-Repeat Binding Factors (CBFs) are DNAbinding transcriptional activators of gene pathways imparting freezing tolerance. Poaceae contain three CBF subfamilies, two of which, HvCBF3/CBFIII and HvCBF4/CBFIV, are unique to this taxon. To gain mechanistic insight into HvCBF4/CBFIV CBFs we overexpressed Hv-CBF2A in spring barley (Hordeum vulgare) cultivar ‘Golden Promise’. The Hv-CBF2A overexpressing lines exhibited stunted growth, poor yield, and greater freezing tolerance compared to non-transformed ‘Golden Promise’. Differences in freezing tolerance were apparent only upon cold acclimation. During cold acclimation freezing tolerance of the Hv-CBF2A overexpressing lines increased more rapidly than that of ‘Golden Promise’ and paralleled the freezing tolerance of the winter hardy barley ‘Dicktoo’. Transcript levels of candidate CBF target genes, COR14B and DHN5 were increased in the overexpressor lines at warm temperatures, and at cold temperatures they accumulated to much higher levels in the Hv-CBF2A overexpressors than in ‘Golden Promise’. Hv-CBF2A overexpression also increased transcript levels of other CBF genes at FROST RESISTANCE-H2-H2 (FR-H2) possessing CRT/DRE sites in their upstream regions, the most notable of which was CBF12. CBF12 transcript levels exhibited a relatively constant incremental increase above levels in ‘Golden Promise’ both at warm and cold. These data indicate that Hv-CBF2A activates target genes at warm temperatures and that transcript accumulation for some of these targets is greatly enhanced by cold temperatures

A comparison of career satisfaction amongst dental healthcare professionals across three health care systems: Comparison of data from the United Kingdom, New Zealand and Trinidad & Tobago

BACKGROUND: The aim of this study was to compare the expressed levels of career satisfaction of three groups of comparable dental healthcare professionals, working in Trinidad, the United Kingdom and New Zealand. METHODS: Three questionnaire surveys were carried out of comparable dental healthcare professionals. Dental nurses in Trinidad and dental therapists in the UK and New Zealand. Questionnaires were sent to all registered dental nurses or dental therapists. RESULTS: Career satisfaction was lowest amongst Dental Therapists working in Trinidad and Tobago. Approximately 59% of the Therapists working in New Zealand reported stated that they felt they were not a valued member of the dental team, the corresponding proportion in the United Kingdom was 32%, and for Trinidad 39%. CONCLUSION: Dental therapists working in different healthcare systems report different levels of satisfaction with their career

Ion implantation in nanodiamonds: Size effect and energy dependence

Nanoparticles are ubiquitous in nature and are increasingly important for technology. They are subject to bombardment by ionizing radiation in a diverse range of environments. In particular, nanodiamonds represent a variety of nanoparticles of significant fundamental and applied interest. Here we present a combined experimental and computational study of the behaviour of nanodiamonds under irradiation by xenon ions. Unexpectedly, we observed a pronounced size effect on the radiation resistance of the nanodiamonds: particles larger than 8 nm behave similarly to macroscopic diamond (i.e. characterized by high radiation resistance) whereas smaller particles can be completely destroyed by a single impact from an ion in a defined energy range. This latter observation is explained by extreme heating of the nanodiamonds by the penetrating ion. The obtained results are not limited to nanodiamonds, making them of interest for several fields, putting constraints on processes for the controlled modification of nanodiamonds, on the survival of dust in astrophysical environments, and on the behaviour of actinides released from nuclear waste into the environment

The role of dimensionality in neuronal network dynamics

The research leading to these results has received funding from the European Union’s Seventh Framework Programme under grant agreement FP7 ICT 2011 – 284553 (Acronym: Si-CODE), the NEUROSCAFFOLDS Project n. 604263, the National Natural Science Foundation of China (Grant number: 51361130033) and the Ministry of Science and Technology of China (973 Grant number: 2014CB965003)

Mapping carcass and meat quality QTL on Sus Scrofa chromosome 2 in commercial finishing pigs

Quantitative trait loci (QTL) affecting carcass and meat quality located on SSC2 were identified using variance component methods. A large number of traits involved in meat and carcass quality was detected in a commercial crossbred population: 1855 pigs sired by 17 boars from a synthetic line, which where homozygous (A/A) for IGF2. Using combined linkage and linkage disequilibrium mapping (LDLA), several QTL significantly affecting loin muscle mass, ham weight and ham muscles (outer ham and knuckle ham) and meat quality traits, such as Minolta-L* and -b*, ultimate pH and Japanese colour score were detected. These results agreed well with previous QTL-studies involving SSC2. Since our study is carried out on crossbreds, different QTL may be segregating in the parental lines. To address this question, we compared models with a single QTL-variance component with models allowing for separate sire and dam QTL-variance components. The same QTL were identified using a single QTL variance component model compared to a model allowing for separate variances with minor differences with respect to QTL location. However, the variance component method made it possible to detect QTL segregating in the paternal line (e.g. HAMB), the maternal lines (e.g. Ham) or in both (e.g. pHu). Combining association and linkage information among haplotypes improved slightly the significance of the QTL compared to an analysis using linkage information only

Molecular Correlates of Social Dominance: A Novel Role for Ependymin in Aggression

Theoretical and empirical studies have sought to explain the formation and maintenance of social relationships within groups. The resulting dominance hierarchies have significant fitness and survival consequences dependent upon social status. We hypothesised that each position or rank within a group has a distinctive brain gene expression profile that correlates with behavioural phenotype. Furthermore, transitions in rank position should determine which genes shift in expression concurrent with the new dominance status. We used a custom cDNA microarray to profile brain transcript expression in a model species, the rainbow trout, which forms tractable linear hierarchies. Dominant, subdominant and submissive individuals had distinctive transcript profiles with 110 gene probes identified using conservative statistical analyses. By removing the dominant, we characterised the changes in transcript expression in sub-dominant individuals that became dominant demonstrating that the molecular transition occurred within 48 hours. A strong, novel candidate gene, ependymin, which was highly expressed in both the transcript and protein in subdominants relative to dominants, was tested further. Using antibody injection to inactivate ependymin in pairs of dominant and subdominant zebrafish, the subdominant fish exhibited a substantial increase in aggression in parallel with an enhanced competitive ability. This is the first study to characterise the molecular signatures of dominance status within groups and the first to implicate ependymin in control of aggressive behaviour. It also provides evidence for indirect genetic effect models in which genotype/phenotype of an individual is influenced by conspecific interactions within a group. The variation in the molecular profile of each individual within a group may offer a new explanation of intraspecific variation in gene expression within undefined groups of animals and provides new candidates for empirical study