Peridermal cell patterning in the feather-forming skin of the chick embryo

The shape, distribution, and orientation of peridermal cells were examined in the dorsolumbar skin of $\text{7}\text{1}\text{2}\text{-}\text{day}$ chick embryos. Most feather rudiments of middorsal and lateral rows showed a marked cephalocaudal polarity. A similar polarity was found in the prospective rudiments of skin areas lateral to the last-formed row. On the cranial slope and apex of rudiments, cells are convex and predominantly elongated at right angles with respect to the cephalocaudal axis, whereas on the caudal slope, most cells are flat, polygonal, surrounded by a border-line ridge, and oriented predominantly with their long axis parallel to the cephalocaudal axis. The significance of this pattern is discussed in view of the fact that the epidermis is the determinant tissue in feather orientation.     

A novel nitrilase, arylacetonitrilase, of Alcaligenes faecalis JM3. Purification and characterization

A new type of nitrilase, arylacetonitrilase, has been purified from isovaleronitrile-induced cells of Alcaligenes faecalis JM3 in four steps. The purity of the enzyme was confirmed by SDS/polyacrylamide gel electrophoresis, ampholyte electrofocusing and double immunodiffusion in agarose. The enzyme has a molecular mass of about 275 kDa and consists of six subunits of identical molecular mass. The purified enzyme exhibits a pH optimum of 7.5 and a temperature optimum of 45 degrees C. The enzyme is specific for arylacetonitriles such as 2-thiophenacetonitrile, p-tolyacetonitrile, p-chlorobenzylcyanide, p-fluorobenzylcyanide and 3-pyridylacetonitrile. The enzyme stoichiometrically catalyzes the hydrolysis of arylacetonitrile to arylacetic acid and ammonia, no formation of amide occurring. However, the enzyme does not attack nitrile groups attached to aromatic and heteroaromatic rings, which are hydrolyzed preferably by the nitrilases known previously. The enzyme requires thiol compounds such as dithiothreitol and 2-mercaptoethanol to exhibit its maximum activity.     

A Taxonomic Search Engine: Federating taxonomic databases using web services

Background  

The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism.     

Radiographic joint damage in rheumatoid arthritis is associated with differences in cartilage turnover and can be predicted by serum biomarkers: an evaluation from 1 to 4 years after diagnosis

Introduction  

The objective of this study was to determine whether serum biomarkers for degradation and synthesis of the extracellular matrix of cartilage are associated with, and can predict, radiographic damage in patients with rheumatoid arthritis (RA).     

3-hydroxy-5-methylproline, a new amino acid identified as a component of actinomycin Z1.

3-Hydroxy-5-methylproline has been identified in hydrolysates of actinomycin Z₁ by ion-exchange and paper chromatography, paper electrophoresis, gas chromatography and mass spectrometry in comparison with the synthetic compound. The stereochemistry of this amino acid is under investigation. The amino acid composition of actinomycin Z₁ thus consists of threonine, hydroxythreonine, D-valine(2), 4-oxo-5-methylproline, 3-hydroxy-5-methylproline, sarcosine(2), N-methylalanine and N-methylvaline.     

A dynamic model for genome-wide association studies

Although genome-wide association studies (GWAS) are widely used to identify the genetic and environmental etiology of a trait, several key issues related to their statistical power and biological relevance have remained unexplored. Here, we describe a novel statistical approach, called functional GWAS or fGWAS, to analyze the genetic control of traits by integrating biological principles of trait formation into the GWAS framework through mathematical and statistical bridges. fGWAS can address many fundamental questions, such as the patterns of genetic control over development, the duration of genetic effects, as well as what causes developmental trajectories to change or stop changing. In statistics, fGWAS displays increased power for gene detection by capitalizing on cumulative phenotypic variation in a longitudinal trait over time and increased robustness for manipulating sparse longitudinal data.     

Effect of surface nanoscale topography on elastic modulus of individual osteoblastic cells as determined by atomic force microscopy

Mechanical stimulation of osteoblasts by fluid flow promotes a variety of pro-differentiation effects and improving the efficiency of these mechanical signals could encourage specific differentiation pathways. One way this could be accomplished is by altering mechanical properties of osteoblasts. In this study, murine osteoblastic MC3T3-E1 cells were cultured on surfaces covered with nanometer-sized islands to examine the hypothesis that the elastic modulus of osteoblastic cells is affected by nanoscale topography. Nanoislands were produced by polymer demixing of polystyrene and poly(bromostyrene), which leads to a segregated polymer system and formation of nanometer-sized topographical features. The elastic modulus of MC3T3-E1 cells was determined using atomic force microscopy in conjunction with the Hertz mathematical model. Osteoblastic cells cultured on nanotopographic surfaces (11-38 nm high islands) had a different distribution of cellular modulus values, e.g., the distribution shifted toward higher modulus values, relative to cells on flat control surfaces. There were also differences in cell modulus distribution between two flat controls as surface chemistry was changed between polystyrene and glass. Taken together, our results demonstrate that both surface nanotopography and chemistry affect the mechanical properties of cells and may provide new methods for altering the response of cells to external mechanical signals.     

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities

Background

To determine which changes in the host cell genome are crucial for cervical carcinogenesis, a longitudinal in vitro model system of HPV-transformed keratinocytes was profiled in a genome-wide manner. Four cell lines affected with either HPV16 or HPV18 were assayed at 8 sequential time points for gene expression (mRNA) and gene copy number (DNA) using high-resolution microarrays. Available methods for temporal differential expression analysis are not designed for integrative genomic studies.

Results

Here, we present a method that allows for the identification of differential gene expression associated with DNA copy number changes over time. The temporal variation in gene expression is described by a generalized linear mixed model employing low-rank thin-plate splines. Model parameters are estimated with an empirical Bayes procedure, which exploits integrated nested Laplace approximation for fast computation. Iteratively, posteriors of hyperparameters and model parameters are estimated. The empirical Bayes procedure shrinks multiple dispersion-related parameters. Shrinkage leads to more stable estimates of the model parameters, better control of false positives and improvement of reproducibility. In addition, to make estimates of the DNA copy number more stable, model parameters are also estimated in a multivariate way using triplets of features, imposing a spatial prior for the copy number effect.

Conclusion

With the proposed method for analysis of time-course multilevel molecular data, more profound insight may be gained through the identification of temporal differential expression induced by DNA copy number abnormalities. In particular, in the analysis of an integrative oncogenomics study with a time-course set-up our method finds genes previously reported to be involved in cervical carcinogenesis. Furthermore, the proposed method yields improvements in sensitivity, specificity and reproducibility compared to existing methods. Finally, the proposed method is able to handle count (RNAseq) data from time course experiments as is shown on a real data set.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-327) contains supplementary material, which is available to authorized users.     

Spatiotemporal changes in the genetic diversity of harmful algal blooms caused by the toxic dinoflagellate Alexandrium minutum

Organisms with sexual and asexual reproductive systems benefit from both types of reproduction. Sexual recombination generates new combinations of alleles, whereas clonality favours the spread of the fittest genotype through the entire population. Therefore, the rate of sexual vs. clonal reproduction has a major influence on the demography and genetic structure of natural populations. We addressed the effect of reproductive system on populations of the dinoflagellate Alexandrium minutum. More specifically, we monitored the spatiotemporal genetic diversity during and between bloom events in two estuaries separated by 150 km for two consecutive years. An analysis of population genetic patterns using microsatellite markers revealed surprisingly high genotypic and genetic diversity. Moreover, there was significant spatial and temporal genetic differentiation during and between bloom events. Our results demonstrate that (i) interannual genetic differentiation can be very high, (ii) estuaries are partially isolated during bloom events and (iii) genetic diversity can change rapidly during a bloom event. This rapid genetic change may reflect selective effects that are nevertheless not strong enough to reduce allelic diversity. Thus, sexual reproduction and/or migration may regularly erase any genetic structure produced within estuaries during a bloom event.