Extraction of PCR-quality plant and microbial DNA from total rumen contents

DNA from rumen digesta has several diagnostic applications such as studying microbial community dynamics, transgene/DNA stability, and population typing of various rumen bacteria. Several DNA extraction procedures are described in the literature for rumen digesta, which describe the removal of tannins, polysaccharides, and other PCR inhibitors. Some of these protocols are time-consuming and impractical when handling a large number of samples routinely. Here we describe a rapid method for the extraction of PCR-quality plant and microbial DNA from total rumen contents that is based on modifications in the cetyltrimethylammonium bromide procedure followed by cleanup using a Qiagen column. This procedure is highly reproducible and relatively short, once the initial grinding of the samples is performed, and it consistently yields PCR-quality DNA.     

Mitogen-activated protein kinases in normal and (pre)neoplastic ovarian surface epithelium

Mitogen-activated protein kinases (MAPKs) are a group of serine/threonine kinases which are activated in response to a diverse array of extracellular stimuli and mediate signal transduction from the cell surface to the nucleus. It has been demonstrated that MAPKs are activated by external stimuli including chemotherapeutic agents, growth factors and reproductive hormones in ovarian surface epithelial cells. Thus, the MAPK signaling pathway may play an important role in the regulation of proliferation, survival and apoptosis in response to these external stimuli in ovarian cancer. In this article, an activation of the MAPK signaling cascade by several key reproductive hormones and growth factors in epithelial ovarian cancer is reviewed.     

Possible Involvement of GABAA and GABAB Receptors in the Inhibitory Action of Lindane on Transmitter Release from Cerebellar Granule Neurons

Cerebellar granule cells in culture express receptors for GABA belonging to the GABA_A and GABA_B classes. In order to characterize the ability of the insecticide lindane to interact with these receptors cells were grown in either plain culture media or media containing 150 M THIP as this is known to influence the properties of both GABA_A and GABA_B receptors. It was found that lindane regardless of the culture condition inhibited evoked (40 mM K⁺) release of neurotransmitter ([³H]D-aspartate as label for glutamate). In naive cells both GABA_A and GABA_B receptor active drugs prevented the inhibitory action of lindane but in THIP treated cultures none of the GABA_A and GABA_B receptor active drugs had any effect on the inhibitory action of lindane. This lack of effect was not due to inability of baclofen itself to inhibit transmitter release. It is concluded that lindane dependent on the state of the GABA_A and GABA_B receptors is able to indirectly interfere with both GABA_A and GABA_B receptors. In case of the latter receptors it was shown using [³H]baclofen to label the receptors that lindane could not displace the ligand confirming that lindane is likely to exert its action at a site different from the agonist binding site.     

Competitive interactions and the effect of herbivory on Bt-Brassica napus, Brassica rapa and Lolium perenne

1.  The probability of a transgenic crop establishing a feral population outside cultivated areas and possibly outcompeting naturally occurring species needs to be assessed to make an ecological risk assessment of the transgenic crop.
2.  The interaction between herbivory and competition is thought to determine the ecological success of insect-resistant plants, and this interaction was investigated in a competition experiment with transgenic insect-resistant Bt- Brassica napus , Brassica rapa , Lolium perenne , and herbivory from the large white butterfly Pieris brassicae .
3.  As expected, herbivory had a negative effect on the biomass of B. rapa at high plant densities. The competitive ability of L. perenne , when growing with B. rapa , increased significantly with the level of herbivory on B. rapa .
4.  To predict the effect of herbivory in a natural ecosystem, plant competition between the two annual Brassica species was analysed in a population ecological model. It was concluded that it is probable that transgenic Bt- B. napus plants may invade a natural habitat if herbivory is sufficiently high and the habitat is suitable for B. napus .
5.   Synthesis and applications . The results indicate that it is important to study the interaction between herbivory and competition when assessing the ecological risk of insect-resistant genetically modified crops. Furthermore, combining ecological data from manipulated experiments with population ecological modelling is a fruitful approach when conducting environmental risk assessments.     

Ecological hierarchies and self-organisation – Pattern analysis,modelling and process integration across scales

A continuing discussion in applied and theoretical ecology focuses on the relationship of different organisational levels and on how ecological systems interact across scales. We address principal approaches to cope with complex across-level issues in ecology by applying elements of hierarchy theory and the theory of complex adaptive systems. A top-down approach, often characterised by the use of statistical techniques, can be applied to analyse large-scale dynamics and identify constraints exerted on lower levels. Current developments are illustrated with examples from the analysis of within-community spatial patterns and large-scale vegetation patterns. A bottom-up approach allows one to elucidate how interactions of individuals shape dynamics at higher levels in a self-organisation process; e.g., population development and community composition. This may be facilitated by various modelling tools, which provide the distinction between focal levels and resulting properties. For instance, resilience in grassland communities has been analysed with a cellular automaton approach, and the driving forces in rodent population oscillations have been identified with an agent-based model. Both modelling tools illustrate the principles of analysing higher level processes by representing the interactions of basic components.The focus of most ecological investigations on either top-down or bottom-up approaches may not be appropriate, if strong cross-scale relationships predominate. Here, we propose an ‘across-scale-approach’, closely interweaving the inherent potentials of both approaches. This combination of analytical and synthesising approaches will enable ecologists to establish a more coherent access to cross-level interactions in ecological systems.     

Antiproliferative effect of growth hormone-releasing hormone (GHRH) antagonist on ovarian cancer cells through the EGFR-Akt pathway

Background  

Antagonists of growth hormone-releasing hormone (GHRH) are being developed for the treatment of various human cancers.     

An improved procedure for gene selection from microarray experiments using false discovery rate criterion

Background  

A large number of genes usually show differential expressions in a microarray experiment with two types of tissues, and the p-values of a proper statistical test are often used to quantify the significance of these differences. The genes with small p-values are then picked as the genes responsible for the differences in the tissue RNA expressions. One key question is what should be the threshold to consider the p-values small. There is always a trade off between this threshold and the rate of false claims. Recent statistical literature shows that the false discovery rate (FDR) criterion is a powerful and reasonable criterion to pick those genes with differential expression. Moreover, the power of detection can be increased by knowing the number of non-differential expression genes. While this number is unknown in practice, there are methods to estimate it from data. The purpose of this paper is to present a new method of estimating this number and use it for the FDR procedure construction.     

A bivariate quantitative genetic model for a threshold trait and a survival trait

Many of the functional traits considered in animal breeding can be analyzed as threshold traits or survival traits with examples including disease traits, conformation scores, calving difficulty and longevity. In this paper we derive and implement a bivariate quantitative genetic model for a threshold character and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted in which model parameters were augmented with unobserved liabilities associated with the threshold trait. The fully conditional posterior distributions associated with parameters of the threshold trait reduced to well known distributions. For the survival trait the two baseline Weibull parameters were updated jointly by a Metropolis-Hastings step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. The Gibbs sampler was tested in a simulation study and illustrated in a joint analysis of calving difficulty and longevity of dairy cattle. The simulation study showed that the estimated marginal posterior distributions covered well and placed high density to the true values used in the simulation of data. The data analysis of calving difficulty and longevity showed that genetic variation exists for both traits. The additive genetic correlation was moderately favorable with marginal posterior mean equal to 0.37 and 95% central posterior credibility interval ranging between 0.11 and 0.61. Therefore, this study suggests that selection for improving one of the two traits will be beneficial for the other trait as well.