Teaching aldosterone regulation and basic scientific principles using a classic paper by Dr. James O. Davis and colleagues

Classroom discussion of scientific articles can be an effective means of teaching scientific principles and methodology to both undergraduate and graduate science students. The availability of classic papers from the American Physiological Society Legacy Project has made it possible to access articles dating back to the early portions of the 20th century. In this article, we discuss a classic paper from the laboratory of Dr. James O. Davis on the regulation of aldosterone synthesis from the adrenal zona glomerulosa cell. Dr. Davis has conducted much of the seminal research investigating the renin-angiotensin system and the regulation of aldosterone release by angiotensin II. In addition to a characterization of the effects of ACTH on aldosterone regulation, this study is useful for discussing the basic principles of negative feedback pathways of the hypothalamic-pituitary axis. This study also provides examples of early bioassay techniques for the detection of angiotensin II and of the importance of quantitative measurements when investigating physiological responses. Three figures and one table are reproduced from the original article along with a series of discussion questions designed to facilitate discovery learning.     

Quantitative trait loci for IQ and other complex traits: single-nucleotide polymorphism genotyping using pooled DNA and microarrays

Similar to other complex traits, it is likely that many DNA polymorphisms of small effect size [quantitative trait loci (QTLs)] are responsible for the high heritability of intelligence, in addition to many rare monogenic disorders known to contribute to lowered intelligence. We review the current status of approaches to identify QTLs associations for intelligence employing genome-wide strategies using pooled DNA from many individuals and evaluate the innovative approach of microarray analysis to genotype DNA pools for large numbers of single nucleotide polymorphisms.     

In vivo detection of secreted proteins from wounded skin using capillary ultrafiltration probes and mass spectrometric proteomics

The identification of in vivo secreted proteins is a major challenge in systems biology. Here we report a novel technique using capillary ultrafiltration (CUF) probes to identify the secreted proteins involved in wound healing. CUF probes, which use semipermeable membrane hollow fibers to continuously capture secreted proteins, were used to sample skin wound fluids. To identify low-abundance proteins, we digested the CUF probe-collected wound fluid with trypsin and then directly subjected it to MS without using 2-DE separation. Two protein fragments with masses of 1565.7 and 1694.8 Da were identified by MS as peptides of thymosin beta10 and beta4, respectively. This is the first identification of thymosin beta10 as an in vivo constituent of the skin wound fluid. The LKKTETQ peptide, a common actin-binding domain of thymosin beta4 and beta10, significantly enhanced skin wound healing in vitro and in vivo. Our data suggest that the enhancement of wound healing by LKKTETQ may be mediated by purinergic receptors. The technique of using CUF probes linked to mass spectrometric proteomics represents a powerful method to identify in vivo secreted proteins, and may be applicable for identification of proteins relevant in various human diseases.     

Myriaporone 3/4 structure--activity relationship studies define a pharmacophore targeting eukaryotic protein synthesis

Myriaporones are naturally occurring compounds which structurally resemble the southern hemisphere of the tedanolide family of macrolide antitumor agents. Despite the fact that myriaporone 3/4 represents only a portion of tedanolide, it nonetheless retains much of its biological activity. We show here that like tedanolide, myriaporone 3/4 inhibits protein synthesis and proliferation of mammalian cells with low nanomolar potencies but displays no prokaryotic growth inhibitory effect. Moreover, myriaporone 3/4 displays a very rapid, reversible and p21-independent activity to block S phase progression in mammalian cells. Structure-activity relationship studies revealed that the C18-C19 epoxide and the C14 hydroxymethyl group (tedanolide numbering) of myriaporone 3/4 are required for cell cycle inhibition. These constitute previously unidentified and/or novel pharmacophores for myriaporone 3/4. Our results show that the important biological activities associated with the structurally complex tedanolides are present and can be harnessed in the chemically much simpler myriaporones. This greatly increases the value of the latter as investigative tools for biochemical research as well as for development of potential therapeutics.     

Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations

The fixation of a beneficial mutation represents the first step in adaptation, and the average effect of such mutations is therefore a fundamental property of evolving populations. It is nevertheless poorly characterized because the rarity of beneficial mutations makes it difficult to obtain reliable estimates of fitness. We obtained 68 genotypes each containing a single fixed beneficial mutation from experimental populations of Pseudomonas fluorescens, evolving in medium with serine as the sole carbon source and estimated the selective advantage of each by competition with the ancestor. The distribution of selection coefficients is modal and closely resembles the Weibull distribution. The average selection coefficient (2.1) and beneficial mutation rate (3.8x10(-8)) are high relative to previous studies, possibly because the ancestral population grows poorly in serine-limited medium. Our experiment suggests that the initial stages of adaptation to stressful environments will involve the substitution of mutations with large effect on fitness.     

Quantifying the Gurken morphogen gradient in Drosophila oogenesis

Quantitative information about the distribution of morphogens is crucial for understanding their effects on cell-fate determination, yet it is difficult to obtain through direct measurements. We have developed a parameter estimation approach for quantifying the spatial distribution of Gurken, a TGFalpha-like EGFR ligand that acts as a morphogen in Drosophila oogenesis. Modeling of Gurken/EGFR system shows that the shape of the Gurken gradient is controlled by a single dimensionless parameter, the Thiele modulus, which reflects the relative importance of ligand diffusion and degradation. By combining the model with genetic alterations of EGFR levels, we have estimated the value of the Thiele modulus in the wild-type egg chamber. This provides a direct characterization of the shape of the Gurken gradient and demonstrates how parameter estimation techniques can be used to quantify morphogen gradients in development.     

Quantitative proteomic analysis of drug-induced changes in mycobacteria

A new approach for qualitative and quantitative proteomic analysis using capillary liquid chromatography and mass spectrometry to study the protein expression response in mycobacteria following isoniazid treatment is discussed. In keeping with known effects on the fatty acid synthase II pathway, proteins encoded by the kas operon (AcpM, KasA, KasB, Accd6) were significantly overexpressed, as were those involved in iron metabolism and cell division suggesting a complex interplay of metabolic events leading to cell death.     

The marine viromes of four oceanic regions

Viruses are the most common biological entities in the marine environment. There has not been a global survey of these viruses, and consequently, it is not known what types of viruses are in Earth's oceans or how they are distributed. Metagenomic analyses of 184 viral assemblages collected over a decade and representing 68 sites in four major oceanic regions showed that most of the viral sequences were not similar to those in the current databases. There was a distinct “marine-ness” quality to the viral assemblages. Global diversity was very high, presumably several hundred thousand of species, and regional richness varied on a North-South latitudinal gradient. The marine regions had different assemblages of viruses. Cyanophages and a newly discovered clade of single-stranded DNA phages dominated the Sargasso Sea sample, whereas prophage-like sequences were most common in the Arctic. However most viral species were found to be widespread. With a majority of shared species between oceanic regions, most of the differences between viral assemblages seemed to be explained by variation in the occurrence of the most common viral species and not by exclusion of different viral genomes. These results support the idea that viruses are widely dispersed and that local environmental conditions enrich for certain viral types through selective pressure.     

Probing SWI/SNF remodeling of the nucleosome by unzipping single DNA molecules

Chromatin-remodeling enzymes can overcome strong histone-DNA interactions within the nucleosome to regulate access of DNA-binding factors to the genetic code. By unzipping individual DNA duplexes, each containing a uniquely positioned nucleosome flanked by long segments of DNA, we directly probed histone-DNA interactions. The resulting disruption-force signatures were characteristic of the types and locations of interactions and allowed measurement of the positions of nucleosomes with 2.6-base-pair (bp) precision. Nucleosomes remodeled by yeast SWI/SNF were moved bidirectionally along the DNA, resulting in a continuous position distribution. The characteristic distance of motion was approximately 28 bp per remodeling event, and each event occurred with a catalytic efficiency of 0.4 min(-1) per nM SWI/SNF. Remodeled nucleosomes had essentially identical disruption signatures to those of unremodeled nucleosomes, indicating that their overall structure remained canonical. These results impose substantial constraints on the mechanism of SWI/SNF remodeling.