Determinants of expression variability

The amount of tissue-specific expression variability (EV) across individuals is an essential characteristic of a gene and believed to have evolved, in part, under functional constraints. However, the determinants and functional implications of EV are only beginning to be investigated. Our analyses based on multiple expression profiles in 41 primary human tissues show that a gene’s EV is significantly correlated with a number of features pertaining to the genomic, epigenomic, regulatory, polymorphic, functional, structural and network characteristics of the gene. We found that (i) EV of a gene is encoded, in part, by its genomic context and is further influenced by the epigenome; (ii) strong promoters induce less variable expression; (iii) less variable gene loci evolve under purifying selection against copy number polymorphisms; (iv) genes that encode inherently disordered or highly interacting proteins exhibit lower variability; and (v) genes with less variable expression are enriched for house-keeping functions, while genes with highly variable expression tend to function in development and extra-cellular response and are associated with human diseases. Thus, our analysis reveals a number of potential mediators as well as functional and evolutionary correlates of EV, and provides new insights into the inherent variability in eukaryotic gene expression.     

Investigating Models of Protein Function and Allostery With a Widespread Mutational Analysis of a Light-Activated Protein

To investigate the relationship between a protein’s sequence and its biophysical properties, we studied the effects of more than 100 mutations in Avena sativa light-oxygen-voltage domain 2, a model protein of the Per-Arnt-Sim family. The A. sativa light–oxygen–voltage domain 2 undergoes a photocycle with a conformational change involving the unfolding of the terminal helices. Whereas selection studies typically search for winners in a large population and fail to characterize many sites, we characterized the biophysical consequences of mutations throughout the protein using NMR, circular dichroism, and ultraviolet/visible spectroscopy. Despite our intention to introduce highly disruptive substitutions, most had modest or no effect on function, and many could even be considered to be more photoactive. Substitutions at evolutionarily conserved sites can have minimal effect, whereas those at nonconserved positions can have large effects, contrary to the view that the effects of mutations, especially at conserved positions, are predictable. Using predictive models, we found that the effects of mutations on biophysical function and allostery reflect a complex mixture of multiple characteristics including location, character, electrostatics, and chemistry.     

Untersuchungen Über Auslösung und Hemmung der Regeneration beim Axolotl

Ohne ZusammenfassungAls Festgabe für Prof. Dr. Hans Driesch in Verehrung gewidmet vom Verfasser.Diese Arbeit war für die ProfessorDriesch gewidmeten Bände dieses Archivs bestimmt. Durch einen Unglücksfall hat sich jedoch ihre Vollendung verspätet und so erscheint sie erst jetzt nachträglich. Sie soll die Gefühle derselben tiefen Verehrung für den Jubilar bezeugen, welche die Verfasser der in den Festbänden publizierten Arbeiten ihm zum Ausdruck brachten.     

Free fatty acids activate a vigorous Ca(2+):2H(+) antiport activity in yeast mitochondria.

The accumulation and retention of Ca(2+) by yeast mitochondria (Saccharomyces cerevisiae) mediated by ionophore ETH 129 occurs with a variable efficiency in different preparations. Ineffective Ca(2+) transport and a depressed membrane potential occur in parallel, are exacerbated in parallel by exogenous free fatty acids, and are corrected in parallel by the addition of bovine serum albumin. Bovine serum albumin is not required to develop a high membrane potential when either Ca(2+) or ETH 129 are absent, and when both are present membrane potential is restored by the addition of EGTA in a concentration-dependent manner. Respiration and swelling data indicate that the permeability transition pore does not open in yeast mitochondria that are treated with Ca(2+) and ETH 129, whereas fatty acid concentration studies and the inaction of carboxyatractyloside indicate that fatty acid-derived uncoupling does not underlie the other observations. It is concluded that yeast mitochondria contain a previously unrecognized Ca(2+):2H(+) antiporter that is highly active in the presence of free fatty acids and leads to a futile cycle of Ca(2+) accumulation and release when exogenous Ca(2+) and ETH 129 are available. It is also shown that isolated yeast mitochondria degrade their phospholipids at a relatively rapid rate. The activity responsible is also previously unrecognized. It is Ca(2+)-independent, little affected by the presence or absence of a respiratory substrate, and leads to the hydrolysis of ester linkages at both the sn-1 and sn-2 positions of the glycerophospholipids. The products of this activity, through their actions on the antiporter, explain the variable behavior of yeast mitochondria treated with Ca(2+) plus ETH 129.     

Cultured circular smooth muscle from the rabbit colon

Summary Although cultured vascular smooth muscle cells have been extensively characterized and investigated, there are very few studies of cultured intestinal smooth muscle cells. The aim of this study was to culture colonic smooth muscle (CSM) cells from the rabbit colon. Freshly isolated CSM cells from the circular muscle layer of the distal colon were prepared by collagenase digestion. In primary culture, CSM cells attached to the culture vessels by 48 to 72 h, proliferated by 3 to 7 d, and reached confluency by 14 to 17 d with a “hill-and-valley” pattern. Spontaneous contractions were not observed at any time at 21° or 37° C. Confluent primary cultures were greater than 95% CSM cells, as identified by intensely positive immunofluorescent staining to smooth muscle actin-specific CGA7 and muscle-specific HHF-35 monoclonal antibodies. Transmission electron microscopy of freshly isolated and proliferating CSM cells revealed ultrastructural features consistent with smooth muscle cells. We successfully cultured CSM cells of the rabbit from freshly isolated cells and validated these CSM cells by electron microscopy and immunocytochemical staining. These highly pure primary cultures may be used to investigate numerous aspects of CSM cell metabolism and physiology. These studies were supported by the National Institutes of Health grant to the Inflammatory Bowel Disease Center (Bethesda, MD) P30-AM-32200 and R01-DK-31147. Dr. Kao is the recipient of a Research Career Development Award from the National Foundation for Ileitis and Colitis, Inc. A preliminary report of this work was presented at the American Motility Society Meeting, Houston, TX, in October 1986, and appeared in abstract form inGastroenterology 91: 1057; 1986.     

The presence or absence of light during flotation restricted environmental stimulation: Effects on plasma cortisol,blood pressure,and mood

This study examined the effect of light on relaxation associated with flotation restricted environmental stimulation therapy (REST), as measured by plasma cortisol, mean arterial pressure, and psychometric parameters. Twenty-one subjects were paired by baseline cortisol levels into two groups: one experiencing flotation REST in the presence of light (REST-L) and one experiencing flotation REST in the absence of light (REST-D). Subjects were 15 male and 6 female students aged 22–28 in normal health who had not experienced REST. Repeated flotation REST (8 sessions) either with light or without light was associated with a decrease in plasma cortisol and a decrease in mean arterial pressure, with no differences in effectiveness between groups. The psychometric assessment of mood, using the POMS scale, before and after sessions 1 and 8 revealed mood state improvement in both REST-L and REST-D groups. These data suggest that the presence of light did not compromise the flotation REST experience, as evidenced by the lack of difference between REST-L and REST-D groups.