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.     

Lysine-derived cross-links in the egg shell membrane

Egg shell membrane protein contains significant quantities of the lysine-derived aldehyde, allysine, and its aldol condensation product. NaB³H₄ reduction followed by alkaline hydrolysis of purified protein revealed that there were six residues/1000 of both allysine and the reduced aldol while only traces of desmosine and isodesmosine were detected. The amino acid composition of the membrane protein did not resemble that of mammalian elastin.     

Frequent mowing is better than grazing for the conservation value of lowland tussock grasssland at Pontville,Tasmania

Abstract The effects of an unusual high frequency mowing regime, which involved the removal of slash, were compared to moderate grazing through the method of paired quadrats across a fenceline, which was orthogonal to a weak environmental gradient. The mown plots proved superior in their conservation characteristics to the moderately grazed plots. The mowing regime produced greater cover of rare or threatened species, greater native cover and lesser exotic grass cover. It thus presents an opportunity for maintaining or improving the condition of previously grazed remnants in reserves without resorting to the use of stock or fire for biomass reduction.     

The presence of chlorophyll b and the estimation of phaeopigments in marine phytoplankton

A reverse-phase h.p.l.c. technique was used to estimate theconcentration of chlorophyll b in phytoplankton cultures, fecalpellets of Calanus pacificus, and suspended paniculate matterfrom the Central North Pacific, Oregon coastal waters, and DabobBay (a temperate fjord in Puget Sound, WA, USA). The purposewas to assess the distribution of this pigment in the euphoticzone and its effect on the fluorometnc estimation of phaeopigments.Analyses of natural waters confirm high chlorophyll b concentrations(median mass ratio of b:a > 0.3) at the depth of the chlorophylla maximum in tropical waters while values for temperate planktonare relatively low (median mass ratio of chl b:a = 0.05) andpatchy. Zooplankton fecal pellets showed a significant enrichmentin chlorophyll b, suggesting grazing as a mechanism to explainhigh concentrations of this pigment at the bottom of the euphoticzone. It is estimated that the presence of chlorophyll b couldcause an average overestimation of phaeopigment concentrationby the fluorometnc technique of 38% between 0 and 200 m in theCentral North Pacific. This effect is more pronounced at thelayer of chlorophyll b maximum (120–140 m). ¹Present address: Marine Biology Research Division, A-002, ScrippsInstitution of Oceanography, La Jolla, CA 92093, USA     

Effect of synthetic auxins on callus induction from tea stem tissue

A study was initiated to establish an in vitro culture protocol for tea (Camellia sinensis). Explant sources, disinfestation methods and culture media were examined. Segments (divots) were dissected from greenwood stem (current year growth) internodes of field grown plants. Disinfestation was achieved by separate treatments of 3.75% sodium hypochlorite and 7.5% CaCl₂. MS medium with sucrose (30 g/L), inositol (100 mg/L) and thiamine-HCl (1.3 mg/L) and kinetin was used with combinations of the auxins: (2,4-dichlorophenoxy) acetic acid (2,4-D), (2,4,5-trichlorophenoxy) acetic acid (2,4,5-T), (naphthalene) acetic acid (NAA) and 4-amino-3,5,6-trichloro-2-pyridinecarboxylic acid (Picloram). Picloram (10^-7M) induced the most callus proliferation without kinetin. At a constant level of kinetin (10^-5M), the concentrations inducing the most callus growth were 10^-7M for 2,4-D, 10^-6M for 2,4,5-T, 10^-7M for Picloram and 10^-8M for NAA. A factorial test of 2,4,5-T and kinetin concentrations showed the optimum for callus growth was 10^-7M and 10^-5M, respectively.Technical Contribution No. 2532 of the South Carolina Agricultural Experiment Station, Clemson University.Graduate Research Assistant and Professor, respectively.     

Lake-watershed acidification in the North Branch of the Moose River: Introduction

An integrated analysis of a terrestrial-aquatic ecosystem, the North Branch of the Moose River in the Adirondack region of New York, was conducted. This basin contains a large number of interconnected surface waters that exhibit marked gradients in pH and acid neutralizing capacity (ANC). As a result, the basin has been the focus of research activity, including the Regional Integrated Lake-Watershed Acidification Study (RILWAS). The objective of the current analysis was to use the North Branch of the Moose River as a case study to:

1. Evaluate processes regulating the acid-base chemistry of surface waters.
2. To assess the effects of surface water acidification on fish populations.

The observations of this study were consistent with the model of surface water acidification developed during the Integrated Lake-Watershed Acidification Study (ILWAS). The processes depicted in the original ILWAS simulation model were adequate to describe the acid-base chemistry of surface waters in the North Branch of the Moose River. However, the reduction of SO ₄ ^2? in lake sediments, a process not represented in the original model, proved to be a significant source of acid neutralizing capacity (ANC) for some of these waters. As a result, reduction processes were added to the model. Analysis of in-situ bioassay and survey data indicate that acid-sensitive fish species have disappeared from the more acidic areas of the basin over the last half century. Paleoecological analyses indicate that pH has decreased from the high 5's to about 5 in Big Moose Lake during this period. ILWAS model simulations indicate that the pH of Big Moose Lake would increase by at least 0.1 to 0.5 pH units (depending on the season) in response to a 50% reduction in total atmospheric S deposition. Considerable variability in processes regulating acid/base chemistry was evident in the North Branch of the Moose River. Therefore, regional assessments of past or possible future effects of acidic deposition require widespread application of ILWAS theory within the Adirondack region and other potentially acid-sensitive areas.     

Big Moose Basin: simulation of response to acidic deposition

The ILWAS model has been enhanced for application to multiple-lake hydrologic basins. This version of the model has been applied to the Big Moose basin, which includes Big Moose Lake and its tributary streams, lakes, and watersheds. The basin, as defined, includes an area of 96 km², with over 20 lakes and ponds, and 70 km of streams. Hydrologic and chemical calibrations have been made using data from seven sampling stations. When total atmospheric sulfur loading to the basin is halved, the model predicts, after four years of simulation, a decreasing sulfate concentration and to a lesser extent a rising alkalinity at Big Moose Lake outlet. At the end of four years, the results show an increase in pH of 0.1 to 0.5 pH units depending upon season.