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.     

Potential for mating disruption of Sparganothis sulfureana (Lepidoptera: Tortricidae) in cranberries.

The feasibility of disrupting mating of Sparganothis fruitworm with a sprayable microencapsulated formulation of (E)-11-tetradecenyl acetate (E11-14:Ac), the major pheromone component, was evaluated in New Jersey during 1996 and 1997 seasons. In both years, application of encapsulated E11-14:Ac, at 25-187.5 g (AI)/ha, reduced the incidence of mating of virgin females placed in treated plots relative to those placed in control plots. Pheromone trap catches were lower in pheromone treated plots, indicating that fewer male moths were able to locate the traps in treated plots. Larval density and fruit damage were significantly lower in plots treated with 62.5,125, or 187.5 g (AI)/ha of pheromone than in the untreated control. Air and foliage samples were collected to determine the air titers and foliage residuals of E11-14:Ac throughout the adult flight during 1996 and 1997. E11-14:Ac levels in air and foliage samples, declined sharply one wk after the pheromone application. However, detectable levels of E11-14:Ac were present in both air and foliage samples throughout the 3- to 4-wk period after the pheromone application. Multiple applications of pheromone at lower rates may be more effective in maintaining pheromone levels than a single dose at higher rates. These results suggest that mating disruption is a promising strategy to manage Sparganothis fruitworm in cranberries.     

Growth and analysis of crystal forms of toxic shock syndrome toxin 1

Native toxic shock syndrom toxin 1 (TSST-1) purified from Staphylococcus aurius has been crystallized in four different forms. The highest resolution data (2.05 Å) was collected from orthorhombic crystals belonging to the space group C222₁. The unit cell dimension are a = 108.7 Å, b = 177.5 Å, c = 97.6 Å. Rotation function analysis of this from indicates that there is trimer of toxin molecules in the asymmetric unit with a local 3-fold axis parallel to the crystallographic c axis. Crystals of a double mutant of TSST-1 have been grown which has a single molecule in the asymmetric unit and diffract to 1.9 Å. The space group is P2₁ with unit cell parameters of a = 44.4 Å, b = 34.0 Å, c = 55.2 Å, β = 93.0°. © 1993 Wiley-Liss, Inc.     

Organization of the mitochondrial Cob 2 pseudogene in different lines of rice

In the fertile rice line IR 36 there are two copies of the apocytochrome b (cob) gene: a functional copy, cob 1, and a pseudogene, cob 2 (Kaleikau et al. 1992). In a survey of diverse rice lines, we found that cob 2 was absent in the wild abortive(WA)-type cytoplasmic male-sterile cytoplasm, but was present in the fertile lines. While cob 1 was conserved among all the lines, fertile and sterile, the cob 2 region was different in the fertile lines tested. The 5′ regions of most cob 2 loci were similar to cob 1 (about 4 kb of the flanking region and most of the coding region), but the 3′ region varied among different fertile lines. The point of divergence, the break-point, from the cob 1 sequence was conserved in all the cob 2 regions tested. In all the cob 2 regions, this break-point seems to be linked to the variable region of cob 2 through a conserved 192-bp segment, which is not a part of cob 1. It is proposed that the cob 2 regions could have been produced by recombination or insertion events involving cob 1 and the 192-bp segment which is present at different locations in the mitochondrial genomes of the various rice lines.     

Optimal local propensities for model proteins

Lattice models of proteins were used to examine the role of local propensities in stabilizing the native state of a protein, using techniques drawn from spin-glass theory to characterize the free-energy landscapes. In the strong evolutionary limit, optimal conditions for folding are achieved when the contributions from local interactions to the stability of the native state is small. Further increasing the local interactions rapidly decreases the foldability. © 1995 Wiley-Liss, Inc.     

A new technique of depositing phospholipid bilayers on quartz surfaces: its use in membrane spin-label studies

We have developed a new improved technique termed the parallel-beam spattering (PBS) method for depositing phospholipid bilayers on quartz surfaces. This technique involves atomizing the phospholipid mixture with a stream of nitrogen gas and passing this atomized mixture through two orifices separated by a distance to achieve a parallel beam of atomized particles before deposition on the quartz plate. A static electric field can easily be applied to the quartz surface. Also a goniometer of new design has been constructed to allow precise positioning of the deposited phospholipid bilayers with reference to the magnetic field. We have utilized the PBS method to deposit phosphatidylcholine/nitroxyl labeled cholestane mixtures on quartz plates and have found that hydrated bilayers of these mixtures yield ESR spectra with essentially the same characteristics as those obtained using more conventional techniques. The distinct advantage of the new technique for depositing bilayers is that there is no spectral anomaly present which usually is present when the more conventional method of depositing bilayers is used. The spectral anomaly is apparently caused by a portion of the bilayers aligned in directions not directly parallel to the quartz surface. For precision work the spectral anomaly is unacceptable. It is not observed with the new PBS method which has yielded highly reproducible results.     

Labelling the blueberry leaftier, Croesia curvalana with foliar sprays of rubidium chloride

The feasibility of labelling blueberry leaftier by rearing the larvae on blueberry plants treated with foliar sprays of rubidium chloride (RbCl) at concentrations of 1000, 5000, 10 000 and 20 000 ppm were assessed. RbCl sprays above 5000 ppm significantly reduced survivorship to adult stage. The adult longevity, fecundity and mating were not affected when the larvae were reared on foliage treated with 5000 ppm RbCl solution. Reciprocal matings of 5000 ppm treated moths with untreated moths revealed transfer of label above the 0.1 µg Rb/insect threshold level from treated males to untreated females (in 8 out of 13 pairs) and vice versa (in 1 out of 9 pairs). Considerable loss of Rb (56–64%) occurred from the leaves over a 15 day period. All of the moths and pupae collected from the RbCl treated plots in 1989 and 1990 respectively, had a Rb content higher than the threshold level. In a preliminary dispersal study, marked male and female moths were found in sweepnet samples collected 20 and 60 m from the centre of the treated field. Labelled male moths were also captured in pheromone traps arranged in a circle, 40 m from the treated plot.