Effective water model for Monte Carlo simulations of proteins

We present an effective theory for water. Our goal is to formulate on accurate model for the effects of solvation on protein dynamics, without incurring the huge computational cost and the slow temporal evolution typical of molecular dynamics simulations of liquids. We replace the individual water molecules in an all-atom potential with a local dielectric density field, with self interactions given by the Landau-Ginzburg free energy and external interactions by Lennard-Jones forces at the surface of the protein atoms. We explore conformational space with finite temperature Monte Carlo dynamics, using parallel Langevin and Fourier acceleration algorithms well suited to data-parallel computer architectures such as the Connection Machine. To establish the validity of our approximations, we compare our electrostatic contribution to the solvalion energy with the results of Lim, Bashford, and Karplus using a conventional static continuum dielectric cavity model, and the non electrostatic contributions with estimates of hydrophohic surface free energy. Our model can also accommodate ionic charges and temperature fluctuations, We propose future investigations extending our effective theory of solvation to include explicit orientational entropy and hydroxen-bonding terms. © 1995 John Wiley & Sons, Inc.     

Water balance of conifer logs in early stages of decomposition

Seasonal and long-term changes in the water balance of conifer logs during the first 8 years of decomposition were studied in an old-growth Pseudotsuga/Tsuga forest in the Oregon Cascade Mountains. Measurements were made of the moisture content of outer bark, inner bark, sapwood, and heartwood and of the flow of water into and out of logs of four species (Abies amabilis, Pseudotsuga menziesii, Thuja plicata, and Tsuga heterophylla). After the logs had decomposed from 1 to 2 years, 38–47% of the canopy throughfall landing upon them ran off the surface, 29–34% leached from the bottom, and 21–30% was absorbed and evaporated. After 8 years of decomposition, water entering and then leaching from logs increased 1.3 times while runoff decreased a similar amount. The proportion of water stored by and evaporated from logs in this study indicates that in old growth forests they may intercept 2–5% of the canopy throughfall to the forest floor and that, even in early stages of decomposition, they may affect the hydrological cycle of Pacific Northwest old-growth forests.This is paper 2945 of the Forest Research Laboratory, Oregon State University, Corvallis     

Absence of Linkage Between Human Obesity and the Mouse Agouti Homologous Region (20q11.2) or Other Markers Spanning Chromosome 20q

XU, WEIZHEN, DANIELLE R REED, YUAN DING AND R ARLEN PRICE. Absence of linkage between human obesity and the mouse agouti homologous region (20q11.2) or other markers spanning chromosome 20q. Obes Res. Mutant alleles of the agouti gene cause obesity in the mouse and the homologous gene in humans has been mapped to chromosome 20q11.2. An allelic variant of the agouti gene could account for obesity in humans and we tested this hypothesis by genotyping 210 sibling pairs from 45 families segregating an obesity phenotype. Using sibling pair linear regression analysis, evidence for linkage between obesity and markers flanking the agouti locus and other markers spanning chromosome 20q was assessed. We found no correlation between identity-by-descent at these markers and obesity differences within pairs. In the mouse, obesity caused by mutations of the agouti gene develops later in life, so a subset of families with adult-onset obesity were also tested for linkage, with negative results. Although it is not possible to exclude alleles of the agouti gene as a contributor to obesity in humans, the absence of positive linkage in this study suggests that either the agouti gene has small effects or the allele frequency is low.     

Evidence of Increased Oxidative Damage in Both Sporadic and Familial Amyotrophic Lateral Sclerosis

Abstract: Some cases of autosomal dominant familial amyotrophic lateral sclerosis (FALS) are associated with mutations in the gene encoding Cu/Zn superoxide dismutase (SOD1), suggesting that oxidative damage may play a role in ALS pathogenesis. To further investigate the biochemical features of FALS and sporadic ALS (SALS), we examined markers of oxidative damage to protein, lipids, and DNA in motor cortex (Brodmann area 4), parietal cortex (Brodmann area 40), and cerebellum from control subjects, FALS patients with and without known SOD mutations, SALS patients, and disease controls (Pick's disease, progressive supranuclear palsy, diffuse Lewy body disease). Protein carbonyl and nuclear DNA 8-hydroxy-2'-deoxyguanosine (OH⁸dG) levels were increased in SALS motor cortex but not in FALS patients. Malondialdehyde levels showed no significant changes. Immunohistochemical studies showed increased neuronal staining for hemeoxygenase-1, malondialdehyde-modified protein, and OH⁸dG in both SALS and FALS spinal cord. These studies therefore provide further evidence that oxidative damage may play a role in the pathogenesis of neuronal degeneration in both SALS and FALS.     

Plant compensation, natural biological control, and herbivory by Aphis gossypii on pre-reproductive cotton: the anatomy of a non-pest

Crop plant compensation for herbivory and the population dynamics of herbivores are two key elements in defining an herbivore's pest status. We studied the dynamics of natural, unmanipulated populations of the aphid Aphis gossypii on seedling plantings of cotton, Gossypium hirsutum and Gossypium barbadense, over a 4-year period in California's Central Valley. Aphid populations colonized all plantings, but reached densities in excess of 0.5 aphids/leaf during only one year (1991), when outbreaks occurred. Outbreak populations were, however, ephemeral; predation and parasitism suppressed aphid populations prior to the initiation of flower bud production, when cotton plant growth may become photosynthate-limited. Effective natural biological control was observed despite the action of hyperparasitoids and the heavy mortality of immature parasitoids that occurred when predators consumed parasitized aphids.We conducted manipulative experiments during 1991 and 1992 to quantify the ability of pre-reproductive G. hirsutum to compensate for aphid herbivory. In 1991 aphid populations in the high-damage treatment reached densities as high as any observed naturally during the past 37 years. Damage symptoms were severe: leaf area was reduced by up to 58% and total above-ground plant biomass was reduced by 45%. By the time of crop harvest, however, plants had compensated fully for the early damage in each of the three traits that define cotton's economic value: the timing of crop maturation, the yield of cotton fiber, and the quality of cotton fiber. Aphid feeding damage did, however, produce some changes in plant architecture that persisted throughout the growing season, including a decrease in the number of vegetative branches. In 1992 aphid populations and associated damage were much lighter, but the qualitative responses to herbivory were consistent with those observed in 1991. Plant compensation for early damage was complete for economically significant measures, and vegetative branch production was again suppressed in mature cotton plants. There was no evidence for a change in the suitability of G. hirsutum as a host plant for A. gossypii as a result of early damage (induced resistance).We conclude that pre-reproductive G. hirsutum, which has not yet begun strong allocations to reproductive structures or established architectural complexity, has retained effective means of compensating for herbivory. In contrast to other systems exhibiting strong compensation, G. hirsutum appears to compensate in part by enhancing apical dominance. The recognition of early-season A. gossypii as non-pests is critical to the sustainability of cotton production, because it will allow growers to forego pesticide applications that accelerate the evolution of pesticide-resistance and disrupt natural communities of predators and parasitoids.Deceased, formerly at the Shafter Research Station, 17053 Shafter Ave., Shafter, CA 93263, USA     

Nitrite accumulation in a sequencing batch reactor during the aerobic phase of biological nitrogen removal

Accumulation of nitrite occurred during the aerobic phase of a sequencing batch reactor (SBR) operating to remove nitrogen from synthetic waste water. Although present, heterotrophic nitrifiers were not involved in the nitrification of the SBR. The activity of autotrophic nitrite oxidizers was reduced in the SBR where free ammonia was the main inhibitor for the nitrite oxidation. Nitrite build-up in the SBR was reduced when the aerobic phase was extended. All the ammonia could be oxidized when the aerobic phase was longer than four hours. The accumulated nitrite and nitrate were removed completely in the post-anoxic phase.     

Electron tunneling in proteins: role of the intervening medium

Analysis of electron-transfer (ET) kinetics data obtained from experiments on Ru-modified proteins (azurin, cytochrome c, myoglobin) and the bacterial photosynthetic reaction center reveals that distant donor-acceptor electronic couplings depend upon the secondary structure of the intervening polypeptide matrix. The β-sheet azurin structure efficiently and isotropically mediates coupling with an exponential distance-decay constant of 1.1?Å^–1. The experimentally derived distance-decay constant of 1.4?Å^–1 for long-range ET in myoglobin and the reaction center suggests that hydrogen-bond couplings are weaker through α helices than across β sheets. The donor-acceptor interactions of systems with comparable tunneling energies fall into two coupling zones: the β zone (bounded by distance-decay constants of 0.9?and 1.15 Å^–1) includes all the β-sheet (azurin) couplings and all but one coupling in cytochrome c; the α zone (boundaries: 1.25 and 1.6?Å^–1) includes less strongly coupled donor-acceptor pairs in myoglobin and the reaction center as well as a relatively weakly coupled pair in cytochrome c.     

Molecular and phenotypic analysis of the S. cerevisiae MNN10 gene identifies a family of related glycosyltransferases

The Saccharomyces cerevisiae mnn10 mutant is defective in thesynthesis of N-linked oligosaccharides (Ballou et al., 1989).This mutation has no effect on O-linked sugars, but resultsin the accumulation of glycoproteins that contain severely truncatedN-linked outer-chain oligosaccharides. We have cloned the MNN10gene by complementation of the hygromycin B sensitivity conferredby the mutant phenotype. Sequence analysis predicts that Mnn10pis a 46.7 kDa type II membrane protein with structural featurescharacteristic of a glycosyltransferase. Subcellular fractionationdata indicate that most of the Mnn10 protein cofractionateswith Golgi markers and away from markers for the endoplasmicreticulum (ER), suggesting Mnn10p is localized to the Golgicomplex. A comparison of the Mnn10 protein sequence to proteinsin the two different databases identified five proteins thatare homologous to Mnn10p, including a well characterized Schizosaccharomycespombe