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PubMed2004

The well-tempered auxiliary-field Monte Carlo.

The auxiliary-field Monte Carlo (AFMC) is a method for computing ground-state and excited-state energies and other properties of electrons in molecules. For a given basis set, AFMC is an approximation to full-configuration interaction and the accuracy is determined predominantly by an inverse temperature "beta" parameter. A considerable amount of the dynamical correlation energy is recovered even at small values of beta. Yet, nondynamical correlation energy is inefficiently treated by AFMC. This is because the statistical error grows with beta, warranting increasing amount of Monte Carlo sampling. A recently introduced multi-determinant variant of AFMC is studied, and the method can be tuned by balancing the sizes of the determinantal space and the beta-parameter with respect to a predefined target accuracy. The well-tempered AFMC is considerably more efficient than a naive AFMC. As a welcome "byproduct" low lying excitation energies of the molecule are supplied as well. We demonstrate the principles on dissociating hydrogen molecule and torsion of ethylene where we calculate the (unoptimized) torsional barrier and the vertical singlet-triplet splitting.

Journal Article↗
PubMed2005

Optimal allocation of replicas in parallel tempering simulations.

We have studied the efficiency of parallel tempering simulations for a variety of systems including a coarse-grained protein, an atomistic model polypeptide, and the Lennard-Jones fluid. A scheme is proposed for the optimal allocation of temperatures in these simulations. The method is compared to the existing empirical approaches used for this purpose. Accuracy associated with the computed thermodynamic quantities such as specific heat is also computed and their dependence on the trial-exchange acceptance rate is reported.

Bacterial Proteins↗
PubMed1994

Ovulatory activity, hormonal induction of ovulation and fertility of young Cashmere and Angora female goats in a temperate environment.

Reproductive parameters of young Cashmere and Angora goats born between 1988 and 1990 and grazed on temperate pastures in southern Australia were examined with a view to reducing the age of first breeding. Females born in August or October of 1989 and 1990 were examined each month by laparoscopy to determine natural ovulatory activity when 6-19-months old. Cashmeres commenced ovulating as young as 7 months of age or as light as 12 kg. Almost all Cashmeres were ovulating by 8-10 months of age at a liveweight of at least 18 kg, and their breeding season extended from April to October. By comparison with Cashmeres, Angoras grew more slowly, fewer ovulated, they commenced ovulation later, their ovulation rates were lower and their breeding season was shorter. A stratified sample of these females was injected with 200 I.U. or 400 I.U. of pregnant mare serum gonadotrophin (PMSG) after treatment with controlled internal drug release (CIDR) devices for 16-18 days to induce ovulation at 6, 9, 12, 15 and 19 months of age. Ovulation rates after CIDR-PMSG treatment were higher for Cashmeres than for Angoras and tended to be higher for females injected with 400 I.U. PMSG than 200 I.U. PMSG. The proportion of females remaining anovulatory after exogenous hormonal treatment was higher for Angoras than for Cashmeres (38% and 10% respectively) but it was not affected by the dose of PMSG or age. For kids born in 1989, the kidding rates to insemination (with follow-up mating) after CIDR-PMSG treatment for 8-month-old and 20-month-old Cashmeres (in the breeding season) were similar (75.0% and 83.8% respectively) but the rate for 14-month-old Cashmeres was only 10.0% (in the non-breeding period). The kidding rates for Angoras bred at 8, 14 and 20 months of age were 8.4%, 20.0% and 30.0% respectively. Ovulatory activity and fertility in the non-breeding period, with or without CIDR-PMSG treatment, did not improve with melatonin treatment.

Animals↗
PubMed2004

Neutrality, niches, and dispersal in a temperate forest understory.

A fundamental goal of ecology is to understand what controls the distribution and abundance of species. Both environmental niches and trade-offs among species in dispersal and competitive ability have traditionally been cited as determinants of plant community composition. More recently, neutral models have shown that communities of species with identical life-history characteristics and no adaptation to environmental niches can form spatial distribution patterns similar to those found in nature, so long as the species have a limited dispersal distance. If there is a strong correlation between geographic distance and change in environmental conditions, however, such spatial patterns can arise through either neutral or niche-based processes. To test these competing theories, we developed a sampling design that decoupled distance and environment in the understory plant communities of an old-growth, temperate forest. We found strong evidence of niche-structuring but almost no support for neutral predictions. Dispersal limitation acted in conjunction with environmental gradients to determine species' distributions, and both functional and phylogenetic constraints appear to contribute to the niche differentiation that structures community assembly. Our results indicate that testing a neutral hypothesis without accounting for environmental gradients will at best cause unexplained variation in plant distributions and may well provide misleading support for neutrality because of a correlation between geographic distance and environment.

Analysis of Variance↗
PubMed2005

Energy landscape of amyloidogenic peptide oligomerization by parallel-tempering molecular dynamics simulation: significant role of Asn ladder.

Recent evidence suggests that amyloidogenic oligomers may be the toxic species in cell cultures. Thus, it is crucial to understand their structure and oligomerization mechanism in atomistic detail. By employing tens of fast central processing units and an advanced phase-space sampling algorithm, parallel-tempering molecular dynamics, we have explored the energy landscape of amyloidogenic peptide oligomerization in explicit water. A pentapeptide, DFNKF, derived from human calcitonin and its mutant, DFAKF, was simulated with a total simulation time of approximately 500 ns. The detailed oligomerization process of a DFNKF parallel beta-sheet formation at 300 K has been characterized. The assembly of a parallel beta-sheet from the amorphous state mainly occurs via a "bottleneck" channel where the interstrand Asn-Asn stacking is the major interaction. The interactions of Asn-Asn stacking include both backbone and side-chain hydrogen bonds. The Asn-Asn interactions work like "glue" by sticking the DFNKF strands together and assist the "on-pathway" oligomerization. The Asn-Asn stacking observed here is similar to the Asn ladder commonly found in globular beta-helix proteins. A control run shows that when Asn is mutated to Ala, the stability and population of the DFAKF parallel beta-sheet is decreased. Furthermore, our in vitro mutagenesis experiments show that the ability of DFAKF peptides to form amyloid fibrils is significantly reduced, in agreement with the simulations. Knowledge of the energy landscape of oligomerization may provide hints for rational drug design, preventing amyloid-associated diseases.

Algorithms↗
PubMed1971

Comparison of faunal equilibrium turnover rates on a tropical island and a temperate island.

Rates of immigration and extinction of bird species on a tropical island, Karkar in the southwest Pacific Ocean, have been estimated from surveys made in 1914 and in 1969. Compared to a temperate-zone island of similar size and isolation (Santa Cruz off southern California), Karkar has a similar extinction rate, but a lower immigration rate expressed as a fraction of the mainland species pool, due to the sedentariness of many tropical forest birds. The probability of extinction is highest for species that are rare (due to narrow habitat requirements, large territory size, competition, recency of colonization, or marginal suitability of habitat), species with "in-and-out" tactics, and populations on small islands.

Journal Article↗
PubMed1976

Classification of irreducible tempered representations of semisimple Lie groups.

For each connected real semisimple matrix group, one obtains a constructive list of the irreducible tempered unitary representations and their characters. These irreducible representations all turn out to be instances of a more general kind of representation, here called basic. The result completes Langland's classification of all irreducible admissible representations for such groups. Since not all basic representations are irreducible, a study is made of character identities relating different basic representations and of the commuting algebra for each basic representation.

Journal Article↗
PubMed1999

Isolation of a temperate bacteriophage encoding the type III effector protein SopE from an epidemic Salmonella typhimurium strain.

Salmonella typhimurium employs the specialized type III secretion system encoded in pathogenicity island 1 (SPI1) to translocate effector proteins into host cells and to modulate host cell signal transduction. The SPI1 type III system and the effector proteins are conserved among all salmonellae and are thought to be acquired by horizontal gene transfer. The genetic mechanisms mediating this horizontal transfer are unknown. Here, we describe that SopE, a SPI1-dependent translocated effector protein, is present in relatively few S. typhimurium isolates. We have isolated a temperate phage that encodes SopE. Phage morphology and DNA hybridization, as well as partial sequence information, suggest that this phage (SopEPhi) is a new member of the P2 family of bacteriophages. By lysogenic conversion this phage can horizontally transfer genes between different S. typhimurium strains. Strikingly, most of the isolates harboring SopEPhi belong to the small group of epidemic strains of S. typhimurium that have been responsible for a large percentage of human and animal salmonellosis and have persisted for a long period of time. Our data suggest that horizontal transfer of type III dependent effector proteins by lysogenic infection with bacteriophages (lysogenic conversion) may provide an efficient mechanism for fine-tuning the interaction of Salmonella spp. with their hosts.

Bacterial Proteins↗
PubMed2000

Catalytic tempering: A method for sampling rough energy landscapes by Monte Carlo.

A new Monte Carlo algorithm is presented for the efficient sampling of the Boltzmann distribution of configurations of systems with rough energy landscapes. The method is based on the introduction of a fictitious coordinate y so that the dimensionality of the system is increased by one. This augmented system has a potential surface and a temperature that is made to depend on the new coordinate y in such a way that for a small strip of the y space, called the "normal region," the temperature is set equal to the temperature desired and the potential is the original rough energy potential. To enhance barrier crossing outside the "normal region," the energy barriers are reduced by truncation (with preservation of the potential minima) and the temperature is made to increase with ||y ||. The method, called catalytic tempering or CAT, is found to greatly improve the rate of convergence of Monte Carlo sampling in model systems and to eliminate the quasi-ergodic behavior often found in the sampling of rough energy landscapes.

Journal Article↗
PubMed1979

The development of Onchocerca volvulus in two temperate blackfly species, Simulium ornatum Meigen and Simulium lineatum Meigen.

In view of the promise shown by temperate simuliids for laboratory colonization, the ability of Simulium ornatum and S. lineatum to support the development of Onchocerca volvulus was investigated. An injection technique is described for the introduction of O. volvulus microfilariae from a chimpanzee into female simuliids in the absence of a bloodmeal. RPMI 1640 medium, with penicillin, streptomycin and foetal calf serum, proved satisfactory as an inoculation medium. Third stage larvae were obtained in both S. ornatum and S. lineatum after seven days at 27 degrees C. The rate of development of the parasite in S. ornatum is recorded.

Animals↗
PubMed1984

Peritrophic membrane formation in three temperate simuliids, Simulium ornatum, S. equinum and S. lineatum, with respect to the migration of onchocercal microfilariae.

Engorged females of three temperate simuliid species, Simulium ornatum, S. lineatum and S. equinum, were collected immediately after their bloodfeeds from a cow host. Midguts were dissected out at selected time intervals thereafter, from two minutes to 24 hours post engorgement (p.e.) and peritrophic membrane formation observed. There was an initial rapid secretion of peritrophic membrane (PM) material from the midgut epithelium. The peritrophic membrane produced is Type 1, being formed by delamination from the entire midgut epithelium. This secretory phase continued for approximately two hours p.e. in all three species and was followed by a period of organization within the membrane. At between 12 and 24 hours p.e., the PM appeared more organized and was associated with the formation of several distinct laminae in both S. ornatum and S. lineatum, although in S. equinum it consisted of only a single homogenous layer. Both the rate of secretion and the resulting morphological appearance of the PM appeared species-specific and there was great variation in its thickness in all three species at all time intervals examined. It is suggested that microfilariae penetrate the PM during the initial period of its secretion before it has condensed to form a distinct structure. Furthermore, the migration of microfilariae may be restricted to, or enhanced by, the presence of very thin areas within the membrane where erythrocytes lie almost adjacent to the midgut epithelium.

Animals↗
PubMed2004

Short-term sequestration of slurry-derived carbon into particle size fractions of a temperate grassland soil.

Surface application of animal wastes in intensive grassland systems has caused growing environmental problems during the last decade and, therefore, increasing public and scientific concern. In the present study we examined if the natural abundance 13C stable isotope tracer techniques could be used to investigate a poorly defined aspect of waste application, i.e. incorporation of slurry-derived C and its distribution in soil organic matter (SOM) fractions with different turnover times of a pasture soil. C3 and C4 slurries (delta13C(V-PDB) = -30.7/1000 and -21.3/1000, respectively) from cows fed either on a maize (C4) or perennial ryegrass (C3) diet were applied to a C3 soil with a delta13C value of (-30.0+/-0.2)/1000. The cattle slurry was applied at 50 m3 ha(-1). Coarse sand, fine sand, silt, clay and fine clay were isolated from bulk soil samples (0-2 cm depth), freeze-dried and ground prior to total organic C (TOC) using elemental analysis and 13C natural abundance analysis by isotope-ratio mass spectrometry. The stable isotope tracer technique did allow to quantify the short-term sequestration of slurry-derived C in particle-size fractions of the grassland soil. Slurry-derived carbon was sequestered in various amounts in the five particle-size fractions, but most of it was sequestered in the coarse sand fraction during the two week experiment. The preferential input into the coarse sand fraction suggests that only the larger particulate slurry-derived materials were trapped into the soil during the experimental period. Less than 40% of the applied slurry-derived C was sequestered into the soil, suggesting a potential for large losses into the wider environment. The practice of surface spreading of slurry to temperate grassland soils is clearly not efficient, and improvements in slurry application methods, such as incorporation directly into the soil, should therefore be encouraged.

Animals↗
PubMed2004

Stable isotope biogeochemistry of the sulfur cycle in modern marine sediments: I. Seasonal dynamics in a temperate intertidal sandy surface sediment.

A biogeochemical and stable isotope geochemical study was carried out in surface sediments of an organic-matter poor temperate intertidal sandy surface sediment (German Wadden Sea of the North Sea) to investigate the activity of sulfate-reducing bacteria and the dynamics of the vertical partitioning of sedimentary sulfur, iron, and manganese species in relation to the availability of total organic carbon (TOC) and mud contents. The contents and stable isotopic compositions ((34)S/(32)S) of total reduced inorganic sulfur species (TRIS) and dissolved sulfate were measured. Maximum oxygen penetration depths were estimated from the onset of a blackening of the sediments due to FeS accumulation and ranged from 5 to 10 mm below surface (mmbsf). A zone of relatively moderate relative organic-matter enrichment was found between 5 and 20 mmbsf leading to enhanced activities of sulfate-reducing bacteria with sulfate-reduction rates (SRR) up to 350 nmol cm(-3) d(-1). Below this zone, microbial SRR dropped significantly. Depth integrated SRR seem to depend not only on temperature but also on the availability of reactive organic matter. The sulfur-isotopic composition of TRIS was depleted in (34)S by 33-40 per thousand with respect to coexisting dissolved sulfate (constant at about +21 per thousand vs. Vienna-Canyon Diablo Troilite (V-CDT)). Since sulfate reduction is not limited by dissolved sulfate (open system), depth variations of the isotopic composition of TRIS reflect changes in overall isotope effect due to superimposed microbial and abiotic reactions. Most of the solid-phase iron and manganese was bonded to (non-reactive) heavy minerals. However, a layer of reactive Fe(III) and Mn(IV) oxi(hydroxi)des was found in the uppermost sediment section due to re-oxidation of dissolved Fe(II) and Mn(II) species at the sediment-water interface. Metal cycling below the surface is at least partially coupled to intense sulfur cycling.

Carbon↗
PubMed1964

THE ROLE OF TEMPERATE BACTERIOPHAGE IN THE PRODUCTION OF ERYTHROGENIC TOXIN BY GROUP A STREPTOCOCCI.

Non-lysogenic, non-toxinogenic Group A streptococci when infected by temperate bacteriophages isolated from known scarlatinal toxin-producing strains acquire the capacity to form erythrogenic toxin. This toxin causes a characteristic erythematous reaction in the skin of rabbits and is readily neutralizable by standard scarlatinal antitoxins. The production of toxin appears to be related to the synthesis of mature phage particles since ultraviolet enhancement of phage production results in a concomitant increase in toxin titer. In contrast, there is no increase in the production of another extracellular product, deoxyribonuclease, by these lysogenized streptococci. Furthermore, cellular disruption studies indicate that the toxin probably does not exist in a preformed state within the cell. Double diffusion reactions in agar indicate that a newly formed protein appears in the lysogenic culture filtrate and is absent in the non-lysogenic filtrates.

Animals↗
PubMed2005

Temperature influences whole-animal rates of metabolism but not protein synthesis in a temperate intertidal isopod.

The effects of temperature on two important biological rate processes, whole-body rates of oxygen uptake (M dot o2) and protein synthesis (k(s)), were investigated in the temperate intertidal isopod Ligia oceanica at two different times of the year. Animals were collected in January (winter) and June (summer) and either subjected to an acute temperature change after 24 h (acclimatized) or acclimated to various temperatures for 4 wk. In both cases, M dot o2 increased with temperature, with a Q(10) of 2.2 between 5 degrees and 20 degrees C, but increased in thermal sensitivity at 25 degrees C. Winter isopods were characterized by significantly higher M dot o2 levels, greater thermal sensitivities, and lower thermal tolerances than summer animals. Seasonal differences in M dot o2 persisted after acclimation, indicating that temperature alone was not responsible for the changes. In sharp contrast, whole-body k(s) showed no variation with temperature, although overall rates decreased upon acclimation. In acclimatized animals, k(s) was higher in the summer than in the winter. After acclimation, a compensatory increase in RNA capacity in winter animals reversed this situation. The temperature independence of whole-body k(s) in L. oceanica could ensure survival in a highly liable thermal environment, as thermal tolerances of intertidal invertebrates are thought to be more closely related to protein than to energy metabolism.

Acclimatization↗
PubMed2006

Whole blood-oxygen binding properties of four cold-temperate marine fishes: blood affinity is independent of pH-dependent binding, routine swimming performance, and environmental hypoxia.

The relationship between whole blood-oxygen affinity (P(50)) and pH-dependent binding (i.e., cooperativity and the Bohr [ Phi ] and Root effects) was examined statistically under standardized conditions (10.0 degrees Celsius) in four unrelated cold-temperate marine fishes that differ widely in their swimming performance and their expected responses to hypoxia: cod (Gadus morhua), herring (Clupea harengus), mackerel (Scomber scombrus), and plaice (Pleuronectes platessa). An unexpected difference in blood-oxygen affinity was found (herring>plaice>mackerel>cod), and this was independent of both swimming performance and the predicted low O(2) response of each species. The ecotype of the four marine species was also unrelated to pH-dependent binding because no difference in the Bohr effect was apparent ( Phi varied insignificantly from -0.90 to -1.06), and differences in the magnitude of the cooperative binding reaction were associated only with the presence of the Root effect. Although several reviews propose a generalized link between blood-oxygen affinity and pH-dependent binding, our results advise against overestimating the adaptive functional properties of hemoglobin across unrelated species.

Animals↗
PubMed1987

Physical analysis of PB2, a temperate bacteriophage of Agrobacterium tumefaciens.

We have constructed a detailed physical map of PB2, a temperate bacteriophage of Agrobacterium tumefaciens. The restriction endonucleases Bam HI (3 sites), Eco RI (22 sites), Hind III (19 sites), Hpa I (5 sites), Xba I (1 site), and Xho I (1 site) were used to elucidate the map of infectious PB2 DNA. The map was generated by reciprocal sequential digestions and analysis of partial digestion products of isolated restriction fragments. We have determined the genome size as 66.35 +/- 1.71 kb. The potential of PB2 as a phage-based shuttle vector for the A. tumefaciens-plant transformation system is discussed.

Bacteriophages↗
PubMed2004

Modelling seedling growth rates of 18 temperate arable weed species as a function of the environment and plant traits.

BACKGROUND AND AIMS: The early growth rate of seedlings in the exponential phase is an important eco- physiological trait in crop/weed competition models based on assessments of relative weed green area. An understanding of the role of various plant traits in determining early growth rate may also be useful for identifying contrasting weed strategies for establishment before canopy closure. METHODS: The response of seedling relative growth rate (RGR) to the environment was measured in outdoor sand beds in the autumn and the spring for 18 temperate annual weed species and two crops. Seedling growth was modelled using thermal time and effective day-degrees (combining the effect of temperature and radiation). The contribution of various plant traits in determining variability in RGR was investigated using regression analysis. KEY RESULTS: The effective day-degree model was more effective for describing early weed growth than thermal time. Variability in RGR measured in the autumn was largely determined by differences between the species in net assimilation rate (NAR), whereas in the spring leaf area ratio (LAR) played a larger part. There were differences between the broadleaf and grass species in the relative contribution of NAR and LAR to RGR in both seasons. RGR in the spring was negatively correlated with initial seedling size. CONCLUSIONS: The parameters derived in this study can be used to calibrate empirical models of crop yield loss based on relative weed green area to different growing seasons and assessment dates. The grass weeds, which tended to have large seeds, had a higher investment in roots in the seedling stage, potentially making them more competitive later in the season when resources become limiting.

Environment↗