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PubMed2004

Seasonal dynamics of phytoplankton and planktonic protozoan communities in a northern temperate humic lake: diversity in a dinoflagellate dominated system.

Species diversity and richness, and seasonal population dynamics of phytoplankton, planktonic protozoa, and bacterioplankton sampled from the epilimnion of Crystal Bog in 2000, were examined in order to test the hypothesis that these groups' diversity and abundance patterns might be linked. Crystal Bog, a humic lake in Vilas County, Wisconsin, is part of the North Temperate Lakes Long-Term Ecological Research Site. Phytoplankton and planktonic protozoa were identified and enumerated in a settling chamber with an inverted microscope. Bacterial cells were enumerated with the use of fluorescence 4', 6'-diamidino-2-phenylindole (DAPI)-staining procedures, and automated ribosomal intergenic spacer analysis (ARISA) was used to assess bacterioplankton diversity. Bacterial cell counts showed little seasonal variation and averaged 2.6 x 10(6) cells/mL over the ice-free season. Phytoplankton and planktonic protozoan numbers varied by up to two orders of magnitude and were most numerous in late spring and summer. Dinoflagellates largely dominated Crystal Bog throughout the ice-free period, specifically Peridiniopsis quadridens in the spring, Peridinium limbatum in summer, and Gymnodinium fuscum and P. quadridens in fall. Brief blooms of Cryptomonas, Dinobryon, and Synura occurred between periods of dinoflagellate domination. The dominant dinoflagellate, Peridinium limbatum, was calculated to have a growth rate of 0.065 day(-1) and a doubling time of 10.7 days. Heterotrophic nanoflagellates (HNFs) were a consistent component of the planktonic protozoa; seasonal patterns were determined for three genera of HNFs (Monosiga, Bicosoeca, and Desmarella moniliformis). Three genera of ciliates (Coleps, Strobilidium, and Strombidium) comprised the greater part of the planktonic protozoa in Crystal Bog. The number of species of planktonic protozoa was too low to calculate a diversity index. Shannon-Weaver diversity indices for phytoplankton and bacterioplankton in the epilimnion followed very similar seasonal patterns in this lake, supporting the hypothesis that in freshwaters, diversity patterns of these groups are linked.

Animals↗
PubMed2005

Nutrient and temperature limitation of bacterioplankton growth in temperate lakes.

Limitation of bacterioplankton production by nutrients and temperature was investigated in eight temperate lakes in summer. Six of the lakes were resampled in autumn. The lakes differ in nutrient content, water color, and concentration of dissolved organic carbon. Nutrients (phosphorus, nitrogen, and organic carbon) were added alone and in all possible combinations to filtered lake water inoculated with bacteria from the lake. After incubation for 36-40 h at in situ temperatures (ranging from 7 to 20 degrees C), the response in bacterioplankton production was determined. The effect of increased temperature on bacterioplankton growth was also tested. Bacterioplankton production was often limited by phosphorus alone, organic carbon alone, or the two in combination. Phosphorus limitation of bacterioplankton production was more common in the summer, whereas limitation by organic carbon was more frequently observed in the autumn. There was a close balance between limitation by phosphorus and organic carbon in the epilimnion in the summer. In the hypolimnion in the summer, bacterioplankton growth was primarily phosphorus-limited. The effect of phosphorus additions decreased with increasing phosphorus concentrations in the lakes. However, there were no correlations between the effect of added organic carbon and water color, dissolved organic carbon concentration, or phosphorus concentration. When temperature was low (in the hypolimnion in the summer, and throughout the water column in the autumn) temperature also limited bacterioplankton production. Thus, temperature and inorganic nutrients or organic compounds can limit bacterioplankton growth both alone and simultaneously. However, at low temperatures, temperature is the most important factor influencing bacterioplankton growth.

Bacteria↗
PubMed1999

Protozoan Bacterivory in the Ice and the Water Column of a Cold Temperate Lagoon.

> Abstract Bacterial abundance and bacterivorous protist abundance and activity were examined in ice-brine and water column communities of a cold temperate Japanese lagoon (Saroma-Ko Lagoon, Hokkaido, 44 degreesN, 144 degreesE), during the late winter phase of ice community development (February-March 1992). Bacterial abundance averaged 6 and 1 x 10(5) cells ml-1 in the ice-brine and plankton samples, respectively, and generally decreased during the sampling period. Bacterivorous protists, identified based on direct observation of short-term (<1 h) ingested fluorescently labeled bacteria (FLB) in their food vacuoles, were largely dominated by flagellates, mainly cryothecomonad-type and chrysomonad-like cells and small dinoflagellates of the genus Gymnodinium. Bacterivorous ciliates included mainly the prostomatid Urotricha sp., the scuticociliates Uronema and Cyclidium, the choreotrichs Lohmaniella oviformis and Strobilidium, and the hypotrich Euplotes sp. Protist abundance averaged 4 x 10(3) and 8.1 cells ml-1 in the ice-brine and 0.3 x 10(3) and 1.2 cells ml-1 in the plankton, for flagellates and ciliates, respectively. In contrast to bacteria, the abundance of protists generally increased throughout the sampling period, indicating predator-prey interactions. Protistan bacterivory, measured from the rate of FLB disappearance over 24 h, averaged 36% (ice) and 24% (plankton) of bacterial standing stock and exhibited the same seasonal pattern as for protist abundance. The calculated specific clearance (range, 2-67 nl protozoa-1 h-1) and ingestion (<1-26 particles protozoa-1 h-1) rates were likely to be minimal estimates and grazing impact may have been higher on occasion. Indications for the dependence of "bacterivorous protists" on nonbacterial food items were also provided. Although alternative sources of bacterial loss are likely to be of importance, this study provides evidence for the potential of protozoan assemblages as bacterial grazers in both sea ice-brine biota and water column at the southern limit of sea ice in the northern hemisphere.

Journal Article↗
PubMed1996

phi 20, a temperate bacteriophage isolated from Bacillus anthracis exists as a plasmidial prophage.

This study describes the isolation of temperate B. anthracis phages, from 4 out of 20 B. anthracis strains screened, by use of the inducing agents mitomycin C and UV light. Phage phi 20 isolated from B. anthracis Sterne 34F2 (pXO1+ pXO2-) was shown to have double-stranded DNA of size 48756 bp and a restriction site map showing nine sites for enzymes BamHI, BglII, and SstI is included. The phi 20 genome was found to exist as a plasmidial prophage and the phage itself to have a polyhedral head of diameter 65 nm and tail 217 nm long and 15 nm wide.

Bacillus Phages↗
PubMed2003

In vitro protein synthesis capacities in a cold stenothermal and a temperate eurythermal pectinid.

The translational system was isolated from the gills of the Antarctic scallop Adamussium colbecki (Smith) and the European scallop Aequipecten opercularis (Linnaeus) for in vitro protein synthesis capacities microg protein mg FW(-1) day(-1)) and the translational capacities of RNA (k(RNA in vitro) mg protein mg RNA(-1) day(-1)). In vitro protein synthesis capacity in the cold-adapted pectinid at 0 degrees C was similar to the one found in the temperate scallop at 25 degrees C. These findings might reflect cold compensated rates in Adamussium colbecki, partly explainable by high tissue levels of RNA. Cold-compensated in vitro protein synthesis capacities may further result from increments in the translational capacity of RNA. The thermal sensitivity of the translation machinery was slightly different in the two species, with significantly lower levels of Arrhenius activation energies E(a) and Q(10) in Adamussium colbecki in the temperature range 0-15 degrees C. Reduced protein synthesis and translational capacities were found in vitro in gills of long-term aquarium-maintained Adamussium colbecki and were accounted for by a loss of protein synthesis machinery, i.e. a reduction in RNA levels, as well as a decrease in the amount of protein synthesized per milligram of RNA (RNA translational capacity, k(RNA in vitro)). Such changes may involve food uptake or mirror metabolic depression strategies, like those occurring during winter. Consequences of high in vitro RNA translational capacities found in the permanently cold-adapted species are discussed in the context of seasonal food availability and growth rates at high latitudes.

Adaptation, Physiological↗
PubMed1998

DNA analysis of temperate bacteriophage Aa(phi)23 isolated from actinobacillus actinomycetemcomitans.

The DNA of the temperate bacteriophage Aaphi23 isolated from the oral bacterium Actinobacillus actinomycetemcomitans was examined structurally both in the phage head and in the prophage. The DNA in phage particles comprises 44 kb linear molecules with a terminal redundancy of 1.6 kb, which represent circular permutations. Thus, DNA is packaged into phage heads by the headful mechanism. The Aaphi23 prophage is integrated into the host chromosome.

Aggregatibacter actinomycetemcomitans↗
PubMed1999

Shiga toxins even when different are encoded at identical positions in the genomes of related temperate bacteriophages.

The nucleotide sequence of an 11,142-bp region including the stx2 operon in the genome of the temperate bacteriophage 933W in the EDL933 strain of Escherichia coli O157 was determined and compared to the respective regions derived from other lambdoid bacteriophages. In phage 933W, a region of ORFs interlinked by overlapping start-stop codons (ATGA) was detected preceding the toxin gene. These ORFs show a high degree of sequence identity to genes of the nin region of phage lambda. Immediately downstream of these nin genes we identified an ORF that may code for an anti-terminator similar to the lambda Q protein. It is concluded that toxin expression is directly associated with the initiation of cell lysis. Downstream of the stx2 operon we identified an ORF that is homologous to the holin gene S of bacteriophage PA-2. PCR primers were designed, which, based on a comparison of the phage sequences, appeared to be common to both stx1- and stx2-harbouring phages. However, only seven of the 22 STEC strains investigated from serogroups O157, O26, O103 and O111 yielded the expected PCR amplification product. The data reported here may be useful in developing new strategies for inhibiting the expression of Stx and for developing universal diagnostic primers for use in tracking the origin and evolution of Shiga toxins and the phages that carry them.

Amino Acid Sequence↗
PubMed2003

Leaf display and photosynthesis of tree seedlings in a cool-temperate deciduous broadleaf forest understorey.

To examine a possible convergence in leaf photosynthetic characteristics and leaf display responses to light environment in seedlings of three canopy and two shrub tree species in understorey of cool-temperate deciduous broadleaf forest, relationships between light environment, leaf orientation and leaf light-photosynthetic response were measured. Light capture of the seedlings (17-24 individuals with 2-12 leaves for each species) was assessed with a three dimensional geometric modeling program Y-plant. Leaf photosynthetic characteristics of the five species were found to have acclimated to the understorey light environment, i.e., low light compensation point and high apparent quantum yield. In addition, light-saturated photosynthetic rates were higher in seedlings inhabiting microsites with higher light availability. Efficiencies of light capture and carbon gain of the leaf display were evaluated by simulating the directionalities of light capture and daily photosynthesis for each seedling using hemispherical canopy photography. The results showed that most of the seedlings orientated their leaves in a way to increase the daily photosynthesis during the direct light periods (sunflecks) rather than maximize daily photosynthesis by diffuse light. Simulations also showed that daily photosynthesis would increase only 10% of that on actual leaf display when the leaves orientated to maximize the diffuse light interception. Simulations in which leaf orientations were varied showed that when the leaf display fully maximized direct light interception, the time that leaves were exposed to excessive photon flux density of >800 mumol photons m(-2) s(-1) were doubled. The understorey seedlings studied responded to the given light environments in a way to maximize the efficiency of acquisition and use of light during their short (approximately 3 month) seasonal growth period.

Computer Simulation↗
PubMed2004

Rapid development of phosphorus limitation in temperate rainforest along the Franz Josef soil chronosequence.

The aim of this study was to examine how shifts in soil nutrient availability along a soil chronosequence affected temperate rainforest vegetation. Soil nutrient availability, woody plant diversity, composition and structure, and woody species leaf and litter nutrient concentrations were quantified along the sequence through ecosystem progression and retrogression. In this super-wet, high leaching environment, the chronosequence exhibited rapid soil development and decline within 120000 years. There were strong gradients of soil pH, N, P and C, and these had a profound effect on vegetation. N:P(leaf) increased along the chronosequence as vegetation shifted from being N- to P- limited. However, high N:P(leaf) ratios, which indicate P-limitation, were obtained on soils with both high and low soil P availability. This was because the high N-inputs from an N-fixing shrub caused vegetation to be P-limited in spite of high soil P availability. Woody species nutrient resorption increased with site age, as availability of N and P declined. Soil P declined 8-fold along the sequence and P resorption proficiency decreased from 0.07 to 0.01%, correspondingly. N resorption proficiency decreased from 1.54 to 0.26%, corresponding to shifts in mineralisable N. Woody plant species richness, vegetation cover and tree height increased through ecosystem progression and then declined. During retrogression, the forest became shorter, more open and less diverse, and there were compositional shifts towards stress-tolerant species. Conifers (of the Podocarpaceae) were the only group to increase in richness along the sequence. Conifers maintained a lower N:P(leaf) than other groups, suggesting superior acquisition of P on poor soils. In conclusion, there was evidence that P limitation and retrogressive forests developed on old soils, but N limitation on very young soils was not apparent because of inputs from an abundant N-fixing shrub.

Ecology↗
PubMed2005

Respiration characteristics in temperate rainforest tree species differ along a long-term soil-development chronosequence.

We measured the response of dark respiration (R(d)) to temperature and foliage characteristics in the upper canopies of tree species in temperate rainforest communities in New Zealand along a soil chronosequence (six sites from 6 years to 120,000 years). The chronosequence provided a vegetation gradient characterised by significant changes in soil nutrition. This enabled us to examine the extent to which changes in dark respiration can be applied across forest biomes and the utility of scaling rules in whole-canopy carbon modelling. The response of respiration to temperature in the dominant tree species differed significantly between sites along the sequence. This involved changes in both R(d) at a reference temperature (R(10)) and the extent to which R(d) increased with temperature (described by E(o), a parameter related to the energy of activation, or the change in R(d) over a 10 degrees C range, Q(10)). Site averaged E(o) ranged from 44.4 kJ mol(-1) K(-1) at the 60-year-old site to 26.0 kJ mol(-1) K(-1) at the oldest, most nutrient poor, site. Relationships between respiratory and foliage characteristics indicated that both the temperature response of respiration (E(o) or Q(10)) and the instantaneous rate of respiration increased with both foliar nitrogen and phosphorus content. The ratio of photosynthetic capacity (Whitehead et al. in Oecologia 2005) to respiration (A(max)/R(d)) attained values in excess of 15 for species in the 6- to 120-year-old sites, but thereafter decreased significantly to around five at the 120,000-year-old site. This indicates that shoot carbon acquisition is regulated by nutrient limitations in the retrogressing ecosystems on the oldest sites. Our findings indicate that respiration and its temperature response will vary according to soil age and, therefore, to soil nutrient availability and the stage of forest development. Thus, variability in respiratory characteristics for canopies should be considered when using models to integrate respiration at large spatial scales.

Age Factors↗
PubMed2005

Rodent seed predation promotes differential recruitment among bird-dispersed trees in temperate secondary forests.

We investigated the role of seed predation by rodents in the recruitment of the fleshy-fruited trees Taxus baccata, Ilex aquifolium and Crataegus monogyna in temperate secondary forests in NW Spain. We measured the densities of dispersed seeds, early emerged seedlings, established recruits and adults, at four sites over a period of 2 years. Seed predation among species was compared by seed removal experiments and analysis of rodent larder-hoards. The three species differed markedly in local regeneration patterns. The rank order in the seed rain following decreasing seed density was Ilex, Taxus and Crataegus. However, Crataegus established 3.3 times more seedlings than Taxus. For all species, there was a positive linear relationship between the density of emerged seedlings and seed density, suggesting that recruitment was seed- rather than microsite-limited. A consistent pattern of seed selection among species was exerted by rodents, which preferred Taxus and, secondarily, Ilex seeds to Crataegus seeds. Predation ranking was the inverse of that of seed protection against predators, measured as the mass of woody coat per mass unit of the edible fraction. Recruitment potential, evaluated as the ratio of seedlings to seeds, was negatively related to seed predation, with the rank order Crataegus > Ilex > Taxus. The selective early recruitment limitation exerted by predation may have a demographic effect in the long term, as judged by the positive relationship between early seedling emergence and the density of established recruits. By modulating the pre-emptive competition for seed safe sites, rodents may preclude the progressive exclusion of species that produce low numbers of seeds (i.e. Crataegus) by those dominant in seed number (i.e. Ilex, Taxus), or at least foster the evenness for site occupation among seedlings of different species.

Animals↗
PubMed2005

Fine root chemistry and decomposition in model communities of north-temperate tree species show little response to elevated atmospheric CO2 and varying soil resource availability.

Rising atmospheric [CO2] has the potential to alter soil carbon (C) cycling by increasing the content of recalcitrant constituents in plant litter, thereby decreasing rates of decomposition. Because fine root turnover constitutes a large fraction of annual NPP, changes in fine root decomposition are especially important. These responses will likely be affected by soil resource availability and the life history characteristics of the dominant tree species. We evaluated the effects of elevated atmospheric [CO2] and soil resource availability on the production and chemistry, mycorrhizal colonization, and decomposition of fine roots in an early- and late-successional tree species that are economically and ecologically important in north temperate forests. Open-top chambers were used to expose young trembling aspen (Populus tremuloides) and sugar maple (Acer saccharum) trees to ambient (36 Pa) and elevated (56 Pa) atmospheric CO2. Soil resource availability was composed of two treatments that bracketed the range found in the Upper Lake States, USA. After 2.5 years of growth, sugar maple had greater fine root standing crop due to relatively greater allocation to fine roots (30% of total root biomass) relative to aspen (7% total root biomass). Relative to the low soil resources treatment, aspen fine root biomass increased 76% with increased soil resource availability, but only under elevated [CO2]. Sugar maple fine root biomass increased 26% with increased soil resource availability (relative to the low soil resources treatment), and showed little response to elevated [CO2]. Concentrations of N and soluble phenolics, and C/N ratio in roots were similar for the two species, but aspen had slightly higher lignin and lower condensed tannins contents compared to sugar maple. As predicted by source-sink models of carbon allocation, pooled constituents (C/N ratio, soluble phenolics) increased in response to increased relative carbon availability (elevated [CO2]/low soil resource availability), however, biosynthetically distinct compounds (lignin, starch, condensed tannins) did not always respond as predicted. We found that mycorrhizal colonization of fine roots was not strongly affected by atmospheric [CO2] or soil resource availability, as indicated by root ergosterol contents. Overall, absolute changes in root chemical composition in response to increases in C and soil resource availability were small and had no effect on soil fungal biomass or specific rates of fine root decomposition. We conclude that root contributions to soil carbon cycling will mainly be influenced by fine root production and turnover responses to rising atmospheric [CO2], rather than changes in substrate chemistry.

Atmosphere↗
PubMed2006

Fire season and intensity affect shrub recruitment in temperate sclerophyllous woodlands.

The season in which a fire occurs may regulate plant seedling recruitment because of: (1) the interaction of season and intensity of fire and the temperature requirements for seed release, germination and growth; (2) post-fire rainfall and temperature patterns affecting germination; (3) the interaction of post-fire germination conditions and competition from surrounding vegetation; and (4) the interaction of post-fire germination conditions and seed predators and/or seedling herbivores. This study examined the effects of different fire intensities and fire seasons on the emergence and survival of shrubs representing a range of fire response syndromes from a summer rainfall cool climate region. Replicated experimental burns were conducted in two seasons (spring and autumn) in 2 consecutive years and fuel loads were increased to examine the effects of fire intensity (low intensity and moderate intensity). Post-fire watering treatments partitioned the effects of seasonal temperature from soil moisture. Higher intensity fires resulted in enhanced seedling emergence for hard-seeded species but rarely influenced survival. Spring fires enhanced seedling emergence across all functional groups. Reduced autumn recruitment was related to seasonal temperature inhibiting germination rather than a lack of soil moisture or competition. In Mediterranean-type climate regions, seedling emergence has been related to post-fire rainfall and exposure of seeds to seed predators. We think a similar model may operate in temperate summer rainfall regions where cold-induced dormancy over winter exposes seeds to predators for a longer time and subsequently results in recruitment failure. Our results support the theory that the effect of fire season is more predictable where there are strong seasonal patterns in climate. In this study seasonal temperature rather than rainfall appears to be more influential.

Climate↗
PubMed2006

Leaf anatomy and light acclimation in woody seedlings after gap formation in a cool-temperate deciduous forest.

The photosynthetic light acclimation of fully expanded leaves of tree seedlings in response to gap formation was studied with respect to anatomical and photosynthetic characteristics in a natural cool-temperate deciduous forest. Eight woody species of different functional groups were used; two species each from mid-successional canopy species (Kalopanax pictus and Magnolia obovata), from late-successional canopy species (Quercus crispula and Acer mono), from sub-canopy species (Acer japonicum and Fraxinus lanuginosa) and from vine species (Schizophragma hydrangeoides and Hydrangea petiolaris). The light-saturated rate of photosynthesis (Pmax) increased significantly after gap formation in six species other than vine species. Shade leaves of K. pictus, M. obovata and Q. crispula had vacant spaces along cell walls in mesophyll cells, where chloroplasts were absent. The vacant space was filled after the gap formation by increased chloroplast volume, which in turn increased Pmax. In two Acer species, an increase in the area of mesophyll cells facing the intercellular space enabled the leaves to increase Pmax after maturation. The two vine species did not significantly change their anatomical traits. Although the response and the mechanism of acclimation to light improvement varied from species to species, the increase in the area of chloroplast surface facing the intercellular space per unit leaf area accounted for most of the increase in Pmax, demonstrating the importance of leaf anatomy in increasing Pmax.

Acclimatization↗
PubMed2004

Seasonal variation of arbuscular mycorrhizal fungi in temperate grasslands along a wide hydrologic gradient.

We studied seasonal variation in population attributes of arbuscular mycorrhizal (AM) fungi over 2 years in four sites of temperate grasslands of the Argentinean Flooding Pampas. The sites represent a wide range of soil conditions, hydrologic gradients, and floristic composition. Lotus glaber, a perennial herbaceous legume naturalised in the Flooding Pampas, was dominant at the four plant community sites. Its roots were highly colonised by AM fungi. Temporal variations in spore density, spore type, AM root colonisation, floristic composition and soil chemical characteristics occurred in each site and were different among sites. The duration of flooding had no effect on spore density but depressed AM root colonisation. Eleven different types of spores were recognized and four were identified. Two species dominated at the four sites: Glomus fasciculatum and Glomus intraradices. Spore density was highest in summer (dry season) and lowest in winter (wet season) with intermediate values in autumn and spring. Colonisation of L. glaber roots was highest in summer or spring and lowest in winter or autumn. The relative density of G. fasciculatum and G. intraradices versus Glomus sp. and Acaulospora sp. had distinctive seasonal peaks. These seasonal peaks occurred at all four sites, suggesting differences among AM fungus species with respect to the seasonality of sporulation. Spore density and AM root colonisation when measured at any one time were poorly related to each other. However, spore density was significantly correlated with root colonisation 3 months before, suggesting that high colonisation in one season precedes high sporulation in the next season.

Argentina↗
PubMed1998

A temperate phage with cohesive ends induced by mitomycin C treatment of Lactobacillus casei.

A temperate phage, named PL-2, was induced from Lactobacillus casei ATCC 27092 by mitomycin C treatment of the cells at exponential growth phase. The phage had an isometric head of 45 nm in diameter and a flexible, non-contractile tail, 150 nm long and 10 nm wide, with a sharp tip. Along the tail axis, about 40 regularly spaced striae were seen. The phage DNA had complementary cohesive ends. The restriction enzyme map of the DNA was constructed by using 13 different restriction endonucleases. The size of the DNA was 35.2 kb, 83% in size of that of phage PL-1 lytic for the same Lb. casei strain.

Bacteriophages↗
PubMed1997

Isolation and characterization of bacteriophage BCJA1, a novel temperate bacteriophage active against the alkaliphilic bacterium, Bacillus clarkii.

The isolation and characterization of a novel bacteriophage active against the obligately alkaliphilic bacterium Bacillus clarkii is described. The bacteriophage, designated BCJA1. is a member of the Siphoviridae family with a B1 morphology. It possesses an isometric head, which measures 65 nm between opposite apices, and a noncontractile tail of 195 nm length. It had a buoyant density of 1.518 g/ml and an estimated particle mass of 37 x 10(7) daltons. BCJA1 was stable over the pH range of 6-11. A one-step growth experiment conducted at pH 10 demonstrated a latent period of about 40 min and a burst size of approximately 40. The purified bacteriophage appeared to consist of 10 proteins with the major head and tail proteins likely to be of molecular weight 36500 and 28000, respectively. The genome size was estimated to be between 32.1 and 34.8 kb. The percent G + C content of purified bacteriophage DNA was 45.6. The wildtype bacteriophage is temperate but a clear plaque mutant was isolated.

Bacillus↗
PubMed2005

Protein structure prediction by tempering spatial constraints.

The probability to predict correctly a protein structure can be enhanced through introduction of spatial constraints - either from NMR experiments or from homologous structures. However, the additional constraints lead often to new local energy minima and worse sampling efficiency in simulations. In this work, we present a new parallel tempering variant that alleviates the energy barriers resulting from spatial constraints and therefore yields to an enhanced sampling in structure prediction simulations.

Algorithms↗