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PubMed2005

Replica exchange with solute tempering: a method for sampling biological systems in explicit water.

An innovative replica exchange (parallel tempering) method called replica exchange with solute tempering (REST) for the efficient sampling of aqueous protein solutions is presented here. The method bypasses the poor scaling with system size of standard replica exchange and thus reduces the number of replicas (parallel processes) that must be used. This reduction is accomplished by deforming the Hamiltonian function for each replica in such a way that the acceptance probability for the exchange of replica configurations does not depend on the number of explicit water molecules in the system. For proof of concept, REST is compared with standard replica exchange for an alanine dipeptide molecule in water. The comparisons confirm that REST greatly reduces the number of CPUs required by regular replica exchange and increases the sampling efficiency. This method reduces the CPU time required for calculating thermodynamic averages and for the ab initio folding of proteins in explicit water.

Algorithms↗
PubMed2002

Decoupling of unpolluted temperate forests from rock nutrient sources revealed by natural (87)Sr/(86)Sr and (84)Sr tracer addition.

An experimental tracer addition of (84)Sr to an unpolluted temperate forest site in southern Chile, as well as the natural variation of (87)Sr/(86)Sr within plants and soils, indicates that mechanisms in shallow soil organic horizons are of key importance for retaining and recycling atmospheric cation inputs at scales of decades or less. The dominant tree species Nothofagus nitida feeds nearly exclusively (>90%) on cations of atmospheric origin, despite strong variations in tree size and location in the forest landscape. Our results illustrate that (i) unpolluted temperate forests can become nutritionally decoupled from deeper weathering processes, virtually functioning as atmospherically fed ecosystems, and (ii) base cation turnover times are considerably more rapid than previously recognized in the plant available pool of soil. These results challenge the prevalent paradigm that plants largely feed on rock-derived cations and have important implications for understanding sensitivity of forests to air pollution.

Calcium↗
PubMed2000

Cardiorespiratory and thermoregulatory response of working in fire-fighter protective clothing in a temperate environment.

The cardiorespiratory and thermal responses of two intensities of treadmill exercise were compared for brief periods (12 min) in fire ensemble (FE) but without self contained breathing apparatus, and sports ensemble (SE), in a temperature environment. A further experiment explored the responses of subjects exercising in FE over a prolonged period (60 min). Eighteen male fire-fighters wearing either FE or SE walked on a level treadmill for 6 min at 5 km x h(-1) increasing to 7 km x h(-1) for 6 min. Following a recovery interval of 1 h, the exercise protocol was repeated in the second ensemble; the order of ensemble was balanced. Heart rate (HR), rectal temperature (Tre), VO2 max and rating of perceived exertion (RPE) were monitored continuously under both ensembles. At 7 km x h(-1), VO2 was significantly higher (p<0.05) in FE (36.1 and 39.9 ml x kg(-1) x min(-1)) than in SE and represented 74% VO2 max. There were no changes Tre. In experiment 2, following a rest interval of at least 36 h, eight subjects in FE walked on the treadmill at 6 km x h (gradient 10%) for 60 min also in temperate conditions, where HR, Tre and RPE were recorded at 10-min intervals. During the 60-min exercise in FE, HR reached 161 beats x min(-1) and Tre increased to 38.3 degrees C. Despite considerable subject discomfort, Tre remained below dangerous levels (38.4 degrees C). When RPE were compared with a physiological strain index (PSI) calculated from Tre and HR data over 60 min, there was no significant difference (p<0.05) with a correlation coefficient (r) of 0.98. The results suggest that RPE and PSI are closely related when exercise is sufficiently prolonged or intense to elevate Tre and HR in fire-fighters wearing FE in temperate conditions. If further investigation confirms this relationship for hot humid conditions in which fire-fighters operate, then with training, it may provide individuals with a valid measure of dangerous levels of perceived heat strain.

Analysis of Variance↗
PubMed2005

Quantification of dung carbon incorporation in a temperate grassland soil following spring application using bulk stable carbon isotope determinations.

Herbivore dung constitutes a substantial input of C to temperate grassland soils, and its fate must be determined in order to fully understand nutrient cycling in this ecosystem. This experiment used changes in bulk delta13C values of the 0-1 cm and 1-5 cm soil horizons of a dung-treated temperate grassland soil to approximate percentage applied dung C incorporation over 372 days. Natural abundance 13C-labelled C4 dung (delta13C - 12.6%) and C3 dung (delta13C - 31.3% were produced in a monitored diet switch from ryegrass silage (delta13C - 30.1%) to maize silage (delta13C - 11.6%). The dung was applied to a C3 grassland (delta13C 0-1 cm - 29.9%, 1-5 cm - 30.6%), and dung remains and soil cores from beneath the treatments were sampled at intervals. delta13C values were used to estimate a maximum of 12% applied dung C incorporation in the top 5 cm of the soil after 112 days, which declined to around 8% at the end of the experiment. A significant increase in percentage applied dung C was observed in the top 1 cm of soil, compared with the 1-5 cm horizon, after a substantial rain event after 30 days. However, results of forage fibre analyses of the two dung types revealed significant differences in composition which may affect subsequent calculations of percentage dung incorporation based on bulk delta13C values.

Animal Feed↗
PubMed1986

Radiation preservation of foods of plant origin. Part V. Temperate fruits: pome fruits, stone fruits, and berries.

The current status of research on the application of ionizing radiation for improving the storage of temperate fruits, i.e., apple, pear, peach, nectarine, apricot, cherry, plum, strawberry, bilberry, cranberry, raspberry, and black currant, is reviewed. Changes in fruit metabolism, chemical composition, texture, and organoleptic quality attributes are discussed with reference to the irradiation dose. The feasibility of using radiation either alone or in conjunction with heat treatment, refrigeration, and controlled atmospheres (CA) for the control of storage decay caused by fungal pathogens is considered. Areas of further research are suggested before irradiation could be considered for practical application in some of these temperate fruits. The recent trends in the possible use of irradiation for disinfestation of certain pome and stone fruits and the prospects for the commercial utilization of irradiation for improving the market life of strawberries are discussed.

Carbohydrate Metabolism↗
PubMedDate not supplied

High-energy phosphate metabolism during exercise and recovery in temperate and Antarctic scallops: an in vivo 31P-NMR study.

In vivo (31)P-nuclear magnetic resonance (NMR) spectroscopy was used to measure the levels of ATP, phospho-l-arginine (PLA), and inorganic phosphate in the adductor muscle of the Antarctic scallop Adamussium colbecki and two temperate species, Aequipecten opercularis and Pecten maximus. Graded exercise regimes from light (one to two contractions) to exhausting (failing to respond to further stimulation) were imposed on animals of each species at its habitat temperature (0 degrees vs. 12 degrees C, respectively). NMR spectroscopy allowed noninvasive measurement of metabolite levels and intracellular pH at high time resolution (30-120-s intervals) during exercise and throughout the recovery period. Significant differences were shown between the magnitude and form of the metabolic response with increasing levels of exercise in each species. After exhaustion, short-term (first 15 min) muscle alkalosis was followed by acidosis of up to 0.2 pH units during the recovery process. Aequipecten opercularis had similar resting muscle PLA levels compared with either P. maximus or A. colbecki but used a fivefold greater proportion of this store per contraction and was able to perform only half as many claps (maximum of 24) as the other species before exhaustion. All species regenerated their PLA store at a similar rate despite different environmental temperatures. These findings argue for some cold compensation of muscular performance and recovery capacities in the Antarctic scallop, albeit at levels of performance similar to scallops with low activity lifestyles from temperate latitudes.

Adaptation, Physiological↗
PubMed2003

VO1, a temperate bacteriophage of the type 19A multiresistant epidemic 8249 strain of Streptococcus pneumoniae: analysis of variability of lytic and putative C5 methyltransferase genes.

A temperate bacteriophage (VO1) has been isolated from the Streptococcus pneumoniae type 19F multiresistant epidemic 8249 strain (South African strain). Structural analysis of the specific integration site, protein composition, restriction patterns, and molecular dissection of the lytic system of this phage revealed high sequence similarity with MM1, a temperate phage from the Spain23F-1 strain of pneumococcus, another multiresistant epidemic clone. The different pneumococcal strains sequenced so far exhibit an identical and single attB located in the same site of the genome. Remarkably, the LytA amidase coded by VO1 showed clear differences with that of the host bacterium in contrast with the situation previously documented for bacterial- and phage-coded amidases of pneumococcus. In addition, a new gene (orfmet) putatively coding for a C5 methyltransferase has been identified. A noticeable variability affecting the presence (or absence) of this supernumerary gene(s) in the same region of the genomes of three otherwise highly similar phages (i.e., VO1, MM1, and HB-3) suggests frequent recombinational events leading to introduce variability in this genome region. The peculiarities of genes like lytA and orfmet in VO1 provide interesting insights on mechanisms of horizontal transfer and lysogenic state co-evolution.

Amino Acid Sequence↗
PubMed2005

The leaf size-twig size spectrum of temperate woody species along an altitudinal gradient: an invariant allometric scaling relationship.

BACKGROUND AND AIMS: The leaf size-twig size spectrum is one of the leading dimensions of plant ecological variation, and now it is under development. The purpose of this study was to test whether the relationship between leaf size and twig size is isometric or allometric, and to examine the relationship between plant allometric growth and life history strategies in the spectrum. METHODS: Leaf and stem characters-including leaf and stem mass, total leaf area, individual leaf area, stem cross-sectional area, leaf number and stem length-at the twig level for 59 woody species were investigated along an altitudinal gradient on Changbaishan Mountain in the temperate zone of China. The environmental gradient ranges from temperate broad-leaved mixed forest at low altitude, to conifer forest at middle altitude, and to sub-alpine birch forest at high altitude. The scaling relationships between stem cross-sectional area and stem mass, stem mass and leaf mass, and leaf mass and leaf area at the twig level were simultaneously determined. KEY RESULTS: Twig cross-sectional area was found to have invariant allometric scaling relationships with the stem mass, leaf mass, total leaf area and individual leaf area, all with common slopes being significantly larger than 1, for three altitudinal-zoned vegetation types under investigation. However, leaf mass was found to be isometrically related to stem mass and leaf area along the environmental gradient. Based on the predictions of previous models, the exponent value of the relationship between twig cross-sectional area and total leaf area can be inferred to be 1.5, which falls between the confidence intervals of the relationship at each altitude, and between the confidence intervals of the common slope value (1.17-1.56) of this study. This invariant scaling relationship is assumed to result from the fractural network and/or developmental constraints of plants. The allometric constants (y-intercepts) of the relationships between the stem cross-sectional area and leaf area (both total leaf area and individual leaf area) were found to decrease significantly along the altitudinal gradient. This suggests that the species would support less leaf area at a given twig cross-sectional area with increasing environmental stress. CONCLUSIONS: This study demonstrated that plants respond to the environmental gradient by changing the y-intercepts of the relationship between leaf size-twig size, while keeping the exponent value of the allometric relationship as an invariant constant. The allometric growth in the twig size-leaf size spectrum is related to many other components of plant life history strategy, including the well established life history trade-off between efficiency and safety in the hydraulic transport of water.

Acclimatization↗
PubMed2006

Inheritance of time to flowering in chickpea in a short-season temperate environment.

Time to flowering is central in determining the adaptation and productivity of chickpea in short-season temperate environments. We studied the genetic control of this trait in three crosses, 272-2 x CDC Anna, 298T-9 x CDC Anna, and 298T-9 x CDC Frontier. From each cross, 180 F2 plants and parents were evaluated for time to flowering under greenhouse conditions. In summer 2004, multiple generations including P1, F1, P2, F2, and F2:3 (also called MG5) were evaluated for time to flowering under field conditions. The data on time to flowering in the F(2) populations were continuous in distribution but deviated from normal distribution. The F2:3 families derived from this showed a bimodal distribution for time to flowering, a typical case of major-gene inheritance model with duplicate recessive epistasis. A joint segregation analysis of MG5 also revealed that time to flowering in chickpea was controlled by two major genes along with other polygenes. Late flowering was dominant over early flowering for both major genes with digenic interaction between them, mainly an additive x additive type. This information can be used to formulate the most efficient breeding strategy for improvement of time to flowering in chickpea in short-season temperate environments.

Cicer↗
PubMedDate not supplied

Genotypic and phenotypic variation as stress adaptations in temperate tree species: a review of several case studies.

Species that occupy large geographic ranges or a variety of habitats within a limited area deal with contrasting environmental conditions by genotypic and phenotypic variation. My students and I have studied these forms of ecophysiological variation in temperate tree species in eastern North America by means of a series of field and greenhouse experiments, including controlled studies with Cercis canadensis L., Fraxinus pennsylvanica Marsh., Acer rubrum L., Prunus serotina Ehrh. and Quercus rubra L., in relation to drought stress. These studies have included measurements of gas exchange, tissue water relations and leaf morphology, and have identified genotypic variation at the biome and individual community levels. Xeric genotypes generally had higher net photosynthesis and leaf conductance and lower osmotic and water potentials at incipient wilting than mesic genotypes during drought. Xeric genotypes also produced leaves with greater thickness, leaf mass per area and stomatal density and smaller area than the mesic genotypes, suggesting general coordination among leaf morphology, gas exchange and tissue water relations. Leaf phenotypic plasticity to different light environments occurred in virtually every study species, which represented a wide array of ecological tolerances. In a study of interactions of genotypes with environment, shade plants, but not sun plants, exhibited osmotic adjustment during drought and shade plants had smaller reductions in photosynthesis with decreasing leaf water potential. In that study, sun, but not shade, plants had significant genotypic differences in leaf structure, but with certain variables phenotypic variation exceeded genotype variation. Thus, genotypic variation was not expressed in all phenotypes, and phenotypes responded differentially to stress. Overall, these studies indicate the importance of genotypic and phenotypic variation as stress adaptations in temperate tree species among both distant and nearby sites of contrasting environmental conditions.

Journal Article↗
PubMed1999

Seasonal variations in leaf area index, leaf chlorophyll, and water content; scaling-up to estimate fAPAR and carbon balance in a multilayer, multispecies temperate forest.

Seasonal differences in phenology between coniferous and deciduous tree species need to be considered when developing models to estimate CO(2) exchange in temperate forest ecosystems. Because seasonal variations in CO(2) flux in temperate forests are closely correlated with plant phenology, we quantified the phenology of forest species in a multilayered forest with patches of Scots pine (Pinus sylvestris L.) and oak (Quercus robur L.) in Brasschaat, Belgium. A scaling-up modeling approach was developed to simulate reflectance at the leaf and canopy scales over a one-year cycle. Chlorophyll concentration, water content, specific leaf area and leaf area index of the forest species were measured throughout an entire year (1997). Scaling-up from the leaf to canopy was achieved by linking the PROSPECT and SAIL models. The result is the annual progression of the fraction of absorbed photosynthetically active radiation (fAPAR) in a 1 km(2) forest area, which can be directly related to high-resolution, remotely sensed data.

Journal Article↗
PubMed2002

Rate of stomatal opening, shoot hydraulic conductance and photosynthetic characteristics in relation to leaf abscisic acid concentration in six temperate deciduous trees.

Correlations between leaf abscisic acid concentration ([ABA]), stomatal conductance (gs), rate of stomatal opening in response to an increase in leaf water potential (si), shoot hydraulic conductance (L) and photosynthetic characteristics were examined in saplings of six temperate deciduous tree species: Acer platanoides L., Padus avium Mill., Populus tremula L., Quercus robur L., Salix caprea L. and Tilia cordata Mill. Species-specific values of foliar [ABA] were negatively related to the mean values of gs, si, L and light- and CO2- saturated net photosynthesis (P(max)), thus providing strong correlative evidence of a scaling of foliar gas exchange and hydraulic characteristics with leaf endogenous [ABA]. In addition, we suggest that mean gs, si, L and Pmax for mature leaves may partly be determined by the species-specific [ABA] during leaf growth. The most drought-intolerant species had the lowest [ABA] and the highest gs, suggesting that interspecific differences in [ABA] may be linked to differences in species-specific water-use efficiency. Application of high concentrations of exogenous ABA led to large decreases in gs, si and P(max), further underscoring the direct role of ABA in regulating stomatal opening and photosynthetic rate. Exogenous ABA also decreased L, but the decreases were considerably smaller than the decreases in gs, si and Pmax. Thus, exogenous ABA predominantly affected the stomata directly, but modification of L by ABA may also be an important mechanism of ABA action. We conclude that interspecific variability in endogenous [ABA] during foliage growth and in mature leaves provides an important factor explaining observed differences in L, gs, si and Pmax among temperate deciduous tree species.

Abscisic Acid↗
PubMed2004

Enhancement of understory productivity by asynchronous phenology with overstory competitors in a temperate deciduous forest.

Some saplings and shrubs growing in the understory of temperate deciduous forests extend their periods of leaf display beyond that of the overstory, resulting in periods when understory radiation, and hence productivity, are not limited by the overstory canopy. To assess the importance of the duration of leaf display on the productivity of understory and overstory trees of deciduous forests in the north eastern United States, we applied the simulation model, BIOME-BGC with climate data for Hubbard Brook Experimental Forest, New Hampshire, USA and mean ecophysiological data for species of deciduous, temperate forests. Extension of the overstory leaf display period increased overstory leaf area index (LAI) by only 3 to 4% and productivity by only 2 to 4%. In contrast, extending the growing season of the understory relative to the overstory by one week in both spring and fall, increased understory LAI by 35% and productivity by 32%. A 2-week extension of the growing period in both spring and fall increased understory LAI by 53% and productivity by 55%.

Ecosystem↗
PubMed1996

Sequence and mutational analysis of the common nodBCIJ region of Rhizobium sp. (Oxytropis arctobia) strain N33, a nitrogen-fixing microsymbiont of both arctic and temperate legumes.

By heterologous hybridization, we have identified the common nodulation genes nodBCIJ of Rhizobium sp. strain N33 within a 8.2-kb PstI fragment. The nodBCIJ genes are located within a 4,620-bp region which also included a consensus nod box promoter. The four open reading frames coding for the nodBCIJ genes contain 657, 1,353, 915, and 789 nucleotides, respectively. We found that the nodA gene was not adjacent to the nodB gene, unlike the situation in many rhizobia. The DNA of the nodBCIJ genes of Rhizobium sp. strain N33 were found to be homologous to the corresponding genes of other rhizobia except for the 3'-coding region of the nodC gene. The deduced NodC protein was the longest of the rhizobia except Bradyrhizobium japonicum. Tn5 mutagenesis of the common nod region of strain N33 revealed that the nodBC genes were essential for nodulation on their temperate hosts Onobrychis viciifolia and Astragalus cicer. By contrast, mutations in the nodI and nodJ genes produced a Nod+ phenotype with a reduced number of nodules on the temperate hosts. Nodules formed on Onobrychis viciifolia by either nodI or nodJ mutants were approximately 10 times smaller than nodules formed by the wild type strain: this reduction in nodule size was not observed on Astragalus cicer.

Amino Acid Sequence↗
PubMed1975

Characterization of different plaque-forming and defective temperate phages in Agrobacterium.

Four Agrobacterium tumefaciens temperate phages (PB2A, PB6(omega), PV-1(LV-1) and PS8), were shown to have the same genome size. Moreover hybridization experiments by the heteroduplex method and electron microscopy showed a 100% homology between these four phage genomes. Indications for lysogeny were found by direct means for the Agrobacterum timefaciens strain 396, Agrobacterium radiobacter strain 8149 and Agrobacterium species 0362 and by the electron microscope negative staining technique for the A.tumefaciens strains b6-806,b6-6,b6s3,b2as,cv-1,4452,11156,11158,396, and 925; for A.radiobacter strains tr-1 and 8149, the latter being bi-lysogenic, and for the A. species 0362. These isolated phage particles, most of which appear to be defective, could be grouped into different classes. No particles could be detected in the lysates of A. tumefaciens RV3, A. radiobacter strains 4718 and S1005, and A. species 0363. Further characterization by genome size was carried out for the defective temperate phages PB6-806, P4452,P8149 and P0362. No evidence for homology between PB6-806 and PB6 omega could be found. The defective phages PB6-806 and P4452 showed the same morphology but a different genome size, whereas the two phages P0362 and P8149 had a very different morphology and genome size.

Bacteriolysis↗
PubMed1990

Phi SC623, a temperate actinophage of Streptomyces coelicolor Müller, and its relatives phi SC347 and phi SC681.

Three species-specific, temperate actinophages of Streptomyces coelicolor Müller, phi SC623, phi SC347 and phi SC681, were compared with respect to host range, virion structure, antiserum cross-inactivation, DNA-restriction pattern, DNA hybridization, and DNA base composition. The restriction map of phi SC623 (57 kb) was established with eight restriction enzymes; the homologies of this phage with phi SC347 and phi SC681 suggested that it might be a hybrid phage composed of approximately equal parts homologous to one of the other two phages. No homology was detected between phi SC623 and R4, a temperate, wide-host-range phage which can also lysogenize S. coelicolor Müller.

Bacteriophages↗
PubMed1997

Sequence analysis and characterization of phi O1205, a temperate bacteriophage infecting Streptococcus thermophilus CNRZ1205.

The complete nucleotide sequence of phi O1205, a temperate bacteriophage infecting Streptococcus thermophilus strain CNRZ1205, was determined. The phage genome has a unit length of 43,075 bp and appears to be packaged by the so-called headful mechanism. The genomic organization and structure of phi O1205 resemble those of several temperate lactococcal phages that display a life-cycle-specific organization, where ORFs believed to be involved in the lysogenic life-cycle are clustered and arranged in an orientation opposite to the ORFs supposedly involved in the lytic life-cycle. Database searches revealed putative functions for several identified ORFs and further indicated that phi O1205 is genetically related to a particular group of lactococcal phages. Three genes encoding the major structural proteins were identified on the phi O1205 genome. The phage attachment site attP, the bacterial attachment site attB, and the two phage/chromosome junctions attL and attR were identified and found to contain a 40 bp common core sequence.

Amino Acid Sequence↗
PubMed2000

Parallel excluded volume tempering for polymer melts.

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts that makes use of both parallel tempering and large-scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large-scale Monte Carlo moves through attempted pivot and translation moves that reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as N=60 monomers, however at this chain length the large-scale Monte Carlo moves were ineffective. For even longer chains, the speedup becomes substantial, as observed from preliminary data for N=200. We also compare our scheme to the end bridging algorithm of Theodorou et al. For N=60, end bridging must allow a polydispersity of more than 10% in order to relax the end-to-end vector more quickly than our method. The comparison is, however, hampered by the fact that the end-to-end vector becomes a somewhat artificial quantity when one implements end bridging, and is perhaps no longer the slowest dynamic variable.

Algorithms↗