Shoot Growth and Mortality Patterns of Urtica dioica, a Clonal Forb

The growth and mortality patterns of the clonal forb Urticadioica were investigated at the level of the individual shootin two growing seasons, 1991 and 1992, in a natural stand. Shootheight and diameter at ground level of each shoot tagged inspring were measured repeatedly five times during the growingseason. Dry weights of these repeatedly measured shoots wereestimated using an allometric relationship between dry weight,height and diameter of harvested shoots. A large decrease inshoot density occurred with stand development from the beginningof the growing season in both the years: (1) shoot survivalrate was about 30% at the end of the growing season; (2) shootmortality rate per 10 x 10 cm subplot between censuses was positivelydependent on shoot density per subplot; (3) the mortality rateof individual shoots was negatively dependent on shoot size(height, diameter and weight) at each growing stage, suggestingone-sided competition between living and dying shoots; (4) shootsize (height, diameter and weight) variability in terms of thecoefficient of variation and skewness decreased in accordancewith shoot mortality. Symmetric competition between living shootswas detected by regression analysis based on a model for individualshoot growth considering the degree of competitive asymmetry.However, the competitive effect on individual shoot growth wasvery small (nearly absent). The mortality pattern of Urticadioica indicates that shoot self-thinning occurred from theearly growing stage as in non-clonal crowded monospecific stands,and contrasts with many clonal plants where shoot self-thinningrarely occurs or, if any, is confined only to a short periodof the later growing stage. The pattern of growth and competitionbetween living shoots of Urtica dioica contrasts with non-clonalcrowded plants undergoing intense competition (usually asymmetric)between individuals, but is a common feature of many clonalplants where shoot competition is supposed to be reduced by'physiological integration' between shoots. These form a newpattern not reported yet for clonal plants. It is pointed outthat clonal plants show a wider spectrum of the growth, competitionand mortality patterns of shoots than non-clonals. Some possiblemechanisms for the pattern of Urtica dioica are discussed.Copyright1995, 1999 Academic Press Shoot competition, diffusion model, individual shoot growth, shoot self-thinning, shoot size variability, Urtica dioica L     

Mass Mortality Events in the NW Adriatic Sea: Phase Shift from Slow- to Fast-Growing Organisms

Massive outbreaks are increasing all over the world, which are likely related to climate change. The North Adriatic Sea, a sub-basin of the Mediterranean Sea, is a shallow semi-closed sea receiving high nutrients inputs from important rivers. These inputs sustain the highest productive basin of the Mediterranean Sea. Moreover, this area shows a high number of endemisms probably due to the high diversity of environmental conditions and the conspicuous food availability. Here, we documented two massive mortalities (2009 and 2011) and the pattern of recovery of the affected biocoenoses in the next two years. Results show an impressive and fast shift of the benthic assemblage from a biocoenosis mainly composed of slow-growing and long-lived species to a biocoenosis dominated by fast-growing and short-lived species. The sponge Chondrosia reniformis, one of the key species of this assemblage, which had never been involved in previous massive mortality events in the Mediterranean Sea, reduced its coverage by 70%, and only few small specimens survived. All the damaged sponges, together with many associated organisms, were detached by rough-sea conditions, leaving large bare areas on the rocky wall. Almost three years after the disease, the survived specimens of C. reniformis did not increase significantly in size, while the bare areas were colonized by fast-growing species such as stoloniferans, hydrozoans, mussels, algae, serpulids and bryozoans. Cnidarians were more resilient than massive sponges since they quickly recovered in less than one month. In the study area, the last two outbreaks caused a reduction in the filtration efficiency of the local benthic assemblage by over 60%. The analysis of the times series of wave heights and temperature revealed that the conditions in summer 2011 were not so extreme as to justify severe mass mortality, suggesting the occurrence of other factors which triggered the disease. The long-term observations of a benthic assemblage in the NW Adriatic Sea allowed us to monitor its dynamics before, during and after the mortality event. The N Adriatic Sea responds quickly to climatic anomalies and other environmental stresses because of the reduced dimension of the basin. The long-term consequences of frequent mass mortality episodes in this area could promote the shift from biocoenoses dominated by slow-growing and long-lived species to assemblages dominated by plastic and short life cycle species.     

Probabilistic Model of Microbial Cell Growth,Division, and Mortality

After a short time interval of length δt during microbial growth, an individual cell can be found to be divided with probability P_d(t)δt, dead with probability P_m(t)δt, or alive but undivided with the probability 1 − [P_d(t) + P_m(t)]δt, where t is time, P_d(t) expresses the probability of division for an individual cell per unit of time, and P_m(t) expresses the probability of mortality per unit of time. These probabilities may change with the state of the population and the habitat''s properties and are therefore functions of time. This scenario translates into a model that is presented in stochastic and deterministic versions. The first, a stochastic process model, monitors the fates of individual cells and determines cell numbers. It is particularly suitable for small populations such as those that may exist in the case of casual contamination of a food by a pathogen. The second, which can be regarded as a large-population limit of the stochastic model, is a continuous mathematical expression that describes the population''s size as a function of time. It is suitable for large microbial populations such as those present in unprocessed foods. Exponential or logistic growth with or without lag, inactivation with or without a “shoulder,” and transitions between growth and inactivation are all manifestations of the underlying probability structure of the model. With temperature-dependent parameters, the model can be used to simulate nonisothermal growth and inactivation patterns. The same concept applies to other factors that promote or inhibit microorganisms, such as pH and the presence of antimicrobials, etc. With P_d(t) and P_m(t) in the form of logistic functions, the model can simulate all commonly observed growth/mortality patterns. Estimates of the changing probability parameters can be obtained with both the stochastic and deterministic versions of the model, as demonstrated with simulated data.     

A Modified In vitro Invasion Assay to Determine the Potential Role of Hormones,Cytokines and/or Growth Factors in Mediating Cancer Cell Invasion

Blood serum serves as a chemoattractant towards which cancer cells migrate and invade, facilitating their intravasation into microvessels. However, the actual molecules towards which the cells migrate remain elusive. This modified invasion assay has been developed to identify targets which drive cell migration and invasion. This technique compares the invasion index under three conditions to determine whether a specific hormone, growth factor, or cytokine plays a role in mediating the invasive potential of a cancer cell. These conditions include i) normal fetal bovine serum (FBS), ii) charcoal-stripped FBS (CS-FBS), which removes hormones, growth factors, and cytokines and iii) CS-FBS + molecule (denoted “X”). A significant change in cell invasion with CS-FBS as compared to FBS, indicates the involvement of hormones, cytokines or growth factors in mediating the change. Individual molecules can then be added back to CS-FBS to assay their ability to reverse or rescue the invasion phenotype. Furthermore, two or more factors can be combined to evaluate the additive or synergistic effects of multiple molecules in driving or inhibiting invasion. Overall, this method enables the investigator to determine whether hormones, cytokines, and/or growth factors play a role in cell invasion by serving as chemoattractants or inhibitors of invasion for a particular type of cancer cell or a specific mutant. By identifying specific chemoattractants and inhibitors, this modified invasion assay may help to elucidate signaling pathways that direct cancer cell invasion.     

Environmental and Ontogenetic Effects on Intraspecific Trait Variation of a Macrophyte Species across Five Ecological Scales

Although functional trait variability is increasingly used in community ecology, the scale- and size-dependent aspects of trait variation are usually disregarded. Here we quantified the spatial structure of shoot height, branch length, root/shoot ratio and leaf number in a macrophyte species Potamogeton maackianus, and then disentangled the environmental and ontogenetic effects on these traits. Using a hierarchical nested design, we measured the four traits from 681 individuals across five ecological scales: lake, transect, depth stratus, quadrat and individual. A notable high trait variation (coefficient variation: 48–112%) was observed within species. These traits differed in the spatial structure, depending on environmental factors of different scales. Shoot height and branch length were most responsive to lake, transect and depth stratus scales, while root/shoot ratio and leaf number to quadrat and individual scales. The trait variations caused by environment are nearly three times higher than that caused by ontogeny, with ontogenetic variance ranging from 21% (leaf number) to 33% (branch length) of total variance. Remarkably, these traits showed non-negligible ontogenetic variation (0–60%) in each ecological scale, and significant shifts in allometric trajectories at lake and depth stratus scales. Our results highlight that environmental filtering processes can sort individuals within species with traits values adaptive to environmental changes and ontogenetic variation of functional traits was non-negligible across the five ecological scales.     

Environmental Stress, Bottom-up Effects, and Community Dynamics: Integrating Molecular-Physiological and Ecological Approaches

Environmental stress and nutrient/productivity models predict the responses of community structure along gradients of physical conditions and bottom-up effects. Although both models have succeeded in helping to understand variation in ecological communities, most tests have been qualitative. Until recently, two roadblocks to more quantitative tests in marine environments have been a lack of (1) inexpensive, field-deployable technology for quantifying (e.g.) temperature, light, salinity, chlorophyll, and productivity, and (2) methods of quantifying the sub-organismal mechanisms linking environmental conditions to their ecological expression. The advent of inexpensive remote-sensing technology, adoption of molecular techniques such as quantification of heat-shock proteins and RNA:DNA ratios, and the formation of interdisciplinary alliances between ecologists and physiologists has begun to overcome these roadblocks. An integrated eco-physiological approach focuses on the determinants of: distributional limits among microhabitat patches and along (local-scale) environmental gradients (e.g., zonation); among-site (mesoscale) differences in community pattern; and geographic (macroscale) differences in ecosystem structure. These approaches promise new insights into the physiological mechanisms underlying variation in processes such as species interactions, physical disturbance, survival and growth. Here, we review two classes of models for community dynamics, and present examples of ecological studies of these models in consumer-prey systems. We illustrate the power of new molecular tools to characterize the sub-organismal responses of some of the same consumers and prey to thermal stress and food concentration. Ecological and physiological evidence tends to be consistent with model predictions, supporting our argument that we are poised to make major advances in the mechanistic understanding of community dynamics along key environmental gradients.     

Exploring Bacterioplankton Growth and Protein Synthesis to Determine Conversion Factors Across a Gradient of Dissolved Organic Matter

The effect of bacterial specific growth rates of abundance (micro) and protein synthesis (b) on conversion factor (CF) variability was explored in order to provide an alternative approach to the controversial application of just one universal CF to field data. Nine regrowth cultures (RCs) were set up from very diverse aquatic ecosystems, controlling temperature and adding N and P to avoid mineral limitation and force organic carbon limitation. The values of micro varied one order of magnitude from 0.26 to 3.34 d(-1), whereas b values varied two orders of magnitude from 0.28 to 34.87 d(-1). We found no relationships between micro or b values and the dissolved organic carbon (DOC) concentration or the dissolved organic matter (DOM) quality indexes assayed. Abundance and protein synthesis increased exponentially and synchronously in four RCs, leading to balanced growth (micro = b). In contrast, abundance and protein synthesis increased logistically in the other five RCs and b values were significantly higher than g values, leading to unbalanced growth (micro not equal b). CFs ranged from 0.0062 to 0.0576 x 10(18) cells mol leucine(-1) with an average of 0.0305 x 10(18) cells mol leucine(-1). CFs obtained in RCs with balanced growth were generally higher than CFs obtained in RCs with unbalanced growth and were not alike, impeding the establishment of an upper limit for CFs. A positive and significant relationship (n = 8, p < 0.0 1, r2 = 0.71) was found between CFs and DOC concentration (CF (x10(18) cells mol leucine(-1)) = 0.0104 + 0.0094 DOC (mM)) when the value for the most productive system was excluded. This function permits the estimation of site-specific CFs based on DOC concentration instead of the controversial use of a single CF for different systems.     

The Irreversible C3 to CAM Shift in Well-watered and Salt-stressed Plants of Mesembryanthemum crystallinum is under Strict Ontogenetic Control

The shift from C₃ to CAM was investigated as a function of both leaf and plant age in well-watered and salt-stressed (300 mM NaCl solution) plants of Mesembryanthemum crystallinum. Initiation of a night-time accumulation of malic acid, the decisive criterion of CAM, was followed in plants that were continuously stressed at different points in their life cycle. The deinducibility of CAM was examined after the release from stress by extensively rinsing the potting soil with de-mineralized water. Our results show that in M. crystallinum CAM is under strict developmental control, since CAM appeared only when a certain stage of development of the whole plant was reached. CAM was not present in any plant before this threshold, which was the same in salt-stressed as well as in well-watered plants. The metabolic shift coincided with the change from the seedling to the juvenile growth phase, and not with that from vegetative to reproductive growth, represented by the start of branching. The latter is timed to the end of extension growth. In well-watered plants, after this decisive point in development, a weak nighttime accumulation of malic acid could be measured (? 0.05 mol kg_DW^?1) in the oldest, mature leaves but not in young, developing ones. This “CAM capacity” gradually increased up to 0.2 mol kg_DE^?1 with further plant ageing. Leaf senescence, characterized by wilting and yellowing, diminished the CAM activity. In mature leaves salt stress drastically enhanced the magnitude of diurnal fluctuation in malic acid content. Removal of salt stress did not deinduce CAM activity, but diminished the amplitude of malic acid oscillations to some extent in those plants which had been stressed from early in their life cycle. In these plants, salt stress delayed plant development and growth thus retarding the life cycle. Well-watered plants, for example, branched about three weeks earlier than those that had been stressed continuously from one week after germination. After removal of stress a quasi-preserved earlier developmental stage in relation to the control plants determined the weaker CAM expression.     

Asexual Endophytes in a Native Grass: Tradeoffs in Mortality, Growth, Reproduction, and Alkaloid Production

Neotyphodium endophytes are asexual, seed-borne fungal symbionts that are thought to interact mutualistically with their grass hosts. Benefits include increased growth, reproduction, and resistance to herbivores via endophytic alkaloids. Although these benefits are well established in infected introduced, agronomic grasses, little is known about the cost and benefits of endophyte infection in native grass populations. These populations exist as mosaics of uninfected and infected plants, with the latter often comprised of plants that vary widely in alkaloid content. We tested the costs and benefits of endophyte infections with varying alkaloids in the native grass Achnatherum robustum (sleepygrass). We conducted a 4-year field experiment, where herbivory and water availability were controlled and survival, growth, and reproduction of three maternal plant genotypes [uninfected plants (E−), infected plants with high levels of ergot alkaloids (E+A+), and infected plants with no alkaloids (E+A−)] were monitored over three growing seasons. Generally, E+A+ plants had reduced growth over the three growing seasons and lower seed production than E− or E+A− plants, suggesting a cost of alkaloid production. The reduction in vegetative biomass in E+A+ plants was most pronounced under supplemented water, contrary to the prediction that additional resources would offset the cost of alkaloid production. Also, E+A+ plants showed no advantage in growth, seed production, or reproductive effort under full herbivory relative to E− or E+A− grasses, contrary to the predictions of the defensive mutualism hypothesis. However, E+A+ plants had higher overwintering survival than E+A− plants in early plant ontogeny, suggesting that alkaloids associated with infection may protect against below ground herbivory or harsh winter conditions. Our results suggest that the mosaic of E−, E+A+, and E+A− plants observed in nature may result from varying biotic and abiotic selective factors that maintain the presence of uninfected plants and infected plants that vary in alkaloid production.     

Integrating structure,bioinformatics, and enzymology to discover function: BioH,a new carboxylesterase from Escherichia coli

Structural proteomics projects are generating three-dimensional structures of novel, uncharacterized proteins at an increasing rate. However, structure alone is often insufficient to deduce the specific biochemical function of a protein. Here we determined the function for a protein using a strategy that integrates structural and bioinformatics data with parallel experimental screening for enzymatic activity. BioH is involved in biotin biosynthesis in Escherichia coli and had no previously known biochemical function. The crystal structure of BioH was determined at 1.7 A resolution. An automated procedure was used to compare the structure of BioH with structural templates from a variety of different enzyme active sites. This screen identified a catalytic triad (Ser82, His235, and Asp207) with a configuration similar to that of the catalytic triad of hydrolases. Analysis of BioH with a panel of hydrolase assays revealed a carboxylesterase activity with a preference for short acyl chain substrates. The combined use of structural bioinformatics with experimental screens for detecting enzyme activity could greatly enhance the rate at which function is determined from structure.     

Burning and Grazing Management in a California Grassland: Growth, Mortality, and Recruitment of Nassella pulchra

Abstract Annual grasslands in California are often managed with seasonal grazing and prescribed burning on the assumption that such practices have long‐term benefits for native species. Mature native perennial bunchgrasses, particularly Nassella pulchra (purple needlegrass), are often the focal species, although very little is known about responses at different life history stages. Thus, important questions remain about long‐term population dynamics of both mature plants and seedling recruitment. In plots receiving repeated grazing and burning events over 7 years, mortality of mature plants was threefold higher on mounds than on intermounds and likely reflected increased competition intensity associated with increased resource availability in deeper soil. Burning and grazing treatments had strong positive effects on basal area of mature N. pulchra. However, plants in grazed plots that were not burned contained considerable standing dead biomass. Topographic location strongly influenced growth as intermound plants grew relatively more than mound plants, but the effects on growth of burning and grazing did not vary with topographic location. In mapped plots N. pulchra recruitment was very low, and overall density dropped an average of 31%. However, a significant time‐by‐burning effect indicated that survival was significantly higher in burned plots. After 7 years of repeated treatments, effects of burning and grazing management on mature N. pulchra were positive but not for all phenological stages. Understanding long‐term influence of management on bunchgrass populations may not be easy to determine because short‐term results may not reflect long‐term responses and some life cycle dynamics may be observed only over very long periods.     

Small and Large Ribosomal Subunit Deficiencies Lead to Distinct Gene Expression Signatures that Reflect Cellular Growth Rate

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Application of a Hybrid Forest Growth Model to Evaluate Climate Change Impacts on Productivity,Nutrient Cycling and Mortality in a Montane Forest Ecosystem

Climate change introduces considerable uncertainty in forest management planning and outcomes, potentially undermining efforts at achieving sustainable practices. Here, we describe the development and application of the FORECAST Climate model. Constructed using a hybrid simulation approach, the model includes an explicit representation of the effect of temperature and moisture availability on tree growth and survival, litter decomposition, and nutrient cycling. The model also includes a representation of the impact of increasing atmospheric CO₂ on water use efficiency, but no direct CO₂ fertilization effect. FORECAST Climate was evaluated for its ability to reproduce the effects of historical climate on Douglas-fir and lodgepole pine growth in a montane forest in southern British Columbia, Canada, as measured using tree ring analysis. The model was subsequently used to project the long-term impacts of alternative future climate change scenarios on forest productivity in young and established stands. There was a close association between predicted sapwood production and measured tree ring chronologies, providing confidence that model is able to predict the relative impact of annual climate variability on tree productivity. Simulations of future climate change suggest a modest increase in productivity in young stands of both species related to an increase in growing season length. In contrast, results showed a negative impact on stemwood biomass production (particularly in the case of lodgepole pine) for established stands due to increased moisture stress mortality.     

Recruitment,Growth and Mortality of an Antarctic Hexactinellid Sponge,Anoxycalyx joubini

Polar ecosystems are sensitive to climate forcing, and we often lack baselines to evaluate changes. Here we report a nearly 50-year study in which a sudden shift in the population dynamics of an ecologically important, structure-forming hexactinellid sponge, Anoxycalyx joubini was observed. This is the largest Antarctic sponge, with individuals growing over two meters tall. In order to investigate life history characteristics of Antarctic marine invertebrates, artificial substrata were deployed at a number of sites in the southern portion of the Ross Sea between 1967 and 1975. Over a 22-year period, no growth or settlement was recorded for A. joubini on these substrata; however, in 2004 and 2010, A. joubini was observed to have settled and grown to large sizes on some but not all artificial substrata. This single settlement and growth event correlates with a region-wide shift in phytoplankton productivity driven by the calving of a massive iceberg. We also report almost complete mortality of large sponges followed over 40 years. Given our warming global climate, similar system-wide changes are expected in the future.     

Long-Range Genomic Enrichment,Sequencing, and Assembly to Determine Unknown Sequences Flanking a Known microRNA

Conserved plant microRNAs (miRNAs) modulate important biological processes but little is known about conserved cis-regulatory elements (CREs) surrounding MIRNA genes. We developed a solution-based targeted genomic enrichment methodology to capture, enrich, and sequence flanking genomic regions surrounding conserved MIRNA genes with a locked-nucleic acid (LNA)-modified, biotinylated probe complementary to the mature miRNA sequence. Genomic DNA bound by the probe is captured by streptavidin-coated magnetic beads, amplified, sequenced and assembled de novo to obtain genomic DNA sequences flanking MIRNA locus of interest. We demonstrate the sensitivity and specificity of this enrichment methodology in Arabidopsis thaliana to enrich targeted regions spanning 10–20 kb surrounding known MIR166 and MIR165 loci. Assembly of the sequencing reads successfully recovered all targeted loci. While further optimization for larger, more complex genomes is needed, this method may enable determination of flanking genomic DNA sequence surrounding a known core (like a conserved mature miRNA) from multiple species that currently don''t have a full genome assembly available.