Introducing the biogeographic species pool

The species pool concept has played a central role in the development of ecological theory for at least 60 yr. Surprisingly, there is little consensus as to how one should define the species pool, and consequently, no systematic approach exists. Because the definition of the species pool is essential to infer the processes that shape ecological communities, there is a strong incentive to develop an ecologically realistic definition of the species pool based on repeatable and transparent analytical approaches. Recently, several methodological tools have become available to summarize repeated patterns in the geographic distribution of species, phylogenetic clades and taxonomically broad lineages. Here, we present three analytical approaches that can be used to define what we term ‘the biogeographic species pool’: distance‐based clustering analysis, network modularity analysis, and assemblage dispersion fields. The biogeographic species pool defines the pool of potential community members in a broad sense and represents a first step towards a standardized definition of the species pool for the purpose of comparative ecological, evolutionary and biogeographic studies.     

Phytoplankton biomass response to nitrogen inputs: a method for WFD boundary setting applied to Danish coastal waters

Reference conditions and boundary values between Water Framework Directive status classes were estimated for phytoplankton biomass from empirical relationships relating: (1) nitrogen inputs from land to total nitrogen (TN) concentrations and (2) TN concentrations to chlorophyll a (chl a) concentrations. Different periods during the last >100 years were used to characterise hypothesised ecological status, and a hind-casted time series was used to define boundary values for nitrogen inputs. Nitrogen levels in 35 coastal water bodies around Denmark were significantly related to inputs from land to various degrees (factor of 50) reflecting gradients from open coastal to freshwater-influenced estuaries. Significant differences in the relationship between chl a and TN across sites were found, suggesting that previous response models have been too simple and uncertain. Reference and boundary values for chl a, estimated with a relative uncertainty of 5–20%, varied substantially between sites, and the boundary value between good and moderate status was 6–81% higher than the reference condition with an average of 28%. Differences in bioavailability of nutrient sources and grazing pressure are important factors controlling site-specific phytoplankton biomass, and models for predicting phytoplankton responses to nutrient reductions must account for these. The boundary setting must be adaptive to incorporate improved quantitative knowledge and effects of shifting baselines.     

Capturing, sharing and analysing biophysical data from protein engineering and protein characterization studies

Large amounts of data are being generated annually on the connection between the sequence, structure and function of proteins using site-directed mutagenesis, protein design and directed evolution techniques. These data provide the fundamental building blocks for our understanding of protein function, molecular biology and living organisms in general. However, much experimental data are never deposited in databases and is thus ‘lost’ in journal publications or in PhD theses. At the same time theoretical scientists are in need of large amounts of experimental data for benchmarking and calibrating novel predictive algorithms, and theoretical progress is therefore often hampered by the lack of suitable data to validate or disprove a theoretical assumption. We present PEAT (Protein Engineering Analysis Tool), an application that integrates data deposition, storage and analysis for researchers carrying out protein engineering projects or biophysical characterization of proteins. PEAT contains modules for DNA sequence manipulation, primer design, fitting of biophysical characterization data (enzyme kinetics, circular dichroism spectroscopy, NMR titration data, etc.), and facilitates sharing of experimental data and analyses for a typical university-based research group. PEAT is freely available to academic researchers at http://enzyme.ucd.ie/PEAT.     

Circulating matrix metalloproteinase-9 is associated with cardiovascular risk factors in a middle-aged normal population

Background

Elevated levels of circulating matrix metalloproteinase-9 (MMP-9) have been demonstrated in patients with established coronary artery disease (CAD). The aim of this study was to analyse levels of MMP-9 in a population free from symptomatic CAD and investigate their associations with cardiovascular (CV) risk factors, including C-reactive protein (CRP).

Methods

A cross-sectional study was performed in a population based random sample aged 45–69 (n = 345, 50% women). MMP-9 levels were measured in EDTA-plasma using an ELISA-method. CV risk factors were measured using questionnaires and standard laboratory methods.

Results

Plasma MMP-9 was detectable in all participants, mean 38.9 ng/mL (SD 22.1 ng/mL). Among individuals without reported symptomatic CAD a positive association (p<0.001) was seen, for both men and women, of MMP-9 levels regarding total risk load of eight CV risk factors i.e. blood pressure, dyslipidemia, diabetes, obesity, smoking, alcohol intake, physical activity and fruit and vegetable intake. The association was significant also after adjustment for CRP, and was not driven by a single risk factor alone. In regression models adjusted for age, sex, smoking, alcohol intake and CRP, elevated MMP-9 levels were independently positively associated with systolic blood pressure (p = 0.037), smoking (p<0.001), alcohol intake (p = 0.003) and CRP (p<0.001). The correlation coefficient between MMP-9 and CRP was r = 0.24 (p<0.001).

Conclusions

In a population without reported symptomatic CAD, MMP-9 levels were associated with total CV risk load as well as with single risk factors. This was found also after adjustment for CRP.     

Birth, morphologic, and blood characteristics of free-ranging white-tailed deer neonates

Winter severity is a primary factor influencing deer survival and reproduction in northern climates. Prolonged, harsh winters can adversely affect body condition of does, resulting in depressed morphologic development of neonates. In this study, we captured 59 white-tailed deer (Odocoileus virginianus) neonates (28 in 2001 and 31 in 2002), following two distinctly different winters, one severe and the other historically mild. Vaginal implant transmitters allowed exact age to be determined for 73% of the neonates; new hoof growth was used to estimate age (days) of the other 27%. Birthdate and morphologic measurements of neonates (i.e., birth mass, new hoof growth, hoof length) were compared by sex and capture year. For known-age neonates (n=43), there was a year-by-sex interaction effect (P=0.01) on birthdate, being later for females during spring 2001 compared with 2002, which was consistent with a significant (P=0.03) year-by-sex interaction for total hoof length (22.3 mm [SE=0.9] and 20.3 [SE=0.8] for females and males in 2001; 19.9 [SE=1.0] and 22.1 [SE=1.0] for females and males in 2002). Interestingly, there was no effect of year on birth mass or birthdate of known-age neonates. A year-by-sex interaction (P=0.04) was determined for birthdates of estimated age (5 yr old were born later (P<0.01) than fawns born to dams 相似文献   

Bacterial Growth on Surfaces: Automated Image Analysis for Quantification of Growth Rate-Related Parameters

A fast routine method for estimating bacterial cell growth rates by using the metachromatic dye acridine orange is described. The method allows simultaneous estimates of cellular RNA and DNA contents of single cells. Acridine orange staining can be used as a nonspecific supplement to quantitative species-specific hybridizations with fluorescence-labelled ribosomal probes to estimate the single-cell concentration of RNA. By automated analysis of digitized images of stained cells, we determined four independent growth rate-related parameters: cellular RNA and DNA contents, cell volume, and the frequency of dividing cells in a cell population. These parameters were used to compare physiological states of liquid-suspended and surface-growing Pseudomonas putida KT2442 in chemostat cultures. The major finding is that the correlation between substrate availability and cellular growth rate found for the free-living cells was not observed for the surface-bound cells; in contrast, the data indicate an almost constant growth rate for attached cells which was independent of the dilution rate in the chemostat.     

Dielectric Study of the Physical State of Electrolytes and Water Within Bacillus cereus Spores

Dielectric measurements revealed that dormant spores of Bacillus cereus have extremely low conductivities at high frequencies (50 MHz) and so must contain remarkably low concentrations of mobile ions both within the core and in the surrounding integuments. Activation, germination, and outgrowth were all accompanied by increases in conductivity of the cells and their suspending medium, and this result indicated that intracellular electrolytes had become ionized and leaked from the spores. High-frequency dielectric constants of spores were consistent with normal states for cell water. These values increased during successive stages of development from dormant spore to vegetative bacillus, and they could be directly related to increases in cell water content. In all, the results refuted a model of the dormant spore involving freely mobile, ionized electrolytes and supported a model involving electrostatically bound electrolytes.     

Passive Electrical Properties of Microorganisms: IV. Studies of the Protoplasts of Micrococcus lysodeikticus

Observations of protoplasts of Micrococcus lysodeikticus show that removal of the cell wall of this organism decreases the dielectric constant by two orders of magnitude. The upper limit of the effective, homogeneous conductivity for the protoplast is 0.001 mho/m as compared with 0.045 mho/m for the intact cell. These results conclusively demonstrate the dominant effect of the cell wall on the low frequency dielectric properties of bacteria.