Rhizosphere carbon flow measurement and implications: from isotopes to reporter genes

Despite the fundamental importance of rhizosphere C-flow in managed and natural systems, reliable measurement/resolution of C-flow and assessment of its consequences have largely remained elusive to soil biologists. Techniques involving both radioactive (¹⁴C) and stable (¹³C) isotopes of carbon have made some progress in terms of studying rhizosphere C-flow. Pulse-chase techniques have been used effectively to study dynamics of C-transfer to the rhizosphere and rhizosphere microbial biomass. The information obtained through pulse-chase is strongly dependent on the chase period following the labelling event. Continuous labelling is primarily used to determine plant inputs to soil over an extended time period and includes all kinds of C input – from root turnover, root respiration, root exudation, production of mucilage, etc. One of the main constraints to both approaches is that distinguishing root from microbial respiration is difficult, if not impossible. ¹³C techniques have gone some way towards resolving this difficulty, although ¹³C signatures in the plant–soil system are not easy to interpret and detailed resolution of carbon flow through different components of the rhizosphere biomass is unlikely to be achieved in such an inherently `noisy' system. Recent developments in molecular biology now provide a new opportunity to resolve rhizosphere C-flow and its implications. Reporter gene systems where, for example, rhizobacteria are marked with lux and unstable gfp reporters, overcome the difficulty of distinguishing root and microbial C fluxes and complement the isotopic and more traditional approaches. Reporter systems have now begun to resolve the competitive C sink strengths of different components of the rhizosphere microbial community and assess how a rhizobacterial inoculum may change C-flow in applications such as disease control and rhizoremediation of contaminated land. Fusion of reporter genes to nutrient (N and P) starvation genes in rhizobacteria has also enabled in situ characterisation of nutrient depletion around the root and assessment of the impact of changes in C-flow (such as those induced by climate change) on nutrient depletion dynamics. The availability of an integrated approach involving isotopic, molecular biological and other techniques now offers an exciting new era where reliable measurement and resolution of rhizosphere C-flow (and its consequences) can contribute to our understanding of ecosystem function and to management of crop-microbe interactions.     

Theoretic considerations regarding slow cooling and vitrification during cryopreservation

This review presents the methodology of using theoretic models for development of cryopreservation protocols by designing specific cooling profiles and selecting appropriate external conditions to optimize cryopreservation survival. Biophysical events during the processes of cryopreservation were examined and corresponding theoretic equations were used to simulate cryopreservation procedures under various slow cooling conditions for rat zygotes in the presence of DMSO, using a 0.25-mL plastic straw as the container. Simulation revealed three regions with their own characteristics and cryopreservation relevance. In addition, this review discusses vitrification cryopreservation using two-step additions. The effects of exposure durations and exposure temperatures on cell survival and subsequent development rates were examined in a series of cryopreservation experiments. Values of accumulative osmotic damage were used to quantitatively examine the magnitude of the associated osmotic damage during cryoprotective agent (CPA) additions and dilutions. In these investigations, oocyte blastocyst rates were highly correlated with the values of accumulative osmotic damage in the processes of CPA additions/dilutions. This review emphasizes the most essential step of the selection of the cell container in the process of cryopreservation, and provides practical suggestions and guidelines for optimizing slow cooling protocols. The review stresses that conducting CPA addition steps at 25 °C would be preferable for vitrification. It also suggests that the final dilution process needs more systematic research to optimize vitrification procedures.     

Collecting And Measuring Wound Exudate Biochemical Mediators In Surgical Wounds

We describe a methodology by which we are able to collect and measure biochemical inflammatory and nociceptive mediators at the surgical wound site. Collecting site-specific biochemical markers is important to understand the relationship between levels in serum and surgical wound, determine any associations between mediator release, pain, analgesic use and other outcomes of interest, and evaluate the effect of systemic and peripheral drug administration on surgical wound biochemistry. This methodology has been applied to healthy women undergoing elective cesarean delivery with spinal anesthesia. We have measured wound exudate and serum mediators at the same time intervals as patient''s pain scores and analgesics consumption for up to 48 hours post-cesarean delivery. Using this methodology we have been able to detect various biochemical mediators including nerve growth factor (NGF), prostaglandin E2 (PG-E2) substance P, IL-1β, IL-2, IL-4, IL-6, IL-7, IL-8, IL-10, IL-12, IL-13, IL-17, TNFα, INFγ, G-CSF, GM-CSF, MCP-1 and MIP-1β. Studies applying this human surgical wound bioassay have found no correlations between wound and serum cytokine concentrations or their time-release profile (J Pain. 2008; 9(7):650-7).¹ We also documented the utility of the technique to identify drug-mediated changes in wound cytokine content (Anesth Analg 2010; 111:1452-9).²     

Molecular modeling and analysis of human and plant endo-β-N-acetyl- glucosaminidases for mutations effects on function

Endo- β-N-acetylgucosaminidases (ENGases) are the enzymes that catalyze both hydrolysis and transglycosylation reactions. It is of interest to study ENGases because of their ability to synthesize glycopeptides. Homology models of Human, Arabidopsis thaliana and Sorghum ENGases were developed and their active sites marked based on information available from Arthrobacter protophormiae (PDB ID: 3FHQ) ENGase. Further, these models were docked with the natural substrate GlcNAc-Asn and the inhibitor Man₃GlcNAc-thiazoline. The catalytic triad of Asn, Glu and Tyr (N171, E173 and Y205 of bacteria) were found to be conserved across the phyla. The crucial Y299F mutation showing 3 times higher transglycosylation activity than in wild type Endo-A is known. The hydrolytic activity remained unchanged in bacteria, while the transglycosylation activity increased. This Y to F change is found to be naturally evolved and should be attributing higher transglycosylation rates in human and Arabidopsis thaliana ENGases. Ligand interactions Ligplots revealed the interaction of amino acids with hydrophobic side chains and polar uncharged side chain amino acids. Thus, structure based molecular model-ligand interactions provide insights into the catalytic mechanism of ENGases and assist in the rational engineering of ENGases.     

The relationship of body size to survivorship of hatchling snapping turtles (Chelydra serpentina): an evaluation of the “bigger is better” hypothesis

In many organisms, body size is positively correlated with traits that are presumably related to fitness. If directional selection frequently favors larger offspring (the “bigger is better” hypothesis), the results of such selection should be detectable with field experiments. We tested the “bigger is better” hypothesis in hatchling snapping turtles (Chelydra serpentina) by conducting one long-term and three short-term experiments on the University of Michigan E.S. George Reserve in southeastern Michigan. In the fall of 1995 and 1996, we released hatchlings at artificial nests separated from the nearest wetland by fences. We recorded the proportion of hatchlings recaptured, the time it took hatchlings to move to fences from artificial nests 45, 55, and 80 m away, and dispersion along the fence. We determined whether the response variables and probability of recapture at fences were associated with hatchling body size. During 1995, average travel times of hatchlings from the experimental nests were not related to distance from the fence; however, time to recapture was positively correlated with dispersion from the zero point on the fence, and the maximum time to reach the fence was almost twice as long for hatchlings from the 80-m nest compared to those from the 45-m nest. Sixty-seven percent of the hatchlings reached the fence and the proportions doing so from each nest were not different. Body size was not significantly related to probability of recapture in either of the 1995 experiments. In 1996, 59% of released hatchlings were recaptured. Time to recapture was not related to dispersion from the zero point or to body size. Cubic spline analysis suggested stabilizing selection on body size. We also conducted a set of long-term hatchling release experiments between 1980–1993 to compare the survival of hatchlings released at nest sites to that of hatchlings released directly into marshes, and we looked for relationships between survivorship and hatchling body size. During 7 years in which more than 30 hatchlings were released, 413 hatchlings were released directly into the marsh and 262 were released at nests: their probability of survival did not differ. Over all years, for both release groups combined and for each group separately, survival was not related to body size. In 1983 alone, survival was also not related to body size for either group or for both groups combined. In our three short-term experiments and one long-term experiment, we found no evidence to support the “bigger is better” hypothesis. When selection on body size did occur, selection was stabilizing, not directional for larger size. Received: 4 June 1998 / Accepted: 24 June 1999     

Differences in ratings of intensity and pleasantness for the capsaicin burn between chili likers and non-likers; implications for liking development

If liking for the chili burn is acquired, then the relationshipbetween ratings of burn intensity and pleasantness in chilinon-likers should be representative of the inital response patternto chili, and in chili likers, the final acquired response pattern.Close examination of these relationships may provide insightsinto the mechanisms that mediate liking development. The experimentreported here asked chili likers (frequent users) and non-likers(very infrequent users) to make burn intensity and pleasantnessjudgements for an ascending series of capsaicin concentrationsin an attempt to define the relationship between these variables.Non-likers were found to be indifferent to low to moderate burnintensities, which were liked by chili likers. Both groups dislikedstrong burn intensities. These data provide preliminary supportfor a model of liking development whereby initially indifferentresponses develop into liking responses apparently independentof sensory changes. ² Present address: CSIRO, Sensory Research Centre, PO Box 52.North Ryde, NSW 2113, Australia.     

The three-spined stickleback as an environmental sentinel: effects of stressors on whole-body physiological indices

Indicators of a generalized stress response (changes in cortisol, glucose, RNA: DNA ratio and total protein) when measured in whole-body preparations of individual three-spined sticklebacks Gasterosteus aculeatus displayed significant alterations in response to acute (hours) and chronic (days) disturbances and food withdrawal. In addition, changes in alkali-labile phosphorous, a specific biomarker of exposure to oestrogenic contaminants, could be detected in whole-body preparations of oestrogen-exposed three-spined sticklebacks confirming that the measurement of biomarkers normally assessed in a specific tissue can be equally possible in whole fish.