Scaling up evolutionary responses to elevated CO2: lessons from Arabidopsis

Results from norm of reaction studies and selection experiments indicate that elevated CO₂ will act as a selective agent on natural plant populations, especially for C₃ species that are most sensitive to changes in atmospheric CO₂ concentration. Evolutionary responses to CO₂ may alter plant physiology, development rate, growth, and reproduction in ways that cannot be predicted from single generation studies. Moreover, ecological and evolutionary changes in plant communities will have a range of consequences at higher spatial scales and may cause substantial deviations from ecosystem level predictions based on short‐term responses to elevated CO₂. Therefore, steps need to be taken to identify the plant traits that are most likely to evolve at elevated CO₂, and to understand how these changes may affect net primary productivity within ecosystems. These processes may range in scale from molecular and physiological changes that occur among genotypes at the individual and population levels, to changes in community‐ and ecosystem‐level productivity that result from the integrative effects of different plant species evolving simultaneously. In this review, we (1) synthesize recent studies investigating the role of atmospheric CO₂ as a selective agent on plants, (2) discuss possible control points during plant development that may change in response to selection at elevated CO₂ with an emphasis at the primary molecular level, and (3) provide a quantitative framework for scaling the evolutionary effects of CO₂ on plants in order to determine changes in community and ecosystem productivity. Furthermore, this review points out that studies integrating the effects of plant evolution in response to elevated CO₂ are lacking, and therefore more attention needs be devoted to this issue among the global change research community.     

Fingerprinting Diazotroph Communities in the Chesapeake Bay by Using a DNA Macroarray

Investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on PCR amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifH. Recent work has suggested that DNA macroarrays provide semiquantitative fingerprints of diversity within mixtures of nifH amplicons (G. F. Steward, B. D. Jenkins, B. B. Ward, and J. P. Zehr, Appl. Environ. Microbiol. 70:1455-1465, 2004). Here we report the application of macroarrays for a study in the Chesapeake Bay. Samples from different locations in the bay yielded distinct fingerprints. Analysis of replicates and samples from different locations by cluster analysis showed that replicates clustered together, whereas different samples formed distinct clusters. There was a correspondence between the hybridization pattern observed and that predicted from the distribution of sequence types in a corresponding clone library. Some discrepancies between the methods were observed which are likely a result of the high nifH sequence diversity in the Chesapeake Bay and the limited number of sequences represented on this version of the array. Analyses of sequences in the clone library indicate that the Chesapeake Bay harbors unique, phylogenetically diverse diazotrophs. The macroarray hybridization patterns suggest that there are spatially variable communities of diazotrophs, which have been confirmed by quantitative PCR methods (S. M. Short, B. D. Jenkins, and J. P. Zehr, Appl. Environ. Microbiol., in press). The results show that DNA macroarrays have great potential for mapping the spatial and temporal variability of functional gene diversity in the environment.     

Measuring Topological Congruence by Extending Character Techniques

A measure of topological congruence which is an extension of the Mickevich–Farris character incongruence metric ( i.e. , ILD; Mickevich and Farris, 1981) is proposed. Group inclusion characters (1 = member of a clade; 0 = not a member) are constructed for each topology to be considered. The sets of characters derived from the topologies are then compared for character incongruence due to data set combination. Each homoplasy signifies a disagreement among topological statements. The value is normalized for potential maximum incongruence to adjust values for unresolved topologies. This measure is compared to other topological and character congruence techniques and explored in test data.     

The effects of habitat- and diet-based cues on association preferences in three-spined sticklebacks

A number of recent articles have investigated the potentialof familiarity preferences to influence group membership infree-ranging animals. However, it is not clear to which extentindividual recognition or a more general recognition of a groupodor is responsible for familiarity preferences. First, we testedthe sensory basis of the recognition of familiars in stickleback.When allowed to choose between a familiar and a nonfamiliarstimulus shoal on the basis of both visual and chemical communication,visual communication only, and chemical communication only,the preference of focal fish for familiars was shown to dependon the presence of chemical cues. We subsequently investigatedthe effects of recent habitat and diet on shoaling preferencesin the three-spined stickleback (Gasterosteus aculeatus). Experimentalfish were divided into four treatment groups consisting of twowater treatments (saline and freshwater) and two diet treatments(Daphnia spp. and bloodworm). Focal fish subsequently showedsignificant association preferences for groups of nonfamiliarfish that had undergone the same water or diet treatment asthemselves. These data indicate that individual recognitionis not a prerequisite for the expression of association preferences.     

Characterisation of micromonosporae from aquatic environments using molecular taxonomic methods

Large numbers of strains assigned to the genus Micromonospora on the basis of typical colonial and pigmentation features were isolated from diverse aquatic sediments using a standard selective isolation procedure. Two hundred and six isolates and eight representatives of the genus Micromonospora were assigned to 24 multimembered groups based on a numerical analysis of banding patterns generated using BOX and ERIC primers. Representatives of multimembered groups encompassing isolated micromonosporae were the subject of 16S rRNA gene sequencing analyses. Good congruence was found between the molecular fingerprinting and 16S rRNA sequence data indicating that the groups based upon the former are taxonomically meaningful. Nearly all of the isolates that were chosen for the 16S rRNA gene sequencing analyses showed that the ecosystems studied are a rich source of novel micromonosporae. These findings have implications for high throughput screening for novel micromonosporae as BOX and ERIC fingerprinting, which is rapid and reproducible, can be applied as a robust dereplication procedure to indicate which environmental isolates have been cultured previously.     

Repeat-protein folding: new insights into origins of cooperativity, stability, and topology

Although our understanding of globular protein folding continues to advance, the irregular tertiary structures and high cooperativity of globular proteins complicates energetic dissection. Recently, proteins with regular, repetitive tertiary structures have been identified that sidestep limitations imposed by globular protein architecture. Here we review recent studies of repeat-protein folding. These studies uniquely advance our understanding of both the energetics and kinetics of protein folding. Equilibrium studies provide detailed maps of local stabilities, access to energy landscapes, insights into cooperativity, determination of nearest-neighbor interaction parameters using statistical thermodynamics, relationships between consensus sequences and repeat-protein stability. Kinetic studies provide insight into the influence of short-range topology on folding rates, the degree to which folding proceeds by parallel (versus localized) pathways, and the factors that select among multiple potential pathways. The recent application of force spectroscopy to repeat-protein unfolding is providing a unique route to test and extend many of these findings.     

Regulation of the paracellular Na+ and Cl- conductances by the NaCl-generated osmotic gradient in a manner dependent on the direction of osmotic gradients

In the present study, we investigated the effect of osmolality on the paracellular ion conductance (Gp) composed of the Na⁺ conductance (G_Na) and the Cl⁻ conductance (G_Cl). An osmotic gradient generated by NaCl with relatively apical hypertonicity (NaCl-absorption-direction) induced a large increase in the G_Na associated with a small increase in the G_Cl, whereas an osmotic gradient generated by NaCl with relatively basolateral hypertonicity (NaCl-secretion-direction) induced small increases in the G_Na and the G_Cl. These increases in the Gp caused by NaCl-generated osmotic gradients were diminished by the application of sucrose canceling the NaCl-generated osmotic gradient. The osmotic gradient generated by basolateral application of sucrose without any NaCl gradients had little effects on the Gp. However, this basolateral application of sucrose produced a precondition drastically quickening the time course of the action of the NaCl-generated osmotic gradient on the Gp. Further, we found that application of the basolateral hypotonicity generated by reduction of NaCl concentration shifted the localization of claudin-1 to the apical from the basolateral side. These results indicate that the osmotic gradient regulates the paracellular ion conductive pathway of tight junctions via a mechanism dependent on the direction of NaCl gradients associated with a shift of claudin-1 localization to the apical side in renal A6 epithelial cells.     

Comprehensive proteomics analysis of autophagy-deficient mouse liver

Autophagy is a bulk protein degradation system for the entire organelles and cytoplasmic proteins. Previously, we have shown the liver dysfunction by autophagy deficiency. To examine the pathological effect of autophagy deficiency, we examined protein composition and their levels in autophagy-deficient liver by the proteomic analysis. While impaired autophagy led to an increase in total protein mass, the protein composition was largely unchanged, consistent with non-selective proteins/organelles degradation of autophagy. However, a series of oxidative stress-inducible proteins, including glutathione S-transferase families, protein disulfide isomerase and glucose-regulated proteins were specifically increased in autophagy-deficient liver, probably due to enhanced gene expression, which is induced by accumulation of Nrf2 in the nuclei of mutant hepatocytes. Our results suggest that autophagy deficiency causes oxidative stress, and such stress might be the main cause of liver injury in autophagy-deficient liver.     

Exposure to perflubron is associated with decreased Syk phosphorylation in human neutrophils.

Liquid ventilation with perflubron is associated with reduced neutrophil recruitment into the lung during acute injury. Perflubron also reduces chemotactic responses, the respiratory burst, and cytokine production in neutrophils and in alveolar macrophages in vitro. In the current studies, the effect of perflubron on neutrophil chemotaxis to formyl-Met-Leu-Phe (fMLP) and phagocytosis of opsonized sheep erythrocytes (EA) correlated with decreased phosphorylation of Syk, an important intracellular second messenger in pathways regulating neutrophil functional responses. Brief (5 min) exposure of neutrophils to perflubron resulted in a dose-dependent reduction in chemotaxis to fMLP and reduced phagocytosis of EA but no apparent morphological changes as seen by electron microscopy. Concurrently, there was a reduction in both total cytosolic tyrosine phosphorylation and Syk phosphorylation. Binding studies indicated that this effect was neither a result of impaired ligand-receptor affinity nor a change in the number of fMLP receptors available on the neutrophil surface. These results suggest that perflubron nonspecifically affects cellular activation as measured by tyrosine phosphorylation perhaps by interfering with transmembrane signal transduction.