Conditional mutagenesis by oligonucleotide-mediated integration of loxP sites in zebrafish.

Many eukaryotic genes play essential roles in multiple biological processes in several different tissues. Conditional mutants are needed to analyze genes with such pleiotropic functions. In vertebrates, conditional gene inactivation has only been feasible in the mouse, leaving other model systems to rely on surrogate experimental approaches such as overexpression of dominant negative proteins and antisense-based tools.

Progress in Remote Sensing of Photosynthetic Activity over the Amazon Basin.

Although quantifying the massive exchange of carbon that takes place over the Amazon Basin remains a challenge, progress is being made as the remote sensing community moves from using traditional, reflectance-based vegetation indices, such as the Normalized Difference Vegetation Index (NDVI), to the more functional Photochemical Reflectance Index (PRI). This new index, together with satellite-derived estimates of canopy light interception and Sun-Induced Fluorescence (SIF), provide improved estimates of Gross Primary Production (GPP). This paper traces the development of these new approaches, compares the results of their analyses from multiple years of data acquired across the Amazon Basin and suggests further improvements in instrument design, data acquisition and processing.

Water relations in tree physiology: where to from here?

We look back over 50 years of research into the water relations of trees, with the objective of assessing the maturity of the topic in terms of the idea of a paradigm, put forward by Kuhn in 1962. Our brief review indicates that the physical processes underlying the calculation of transpiration are well understood and accepted, and knowledge of those processes can be applied if information about the leaf area of trees, and stomatal conductance, is available. Considerable progress has been made in understanding the factors governing stomatal responses to environment, with insights into how the hydraulic conducting system of trees determines the maximum aperture of stomata.

Internal epitope tagging informed by relative lack of sequence conservation.

Many experimental techniques rely on specific recognition and stringent binding of proteins by antibodies. This can readily be achieved by introducing an epitope tag. We employed an approach that uses a relative lack of evolutionary conservation to inform epitope tag site selection, followed by integration of the tag-coding sequence into the endogenous locus in zebrafish.

An ecoregion assessment of projected tree species vulnerabilities in western North America through the 21st century.

Forest ecosystems across western North America will likely see shifts in both tree species dominance and composition over the rest of this century in response to climate change. Our objective in this study was to identify which ecological regions might expect the greatest changes to occur. We used the process-based growth model 3-PG, to provide estimates of tree species responses to changes in environmental conditions and to evaluate the extent that species are resilient to shifts in climate over the rest of this century.

Predicting large wildfires across western North America by modeling seasonal variation in soil water balance.

A lengthening of the fire season, coupled with higher temperatures, increases the probability of fires throughout much of western North America. Although regional variation in the frequency of fires is well established, attempts to predict the occurrence of fire at a spatial resolution <10 km have generally been unsuccessful. We hypothesized that predictions of fires might be improved if depletion of soil water reserves were coupled more directly to maximum leaf area index (LAI) and stomatal behavior.

Evaluating theories of drought-induced vegetation mortality using a multimodel-experiment framework.

Model-data comparisons of plant physiological processes provide an understanding of mechanisms underlying vegetation responses to climate. We simulated the physiology of a piñon pine-juniper woodland (Pinus edulis-Juniperus monosperma) that experienced mortality during a 5 yr precipitation-reduction experiment, allowing a framework with which to examine our knowledge of drought-induced tree mortality. We used six models designed for scales ranging from individual plants to a global level, all containing state-of-the-art representations of the internal hydraulic and carbohydrate dynamics of woody plants.

Satellite observed widespread decline in Mongolian grasslands largely due to overgrazing.

The Mongolian Steppe is one of the largest remaining grassland ecosystems. Recent studies have reported widespread decline of vegetation across the steppe and about 70% of this ecosystem is now considered degraded. Among the scientific community there has been an active debate about whether the observed degradation is related to climate, or over-grazing, or both.

Satellite-derived estimates of forest leaf area index in southwest Western Australia are not tightly coupled to interannual variations in rainfall: implications for groundwater decline in a drying climate.

There is increasing concern that widespread forest decline could occur in regions of the world where droughts are predicted to increase in frequency and severity as a result of climate change. The average annual leaf area index (LAI) is an indicator of canopy cover and the difference between the annual maximum and minimum LAI is an indicator of annual leaf turnover. In this study, we analyzed satellite-derived estimates of monthly LAI across forested coastal catchments of southwest Western Australia over a 12 year period (2000-2011) that included the driest year on record for the last 60 years.

Predicting tree diversity across the United States as a function of modeled gross primary production.

At the regional and continental scale, ecologists have theorized that spatial variation in biodiversity can be interpreted as a response to differences in climate. To test this theory we assumed that ecological constraints associated with current climatic conditions (2000-2004) might best be correlated with tree richness if expressed through satellite-derived measures of gross primary production (GPP), rather than the more commonly used, but less consistently derived, net primary production. To evaluate current patterns in tree diversity across the contiguous United States we acquired information on tree composition from the USDA Forest Service's Forest Inventory and Analysis program that represented more than 17,4000 survey plots.

Physiological girdling of pine trees via phloem chilling: proof of concept.

Quantifying below-ground carbon (C) allocation is particularly difficult as methods usually disturb the root-mycorrhizal-soil continuum. We reduced C allocation below ground of loblolly pine trees by: (1) physically girdling trees and (2) physiologically girdling pine trees by chilling the phloem. Chilling reduced cambium temperatures by approximately 18 degrees C.

Gas-phase rate coefficients for the reactions of nitrate radicals with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene at room temperature.

Rate coefficients for reactions of nitrate radicals (NO3) with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene were determined to be (6.55 +/- 0.78)x 10(-13) cm3 molecule(-1) s(-1), (3.

Structural and biochemical analyses of DNA and RNA binding by a bifunctional homing endonuclease and group I intron splicing factor.

We determined the crystal structure of a bifunctional group I intron splicing factor and homing endonuclease, termed the I-AniI maturase, in complex with its DNA target at 2.6 A resolution. The structure demonstrates the remarkable structural conservation of the beta-sheet DNA-binding motif between highly divergent enzyme subfamilies.

In vitro analysis of the relationship between endonuclease and maturase activities in the bi-functional group I intron-encoded protein, I-AniI.

The AnCOB group I intron from Aspergillus nidulans encodes a homing DNA endonuclease called I-AniI which also functions as a maturase, assisting in AnCOB intron RNA splicing. In this investigation we biochemically characterized the endonuclease activity of I-AniI in vitro and utilized competition assays to probe the relationship between the RNA- and DNA-binding sites. Despite functioning as an RNA maturase, I-AniI still retains several characteristic properties of homing endonucleases including relaxed substrate specificity, DNA cleavage product retention and instability in the reaction buffer, which suggest that the protein has not undergone dramatic structural adaptations to function as an RNA-binding protein.

Lessons learned while extending physiological principles from growth chambers to satellite studies.

Over the last three decades, physiological principles established in laboratory studies have been applied to systems at progressively larger scales and are now firmly merged into the fields of ecology, ecosystem modeling, forest protection, and global change research. To expand the vision of any field requires that scientists from different disciplines build a bridge across the chasm that normally exists between the knowledge bases and perspectives of different fields. Bridges are built most quickly when representatives of different disciplines see the possibility of mutual advantage in collaboration and seek to quickly demonstrate that potential.

Effects of branch length on carbon isotope discrimination in Pinus radiata.

Gas exchange was measured on a pruned Pinus radiata D. Don hedge and on a long-branch P. radiata tree near Hamilton, New Zealand, in spring 1993 when soil water content was close to field capacity.

Woody tissue maintenance respiration of four conifers in contrasting climates.

We estimate maintenance respiration for boles of four temperate conifers (ponderosa pine, western hemlock, red pine, and slash pine) from CO efflux measurements in autumn, when construction respiration is low or negligible. Maintenance respiration of stems was linearly related to sapwood volume for all species; at 10°C, respiration per unit sapwood volume ranged from 4.8 to 8.