A state and transition model for the eastern Monte Phytogeographycal Province in Rio Negro

We developed a functional model for a shrub steppe vegetation of the eastern Monte Phytogeographical Province in Río Negro (Argentina) with six stable states and 12 transitions, based on the woody encroachment degree, characteristics of the herbaceous layer and the soil surface, and biological crust cover. Information was obtained from letters of naturalists and travelers along the region since the late eighteenth century, reports of old settlers, and our own research work. On the Monte, different functional groups can be distinguished. Our work focused on the three most conspicuous to analyze the dynamics of the system: shrubs, grasses and biological crust. The shrub layer is only affected by large-scale disturbances (fire, mechanical clearing) which maintain the balance between grasses and shrubs in the system. Mechanical clearing with soil removal also causes a decrease in grass cover and vegetation diversity. This layer, however, is most frequently affected by intensive and continuous grazing, which reduces the occurrence of fires and shifts the equilibrium toward the shrubs. All disturbances in general deteriorate the biological crust that covers the soil, which offers situations of facilitation for the regeneration of the herbaceous layer. Grazing and mechanical clearing reduce soil cover and promote the development of soil compaction, which reduce water infiltration and germination and/or seedling establishment, and this creates deteriorated states difficult to reverse. Those states can also be produced by tillage for agriculture and stubble grazing. Some of the transitions that we describe can be favored through grassland management strategies, in order to reach higher states of pastoral value and reverse deteriorating situations.     

Ecomorphology of morpho‐functional relationships in the family of sparidae: A quantitative statistic approach

In many fish species, morphological similarity can be considered as a proxy for similarities in habitat use. The Sparidae family includes species that are recognized for common morphological features such as structure and positioning of the fins and specialized dentition. The aim of this study was to quantitatively describe the relationship of body shape morphology with habitat use, trophic level, and systematics in the majority of known Sparidae species (N = 92). This ecomorphological comparison was performed with a geometric morphometric approach considering as variables the Trophic Index (TROPH), the habitat (i.e., classified as demersal, benthopelagic and reef associated) and the phylogenetic relationship of species at the subfamily level. The analysis by the TROPH variable showed a positive relation with shape because the morphological features of all the species are strongly correlated with their trophic behavior (e.g., herbivore species have a smaller mouth gap that make them able to feed upon sessile resources). The morphological analysis according to the Habitat variable was used to classify species according to a feeding‐habitat niche in terms of portion of the water column and seabed space where species mostly perform their behavioral activities. We described three kinds of morphological designs in relation to a benthopelagic, demersal and reef‐associated habit. The six subfamily groups were morphologically well distinguishable and the cladogram relative to Mahalanobis' morphological distances was compared with those proposed by other authors. We also quantified the phylogenetic relationship among the different subfamilies based on the analysis of shape in relation to trophic ecology, confirming the observations of the authors. J. Morphol., 2009. © 2009 Wiley‐Liss, Inc.     

An Urban Metabolism and Carbon Footprint Analysis of the Jing–Jin–Ji Regional Agglomeration

Urban energy metabolism includes processes for exploiting, transforming, and consuming energy, as well as processes for recycling by‐products and wastes. Embodied energy is the energy consumed during all of these activities, both directly and indirectly. Multiregional input‐output (MRIO) analysis can calculate the energy consumption embodied in flows among sectors for multiple cities or regions. Our goal was to address a problem apparent in previous research, which was insufficient attention to indirect energy flows. We combined MRIO analysis with ecological network analysis to calculate the embodied energy consumption and the energy‐related carbon footprints of five sectors in three regions that comprise the Jing‐Jin‐Ji agglomeration, using data from 2002 and 2007. Our analysis traced metabolic processes of sectors from the perspective of final consumption. Based on the embodied energy analysis, we quantified the indirect energy consumption implied in exchanges of sectors and its distribution and identified the relationships formed through the indirect consumption to analyze the roles of providers and receivers in the system. Results showed that the embodied energy consumption for the Jing‐Jin‐Ji region increased from 2002 to 2007 as a result of increased energy consumption in Tianjin and Hebei. Overall, consumption of Beijing decreased likely attributable to the fact that government policies relocated industries during this time in anticipation of the Olympic Games. The relationships among sectors changed: Beijing changed from a net exporter to an importer, whereas Hebei changed from a net importer of energy from Beijing to an exporter to Beijing, and Tianjin served as an importer in both years.     

Seasonal shifts in the importance of bottom–up and top–down factors on stream periphyton community structure

We examined the importance of temporal variability in top–down and bottom–up effects on the accumulation of stream periphyton, which are complex associations of autotrophic and heterotrophic microorganisms. Periphyton contributes to primary production and nutrient cycling and serves as a food resource for herbivores (grazers). Periphyton growth is often limited by the availability of nitrogen and phosphorus, and biomass can be controlled by grazers. In this study we experimentally manipulated nutrients and grazers simultaneously to determine the relative contribution of bottom–up and top–down controls on periphyton over time. We used nutrient diffusing substrates to regulate nutrient concentrations and an underwater electric field to exclude grazing insects in three sequential 16–17 day experiments from August to October in montane Colorado, USA. We measured algal biomass, periphyton organic mass, and algal community composition in each experiment and determined densities of streambed insect species, including grazers. Phosphorus was the primary limiting nutrient for algal biomass, but it did not influence periphyton organic mass across all experiments. Effects of nutrient additions on algal biomass and community composition decreased between August and October. Grazed substrates supported reduced periphyton biomass only in the first experiment, corresponding to high benthic abundances of a dominant mayfly grazer (Rhithrogena spp.). Grazed substrates in the first experiment also showed altered algal community composition with reduced diatom relative abundances, presumably in response to selective grazing. We showed that top–down grazing effects were strongest in late summer when grazers were abundant. The effects of phosphorus additions on algal biomass likely decreased over time because temperature became more limiting to growth than nutrients, and because reduced current velocity decreased nutrient uptake rates. These results suggest that investigators should proceed with caution when extending findings based on short‐term experiments. Furthermore, these results support the need for additional seasonal‐scale field research in stream ecology.     

Effect of feeding tree leaves as supplements on the nutrient digestion and rumen fermentation pattern in sheep grazing on semi-arid range of India – I

A study was carried out to determine the effect of feeding different tree leaves as supplements on nutrient digestion, rumen fermentation and blood parameters of sheep grazing on a semi-arid rangeland. Thirty adult Malpura rams of uniform body weight (39.0 ± 0.75) were divided into five groups of six each. They were grazed as a single flock from 08.00 to 17.00 h on a semi-arid rangeland. After the end of the grazing period, the first group (G1), which was not provided with any supplementation, served as the control. The second group (G2) was supplemented with 200 g of a concentrate mixture per head per day, whereas the third, fourth and fifth groups (G3–G5) were provided with approximately 200 g DM d⁻¹ of freshly cut foliage from Prosopis cineraria, Acacia nilotica and Albezia lebbek. The foliage from P. cineraria contained 133.4 g kg⁻¹ DM condensed tannin (CT) with protein precipitating capacity (PPC) of 66 g kg⁻¹ DM, whereas A. nilotica contained 18.9 g kg⁻¹ DM hydrolysable tannin (HT) with PPC of 11.5 g kg⁻¹ DM. However, A. lebbek did not contain any tannin. The protein contents were 119, 139 and 194 g kg⁻¹ DM, respectively. The DMI (g d⁻¹) was 688, 916, 1024, 1003, 999 in G1, G2, G3, G4 and G5, respectively. Digestible crude protein (DCP) and metabolizable energy (ME) intakes in supplemented groups G2–G5 were higher (P < 0.05) than in the control (G1). Supplementation improved the DM digestibility in all groups, whereas CP digestibility was lower (P < 0.05) in G3 compared to G2, G4 and G5. Rumen fermentation study conducted 6 h after supplementation revealed that total N, ammonia N, and total VFA levels were lower (P < 0.05) in G3 compared to the other supplemented groups. Although the haemoglobin (Hb) levels were similar among groups, blood urea N (BUN) was lowest in G3 compared to the other groups. The initial body weights were similar among groups (mean 39 kg). After 60 days of experimental feeding, all groups maintained their body weight, except the control group (G1), which lost body weight. It was observed, that supplementation with tree leaves containing CT like P. cineraria helps in better rumen fermentation pattern by preventing excessive loss of nitrogen. It was concluded that maximum nutritional benefits of tree leaves could be harvested, if used as supplement rather than as a sole feed.     

A population biological approach to the collective dynamics of countries undergoing demographic transition

Birth rates have been declining in higher-income countries since the middle of the 19th century. A growing number of other countries have entered this demographic transition to lower fertility, as socioeconomic development continues. Analyses of this demographic transition vary widely, but most analyze individual populations in isolation from others, and most come from fields outside the biological sciences. Here, we develop a population biological model of population dynamics in higher-income countries. Individual countries evolve through density-regulated growth, where gradual evolution toward higher population densities boosts productivity (and hence socioeconomic growth) through economics of agglomeration and scale, in turn reducing birth rates. The exchange of technology and capital between countries can further boost productivity gains in any given country, thus contributing to its demographic transition. As a result, countries can down-regulate one another's population growth through mutual improvements in productivity. The model is fitted to time series data on population size, GDP per capita, and birth rates for the United States, the United Kingdom, and France. The metapopulation dynamics are also characterized across a range of parameter values close to the fitted values. This work may help advance population biological approaches to understanding the implications of the fertility demographic transition for modern human populations. This is relevant to developing long-term predictions of the earth's total population size, which must be based upon a model that incorporates underlying mechanisms.     

Patterns of resistance and resilience of the stress-tolerant coral Siderastrea radians (Pallas) to sub-optimal salinity and sediment burial

The coastal lagoons of south Florida, U.S., experience fluctuating levels of sedimentation and salinity and contain only a subset of the coral species found at the adjacent reefs of the Florida Reef Tract. The dominant species within these habitats is Siderastrea radians, which can reach densities of up to 68 colonies m^- 2 and is commonly exposed to salinity extremes (< 10 psu to > 37 psu) and chronic sediment burial. In this study, we document the patterns of resistance and resilience of S. radians to sub-optimal salinity levels and sediment burial in a series of short-term, long-term, acute, chronic, single-stressor, and sequential-stressor experiments.S. radians displayed remarkable patterns of resistance and resilience and mortality was documented only under prolonged (≥ 48 h) continuous exposure to salinity extremes (15 and 45 psu) and chronic sediment burial. A reduction in photosynthetic rates was documented for all salinity exposures and the decrease in photosynthesis was linearly related to exposure time. Negative impacts on photosynthetic rates were more severe under low salinity (15 psu) than under high salinity (45 psu). Corals exposed to intermediate, low-salinity levels (25 psu), exhibited initial declines in photosynthesis that were followed by temporary increases that may represent transient acclimatization patterns. The impacts of sediment burial were influenced by the duration of the burial period and ranged from a temporary reduction in photosynthesis to significant reductions in growth and tissue mortality. The maintenance of P/R ratios > 1 and the rapid (< 24 h) recovery of photosynthetic rates after burial periods of 2-24 h indicates that S. radians is able to resist short-term burial periods with minor physiological consequences. However, as burial periods increase and colonies become covered at multiple chronic intervals, sediment burial resulted in extended photosynthetic recovery periods, reduced growth, and mortality. Under normal conditions (i.e., no salinity stress), S. radians was very effective at clearing sediments, and > 50% of the colonies' surface area was cleared within 1 h. However, clearing rates were influenced by physiological status, and prior exposure to sub-optimal salinity significantly reduced the clearing rates of stressed colonies.The response of S. radians to disturbance documented in this study characterizes this species as highly stress-tolerant and provides an explanation for its present high abundance in both reef and marginal environments. Moreover, the key life-history attributes of S. radians, such as brooding reproductive strategy, small colony size, high stress-tolerance, and high recruitment rates, suggest the potential for this species to replace reef-building taxa under increased disturbance scenarios in Florida and elsewhere in the region.     

A model of the transition state in the alkaline phosphatase reaction

A high resolution crystal structure of Escherichia coli alkaline phosphatase in the presence of vanadate has been refined to 1.9 A resolution. The vanadate ion takes on a trigonal bipyramidal geometry and is covalently bound by the active site serine nucleophile. A coordinated water molecule occupies the axial position opposite the serine nucleophile, whereas the equatorial oxygen atoms of the vanadate ion are stabilized by interactions with both Arg-166 and the zinc metal ions of the active site. This structural complex supports the in-line displacement mechanism of phosphomonoester hydrolysis by alkaline phosphatase and provides a model for the proposed transition state in the enzyme-catalyzed reaction.     

Abiotic factors modulate post-drought growth resilience of Scots pine plantations and rear-edge Scots pine and oak forests

The proportion of planted forests in the Mediterranean Basin is one of the largest in the world. These plantations are dominated by pine species and present a series of characteristics such as low elevation, high competition or small tree size that make them more vulnerable to droughts. However, quantitative assessments of their post-drought growth resilience in accordance with species, site factors and tree characteristics are lacking. In this study we sampled 164 trees at four forest sites located in the drought-prone Sierra Nevada, southeastern Spain. We compared growth responsiveness to drought in rear-edge planted vs. relic natural Scots pine (Pinus sylvestris) and coexisting Pyrenean oak (Quercus pyrenaica) stands. Our objective was to characterize and compare the different growth responses to drought between species and sites and the effect of the main physiographic factors (altitude, aspect, and slope) on these responses since the influence of these factors on post-drought resistance and resilience has received little attention to date. Our results reveal that the planted pine sites with the lowest mean growth rates displayed greater resistance during drought, and that higher altitude was associated with improved resistance and/or resilience for all species and sites. Natural pine and Pyrenean oak stands were better adapted to the dry climatic conditions of the Mediterranean region where the study was undertaken, displaying greater resistance and/or resilience and lower influence of drought on growth in comparison to stands of planted pines. These results suggest that promoting the conservation of high-elevation pine plantations and enhancing the regeneration of natural pine and oak may improve the resistance and resilience of these drought-prone forest ecosystems.     

A rule-based model for the functional analysis of vegetation change in Australasian grasslands

Abstract. Grasslands encompass a broad array of vegetation and climatic zones. We describe the first developments towards a rule-based functional model for predicting vegetation structure in Australian and New Zealand pastures and rangelands. The approach aims to predict the combined effects of climate and disturbance by humans and grazing livestock, and to provide a level of resolution needed for predicting changes in pastures and rangelands. We enlisted expert knowledge to develop: (1) a minimum set of critical traits; (2) rules relating site variables to favoured plant attributes; (3) rules relating attributes to plant functional traits, and (4) rules relating plant functional types to likely plant communities. We tested the resulting model by deriving some simple predictions of plant communities of some existing pasture and rangeland sites in Australia and New Zealand, with differing climatic and human disturbance inputs. The results indicate that this first model is able to predict plant communities with varying success rates, and with the best results in cases where there are extreme climates or high management inputs. Key sensitivities in the model where further research is required include: (1) the urgent need for more explicit understanding of the key plant functional attributes favoured by differing climates and disturbance regimes, (2) the functional relationships between these plant functional attributes and recognisable plant functional types in vegetation, and (3) the assembly rules for the coexistence of these different plant functional types in major plant communities. The same understanding is required for subsequent process-based modelling development.     

The traits of “trait ecologists”: An analysis of the use of trait and functional trait terminology

Trait and functional trait approaches have revolutionized ecology improving our understanding of community assembly, species coexistence, and biodiversity loss. Focusing on traits promotes comparability across spatial and organizational scales, but terms must be used consistently. While several papers have offered definitions, it remains unclear how ecologists operationalize “trait” and “functional trait” terms. Here, we evaluate how researchers and the published literatures use these terms and explore differences among subdisciplines and study systems (taxa and biome). By conducting both a survey and a literature review, we test the hypothesis that ecologists’ working definition of “trait” is adapted or altered when confronting the realities of collecting, analyzing and presenting data. From 486 survey responses and 712 reviewed papers, we identified inconsistencies in the understanding and use of terminology among researchers, but also limited inclusion of definitions within the published literature. Discrepancies were not explained by subdiscipline, system of study, or respondent characteristics, suggesting there could be an inconsistent understanding even among those working in related topics. Consistencies among survey responses included the use of morphological, phonological, and physiological traits. Previous studies have called for unification of terminology; yet, our study shows that proposed definitions are not consistently used or accepted. Sources of disagreement include trait heritability, defining and interpreting function, and dealing with organisms in which individuals are not clearly recognizable. We discuss and offer guidelines for overcoming these disagreements. The diversity of life on Earth means traits can represent different features that can be measured and reported in different ways, and thus, narrow definitions that work for one system will fail in others. We recommend ecologists embrace the breadth of biodiversity using a simplified definition of “trait” more consistent with its common use. Trait‐based approaches will be most powerful if we accept that traits are at least as diverse as trait ecologists.     

Stability of complex food webs: resilience, resistance and the average interaction strength

In the face of stochastic climatic perturbations, the overall stability of an ecosystem will be determined by the balance between its resilience and its resistance, but their relative importance is still unknown. Using aquatic food web models we study ecosystem stability as a function of food web complexity. We measured three dynamical stability properties: resilience, resistance, and variability. Specifically, we evaluate how a decrease in the strength of predator-prey interactions with food web complexity, reflecting a decrease in predation efficiency with the number of prey per predator, affects the overall stability of the ecosystem. We find that in mass conservative ecosystems, a lower interaction strength slows down the mass cycling rate in the system and this increases its resistance to perturbations of the growth rate of primary producers. Furthermore, we show that the overall stability of the food webs is mostly given by their resistance, and not by their resilience. Resilience and resistance display opposite trends, although they are shown not to be simply opposite concepts but rather independent properties. The ecological implication is that weaker predator-prey interactions in closed ecosystems can stabilize food web dynamics by increasing its resistance to climatic perturbations.     

Environmental drivers of species composition and functional diversity of dung beetles along the Atlantic Forest–Pampa transition zone

Human activities are causing a rapid loss of biodiversity, which impairs ecosystem functions and services. Therefore, understanding which processes shape how biodiversity is distributed along spatial and environmental gradients is a first step to guide conservation and management efforts. We aimed to determine the relative explanatory importance of biogeographic, environmental, landscape and spatial variables on assemblage dissimilarities and functional diversity of dung beetles along the Atlantic Forest–Pampa (i.e. forest–grassland) transition zone located in Southeast South America. We described each site according to their biogeographic position, environmental conditions, landscape features and spatial patterns. The compositional dissimilarity was partitioned into turnover and nestedness components of β‐diversity. Mantel tests and generalised dissimilarity models were used to relate β‐diversity and its components to biogeographic, environmental, landscape and spatial variables. Variation partitioning analysis was used to estimate the pure and shared variation in species composition and functional diversity explained by the four categories of predictors. Biome domain was the main factor causing dung beetle compositional dissimilarity, with a high species replacement between Atlantic Forest and Pampa. Biogeographic, environmental, landscape and spatial distances also affected the patterns of dung beetle dissimilarity and β‐diversity components. The shared effects of the four sets of predictors explained most of the variation in dung beetle composition. A similar response pattern was found for dung beetle functional diversity, which excluded biogeographic effects. Only the pure effects of environmental and spatial predictors were significant for species composition and functional diversity. Our results indicate that dung beetle species composition and functional diversity are jointly driven by environmental, landscape and spatial predictors with higher pure environmental and spatial effects. The forest–grassland transition zone promotes a strong species and trait replacement highly influenced both by environmental filtering and dispersal limitation.     

A new SEIR epidemic model with applications to the theory of eradication and control of diseases, and to the calculation of R0

We present a novel SEIR (susceptible-exposure-infective-recovered) model that is suitable for modeling the eradication of diseases by mass vaccination or control of diseases by case isolation combined with contact tracing, incorporating the vaccine efficacy or the control efficacy into the model. Moreover, relying on this novel SEIR model and some probabilistic arguments, we have found four formulas that are suitable for estimating the basic reproductive numbers R(0) in terms of the ratio of the mean infectious period to the mean latent period of a disease. The ranges of R(0) for most known diseases, that are calculated by our formulas, coincide very well with the values of R(0) estimated by the usual method of fitting the models to observed data.     

Modeling the hazard of transition into the absorbing state in the illness-death model

The illness-death model is the simplest multistate model where the transition from the initial state 0 to the absorbing state 2 may involve an intermediate state 1 (e.g., disease relapse). The impact of the transition into state 1 on the subsequent transition hazard to state 2 enables insight to be gained into the disease evolution. The standard approach of analysis is modeling the transition hazards from 0 to 2 and from 1 to 2, including time to illness as a time-varying covariate and measuring time from origin even after transition into state 1. The hazard from 1 to 2 can be also modeled separately using only patients in state 1, measuring time from illness and including time to illness as a fixed covariate. A recently proposed approach is a model where time after the transition into state 1 is measured in both scales and time to illness is included as a time-varying covariate. Another possibility is a model where time after transition into state 1 is measured only from illness and time to illness is included as a fixed covariate. Through theoretical reasoning and simulation protocols, we discuss the use of these models and we develop a practical strategy aiming to (a) validate the properties of the illness-death process, (b) estimate the impact of time to illness on the hazard from state 1 to 2, and (c) quantify the impact that the transition into state 1 has on the hazard of the absorbing state. The strategy is also applied to a literature dataset on diabetes.     

Effect of tree leaf as supplementation on nutrient digestion and rumen fermentation pattern in sheep grazing semi-arid range of India – II

A study was conducted to evaluate the effects of supplementing with different tree leaves on nutrient digestion, rumen fermentation and blood parameters of sheep. Thirty adult Malpura rams (39.0 ± 0.56 kg) were divided into five groups of six each. They were grazed as a single flock on a semi-arid rangeland and after the end of routine grazing period (08:00–17:00 h), first group (G1), which was not provided with any supplementation, served as control group. Second group (G2) was supplemented with 200 g of a conventional concentrate mixture per head per day, whereas third, fourth and fifth groups (G3, G4 and G5) were supplemented with approximately 200 g dry matter (DM) per day freshly cut foliage from Ailanthes excelsa, Azardirachta indica and Bauhinia racemosa, respectively. Protein content (g kg⁻¹ DM) in A. excelsa, A. indica and B. racemosa foliage was 197, 128 and 132, respectively. A. indica and B. racemosa foliages also contained 123.2 and 211.2 g kg⁻¹ DM condensed tannin (CT) with protein precipitating capacity (PPC) of 16.5 and 46.5 g kg⁻¹ DM. None of the tree leaves contained hydrolysable tannin (HT). Dry matter intake (DMI, g day⁻¹) was 591, 766, 865, 974 and 939 in G1, G2, G3, G4 and G5, respectively. Digestible crude protein (DCP) and metabolisable energy (ME) intakes in supplemented groups G2–G5 were higher (P < 0.05) compared to control (G1). Supplementation improved digestibility of all nutrients in all groups. Rumen fermentation study indicated lower (P < 0.05) ammonia and total N in the rumen liquor collected from G5 sheep compared to the other supplemented groups. Although haemoglobin (Hb, g dl⁻¹) levels showed small changes among groups, blood urea nitrogen (BUN, mg dl⁻¹) was lowest in G5 compared to the other groups. Initial BW were similar among the groups. After 60 days of experimental feeding, all animals maintained their BW, except sheep in the control group (G1), which lost BW. Results indicate that for adult sheep grazing on a semi-arid range, supplementation with a concentrate mixture could be replaced by tree leaves like A. excelsa, A. indica and B. racemosa, during the lean season to maintain their BW. In addition, supplementing with tree leaves containing condensed tannin has advantages in terms of N utilization.     

The dynamics of a Lotka–Volterra predator–prey model with state dependent impulsive harvest for predator

According to the economic and biological aspects of renewable resources management, we propose a Lotka–Volterra predator–prey model with state dependent impulsive harvest. By using the Poincaré map, some conditions for the existence and stability of positive periodic solution are obtained. Moreover, we show that there is no periodic solution with order larger than or equal to three under some conditions. Numerical results are carried out to illustrate the feasibility of our main results. The bifurcation diagrams of periodic solutions are obtained by using the numerical simulations, and it is shown that a chaotic solution is generated via a cascade of period-doubling bifurcations, which implies that the presence of pulses makes the dynamic behavior more complex.     

Electrostatic interactions in the denatured state and in the transition state for protein folding: effects of denatured state interactions on the analysis of transition state structure

The development of electrostatic interactions during the folding of the N-terminal domain of the ribosomal protein L9 (NTL9) is investigated by pH-dependent rate equilibrium free energy relationships. We show that Asp8, among six acidic residues, is involved in non-native, electrostatic interactions with K12 in the transition state for folding as well as in the denatured state. The perturbed native state pK(a) of D8 (pK(a) = 3.0) appears to be maintained through non-native interactions in both the transition state and the denatured state. Mutational effects on the stability of the transition state for protein (un)folding are often analyzed in respect to change in ground states. Thus, the interpretation of transition state analysis critically depends on an understanding of mutational effects on both the native and denatured state. Increasing evidence for structurally biased denatured states under physiological conditions raises concerns about possible denatured state effects on folding studies. We show that the structural interpretation of transition state analysis can be altered dramatically by denatured state effects.