How strong are side chain interactions in the folding intermediate?

Influence of 12 nonpolar amino acids residues from the hydrophobic core of apomyoglobin on stability of its native state and folding intermediate was studied. Six of the selected residues are from the A, G and H helices; these are conserved in structure of the globin family, although nonfunctional, that is, not involved in heme binding. The rest are nonconserved hydrophobic residues that belong to the B, C, D, and E helices. Each residue was substituted by alanine, and equilibrium pH‐induced transitions in apomyoglobin and its mutants were studied by circular dichroism and fluorescent spectroscopy. The obtained results allowed estimating changes in their free energy during formation of the intermediate state. It was first shown that the strength of side chain interactions in the apomyoglobin intermediate state amounts to 15–50% of that in its native state for conserved residues, and practically to 0% for nonconserved residues. These results allow a better understanding of interactions occurring in the intermediate state and shed light on involvement of certain residues in protein folding at different stages.     

Microbial βγ-crystallins

βγ-Crystallins have emerged as a superfamily of structurally homologous proteins with representatives across the domains of life. A major portion of this superfamily is constituted by members from microorganisms. This superfamily has also been recognized as a novel group of Ca²⁺-binding proteins with huge diversity. The βγ domain shows variable properties in Ca²⁺ binding, stability and association with other domains. The various members present a series of evolutionary adaptations culminating in great diversity in properties and functions. Most of the predicted βγ-crystallins are yet to be characterized experimentally. In this review, we outline the distinctive features of microbial βγ-crystallins and their position in the βγ-crystallin superfamily.     

Hydrophobic interactions are the prevalent force in bromelain:Fab’ complex

Antibromelain polyclonal antibodies against stem bromelain were raised in male albino rabbits and the Fab’ monomers isolated from the IgG of the immune sera as reported in our earlier communication (Gupta, P., Khan, R. H., and Saleemuddin, M. (2003) Biochim. Biophys. Acta, 1646, 131–135). Further, as evident from that communication, bromelain:Fab’ complex has 1: 1 stoichiometry. The stability of bromelain:Fab’ complex (1: 1) was investigated by far and near-UV CD and fluorescence measurements. Addition of up to 1.8 M NaCl caused no significant changes in fluorescence signals and near-UV CD peak pattern. However, the spectral studies together with gel filtration studies suggest dissociation of the complex beyond 5% (v/v) methanol. These results show that hydrophobic interactions play a pronounced role in the binding of Fab’ to bromelain while electrostatic interactions may be less crucial.     

How context dependent are species interactions?

The net effects of interspecific species interactions on individuals and populations vary in both sign (?, 0, +) and magnitude (strong to weak). Interaction outcomes are context‐dependent when the sign and/or magnitude change as a function of the biotic or abiotic context. While context dependency appears to be common, its distribution in nature is poorly described. Here, we used meta‐analysis to quantify variation in species interaction outcomes (competition, mutualism, or predation) for 247 published articles. Contrary to our expectations, variation in the magnitude of effect sizes did not differ among species interactions, and while mutualism was most likely to change sign across contexts (and predation least likely), mutualism did not strongly differ from competition. Both the magnitude and sign of species interactions varied the most along spatial and abiotic gradients, and least as a function of the presence/absence of a third species. However, the degree of context dependency across these context types was not consistent among mutualism, competition and predation studies. Surprisingly, study location and ecosystem type varied in the degree of context dependency, with laboratory studies showing the highest variation in outcomes. We urge that studying context dependency per se, rather than focusing only on mean outcomes, can provide a general method for describing patterns of variation in nature.     

Vertebrate-like βγ-crystallins in the ocular lenses of a copepod

The diverse crystallins are water-soluble proteins that are responsible for the optical properties of cellular lenses of animal eyes. While all vertebrate lenses contain physiological stress-related - and -crystallins, some also contain taxon-specific, often enzyme-related crystallins. To date, the - and -crystallins have been found only in vertebrate lenses. Here we report lenses from an invertebrate, the pontellid copepod Anomalocera ornata, accumulate -crystallin family members as judged by immunocytochemistry, western immunoblotting and microsequencing. Our data provide the first example of -crystallin members in an invertebrate lens, establishing that the use of this protein family as lens crystallins is not confined to vertebrates.     

Latitudinal trends in plant‐pollinator interactions: are tropical plants more specialised?

The increase in richness of species and higher taxa going from higher to lower latitudes is one of the most studied global biogeographical patterns. Latitudinal trends in the interactions between species have, in contrast, hardly been studied at all, probably because recording interactions is much less straightforward than counting species. We have assembled two independent data sets which suggest that plant-pollinator interactions are not more ecologically specialised in the tropics compared to temperate latitudes. This is in contrast to a prevailing view that tropical ecological interactions tend towards higher specificity than their temperate counterparts.     

Predator–prey interactions and metabolic rates are altered in stable and unstable groups in a social fish

Understanding the determinants and consequences of predation effort, success and prey responses is important since these factors affect the fitness of predators and prey. When predators are also invasive species, the impacts on prey can be particularly far-reaching with ultimate ecosystem-level consequences. However, predators are typically viewed as behaviourally fixed within this interaction and it is unclear how variation in predator social dynamics affects predator–prey interactions. Using the invasive eastern mosquitofish Gambusia holbrooki and a native glass shrimp Paratya australiensis in Australia, we investigated how varying levels of social conflict within predator groups influences predator–prey interactions. By experimentally manipulating group stability of G. holbrooki, we show that rates of social conflict were lower in groups with large size differences, but that routine metabolic rates were higher in groups with large size differences. Predation effort and success did not vary depending on group stability, but in stable groups predation effort by aggressive dominants was greater than subordinates. The anti-predator responses of prey to the stability of predator groups were mixed. While more prey utilized shelters when exposed to stable compared to unstable groups of predators, a greater proportion were sedentary when predator groups were unstable. Overall, this study demonstrates predator group stability is modulated by differences in body size and can influence prey responses. Further, it reveals a hidden metabolic cost of living in stable groups despite reduced overt social conflict. For invasive species management, it is therefore important to consider the behavioural and physiological plasticity of the invasive predators, whose complex social interactions and metabolic demands can modulate patterns of predator–prey interactions.     

Incorporating biotic factors in species distribution modeling: are interactions with soil microbes important?

It is increasingly recognized that species distributions are driven by both abiotic factors and biotic interactions. Despite much recent work incorporating competition, predation, and mutualism into species distribution models (SDMs), the focus has been confined to aboveground macroscopic interactions. Biotic interactions between plants and soil microbial communities are understudied as potentially important drivers of plant distributions. Some soil bacteria promote plant growth by cycling nutrients, while others are pathogenic; thus they have a high potential for influencing plant occurrence. We investigated the influence of soil bacterial clades on the distributions of bryophytes and 12 vascular plant species in a high elevation talus‐field ecosystem in the Rocky Mountain Front Range, Colorado, USA. We used an information‐theoretic criterion (AICc) modeling approach to compare SDMs with the following different sets of predictors: abiotic variables, abiotic variables and other plant abundances, abiotic variables and soil bacteria clade relative abundances, and a full model with abiotic factors, plant abundances, and bacteria relative abundances. We predicted that bacteria would influence plant distributions both positively and negatively, and that these interactions would improve prediction of plant species distributions. We found that inclusion of either plant or bacteria biotic predictors generally improved the fit, deviance explained, and predictive power of the SDMs, and for the majority of the species, adding information on both other plants and bacteria yielded the best model. Interactions between the modeled species and biotic predictors were both positive and negative, suggesting the presence of competition, parasitism, and facilitation. While our results indicate that plant–plant co‐occurrences are a stronger driver of plant distributions than plant–bacteria co‐occurrences, they also show that bacteria can explain parts of plant distributions that remain unexplained by abiotic and plant predictors. Our results provide further support for including biotic factors in SDMs, and suggest that belowground factors be considered as well.     

Plant hormone interactions: how complex are they?

Models describing plant hormone interactions are often complex and web-like. Here we assess several suggested interactions within one experimental system, elongating pea internodes. Results from this system indicate that at least some suggested interactions between auxin, gibberellins (GAs), brassinosteroids (BRs), abscisic acid (ABA) and ethylene do not occur in this system or occur in the reverse direction to that suggested. Furthermore, some of the interactions are relatively weak and may be of little physiological relevance. This is especially true if plant hormones are assumed to show a log-linear response curve as many empirical results suggest. Although there is strong evidence to support some interactions between hormones (e.g. auxin stimulating ethylene and bioactive GA levels), at least some of the web-like complexities do not appear to be justified or are overstated. Simpler and more targeted models may be developed by dissecting out key interactions with major physiological effects.     

How relevant are house dust mite-fungal interactions in laboratory culture to the natural dust system?

Both house dust and house dust mitesDermatophagoides pteronyssinus contained a wider range of fungi than laboratory mite cultures. In total, nine species of fungi were isolated fromD. pteronyssinus in house dust, and these included three xerophilic species (Eurotium amstelodami, Aspergillus penicillioides andWallemia sebi) commonly found in laboratory cultures ofD. pteronyssinus. It is concluded that mites do interact with a similar range of fungi in natural dust and in laboratory culture, but that the diversity of fungal species in the laboratory is reduced and the density of individual fungal species in culture exceeds that of house dust. In a second experiment, dust samples were incubated at room temperature with 75% relative humidity. The diversity of fungi invariably declined from up to 13 genera to the few species recorded in laboratory culture. This suggests that the dominance of xerophilic fungi in laboratory mite rearings is mediated primarily by low relative humidity, and the exclusion of air-borne spores.     

ERRATUM: Vertebrate-like βγ-crystallins in the ocular lenses of a copepod

We previously reported that the ocular lenses of the pontellid copepod Anomalocera ornata possess vertebrate-like β- and γ-crystallins. We cannot repeat our earlier data suggesting that the copepod lens crystallins belong to the β- and γ-crystallin family of proteins. Our new data are consistent with the copepod crystallins being novel proteins.     

Subunit–subunit interactions are weakened in mutant forms of acetohydroxy acid synthase insensitive to valine inhibition

In acetohydroxy acid synthase from Streptomyces cinnamonensis mutants affected in valine regulation, the impact of mutations on interactions between the catalytic and the regulatory subunits was examined using yeast two-hybrid system. Mutations in the catalytic and the regulatory subunits were projected into homology models of the respective proteins. Two changes in the catalytic subunit, E139A (α domain) and ΔQ217 (β domain), both located on the surface of the catalytic subunit dimer, lowered the interaction with the regulatory subunit. Three consecutive changes in the N-terminal part of the regulatory subunit were examined. Changes G16D and V17D in a loop and adjacent α-helix of ACT domain affected the interaction considerably, indicating that this region might be in contact with the catalytic subunit during allosteric regulation. In contrast, the adjacent mutation L18F did not influence the interaction at all. Thus, L18 might participate in valine binding or conformational change transfer within the regulatory subunits. Shortening of the regulatory subunit to 107 residues reduced the interaction essentially, suggesting that the C-terminal part of the regulatory subunit is also important for the catalytic subunit binding.     

Ectoparasites: are they the proximate cause of cleaning interactions?

We tested the importance of ectoparasites in cleaning symbioses by comparing the activity of Caribbean cleaning gobies ( Elacatinus evelynae ) and of their clients during three daily periods (early morning, midday and late afternoon) in which ectoparasite availability varied naturally. Emergence from the benthos of gnathiid isopod larvae, the main target of cleaning goby predation, was higher at night, when cleaners are inactive, than during the day. Overall ectoparasite loads also tended to be higher on clients in the morning. This coincided with higher rates of visits to cleaning stations by client fish in the morning than at midday, but high rates of client visits were also recorded in the late afternoon. Clients were more likely to adopt stereotypical incitation poses, which increase the likelihood of being cleaned, in the morning than later in the day. Inspection bouts by cleaning gobies were longest in the morning. Cleaner and client behaviours therefore change predictably in response to natural diurnal variation in ectoparasite availability. These results add to a growing number of studies supporting the idea that cleaning symbioses are mutualisms dependent on ectoparasite removal.     

Chemo–ecological interactions in Antarctic bryozoans

The role of bioactive metabolites in ecological interactions involving Antarctic bryozoans has been scarcely studied. Bryozoans are one of the most abundant and diverse members of the Antarctic benthos and are preyed upon by diverse kinds of predators. They seem to be casual food items of the common Antarctic sea urchin Sterechinus neumayeri and the ubiquitous omnivorous amphipod Cheirimedon femoratus. In this study, the cytotoxic activity against embryos and sperm of the sea urchin S. neumayeri and the substrate preferences of the amphipod C. femoratus were assessed using organic extracts from Antarctic bryozoans, in order to determine the presence of chemical defenses. New adapted protocols were designed using a solidifying gel for simulating bryozoans’ surface. We analyzed 32 organic extracts from 16 samples that belonged to 13 different bryozoan species. No cytotoxicity was detected against embryos of S. neumayeri, while 12 of the 13 bryozoan species were cytotoxic to sperm at natural concentrations. In the substrate preference assays, the amphipod C. femoratus was repelled by ten species. The variable bioactivities found in both types of organic partitions of extracts indicated the presence of both lipophilic and hydrophilic defenses. Inter- and intraspecific variability of chemical defenses was detected also, suggesting environmental-induced responses, symbiotic production, and/or genetic variability. Possible alternative defensive mechanisms are also discussed for species with low or no chemical defense. Our results clearly support the fact that chemically mediated bioactivity in Antarctic bryozoans is common, and there is a likely ecological role of cytotoxic and repellent compounds for their protection.     

Nitrogen–climate interactions in US agriculture

Agriculture in the United States (US) cycles large quantities of nitrogen (N) to produce food, fuel, and fiber and is a major source of excess reactive nitrogen (Nr) in the environment. Nitrogen lost from cropping systems and animal operations moves to waterways, groundwater, and the atmosphere. Changes in climate and climate variability may further affect the ability of agricultural systems to conserve N. The N that escapes affects climate directly through the emissions of nitrous oxide (N₂O), and indirectly through the loss of nitrate (NO₃ ^?), nitrogen oxides (NO _x ) and ammonia to downstream and downwind ecosystems that then emit some of the N received as N₂O and NO _x . Emissions of NO _x lead to the formation of tropospheric ozone, a greenhouse gas that can also harm crops directly. There are many opportunities to mitigate the impact of agricultural N on climate and the impact of climate on agricultural N. Some are available today; many need further research; and all await effective incentives to become adopted. Research needs can be grouped into four major categories: (1) an improved understanding of agricultural N cycle responses to changing climate; (2) a systems-level understanding of important crop and animal systems sufficient to identify key interactions and feedbacks; (3) the further development and testing of quantitative models capable of predicting N-climate interactions with confidence across a wide variety of crop-soil-climate combinations; and (4) socioecological research to better understand the incentives necessary to achieve meaningful deployment of realistic solutions.     

Land�CWater interactions in the amazon

Biogeochemistry is hosting this special thematic issue devoted to studies of land?Cwater interactions, as part of the Large-scale Biosphere?CAtmosphere Experiment in Amazônia (LBA). This compilation of papers covers a broad range of topics with a common theme of coupling land and water processes, across pristine and impacted systems. Findings highlighted that hydrologic flowpaths are clearly important across basin size and structure in determining how water and solutes reach streams. Land-use changes have pronounced impacts on flowpaths, and subsequently, on stream chemistry, from small streams to large rivers. Carbon is produced and transformed across a broad array of fluvial environments and wetlands. Surface waters are not only driven by, but provide feedback to, the atmosphere.