Names are key to the big new biology

Those who seek answers to big, broad questions about biology, especially questions emphasizing the organism (taxonomy, evolution and ecology), will soon benefit from an emerging names-based infrastructure. It will draw on the almost universal association of organism names with biological information to index and interconnect information distributed across the Internet. The result will be a virtual data commons, expanding as further data are shared, allowing biology to become more of a 'big science'. Informatics devices will exploit this 'big new biology', revitalizing comparative biology with a broad perspective to reveal previously inaccessible trends and discontinuities, so helping us to reveal unfamiliar biological truths. Here, we review the first components of this freely available, participatory and semantic Global Names Architecture.     

Mutation breeding of grain legumes

Summary Grain legumes are an important group of crop plants. They provide an essential source of protein food for many developing countries, but their production has gone down in favour of more profitable crops like cereals. Therefore, genetic improvement of grain legumes is urgently needed. The primary aim of grain legume breeding must be the increase of production through adaptation to more advanced cropping schemes and reduction of crop losses. Symbiotic nitrogen fixation as developed by natural evolution does not always seem to be compatible with the needed substantial increase in yield: It is not supplying sufficient nitrogen and supplementation by fertilizer is rather uneconomic. By genetic manipulation of the plant's regulatory system nitrogen fixation may become more effective and tolerant to high soil nitrogen levels. Through a number of mutation breeding projects in different countries involving all important grain legume species it has been proven that mutation induction is a good tool for supplementing the genetic variation available from natural evolution and from selection by man. High-yielding cultivars have been developed from induced mutants, which eventually also possess a more efficient nitrogen fixation capacity.     

Knowledge sharing and collaboration in translational research, and the DC-THERA Directory

Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of 'big data' research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namely how the knowledge generated within the project can be made available beyond its boundaries and life-time. DC-THERA is a European 'Network of Excellence' (NoE) that spawned a very large collaborative and interdisciplinary research community, focusing on the development of novel immunotherapies derived from fundamental research in dendritic cell immunobiology. In this article we introduce the DC-THERA Directory, which is an information system designed to support knowledge management for this research community and beyond. We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science.     

Gel filtration studies of serum growth hormone in acromegaly following bromocriptine administration.

Sera of 7 patients with active acromegaly were fractionated by Sephadex G-100 chromatography and the effects of bromocriptine on the concentrations of total growth hormone (hGH) and its different molecular forms studied. Three immunoreactive peaks were observed, corresponding to molecular weights of about 20,000 ('little hGH'), 40,000 ('big hGH'), and more than 100,000 ('big big hGH') Following bromocriptine administration, there was significantly more reduction of 'little hGH' than of 'big big hGH'. Careful interpretation of these changes is required in view of the possible influences of sample storage and handling on hGH heterogeneity. We suggest that either bromocriptine acts differentially on the release of 'little' and 'big big hGH', or that these components differ in their metabolic half-life. However, even the suppression of 'little hGH' is insufficient to explain the clinical response of the disease to bromocriptine.     

Grand challenges in migration biology

Billions of animals migrate each year. To successfully reach their destination, migrants must have evolved an appropriate genetic program and suitable developmental, morphological, physiological, biomechanical, behavioral, and life-history traits. Moreover, they must interact successfully with biotic and abiotic factors in their environment. Migration therefore provides an excellent model system in which to address several of the "grand challenges" in organismal biology. Previous research on migration, however, has often focused on a single aspect of the phenomenon, largely due to methodological, geographical, or financial constraints. Integrative migration biology asks 'big questions' such as how, when, where, and why animals migrate, which can be answered by examining the process from multiple ecological and evolutionary perspectives, incorporating multifaceted knowledge from various other scientific disciplines, and using new technologies and modeling approaches, all within the context of an annual cycle. Adopting an integrative research strategy will provide a better understanding of the interactions between biological levels of organization, of what role migrants play in disease transmission, and of how to conserve migrants and the habitats upon which they depend.     

Seeing and knowing in twenty-first century genetic medicine: the clinical pedigree as epistemological tool and hybrid risk technique

This paper explores the clinical pedigree as a risk technique within the context of the predictive genetic testing (PGT) clinic. We situate the PGT clinic as a site of genetic governance in that it is a site both for the production of knowledge about genetic risk and for intervening in the everyday lives of individuals and their families who learn to cultivate their relations with themselves and their biological relatives in relation to genetic risk knowledge. Drawing on literature of the pedigree as socially constructed and on notions of risk governance, we suggest that the pedigree operates as an epistemological tool and risk technique – that is, as a visual device that assists in organizing the social relations of knowledge production and aids in effecting shifts in patient subjectivity in ways that are consistent with neoliberal notions of active citizenship.     

Genetic studies in rat models: insights into cardiovascular disease

PURPOSE OF REVIEW: Limited to 2003-2004 publications, this review focuses on 'big picture' concepts learned from rat genetic studies of cardiovascular disease. RECENT DEVELOPMENTS: Analysis reveals insights into pathogenic paradigms, as well as experimental perspectives into rat-based systems of analyses of complex cardiovascular disease. Key concepts are forwarded. Multiple susceptibility genes underlie several quantitative trait loci for blood pressure suggesting a 'quantitative trait loci cluster' concept; hypertension end-organ disease quantitative trait loci are distinct from blood pressure quantitative trait loci indicating differential susceptibility paradigms for hypertension and each complication (stroke, renal disease, cardiac hypertrophy); distinct blood pressure quantitative trait loci are found in males and females indicating gender-specific susceptibility; and genetic subtypes comprise polygenic hypertension in rat models suggesting a genetic basis for clinical heterogeneity of human essential hypertension. Gender specific genetic susceptibility plays a key role in coronary artery disease susceptibility; multiple distinct quantitative trait loci underlie hyperlipidemia and type-2 diabetes, indicating multiple susceptibilities in risk factors for cardiovascular disease. Studies in transgenic inbred rat-strain models demonstrate value for serial, complex, cardiovascular pathophysiological analyses within a genetic context. SUMMARY: Cognizant of the limitations of animal model studies, observations from rat genetic studies provide insight into respective modeled human cardiovascular diseases and risk factor susceptibility, as well as systematically dissect the multifaceted complexities apparent in human complex cardiovascular disease. Given the recapitulation of many features of human cardiovascular disease, the value of rat model-based genetic studies for complex cardiovascular disease is unequivocal, thus mandating the expansion of resources for maximization of rat-based genetic studies.     

A mechanistic model for partial preferences

Classic prey optimal foraging model assumes that individual predators are globally omniscient; that is, they have exact knowledge of prey population densities in the environment. This study examines a spatially explicit individual-based model of a one-predator two-prey system where individual predators are assumed to be omniscient only locally, i.e., to know prey population densities only in the range of their perception. Due to local variations in prey numbers, the probability of acceptance of less profitable prey shifts from the zero-one rule to a gradually decreasing function, for which an explicit formula is derived, giving way to partial preferences. A corresponding predator functional response to more profitable prey is shown to have a sigmoid-like form.     

Suppression mechanisms of COX assembly defects in yeast and human: insights into the COX assembly process

Eukaryotic cytochrome c oxidase (COX) is the terminal enzyme of the mitochondrial respiratory chain. COX is a multimeric enzyme formed by subunits of dual genetic origin whose assembly is intricate and highly regulated. In addition to the structural subunits, a large number of accessory factors are required to build the holoenzyme. The function of these factors is required in all stages of the assembly process. They are relevant to human health because devastating human disorders have been associated with mutations in nuclear genes encoding conserved COX assembly factors. The study of yeast strains and human cell lines from patients carrying mutations in structural subunits and COX assembly factors has been invaluable to attain the current state of knowledge, even if still fragmentary, of the COX assembly process. After the identification of the genes involved, the isolation and characterization of genetic and metabolic suppressors of COX assembly defects, reviewed here, have become a profitable strategy to gain insight into their functions and the pathways in which they operate. Additionally, they have the potential to provide useful information for devising therapeutic approaches to combat human disorders associated with COX deficiency.     

Optimal foraging and risk of claw damage: How flexible are shore crabs in their prey size selectivity?

Understanding the behavioural mechanisms that underlie prey size preference of predators is an essential component of unravelling the processes that govern predator-prey dynamics. In marine systems, despite being able to consume larger and more profitable prey, many molluscivorous predators show a preference for smaller, less profitable prey, most likely to minimize the risk of damaging feeding extremities. Here we assessed the flexibility of this prey size preference. We observed that shore crabs (Carcinus maenas) that were food deprived, and which were offered mussels (Mytilus edulis) of different sizes in dichotomous preference tests, preferred smaller, less profitable mussels. The same result was observed for crabs foraging with a conspecific competitor. Only crabs that were conditioned to feed on the larger, most profitable mussels shifted their prey size preference and ranked the most profitable mussels as highest. Although shore crabs showed flexibility in prey size preference, through which they would be able to cope with environmental variability, our results in general emphasize preference for smaller prey. We discuss the possibility that crabs maximize their long-term feeding rate, in which case it can be optimal to select these smaller mussels.     

Genetic structure and a selected core set of Brazilian soybean cultivars

Soybean is one of the most valuable and profitable oil crop species and a thorough knowledge of the genetic structure of this crop is necessary for developing the best breeding strategies. In this study, a representative collection of soybean cultivars recommended for farming in all Brazilian regions was genotyped using 27 simple sequence repeat (SSR) loci. A total of 130 alleles were detected, with an average allelic number of 4.81 per locus. These alleles determined the core set that best represented this soybean germplasm. The Bayesian analysis revealed the presence of two clusters or subgroups within the whole collection (435 soybean cultivars) and the core set (31 entries). Cultivars of similar origin (ancestral) were clustered into the same groups in both analyses. The genetic diversity parameters, based on the SSR loci, revealed high similarity between the whole collection and core set. Differences between the two clusters detected in the core set were attributed more to the frequency of their ancestors than to their genetic base. In terms of ancestry, divergent groups were presented and a panel is shown which may foster efficient breeding programs and aid soybean breeders in planning reliable crossings in the development of new varieties.     

Patch choice under predation hazard

In this paper we study optimal animal movement in heterogeneous environments consisting of several food patches in which animals trade-off energy gain versus predation risk. We derive a myopic optimization rule describing optimal animal movements by fitness maximization assuming an animal state is described by a single quantity (such as weight, size, or energy reserves). This rule predicts a critical state at which an animal should switch from a more dangerous and more profitable patch to a less dangerous and less profitable patch. Qualitatively, there are two types of behavior: either the animal switches from one patch to another and stays in the new patch for some time before it switches again, or the animal switches between two patches instantaneously. The former case happens if animal state growth is positive in all patches, while the latter case happens if animal state growth is negative in one patch. In particular, this happens if one patch is a refuge. We consider in detail two special cases. The first one assumes a linear animal state growth while the second assumes a saturating animal state growth described by the von Bertalanffy curve. For the first model the proportion of time spent in the more profitable and more risky patch increases with profitability of this patch when state growth is positive in both patches. On contrary, if state growth is negative in the less profitable and safer patch, animals spend proportionally less time in the more profitable and more risky patch as its profitability increases. As a function of the predation risk in the more profitable patch the time spent there proportionally decreases. When animal state growth is described by the saturating curve, time spent in the more risky patch is a hump-shaped curve if state growth is positive in both patches. Our results extend the mu/f rule, which predicts that animals should behave in such a way as to minimize mortality risk to resource intake ratio.     

Warning signals evolve to disengage Batesian mimics

Prey that are unprofitable to attack are typically conspicuous in appearance. Conventional theory assumes that these warning signals have evolved in response to predator receiver biases. However, such biases might be a symptom rather than a cause of warning signals. We therefore examine an alternative theory: that conspicuousness evolves in unprofitable prey to avoid confusion with profitable prey. One might wonder why unprofitable prey do not find a cryptic means to be distinct from profitable prey, reducing both their risk of confusion with profitable prey and their rate of detection by predators. Here we present the first coevolutionary model to allow for Batesian mimicry and signals with different levels of detectability. We find that unprofitable prey do indeed evolve ways of distinguishing themselves using cryptic signals, particularly when appearance traits can evolve in multiple dimensions. However, conspicuous warning signals readily evolve in unprofitable prey when there are more ways to look different from the background than to match it. Moreover, the more unprofitable the prey species, the higher its evolved conspicuousness. Our results provide strong support for the argument that unprofitable species evolve conspicuous signals to avoid confusion with profitable prey and indicate that peak shift in conspicuousness-linked traits is a major factor in its establishment.     

Gene flow between insular, coastal and interior populations of brown bears in Alaska

The brown bears of coastal Alaska have been recently regarded as comprising from one to three distinct genetic groups. We sampled brown bears from each of the regions for which hypotheses of genetic uniqueness have been made, including the bears of the Kodiak Archipelago and the bears of Admiralty, Baranof and Chichagof (ABC) Islands in southeast Alaska. These samples were analysed with a suite of nuclear microsatellite markers. The 'big brown bears' of coastal Alaska were found to be part of the continuous continental distribution of brown bears, and not genetically isolated from the physically smaller 'grizzly bears' of the interior. By contrast, Kodiak brown bears appear to have experienced little or no genetic exchange with continental populations in recent generations. The bears of the ABC Islands, which have previously been shown to undergo little or no female-mediated gene flow with mainland populations, were found not to be genetically isolated from mainland bears. The data from the four insular populations indicate that female and male dispersal can be reduced or eliminated by water barriers of 2–4 km and 7km in width, respectively.     

The influence of predation risk on diet selectivity: A theoretical analysis

Studies that have examined the effect of experimental increases in predation risk on diet selectivity have shown both decreased and increased diet selectivity. A possible explanation for these disparate results emerges from an examination of the prey sets used in these studies, which differed in the relationship between the values of risk components associated with the capture of different prey types (‘danger’) and their profitabilities. When less profitable prey were more dangerous, selectivity increased with predation risk. When prey were equally dangerous, selectivity did not change. Finally, when the more profitable prey were also more dangerous, selectivity decreased with risk. Here, we examine theoretically the influence of a forager's estimate of the probability that a predator is present (φ) on the selection of diets from prey sets with varying danger–profitability relationships. A dynamic programming model is used to determine the maximum attack time (or distance) for each of two types of prey, differing in their energetic content, for a range of forager energy state and φ levels. The diets which would result if foragers attacked prey according to the rules provided by the dynamic model are then determined. The model results indicate that the prey danger–profitability relationship determines the diet selectivity response to φ, confirming that variation in this relationship could be responsible for the range of experimental results. This revised version was published online in July 2006 with corrections to the Cover Date.     

In situ conservation of crop genetic resources through maintenance of traditional farming systems

A strategy is suggested for in situ conservation of crop genetic resources whereby conservation efforts are linked to rural development projects in Third World countries. We describe development projects that emphasize preservation of traditional farming systems and succeed in sustaining production by relying on the maintenance of biological and genetic diversity in these systems. Basing agricultural development efforts on indigenous knowledge, technology, and social organization can provide important guidelines for the design of cropping systems that allow lowincome farmers to produce subsistence and cash crops without dependence on external inputs and seed supplies. By incorporating landraces and wild relatives of crops into these cropping systems, major achievements in the conservation of crop genetic resources can be obtained.     

State-dependent risk-taking by green sea turtles mediates top-down effects of tiger shark intimidation in a marine ecosystem

1. A predictive framework of community and ecosystem dynamics that applies across systems has remained elusive, in part because non-consumptive predator effects are often ignored. Further, it is unclear how much individual-level detail community models must include. 2. Previous studies of short-lived species suggest that state-dependent decisions add little to our understanding of community dynamics. Body condition-dependent decisions made by long-lived herbivores under risk of predation, however, might have greater community-level effects. This possibility remains largely unexplored, especially in marine environments. 3. In the relatively pristine seagrass community of Shark Bay, Australia, we found that herbivorous green sea turtles (Chelonia mydas Linnaeus, 1758) threatened by tiger sharks (Galeocerdo cuvier Peron and LeSueur, 1822) select microhabitats in a condition-dependent manner. Turtles in poor body condition selected profitable, high-risk microhabitats, while turtles in good body condition, which are more abundant, selected safer, less profitable microhabitats. When predation risk was low, however, turtles in good condition moved into more profitable microhabitats. 4. Condition-dependent use of space by turtles shows that tiger sharks modify the spatio-temporal pattern of turtle grazing and their impacts on ecosystem dynamics (a trait-mediated indirect interaction). Therefore, state-dependent decisions by individuals can have important implications for community dynamics in some situations. 5. Our study suggests that declines in large-bodied sharks may affect ecosystems more substantially than assumed when non-lethal effects of these top predators on mesoconsumers are not considered explicitly.     

Carbon catabolite regulation of secondary metabolite formation,an old but not well-established regulatory system

Secondary microbial metabolites have various functions for the producer microorganisms, which allow them to interact and survive in adverse environments. In addition to these functions, other biological activities may have clinical relevance, as diverse as antimicrobial, anticancer and hypocholesterolaemic effects. These metabolites are usually formed during the idiophase of growth and have a wide diversity in their chemical structures. Their synthesis is under the impact of the type and concentration of the culture media nutrients. Some of the molecular mechanisms that affect the synthesis of secondary metabolites in bacteria (Gram-positive and negative) and fungi are partially known. Moreover, all microorganisms have their peculiarities in the control mechanisms of carbon sources, even those belonging to the same genus. This regulatory knowledge is necessary to establish culture conditions and manipulation methods for genetic improvement and product fermentation. As the carbon source is one of the essential nutritional factors for antibiotic production, its study has been imperative both at the industrial and research levels. This review aims to draw the utmost recent advances performed to clarify the molecular mechanisms of the negative effect exerted by the carbon source on the secondary metabolite formation, emphasizing those found in Streptomyces, one of the genera most profitable antibiotic producers.     

Prey selection by plovers: Optimal foraging in mixed-species groups

Prey (earthworm) size selection was investigated in lapwings (Vanellus vanellus) and golden plovers (Pluvialis apricaria) feeding in mixed species flocks and compared with that predicted by an optimal foraging model based on energy intake. As well as the usual constraints of searching and handling time, our model incorporated the difficulty of capturing concealed prey, the orientation time needed to locate prey and the risk of theft by gulls (Larus ridibundus). When costs were taken into account, small worms turned out to be the most profitable. The relative profitability of size classes changed when gulls were present and birds shifted their intake accordingly so that they always took mainly the most profitable worms. Birds were expected to do best by taking the three most profitable size classes and the size range taken was consistent with this. In addition there was an inverse relationship between the probabilities of taking profitable and unprofitable worm sizes. Observations of birds were supported by field enclosure experiments which prevented birds feeding in certain areas. Departures from predictions of the model are interpreted as sampling errors due to birds using depth as an approximate indicator of worm size.     

Testing participation in BRCA1/2-positive families: initiator role of index cases

The objectives of this study were to: (1) describe diffusion of information by affected women in whom a mutation has been identified (index cases) to their families and testing participation among high-risk relatives; (2) assess information recall and understanding by index cases and their satisfaction with the testing process; and (3) determine the factors associated with higher/lower testing decision in the family. Thirty index cases completed a self-administered questionnaire assessing their personal and family characteristics and their satisfaction with their own genetic testing process and a telephone interview to evaluate their knowledge about the risk of a genetic predisposition to breast and ovarian cancer, the type and number of close relatives that they informed, and the difficulties that they encountered. Information about breast/ovarian cancer risk and test availability was generally well transmitted (75%), predominantly (88%) to first-degree relatives. In contrast, testing participation was low (15%) and essentially occurred among sisters and daughters. There was a general lack of knowledge despite a high level of satisfaction regarding the information given by the geneticist. Family support and the knowledge of index cases about the risk of transmission of BRCA1/2 mutations by women were found to be positively and significantly associated with the testing decision among first-degree relatives. Difficulties in informing relatives appeared to be related to poor understanding of the information by index cases, as well as fear, and avoidance among close relatives. A major challenge for genetic counseling is to ensure that consulting patients not only receive complete understanding but also understand this information and anticipate the impact of the test result before deciding to take the test.