Towards defining the nuclear proteome

Background

The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered.

Results

We report direct evidence for 2,568 mammalian proteins within the nuclear proteome: the nuclear subcellular localization of 1,529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and an additional 1,039 proteins for which clear experimental evidence is documented in published literature. This is direct evidence that the nuclear proteome consists of at least 14% of the entire proteome. This dataset was used to evaluate computational approaches designed to identify additional nuclear proteins.

Conclusion

This represents direct experimental evidence that the nuclear proteome consists of at least 14% of the entire proteome. This high-quality nuclear proteome dataset was used to evaluate computational approaches designed to identify additional nuclear proteins. Based on this analysis, researchers can determine the stringency and types of lines of evidence they consider to infer the size and complement of the nuclear proteome.     

Towards defining aquatic ecosystem health for the Great Lakes

The Canada — U.S. Great Lakes Water Quality Agreement defines Areas of Concern as geographic areas that fail to meet the general or specific objectives of the Great Lakes Water Quality Agreement where such failure has caused or is likely to cause impairment of beneficial use or the area's ability to support aquatic life. Impairment of beneficial use is defined by the Agreement as a change in the physical, chemical or biological integrity sufficient to cause any one of 14 designated use impairments. In 1987 the International Joint Commission's Great Lakes Water Quality Board (GLWQB) recommended that criteria be developed to determine when ecosystem conditions have been impacted enough to warrant designation as an Area of Concern and when conditions have improved sufficiently to be delisted. Based on scientific input and policy considerations, the GLWQB adopted, in principle, a set of quantitative and qualitative listing/delisting criteria for each of the 14 use impairments. These criteria can be uniformly applied throughout the basin. Further, the GLWQB recommended future refinement of these criteria based on advances in science and public input.     

Towards a common strategy for transducing olfactory information

Olfactory receptor cells in phylogenetically diverse animals are strikingly similar, notwithstanding species-specific differences in organizational details. As we learn more about how olfactory receptor cells function, we see the first evidence that phylogenetic similarity may extend to the functional level. Conservation of form and function in phylogenetically diverse animals would suggest the presence of a fundamental strategy for detecting and discriminating odors. Emerging data on how olfactory receptor cells transduce odor information offers some insight into what this still unresolved strategy may be.     

Towards a matrix mechanics framework for dynamic protein network

Protein–protein interaction networks are currently visualized by software generated interaction webs based upon static experimental data. Current state is limited to static, mostly non-compartmental network and non time resolved protein interactions. A satisfactory mathematical foundation for particle interactions within a viscous liquid state (situation within the cytoplasm) does not exist nor do current computer programs enable building dynamic interaction networks for time resolved interactions. Building mathematical foundation for intracellular protein interactions can be achieved in two increments (a) trigger and capture the dynamic molecular changes for a select subset of proteins using several model systems and high throughput time resolved proteomics and, (b) use this information to build the mathematical foundation and computational algorithm for a compartmentalized and dynamic protein interaction network. Such a foundation is expected to provide benefit in at least two spheres: (a) understanding physiology enabling explanation of phenomenon such as incomplete penetrance in genetic disorders and (b) enabling several fold increase in biopharmaceutical production using impure starting materials.     

Towards defining the complement of mammalian WFDC-domain-containing proteins

WFDC (whey/four-disulfide core)-domain-containing proteins are defined by the possession of one or more 40-50 amino acid domains that include eight conserved cysteine residues linked by four characteristic intramolecular disulfide bonds. Some also contain other structural domains, whereas in many the WFDC-domain is the only domain present. The WFDC-domain is not limited to mammals but is widespread across all lineages. There is increasing evidence to suggest that mammalian WFDC-domain-containing proteins are undergoing rapid molecular evolution and as might be expected they exhibit low levels of sequence similarity coupled with multiple examples of species-specific gene acquisition and gene loss. The characteristic structural domain (that is generally encoded by a single exon) makes these proteins relatively easy to identify in databases. This review will outline the repertoire of such domains within the mouse, but similar principles can be applied to the identification of all proteins within individual species.     

Towards a worldwide wood economics spectrum

Wood performs several essential functions in plants, including mechanically supporting aboveground tissue, storing water and other resources, and transporting sap. Woody tissues are likely to face physiological, structural and defensive trade-offs. How a plant optimizes among these competing functions can have major ecological implications, which have been under-appreciated by ecologists compared to the focus they have given to leaf function. To draw together our current understanding of wood function, we identify and collate data on the major wood functional traits, including the largest wood density database to date (8412 taxa), mechanical strength measures and anatomical features, as well as clade-specific features such as secondary chemistry. We then show how wood traits are related to one another, highlighting functional trade-offs, and to ecological and demographic plant features (growth form, growth rate, latitude, ecological setting). We suggest that, similar to the manifold that tree species leaf traits cluster around the 'leaf economics spectrum', a similar 'wood economics spectrum' may be defined. We then discuss the biogeography, evolution and biogeochemistry of the spectrum, and conclude by pointing out the major gaps in our current knowledge of wood functional traits.     

Towards the identification of the common features of bacterial biofilm development.

Microorganisms can live and proliferate as individual cells swimming freely in the environment, or they can grow as highly organized, multicellular communities encased in a self-produced polymeric matrix in close association with surfaces and interfaces. This microbial lifestyle is referred to as biofilms. The intense search over the last few years for factors involved in biofilm development has revealed that distantly related bacterial species recurrently make use of the same elements to produce biofilms. These common elements include a group of proteins containing GGDEF/EAL domains, surface proteins homologous to Bap of Staphylococcus aureus, and some types of exopolysaccharides, such as cellulose and the poly-beta-1,6-N-acetylglucosamine. This review summarizes current knowledge about these three common elements and their role in biofilm development.     

Towards a whole-system framework for wildfire monitoring using Earth observations

Fire seasons have become increasingly variable and extreme due to changing climatological, ecological, and social conditions. Earth observation data are critical for monitoring fires and their impacts. Herein, we present a whole-system framework for identifying and synthesizing fire monitoring objectives and data needs throughout the life cycle of a fire event. The four stages of fire monitoring using Earth observation data include the following: (1) pre-fire vegetation inventories, (2) active-fire monitoring, (3) post-fire assessment, and (4) multi-scale synthesis. We identify the challenges and opportunities associated with current approaches to fire monitoring, highlighting four case studies from North American boreal, montane, and grassland ecosystems. While the case studies are localized to these ecosystems and regional contexts, they provide insights for others experiencing similar monitoring challenges worldwide. The field of remote sensing is experiencing a rapid proliferation of new data sources, providing observations that can inform all aspects of our fire monitoring framework; however, significant challenges for meeting fire monitoring objectives remain. We identify future opportunities for data sharing and rapid co-development of information products using cloud computing that benefits from open-access Earth observation and other geospatial data layers.     

Towards a general framework for including noise impacts in LCA

Purpose  

Several damages have been associated with the exposure of human beings to noise. These include auditory effects, i.e., hearing impairment, but also non-auditory physiological ones such as hypertension and ischemic heart disease, or psychological ones such as annoyance, depression, sleep disturbance, limited performance of cognitive tasks or inadequate cognitive development. Noise can also interfere with intended activities, both in daytime and nighttime. ISO 14'040 also indicated the necessity of introducing noise, together with other less developed impact categories, in a complete LCA study, possibly changing the results of many LCA studies already available. The attempts available in the literature focused on the integration of transportation noise in LCA. Although being considered the most frequent source of intrusive impact, transportation noise is not the only type of noise that can have a malign impact on public health. Several other sources of noise such as industrial or occupational need to be taken into account to have a complete consideration of noise into LCA. Major life cycle inventories (LCI) typically do not contain data on noise emissions yet and characterisation factors are not yet clearly defined. The aim of the present paper is to briefly review what is already available in the field and propose a new framework for the consideration of human health impacts of any type of noise that could be of interest in the LCA practice, providing indications for the introduction of noise in LCI and analysing what data is already available and, in the form of a research agenda, what other resources would be needed to reach a complete coverage of the problem.     

Towards a lightweight generic computational grid framework for biological research

Background  

An increasing number of scientific research projects require access to large-scale computational resources. This is particularly true in the biological field, whether to facilitate the analysis of large high-throughput data sets, or to perform large numbers of complex simulations – a characteristic of the emerging field of systems biology.     

Towards a framework for the study of the neural correlates of aesthetic preference

Aiming to provide a tentative framework for the study of the neural correlates of aesthetic preference, we review three recent neuroimaging studies carried out with the purpose of locating brain activity associated with decisions about the beauty of visual stimuli (Cela-Conde et al., 2004; Kawabata and Zeki, 2004; Vartanian and Goel, 2004). We find that the results of the three studies are not in line with previous neuropsychological data. Moreover, there are no coincidences among their results. However, when they are mapped on to Chatterjee's (2003) neuropsychological model of aesthetic preference it becomes clear that neuroimaging data are not contradictory, but complementary, and their interpretation is enriched. The results of these studies suggest that affective processes have an important role in aesthetic preference, and that they are integrated with cognitive processes to reach a decision regarding the beauty of visual stimuli. Future studies must aim to clarify whether certain methodological procedures are better suited to study any of the particular cognitive operations involved in aesthetic preference, and ascertain the extent to which the proposed framework is compatible with the aesthetic appreciation of musical stimuli.     

A theoretical framework for defining some concepts in evolution.

We present a theoretical framework for biological evolution with the intention of giving precise mathematical definitions of some concepts in evolutionary biology such as fitness, evolutionary pressure, specialization and natural selection. In this framework, such concepts are identified with well-known mathematical terms within the theory of dynamical systems. We also discuss some more general implications in evolution; for instance, the fact that our model naturally exhibits a frequency spectrum of the type 1/f for low frequencies of evolutionary events.     

A common framework for perceptual learning

In this review, we summarize recent evidence that perceptual learning can occur not only under training conditions but also in situations of unattended and passive sensory stimulation. We suggest that the key to learning is to boost stimulus-related activity that is normally insufficient exceed a learning threshold. We discuss how factors such as attention and reinforcement have crucial, permissive roles in learning. We observe, however, that highly optimized stimulation protocols can also boost responses and promote learning. This helps to reconcile observations of how learning can occur (or fail to occur) in seemingly contradictory circumstances, and argues that different processes that affect learning operate through similar mechanisms that are probably based on, and mediated by, neuromodulatory factors.