Where do all the proteins go?

The subcellular localization of a protein can be very informative in identifying its function and in understanding the regulatory mechanisms by which it is controlled. Past efforts to define protein localization have typically entailed methods of immunological and fluorescence-based detection applied to a limited number of gene products. Several current studies are shifting this paradigm – utilizing traditional and novel approaches in molecular biology, proteomics, histochemistry and bioinformatics to define protein localization on a proteome-wide scale. Selected studies highlighting each of these approaches are presented here as an overview of the diverse avenues by which protein localization may be investigated for the identification of new drug targets.     

Where did the finch go? Insights from radio telemetry of the medium ground finch (Geospiza fortis)

Movement patterns and habitat selection of animals have important implications for ecology and evolution. Darwin''s finches are a classic model system for ecological and evolutionary studies, yet their spatial ecology remains poorly studied. We tagged and radio‐tracked five (three females, two males) medium ground finches (Geospiza fortis) to examine the feasibility of telemetry for understanding their movement and habitat use. Based on 143 locations collected during a 3‐week period, we analyzed for the first time home‐range size and habitat selection patterns of finches at El Garrapatero, an arid coastal ecosystem on Santa Cruz Island (Galápagos). The average 95% home range and 50% core area for G. fortis in the breeding season was 20.54 ha ± 4.04 ha SE and 4.03 ha ± 1.11 ha SE, respectively. For most of the finches, their home range covered a diverse set of habitats. Three finches positively selected the dry‐forest habitat, while the other habitats seemed to be either negatively selected or simply neglected by the finches. In addition, we noted a communal roosting behavior in an area close to the ocean, where the vegetation is greener and denser than the more inland dry‐forest vegetation. We show that telemetry on Darwin''s finches provides valuable data to understand the movement ecology of the species. Based on our results, we propose a series of questions about the ecology and evolution of Darwin''s finches that can be addressed using telemetry.     

Where did the BLOSUM62 alignment score matrix come from?

Many sequence alignment programs use the BLOSUM62 score matrix to score pairs of aligned residues. Where did BLOSUM62 come from?     

Where did all the nitrogen go? Fate of nitrogen inputs to large watersheds in the northeastern U.S.A.

To assess the fate of the large amounts of nitrogen (N) brought into the environment by human activities, we constructed N budgets for sixteen large watersheds (475 to 70,189 km²) in the northeastern U.S.A. These watersheds are mainly forested (48–87%), but vary widely with respect to land use and population density. We combined published data and empirical and process models to set up a complete N budget for these sixteen watersheds. Atmospheric deposition, fertilizer application, net feed and food inputs, biological fixation, river discharge, wood accumulation and export, changes in soil N, and denitrification losses in the landscape and in rivers were considered for the period 1988 to 1992. For the whole area, on average 3420 kg of N is imported annually per km² of land. Atmospheric N deposition, N₂ fixation by plants, and N imported in commercial products (fertilizers, food and feed) contributed to the input in roughly equal contributions. We quantified the fate of these inputs by independent estimates of storage and loss terms, except for denitrification from land, which was estimated from the difference between all inputs and all other storage and loss terms. Of the total storage and losses in the watersheds, about half of the N is lost in gaseous form (51%, largely by denitrification). Additional N is lost in riverine export (20%), in food exports (6%), and in wood exports (5%). Change in storage of N in the watersheds in soil organic matter (9%) and wood (9%) accounts for the remainder of the sinks. The presence of appreciable changes in total N storage on land, which we probably under-rather than overestimated, shows that the N budget is not in steady state, so that drainage and denitrification exports of N may well increase further in the future.     

Where did all the Aleut men go? Aleut male attrition and related patterns in Aleutian historical demography and social organization

Historical, economic, and political influences on Aleut demography and social organization are considered in relation to an apparent deficit of Aleut males in the early 20th century. Ethnohistoric records detail persistent waves of explorers, fur hunters, missionaries, bureaucrats, and foreign fishermen coming to the Aleutian region for economic exploitation, with some making it their home. The first major wave consisted of Russian and Siberian crews in pursuit of sea otters and fur seals. These entrepreneurs moved Aleut men to hunting grounds and replaced a large portion of them in the villages. The second wave consisted of Scandinavian and other European immigrants who followed cod, halibut, and herring fisheries and who married into eastern Aleut villages. These movements resulted in two genealogical deficits of Aleut men with concomitant shifts in social organization and economic emphases that contribute to the modern diversity of Aleut society. Aleut evacuation during World War II exacerbated these sex imbalances in the villages of the western Aleutian and Pribilof islands.     

Information extraction from full text scientific articles: Where are the keywords?

Background  

To date, many of the methods for information extraction of biological information from scientific articles are restricted to the abstract of the article. However, full text articles in electronic version, which offer larger sources of data, are currently available. Several questions arise as to whether the effort of scanning full text articles is worthy, or whether the information that can be extracted from the different sections of an article can be relevant.     

Where do the electrons go? How numerous redox processes drive phytochemical diversity

Phytochemistry Reviews - Plants produce structurally and functionally diverse metabolites that are key to many physiological processes such as growth and development, reproduction, defense, and...     

Glioma development: where did it all go wrong?

Investigating the family tree of a tumor to identify its cellular origins is a daunting task. Liu et al. (2011) now use an elegant lineage tracing technique (MADM) to visualize glioma from its earliest stages. They show that mutations originally induced in neural stem cells lie dormant and only trigger malignant transformation following differentiation into oligodendrocyte precursor cells.     

Genetic research in osteoporosis: Where are we? Where should we go next?

Fractures resulting from low bone mass and excessive skeletal fragility (osteoporosis) are common worldwide both in males and females, particularly in later years of life. Both fractures, and the most important predictor of fractures, bone mass, are now known to be strongly heritable. This fact, plus the current growth in genetic science, has led to a surge of genetic research in osteoporosis, mostly in the search for genes and their polymorphisms that are responsible for variation in bone mass. Finding the genetic basis underlying variation in bone mass will lead us to deeper understanding of the biology of bone mass accumulation, maintenance and adaptation to load. This, plus finding the genetic basis for overall variation in fracture risk per se, will facilitate the development of interventions, both pharmaceutical and non-pharmaceutical, to prevent and/or treat osteoporosis successfully. This research has produced a rather large number of gene loci that seem to influence bone mass. The challenge now is to refine the statistical genetics and the phenotypes involved so that we can confidently identify those gene loci that truly influence bone mass, and to find ways to study the genetic basis for the most direct disease outcome of interest, fracture.     

Macroecology in the age of Big Data – Where to go from here?

Recent years have seen an exponential increase in the amount of data available in all sciences and application domains. Macroecology is part of this “Big Data” trend, with a strong rise in the volume of data that we are using for our research. Here, we summarize the most recent developments in macroecology in the age of Big Data that were presented at the 2018 annual meeting of the Specialist Group Macroecology of the Ecological Society of Germany, Austria and Switzerland (GfÖ). Supported by computational advances, macroecology has been a rapidly developing field over recent years. Our meeting highlighted important avenues for further progress in terms of standardized data collection, data integration, method development and process integration. In particular, we focus on (a) important data gaps and new initiatives to close them, for example through space- and airborne sensors, (b) how various data sources and types can be integrated, (c) how uncertainty can be assessed in data-driven analyses and (d) how Big Data and machine learning approaches have opened new ways of investigating processes rather than simply describing patterns. We discuss how Big Data opens up new opportunities, but also poses new challenges to macroecological research. In the future, it will be essential to carefully assess data quality, the reproducibility of data compilation and analytical methods, and the communication of uncertainties. Major progress in the field will depend on the definition of data standards and workflows for macroecology, such that scientific quality and integrity are guaranteed, and collaboration in research projects is made easier.