Opportunities and challenges for the life sciences community

Twenty-first century life sciences have transformed into data-enabled (also called data-intensive, data-driven, or big data) sciences. They principally depend on data-, computation-, and instrumentation-intensive approaches to seek comprehensive understanding of complex biological processes and systems (e.g., ecosystems, complex diseases, environmental, and health challenges). Federal agencies including the National Science Foundation (NSF) have played and continue to play an exceptional leadership role by innovatively addressing the challenges of data-enabled life sciences. Yet even more is required not only to keep up with the current developments, but also to pro-actively enable future research needs. Straightforward access to data, computing, and analysis resources will enable true democratization of research competitions; thus investigators will compete based on the merits and broader impact of their ideas and approaches rather than on the scale of their institutional resources. This is the Final Report for Data-Intensive Science Workshops DISW1 and DISW2. The first NSF-funded Data Intensive Science Workshop (DISW1, Seattle, WA, September 19-20, 2010) overviewed the status of the data-enabled life sciences and identified their challenges and opportunities. This served as a baseline for the second NSF-funded DIS workshop (DISW2, Washington, DC, May 16-17, 2011). Based on the findings of DISW2 the following overarching recommendation to the NSF was proposed: establish a community alliance to be the voice and framework of the data-enabled life sciences. After this Final Report was finished, Data-Enabled Life Sciences Alliance (DELSA, www.delsall.org ) was formed to become a Digital Commons for the life sciences community.     

The early evolution of life: solution to Darwin's dilemma

Recent studies of Precambrian fossils indicate that life on Earth originated earlier than assumed, microscopic life was prevalent in the Precambrian Eon, the tempo and mode of evolution during the Precambrian period were different from other periods, and that only the Precambrian fossil record can be used as evidence of early life. Implications for future research include directing the search for the origin of life away from the geological record, modification of hypotheses about molecular change, use of Precambrian microfossils in dating younger geological units, and progress in defining the nature of major events in early evolution.     

The rapid dissolution of dioecy by experimental evolution

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Data issues in the life sciences

We review technical and sociological issues facing the Life Sciences as they transform into more data-centric disciplines - the "Big New Biology". Three major challenges are: 1) lack of comprehensive standards; 2) lack of incentives for individual scientists to share data; 3) lack of appropriate infrastructure and support. Technological advances with standards, bandwidth, distributed computing, exemplar successes, and a strong presence in the emerging world of Linked Open Data are sufficient to conclude that technical issues will be overcome in the foreseeable future. While motivated to have a shared open infrastructure and data pool, and pressured by funding agencies in move in this direction, the sociological issues determine progress. Major sociological issues include our lack of understanding of the heterogeneous data cultures within Life Sciences, and the impediments to progress include a lack of incentives to build appropriate infrastructures into projects and institutions or to encourage scientists to make data openly available.     

Applications of low-light imaging to life sciences

Photon imaging is a new technique for the quantitative analysis of bioluminescence and chemiluminescence and can be performed both at the macro and micro levels. The high sensitivity and spatial resolution of photon-counting cameras have resulted in the development of new applications in the life sciences. At the macro level, imaging is a valuable tool for the rapid identification of biological samples emitting long-lasting glows in assays using microtitre plates or filter formats (immunoassays, DNA probes, phagocytosis, gene expression, metabolite and drug analysis) and also for in vivo studies of promoter activity. At the micro level, low-light imaging can be used for analysing multiple analytes on micro sensors and for advanced cell analysis (immunocytology, in situ hybridization, identification of cells or tissues expressing the luciferase gene, intracellular or intercellular protein traffic, metabolite analysis and imaging of Ca²⁺ flux and phosphorylation reactions). Two-dimensional photon-counting instrumentation is a versatile and powerful research tool for imaging and is complementary to conventional luminometers. The main applications to the life sciences involve many types of luminescence assays and can be performed on multiple samples in standard and non-standard formats. Photon-counting coupled to imaging is very helpful in selecting microorganisms or cells expressing bioluminescent genes. Measurements can be made in vitro and in vivo with a sensitivity comparable to that of phototube luminometers.     

Applications of PIXE in the life sciences

Biological Trace Element Research - During the last decade, particle-induced X-ray emission spectrometry (PIXE) has been accepted by the analytical chemistry community as a standard method. Instead...     

Online tools to support literature-based discovery in the life sciences

In biomedical research, the amount of experimental data and published scientific information is overwhelming and ever increasing, which may inhibit rather than stimulate scientific progress. Not only are text-mining and information extraction tools needed to render the biomedical literature accessible but the results of these tools can also assist researchers in the formulation and evaluation of novel hypotheses. This requires an additional set of technological approaches that are defined here as literature-based discovery (LBD) tools. Recently, several LBD tools have been developed for this purpose and a few well-motivated, specific and directly testable hypotheses have been published, some of which have even been validated experimentally. This paper presents an overview of recent LBD research and discusses methodology, results and online tools that are available to the scientific community.     

Patent pools and clearinghouses in the life sciences

The biopharmaceutical industry is slowly absorbing the idea of collaborative patent licensing models. Recently, two patent pools for developing countries have been launched: the Pool for Open Innovation against Neglected Tropical Diseases initiated by GlaxoSmithKline (GSK), which is referred to as the BIO Ventures for Global Health (BVGH) pool, and the Medicines Patent Pool (MPP) initiated by UNITAID. Various organizations have recommended using pools or clearinghouses beyond the humanitarian dimension where many patents are owned by many different actors. As a first attempt, MPEG LA, which administers patent pools in various technology fields, is now setting up a clearinghouse for patents related to molecular diagnostics. These examples as well as the results from an empirical study provide useful insights for the design and administration of future pools and clearinghouses in the life sciences.     

Birth of the life sciences in Spain and Portugal

For many centuries, Spain and Portugal were occupied by various nations. The consequent mixing of cultures formed a unique environment in which to do science.     

Melatonin: perspectives in the life sciences

The pineal gland hormone melatonin is now considered an important neuroendocrine component of animal physiology. Although the functional status of melatonin has been well described for subhuman species, there is a paucity of data concerning the physiological role of this hormone in man. This paucity of data has much to do with the limitations of experimental design imposed by the practical and ethical difficulties associated with the study of a nocturnally secreted hormone. The recent advent of salivary melatonin assay has provided a very practical means of monitoring melatonin secretion in long-term longitudinal type community based studies of pineal gland function in human health and disease. The efforts to describe key chronobiological changes in melatonin secretion of possible functional significance have been accompanied by a seemingly less enthusiastic search to describe the nature of the melatonin receptor, another highly important component of the 'melatonin message'. The functional relevance of specific chronobiological changes in melatonin secretion cannot be completely understood without an increased knowledge of melatonin action at the receptor level. The present work describes the recent methodological advance in the investigation of human pineal gland physiology represented by salivary melatonin assay, and discusses the present status of our knowledge of the melatonin receptor.     

Low-light imaging technology in the life sciences

Photon imaging is an increasingly important technique for the measurement and analysis of chemiluminescence and bioluminescence. New high-performance low-light level imaging systems have recently become available for the life science. These systems use advances in camera design and digital image processing and are now being used for a wide range of luminescence applications. They offer good sensitivity for photon detection and large dynamic range, and are suitable for quantitative analysis. This is achieved using a range of software techniques including image arithmetic, histogramming or summing regions of interest, feature extraction and multiple image processing for kinetics or assay screening. Improvements in imageprocessing hardware and software have increased the usefulness of these systems in the biosciences. Low-light imaging is a rapid and non-invasive method for the sensitive detection and analysis of luminescent assays. As such it offers a powerful and sensitive tool for investigating processes, both at the cellular level (luc and lux reporter genes, intracellular signalling) and for measurement of macro samples (immunoassays, gels and blots, tissue sections).