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Biological Questions (biological + question)
Selected AbstractsUse and misuse of the reduced major axis for line-fittingAMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY, Issue 3 2009Richard J. Smith Abstract Many investigators use the reduced major axis (RMA) instead of ordinary least squares (OLS) to define a line of best fit for a bivariate relationship when the variable represented on the X -axis is measured with error. OLS frequently is described as requiring the assumption that X is measured without error while RMA incorporates an assumption that there is error in X. Although an RMA fit actually involves a very specific pattern of error variance, investigators have prioritized the presence versus the absence of error rather than the pattern of error in selecting between the two methods. Another difference between RMA and OLS is that RMA is symmetric, meaning that a single line defines the bivariate relationship, regardless of which variable is X and which is Y, while OLS is asymmetric, so that the slope and resulting interpretation of the data are changed when the variables assigned to X and Y are reversed. The concept of error is reviewed and expanded from previous discussions, and it is argued that the symmetry-asymmetry issue should be the criterion by which investigators choose between RMA and OLS. This is a biological question about the relationship between variables. It is determined by the investigator, not dictated by the pattern of error in the data. If X is measured with error but OLS should be used because the biological question is asymmetric, there are several methods available for adjusting the OLS slope to reflect the bias due to error. RMA is being used in many analyses for which OLS would be more appropriate. Am J Phys Anthropol, 2009. © 2009 Wiley-Liss, Inc. [source] Capturing Complex Protein Gradients on Biomimetic Hydrogels for Cell-Based AssaysADVANCED FUNCTIONAL MATERIALS, Issue 21 2009Steffen Cosson Abstract A versatile strategy to rapidly immobilize complex gradients of virtually any desired protein on soft poly(ethylene glycol) (PEG) hydrogel surfaces that are reminiscent of natural extracellular matrices (ECM) is reported. A microfluidic chip is used to generate steady-state gradients of biotinylated or Fc-tagged fusion proteins that are captured and bound to the surface in less than 5,min by NeutrAvidin or ProteinA, displayed on the surface. The selectivity and orthogonality of the binding schemes enables the formation of parallel and orthogonal overlapping gradients of multiple proteins, which is not possible on conventional cell culture substrates. After patterning, the hydrogels are released from the microfluidic chip and used for cell culture. This novel platform is validated by conducting single-cell migration experiments using time-lapse microscopy. The orientation of cell migration, as well as the migration rate of primary human fibroblasts, depends on the concentration of an immobilized fibronectin fragment. This technique can be readily applied to other proteins to address a wealth of biological questions with different cell types. [source] Molecular imaging of regional brain tumor biologyJOURNAL OF CELLULAR BIOCHEMISTRY, Issue S39 2002A.M. Spence Abstract Energy metabolism measurements in gliomas in vivo are now performed widely with positron emission tomography (PET). This capability has developed from a large number of basic and clinical science investigations that have cross fertilized one another. This article presents several areas that exemplify questions that have been explored over the last two decades. While the application of PET with [18F]-2-fluoro-2-deoxyglucose (FDG-PET) has proven useful for grading and prognosis assessments, this approach is less clinically suitable for assessing response to therapy, even though results to date raise very intriguing biological questions. Integration of metabolic imaging results into glioma therapy protocols is a recent and only preliminarily tapped method that may prove useful in additional trials that target DNA or membrane biosynthesis, or resistance mechanisms such as hypoxia. There are exciting future directions for molecular imaging that will undoubtedly be fruitful to explore, especially apoptosis, angiogenesis and expression of mutations of genes, e.g., epidermal growth factor receptor, that promote or suppress cellular malignant behavior. J. Cell. Biochem. Suppl. 39: 25,35, 2002. © 2002 Wiley-Liss, Inc. [source] Habitat saturation and the spatial evolutionary ecology of altruismJOURNAL OF EVOLUTIONARY BIOLOGY, Issue 7 2009S. LION Abstract Under which ecological conditions should individuals help their neighbours? We investigate the effect of habitat saturation on the evolution of helping behaviours in a spatially structured population. We combine the formalisms of population genetics and spatial moment equations to tease out the effects of various physiological (direct benefits and costs of helping) and ecological parameters (such as the density of empty sites) on the selection gradient on helping. Our analysis highlights the crucial importance of demography for the evolution of helping behaviours. It shows that habitat saturation can have contrasting effects, depending on the form of competition (direct vs. indirect competition) and on the conditionality of helping. In our attempt to bridge the gap between spatial ecology and population genetics, we derive an expression for relatedness that takes into account both habitat saturation and the spatial structure of genetic variation. This analysis helps clarify discrepancies in the results obtained by previous theoretical studies. It also provides a theoretical framework taking into account the interplay between demography and kin selection, in which new biological questions can be explored. [source] Probing protein function by chemical modification,JOURNAL OF PEPTIDE SCIENCE, Issue 10 2010Yao-Wen Wu Abstract Labeling proteins with synthetic probes, such as fluorophores, affinity tags, and other functional labels is enormously useful for characterizing protein function in vitro, in live cells, or in whole organisms. Recent advancements of chemical methods have substantially expanded the tools that are applicable to modify proteins. In this review, we discuss some important chemical methods for site-specific protein modification and highlight the application of established techniques to tackle biological questions. Copyright © 2010 European Peptide Society and John Wiley & Sons, Ltd. [source] 71 Proteomics of haematococcus pluvialis: new opportunities for study of genomics of a non-sequenced speciesJOURNAL OF PHYCOLOGY, Issue 2003Q. Hu The green alga, Haematococcus pluvialis, has become a model organism for commercial production of the high-value carotenoid astaxanthin. H. Pluvialis has also drawn significant scientific attention because fundamental biological questions relating to the massive cellular accumulation of astaxanthin have to be addressed in order to improve the yield and quality of the algal biomass. However, research has been impeded by the lack of molecular background information on this non-sequenced species. A combination of classical biochemistry with a state-of-the-art proteomic approach was used to address these questions. This was possible by taking advantage of information already available for homologous genes/gene-products in organisms whose genomes have been sequenced. The approach involved isolation of subsets of the proteome from subcellular compartments/organelles of an organism by one- or two-dimensional electrophoresis (1-DE or 2-DE) and their identification by N-terminal sequencing and peptide mass fingerprinting (PMF), involving matrix-assisted laser desorption/ionization and time-of-flight (MALDI-TOF) mass spectrometry coupled with bioinformatics. Based upon the information obtained from the combined methods, expression and physiological functions of specific genes/encoded proteins may be deduced. Examples include profiling of cell wall proteins, biogenesis and protein composition of lipid bodies, and expression patterns of soluble proteins under stress conditions. Advantages and limitations of the method for non-sequenced organisms and for cross-species protein identification will also be discussed. [source] Toward Understanding the Mechanism of Chromophore-assisted Laser Inactivation,Evidence for the Primary Photochemical Steps,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 2 2005Elke Horstkotte ABSTRACT Chromophore-assisted laser inactivation (CALI) is a lightmediated technique used to selectively inactivate proteins of interest to elucidate their biological function. CALI has potential applications to a wide array of biological questions, and its efficiency allows for high-throughput application. A solid understanding of its underlying photochemical mechanism is still missing. In this study, we address the CALI mechanism using a simplified model system consisting of the enzyme ,-galactosidase as target protein and the common dye fluorescein. We demonstrate that protein photoinactivation is independent from dye photobleaching and provide evidence that the first singlet state of the chromophore is the relevant transient state for the initiation of CALI. Furthermore, the inactivation process was shown to be dependent on oxygen and likely to be based on photooxidation of the target protein via singlet oxygen. The simple model system used in this study may be further applied to identify and optimize other CALI chromophores. [source] Fish proteome analysis: Model organisms and non-sequenced speciesPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 4 2010Ignasi Forné Abstract In the last decade, proteomic technologies have been increasingly used in fish biology research. Proteomics has been applied primarily to investigate the physiology, development biology and the impact of contaminants in fish model organisms, such as zebrafish (Danio rerio), as well as in some commercial species produced in aquaculture, mainly salmonids and cyprinids. However, the lack of previous genetic information on most fish species has been a major drawback for a more general application of the different proteomic technologies currently available. Also, many teleosts of interest in biological research and with potential application in aquaculture hold unique physiological characteristics that cannot be directly addressed from the study of small laboratory fish models. This review describes proteomic approaches that have been used to investigate diverse biological questions in model and non-model fish species. We will also evaluate the current possibilities to integrate fish proteomics with other "omic" approaches, as well as with additional complementary techniques, in order to address the future challenges in fish biology research. [source] Voltage-gated proton channels: what's next?THE JOURNAL OF PHYSIOLOGY, Issue 22 2008Thomas E. DeCoursey This review is an attempt to identify and place in context some of the many questions about voltage-gated proton channels that remain unsolved. As the gene was identified only 2 years ago, the situation is very different than in fields where the gene has been known for decades. For the proton channel, most of the obvious and less obvious structure,function questions are still wide open. Remarkably, the proton channel protein strongly resembles the voltage-sensing domain of many voltage-gated ion channels, and thus offers a novel approach to study gating mechanisms. Another surprise is that the proton channel appears to function as a dimer, with two separate conduction pathways. A number of significant biological questions remain in dispute, unanswered, or in some cases, not yet asked. This latter deficit is ascribable to the intrinsic difficulty in evaluating the importance of one component in a complex system, and in addition, to the lack, until recently, of a means of performing an unambiguous lesion experiment, that is, of selectively eliminating the molecule in question. We still lack a potent, selective pharmacological inhibitor, but the identification of the gene has allowed the development of powerful new tools including proton channel antibodies, siRNA and knockout mice. [source] A perspective of synthetic biology: Assembling building blocks for novel functionsBIOTECHNOLOGY JOURNAL, Issue 6 2006Pengcheng Fu ProfessorArticle first published online: 19 MAY 200 Abstract Synthetic biology is a recently emerging field that applies engineering formalisms to design and construct new biological parts, devices, and systems for novel functions or life forms that do not exist in nature. Synthetic biology relies on and shares tools from genetic engineering, bioengineering, systems biology and many other engineering disciplines. It is also different from these subjects, in both insights and approach. Applications of synthetic biology have great potential for novel contributions to established fields and for offering opportunities to answer fundamentally new biological questions. This article does not aim at a thorough survey of the literature and detailing progress in all different directions. Instead, it is intended to communicate a way of thinking for synthetic biology in which basic functional elements are defined and assembled into living systems or biomaterials with new properties and behaviors. Four major application areas with a common theme are discussed and a procedure (or "protocol") for a standard synthetic biology work is suggested. [source] | |||||||||||||