A proteomics approach to understanding protein ubiquitination

There is a growing need for techniques that can identify and characterize protein modifications on a large or global scale. We report here a proteomics approach to enrich, recover, and identify ubiquitin conjugates from Saccharomyces cerevisiae lysate. Ubiquitin conjugates from a strain expressing 6xHis-tagged ubiquitin were isolated, proteolyzed with trypsin and analyzed by multidimensional liquid chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for amino acid sequence determination. We identified 1,075 proteins from the sample. In addition, we detected 110 precise ubiquitination sites present in 72 ubiquitin-protein conjugates. Finally, ubiquitin itself was found to be modified at seven lysine residues providing evidence for unexpected diversity in polyubiquitin chain topology in vivo. The methodology described here provides a general tool for the large-scale analysis and characterization of protein ubiquitination.     

A field-theoretic approach to understanding scale-free neocortical dynamics

A mesoscopic field-theoretic approach is compared with neural network and brain imaging approaches to understanding brain dynamics. Analysis of high spatiotemporal resolution rabbit electroencephalogram (EEG) reveals neural fields in the form of spatial patterns in amplitude (AM) and phase (PM) modulation of gamma and beta carrier waves that serve to classify EEGs from trials with differing conditioned stimuli (CS+/−). Paleocortex exemplified by olfactory EEG has one AM–PM pattern at a time that forms by an input-dependent phase transition. Neocortex shows multiple overlapping AM–PM patterns before and during presentation of CSs. Modeling suggests that neocortex is stabilized in a scale-free state of self-organized criticality, enabling cooperative domains to form virtually instantaneously by phase transitions ranging in size from a few hypercolumns to an entire hemisphere. Self-organized local domains precede formation of global domains that supervene and contribute global modulations to local domains. This mechanism is proposed to explain Gestalt formation in perception.     

A genomic approach to the understanding of Xylella fastidiosa pathogenicity

Xylella fastidiosa is a fastidious, xylem-limited bacterium that causes several economically important plant diseases, including citrus variegated chlorosis (CVC). X. fastidiosa is the first plant pathogen to have its genome completely sequenced. In addition, it is probably the least previously studied of any organism for which the complete genome sequence is available. Several pathogenicity-related genes have been identified in the X. fastidiosa genome by similarity with other bacterial genes involved in pathogenesis in plants, as well as in animals. The X. fastidiosa genome encodes different classes of proteins directly or indirectly involved in cell-cell interactions, degradation of plant cell walls, iron homeostasis, anti-oxidant responses, synthesis of toxins, and regulation of pathogenicity. Neither genes encoding members of the type III protein secretion system nor avirulence-like genes have been identified in X. fastidiosa.     

A generalised approach to the study and understanding of adaptive evolution

Evolutionary theory has made large impacts on our understanding and management of the world, in part because it has been able to incorporate new data and new insights successfully. Nonetheless, there is currently a tension between certain biological phenomena and mainstream evolutionary theory. For example, how does the inheritance of molecular epigenetic changes fit into mainstream evolutionary theory? Is niche construction an evolutionary process? Is local adaptation via habitat choice also adaptive evolution? These examples suggest there is scope (and perhaps even a need) to broaden our views on evolution. We identify three aspects whose incorporation into a single framework would enable a more generalised approach to the understanding and study of adaptive evolution: (i) a broadened view of extended phenotypes; (ii) that traits can respond to each other; and (iii) that inheritance can be non-genetic. We use causal modelling to integrate these three aspects with established views on the variables and mechanisms that drive and allow for adaptive evolution. Our causal model identifies natural selection and non-genetic inheritance of adaptive parental responses as two complementary yet distinct and independent drivers of adaptive evolution. Both drivers are compatible with the Price equation; specifically, non-genetic inheritance of parental responses is captured by an often-neglected component of the Price equation. Our causal model is general and simplified, but can be adjusted flexibly in terms of variables and causal connections, depending on the research question and/or biological system. By revisiting the three examples given above, we show how to use it as a heuristic tool to clarify conceptual issues and to help design empirical research. In contrast to a gene-centric view defining evolution only in terms of genetic change, our generalised approach allows us to see evolution as a change in the whole causal structure, consisting not just of genetic but also of phenotypic and environmental variables.     

Replica-exchange molecular dynamics simulation for understanding the initial process of amyloid peptide aggregation

We applied replica-exchange molecular dynamics simulation to five fragments of amyloid-β peptide in order to study the mechanism of amyloid fibril formation. In this study, we calculated the free energy by focusing on how to form the β-structures to obtain the dominant structures. We classify the obtained β-structures and elucidate the order of β-structure assembly.     

A new approach to understanding the initial step in visual transduction.

Data from picosecond spectroscopic studies of the formation kinetics of bathorhodopsin upon photolysis of rhodopsin and isorhodopsin was analyzed in terms of the Englman-Jortner theory of radiationless transitions. It was found that low frequency vibrations of the protein and/or chromophore are important in coupling bathorhodopsin to its precursor. The results were consistent with a mechanism for bathorhodopsin formation involving only a simple chromophore isomerization. A similar analysis of the formation kinetics of the K state of bacteriorhodopsin showed that different low frequency vibrations than those calculated for rhodopsin couple it to its precursor. The frequency of these vibrations increases upon deuteration for rhodopsin, while it decreases upon deuteration for bacteriorhodopsin. This points out the importance the specific protein matrix has on the primary photolysis reaction.     

A proteomic approach to understanding the pathogenesis of idiopathic macular hole formation

Idiopathic macular holes (IMH) are full-thickness defects of retinal tissue that cause severe vision loss due to disruption of the anatomic fovea. Abnormal vitreous traction is involved in the formation of macular holes. Both glial cells and hyalocytes contribute to epiretinal membrane formation in IMH. In order to gain further insight into the pathophysiology of IMH, we conducted a discovery phase investigation of the vitreous proteome in four patients with macular holes and six controls using one-dimensional gel fractionation and liquid chromatography–tandem mass spectrometry analyses on an Orbitrap Elite mass spectrometer. Of a total of 5912 vitreous proteins, 32 proteins had increased and 39 proteins had decreased expression in IMH compared with controls, using a false discovery rate approach with p value < 0.001 and q value < 0.05. IMH was associated with increased expression of proteins in the complement pathway, α-2-macroglobulin, a major inducer of Müller glial cell migration, fibrinogen, and extracellular matrix proteins, and decreased expression of proteins involved in protein folding and actin filament binding. A proteomic approach revealed proteins and biological pathways that may be involved in the pathogenesis of IMH and could be targeted for future studies.     

Family mealtimes: A contextual approach to understanding childhood obesity

There has been a growing interest in the role that shared family mealtimes may play in promoting the health and well-being of children. Families that regularly eat their main meal together four or more times a week are more likely to have children who do better in school, are of average weight, less likely to use drugs and alcohol at an early age, and consume more fruits and vegetables. The mere fact that families eat together does not address the process by which shared family mealtimes may protect children from unhealthy weight gain. Just as there is no simple explanation for the rising rates of obesity, the link between shared family mealtimes and childhood obesity is a complex one including socioeconomic and cultural context. In this paper, we provide an overview of how shared family mealtimes are embedded in a socio-cultural context that may either support or derail healthy eating patterns for children and youth. Evidence from an observational study of 200 family mealtimes demonstrates the complex interplay between socio-economic factors, family mealtime behaviors, and child obesity status. Families who had a child of healthy weight spent more time engaged with each other during the meal, expressed more positive communication, and considered mealtimes more important and meaningful than families who had a child who was overweight or obese. Using a cumulative risk model, it was found that the combination of family level and neighborhood risk factors predicted child overweight status. Recommendations are made for future research directions and policies directed toward families living in diverse economic circumstances.     

A post-genomic approach to understanding sphingolipid metabolism in Arabidopsis thaliana

AIMS: To highlight the importance of sphingolipids and their metabolites in plant biology. SCOPE: The completion of the arabidopsis genome provides a platform for the identification and functional characterization of genes involved in sphingolipid biosynthesis. Using the yeast Saccharomyces cerevisiae as an experimental model, this review annotates arabidopsis open reading frames likely to be involved in sphingolipid metabolism. A number of these open reading frames have already been subject to functional characterization, though the majority still awaits investigation. Plant-specific aspects of sphingolipid biology (such as enhanced long chain base heterogeneity) are considered in the context of the emerging roles for these lipids in plant form and function. CONCLUSIONS: Arabidopsis provides an excellent genetic and post-genomic model for the characterization of the roles of sphingolipids in higher plants.     

An integrative approach to understanding mechanosensation

The ability for a living organism to sense and respond to its external environment is crucial to its survival. Understanding mechanosensation, the mechanism by which organisms react in response to mechanical stimuli, presents many interesting and challenging problems for both experimental and computational biologists. A major difficulty in studying mechanosensors is their inherent multiscale nature. The systems involved in mechanosesnsing can span eight orders of magnitude in length scale and up to 10 orders of magnitude in time scale. Trying to ascertain information across these length and time scales simultaneously is challenging. This problem has led to the need to approach these types of problems using an integrative approach, combining both computational and experimental biology. This review classifies the major types of mechanosensors and explains methods that have been employed in understanding their behavior, both using modeling and experimental techniques. Multiscale modeling methods combined with experimental techniques in an integrative approach are suggested as ways of undertaking the study of such systems.     

A new approach to understanding the molecular mechanisms through which estrogens affect cognition

Traditional approaches to the study of hormones and cognition have been primarily observational or correlational in nature. Because this work does not permit causal relationships to be identified, very little is known about the specific molecules and cellular events through which hormones affect cognitive function. In this review, we propose a new approach to study hormones and memory, where the systematic blocking of cellular events can reveal which such events are necessary for hormones to influence memory consolidation. The discussion will focus on the modulation of the hippocampus and hippocampal memory by estrogens, given the extensive literature on this subject, and will illustrate how the application of this approach is beginning to reveal important new information about the molecular mechanisms through which estrogens modulate memory consolidation. The clinical relevance of this work will also be discussed.     

A theoretical approach to understanding of the vestibular perception organization in microgravity condition

This paper should be viewed as a part of our attempts to arrive at a quantitative understanding of some contradictory experimental phenomena in the vestibular perception. The most popular remains the Steinhausen's model of perception, in which the endolymph circulation, caused by the angular acceleration, is "measured" by the displacement of cupulae diaphragm. Though displacements of the cupulae top were experimentally observed, the thorough mathematical analysis shows that the applicated stop-stimuli were too much over the range of adequate stimulation conditions, so the cupulae was teared off from its normal position. The more natural mechanism of perception was proposed by McLaren & Hillman. It was experimentally demonstrated that the cupulae diaphragm remained margin attached during the normal stimulation conditions only with its bottom moved according to the value of the applicated angular acceleration. A question only arises, how will be the hair cells excited by low level stimulation, when elastic deformations of the cupulae are small and there is no visible shift of the cupulae bottom? The response is to find in the third mechanism formulated by Schmaltz, which connected the excitation of hair cells with the process of endolymph diffusion through the cupulae towards the subcupulae space.     

A synthesis approach to understanding repeated peptides conserved in mineralization proteins

We created artificial proteins that contained repeats of a short peptide motif, Asn-Gly-Asx. In nature this motif is repeated within shell proteins as an idiosyncratic domain, while in vitro it has been shown to suppress calcification. The motif was embedded within peptide sequences that did or did not have the ability to form secondary structures, which provided the motif with a variety of physicochemical properties. Although a short synthetic peptide containing the motif did not inhibit calcification in vitro, some of the artificial proteins carrying repeats of the motif did show robust suppression of calcification. Artificial proteins lacking the motif did not exhibit suppressive activity. Likewise, one construct containing multiple repeats of the motifs also did not exert an inhibitory effect on calcification. Apparently, carrying the Asn-Gly-Asx motif is not, by itself, sufficient for expression of its cryptic activity; instead, certain physicochemical properties of the polypeptides mediate its manifestation. We anticipate that syntheses using "motif programming", such as the one described here, will shed light on the origin of repetitive sequences as well as on the evolution of biomineralization proteins.     

A flexible approach for understanding protein stability

A distance constraint model (DCM) is presented that identifies flexible regions within protein structure consistent with specified thermodynamic condition. The DCM is based on a rigorous free energy decomposition scheme representing structure as fluctuating constraint topologies. Entropy non-additivity is problematic for naive decompositions, limiting the success of heat capacity predictions. The DCM resolves non-additivity by summing over independent entropic components determined by an efficient network-rigidity algorithm. A minimal 3-parameter DCM is demonstrated to accurately reproduce experimental heat capacity curves. Free energy landscapes and quantitative stability-flexibility relationships are obtained in terms of global flexibility. Several connections to experiment are made.     

PharmEcology: A pharmacological approach to understanding plant-herbivore interactions: an introduction to the symposium

A central goal in understanding the ecology and evolution of animals is to identify factors that constrain or expand breadth of diet. Selection of diet in many animals is often constrained by chemical deterrents (i.e., secondary metabolites) in available food items. The integration of chemistry and ecology has led to a significant understanding of the chemical complexity of prey (e.g., animals, plants, and algae) and the resultant foraging behavior of consumers. However, most of the literature on chemical defenses of marine and terrestrial prey lacks a mechanistic understanding of how consumers tolerate, or avoid, chemically-defended foods. In order to understand ecological patterns of foraging and co-evolutionary relationships between prey and consumers, we must advance our understanding of the physiological mechanisms responsible for chemical interactions. Such mechanistic studies require the integration of the discipline of pharmacology with ecology, which we call "PharmEcology." Pharmacology provides the tools and insight to investigate the fate (what the body does to a chemical) and action (what a chemical does to the body) of chemicals in living organisms, whereas ecology provides the insight into the interactions between organisms (e.g., herbivores) and their environment (e.g., plants). Although, the general concepts of pharmacology were introduced to ecologists studying plant-herbivore interactions over 30 years ago, the empirical use of pharmacology to understand mechanisms of chemical interactions has remained limited. Moreover, many of the recent biochemical, molecular and technical advances in pharmacology have yet to be utilized by ecologists. The PharmEcology symposium held at a meeting of the Society for Integrative and Comparative Biology in January of 2009 was developed to define novel research directions at the interface of pharmacology and ecology.