Stable carbon isotopes of lipid biomarkers: analysis of metabolites and metabolic fates of environmental microorganisms

Lipid biomarkers are specific compounds that are characteristic of certain groups or species of microorganisms. The use of natural or labeled carbon isotopes of lipid biomarkers has enabled a better understanding of carbon flow pathways at the molecular level. Recent advances include, but are not limited to, the elucidation of mechanisms of anaerobic methane oxidation mediated by syntrophic sulfate-reducing bacteria and Archaea, linking microbial populations with specific microbial processes or bacterial transport mechanisms in natural or contaminated environments, and elucidation of the biosynthetic pathways of cellular material.     

Genetic ecotoxicology: The genotypic diversity approach

Organismal responses at the genetic level to exposure to environmental genotoxicants have been well documented. An elucidation of the molecular mechanisms involved with these responses, as well as an assessment of the changes that may occur to the genetic material, will provide an understanding of the potential for deleterious consequences at higher levels of biological organization. Moreover, modern procedures of molecular biology offer the hope that alterations and changes to genetic material can be readily detected.     

Defining species: a multi-level approach

Different concepts define species at the pattern-level grouping of organisms into discrete clusters, the level of the processes operating within and between populations leading to the formation and maintenance of these clusters, or the level of the inner-organismic genetic and molecular mechanisms that contribute to species cohesion or promote speciation. I argue that, unlike single-level approaches, a multi-level framework takes into account the complex sequences of cause-effect reinforcements leading to the formation and maintenance of various patterns, and allows for revisions and refinements of pattern-based characterizations in light of the gradual elucidation of the causes and mechanisms contributing to pattern formation and maintenance.     

Epistasis and intramolecular networks in protein evolution

Proteins are molecular machines composed of complex, highly connected amino acid networks. Their functional optimization requires the reorganization of these intramolecular networks by evolution. In this review, we discuss the mechanisms by which epistasis, that is, the dependence of the effect of a mutation on the genetic background, rewires intramolecular interactions to alter protein function. Deciphering the biophysical basis of epistasis is crucial to our understanding of evolutionary dynamics and the elucidation of sequence-structure-function relationships. We featured recent studies that provide insights into the molecular mechanisms giving rise to epistasis, particularly at the structural level. These studies illustrate the convoluted and fascinating nature of the intramolecular networks co-opted by epistasis during the evolution of protein function.     

A DELLAcate balance: the role of gibberellin in plant morphogenesis

The importance of gibberellin (GA) in vegetative and reproductive development has been known for some time. Recent studies have uncovered new roles of GA in leaf differentiation, photomorphogenesis and pollen-tube growth. Significant contributions to our understanding of GA-regulated morphogenesis include the identification of upstream regulators of GA biosynthesis, the elucidation of the function of GA signaling components, and the isolation of downstream targets. In addition, the mechanisms of interactions between GA and other hormone pathways are beginning to be revealed at the molecular level.     

Somatic cell genetics resource for research in aging. The National Institutes of Health plan for an expanded program in cellular aging.

A mutant cell bank in support of research in aging has been established at the Institute for Medical Research, Camden, N.J. The bank is under contract support of the Adult Development and Aging Program of the National Institute of child Health and Human Development. We anticipate that the bank, with associated services such as an annual workshop, will facilitate the growth of the NIH grant-supported cellular aging research program and thus contribute to the elucidation of mechanisms in human aging at the cellular and molecular level.     

The molecular basis of cytokinin action

Current understanding of cytokinin (CK) physiology at the cellular level results largely from the manipulation of endogenous CK levels by either application of exogenous CKs or the expression of CK biosynthetic transgenes, as well as the characterisation of single gene mutants. Cytokinins modulate changes in plant gene expression, which are in turn assumed to effect physiological and morphological changes with which CK action is associated. Presently, a major focus of investigation is elucidation of the biochemical events leading from the perception of CK to the manifestation of a response. Analysis of the expression patterns of CK-regulated genes and identification of their products provides one means of investigating CK action at the molecular level. Biochemical approaches have led to the identification of several soluble CK-binding proteins, although their functional roles in CK signalling largely remain uncertain. Conclusive identification of a bona fide CK receptor has yet to be achieved, although several potential candidates have been suggested. Pharmacological and molecular genetic strategies have implicated the involvement of signalling mechanisms likely to be involved in CK action. The apparent involvement of fluctuations in the concentration of intracellular Ca²⁺, changes in protein phosphorylation as well as DNA and/or protein methylation provide information concerning the types of proteins likely to be involved in the process. Dissection of CK signal transduction chains and elucidation of their interaction with other pathways that regulate plant growth and development is likely to be essential in understanding the mode of action of this poorly understood class of plant growth regulator. However, integration of this knowledge with an improved understanding of the mechanisms whereby overall hormone homeostasis is regulated at the metabolic level will be necessary for comprehensive appreciation of the influence of CKs on plant morphology and physiology.     

A role for convergent evolution in the secretory life of cells

The role of convergent evolution in biological adaptation is increasingly appreciated. Many clear examples have been described at the level of individual proteins and for organismal morphology, and convergent mechanisms have even been invoked to account for similar community structures that are shared between ecosystems. At the cellular level, an important area that has received scant attention is the potential influence of convergent evolution on complex subcellular features, such as organelles. Here, we show that existing data strongly argue that convergent evolution underlies the similar properties of specialized secretory vesicles, called dense core granules, in the animal and ciliate lineages. We discuss both the criteria for judging convergent evolution and the contribution that such evolutionary analysis can make to improve our understanding of processes in cell biology. The elucidation of these underlying evolutionary relationships is vital because cellular structures that are assumed to be analogous, owing to shared features, might in fact be governed by different molecular mechanisms.     

Apoptosis: the germs of death

From the initial recognition that programmed cell suicide existed, to the elucidation of the underlying death and survival pathways at the molecular level, the story of apoptosis has unfolded rapidly. But much still remains to be discovered.     

Lactoferrin and host defence: an overview of its immuno-modulating and anti-inflammatory properties

Lactoferrin is a member of the transferrin family of iron-binding glycoproteins that is abundantly expressed and secreted from glandular epithelial cells. In secretions, such as milk and fluids of the intestinal tract, lactoferrin is an important component of the first line of host defence. During the inflammatory process, lactoferrin, a prominent component of the secondary granules of neutrophils (PMNs), is released in infected tissues and in blood and then it is rapidly cleared by the liver. In addition to the antimicrobial properties of lactoferrin, a set of studies has focused on its ability to modulate the inflammatory process and the overall immune response. Though many in vitro and in vivo studies report clear regulation of the immune response and protective effect against infection and septic shock by lactoferrin, elucidation of all the cellular and molecular mechanisms of action is far from being achieved. At the cellular level, lactoferrin modulates the migration, maturation and function of immune cells. At the molecular level and in addition to iron binding, interactions of lactoferrin with a plethora of compounds, either soluble or membrane molecules, account for its modulatory properties. This paper reviews our current understanding of the cellular and molecular mechanisms that explain the regulatory properties of lactoferrin in host defence.     

Model Organisms Proteomics—From Holobionts to Human Nutrition

Model organisms are an important tool for the development and validation of analytical approaches for proteomics and for the study of basic mechanisms of biological processes. The Initiative on Model Organism Proteomics (iMOP) organized a session during the 11th HUPO world congress in Boston in 2012, highlighting the potential of proteomics studies in model organism for the elucidation of important mechanisms regulating the interaction of humans with its environment. Major subjects were the use of model organisms for the study of molecular events triggering the interaction of host organisms with the surrounding microbiota and the elucidation of the complex influence of nutrition on the health of human beings.     

A trace of silence: memory and microRNA at the synapse

Identifying the neural circuits that mediate particular behaviors and uncovering their plasticity is an endeavor at the heart of neuroscience. This effort is allied with the elucidation of plasticity mechanisms, because the molecular determinants of plasticity can be markers for the neurons and synapses that are modified by experience. Of particular interest is protein synthesis localized to the synapse, which might establish and maintain the stable modification of neuronal properties, including the pattern and strength of synaptic connections. Recent studies reveal that microRNAs and the RISC pathway regulate synaptic protein synthesis. Is synaptic activity of the RISC pathway a molecular signature of memory?     

Large-scale prediction of protein-protein interactions from structures

Background  

The prediction of protein-protein interactions is an important step toward the elucidation of protein functions and the understanding of the molecular mechanisms inside the cell. While experimental methods for identifying these interactions remain costly and often noisy, the increasing quantity of solved 3D protein structures suggests that in silico methods to predict interactions between two protein structures will play an increasingly important role in screening candidate interacting pairs. Approaches using the knowledge of the structure are presumably more accurate than those based on sequence only. Approaches based on docking protein structures solve a variant of this problem, but these methods remain very computationally intensive and will not scale in the near future to the detection of interactions at the level of an interactome, involving millions of candidate pairs of proteins.     

Modulation of signal transduction by vitamin E

The ability of vitamin E to modulate signal transduction and gene expression has been observed in numerous studies; however, the detailed molecular mechanisms involved are often not clear. The eight natural vitamin E analogues and synthetic derivatives affect signal transduction with different potency, possibly reflecting their different ability to interact with specific proteins. Vitamin E modulates the activity of several enzymes involved in signal transduction, such as protein kinase C, protein kinase B, protein tyrosine kinases, 5-, 12-, and 15-lipoxygenases, cyclooxygenase-2, phospholipase A2, protein phosphatase 2A, protein tyrosine phosphatase, and diacylglycerol kinase. Activation of some these enzymes after stimulation of cell surface receptors with growth factors or cytokines can be normalized by vitamin E. At the molecular level, the translocation of several of these enzymes to the plasma membrane is affected by vitamin E, suggesting that the modulation of protein-membrane interactions may be a common theme for vitamin E action. In this review the main effects of vitamin E on enzymes involved in signal transduction are summarized and the possible mechanisms leading to enzyme modulation evaluated. The elucidation of the molecular and cellular events affected by vitamin E could reveal novel strategies and molecular targets for developing similarly acting compounds.     

Study on the multiple mechanisms underlying the reaction between hydroxyl radical and phenolic compounds by qualitative structure and activity relationship

The activity–structure relationships (ASR) of phenolic compounds as hydroxyl-radical scavengers have mostly been studied and discussed with regard to their iron-chelating and hydrogen-donation properties in Fenton-type system, but extensive elucidation of multiple mechanisms underlying the hydroxyl radical scavenging reaction is out of obtaining up to now. In the present paper, a series of phenolic compounds was studied for their reactivity with hydroxyl radical by computed chemistry and deoxyribose degradation assay. The rate constant (K_S), an index dependent markedly on the reaction mechanism and intrinsic reactivity of antioxidants, was found to have good correlation with hydroxyl O–H bond strength (ΔH_f), electron-donating ability (ionization potential approximated by HOMO energy level), enthalpy of single electron transfer (E_a), and spin distribution of phenoxyl radicals (Ds^r) after H-abstraction. Moreover, the theoretical parameters were highly intercorrelated, suggesting that multiple mechanisms co-exist in the hydroxyl-radical-scavenging reaction and interact with each other. Multi-linear regression analysis indicated that, in addition to H-atom transfer, electron transfer process and stability of the resulted phenoxyl radicals also significantly influence the reactivity of quenching hydroxyl radicals. The QSAR model so established here was based on the elucidation of the complex molecular mechanisms, and may reasonably predict the antioxidant activity using simple experimental and calculated parameters.     

Characterization of mitochondrial proteome in a severe case of ETF-QO deficiency

Multiple acyl-CoA dehydrogenase deficiency (MADD) is a mitochondrial fatty acid oxidation disorder caused by mutations that affect electron transfer flavoprotein (ETF) or ETF:ubiquinone oxidoreductase (ETF-QO) or even due to unidentified disturbances of riboflavin metabolism. Besides all the available data on the molecular basis of FAO disorders, including MADD, the pathophysiological mechanisms underlying clinical phenotype development, namely at the mitochondrial level, are poorly understood. In order to contribute to the elucidation of these mechanisms, we isolated mitochondria from cultured fibroblasts, from a patient with a severe MADD presentation due to ETF-QO deficiency, characterize its mitochondrial proteome and compare it with normal controls. The used approach (2-DE-MS/MS) allowed the positive identification of 287 proteins in both patient and controls, presenting 35 of the significant differences in their relative abundance. Among the differentially expressed are proteins associated to binding/folding functions, mitochondrial antioxidant enzymes as well as proteins associated to apoptotic events. The overexpression of chaperones like Hsp60 or mitochondrial Grp75, antioxidant enzymes and apoptotic proteins reflects the mitochondrial response to a complete absence of ETF-QO. Our study provides a global perspective of the mitochondrial proteome plasticity in a severe case of MADD and highlights the main molecular pathways involved in its pathogenesis.