Resolvins: natural agonists for resolution of pulmonary inflammation

Inappropriate or excessive pulmonary inflammation can contribute to chronic lung diseases. In health, the resolution of inflammation is an active process that terminates inflammatory responses. The recent identification of endogenous lipid-derived mediators of resolution has provided a window to explore the pathobiology of inflammatory disease and structural templates for the design of novel pro-resolving therapeutics. Resolvins (resolution-phase interaction products) are a family of pro-resolving mediators that are enzymatically generated from essential omega-3 polyunsaturated fatty acids. Two molecular series of resolvins have been characterised, namely E- and D-series resolvins which possess distinct structural, biochemical and pharmacological properties. Acting as agonists at specific receptors (CMKLR1, BLT1, ALX/FPR2 and GPR32), resolvins can signal for potent counter-regulatory effects on leukocyte functions, including preventing uncontrolled neutrophil swarming, decreasing the generation of cytokines, chemokines and reactive oxygen species and promoting clearance of apoptotic neutrophils from inflamed tissues. Hence, resolvins provide mechanisms for cytoprotection of host tissues to the potentially detrimental effects of unresolved inflammation. This review highlights recent experimental findings in resolvin research, and the impact of these stereospecific molecules on the resolution of pulmonary inflammation and tissue catabasis.     

Molecular circuits of resolution: formation and actions of resolvins and protectins

The cellular events underlying the resolution of acute inflammation are not known in molecular terms. To identify anti-inflammatory and proresolving circuits, we investigated the temporal and differential changes in self-resolving murine exudates using mass spectrometry-based proteomics and lipidomics. Key resolution components were defined as resolution indices including Psi(max), the maximal neutrophil numbers that are present during the inflammatory response; T(max), the time when Psi(max) occurs; and the resolution interval (R(i)) from T(max) to T(50) when neutrophil numbers reach half Psi(max). The onset of resolution was at approximately 12 h with proteomic analysis showing both haptoglobin and S100A9 levels were maximal and other exudate proteins were dynamically regulated. Eicosanoids and polyunsaturated fatty acids first appeared within 4 h. Interestingly, the docosahexaenoic acid-derived anti-inflammatory lipid mediator 10,17S-docosatriene was generated during the R(i). Administration of aspirin-triggered lipoxin A(4) analog, resolvin E1, or 10,17S-docosatriene each either activated and/or accelerated resolution. For example, aspirin-triggered lipoxin A(4) analog reduced Psi(max), resolvin E1 decreased both Psi(max) and T(max), whereas 10,17S-docosatriene reduced Psi(max), T(max), and shortened R(i). Also, aspirin-triggered lipoxin A(4) analog markedly inhibited proinflammatory cytokines and chemokines at 4 h (20-50% inhibition), whereas resolvin E1 and 10,17S-docosatriene's inhibitory actions were maximal at 12 h (30-80% inhibition). Moreover, aspirin-triggered lipoxin A(4) analog evoked release of the antiphlogistic cytokine TGF-beta. These results characterize the first molecular resolution circuits and their major components activated by specific novel lipid mediators (i.e., resolvin E1 and 10,17S-docosatriene) to promote resolution.     

Natural killer lymphocytes: biology,development, and function

Natural killer (NK) lymphocytes represent the first line of defense against virally infected cells and tumor cells. The role of NK cells in immune responses has been markedly explored, mainly due to the identification of NK cell receptors and their ligands, but also through the analysis of mechanisms underlying the effects of various cytokines on NK cell development and function. A population of lymphocytes that shares function and receptors with NK cells is represented by natural killer T (NKT) cells. NKT lymphocytes are regulators of both innate and adaptive immune responses, but have also been reported to function as effector antitumor cells. The marked progress in our understanding of the biology, development, and function of NK/NKT cells has provided the basis for their potential application in tumor clinical trials.This work was presented at the first Cancer Immunology and Immunotherapy Summer School, 8–13 September 2003, Ionian Village, Bartholomeio, Peloponnese, Greece.     

Natural products from synthetic biology

DNA sequencing has uncovered microbial secondary metabolic potential that never surfaced in fermentation based screens. Deep and cheap sequencing of a genus such as Streptomyces can rapidly expose hundreds of metabolic genes and operons. Meanwhile, synthetic biologists, in their quest to engineer advanced biofuels, are mastering metabolic engineering. Natural products, a reliable source of new therapeutic leads for many years, have fallen into disfavor with drug discoverers partly because these molecules are rarely available as pure compounds and sourcing is often problematic. The convergence of next generation sequencing and synthetic biology, along with less spectacular progress in analytic technologies such as mass spectroscopy, opens the door to the creation of large, reliable libraries of pure natural products for drug discovery.     

PALM reading: Seeing the future of cell biology at higher resolution

The inherent resolution limit of the light microscope has been a limiting factor in investigations of many fields of cell biology. A recent paper in Science by Betzig and coworkers describes a new method that can push the limit significantly lower.     

Natural strategies for the spatial optimization of metabolism in synthetic biology

Metabolism is a highly interconnected web of chemical reactions that power life. Though the stoichiometry of metabolism is well understood, the multidimensional aspects of metabolic regulation in time and space remain difficult to define, model and engineer. Complex metabolic conversions can be performed by multiple species working cooperatively and exchanging metabolites via structured networks of organisms and resources. Within cells, metabolism is spatially regulated via sequestration in subcellular compartments and through the assembly of multienzyme complexes. Metabolic engineering and synthetic biology have had success in engineering metabolism in the first and second dimensions, designing linear metabolic pathways and channeling metabolic flux. More recently, engineering of the third dimension has improved output of engineered pathways through isolation and organization of multicell and multienzyme complexes. This review highlights natural and synthetic examples of three-dimensional metabolism both inter- and intracellularly, offering tools and perspectives for biological design.     

Cell and molecular biology of bryophytes: ultimate limits to the resolution of phylogenetic problems

Ultrastructure, biochemistry and 5S rRNA sequences link tracheophytes, bryophytes and charalean green algae, but the precise interrelationships between these groups remain unclear. Further major clarification now awaits primary sequence data. These are also needed to determine directionality in possible evolutionary trends within the bryophytes, but are unlikely to overturn current schemes of classification or phylogeny. Comparative ultrastructural studies of spermatogenesis, sporogenesis, the cytoskeleton and plastids reinforce biochemical and morphogenetic evidence for the wide phyletic discontinuities between mosses, hepatics and hornworts, and also rule out direct lines of descent between them. Direct ancestral lineages from charalean algae to bryophytes and to tracheophytes are also unlikely. EM studies of gametophyte/sporophyte junctions, plus immunological investigations of bryophyte cytoskeletons, are likely to accentuate the differences between mosses, hepatirs and hornworts. Other priorities for systematics include elucidation of oil body ultrastructure, analysis of the changes in nuclear proteins during spermatogenesis and a detailed comparison of bryophyte and charalean plastids. The combined evidence from ultrastrueture, biochemistry, morphology and morphogenesis warrants general acceptance of the polyphyletic origin of the bryophytes. Ultrastructural attributes should be more widely used in bryophyte systematics.     

Natural biology of polyomavirus middle T antigen.

"It has been commented by someone that 'polyoma' is an adjective composed of a prefix and suffix, with no root between--a meatless linguistic sandwich" (C. J. Dawe). The very name "polyomavirus" is a vague mantel: a name given before our understanding of these viral agents was clear but implying a clear tumor life-style, as noted by the late C. J. Dawe. However, polyomavirus are not by nature tumor-inducing agents. Since it is the purpose of this review to consider the natural function of middle T antigen (MT), encoded by one of the seemingly crucial transforming genes of polyomavirus, we will reconsider and redefine the virus and its MT gene in the context of its natural biology and function. This review was motivated by our recent in vivo analysis of MT function. Using intranasal inoculation of adult SCID mice, we have shown that polyomavirus can replicate with an MT lacking all functions associated with transformation to similar levels to wild-type virus. These observations, along with an almost indistinguishable replication of all MT mutants with respect to wild-type viruses in adult competent mice, illustrate that MT can have a play subtle role in acute replication and persistence. The most notable effect of MT mutants was in infections of newborns, indicating that polyomavirus may be highly adapted to replication in newborn lungs. It is from this context that our current understanding of this well-studied virus and gene is presented.     

High resolution 3D perspective of Plasmodium biology: advancing into a new era

Apicomplexan parasites exhibit a great variety of complex life cycles that require adaptation to different niches of parasitism. They invade different host cells and highjack their biological functions. Plasmodium falciparum, responsible for the deadliest form of human malaria, causes disease while completely remodeling the erythrocytes of its human host through mechanisms that are only partly understood. Recent developments in ultrastructural technologies offer new opportunities to investigate fundamental aspects in the biology of the parasite in a three-dimensional (3D) perspective. Here we bring together recent work on host cell invasion, hemoglobin uptake, protein export and nuclear dynamics. A comprehensive 3D view of the ultrastructural biology of the parasite may shed new light on cellular mechanisms that underlie the pathogenicity of P. falciparum.     

Synthetic biology: a foundation for multi-scale molecular biology

The field of synthetic biology has made rapid progress in a number of areas including method development, novel applications and community building. In seeking to make biology "engineerable," synthetic biology is increasing the accessibility of biological research to researchers of all experience levels and backgrounds. One of the underlying strengths of synthetic biology is that it may establish the framework for a rigorous bottom-up approach to studying biology starting at the DNA level. Building upon the existing framework established largely by the Registry of Standard Biological Parts, careful consideration of future goals may lead to integrated multi- scale approaches to biology. Here we describe some of the current challenges that need to be addressed or considered in detail to continue the development of synthetic biology. Specifically, discussion on the areas of elucidating biological principles, computational methods and experimental construction methodologies are presented.     

Non-steroidal dissociated glucocorticoid agonists: indoles as A-ring mimetics and function-regulating pharmacophores

We report a SAR of non-steroidal glucocorticoid mimetics that utilize indoles as A-ring mimetics. Detailed SAR is discussed with a focus on improving PR and MR selectivity, GR agonism, and in vitro dissociation profile. SAR analysis led to compound (R)-33 which showed high PR and MR selectivity, potent agonist activity, and reduced transactivation activity in the MMTV and aromatase assays. The compound is equipotent to prednisolone in the LPS-TNF model of inflammation. In mouse CIA, at 30 mg/kg compound (R)-33 inhibited disease progression with an efficacy similar to the 3 mg/kg dose of prednisolone.     

New tools and new biology: Recent miniaturized systems for molecular and cellular biology

Recent advances in applied physics and chemistry have led to the development of novel microfluidic systems. Microfluidic systems allow minute amounts of reagents to be processed using μm-scale channels and offer several advantages over conventional analytical devices for use in biological sciences: faster, more accurate and more reproducible analytical performance, reduced cell and reagent consumption, portability, and integration of functional components in a single chip. In this review, we introduce how microfluidics has been applied to biological sciences. We first present an overview of the fabrication of microfluidic systems and describe the distinct technologies available for biological research. We then present examples of microsystems used in biological sciences, focusing on applications in molecular and cellular biology.     

Resolvins Decrease Oxidative Stress Mediated Macrophage and Epithelial Cell Interaction through Decreased Cytokine Secretion

Background

Inflammation is a key hallmark of ALI and is mediated through ungoverned cytokine signaling. One such cytokine, interleukin-1beta (IL-1β) has been demonstrated to be the most bioactive cytokine in ALI patients. Macrophages are the key players responsible for IL-1β secretion into the alveolar space. Following the binding of IL-1β to its receptor, “activated” alveolar epithelial cells show enhanced barrier dysfunction, adhesion molecule expression, cytokine secretion, and leukocyte attachment. More importantly, it is an important communication molecule between the macrophage and alveolar epithelium. While the molecular determinants of this inflammatory event have been well documented, endogenous resolution processes that decrease IL-1β secretion and resolve alveolar epithelial cell activation and tissue inflammation have not been well characterized. Lipid mediator Aspirin-Triggered Resolvin D1 (AT-RvD1) has demonstrated potent pro-resolutionary effects in vivo models of lung injury; however, the contribution of the alveoli to the protective benefits of this molecule has not been well documented. In this study, we demonstrate that AT-RvD1 treatment lead to a significant decrease in oxidant induced macrophage IL-1β secretion and production, IL-1β-mediated cytokine secretion, adhesion molecule expression, leukocyte adhesion and inflammatory signaling.

Methods

THP-1 macrophages were treated with hydrogen peroxide and extracellular ATP in the presence or absence of AT-RvD1 (1000–0.1 nM). A549 alveolar-like epithelial cells were treated with IL-1β (10 ng/mL) in the presence or absence of AT-RvD1 (0.1 μM). Following treatment, cell lysate and cell culture supernatants were collected for Western blot, qPCR and ELISA analysis of pro-inflammatory molecules. Functional consequences of IL-1β induced alveolar epithelial cell and macrophage activation were also measured following treatment with IL-1β ± AT-RvD1.

Results

Results demonstrate that macrophages exposed to H₂O₂ and ATP in the presence of resolvins show decreased IL-1β production and activity. A549 cells treated with IL-1β in the presence of AT-RvD1 show a reduced level of proinflammatory cytokines IL-6 and IL-8. Further, IL-1β-mediated adhesion molecule expression was also reduced with AT-RvD1 treatment, which was correlated with decreased leukocyte adhesion. AT-RvD1 treatment demonstrated reduced MAP-Kinase signaling. Taken together, our results demonstrate AT-RvD1 treatment reduced IL-1β-mediated alveolar epithelial cell activation. This is a key step in unraveling the protective effects of resolvins, especially AT-RvD1, during injury.     

Structure of the type III pantothenate kinase from Bacillus anthracis at 2.0 A resolution: implications for coenzyme A-dependent redox biology

Coenzyme A (CoASH) is the major low-molecular weight thiol in Staphylococcus aureus and a number of other bacteria; the crystal structure of the S. aureus coenzyme A-disulfide reductase (CoADR), which maintains the reduced intracellular state of CoASH, has recently been reported [Mallett, T.C., Wallen, J.R., Karplus, P.A., Sakai, H., Tsukihara, T., and Claiborne, A. (2006) Biochemistry 45, 11278-89]. In this report we demonstrate that CoASH is the major thiol in Bacillus anthracis; a bioinformatics analysis indicates that three of the four proteins responsible for the conversion of pantothenate (Pan) to CoASH in Escherichia coli are conserved in B. anthracis. In contrast, a novel type III pantothenate kinase (PanK) catalyzes the first committed step in the biosynthetic pathway in B. anthracis; unlike the E. coli type I PanK, this enzyme is not subject to feedback inhibition by CoASH. The crystal structure of B. anthracis PanK (BaPanK), solved using multiwavelength anomalous dispersion data and refined at a resolution of 2.0 A, demonstrates that BaPanK is a new member of the Acetate and Sugar Kinase/Hsc70/Actin (ASKHA) superfamily. The Pan and ATP substrates have been modeled into the active-site cleft; in addition to providing a clear rationale for the absence of CoASH inhibition, analysis of the Pan-binding pocket has led to the development of two new structure-based motifs (the PAN and INTERFACE motifs). Our analyses also suggest that the type III PanK in the spore-forming B. anthracis plays an essential role in the novel thiol/disulfide redox biology of this category A biodefense pathogen.     

Natural genetic engineering of plant cells: the molecular biology of crown gall and hairy root disease

During the past decade, the molecular mechanisms of crown gall and hairy root development have been elucidated in considerable detail. It now appears that the genetic colonization of plant cells by Agrobacterium evolved by continual adaptation of groups of genes that existed long before the evolution of this plant-microbe association. This is most evident for the signal transduction system leading to vir gene induction, and for the early steps of T-DNA transfer to plant cells which have probably evolved from the bacterial conjugation and protein export machinery. However, the later steps, i.e. nuclear targeting of the T-DNA-protein complex, and integration into the host genome by illegitimate recombination are reminiscent of viral infection, where the T-complex resembles a viral particle. The present article reviews the current knowledge of the molecular basis of crown gall and hairy root tumorigenesis, with some emphasis on the mechanisms of signal exchange between plants and bacteria, as well as of T-DNA excision, transfer, integration and expression.The authors are with Plant Molecular Biology, Department of Biology, Biozentrum, Marie-Curie-Str. 9, University of Frankfurt am Main, D-60439 Frankfurt, Germany