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Proteomics of the peroxisome.

Genomes provide us with a blue print for the potential of a cell. However, the activity of a cell is expressed in its proteome. Full understanding of the complexity of cells demands a comprehensive view of the proteome; its interactions, activity states and organization. Comprehensive proteomic approaches applied to peroxisomes have yielded new insights into the organelle and its dynamic interplay with other cellular structures. As technologies and methodologies improve, proteomics hold the promise for new discoveries of peroxisome function and a full description of this dynamic organelle.

Arabidopsis↗

Regulation of connexin biosynthesis, assembly, gap junction formation, and removal.

Gap junctions (GJs) are the only known cellular structures that allow a direct transfer of signaling molecules from cell-to-cell by forming hydrophilic channels that bridge the opposing membranes of neighboring cells. The crucial role of GJ-mediated intercellular communication (GJIC) for coordination of development, tissue function, and cell homeostasis is now well documented. In addition, recent findings have fueled the novel concepts that connexins, although redundant, have unique and specific functions, that GJIC may play a significant role in unstable, transient cell-cell contacts, and that GJ hemi-channels by themselves may function in intra-/extracellular signaling. Assembly of these channels is a complicated, highly regulated process that includes biosynthesis of the connexin subunit proteins on endoplasmic reticulum membranes, oligomerization of compatible subunits into hexameric hemi-channels (connexons), delivery of the connexons to the plasma membrane, head-on docking of compatible connexons in the extracellular space at distinct locations, arrangement of channels into dynamic, spatially and temporally organized GJ channel aggregates (so-called plaques), and coordinated removal of channels into the cytoplasm followed by their degradation. Here we review the current knowledge of the processes that lead to GJ biosynthesis and degradation, draw comparisons to other membrane proteins, highlight novel findings, point out contradictory observations, and provide some provocative suggestive solutions.

Animals↗

The human pituitary nitroproteome: detection of nitrotyrosyl-proteins with two-dimensional Western blotting, and amino acid sequence determination with mass spectrometry.

Nitric oxide is an important mediator that participates in reduction-oxidation (redox) mechanisms and in cellular signal transduction pathways. Two types of post-translational modifications are induced by nitric oxide: S-nitrosylation of cysteine residues and nitration of tyrosine residues. Two-dimensional gel electrophoresis-based Western blotting was used to detect, and liquid chromatography (LC)-tandem mass spectrometry (MS/MS) to determine the amino acid sequence of, several different nitrated proteins in the human pituitary. Proteins from several 2D gel spots, which corresponded to the strongly positive anti-nitrotyrosine Western blot spots, were subjected to in-gel trypsin-digestion and LC-MS/MS analysis. MS/MS, SEQUEST analysis, and de novo sequencing were used to determine the nitration site of each nitrated peptide. A total of four different nitrated peptides were characterized and were matched to four different proteins: synaptosomal-associated protein, actin, immunoglobulin alpha Fc receptor, and cGMP-dependent protein kinase 2. Those nitrotyrosyl-proteins participate in neurotransmission, cellular immunity, and cellular structure and mobility.

Amino Acid Sequence↗

Inkjet printing for high-throughput cell patterning.

The adaptation of inkjet printing technology to the complex fields of tissue engineering and biomaterial development presents the potential to increase progress in these emerging technologies through the implementation of this high-throughput capability via automated processes to enable precise control and repeatability. In this paper, a method of applying high-throughput inkjet printing to control cellular attachment and proliferation by precise, automated deposition of collagen is presented. The results indicate that commercial inkjet printing technology can be used to create viable cellular patterns with a resolution of 350 microm through the deposition of biologically active proteins. This method demonstrates a combination of off-the-shelf inkjet printing and biomaterials and has potential to be adapted to tissue engineering and colony patterning applications. Adapting this method into the three-dimensional construction of cellular structures for eventual high-throughput tissue engineering using a bottom-up approach is possible.

Animals↗

The self-setting properties and in vitro bioactivity of tricalcium silicate.

In this study, tricalcium silicate (Ca(3)SiO(5)), as a new promising injectable bioactive material, was employed to investigate its physical and chemical properties for an injectable bioactive cement filler. The workable Ca(3)SiO(5) pastes with a liquid to powder (L/P) ratio of 0.8--.2 mlg(-1)could be injected for 15--60 min (nozzle diameter 2.0mm). The setting process yielded cellular structures with compressive strength of 6.4--20.2 MPa after 2--28 days. The in vitro bioactivity of Ca(3)SiO(5) paste was investigated by soaking in simulated body fluid (SBF) for various periods. The result showed that the Ca(3)SiO(5) paste could induce hydroxyapatite (HA) formation and dissolve slowly in SBF. The result of indirect cytotoxicity evaluation indicated that Ca(3)SiO(5) paste had a stimulatory effect on cell growth in a certain concentration range. The exothermic process showed that Ca(3)SiO(5) had lower heat evolution rate during the hydration as compared to calcium phosphate cement (CPC). Our results indicated that Ca(3)SiO(5) paste was bioactive and dissolvable, and it is a progressive candidate for further investigation as injectable tissue repairing substitute.

Animals↗

A mathematical model to determine molecular kinetic rate constants under non-steady state conditions using fluorescence recovery after photobleaching (FRAP).

Fluorescence recovery after photobleaching (FRAP) analyses of binding and unbinding of molecules that interact with insoluble scaffolds, such as the cytoskeleton and nuclear matrix, in living cells commonly assume that this process is at equilibrium over the time scale of fluorescence recovery. This assumption breaks down for relatively fast intracellular processes like focal adhesion assembly at the leading edge of a migrating cell, or changes of transcriptional activation in the nucleus, that can occur in a matter of a few minutes. In this paper, we formulate a mathematical model that permits FRAP to be used to determine kinetic rate constants of molecules that interact with insoluble cellular structures under non-steady state conditions. We show that unlike steady state FRAP, fluorescence recovery time scales under these unsteady conditions are determined not only by unbinding rates, but also by the overall assembly and disassembly dynamics of the structural scaffold which supports these binding interactions. Experimental data from FRAP analysis and quantification of scaffold assembly dynamics may be combined and used with our mathematical model to estimate kinetic rate constants, as well as the apparent rate constant of scaffold assembly and disassembly.

Fluorescence Recovery After Photobleaching↗

Microbial-gut interactions in health and disease. Epithelial cell responses.

Pathogenic bacteria use many strategies to secure their survival within the host. Enteropathogens exploit intestinal epithelial cells in many ways, including the manipulation of normal cellular functioning, or of cellular structural components, or by the induction of signalling pathways, such as the production of pro-inflammatory cytokines. However, the enterocyte warns the host of impending danger and, in turn, elicits a protective response. Pathogens are detected by epithelial cells owing to their vast array of surface antigens and secreted products. Epithelial cells have developed both extracellular and intracellular sensing proteins that function as a first line of defence against pathogens; this is followed by acquired immunity, namely IgA, which is used as reinforcement. Thus, in a game of constant attack and defence, the pathogen and the enterocyte aim to outsmart each other in an effort to survive.

Enterobacteriaceae↗

Acute social defeat reduces neurotrophin expression in brain cortical and subcortical areas in mice.

Acute social defeat in mice activates the hypothalamic-pituitary-adrenal axis (HPA) and induces long-term behavioral changes, including exaggerated fear responses and inhibition of territorial behavior. Stress-induced hormonal and neurotransmitter release may contribute to disruption of expression of genes important for cell survival, neuronal plasticity, and neuronal remodeling. Brain-derived neurotrophic factor (BDNF) is a neurotrophic factor associated with structural cellular changes that occur during nervous system development and contributes to neural plasticity in the adult brain. In rats, acute (1-2 h) restraint stress transiently reduces BDNF mRNA expression in the hippocampus, a region important in the memory and in HPA regulation; restraint stress also decreases BDNF expression in the basolateral amygdala (BLA), a region important for fear consolidation and emotional memory. We hypothesized that a brief (10 min) exposure to intense social stress, a more naturalistic stressor than restraint stress, would also reduce BDNF mRNA in the hippocampus and BLA of mice. In the present study, we examined the time course of expression of BDNF mRNA expression in the hippocampus and amygdala, as well as other subcortical and cortical brain regions, following acute social stress. In situ hybridization analysis for BDNF mRNA expression showed that there was a significant decrease in BDNF mRNA expression in all regions studied in mice 24 h after social defeat when compared to control (naive) mice (P<0.05). These findings support our hypothesis that BDNF mRNA levels are reduced by social stress, and may have implications for brain plasticity and behavioral changes following social stress.

Animals↗

Fusion pore regulation of transmitter release.

During the last decade a wealth of new information about the properties of the exocytotic fusion pore is changing our current view of exocytosis. The exocytotic fusion pore, a necessary stage before the full merging of the vesicle membrane with the plasma membrane, is becoming a key cellular structure that might critically control the amount of neurotransmitter released into the synaptic cleft and that can be subjected to control by second messengers and phosphorylated proteins. Fusion pores form, expand to fully merge membranes, or can close leaving an intact and identical synaptic vesicle in place for a new round of exocytosis. Transient formation of fusion pores is the mechanistic representation of the "kiss-and-run" hypothesis of transmitter release and offers new alternatives for synaptic vesicle recycling besides to the classical mechanism mediated by clathrin coat endocytosis. For vesicle recycling transient fusion pores ensures a fast mechanism for maintaining an active pool of synaptic vesicles. The size reached by transient fusion pores and the time spent on the open state can determine the release of subquantal synaptic transmission, which could be a mechanism of synaptic potentiation. In this review we will described the electrophysiological and fluorescence methods that contribute to further explore the biophysical properties of the exocytotic fusion pore and the relevant experiments obtained by these methods.

Animals↗

LVAD-induced reverse remodeling: basic and clinical implications for myocardial recovery.

BACKGROUND: With improved technology, increasing clinical experience, and expanding indications for use, left ventricular assist devices (LVADs) are assuming a greater role in the care of patients with end-stage heart failure. Early in the course of LVAD use as a bridge to transplant, it became evident that some patients exhibit substantial recovery of ventricular function, which led to the concept of reverse remodeling. METHODS AND RESULTS: Herein we summarize and integrate insights derived from a multitude of studies that have investigated how LVAD support influences ventricular structural, cellular, extracellular matrix, molecular, biochemical, and metabolic characteristics of the end-stage failing heart. The focus includes a review of the extent and sustainability of reverse remodeling, the important advances in understanding of the pathophysiology of heart failure derived from these studies and the implications of these findings for development of new therapeutic strategies. CONCLUSION: In brief, studies of LVAD-heart interactions have led to the understanding that although we once considered the end-stage failing heart of patients near death to be irreversibly diseased, when given sufficient mechanical unloading and restoration of more normal neurohormonal milieu, a relatively large degree of myocardial recovery is possible. Comparison of effects on right and left ventricles have provided mechanistic insights by implicating hemodynamic unloading as primarily regulating certain aspects of reverse remodeling, neurohormonal factors as regulating other aspects, and joint regulation of still other aspects. As such these observations have driven a shift of thinking of chronic heart failure as a progressive irreversible disease process to a potentially treatable entity.

Heart↗

The lipid composition of hypodermal membranes from the blue crab (Callinectes sapidus) changes during the molt cycle and alters hypodermal calcium permeability.

Crustaceans are covered by a cuticle that does not grow. In order for an individual to grow, the cuticle must periodically be shed (ecdysis). Replacement of the old cuticle with a new one depends on processes that require precise timing and control, yet the nature and location of these controls remain unclear. A candidate site for them is within the hypodermal microvilli. These cellular structures extend through pore canals deep into the acellular cuticular matrix. Changes in the lipid composition of hypodermal microvilli could modulate water and ion fluxes and enzyme activities during critical stages of the molt cycle; however, the lipid composition of these structures has not been assessed during the molt cycle. Data presented here show that phospholipids isolated from hypodermal microvilli of Callinectes sapidus initially have elevated levels of n-6 fatty acids that decline steadily beginning just after ecdysis. Experiments with liposomes reveal that n-6 fatty acids decrease the calcium permeability of membranes, suggesting that the initially elevated levels in the cuticle may function to reduce calcium flux from the cuticle into the hypodermis. In addition, the ratio of cholesterol to phospholipid and the proportion of oleic acid in membrane phospholipids are maximal at 6 h post-ecdysis. It is known that changes in cholesterol and oleic acid content alter membrane permeability to water. It is, therefore possible that water flux through hypodermal membranes is also modulated in the early post-molt cuticle. Changes in microvillar lipid composition might serve importantly to control biomineralization in the post-ecdysal cuticle.

Animals↗

Microtubule plus-end-tracking proteins: mechanisms and functions.

Microtubule plus-end-tracking proteins (+TIPs) are a diverse group of molecules that display dynamic accumulation at the distal ends of growing microtubules. Specific binding to the growing microtubule tip coupled with quick detachment from the older lattice, plus-end-directed transport, and association with other +TIPs can all contribute to this protein localisation. +TIPs act mainly as microtubule-stabilising factors and at the same time often link microtubule ends to various cellular structures, such as the cell cortex or kinetochores. Regulation of the activity of +TIPs has profound effects on the shape of the microtubule network and plays an essential role in cell division, motility and morphogenesis.

Animals↗

The nuclear envelope: form and reformation.

The membrane system that encloses genomic DNA is referred to as the nuclear envelope. However, with emerging roles in signaling and gene expression, these membranes clearly serve as more than just a physical barrier separating the nucleus and cytoplasm. Recent progress in our understanding of nuclear envelope architecture and composition has also revealed an intriguing connection between constituents of the nuclear envelope and human disease, providing further impetus to decipher this cellular structure and the dramatic remodeling process it undergoes with each cell division.

Animals↗

Microtubule polymerases and depolymerases.

The variety of shapes and sizes of the microtubule cytoskeleton is as great as the number of different cell types. This large variety is a consequence of the dynamic properties of microtubules, which allow them to adopt distributions of arbitrary size and form. How is the distribution of microtubule lengths controlled? Recent work suggests that the length distribution is controlled, at least in part, by the activity of microtubule polymerases and depolymerases, which accelerate microtubule growth and shrinkage. Specifically, biochemical and single-molecule studies have shown how MCAK (kinesin-13) and Kip3p (kinesin-8) accelerate depolymerization and how XMAP215 may accelerate growth. Studies on the yeast Dam1 complex have shown how proteins can couple a cellular structure, the kinetochore, to the ends of polymerizing and depolymerizing microtubules.

Animals↗

Regulation of the myosin-directed chaperone UNC-45 by a novel E3/E4-multiubiquitylation complex in C. elegans.

The organization of the motor protein myosin into motile cellular structures requires precise temporal and spatial control. Caenorhabditis elegans UNC-45 facilitates this by functioning both as a chaperone and as a Hsp90 cochaperone for myosin during thick filament assembly. Consequently, mutations in C. elegans unc-45 result in paralyzed animals with severe myofibril disorganization in striated body wall muscles. Here, we report a new E3/E4 complex, formed by CHN-1, the C. elegans ortholog of CHIP (carboxyl terminus of Hsc70-interacting protein), and UFD-2, an enzyme known to have ubiquitin conjugating E4 activity in yeast, as necessary and sufficient to multiubiquitylate UNC-45 in vitro. The phenotype of unc-45 temperature-sensitive animals is partially suppressed by chn-1 loss of function, while UNC-45 overexpression in worms deficient for chn-1 results in severely disorganized muscle cells. These results identify CHN-1 and UFD-2 as a functional E3/E4 complex and UNC-45 as its physiologically relevant substrate.

Animals↗

The casein kinase 1 family: participation in multiple cellular processes in eukaryotes.

Phosphorylation of serine, threonine and tyrosine residues by cellular protein kinases plays an important role in the regulation of various cellular processes. The serine/threonine specific casein kinase 1 and 2 protein kinase families--(CK1 and CK2)--were among the first protein kinases that had been described. In recent years our knowledge of the regulation and function of mammalian CK1 kinase family members has rapidly increased. Extracellular stimuli, the subcellular localization of CK1 isoforms, their interaction with various cellular structures and proteins, as well as autophosphorylation and proteolytic cleavage of their C-terminal regulatory domains influence CK1 kinase activity. Mammalian CK1 isoforms phosphorylate many different substrates among them key regulatory proteins involved in the control of cell differentiation, proliferation, chromosome segregation and circadian rhythms. Deregulation and/or the incidence of mutations in the coding sequence of CK1 isoforms have been linked to neurodegenerative diseases and cancer. This review will summarize our current knowledge about the function and regulation of mammalian CK1 isoforms.

Amino Acid Sequence↗

An in vitro screen of bacterial lipopolysaccharide biosynthetic enzymes identifies an inhibitor of ADP-heptose biosynthesis.

The lipopolysaccharide (LPS)-rich outer membrane of gram-negative bacteria provides a protective barrier that insulates these organisms from the action of numerous antibiotics. Breach of the LPS layer can therefore provide access to the cell interior to otherwise impermeant toxic molecules and can expose vulnerable binding sites for immune system components such as complement. Inhibition of LPS biosynthesis, leading to a truncated LPS molecule, is an alternative strategy for antibacterial drug development in which this vital cellular structure is weakened. A significant challenge for in vitro screens of small molecules for inhibition of LPS biosynthesis is the difficulty in accessing the complex carbohydrate substrates. We have optimized an assay of the enzymes required for LPS heptose biosynthesis that simultaneously surveys five enzyme activities by using commercially available substrates and report its use in a small-molecule screen that identifies an inhibitor of heptose synthesis.

Adenosine Diphosphate Sugars↗

Deformation and nano-rheology of red blood cells: an AFM investigation.

Interaction forces, deformation and nano-rheology of individual red blood cells in physiologically relevant solution conditions have been determined by colloid probe atomic force microscopy (AFM). On approach of the physically immobilised cell and silica glass spherical probe surfaces, deformation of the red blood cell was observed in the force curves. At low levels of deformation, spring constants were determined in the range 3-6 m Nm(-1), whereas for higher levels of deformation, the forces increase non-linearly and on retraction, significant force curve hysteresis is observed (i.e. lower forces upon retraction). The extent of force curve hysteresis was dependent on both the drive velocity and loading force, typical of a viscoelastic system. The response of the red blood cell has been described by viscoelastic theory, where the short and long time scale elastic moduli and relaxation times are determined, i.e. the cell's nano-rheological properties elucidated. In addition to a time independent elastic modulus of 4.0 x 10(3)Nm(-2) at low levels of deformation, time-dependent elastic moduli ranges are observed (3.5 x 10(4) to 5.5 x 10(4)Nm(-2) at intermediate levels of deformation and 1.5 x 10(5) to 3.0 x 10(5)Nm(-2) at higher levels of deformation). That is, one elastic and more than one viscoelastic response to the red blood cell deformation is evident, which is considered to reflect the cellular structure.

Cells, Immobilized↗