Fishing out proteins that bind to titin

Another giant protein has been detected in cross-striated muscle cells. Given the name obscurin, it was discovered in a yeast two-hybrid screen in which the bait was a small region of titin that is localized near the Z-band. Obscurin is about 720 kD, similar in molecular weight to nebulin, but present at about one tenth the level (Young et al., 2001). Like titin, obscurin contains multiple immunoglobulin-like domains linked in tandem, but in contrast to titin it contains just two fibronectin-like domains. It also contains sequences that suggest obscurin may have roles in signal transduction. During embryonic development, its localization changes from the Z-band to the M-band. With these intriguing properties, obscurin may not remain obscure for long

Assembly and Dynamics of Myofibrils

We review some of the problems in determining how myofibrils may be assembled and just as importantly how this contractile structure may be renewed by sarcomeric proteins moving between the sarcomere and the cytoplasm. We also address in this personal review the recent evidence that indicates that the assembly and dynamics of myofibrils are conserved whether the cells are analyzed in situ or in tissue culture conditions. We suggest that myofibrillogenesis is a fundamentally conserved process, comparable to protein synthesis, mitosis, or cytokinesis, whether examined in situ or in vitro

Sites of monomeric actin incorporation in living PTK2 and REF-52 cells

The purpose of this study was to analyze where monomeric actin first becomes incorporated into the sarcomeric units of the stress fibers. We microinjected fluorescently labeled actin monomers into two cell lines that differ in the sarcomeric spacings of ␣-actinin and nonmuscle myosin II along their stress fibers: REF-52, a fibroblast cell line, and PtK2, an epithelial cell line. The cells were fixed at selected times after microinjection (30 s and longer) and then stained with an ␣-actinin antibody. Localization of the labeled actin and ␣-actinin antibody were recorded with low level light cameras. In both cell types, the initial sites of incorporation were in focal contacts, lamellipodia and in punctate regions of the stress fibers that corresponded to the ␣-actinin rich dense bodies. The adherent junctions between the epithelial PtK2 cells were also initial sites of incorporation. At longer times of incorporation, the actin fluorescence extended along the stress fibers and became almost uniform. We saw no difference in the pattern of incorporation in peripheral and perinuclear regions of the stress fibers. We propose that rapid incorporation of monomeric actin occurs at the cellular sites where the barbed ends of actin filaments are concentrated: at the edges of lamellipodia, the adherens junctions, the attachment plaques and in the dense bodies that mark out the sarcomeric subunits of the stress fibers. Cell Motil

Mitochondrial DNA Variant Discovery and Evaluation in Human Cardiomyopathies through Next-Generation Sequencing

Mutations in mitochondrial DNA (mtDNA) may cause maternally-inherited cardiomyopathy and heart failure. In homoplasmy all mtDNA copies contain the mutation. In heteroplasmy there is a mixture of normal and mutant copies of mtDNA. The clinical phenotype of an affected individual depends on the type of genetic defect and the ratios of mutant and normal mtDNA in affected tissues. We aimed at determining the sensitivity of next-generation sequencing compared to Sanger sequencing for mutation detection in patients with mitochondrial cardiomyopathy. We studied 18 patients with mitochondrial cardiomyopathy and two with suspected mitochondrial disease. We “shotgun” sequenced PCR-amplified mtDNA and multiplexed using a single run on Roche's 454 Genome Sequencer. By mapping to the reference sequence, we obtained 1,300× average coverage per case and identified high-confidence variants. By comparing these to >400 mtDNA substitution variants detected by Sanger, we found 98% concordance in variant detection. Simulation studies showed that >95% of the homoplasmic variants were detected at a minimum sequence coverage of 20× while heteroplasmic variants required >200× coverage. Several Sanger “misses” were detected by 454 sequencing. These included the novel heteroplasmic 7501T>C in tRNA serine 1 in a patient with sudden cardiac death. These results support a potential role of next-generation sequencing in the discovery of novel mtDNA variants with heteroplasmy below the level reliably detected with Sanger sequencing. We hope that this will assist in the identification of mtDNA mutations and key genetic determinants for cardiomyopathy and mitochondrial disease

Molecular diagnosis of Burkitt\u27s lymphoma.

BACKGROUND: The distinction between Burkitt\u27s lymphoma and diffuse large-B-cell lymphoma is crucial because these two types of lymphoma require different treatments. We examined whether gene-expression profiling could reliably distinguish Burkitt\u27s lymphoma from diffuse large-B-cell lymphoma. METHODS: Tumor-biopsy specimens from 303 patients with aggressive lymphomas were profiled for gene expression and were also classified according to morphology, immunohistochemistry, and detection of the t(8;14) c-myc translocation. RESULTS: A classifier based on gene expression correctly identified all 25 pathologically verified cases of classic Burkitt\u27s lymphoma. Burkitt\u27s lymphoma was readily distinguished from diffuse large-B-cell lymphoma by the high level of expression of c-myc target genes, the expression of a subgroup of germinal-center B-cell genes, and the low level of expression of major-histocompatibility-complex class I genes and nuclear factor-kappaB target genes. Eight specimens with a pathological diagnosis of diffuse large-B-cell lymphoma had the typical gene-expression profile of Burkitt\u27s lymphoma, suggesting they represent cases of Burkitt\u27s lymphoma that are difficult to diagnose by current methods. Among 28 of the patients with a molecular diagnosis of Burkitt\u27s lymphoma, the overall survival was superior among those who had received intensive chemotherapy regimens instead of lower-dose regimens. CONCLUSIONS: Gene-expression profiling is an accurate, quantitative method for distinguishing Burkitt\u27s lymphoma from diffuse large-B-cell lymphoma

25th annual computational neuroscience meeting: CNS-2016

The same neuron may play different functional roles in the neural circuits to which it belongs. For example, neurons in the Tritonia pedal ganglia may participate in variable phases of the swim motor rhythms [1]. While such neuronal functional variability is likely to play a major role the delivery of the functionality of neural systems, it is difficult to study it in most nervous systems. We work on the pyloric rhythm network of the crustacean stomatogastric ganglion (STG) [2]. Typically network models of the STG treat neurons of the same functional type as a single model neuron (e.g. PD neurons), assuming the same conductance parameters for these neurons and implying their synchronous firing [3, 4]. However, simultaneous recording of PD neurons shows differences between the timings of spikes of these neurons. This may indicate functional variability of these neurons. Here we modelled separately the two PD neurons of the STG in a multi-neuron model of the pyloric network. Our neuron models comply with known correlations between conductance parameters of ionic currents. Our results reproduce the experimental finding of increasing spike time distance between spikes originating from the two model PD neurons during their synchronised burst phase. The PD neuron with the larger calcium conductance generates its spikes before the other PD neuron. Larger potassium conductance values in the follower neuron imply longer delays between spikes, see Fig. 17.Neuromodulators change the conductance parameters of neurons and maintain the ratios of these parameters [5]. Our results show that such changes may shift the individual contribution of two PD neurons to the PD-phase of the pyloric rhythm altering their functionality within this rhythm. Our work paves the way towards an accessible experimental and computational framework for the analysis of the mechanisms and impact of functional variability of neurons within the neural circuits to which they belong

Differential effects of Latrunculin-A on myofibrils in cultures of skeletal muscle cells: insights into mechanisms of myofibrillogenesis. Cell Motil Cytoskeleton. 2005; 62:35–47. [PubMed: 16080205

To test different models of myofibrillogenesis, we followed live cells expressing Green Fluorescent Proteins ligated to either actin or alpha-actinin and analyzed stress fibers, premyofibrils, and myofibrils in quail myotube cultures. Actin filaments in the three types of fibers were compared by analyzing the effects of Latrunculin-A (Lat-A), a monomeric actin binding macrolide drug (M.W. ¼ 422 Daltons), on stress fibers in fibroblasts and on myofibrils in skeletal myotubes in the same culture. Lat-A, at low concentrations (0.2 mM), induced the loss of stress fibers in fibroblasts within a few hours and within 10 min when Lat-A was increased to 1.0 mM. The effect was reversible with reformation of the stress fibers when the drug was removed. In contrast to the Lat-A induced disassembly of stress fibers in fibroblasts, assembling myofibrils in the skeletal muscle cells were not affected by 1.0-mM concentrations of Lat-A. With increasing concentrations of Lat-A (up to 5 mM), and increasing incubation times, however, the drug induced premyofibrils, the precursors of mature myofibrils, to disassemble and the accumulation of mature myofibrils to be halted. Removal of the drug led to the reformation of premyofibrils and the resumption of myofibrillogenesis in the spreading edges of the myotubes. In contrast, the mature myofibrils in the central shaft of the myotubes were stable in doses of Lat-A as high as 50 mM. The newly assembled mature myofibrils located adjacent to the premyofibrils at the ends and sides of the myotube were intermediate in sensitivity to Lat-A, disassembling when exposed to 10 mM Lat-A for one hour. To determine how a change in the actin filaments during myofibrillogenesis might confer greater resistance to depolymerization by Lat-A, we stained the myotubes with an antibody directed against CapZ, a protein that blocks the release of monomer actin from the barbed ends of actin filaments. CapZ was absent from premyofibrils. It was distributed uniformly along nascent myofibrils where F-actin was unstriated, and was localized in a clearly striated Z-band pattern in the mature myofibrils where F-actin patterns were fully striated. These Lat-A and CapZ results are discussed in the context of various models of myofibrillogenesis. Cell Motil

SARCOPLASMIC RETICULUM IN THE ADDUCTOR MUSCLES OF A BERMUDA SCALLOP: COMPARISON OF SMOOTH VERSUS CROSS-STRIATED PORTIONS

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