A simulation model of <Emphasis Type="Italic">Escherichia coli</Emphasis> osmoregulatory switch using E-CELL system

Background  

Bacterial signal transduction mechanism referred to as a "two component regulatory systems" contributes to the overall adaptability of the bacteria by regulating the gene expression. Osmoregulation is one of the well-studied two component regulatory systems comprising of the sensor, EnvZ and the cognate response regulator, OmpR, which together control the expression of OmpC and OmpF porins in response to the osmolyte concentration.     

Quantification of the glycogen cascade system: the ultrasensitive responses of liver glycogen synthase and muscle phosphorylase are due to distinctive regulatory designs

Background

Signaling pathways include intricate networks of reversible covalent modification cycles. Such multicyclic enzyme cascades amplify the input stimulus, cause integration of multiple signals and exhibit sensitive output responses. Regulation of glycogen synthase and phosphorylase by reversible covalent modification cycles exemplifies signal transduction by enzyme cascades. Although this system for regulating glycogen synthesis and breakdown appears similar in all tissues, subtle differences have been identified. For example, phosphatase-1, a dephosphorylating enzyme of the system, is regulated quite differently in muscle and liver. Do these small differences in regulatory architecture affect the overall performance of the glycogen cascade in a specific tissue? We address this question by analyzing the regulatory structure of the glycogen cascade system in liver and muscle cells at steady state.

Results

The glycogen cascade system in liver and muscle cells was analyzed at steady state and the results were compared with literature data. We found that the cascade system exhibits highly sensitive switch-like responses to changes in cyclic AMP concentration and the outputs are surprisingly different in the two tissues. In muscle, glycogen phosphorylase is more sensitive than glycogen synthase to cyclic AMP, while the opposite is observed in liver. Furthermore, when the liver undergoes a transition from starved to fed-state, the futile cycle of simultaneous glycogen synthesis and degradation switches to reciprocal regulation. Under such a transition, different proportions of active glycogen synthase and phosphorylase can coexist due to the varying inhibition of glycogen-synthase phosphatase by active phosphorylase.

Conclusion

The highly sensitive responses of glycogen synthase in liver and phosphorylase in muscle to primary stimuli can be attributed to distinctive regulatory designs in the glycogen cascade system. The different sensitivities of these two enzymes may exemplify the adaptive strategies employed by liver and muscle cells to meet specific cellular demands.

     

Detailed protein sequence alignment based on Spectral Similarity Score (SSS)

Background  

The chemical property and biological function of a protein is a direct consequence of its primary structure. Several algorithms have been developed which determine alignment and similarity of primary protein sequences. However, character based similarity cannot provide insight into the structural aspects of a protein. We present a method based on spectral similarity to compare subsequences of amino acids that behave similarly but are not aligned well by considering amino acids as mere characters. This approach finds a similarity score between sequences based on any given attribute, like hydrophobicity of amino acids, on the basis of spectral information after partial conversion to the frequency domain.     

Mitochondria regulate Ca2+ wave initiation and inositol trisphosphate signal transduction in oligodendrocyte progenitors

Mitochondria in oligodendrocyte progenitor cells (OPs) take up and release cytosolic Ca2+ during agonist-evoked Ca2+ waves, but it is not clear whether or how they regulate Ca2+ signaling in OPs. We asked whether mitochondria play an active role during agonist-evoked Ca2+ release from intracellular stores. Ca2+ puffs, wave initiation, and wave propagation were measured in fluo-4 loaded OP processes using linescan confocal microscopy. Mitochondrial depolarization, measured by tetramethyl rhodamine ethyl ester (TMRE) fluorescence, accompanied Ca2+ puffs and waves. In addition, waves initiated only where mitochondria were localized. To determine whether energized mitochondria were necessary for wave generation, we blocked mitochondrial function with the electron transport chain inhibitor antimycin A (AA) in combination with oligomycin. AA decreased wave speed and puff probability. These effects were not due to global changes in ATP. We found that AA increased cytosolic Ca2+, markedly reduced agonist-evoked inositol trisphosphate (IP3) production, and also enhanced phosphatidylinositol 4,5-bisphosphate (PIP2) binding to the Ca2+ dependent protein gelsolin. Thus, the reduction in puff probability and wave speed after AA treatment may be explained by competition for PIP2 between phospholipase C and gelsolin. Energized mitochondria and low cytosolic Ca2+ concentration may be required to maintain PIP2, a substrate for IP3 signal transduction.     

The effect of limited interlaminar decompression versus complete laminectomy on intrathecal volume in degenerative lumbar spinal stenosis.

INTRODUCTION: There is a controversial discussion about the adequate surgical procedure for degenerative lumbar spinal stenosis. Due to the observation that the degenerative lumbar spinal stenosis takes place predominantly at the interlaminar region on the level of the disc involving facets and bulging of the ligamentum flavum, resection of the whole lamina might not be necessary. A biomechanical study was designed to assess the effect of different decompression techniques using cadaver lumbar spine models. METHODS: Twelve cadaver spines with CT verified degenerative lumbar spinal stenosis were dissected in order to measure the volume of the dural sac at different flexion and extension angles. Each segment (L3/4, L4/5) was decompressed first by limited interlaminar decompression and second by complete laminectomy. Intrathecal volume measurements were taken initially, after limited interlaminar decompression and after complete laminectomy. RESULTS: Before surgical procedure, the cadaver spines showed an increase of the intrathecal volume in flexion and decrease in extension. After limited interlaminar decompression, there was a significant reduction of volume loss in extension. There was no significant additional reduction of volume loss in extension after complete laminectomy in comparison to limited interlaminar decompression. CONCLUSION: The results allow to conclude that limited interlaminar decompression is efficient for decompression in degenerative lumbar spinal stenosis.     

IL-22 is expressed by Th17 cells in an IL-23-dependent fashion, but not required for the development of autoimmune encephalomyelitis

Lately, IL-17-secreting Th cells have received an overwhelming amount of attention and are now widely held to be the major pathogenic population in autoimmune diseases. In particular, IL-22-secreting Th17 cells were shown to specifically mark the highly pathogenic population of self-reactive T cells in experimental autoimmune encephalomyelitis (EAE). As IL-17A itself was found to only play a minor role during the development of EAE, IL-22 is now postulated to contribute to the pathogenic function of Th17 cells. The goal of this study was to determine the role and function of IL-22 during the development of CNS autoimmunity in vivo. We found that CNS-invading encephalitogenic Th17 cells coexpress IL-22 and that IL-22 is specifically induced by IL-23 in autoimmune-pathogenic CD4+ T cells in a time- and dose-dependent manner. We next generated IL-22-/- mice, which--in contrast to the prediction that expression of inflammatory cytokines by CNS-invading T cells inevitably confers pathogenic function--turned out to be fully susceptible to EAE. Taken together, we show that self-reactive Th cells coexpress IL-17 and IL-22, but that the latter also does not appear to be directly involved in autoimmune pathogenesis of the CNS.     

Accidental experiments: ecological and evolutionary insights and opportunities derived from global change

Humans are the dominant ecological and evolutionary force on the planet today, transforming habitats, polluting environments, changing climates, introducing new species, and causing other species to decline in number or go extinct. These worrying anthropogenic impacts, collectively termed global change, are often viewed as a confounding factor to minimize in basic studies and a problem to resolve or quantify in applied studies. However, these ‘accidental experiments’ also represent opportunities to gain fundamental insight into ecological and evolutionary processes, especially when they result in perturbations that are large or long in duration and difficult or unethical to impose experimentally. We demonstrate this by describing important fundamental insights already gained from studies which utilize global change factors as accidental experiments. In doing so, we highlight why accidental experiments are sometimes more likely to yield insights than traditional approaches. Next, we argue that emerging environmental problems can provide even more opportunities for scientific discovery in the future, and provide both examples and guidelines for moving forward. We recommend 1) a greater flow of information between basic and applied subfields of ecology and evolution to identify emerging opportunities; 2) considering the advantages of the ‘accidental experiment’ approach relative to more traditional approaches; and 3) planning for the challenges inherent to uncontrolled accidental experiments. We emphasize that we do not view the accidental experiments provided by global change as replacements for scientific studies quantifying the magnitude of anthropogenic impacts or outlining strategies for mitigating impacts. Instead, we believe that accidental experiments are uniquely situated to provide insights into evolutionary and ecological processes that ultimately allow us to better predict and manage change on our human‐dominated planet. Synthesis Humans have an increasingly large impact on the planet. In response, ecologists and evolutionary biologists are dedicating increasing scientific attention to global change, largely with studies documenting biological effects and testing strategies to avoid or reverse negative impacts. In this article, we analyze global change from a different perspective, and suggest that human impacts on the environment also serve as valuable ‘accidental experiments’ that can provide fundamental scientific insight. We highlight and synthesize examples of studies taking this approach, and give guidance for gaining future insights from these unfortunate ‘accidental experiments’.     

Regulator of G protein signaling 2 inhibits Gαq-dependent uveal melanoma cell growth

Activating mutations in Gα_q/11 are a major driver of uveal melanoma (UM), the most common intraocular cancer in adults. While progress has recently been made in targeting Gα_q/11 for UM therapy, the crucial role for these proteins in normal physiology and their high structural similarity with many other important GTPase proteins renders this approach challenging. The aim of the current study was to validate whether a key regulator of Gq signaling, regulator of G protein signaling 2 (RGS2), can inhibit Gα_q-mediated UM cell growth. We used two UM cell lines, 92.1 and Mel-202, which both contain the most common activating mutation Gα_q^Q209L and developed stable cell lines with doxycycline-inducible RGS2 protein expression. Using cell viability assays, we showed that RGS2 could inhibit cell growth in both of these UM cell lines. We also found that this effect was independent of the canonical GTPase-activating protein activity of RGS2 but was dependent on the association between RGS2 and Gα_q. Furthermore, RGS2 induction resulted in only partial reduction in cell growth as compared to siRNA-mediated Gαq knockdown, perhaps because RGS2 was only able to reduce mitogen-activated protein kinase signaling downstream of phospholipase Cβ, while leaving activation of the Hippo signaling mediators yes-associated protein 1/TAZ, the other major pathway downstream of Gα_q, unaffected. Taken together, our data indicate that RGS2 can inhibit UM cancer cell growth by associating with Gα_q^Q209L as a partial effector antagonist.