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1.  Heterogeneous kinetics of AKT signaling in individual cells are accounted for by variable protein concentration 
In most solid cancers, cells harboring oncogenic mutations represent only a sub-fraction of the entire population. Within this sub-fraction the expression level of mutated proteins can vary significantly due to cellular variability limiting the efficiency of targeted therapy. To address the causes of the heterogeneity, we performed a systematic analysis of one of the most frequently mutated pathways in cancer cells, the phosphatidylinositol 3 kinase (PI3K) signaling pathway. Among others PI3K signaling is activated by the hepatocyte growth factor (HGF) that regulates proliferation of hepatocytes during liver regeneration but also fosters tumor cell proliferation. HGF-mediated responses of PI3K signaling were monitored both at the single cell and cell population level in primary mouse hepatocytes and in the hepatoma cell line Hepa1_6. Interestingly, we observed that the HGF-mediated AKT responses at the level of individual cells is rather heterogeneous. However, the overall average behavior of the single cells strongly resembled the dynamics of AKT activation determined at the cell population level. To gain insights into the molecular cause for the observed heterogeneous behavior of individual cells, we employed dynamic mathematical modeling in a stochastic framework. Our analysis demonstrated that intrinsic noise was not sufficient to explain the observed kinetic behavior, but rather the importance of extrinsic noise has to be considered. Thus, distinct from gene expression in the examined signaling pathway fluctuations of the reaction rates has only a minor impact whereas variability in the concentration of the various signaling components even in a clonal cell population is a key determinant for the kinetic behavior.
doi:10.3389/fphys.2012.00451
PMCID: PMC3508424  PMID: 23226133
mathematical modeling; HGF; PI3 kinase; AKT; single cell heterogeneity; live cell imaging; primary hepatocytes; hepatocellular carcinoma
2.  Heterogeneity in the penumbra 
Original experimental studies in nonhuman primate models of focal ischemia showed flow-related changes in evoked potentials that suggested a circumferential zone of low regional cerebral blood flow with normal K+ homeostasis, around a core of permanent injury in the striatum or the cortex. This became the basis for the definition of the ischemic penumbra. Imaging techniques of the time suggested a homogeneous core of injury, while positing a surrounding ‘penumbral' region that could be salvaged. However, both molecular studies and observations of vascular integrity indicate a more complex and dynamic situation in the ischemic core that also changes with time. The microvascular, cellular, and molecular events in the acute setting are compatible with heterogeneity of the injury within the injury center, which at early time points can be described as multiple ‘mini-cores' associated with multiple ‘mini-penumbras'. These observations suggest the progression of injury from many small foci to a homogeneous defect over time after the onset of ischemia. Recent observations with updated imaging techniques and data processing support these dynamic changes within the core and the penumbra in humans following focal ischemia.
doi:10.1038/jcbfm.2011.93
PMCID: PMC3185890  PMID: 21731034
focal ischemia; imaging; ischemic penumbra; metabolic characteristics; microvessel characteristics; molecular characteristics
3.  Stress-Coping and Cortisol Analysis in Patients with Non-Syndromic Cleft Lip and Palate: An Explorative Study 
PLoS ONE  2012;7(7):e41015.
Background
Non-syndromic clefts of the orofacial region occur in approximately 1 per 500 to 2,500 live births, depending on geographical area and ethnicity. It can be supposed that the disruption of the normal facial structure and the long-standing pressure of treatment from birth to adulthood bring about a range of life stressors which may lead to a long-lasting impact on affected subjects throughout their lives. Therefore, the present study aimed to assess different aspects of psychosocial stress in affected individuals.
Methods
The study was divided into two parts: first, the Trier Social Stress Test which involves uncontrollability and high levels of social-evaluative stress under real conditions and second, the query of various aspects of coping with psychosocial stress. The test group consisted of 30 affected adult subjects, and an equally sized control group of unaffected volunteers. Cortisol dysregulation was determined by saliva samples before and after stress induction. Meanwhile, participants were asked to complete the SVF 120 stress-coping questionnaire.
Results
The analysis of saliva samples showed a similar baseline concentration as well as a similar increase in cortisol levels after stress induction for both groups. Subsequently, the decline in cortisol concentrations was significantly faster in the CLP group (course: p<0.001; groups: p = 0.102; interaction: p = 0.167). The evaluation of the stress-coping questionnaire revealed a significantly shorter rumination about a stressful event in individuals with CLP-related malformations (p = 0.03).
Conclusion
We conclude that adults with CLP have significantly better stress-coping strategies than their healthy peers.
Trial Registration
German Clinical Trials Organization DRKS00003466
doi:10.1371/journal.pone.0041015
PMCID: PMC3401206  PMID: 22911731
4.  Translational Control of Cell Division by Elongator 
Cell reports  2012;1(5):424-433.
SUMMARY
Elongator is required for the synthesis of the mcm5s2 modification found on tRNAs recognizing AA-ending codons. In order to obtain a global picture of the role of Elongator in translation, we used reverse protein arrays to screen the fission yeast proteome for translation defects. Unexpectedly, this revealed that Elongator inactivation mainly affected three specific functional groups including proteins implicated in cell division. The absence of Elongator results in a delay in mitosis onset and cytokinesis defects. We demonstrate that the kinase Cdr2, which is a central regulator of mitosis and cytokinesis, is under translational control by Elongator due to the Lysine codon usage bias of the cdr2 coding sequence. These findings uncover a mechanism by which the codon usage, coupled to tRNA modifications, fundamentally contributes to gene expression and cellular functions.
doi:10.1016/j.celrep.2012.04.001
PMCID: PMC3388810  PMID: 22768388
5.  Crossed cerebellar diaschisis after stroke: can perfusion-weighted MRI show functional inactivation? 
In this study, we aimed to assess the detection of crossed cerebellar diaschisis (CCD) following stroke by perfusion-weighted magnetic resonance imaging (PW-MRI) in comparison with positron emission tomography (PET). Both PW-MRI and 15O-water-PET were performed in acute and subacute hemispheric stroke patients. The degree of CCD was defined by regions of interest placed in the cerebellar hemispheres ipsilateral (I) and contralateral (C) to the supratentorial lesion. An asymmetry index (AI=C/I) was calculated for PET-cerebral blood flow (CBF) and MRI-based maps of CBF, cerebral blood volume (CBV), mean transit time (MTT), and time to peak (TTP). The resulting AI values were compared by Bland–Altman (BA) plots and receiver operating characteristic analysis to detect the degree and presence of CCD. A total of 26 imaging procedures were performed (median age 57 years, 20/26 imaged within 48 hours after stroke). In BA plots, all four PW-MRI maps could not reliably reflect the degree of CCD. In receiver operating characteristic analysis for detection of CCD, PW-CBF performed poorly (accuracy 0.61), whereas CBV, MTT, and TTP failed (accuracy <0.60). On the basis of our findings, PW-MRI at 1.5 T is not suited to depict CCD after stroke.
doi:10.1038/jcbfm.2011.15
PMCID: PMC3130318  PMID: 21386854
crossed cerebellar diaschisis; perfusion-weighted imaging; positron emission tomography; remote inactivation; stroke
6.  Regulation of transcriptome, translation, and proteome in response to environmental stress in fission yeast 
Genome Biology  2012;13(4):R25.
Background
Gene expression is controlled globally and at multiple levels in response to environmental stress, but the relationships among these dynamic regulatory changes are not clear. Here we analyzed global regulation during different stress conditions in fission yeast, Schizosaccharomyces pombe, combining dynamic genome-wide data on mRNA, translation, and protein profiles.
Results
We observed a strong overall concordance between changes in mRNAs and co-directional changes in translation, for both induced and repressed genes, in response to three conditions: oxidative stress, heat shock, and DNA damage. However, approximately 200 genes each under oxidative and heat stress conditions showed discordant regulation with respect to mRNA and translation profiles, with genes and patterns of regulation being stress-specific. For oxidative stress, we also measured dynamic profiles for 2,147 proteins, comprising 43% of the proteome. The mRNAs induced during oxidative stress strongly correlated with increased protein expression, while repressed mRNAs did not relate to the corresponding protein profiles. Overall changes in relative protein expression correlated better with changes in mRNA expression than with changes in translational efficiency.
Conclusions
These data highlight a global coordination and fine-tuning of gene regulation during stress that mostly acts in the same direction at the levels of transcription and translation. In the oxidative stress condition analyzed, transcription dominates translation to control protein abundance. The concordant regulation of transcription and translation leads to the expected adjustment in protein expression only for up-regulated mRNAs. These patterns of control might reflect the need to balance protein production for stress survival given a limited translational capacity.
doi:10.1186/gb-2012-13-4-r25
PMCID: PMC3446299  PMID: 22512868
7.  Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice 
Drug conjugates have been studied extensively in preclinical in vitro and in vivo models but to date only a few compounds have progressed to the clinical setting. This situation is now changing with the publication of studies demonstrating a significant impact on clinical practice and highlighting the potential of this new class of targeted therapies. This review summarizes the pharmacological and molecular background of the main drug conjugation systems, namely antibody drug conjugates (ADCs), immunotoxins and immunoliposomes. All these compounds combine the specific targeting moiety of an antibody or similar construct with the efficacy of a toxic drug. The aim of this strategy is to target tumor cells specifically while sparing normal tissue, thus resulting in high efficacy and low toxicity. Recently, several strategies have been investigated in phase I clinical trials and some have entered phase III clinical development. This review provides a detailed overview of various strategies and critically discusses the most relevant achievements. Examples of the most advanced compounds include T-DM1 and brentuximab vedotin. However, additional promising strategies such as immunotoxins and immunoliposmes are already in clinical development. In summary, targeted drug delivery by drug conjugates is a new emerging class of anti-cancer therapy that may play a major role in the future.
doi:10.3390/ijms131216020
PMCID: PMC3546676  PMID: 23443108
targeted therapy; drug conjugates; antibody drug conjugates; immunotoxins; immunoliposomes
8.  Complex c-di-GMP Signaling Networks Mediate Transition between Virulence Properties and Biofilm Formation in Salmonella enterica Serovar Typhimurium 
PLoS ONE  2011;6(12):e28351.
Upon Salmonella enterica serovar Typhimurium infection of the gut, an early line of defense is the gastrointestinal epithelium which senses the pathogen and intrusion along the epithelial barrier is one of the first events towards disease. Recently, we showed that high intracellular amounts of the secondary messenger c-di-GMP in S. typhimurium inhibited invasion and abolished induction of a pro-inflammatory immune response in the colonic epithelial cell line HT-29 suggesting regulation of transition between biofilm formation and virulence by c-di-GMP in the intestine. Here we show that highly complex c-di-GMP signaling networks consisting of distinct groups of c-di-GMP synthesizing and degrading proteins modulate the virulence phenotypes invasion, IL-8 production and in vivo colonization in the streptomycin-treated mouse model implying a spatial and timely modulation of virulence properties in S. typhimurium by c-di-GMP signaling. Inhibition of the invasion and IL-8 induction phenotype by c-di-GMP (partially) requires the major biofilm activator CsgD and/or BcsA, the synthase for the extracellular matrix component cellulose. Inhibition of the invasion phenotype is associated with inhibition of secretion of the type three secretion system effector protein SipA, which requires c-di-GMP metabolizing proteins, but not their catalytic activity. Our findings show that c-di-GMP signaling is at least equally important in the regulation of Salmonella-host interaction as in the regulation of biofilm formation at ambient temperature.
doi:10.1371/journal.pone.0028351
PMCID: PMC3229569  PMID: 22164276
9.  Widespread Cotranslational Formation of Protein Complexes 
PLoS Genetics  2011;7(12):e1002398.
Most cellular processes are conducted by multi-protein complexes. However, little is known about how these complexes are assembled. In particular, it is not known if they are formed while one or more members of the complexes are being translated (cotranslational assembly). We took a genomic approach to address this question, by systematically identifying mRNAs associated with specific proteins. In a sample of 31 proteins from Schizosaccharomyces pombe that did not contain RNA–binding domains, we found that ∼38% copurify with mRNAs that encode interacting proteins. For example, the cyclin-dependent kinase Cdc2p associates with the rum1 and cdc18 mRNAs, which encode, respectively, an inhibitor of Cdc2p kinase activity and an essential regulator of DNA replication. Both proteins interact with Cdc2p and are key cell cycle regulators. We obtained analogous results with proteins with different structures and cellular functions (kinesins, protein kinases, transcription factors, proteasome components, etc.). We showed that copurification of a bait protein and of specific mRNAs was dependent on the presence of the proteins encoded by the interacting mRNAs and on polysomal integrity. These results indicate that these observed associations reflect the cotranslational interaction between the bait and the nascent proteins encoded by the interacting mRNAs. Therefore, we show that the cotranslational formation of protein–protein interactions is a widespread phenomenon.
Author Summary
Most proteins do not function in isolation. Instead, they associate with other proteins to form complexes. Little is known about the assembly of protein complexes within cells. One possibility is that proteins are completely synthesised before they bind to each other. An alternative is that proteins attach to each other as they are being translated in the ribosome (called cotranslational assembly). To investigate if cells use cotranslational assembly to form complexes, we identified mRNAs associated with specific proteins. The expectation is that if protein A binds to protein B as protein B is being translated, A will associate indirectly to the mRNA encoding B. Indeed, we found that for ∼40% of proteins (out of a sample of over 30) this was the case. Proteins associated with a small number of mRNAs, most of which encoded known or predicted interacting proteins. We found examples of this phenomenon in proteins with different functions and structures, indicating that cotranslational assembly is widespread. Cotranslational assembly might be required for certain proteins to associate, or it might be important in cases where the early formation of a protein complex is beneficial, such as when a protein is toxic or unstable unless bound to a partner.
doi:10.1371/journal.pgen.1002398
PMCID: PMC3228823  PMID: 22144913
10.  Reversible dysfunction of receptors in traumatic brain injury? 
In many brain disorders reduced binding of central benzodiazepine receptor ligands indicates irreversible neuronal damage. The data presented by Koizumi et al (2010) demonstrate that this is not the case in traumatic brain injury suggesting different pathogenetic mechanisms leading to tissue damage. The proof for this hypothesis requires further studies that should also consider thresholds of ligand binding as indicators of irreversible damage.
doi:10.1038/jcbfm.2010.131
PMCID: PMC3023408  PMID: 20700134
Alzheimer's disease; brain imagery; brain ischemia; brain recovery; cerebral blood flow
11.  Stroke: Working toward a Prioritized World Agenda 
Background and Purpose
The aim of the Synergium was to devise and prioritize new ways of accelerating progress in reducing the risks, effects, and consequences of stroke.
Methods
Preliminary work was performed by 7 working groups of stroke leaders followed by a synergium (a forum for working synergistically together) with approximately 100 additional participants. The resulting draft document had further input from contributors outside the synergium.
Results
Recommendations of the Synergium are: Basic Science, Drug Development and Technology: There is a need to develop: (1) New systems of working together to break down the prevalent ‘silo’ mentality; (2) New models of vertically integrated basic, clinical, and epidemiological disciplines; and (3) Efficient methods of identifying other relevant areas of science. Stroke Prevention: (1) Establish a global chronic disease prevention initiative with stroke as a major focus. (2) Recognize not only abrupt clinical stroke, but subtle subclinical stroke, the commonest type of cerebrovascular disease, leading to impairments of executive function. (3) Develop, implement and evaluate a population approach for stroke prevention. (4) Develop public health communication strategies using traditional and novel (e.g., social media/marketing) techniques. Acute Stroke Management: Continue the establishment of stroke centers, stroke units, regional systems of emergency stroke care and telestroke networks. Brain Recovery and Rehabilitation: (1) Translate best neuroscience, including animal and human studies, into poststroke recovery research and clinical care. (2) Standardize poststroke rehabilitation based on best evidence. (3) Develop consensus on, then implementation of, standardized clinical and surrogate assessments. (4) Carry out rigorous clinical research to advance stroke recovery. Into the 21st Century: Web, Technology and Communications: (1) Work toward global unrestricted access to stroke-related information. (2) Build centralized electronic archives and registries. Foster Cooperation Among Stakeholders (large stroke organizations, nongovernmental organizations, governments, patient organizations and industry) to enhance stroke care. Educate and energize professionals, patients, the public and policy makers by using a ‘Brain Health’ concept that enables promotion of preventive measures.
Conclusions
To accelerate progress in stroke, we must reach beyond the current status scientifically, conceptually, and pragmatically. Advances can be made not only by doing, but ceasing to do. Significant savings in time, money, and effort could result from discontinuing practices driven by unsubstantiated opinion, unproven approaches, and financial gain. Systematic integration of knowledge into programs coupled with careful evaluation can speed the pace of progress.
doi:10.1159/000315099
PMCID: PMC3221270  PMID: 20516682
Prevention; Rehabilitation; Stroke; Translational; Treatment
12.  Effects of upper-frequency boundary and spectral warping on speech intelligibility in electrical stimulation 
Speech understanding was tested for seven listeners using 12-electrode Med-El cochlear implants (CIs) and six normal-hearing listeners using a CI simulation. Eighteen different types of processing were evaluated, which varied the frequency-to-tonotopic place mapping and the upper boundary of the frequency and stimulation range. Spectrally unwarped and warped conditions were included. Unlike previous studies on this topic, the lower boundary of the frequency and stimulation range was fixed while the upper boundary was varied. For the unwarped conditions, only eight to ten channels were needed in both quiet and noise to achieve no significant degradation in speech understanding compared to the normal 12-electrode speech processing. The unwarped conditions were often the best conditions for understanding speech; however, small changes in frequency-to-place mapping (<0.77 octaves for the most basal electrode) yielded no significant degradation in performance from the nearest unwarped condition. A second experiment measured the effect of feedback training for both the unwarped and warped conditions. Improvements were found for the unwarped and frequency-expanded conditions, but not for the compressed condition. These results have implications for new CI processing strategies, such as the inclusion of spectral localization cues.
doi:10.1121/1.2831738
PMCID: PMC3061454  PMID: 18397034
13.  EFFECTS OF LOW-FREQUENCY ULTRASOUND ON MICROCIRCULATION IN VENOUS LEG ULCERS 
Indian Journal of Dermatology  2011;56(2):174-179.
Background:
Therapeutic low-frequency ultrasound (US) has been used for many years to improve wound healing in chronic wounds like venous leg ulcers. No human data are available for the possible effects of single US applications on microcirculation and their frequency-dependency.
Aims:
To investigated the role of therapeutic low-frequency US on microcirculation of venous leg ulcers in vivo.
Patients and Methods:
This is a pilot study on an inpatient basis. We use a newly developed low-frequency continuous-wave US-equipment composed of a US transducer based on piezo-fiber composites that allow the change of frequency. In this study, we apply US of 34 kHz, 53.5 kHz, and 75 kHz respectively. Twelve patients with chronic venous leg ulcers are analyzed. As an adjunct to good ulcer care, therapeutic US is applied, non-contacting, once a day, in a subaqual position for 10 minutes. Microcirculation is assessed in the ulcers adjacent to skin before US-therapy, immediately after the treatment and 30 minutes later. We use a micro-light guide spectrophotometer (O2C, LEA Medizintechnik GmbH, Gieίen, Germany) for calculation of blood flow velocity, hemoglobin oxygen saturation (SCO2) and relative hemoglobin concentration (rHb) in 2 and 8 mm depth. Contact-free remission spectroscopy (SkinREM3, Color Control Chemnitz GmbH, Chemnitz, Germany) allows contact free measurements in the VIS-NIR range of the spectrum (400 ± 1600 nm).
Results:
It is seen that therapeutic US is well tolerated. One patient dropped out from a treatment series since he developed erysipelas responding to standard antibiotic. Effects were seen at 34 kHz only. The SO2 values increased after single US application. The values for rHb were higher in the superficial layer of the wound bed (depth 2 mm) compared to deeper parts (8 mm depth). US treatment did not result in significant changes of rHb and blood cell velocity. The data obtained by remission spectroscopy disclose an increase of oxygenized hemoglobin.
Conclusions:
The major findings are that continuous-wave low-frequency US of 34 kHz, but not, 53.5 kHz or 75 kHz, has a temporary stimulatory effect on microcirculation mainly due to an improved oxygenation. Further studies with treatment series are necessary.
doi:10.4103/0019-5154.80412
PMCID: PMC3108517  PMID: 21716543
Venous leg ulcers; microcirculation; low-frequency ultrasound; spectroscopy; hemoglobin; oxygen
14.  Chemical genetics approach to restoring p27Kip1 reveals novel compounds with antiproliferative activity in prostate cancer cells 
BMC Biology  2010;8:153.
Background
The cyclin-dependent kinase (CDK) inhibitor p27Kip1 is downregulated in a majority of human cancers due to ectopic proteolysis by the ubiquitin-proteasome pathway. The expression of p27 is subject to multiple mechanisms of control involving several transcription factors, kinase pathways and at least three different ubiquitin ligases (SCFSKP2, KPC, Pirh2), which regulate p27 transcription, translation, protein stability and subcellular localization. Using a chemical genetics approach, we have asked whether this control network can be modulated by small molecules such that p27 protein expression is restored in cancer cells.
Results
We developed a cell-based assay for measuring the levels of endogenous nuclear p27 in a high throughput screening format employing LNCaP prostate cancer cells engineered to overexpress SKP2. The assay platform was optimized to Z' factors of 0.48 - 0.6 and piloted by screening a total of 7368 chemical compounds. During the course of this work, we discovered two small molecules of previously unknown biological activity, SMIP001 and SMIP004, which increase the nuclear level of p27 at low micromolar concentrations. SMIPs (small molecule inhibitors of p27 depletion) also upregulate p21Cip1, inhibit cellular CDK2 activity, induce G1 delay, inhibit colony formation in soft agar and exhibit preferential cytotoxicity in LNCaP cells relative to normal human fibroblasts. Unlike SMIP001, SMIP004 was found to downregulate SKP2 and to stabilize p27, although neither SMIP is a proteasome inhibitor. Whereas the screening endpoint - nuclear p27 - was robustly modulated by the compounds, SMIP-mediated cell cycle arrest and apoptosis were not strictly dependent on p27 and p21 - a finding that is explained by parallel inhibitory effects of SMIPs on positive cell cycle regulators, including cyclins E and A, and CDK4.
Conclusions
Our data provide proof-of-principle that the screening platform we developed, using endogenous nuclear p27 as an endpoint, presents an effective means of identifying bioactive molecules with cancer selective antiproliferative activity. This approach, when applied to larger and more diverse sets of compounds with refined drug-like properties, bears the potential of revealing both unknown cellular pathways globally impinging on p27 and novel leads for chemotherapeutics targeting a prominent molecular defect of human cancers.
doi:10.1186/1741-7007-8-153
PMCID: PMC3025922  PMID: 21182779
15.  Current-level discrimination and spectral profile analysis in multi-channel electrical stimulation 
In experiment 1, six cochlear-implant (CI) listeners discriminated a stimulation pattern eliciting equal loudness for each electrode from a stimulation pattern in which the stimulation at one or more electrodes was increased (peak) or decreased (notch). Three cochlear locations and three bandwidths were tested, without and with level roving. Listeners could always detect peaks but not always notches. Increasing the bandwidth beyond two electrodes produced no improvement in just-noticeable differences (JNDs). JNDs for the basal location were higher than for the apical and middle locations, although listeners had highly individual tendencies. In experiment 2, listeners discriminated changes in the peak heights and notch depths. JNDs for higher peaks were better while JNDs for deeper notches were worse than for experiment 1. In experiment 3, listeners discriminated the electrode position of peaks or notches. JNDs were approximately one electrode. In experiment 4, the first three experiments were repeated with large amounts of level roving. There was no evidence that CI listeners performed an across-channel comparison in these tasks.
doi:10.1121/1.2981638
PMCID: PMC3004436  PMID: 19045799
16.  The eIF3 interactome reveals the translasome, a supercomplex linking protein synthesis and degradation machineries 
Molecular cell  2009;36(1):141-152.
Summary
eIF3 promotes translation initiation, but relatively little is known about its full range of activities in the cell. Here, we employed affinity purification and highly sensitive LC-MS/MS to decipher the fission yeast eIF3 interactome, which was found to contain 230 proteins. eIF3 assembles into a large supercomplex, the translasome, which contains elongation factors, tRNA-synthetases, 40S and 60S ribosomal proteins, chaperones, and the proteasome. eIF3 also associates with ribosome biogenesis factors and the importins-β Kap123p and Sal3p. Our genetic data indicated that the binding to both importins-β is essential for cell growth, and photobleaching experiments revealed a critical role for Sal3p in the nuclear import of one of the translasome constituents, the proteasome. Our data reveal the breadth of the eIF3 interactome and suggest that factors involved in translation initiation, ribosome biogenesis, translation elongation, quality control, and transport are physically linked to facilitate efficient protein synthesis.
doi:10.1016/j.molcel.2009.09.026
PMCID: PMC2789680  PMID: 19818717
17.  F-Box-directed CRL complex assembly and regulation by the CSN and CAND1 
Molecular cell  2009;35(5):586-597.
Summary
The COP9 signalosome (CSN) is thought to maintain the stability of cullin-RING ubiquitin ligases (CRL) by limiting the autocatalytic destruction of substrate adapters such as F-box proteins (FBPs). CAND1, a protein associated with unneddylated CUL1, was proposed to assist in this role in an as yet unclear fashion. We found that only a subset of S. pombe FBPs, which feature a critical F-box proline that promotes their interaction with CUL1, required CSN for stability. Unlike the CRL3 adapter Btb3p, none of the CSN-sensitive FBPs were affected by deletion of ubp12. Contrary to current models, CAND1 does not control adapter stability, but maintains the cellular balance of CRL1 complexes by preventing rare FBPs from being out-competed for binding to CUL1 by more ample adapters. These findings were integrated into a refined model of CRL control where substrate availability toggles CRLs between independent CSN and CAND1 cycles.
doi:10.1016/j.molcel.2009.07.024
PMCID: PMC2779159  PMID: 19748355
18.  Comprehensive proteomic analysis of Schizosaccharomyces pombe by two-dimensional HPLC-tandem mass spectrometry 
Methods (San Diego, Calif.)  2009;48(3):311-319.
We describe a detailed and widely applicable method for comprehensive proteomic profiling of the fission yeast Schizosaccharomyces pombe by 2-dimensional high performance liquid chromatography-electrospray ionization-tandem mass spectrometry that demonstrates high sensitivity and robust operation. Steps ranging from the preparation of total proteins, digestion of proteins to peptides, and separation of peptides by two-dimensional (1. strong cation exchange and 2. reversed-phase) high performance liquid chromatography followed by tandem mass spectrometry and data processing have been optimized for our instrumentation platform. Using this technology, we identify ca. 3400 proteins per sample and have identified an estimated 4600 proteins in vegetative cells (equal to ca. 90 % of the predicted S. pombe proteome) at a false discovery rate of ≤ 0.02. Considering the fact that ~500 genes are strongly induced during sexual differentiation, and sexual differentiation was not included in our experiments, the proteomic profiling technique affords what should be virtually complete coverage of the vegetative S. pombe proteome. In addition, these methods are widely applicable, having been used for proteomic profiling of several other organisms.
doi:10.1016/j.ymeth.2009.02.023
PMCID: PMC2710416  PMID: 19272449
Multidimensional liquid chromatography; tandem mass spectrometry; proteomic profiling; Schizosaccharomyces pombe; spectrum counting
19.  Structure of the Heme Biosynthetic Pseudomonas aeruginosa Porphobilinogen Synthase in Complex with the Antibiotic Alaremycin▿  
The recently discovered antibacterial compound alaremycin, produced by Streptomyces sp. A012304, structurally closely resembles 5-aminolevulinic acid, the substrate of porphobilinogen synthase. During the initial steps of heme biosynthesis, two molecules of 5-aminolevulinic acid are asymmetrically condensed to porphobilinogen. Alaremycin was found to efficiently inhibit the growth of both Gram-negative and Gram-positive bacteria. Using the newly created heme-permeable strain Escherichia coli CSA1, we are able to uncouple heme biosynthesis from bacterial growth and demonstrate that alaremycin targets the heme biosynthetic pathway. Further studies focused on the activity of alaremycin against the opportunistic pathogenic bacterium Pseudomonas aeruginosa. The MIC of alaremycin was determined to be 12 mM. Alaremycin was identified as a direct inhibitor of recombinant purified P. aeruginosa porphobilinogen synthase and had a Ki of 1.33 mM. To understand the molecular basis of alaremycin's antibiotic activity at the atomic level, the P. aeruginosa porphobilinogen synthase was cocrystallized with the alaremycin. At 1.75-Å resolution, the crystal structure reveals that the antibiotic efficiently blocks the active site of porphobilinogen synthase. The antibiotic binds as a reduced derivative of 5-acetamido-4-oxo-5-hexenoic acid. The corresponding methyl group is, however, not coordinated by any amino acid residues of the active site, excluding its functional relevance for alaremycin inhibition. Alaremycin is covalently bound by the catalytically important active-site lysine residue 260 and is tightly coordinated by several active-site amino acids. Our data provide a solid structural basis to further improve the activity of alaremycin for rational drug design. Potential approaches are discussed.
doi:10.1128/AAC.00553-09
PMCID: PMC2798535  PMID: 19822707
20.  Recessive multiple epiphyseal dysplasia (rMED) with homozygosity for C653S mutation in the DTDST gene - Phenotype, molecular diagnosis and surgical treatment of habitual dislocation of multilayered patella: Case report 
Background
Multiple epiphyseal dysplasia (MED) is one of the more common generalised skeletal dysplasias. Due to its clinical heterogeneity diagnosis may be difficult. Mutations of at least six separate genes can cause MED. Joint deformities, joint pain and gait disorders are common symptoms.
Case Presentation
We report on a 27-year-old male patient suffering from clinical symptoms of autosomal recessive MED with habitual dislocation of a multilayered patella on both sides, on the surgical treatment and on short-term clinical outcome. Clinical findings were: bilateral hip and knee pain, instability of femorotibial and patellofemoral joints with habitual patella dislocation on both sides, contractures of hip, elbow and second metacarpophalangeal joints. Main radiographic findings were: bilateral dislocated multilayered patella, dysplastic medial tibial plateaus, deformity of both femoral heads and osteoarthritis of the hip joints, and deformity of both radial heads. In the molecular genetic analysis, the DTDST mutation g.1984T > A (p.C653S) was found at the homozygote state. Carrier status was confirmed in the DNA of the patient's parents. The mutation could be considered to be the reason for the patient's disease. Surgical treatment of habitual patella dislocation with medialisation of the tibial tuberosity led to an excellent clinical outcome.
Conclusions
The knowledge of different phenotypes of skeletal dysplasias helps to select genes for genetic analysis. Compared to other DTDST mutations, this is a rather mild phenotype. Molecular diagnosis is important for genetic counselling and for an accurate prognosis. Even in case of a multilayered patella in MED, habitual patella dislocation could be managed successfully by medialisation of the tibial tuberosity.
doi:10.1186/1471-2474-11-110
PMCID: PMC2902411  PMID: 20525296
21.  MIPAS-Family—evaluation of a new multi-modal behavioral training program for pediatric headaches: clinical effects and the impact on quality of life 
The Journal of Headache and Pain  2010;11(3):215-225.
Several meta-analyses have demonstrated that the combination of electrical muscle activity and Temperature Biofeedback could be regarded as gold standard in chronic pediatric headaches. However, these techniques seem to be uneconomical and furthermore they are not directed to improve the social competence as well as resolve possible impairments in daily activities of the child. Therefore, multi-modal behavioral techniques have been proposed, but no studies comparing these with the gold standard were conducted. The present study compared the impact of a new multi-modal behavioral education and training program—MIPAS-Family—with a combined Biofeedback treatment, evaluating clinical efficacy as well as the effect on the quality of life (QoL) of children with chronic headaches. Thirty-four children and adolescents with recurrent headache, ranging from 7 to 16 years, were randomly assigned to the MIPAS-Family (N = 19) or the Biofeedback (N = 15) condition. All patients were diagnosed by the criteria of the International Headache Society. The children and their parents completed headache diaries, diaries of daily living activities and a QoL questionnaire (KINDL®). Both groups showed significant improvements concerning the headache intensity and headache duration. We found no significant differences in the main headache parameters between both treatments. After the treatments, the children were less disturbed by their headaches in the domains school, homework, and leisure time. In conclusion, MIPAS-Family is as effective as Biofeedback but it is more cost-effective and addresses the whole family and the daily activities.
doi:10.1007/s10194-010-0192-5
PMCID: PMC3451914  PMID: 20376520
Pediatric headaches; Biofeedback; MIPAS-Family Program; Education; Behavioral medicine
22.  Developmental changes of the contingent negative variation in migraine and healthy children 
The Journal of Headache and Pain  2009;11(2):105-113.
It has been hypothesized that abnormalities of information processing in migraine may be attributed to impairment of cerebral maturation. However, the most evidences for this hypothesis have come from cross-sectional studies during childhood. We performed a longitudinal study and recorded contingent negative variation (CNV), an event-related slow cortical potential, in migraine children (n = 27) and age-matched healthy individuals (n = 23) in 1998 and 8 years later (2006). Amplitudes of all CNV components were reduced and habituation of the initial CNV (iCNV) increased in the observed time. However, the reduction of the iCNV amplitude was more pronounced in migraine patients who were in remission in 2006 and in healthy subjects and less pronounced in migraineurs with persisting headaches. Patients with the worsened migraine demonstrated the most pronounced loss of iCNV habituation in 1998 and significantly increased iCNV amplitudes in 2006. This longitudinal study supports the hypothesis of impaired cerebral maturation in migraine and shows that migraine manifestation is a key factor interfering with the natural maturation process of central information processing.
doi:10.1007/s10194-009-0180-9
PMCID: PMC3452294  PMID: 20013021
Migraine; Contingent negative variation; Habituation; Maturation
24.  An integrated MR/PET system: prospective applications 
Abdominal Imaging  2008;34(6):668-674.
Radiology is strongly depending on medical imaging technology and consequently directing technological progress. A novel technology can only be established, however, if improved diagnostic accuracy influence on therapeutic management and/or overall reduced cost can be evidenced. It has been demonstrated recently that Magnetic Resonance Imaging (MRI) and Positron Emission Tomography (PET) can technologically be integrated into one single hybrid system. Some scientific arguments on the benefits are obvious, e.g., that simultaneous imaging of morphological and functional information will improve tissue characterization. However, crossfire of questions still remains: What unmet radiological needs are addressed by the novel system? What level of hardware integration is reasonable, or would software-based image co-registration be sufficient? Will MR/PET achieve higher diagnostic accuracy compared to separate imaging? What is the added value compared to other hybrid imaging modalities like PET/CT? And finally, is the system economically reasonable and has the potential to reduce overall costs for therapy planning and monitoring? This article tries to highlight some perspectives of applying an integrated MR/PET system for simultaneous morphologic and functional imaging.
doi:10.1007/s00261-008-9450-2
PMCID: PMC2774419  PMID: 18773235
Magnetic resonance imaging; MRI; Positron emission tomography; PET; MR-PET; Hybrid imaging
25.  [11C]-l-Methionine positron emission tomography in the management of children and young adults with brain tumors 
Journal of Neuro-Oncology  2009;96(2):231-239.
Only a few Methyl-[11C]-l-methionine (MET) positron emission tomography (PET) studies have focused on children and young adults with brain neoplasm. Due to radiation exposure, long scan acquisition time, and the need for sedation in young children MET-PET studies should be restricted to this group of patients when a decision for further therapy is not possible from routine diagnostic procedures alone, e.g., structural imaging. We investigated the diagnostic accuracy of MET-PET for the differentiation between tumorous and non-tumorous lesions in this group of patients. Forty eight MET-PET scans from 39 patients aged from 2 to 21 years (mean 15 ± 5.0 years) were analyzed. The MET tumor-uptake relative to a corresponding control region was calculated. A receiver operating characteristic (ROC) was performed to determine the MET-uptake value that best distinguishes tumorous from non-tumorous brain lesions. A differentiation between tumorous (n = 39) and non-tumorous brain lesions (n = 9) was possible at a threshold of 1.48 of relative MET-uptake with a sensitivity of 83% and a specificity of 92%, respectively. A differentiation between high grade malignant lesions (mean MET-uptake = 2.00 ± 0.46) and low grade tumors (mean MET-uptake = 1.84 ± 0.31) was not possible. There was a significant difference in MET-uptake between the histologically homogeneous subgroups of astrocytoma WHO grade II and anaplastic astrocytoma WHO grade III (P = 0.02). MET-PET might be a useful tool to differentiate tumorous from non-tumorous lesions in children and young adults when a decision for further therapy is difficult or impossible from routine structural imaging procedures alone.
doi:10.1007/s11060-009-9953-x
PMCID: PMC2808525  PMID: 19575148
Brain tumor; Children; PET; Methionine; Molecular imaging

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