43 research outputs found

    The TFIIH components p44/p62 act as a damage sensor during nucleotide excision repair

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    Nucleotide excision repair (NER) protects the genome following exposure to diverse types of DNA damage, including UV light and chemotherapeutics. Mutations in human NER genes lead to diseases such as xeroderma pigmentosum and Cockayne syndrome. In eukaryotes, the major transcription factor TFIIH is the central hub of NER. The core components of TFIIH include the helicases XPB, XPD, and the five core structural subunits. Two of these core-TFIIH proteins, p44 and p62 remain relatively unstudied; although p44 is known to regulate the helicase activity of XPD during NER. p62's role is thought to be structural; however, a recent cryo-EM structure shows p44, p62, and XPD making contacts with each other, implying a more extensive role in DNA repair beyond the structural integrity of TFIIH. Here, we show that p44 stimulates XPD's ATPase, but upon encountering DNA damage further stimulation is only observed when p62 is in the ternary complex. More significantly, we show that the p44/p62 complex binds DNA independently of XPD and diffuses along its backbone, indicating a novel DNA-binding entity in TFIIH. These data support a role for p44/p62 in TFIIH's mechanism of damage detection. This revises our understanding of TFIIH and prompts more extensive investigation of all of the core subunits, for an active role during both DNA repair and transcription

    OmoMYC blunts promoter invasion by oncogenic MYC to inhibit gene expression characteristic of MYC-dependent tumors.

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    MYC genes have both essential roles during normal development and exert oncogenic functions during tumorigenesis. Expression of a dominant-negative allele of MYC, termed OmoMYC, can induce rapid tumor regression in mouse models with little toxicity for normal tissues. How OmoMYC discriminates between physiological and oncogenic functions of MYC is unclear. We have solved the crystal structure of OmoMYC and show that it forms a stable homodimer and as such recognizes DNA in the same manner as the MYC/MAX heterodimer. OmoMYC attenuates both MYC-dependent activation and repression by competing with MYC/MAX for binding to chromatin, effectively lowering MYC/MAX occupancy at its cognate binding sites. OmoMYC causes the largest decreases in promoter occupancy and changes in expression on genes that are invaded by oncogenic MYC levels. A signature of OmoMYC-regulated genes defines subgroups with high MYC levels in multiple tumor entities and identifies novel targets for the eradication of MYC-driven tumors

    Recent advances in quantitative LA-ICP-MS analysis: challenges and solutions in the life sciences and environmental chemistry

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    Erfassung des Ernährungszustandes von Patienten mit Tumoren des Aerodigestivtraktes

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    How to limit the speed of a motor the intricate regulation of the XPB ATPase and translocase in TFIIH

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    The superfamily 2 helicase XPB is an integral part of the general transcription factor TFIIH and assumes essential catalytic functions in transcription initiation and nucleotide excision repair. The ATPase activity of XPB is required in both processes. We investigated the interaction network that regulates XPB via the p52 and p8 subunits with functional mutagenesis based on our crystal structure of the p52 p8 complex and current cryo EM structures. Importantly, we show that XPB s ATPase can be activated either by DNA or by the interaction with the p52 p8 proteins. Intriguingly, we observe that the ATPase activation by p52 p8 is significantly weaker than the activation by DNA and when both p52 p8 and DNA are present, p52 p8 dominates the maximum activation. We therefore define p52 p8 as the master regulator of XPB acting as an activator and speed limiter at the same time. A correlative analysis of the ATPase and translocase activities of XPB shows that XPB only acts as a translocase within the context of complete core TFIIH and that XPA increases the processivity of the translocase complex without altering XPB s ATPase activity. Our data define an intricate network that tightly controls the activity of XPB during transcription and nucleotide excision repai

    Intravenous immunoglobulin in secondary progressive multiple sclerosis: randomised placebo-controlled trial

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    Background Several double-blind placebo-controlled trials of relapsing-remitting multiple sclerosis have shown beneficial effects of intravenous immunoglobulin (IVIG) on relapse rate and disability. The European Study on Intravenous Immunoglobulin in Multiple Sclerosis set out to test IVIG in the secondary progressive phase of the disease. Methods 318 patients with clinically definite secondary progressive multiple sclerosis (mean age 44 years [SD 7]) were randomly assigned IVIG 1 g/kg per month (n = 159) or an equivalent volume of placebo (albumin 0.1%; n = 159) for 27 months. After baseline investigation, clinical assessments were made every 3 months and MRI was repeated after 12 months and 24 months. The primary outcome was confirmed worsening of disability as defined by the time to first confirmed progression on the expanded disability status scale (EDSS). Analyses were by intention to treat. Findings 19 patients in the IVIG group and 39 in the placebo group terminated study treatment prematurely but were included in the analyses. IVIG treatment had no beneficial effect on time to confirmed EDSS progression (hazard ratio 1.11 [95% CI 0.80-1.53] for IVIG versus placebo). The annual relapse rate was 0.46 in both groups. No significant differences between the treatment groups were found in any of the other clinical outcome measures or in the change of T2-lesion load over time. The treatment was generally well tolerated, although deep venous thrombosis, pulmonary embolism, or both occurred in seven patients with risk factors for thromboembolism (IVIG six, placebo one). Interpretation Treatment with IVIG in this study did not show any clinical benefit and therefore cannot be recommended for patients with secondary progressive multiple sclerosis

    LipidMatch: an automated workflow for rule-based lipid identification using untargeted high-resolution tandem mass spectrometry data

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    Abstract Background Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. Results We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows. LipidMatch currently has over 250,000 lipid species spanning 56 lipid types contained in in silico fragmentation libraries. Unique fragmentation libraries, compared to other open source software, include oxidized lipids, bile acids, sphingosines, and previously uncharacterized adducts, including ammoniated cardiolipins. LipidMatch uses rule-based identification. For each lipid type, the user can select which fragments must be observed for identification. Rule-based identification allows for correct annotation of lipids based on the fragments observed, unlike typical identification based solely on spectral similarity scores, where over-reporting structural details that are not conferred by fragmentation data is common. Another unique feature of LipidMatch is ranking lipid identifications for a given feature by the sum of fragment intensities. For each lipid candidate, the intensities of experimental fragments with exact mass matches to expected in silico fragments are summed. The lipid identifications with the greatest summed intensity using this ranking algorithm were comparable to other lipid identification software annotations, MS-DIAL and Greazy. For example, for features with identifications from all 3 software, 92% of LipidMatch identifications by fatty acyl constituents were corroborated by at least one other software in positive mode and 98% in negative ion mode. Conclusions LipidMatch allows users to annotate lipids across a wide range of high resolution tandem mass spectrometry experiments, including imaging experiments, direct infusion experiments, and experiments employing liquid chromatography. LipidMatch leverages the most extensive in silico fragmentation libraries of freely available software. When integrated into a larger lipidomics workflow, LipidMatch may increase the probability of finding lipid-based biomarkers and determining etiology of disease by covering a greater portion of the lipidome and using annotation which does not over-report biologically relevant structural details of identified lipid molecules

    Conserved salt bridge competition triggered by

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    Significance Phosphorylation is a ubiquitous modification that has been implicated in signaling and other functions, but the atomic-level mechanisms are not completely understood. We identify a salt-bridge competition or “theft” mechanism wherein a phosphoserine, but not a phosphomimetic, breaks a pre-existing salt bridge, initiating a partial unfolding event and promoting new protein interactions. Structural elements underlying the theft occurred early in evolution and are found in 10% of homo-oligomers and 30% of hetero-oligomers. These findings identify a facile and evolutionarily accessible mechanism for reorganizing salt bridges and other electrostatic networks with only a single mutation to trigger a functional switch.</jats:p

    Age of onset of recurrent respiratory papillomatosis:a distribution analysis

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    ObjectiveDistribution of age of onset of recurrent respiratory papillomatosis (RRP) is generally described to be bimodal, with peaks at approximately 5 years and 30 years. This assumption has never been scientifically confirmed, and authors tend to refer to an article that does not describe distribution. Knowledge of the distribution of age of onset is important for virological and epidemiological comprehension. The objective of this study was to determine the distribution of age of onset of RRP in a large international sample. DesignCross-sectional distribution analysis. ParticipantsLaryngologists from 12 European hospitals provided information on date of birth and date of onset of all their RRP patients treated between 1998 and 2012. Centers that exclusively treated either patients with juvenile onset RRP or patients with adult onset RRP, or were less accessible for one of these groups, were excluded to prevent skewness. Main outcome measuresA mixture model was implemented to describe distribution of age of onset. The best fitting model was selected using the Bayesian information criterion. ResultsSix hundred and thirty-nine patients were included in the analysis. Age of onset was described by a three component mixture distribution with lognormally distributed components. Recurrent respiratory papillomatosis starts at three median ages 7, 35 and 64 years. ConclusionsDistribution of age of onset of RRP shows three peaks. In addition to the already adopted idea of age peaks at paediatric and adult age, there is an additional peak around the age of 6
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