Genome Binding and Gene Regulation by Stem Cell Transcription Factors

Nearly all cells of an individual organism contain the same genome. However, each cell type transcribes a different set of genes due to the presence of different sets of cell type-specific transcription factors. Such transcription factors bind to regulatory regions such as promoters and enhancers and regulate their activity in gene transcription. Transcription factors interact with each other and form tissue-specific transcription factor networks. Identification of genome binding and gene regulation by transcription factors will enhance our understanding of how transcription factors specify cell types. Chapter 1 serves as a general introduction into eukaryotic transcription regulation and describes the role of enhancers and transcription factors. Chapters 2 – 4 describe the experimental work of this thesis. Chapte

Fysieke belasting op acht melkveehouderijbedrijven : netwerkproject Noordoost Groningen

On eight dairy farms, labour demand and labour efficiency were studied. In 2004, labour demand during a year was calculated using the computer model AgroWerk. To obtain detailed input data for this model the farmers recorded labour times, and all farms were visited to collect input data concerning farm size and farm equipment together with the farmers. Additionally, in 2005 AgroWerk and the ‘Meetlat Kwaliteit van de Arbeid’ (‘Labour Quality Monitor’) were used to calculate physical load of the lower back and the upper extremities for the workers on the farms. Input data were the same as used to calculate labour demand, with additional data concerning distribution of tasks over workers. To calculate the physical load, the computer model uses basic data concerning labour conditions during many tasks that can be done according to several working methods

Early detection of neuropathy in leprosy: A comparison of five tests for field settings

Background: Early detection and treatment of neuropathy in leprosy is important to prevent disabilities. A recent study showed that the Nerve Conduction Studies (NCS) and Warm Detection Thresholds (WDT) tests can detect leprosy neuropathy the earliest. These two tests are not practical under field conditions, however, because they require climate-controlled rooms and highly trained staff and are expensive. We assessed the usefulness of alternative test methods and their sensitivity and specificity to detect neuropathy at an early stage. Methods: Through a literature search we identified five alternative devices that appeared user-friendly, more affordable, portable and/or battery-operated: the Neuropad®, Vibratip™, NC-Stat®DPNCheck™, NeuroQuick and the Thermal Sensibility Tester (TST), assessing respectively sweat function, vibration sensation, nerve conduction, cold sensation and warm sensation. In leprosy patients in Bangladesh, the posterior tibial and sural nerves that tested normal for the monofilament test and voluntary muscle test were assessed with the NCS and WDT as reference standard tests. The alternative devices were then tested on 94 nerves with abnormal WDT and/or NCS results and on 94 unaffected nerves. Sensitivity and specificity were the main outcomes. Results: The NeuroQuick and the TST showed very good sensitivity and specificity. On the sural nerve, the NeuroQuick had both a sensitivity and a specificity of 86%. The TST had a sensitivity of 83% and a specificity of 82%. Both the NC-Stat®DPNCheck™ and Vibratip™ had a high specificity (88% and 100%), but a low sensitivity (16% and 0%). On the posterior tibial nerve, the NeuroQuick and the TST also showed good sensitivity, but the sensitivity was lower than for the sural nerve. The Neuropad® had a sensitivity of 56% and a specificity of 61%. Conclusions: The NeuroQuick and TST are good candidates for further field-testing for reliability and reproducibility. The feasibility of production on a larger scale should be examined

An interaction network of mental disorder proteins in neural stem cells

Mental disorders (MDs) such as intellectual disability (ID), autism spectrum disorders (ASD) and schizophrenia have a strong genetic component. Recently, many gene mutations associated with ID, ASD or schizophrenia have been identified by high-throughput sequencing. A substantial fraction of these mutations are in genes encoding transcriptional regulators. Transcriptional regulators associated with different MDs but acting in the same gene regulatory network provide information on the molecular relation between MDs. Physical interaction between transcriptional regulators is a strong predictor for their cooperation in gene regulation. Here, we biochemically purified transcriptional regulators from neural stem cells, identified their interaction partners by mass spectrometry and assembled a protein interaction network containing 206 proteins, including 68 proteins mutated in MD patients and 52 proteins significantly lacking coding variation in humans. Our network shows molecular connections between established MD proteins and provides a discovery tool for novel MD genes. Network proteins preferentially co-localize on the genome and cooperate in disease-relevant gene regulation. Our results suggest that the observed transcriptional regulators associated with ID, ASD or schizophrenia are part of a transcriptional network in neural stem cells. We find that more severe mutations in network proteins are associated with MDs that include lower intelligence quotient (IQ), suggesting that the level of disruption of a shared transcriptional network correlates with cognitive dysfunction

Convergent Transcription of Interferon-stimulated Genes by TNF-α and IFN-α Augments Antiviral Activity against HCV and HEV

IFN-α has been used for decades to treat chronic hepatitis B and C, and as an off-label treatment for

Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

The locations of transcriptional enhancers and promoters were recently mapped in many mammalian cell types. Proteins that bind those regulatory regions can determine cell identity but have not been systematically identified. Here we purify native enhancers, promoters or heterochromatin from embryonic stem cells by chromatin immunoprecipitations (ChIP) for characteristic histone modifications and identify associated proteins using mass spectrometry (MS). 239 factors are identified and predicted to bind enhancers or promoters with different levels of activity, or heterochromatin. Published genome-wide data indicate a high accuracy of location prediction by ChIP-MS. A quarter of the identified factors are important for pluripotency and includes Oct4, Esrrb, Klf5, Mycn and Dppa2, factors that drive reprogramming to pluripotent stem cells. We determined the genome-wide binding sites of Dppa2 and find that Dppa2 operates outside the classical pluripotency network. Our ChIP-MS method provides a detailed read-out of the transcriptional landscape representative of the investigated cell type

Mediator complex interaction partners organize the transcriptional network that defines neural stem cells

The Mediator complex regulates transcription by connecting enhancers to promoters. High Mediator binding density defines super enhancers, which regulate cell-identity genes and oncogenes. Protein interactions of Mediator may explain its role in these processes but have not been identified comprehensively. Here, we purify Mediator from neural stem cells (NSCs) and identify 75 protein-protein interaction partners. We identify super enhancers in NSCs and show that Mediator-interacting chromatin modifiers colocalize with Mediator at enhancers and super enhancers. Transcription factor families with high affinity for Mediator dominate enhancers and super enhancers and can explain genome-wide Mediator localization. We identify E-box transcription factor Tcf4 as a key regulator of NSCs. Tcf4 interacts with Mediator, colocalizes with Mediator at super enhancers and regulates neurogenic transcription factor genes with super enhancers and broad H3K4me3 domains. Our data suggest that high binding-affinity for Mediator is an important organizing feature in the transcriptional network that determines NSC identity

Acht gesprekken met lectoren over kenniscreatie en kenniscirculatie: inspiratiebundel

In deze inspiratiebundel zijn onder redactie van Josephine Lappie en Jittie Brandsma acht gesprekken met lectoren over kenniscreatie en kenniscirculatie bij elkaar gebracht. Kenniscentra en kenniscirculatie vormen twee belangrijke doelstellingen van lectoraten. In de gesprekken wordt teruggeblikt op de succesfactoren waarmee lectoren kenniscreatie en kenniscirculatie tot nu toe hebben gestimuleerd. En er wordt vooruitgeblikt: Hoe kunnen kenniskringen in de gebundelde vorm als kenniscentra nog beter inspelen op de kansen die voor de Hogeschool Rotterdam voor het oprapen liggen