Functional characterization of ATP-dependent chromatin remodelers of the CHD family of Drosophila

Members of the CHD family (Chromodomain-Helicase-DNA binding) of ATP-dependent chromatin remodelers play key roles at different steps of the transcription cycle. They are essential in regulation of developmental and differentiation programs in multicellular organisms. However, the complexity of these remodelers makes it difficult to study them in higher eukaryotes. In this study, advantage was taken of Drosophila melanogaster as a model organism, which possesses only four CHD family members. In the first part of this study, a novel chromatin remodeler, dCHD3, has been characterized biochemically and functionally. dCHD3 is highly similar to dMi-2 and consequently it possesses similar enzymatic activities in vitro. dCHD3 is a highly active, nucleosome stimulated ATP-dependent chromatin remodeler which slides mononucleosomes in vitro. The chromodomains of dCHD3 seem to be important for substrate recognition and for the remodeling activity of this enzyme. Despite the similarities, dCHD3 and dMi-2 differ significantly in other aspects. In contrast to dMi-2, dCHD3 exists as a monomer in vivo and it is not associated with deacetylase activity. Moreover, dCHD3 expression is restricted to early developmental stages and certain tissues. Finally, dCHD3 cannot compensate for the loss of dMi-2 which suggests that they are not functionally redundant. In the second part of this work, a role of dMi-2 in active transcription has been studied. dMi-2 has been implicated in transcriptional repression as a part of dNuRD or dMec complexes. This study shows that dMi-2 colocalizes with active regions on polytene chromosomes and it is recruited to heat shock genes. Both, reduction of dMi-2 expression in flies or ectopic expression of a catalytically inactive mutant, impair heat shock gene response. Interestingly, 3’ end processing and splicing of some of these genes is affected. In agreement with this, dMi-2 binds to nascent hsp gene transcripts upon heat shock induction. Consequently, these results suggest a role of dMi-2 catalytic activity in co-transcriptional RNA processing. Study of the recruitment mechanism of dMi-2 to heat shock genes suggests that it occurs in a poly(ADP-ribose) dependent manner. Several results support this hypothesis. First, dMi-2 recruitment to hsp70 gene is reduced upon PARP inhibition. Second, dMi-2 binds PAR polymers directly in vitro and several dMi-2 regions, which bind PAR independently in vitro, have been identified. Third, a dMi-2 mutant unable to bind PAR does not localise to active heat shock loci in vivo. Moreover, RNA and PAR compete for dMi-2 binding in vitro suggesting a two-step process for dMi-2 association with active heat shock genes. First, dMi-2 is recruited to the locus via PAR binding followed by association with nascent RNA transcripts. Collectively, these studies suggest, that stress-induced chromatin modification by PARP serves as a scaffold for rapid recruitment of factors that are required for quick and efficient transcriptional response

Extensions in Joint Modeling of Survival and Longitudinal Outcomes

__abstract__ In many medical studies both longitudinal and event history data are collected for each patient. A well-known and broadly studied example is found in AIDS research, where CD4 cell counts taken at different time points are related to the time-to-death. Often such outcomes are separately analyzed. However, in two particular settings a joint modeling approach is required. First, when focus is on the event times and we wish to study the association between the longitudinal responses and the risk for an event, where we need to take into account the fact that the longitudinal response is also an outcome generated by the same subject. Second, when focus is on the longitudinal outcome and events cause dropout. Under specific circumstances the dropout process needs to be accounted in the analysis in order to obtain valid inferences for the longitudinal outcome

Figures, Grounds and Containers. Patient Presentation in Medical Case Reports

This paper studies patient presentation in medical case reports with regard to the concept of space. It examines how the choice of specific linguistic means in the description of diagnosis and treatment can contribute to different modes of patient imaging varying in their spatial configurations. To this end, a corpus of fifty-six medical case reports has been compiled and then analysed at three stages. Firstly, accounts of the diagnosis and treatment of various patients have been investigated to determine whether the vocabulary as well as the grammatical and rhetorical structures employed exemplify general cognitive patterns. Secondly, the results have been interpreted with respect to chosen concepts from the sociology of medicine to explain certain ways of referring to the patients. Thirdly, the results have been considered in relation to the context of the production of medical case reports, as scientific discourses are shaped by the disciplines in which they are used. The analysis of the texts in question reveals that the patients tend to be textually backgrounded, while disease and medical procedures are foregrounded. As a result, there is a tendency to portray the patients in abstraction from their bodies and their mental/bodily reactions

Changes in the content of edible and non-edible components and distribution of tissue components in cockerels and capons

The aim of this study was to determine the effects of castration and age on the content of edible and non-edible components, and the distribution of tissue components in the carcasses of cockerels and capons. The study was conducted on 200 birds (Green-legged Partridge), divided into two sex categories (with 5 replications per group and 20 birds per replication), raised to 28 wk of age. At 8 wk of age, 100 birds were surgically castrated and afterwards at 12 wk of age and at four-wk intervals, 10 intact cockerels and 10 capons were selected randomly and slaughtered. Cockerels, compared with capons, were characterized by a higher proportion of edible components at 24 and 28 wk of age, and a more desirable carcass tissue composition due to a higher content of lean meat in total body weight (BW). Capons had higher abdominal fat content than cockerels, which resulted in a higher percentage of non-edible components in their BW at 24 and 28 wk of age. Differences in the distribution of lean meat in the carcass were noted from 20 wk of age in both castrated and intact birds. The content of breast muscles increased in capons, and the content of leg muscles (thigh and drumstick) increased in cockerels. The results of this study indicate that in view of the optimal lean meat content of the carcass and the optimal distribution of major tissue components, Green-legged Partridge capons should be fattened for a maximum period of 24 wk

Dynamic Predictions with Time-Dependent Covariates in Survival Analysis using Joint Modeling and Landmarking

A key question in clinical practice is accurate prediction of patient prognosis. To this end, nowadays, physicians have at their disposal a variety of tests and biomarkers to aid them in optimizing medical care. These tests are often performed on a regular basis in order to closely follow the progression of the disease. In this setting it is of medical interest to optimally utilize the recorded information and provide medically-relevant summary measures, such as survival probabilities, that will aid in decision making. In this work we present and compare two statistical techniques that provide dynamically-updated estimates of survival probabilities, namely landmark analysis and joint models for longitudinal and time-to-event data. Special attention is given to the functional form linking the longitudinal and event time processes, and to measures of discrimination and calibration in the context of dynamic prediction.Comment: 34 pages, 4 figures. arXiv admin note: substantial text overlap with arXiv:1303.279

Risk preference and indirect utility in portfolio choice problems

Digitised version produced by the EUI Library and made available online in 2020

Recruitment of the ATP-dependent chromatin remodeler dMi-2 to the transcribed region of active heat shock genes

The ATP-dependent chromatin remodeler dMi-2 can play both positive and negative roles in gene transcription. Recently, we have shown that dMi-2 is recruited to the hsp70 gene in a heat shock-dependent manner, and is required to achieve high transcript levels. Here, we use chromatin immunoprecipitation sequencing (ChIP-Seq) to identify other chromatin regions displaying increased dMi-2 binding upon heat shock and to characterize the distribution of dMi-2 over heat shock genes. We show that dMi-2 is recruited to the body of at least seven heat shock genes. Interestingly, dMi-2 binding extends several hundred base pairs beyond the polyadenylation site into the region where transcriptional termination occurs. We find that dMi-2 does not associate with the entire nucleosome-depleted hsp70 locus 87A. Rather, dMi-2 binding is restricted to transcribed regions. Our results suggest that dMi-2 distribution over active heat shock genes are determined by transcriptional activity

New treatment strategies for bipolar disorder in the elderly

Introduction and objective: The purpose of this paper is to systematically review articles and new research in the context of bipolar geriatric patients. Materials and methods: PubMed searches were completed using the key terms bipolar disorder, bipolar elderly, bipolar depression, bipolar elderly treatment and review articles. In addition, references in these resources were searched. Search dates: 2010 to 2022. Description of the state of knowledge: Mental disorders in the context of the elderly concern all depressive disorders. A problem with other disorders such as bipolar disorder is also increasingly recognized. In the elderly, it is quite rare in the general cross-section of society, but it may have a higher percentage, e.g. in nursing homes and care institutions. This review article shows both the difference and the similarities in the course of this disease in older and younger patients. The most important and common aspect for both age groups is psychotherapy with parallel pharmacological treatment. The greatest difficulty in pharmacotherapy in the elderly is polypharmacy and numerous drug interactions, as well as different pharmacodynamics and pharmacokinetics of the drugs used compared to younger patients. Attention should also be paid to the differentiation of bipolar disorder from different types of dementia and other cognitive disorders. Therefore, one should strive to carefully assess the patient's need for a given treatment, establish appropriate periodic monitoring of treatment, and assess the risk of taking or not intervening. This article also aims to review new research and drugs that seem promising, while the individualized and interdisciplinary approach to a geriatric patient with BD is the most important finding of this review. Summary: Bipolar disorder in older people, compared to the younger population, should be treated pharmacologically in combination with psychotherapy. The elderly patient population requires a multidisciplinary approach due to the number of drugs used in a large number of diseases

Multiple Aspects of ATP-Dependent Nucleosome Translocation by RSC and Mi-2 Are Directed by the Underlying DNA Sequence

Contains fulltext : 129351.pdf (publisher's version ) (Open Access)Background Chromosome structure, DNA metabolic processes and cell type identity can all be affected by changing the positions of nucleosomes along chromosomal DNA, a reaction that is catalysed by SNF2-type ATP-driven chromatin remodelers. Recently it was suggested that in vivo, more than 50% of the nucleosome positions can be predicted simply by DNA sequence, especially within promoter regions. This seemingly contrasts with remodeler induced nucleosome mobility. The ability of remodeling enzymes to mobilise nucleosomes over short DNA distances is well documented. However, the nucleosome translocation processivity along DNA remains elusive. Furthermore, it is unknown what determines the initial direction of movement and how new nucleosome positions are adopted. Methodology/Principal Findings We have used AFM imaging and high resolution PAGE of mononucleosomes on 600 and 2500 bp DNA molecules to analyze ATP-dependent nucleosome repositioning by native and recombinant SNF2-type enzymes. We report that the underlying DNA sequence can control the initial direction of translocation, translocation distance, as well as the new positions adopted by nucleosomes upon enzymatic mobilization. Within a strong nucleosomal positioning sequence both recombinant Drosophila Mi-2 (CHD-type) and native RSC from yeast (SWI/SNF-type) repositioned the nucleosome at 10 bp intervals, which are intrinsic to the positioning sequence. Furthermore, RSC-catalyzed nucleosome translocation was noticeably more efficient when beyond the influence of this sequence. Interestingly, under limiting ATP conditions RSC preferred to position the nucleosome with 20 bp intervals within the positioning sequence, suggesting that native RSC preferentially translocates nucleosomes with 15 to 25 bp DNA steps. Conclusions/Significance Nucleosome repositioning thus appears to be influenced by both remodeler intrinsic and DNA sequence specific properties that interplay to define ATPase-catalyzed repositioning. Here we propose a successive three-step framework consisting of initiation, translocation and release steps to describe SNF2-type enzyme mediated nucleosome translocation along DNA. This conceptual framework helps resolve the apparent paradox between the high abundance of ATP-dependent remodelers per nucleus and the relative success of sequence-based predictions of nucleosome positioning in vivo