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Find video protocols related to scientific articles indexed in Pubmed.
Cell microenvironment: confinement and deformation of single cells and their nuclei inside size-adapted microtubes (adv. Healthcare mater. 11/2014).
Adv Healthc Mater
PUBLISHED: 11-11-2014
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Biofunctionalized glass microtube structures serve as transparent cell culture scaffolds and are fabricated to impose spatial confinement on single cells on page 1753. S. Sanchez, C. K. Schmidt, and colleagues demonstrate the influence of the resulting cell deformation on the integrity of the nucleus of human osteosarcoma cells and on cell division. Their findings underline the versatility of the rolled-up microtubes for mimicking space restrictions present in physiological tissues.
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A quantitative 14-3-3 interaction screen connects the nuclear exosome targeting complex to the DNA damage response.
Genes Dev.
PUBLISHED: 09-04-2014
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RNA metabolism is altered following DNA damage, but the underlying mechanisms are not well understood. Through a 14-3-3 interaction screen for DNA damage-induced protein interactions in human cells, we identified protein complexes connected to RNA biology. These include the nuclear exosome targeting (NEXT) complex that regulates turnover of noncoding RNAs termed promoter upstream transcripts (PROMPTs). We show that the NEXT subunit RBM7 is phosphorylated upon DNA damage by the MAPKAPK2 kinase and establish that this mediates 14-3-3 binding and decreases PROMPT binding. These findings and our observation that cells lacking RBM7 display DNA damage hypersensitivity link PROMPT turnover to the DNA damage response.
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tDCS-induced alterations in GABA concentration within primary motor cortex predict motor learning and motor memory: a 7 T magnetic resonance spectroscopy study.
Neuroimage
PUBLISHED: 05-19-2014
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Transcranial direct current stimulation (tDCS) is a non-invasive brain stimulation technique that alters cortical excitability in a polarity specific manner and has been shown to influence learning and memory. tDCS may have both on-line and after-effects on learning and memory, and the latter are thought to be based upon tDCS-induced alterations in neurochemistry and synaptic function. We used ultra-high-field (7 T) magnetic resonance spectroscopy (MRS), together with a robotic force adaptation and de-adaptation task, to investigate whether tDCS-induced alterations in GABA and Glutamate within motor cortex predict motor learning and memory. Note that adaptation to a robot-induced force field has long been considered to be a form of model-based learning that is closely associated with the computation and 'supervised' learning of internal 'forward' models within the cerebellum. Importantly, previous studies have shown that on-line tDCS to the cerebellum, but not to motor cortex, enhances model-based motor learning. Here we demonstrate that anodal tDCS delivered to the hand area of the left primary motor cortex induces a significant reduction in GABA concentration. This effect was specific to GABA, localised to the left motor cortex, and was polarity specific insofar as it was not observed following either cathodal or sham stimulation. Importantly, we show that the magnitude of tDCS-induced alterations in GABA concentration within motor cortex predicts individual differences in both motor learning and motor memory on the robotic force adaptation and de-adaptation task.
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CtIP-mediated resection is essential for viability and can operate independently of BRCA1.
J. Exp. Med.
PUBLISHED: 05-19-2014
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Homologous recombination (HR) is initiated by DNA end resection, a process in which stretches of single-strand DNA (ssDNA) are generated and used for homology search. Factors implicated in resection include nucleases MRE11, EXO1, and DNA2, which process DNA ends into 3' ssDNA overhangs; helicases such as BLM, which unwind DNA; and other proteins such as BRCA1 and CtIP whose functions remain unclear. CDK-mediated phosphorylation of CtIP on T847 is required to promote resection, whereas CDK-dependent phosphorylation of CtIP-S327 is required for interaction with BRCA1. Here, we provide evidence that CtIP functions independently of BRCA1 in promoting DSB end resection. First, using mouse models expressing S327A or T847A mutant CtIP as a sole species, and B cells deficient in CtIP, we show that loss of the CtIP-BRCA1 interaction does not detectably affect resection, maintenance of genomic stability or viability, whereas T847 is essential for these functions. Second, although loss of 53BP1 rescues the embryonic lethality and HR defects in BRCA1-deficient mice, it does not restore viability or genome integrity in CtIP(-/-) mice. Third, the increased resection afforded by loss of 53BP1 and the rescue of BRCA1-deficiency depend on CtIP but not EXO1. Finally, the sensitivity of BRCA1-deficient cells to poly ADP ribose polymerase (PARP) inhibition is partially rescued by the phospho-mimicking mutant CtIP (CtIP-T847E). Thus, in contrast to BRCA1, CtIP has indispensable roles in promoting resection and embryonic development.
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Keeping 53BP1 out of focus in mitosis.
Cell Res.
PUBLISHED: 05-09-2014
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A recent study published in Science reveals the mechanism and biological importance of DNA damage response abrogation in mitotic cells.
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Systematic characterization of deubiquitylating enzymes for roles in maintaining genome integrity.
Nat. Cell Biol.
PUBLISHED: 05-08-2014
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DNA double-strand breaks (DSBs) are perhaps the most toxic of all DNA lesions, with defects in the DNA-damage response to DSBs being associated with various human diseases. Although it is known that DSB repair pathways are tightly regulated by ubiquitylation, we do not yet have a comprehensive understanding of how deubiquitylating enzymes (DUBs) function in DSB responses. Here, by carrying out a multidimensional screening strategy for human DUBs, we identify several with hitherto unknown links to DSB repair, the G2/M DNA-damage checkpoint and genome-integrity maintenance. Phylogenetic analyses reveal functional clustering within certain DUB subgroups, suggesting evolutionally conserved functions and/or related modes of action. Furthermore, we establish that the DUB UCHL5 regulates DSB resection and repair by homologous recombination through protecting its interactor, NFRKB, from degradation. Collectively, our findings extend the list of DUBs promoting the maintenance of genome integrity, and highlight their potential as therapeutic targets for cancer.
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Chemical inhibition of NAT10 corrects defects of laminopathic cells.
Science
PUBLISHED: 05-03-2014
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Down-regulation and mutations of the nuclear-architecture proteins lamin A and C cause misshapen nuclei and altered chromatin organization associated with cancer and laminopathies, including the premature-aging disease Hutchinson-Gilford progeria syndrome (HGPS). Here, we identified the small molecule "Remodelin" that improved nuclear architecture, chromatin organization, and fitness of both human lamin A/C-depleted cells and HGPS-derived patient cells and decreased markers of DNA damage in these cells. Using a combination of chemical, cellular, and genetic approaches, we identified the acetyl-transferase protein NAT10 as the target of Remodelin that mediated nuclear shape rescue in laminopathic cells via microtubule reorganization. These findings provide insights into how NAT10 affects nuclear architecture and suggest alternative strategies for treating laminopathies and aging.
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USP28 is recruited to sites of DNA damage by the tandem BRCT domains of 53BP1 but plays a minor role in double-strand break metabolism.
Mol. Cell. Biol.
PUBLISHED: 03-31-2014
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The DNA damage response (DDR) is critical for genome stability and the suppression of a wide variety of human malignancies, including neurodevelopmental disorders, immunodeficiency, and cancer. In addition, the efficacy of many chemotherapeutic strategies is dictated by the status of the DDR. Ubiquitin-specific protease 28 (USP28) was reported to govern the stability of multiple factors that are critical for diverse aspects of the DDR. Here, we examined the effects of USP28 depletion on the DDR in cells and in vivo. We found that USP28 is recruited to double-strand breaks in a manner that requires the tandem BRCT domains of the DDR protein 53BP1. However, we observed only minor DDR defects in USP28-depleted cells, and mice lacking USP28 showed normal longevity, immunological development, and radiation responses. Our results thus indicate that USP28 is not a critical factor in double-strand break metabolism and is unlikely to be an attractive target for therapeutic intervention aimed at chemotherapy sensitization.
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Where's the silver? Imaging trace silver coverage on the surface of gold nanorods.
J. Am. Chem. Soc.
PUBLISHED: 03-27-2014
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The development of the seeded growth synthesis for gold nanorods provided the first simple, convenient wet chemistry route to these nanomaterials. Over the past decade, the original silver-assisted seeded growth procedure has been the subject of further modifications that have continuously expanded access to anisotropic gold nanoparticles; however, the role of silver in formation of gold nanorods remains poorly understood. We report the first experimental evidence on the position of silver present on gold nanorods using advanced energy dispersive X-ray spectroscopy. Our results indicate the deposition of silver ions on the surface shows no preference for a specific face or axis. Furthermore, we show that the "dog bone" structures developed from gold nanorod solutions show preferential deposition of silver atoms on the ends and in the crevices.
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Increased GABA Contributes to Enhanced Control over Motor Excitability in Tourette Syndrome.
Curr. Biol.
PUBLISHED: 03-14-2014
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Tourette syndrome (TS) is a developmental neurological disorder characterized by vocal and motor tics [1] and associated with cortical-striatal-thalamic-cortical circuit dysfunction [2, 3], hyperexcitability within cortical motor areas [4], and altered intracortical inhibition [4-7]. TS often follows a developmental time course in which tics become increasingly more controlled during adolescence in many individuals [1], who exhibit enhanced control over their volitional movements [8-11]. Importantly, control over motor outputs appears to be brought about by a reduction in the gain of motor excitability [6, 7, 12, 13]. Here we present a neurochemical basis for a localized gain control mechanism. We used ultra-high-field (7 T) magnetic resonance spectroscopy to investigate in vivo concentrations of ?-aminobutyric acid (GABA) within primary and secondary motor areas of individuals with TS. We demonstrate that GABA concentrations within the supplementary motor area (SMA)-a region strongly associated with the genesis of motor tics in TS [14]-are paradoxically elevated in individuals with TS and inversely related to fMRI blood oxygen level-dependent activation. By contrast, GABA concentrations in control sites do not differ from those of a matched control group. Importantly, we also show that GABA concentrations within the SMA are inversely correlated with cortical excitability in primary motor cortex and are predicted by motor tic severity and white-matter microstructure (FA) within a region of the corpus callosum that projects to the SMA within each hemisphere. Based upon these findings, we propose that extrasynaptic GABA contributes to a form of control, based upon localized tonic inhibition within the SMA, that may lead to the suppression of tics.
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Confinement and deformation of single cells and their nuclei inside size-adapted microtubes.
Adv Healthc Mater
PUBLISHED: 03-11-2014
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Rolled-up transparent microtubes are shown to serve as cell culture scaffolds that exactly define the space available for single cell growth. Human U2OS osteosarcoma cells are confined within microtubes of different diameters and the effects of the cell deformation on the integrity of the DNA and cell survival are studied.
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Rolled-up functionalized nanomembranes as three-dimensional cavities for single cell studies.
Nano Lett.
PUBLISHED: 03-10-2014
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We use micropatterning and strain engineering to encapsulate single living mammalian cells into transparent tubular architectures consisting of three-dimensional (3D) rolled-up nanomembranes. By using optical microscopy, we demonstrate that these structures are suitable for the scrutiny of cellular dynamics within confined 3D-microenvironments. We show that spatial confinement of mitotic mammalian cells inside tubular architectures can perturb metaphase plate formation, delay mitotic progression, and cause chromosomal instability in both a transformed and nontransformed human cell line. These findings could provide important clues into how spatial constraints dictate cellular behavior and function.
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Intentional non-adherence to medications by older adults.
Drugs Aging
PUBLISHED: 02-26-2014
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'The extent to which an individual's medication-taking behaviour and/or execution of lifestyle changes, corresponds with agreed recommendations from a healthcare provider', is a highly complex behaviour, defined as adherence. However, intentional non-adherence is regularly observed and results in negative outcomes for patients along with increased healthcare provision costs. Whilst this is a consistent issue amongst adults of all ages, the burden of chronic disease is greatest amongst older adults. As a result, the absolute prevalence of intentional non-adherence is increased in this population. This non-systematic review of intentional non-adherence to medication highlights the extent of the problem amongst older adults. It notes that age, per se, is not a contributory factor in intentionally non-adherent behaviours. Moreover, it describes the difference in methodology required to identify such behaviours in contrast to reports of non-adherence in general: the use of focus groups, semi-structured, one-to-one interviews and questionnaires as opposed to pill counts, electronic medication monitors and analysis of prescription refill rates. Using Leventhal's Common-Sense Model of Self-Regulation, it emphasizes six key factors that may contribute to intentional non-adherence amongst older adults: illness beliefs, the perceived risks (e.g. dependence, adverse effects), benefits and necessity of potential treatments, the patient-practitioner relationship, inter-current physical and mental illnesses, financial constraints and pharmaceutical/pharmacological issues (poly-pharmacy/regimen complexity). It describes the current evidence for each of these aspects and notes the paucity of data validating Leventhal's model in this regard. It also reports on interventions that may address these issues and explicitly acknowledges the lack of evidence-based interventions available to healthcare practitioners. As a result, it highlights five key areas that require urgent research amongst older adults: (1) the overlap between intentional and unintentional non-adherence, particularly amongst those who may be frail or isolated; (2) the potential correlation between symptomatic benefit and intentional vs. unintentional non-adherence to medication; (3) an evaluation of the source of prescribing (i.e. a long-standing provider vs. an acute episode of care) and the patient-prescriber relationship as determinants of intentional and unintentional non-adherence; (4) the decision-making processes leading to selective intentional non-adherence amongst older adults with multiple medical problems; and (5) the development and evaluation of interventions designed to reduce intentional non-adherence, specifically addressing each of the aspects listed above.
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Diels-Alder construction of regiodifferentiated meta-amino phenols and derivatives.
Org. Lett.
PUBLISHED: 02-13-2014
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Synthetic access to regiodifferentiated meta-amino phenols is described. The strategy relies upon distinct deprotonation conditions to afford regioisomeric thermodynamic and kinetic dienes that undergo a tandem Diels-Alder and retro-Diels-Alder sequence with assorted acetylenic dienophiles to afford a range of aromatic products.
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The role of microRNAs in the control of flowering time.
J. Exp. Bot.
PUBLISHED: 01-30-2014
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The onset of flowering in plants is regulated by complex gene networks that integrate multiple environmental and endogenous cues to ensure that flowering occurs at the appropriate time. This is achieved by precise control of the expression of key flowering genes at both the transcriptional and post-transcriptional level. In recent years, a class of small non-coding RNAs, called microRNAs (miRNAs), has been shown to regulate gene expression in a number of plant developmental processes and stress responses. MiRNA-based biotechnology, which harnesses the regulatory functions of such endogenous or artificial miRNAs, therefore represents a highly promising area of research. In this review, the process of plant miRNA biogenesis, their mode of action, and multiple regulatory functions are summarized. The roles of the miR156, miR172, miR159/319, miR390, and miR399 families in the flowering time regulatory network in Arabidopsis thaliana are discussed in depth.
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Enhanced saccadic control in young people with Tourette syndrome despite slowed pro-saccades.
J Neuropsychol
PUBLISHED: 01-24-2014
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Tourette syndrome (TS) is a neurodevelopmental disorder characterized by motor and vocal tics. Tics are repetitive and uncontrolled behaviours that have been associated with basal ganglia dysfunction. We investigated saccadic eye movements in a group of young people with TS but without co-morbid ADHD. Participants performed two tasks. One required them to perform only pro-saccade responses (pure pro-saccade task). The other involved shifting, unpredictably, between executing pro- and anti-saccades (mixed saccade task). We show that in the mixing saccade task, the TS group makes significantly fewer errors than an age-matched control group, while responding equally fast. By contrast, on the pure pro-saccade task, the TS group were shown to be significantly slower to initiate and to complete the saccades (longer movement duration and decreased peak velocity) than controls, while movement amplitude and direction accuracy were not different. These findings demonstrate enhanced shifting ability despite slower reflexive responding in TS and are discussed with respect to a disorder-related adaptation for increased cognitive regulation of behaviour.
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Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks.
Nat. Struct. Mol. Biol.
PUBLISHED: 01-17-2014
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Although both homologous recombination (HR) and nonhomologous end joining can repair DNA double-strand breaks (DSBs), the mechanisms by which one of these pathways is chosen over the other remain unclear. Here we show that transcriptionally active chromatin is preferentially repaired by HR. Using chromatin immunoprecipitation-sequencing (ChIP-seq) to analyze repair of multiple DSBs induced throughout the human genome, we identify an HR-prone subset of DSBs that recruit the HR protein RAD51, undergo resection and rely on RAD51 for efficient repair. These DSBs are located in actively transcribed genes and are targeted to HR repair via the transcription elongation-associated mark trimethylated histone H3 K36. Concordantly, depletion of SETD2, the main H3 K36 trimethyltransferase, severely impedes HR at such DSBs. Our study thereby demonstrates a primary role in DSB repair of the chromatin context in which a break occurs.
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Evidence of a putative deep sea specific microbiome in marine sponges.
PLoS ONE
PUBLISHED: 01-01-2014
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The microbiota of four individual deep water sponges, Lissodendoryx diversichela, Poecillastra compressa, Inflatella pellicula, and Stelletta normani, together with surrounding seawater were analysed by pyrosequencing of a region of the 16S rRNA gene common to Bacteria and Archaea. Due to sampling constraints at depths below 700 m duplicate samples were not collected. The microbial communities of L. diversichela, P. compressa and I. pellicula were typical of low microbial abundance (LMA) sponges while S. normani had a community more typical of high microbial abundance (HMA) sponges. Analysis of the deep sea sponge microbiota revealed that the three LMA-like sponges shared a set of abundant OTUs that were distinct from those associated with sponges from shallow waters. Comparison of the pyrosequencing data with that from shallow water sponges revealed that the microbial communities of all sponges analysed have similar archaeal populations but that the bacterial populations of the deep sea sponges were distinct. Further analysis of the common and abundant OTUs from the three LMA-like sponges placed them within the groups of ammonia oxidising Archaea (Thaumarchaeota) and sulphur oxidising ?-Proteobacteria (Chromatiales). Reads from these two groups made up over 70% of all 16S rRNA genes detected from the three LMA-like sponge samples, providing evidence of a putative common microbial assemblage associated with deep sea LMA sponges.
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Therapeutic benefit of the anesthesiologist-patient relationship.
Anesthesiology
PUBLISHED: 10-17-2013
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The Value of the Preoperative Visit by an Anesthetist: A Study of Doctor-Patient Rapport. By Egbert LD, Battit GE, Turndorf H, and Beecher HK. JAMA 1963; 119:1465-8. Reprinted with permission. Copyright © 1963 American Medical Association. All rights reserved.The psychologic effect of the preoperative visit by an anesthetist has been compared with the effect of pentobarbital for preanesthetic medication. Patients receiving pentobarbital 1 hour before an operation became drowsy but it could not be shown that they became calm. Patients who had received a visit by an anesthetist before operation (informing them about the events which were to occur on the day of operation and about the anesthetic to be administered) were not drowsy but were more likely to be calm on the day of operation. The importance of the preoperative visit probably explains, in part, the difficulties previous investigators have had in showing sedative effects from the barbiturates and narcotics before operation. The tremendous emotional significance to a patient of illness or an operation may explain why physicians are able to exert such influence upon their patients.
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Development and validation of a fall-related impulsive behaviour scale for residential care.
Age Ageing
PUBLISHED: 10-16-2013
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Introduction: impulsivity in older people with cognitive impairment has yet to be examined rigorously as a risk factor for falls. The objective of this study was to evaluate the psychometric properties of a new fall-related impulsive behaviour scale (FIBS) for a cognitively impaired population living in residential care.
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The Hypertension in the Very Elderly Trial - latest data.
Br J Clin Pharmacol
PUBLISHED: 09-21-2013
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Early trials in the field of hypertension focused on adults in their fifties and sixties. However, with the passage of time, a progressive effort has been made to expand the evidence base for treatment in older adults. 2008 saw publication of data from the Hypertension in the Very Elderly Trial which demonstrated significant mortality and morbidity benefits from antihypertensive therapy in octogenarians. More recently, additional data from this cohort has been published suggesting that appropriate anti-hypertensive therapy may lead to a reduction in incident cognitive impairment and fractures, whilst a 1 year open label extension of the main study confirmed many of the original trial findings. This review provides an overview of the Hypertension in the Very Elderly Trial whilst also discursively evaluating the latest data.
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Cognitive change in older women using a computerised battery: a longitudinal quantitative genetic twin study.
Behav. Genet.
PUBLISHED: 08-16-2013
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Cognitive performance is known to change over age 45, especially processing speed. Studies to date indicate that change in performance with ageing is largely environmentally mediated, with little contribution from genetics. We estimated the heritability of a longitudinal battery of computerised cognitive tests including speed measures, using a classical twin design. 324 (127 MZ, 197 DZ) female twins, aged 43-73 at baseline testing, were followed-up after 10 years, using seven measures of the Cambridge Automated Neuropsychological Test battery, four of which were measures of response latency (speed). Results were analysed using univariate and bivariate structural equation modelling. Heritability of longitudinal change was found in 5 of the 7 tests, ranging from 21 to 41%. The genetic aetiology was remarkably stable. The first principle component of change was strongly associated with age (p < 0.001) and heritable at 47% (27-62%). While estimates for heritability increased in all measures over time compared to baseline, these increases were statistically non-significant. This computerised battery showed significant heritability of age-related change in cognition. Focus on this form of change may aid the search for genetic pathways involved in normal and pre-morbid cognitive ageing.
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Risk: benefit of treating high blood pressure in older adults.
Br J Clin Pharmacol
PUBLISHED: 08-06-2013
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Older people (those aged 65 years or over) comprise over 15% of the UKs population and this cohort is growing. Whilst at greatest risk from systemic arterial hypertension (hypertension), its resultant end organ damage and clinically significant cardiovascular disease, this group was initially neglected in clinical trials and thereby denied treatment, with the lack of evidence cited as justification. However since the 1960s, when the first landmark trials in severe diastolic hypertension were published, there has been a progressive attempt to understand the pathophysiology of hypertension and to expand the evidence base for treatment in older adults. In contrast to the participants of the very first randomized trials who had a mean age of 51 years, the recent Hypertension in the Very Elderly Trial demonstrated significant mortality and morbidity benefits from the treatment of both mixed systolic and diastolic hypertension, as well as isolated systolic hypertension in octogenarians. This review highlights the progressive evidence base behind the relative risks and benefits of treating hypertension in older adults.
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A new method for high-resolution imaging of Ku foci to decipher mechanisms of DNA double-strand break repair.
J. Cell Biol.
PUBLISHED: 07-29-2013
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DNA double-strand breaks (DSBs) are the most toxic of all genomic insults, and pathways dealing with their signaling and repair are crucial to prevent cancer and for immune system development. Despite intense investigations, our knowledge of these pathways has been technically limited by our inability to detect the main repair factors at DSBs in cells. In this paper, we present an original method that involves a combination of ribonuclease- and detergent-based preextraction with high-resolution microscopy. This method allows direct visualization of previously hidden repair complexes, including the main DSB sensor Ku, at virtually any type of DSB, including those induced by anticancer agents. We demonstrate its broad range of applications by coupling it to laser microirradiation, super-resolution microscopy, and single-molecule counting to investigate the spatial organization and composition of repair factories. Furthermore, we use our method to monitor DNA repair and identify mechanisms of repair pathway choice, and we show its utility in defining cellular sensitivities and resistance mechanisms to anticancer agents.
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Motor excitability during movement preparation in Tourette syndrome.
J Neuropsychol
PUBLISHED: 07-11-2013
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Tourette syndrome (TS) is a neurodevelopmental disorder characterized by the occurrence of motor and vocal tics. TS has been linked to the impaired operation of cortical-striatal-thalamic-cortical circuits that give rise to hyper-excitability of cortical motor areas, which may be exacerbated by dysfunctional intra-cortical inhibitory mechanisms. That said, many individuals gain control over their tics during adolescence and it has been suggested that this increased control arises as a result of the development of mechanisms that operate to suppress corticospinal excitability (CSE) ahead of volitional movements. Here we used single-pulse transcranial magnetic stimulation (TMS) in conjunction with a manual Go/NoGo task to investigate alterations in CSE ahead of volitional movements in a group of adolescents with TS (N = 10). Our study demonstrated that CSE, as measured by TMS-induced motor-evoked potentials (MEPs), was significantly reduced in the TS group in the period immediately preceding a finger movement. More specifically, we show that individuals with TS, unlike their age-matched controls, do not exhibit the predicted increase in mean MEP amplitude and decrease in MEP variability that immediately precede the execution of volitional movements in typically developing young adults. Finally, we report that the magnitude of the rise in MEP amplitude across the movement preparation period in TS is significantly negatively correlated with clinical measures of motor tic severity, suggesting that individuals with severe motor tics are least able to modulate motor cortical excitability.
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Deubiquitylating enzymes and DNA damage response pathways.
Cell Biochem. Biophys.
PUBLISHED: 05-29-2013
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Covalent post-translational modification of proteins by ubiquitin and ubiquitin-like factors has emerged as a general mechanism to regulate myriad intra-cellular processes. The addition and removal of ubiquitin or ubiquitin-like proteins from factors has recently been demonstrated as a key mechanism to modulate DNA damage response (DDR) pathways. It is thus, timely to evaluate the potential for ubiquitin pathway enzymes as DDR drug targets for therapeutic intervention. The synthetic lethal approach provides exciting opportunities for the development of targeted therapies to treat cancer: most tumours have lost critical DDR pathways, and thus rely more heavily on the remaining pathways, while normal tissues are still equipped with all DDR pathways. Here, we review key deubiquitylating enzymes (DUBs) involved in DDR pathways, and describe how targeting DUBs may lead to selective therapies to treat cancer patients.
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Space can substitute for time in predicting climate-change effects on biodiversity.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 05-20-2013
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"Space-for-time" substitution is widely used in biodiversity modeling to infer past or future trajectories of ecological systems from contemporary spatial patterns. However, the foundational assumption--that drivers of spatial gradients of species composition also drive temporal changes in diversity--rarely is tested. Here, we empirically test the space-for-time assumption by constructing orthogonal datasets of compositional turnover of plant taxa and climatic dissimilarity through time and across space from Late Quaternary pollen records in eastern North America, then modeling climate-driven compositional turnover. Predictions relying on space-for-time substitution were ?72% as accurate as "time-for-time" predictions. However, space-for-time substitution performed poorly during the Holocene when temporal variation in climate was small relative to spatial variation and required subsampling to match the extent of spatial and temporal climatic gradients. Despite this caution, our results generally support the judicious use of space-for-time substitution in modeling community responses to climate change.
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On your mark, get SET(D2), go! H3K36me3 primes DNA mismatch repair.
Cell
PUBLISHED: 04-30-2013
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Trimethylation of histone H3 on Lys36 (H3K36me3) by SETD2 is linked to actively transcribed regions. Li et al. identify a novel role for H3K36me3 that facilitates DNA mismatch repair (MMR) in cells by targeting the MMR machinery to chromatin during the cell cycle, thereby explaining certain cases of MMR-defective cancers.
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KAT5 tyrosine phosphorylation couples chromatin sensing to ATM signalling.
Nature
PUBLISHED: 04-18-2013
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The detection of DNA lesions within chromatin represents a critical step in cellular responses to DNA damage. However, the regulatory mechanisms that couple chromatin sensing to DNA-damage signalling in mammalian cells are not well understood. Here we show that tyrosine phosphorylation of the protein acetyltransferase KAT5 (also known as TIP60) increases after DNA damage in a manner that promotes KAT5 binding to the histone mark H3K9me3. This triggers KAT5-mediated acetylation of the ATM kinase, promoting DNA-damage-checkpoint activation and cell survival. We also establish that chromatin alterations can themselves enhance KAT5 tyrosine phosphorylation and ATM-dependent signalling, and identify the proto-oncogene c-Abl as a mediator of this modification. These findings define KAT5 tyrosine phosphorylation as a key event in the sensing of genomic and chromatin perturbations, and highlight a key role for c-Abl in such processes.
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Gene expression analyses support fallopian tube epithelium as the cell of origin of epithelial ovarian cancer.
Int J Mol Sci
PUBLISHED: 04-09-2013
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Folate receptor alpha (FOLR1/FRA) is reported to be overexpressed in epithelial ovarian cancers (EOC), especially the serous histotype. Further, while dysregulation of the folate-dependent 1-carbon cycle has been implicated in tumorogenesis, little is known relative to the potential mechanism of action of FOLR1 expression in these processes. We therefore investigated the expression of FOLR1, other folate receptors, and genes within the 1-carbon cycle in samples of EOC, normal ovary and fallopian tube on a custom TaqMan Low Density Array. Also included on this array were known markers of EOC such as MSLN, MUC16 and HE4. While few differences were observed in the expression profiles of genes in the 1-carbon cycle, genes previously considered to be overexpressed in EOC (e.g., FOLR1, MSLN, MUC16 and HE4) showed significantly increased expression when comparing EOC to normal ovary. However, when the comparator was changed to normal fallopian tube, these differences were abolished, supporting the hypothesis that EOC derives from fallopian fimbriae and, further, that markers previously considered to be upregulated or overexpressed in EOC are most likely not of ovarian origin, but fallopian in derivation. Our findings therefore support the hypothesis that the cell of origin of EOC is tubal epithelium.
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Dma/RNF8 proteins are evolutionarily conserved E3 ubiquitin ligases that target septins.
Cell Cycle
PUBLISHED: 02-26-2013
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The budding yeast proteins Dma1 and Dma2 are members of the unique FHA-RING domain protein family and are linked to mitotic regulation and septin organization by ill-defined mechanisms. We show that Dma2 has ubiquitin ligase activity, and that septins Shs1 and Cdc11 are likely direct in vivo targets. We further propose that human RNF8, rather than Chfr, is the mammalian Dma homolog. As in yeast, RNF8 localizes to the centrosomes and cell division sites and promotes ubiquitylation of the septin SEPT7, whose depletion increases cell division anomalies. Together, these findings reveal evolutionary and functional conservation of Dma proteins, and suggest that RNF8 maintains genome stability through independent, yet analogous, nuclear and cytoplasmic ubiquitylation activities.
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Regulation of DNA damage responses by ubiquitin and SUMO.
Mol. Cell
PUBLISHED: 02-14-2013
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Ubiquitylation and sumoylation, the covalent attachment of the polypeptides ubiquitin and SUMO, respectively, to target proteins, are pervasive mechanisms for controlling cellular functions. Here, we summarize the key steps and enzymes involved in ubiquitin and SUMO conjugation and provide an overview of how they are crucial for maintaining genome stability. Specifically, we review research that has revealed how ubiquitylation and sumoylation regulate and coordinate various pathways of DNA damage recognition, signaling, and repair at the biochemical, cellular, and whole-organism levels. In addition to providing key insights into the control and importance of DNA repair and associated processes, such work has established paradigms for regulatory control that are likely to extend to other cellular processes and that may provide opportunities for better understanding and treatment of human disease.
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Inserting needles into the body: a meta-analysis of brain activity associated with acupuncture needle stimulation.
J Pain
PUBLISHED: 02-05-2013
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Acupuncture is a therapeutic treatment that is defined as the insertion of needles into the body at specific points (ie, acupoints). Advances in functional neuroimaging have made it possible to study brain responses to acupuncture; however, previous studies have mainly concentrated on acupoint specificity. We wanted to focus on the functional brain responses that occur because of needle insertion into the body. An activation likelihood estimation meta-analysis was carried out to investigate common characteristics of brain responses to acupuncture needle stimulation compared to tactile stimulation. A total of 28 functional magnetic resonance imaging studies, which consisted of 51 acupuncture and 10 tactile stimulation experiments, were selected for the meta-analysis. Following acupuncture needle stimulation, activation in the sensorimotor cortical network, including the insula, thalamus, anterior cingulate cortex, and primary and secondary somatosensory cortices, and deactivation in the limbic-paralimbic neocortical network, including the medial prefrontal cortex, caudate, amygdala, posterior cingulate cortex, and parahippocampus, were detected and assessed. Following control tactile stimulation, weaker patterns of brain responses were detected in areas similar to those stated above. The activation and deactivation patterns following acupuncture stimulation suggest that the hemodynamic responses in the brain simultaneously reflect the sensory, cognitive, and affective dimensions of pain.
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ATM-dependent phosphorylation of heterogeneous nuclear ribonucleoprotein K promotes p53 transcriptional activation in response to DNA damage.
Cell Cycle
PUBLISHED: 01-23-2013
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Previous work has established that heterogeneous nuclear ribonucleoprotein K (hnRNP K) is stabilized in an ATM-dependent manner in response to DNA damage and acts as a cofactor for p53-mediated transcription. Here, we show that in response to DNA damage caused by ionizing radiation, hnRNP K is phosphorylated in an ATM-dependent manner. Furthermore, our data indicate that ATM-dependent hnRNP K phosphorylation is required for its stabilization and its function as a p53 transcriptional cofactor in response to DNA damage. These findings thereby establish hnRNP K as an ATM target and help define how ATM orchestrates p53-dependent transcriptional responses in response to genotoxic stress.
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Exaggerated object affordance and absent automatic inhibition in alien hand syndrome.
Cortex
PUBLISHED: 01-11-2013
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Patients with alien hand syndrome (AHS) experience making apparently deliberate and purposeful movements with their hand against their will. However, the mechanisms contributing to these involuntary actions remain poorly understood. Here, we describe two experimental investigations in a patient with corticobasal syndrome (CBS) with alien hand behaviour in her right hand. First, we show that responses with the alien hand are made significantly more quickly to images of objects which afford an action with that hand compared to objects which afford an action with the unaffected hand. This finding suggests that involuntary grasping behaviours in AHS might be due to exaggerated, automatic motor activation evoked by objects which afford actions with that limb. Second, using a backwards masked priming task, we found normal automatic inhibition of primed responses in the patients unaffected hand, but importantly there was no evidence of such suppression in the alien limb. Taken together, these findings suggest that grasping behaviours in AHS may result from exaggerated object affordance effects, which might potentially arise from disrupted inhibition of automatically evoked responses.
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Archaea Appear to Dominate the Microbiome of Inflatella pellicula Deep Sea Sponges.
PLoS ONE
PUBLISHED: 01-01-2013
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Microbes associated with marine sponges play significant roles in host physiology. Remarkable levels of microbial diversity have been observed in sponges worldwide through both culture-dependent and culture-independent studies. Most studies have focused on the structure of the bacterial communities in sponges and have involved sponges sampled from shallow waters. Here, we used pyrosequencing of 16S rRNA genes to compare the bacterial and archaeal communities associated with two individuals of the marine sponge Inflatella pellicula from the deep-sea, sampled from a depth of 2,900 m, a depth which far exceeds any previous sequence-based report of sponge-associated microbial communities. Sponge-microbial communities were also compared to the microbial community in the surrounding seawater. Sponge-associated microbial communities were dominated by archaeal sequencing reads with a single archaeal OTU, comprising ?60% and ?72% of sequences, being observed from Inflatella pellicula. Archaeal sequencing reads were less abundant in seawater (?11% of sequences). Sponge-associated microbial communities were less diverse and less even than any other sponge-microbial community investigated to date with just 210 and 273 OTUs (97% sequence identity) identified in sponges, with 4 and 6 dominant OTUs comprising ?88% and ?89% of sequences, respectively. Members of the candidate phyla, SAR406, NC10 and ZB3 are reported here from sponges for the first time, increasing the number of bacterial phyla or candidate divisions associated with sponges to 43. A minor cohort from both sponge samples (?0.2% and ?0.3% of sequences) were not classified to phylum level. A single OTU, common to both sponge individuals, dominates these unclassified reads and shares sequence homology with a sponge associated clone which itself has no known close relative and may represent a novel taxon.
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Under-representation of older adults in pharmacokinetic and pharmacodynamic studies: a solvable problem?
Expert Rev Clin Pharmacol
PUBLISHED: 01-01-2013
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The impact of advancing age, with or without the presence of structural and/or functional organ impairment, on the disposition and effects of drugs, demands adequate representation of older adults in pharmacokinetic and pharmacodynamic studies. Currently, however, this group remains poorly represented both in pre- and post-marketing studies. This review discusses recent data on the participation of older adults in pharmacokinetic/pharmacodynamic studies using established databases, the potential barriers to study recruitment and retention and possible strategies to enhance participation in this group. The article also provides a critical appraisal of current regulatory documents on the conduct of such studies.
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Neural correlates of changing intention in the human FEF and IPS.
J. Neurophysiol.
PUBLISHED: 11-23-2011
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Previous research demonstrates that our apparent mental flexibility depends largely on the strength of our prior intention; changing our intention in advance enables a smooth transition from one task to another (e.g., Astle DE, Jackson GM, Swainson R. J Cogn Neurosci 20: 255-267, 2008; Duncan J, Emslie H, Williams P, Johnson R, Freer C. Cogn Psychol 30: 257-303, 1996; Husain M, Parton A, Hodgson TL, Mort D, Rees G. Nat Neurosci 6: 117-118, 2003). However, these necessarily rapid anticipatory mechanisms have been difficult to study in the human brain. We used EEG and magnetoencephalography, specifically event-related potentials and fields (ERPs and ERFs), respectively, to explore the neural correlates of this important aspect of mental flexibility. Subjects performed a manual version of a pro/antisaccade task using preparatory cues to switch between the pro- and antirules. When subjects switched their intention, we observed a positivity over central electrodes, which correlated significantly with our behavioral data; the greater the ERP effect, the stronger the subjects change of intention. ERFs, alongside subject-specific structural MRIs, were used to project into source space. When subjects switched their intention, they showed significantly elevated activity in the right frontal eye field and left intraparietal sulcus (IPS); the greater the left IPS activity on switch trials, the stronger the subjects change of intention. This network has previously been implicated in the top-down control of eye movements, but here we demonstrate its role in the top-down control of a task set, in particular, that it is recruited when we change the task that we intend to perform.
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Design, synthesis, and characterization of nucleic-acid-functionalized gold surfaces for biomarker detection.
Langmuir
PUBLISHED: 09-28-2011
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Nucleic-acid-functionalized gold surfaces have been used extensively for the development of biological sensors. The development of an effective biomarker detection assay requires careful design, synthesis, and characterization of probe components. In this Feature Article, we describe fundamental probe development constraints and provide a critical appraisal of the current methodologies and applications in the field. We discuss critical issues and obstacles that impede the sensitivity and reliability of the sensors to underscore the challenges that must be met to advance the field of biomarker detection.
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Improving recruitment of older people to research through good practice.
Age Ageing
PUBLISHED: 09-11-2011
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There is widespread evidence both of the exclusion of older people from clinical research, and of under-recruitment to clinical trials. This review and opinion piece provides practical advice to assist researchers both to adopt realistic, achievable recruitment rates and to increase the number of older people taking part in research. It analyses 14 consecutive recently published trials, providing the number needed to be screened to recruit one older participant (around 3:1), numbers excluded (up to 49%), drop out rates (5-37%) and whether the planned power was achieved. The value of planning and logistics are outlined, and approaches to optimising recruitment in hospital, primary care and care home settings are discussed, together with the challenges of involving older adults with mental incapacity and those from minority groups in research. The increasingly important task of engaging older members of the public and older patients in research is also discussed. Increasing the participation of older people in research will improve the generalisability of research findings and inform best practice in the clinical management of the growing older population.
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Resolving confusions about urges and intentions.
Cogn Neurosci
PUBLISHED: 09-01-2011
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In our article we considered the nature and the functional anatomy of "urges-for-action," both in the context of everyday behaviors such as yawning, swallowing, and micturition, and in relation to clinical disorders in which the urge-for-action is considered pathological (e.g., Tourette syndrome), and we argued for a key role for the insular and cingulate cortices in experiencing the urge-for-action. Here we seek to address some of the key points raised within several of the interesting commentaries on, and challenges to, our paper.
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Cognitive neuroscience of bodily representations: Psychological processes and neural mechanisms.
Cogn Neurosci
PUBLISHED: 09-01-2011
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The past decade has seen increasing interest within the cognitive neuroscience community in understanding the psychological processes involved in representing the body, and in learning how these processes may be implemented within the brain. This special issue of Cognitive Neuroscience presents six new empirical papers that contribute to this rapidly developing literature, together with two theoretical discussion papers that are accompanied by peer commentaries.
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CtIP Mutations Cause Seckel and Jawad Syndromes.
PLoS Genet.
PUBLISHED: 07-30-2011
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Seckel syndrome is a recessively inherited dwarfism disorder characterized by microcephaly and a unique head profile. Genetically, it constitutes a heterogeneous condition, with several loci mapped (SCKL1-5) but only three disease genes identified: the ATR, CENPJ, and CEP152 genes that control cellular responses to DNA damage. We previously mapped a Seckel syndrome locus to chromosome 18p11.31-q11.2 (SCKL2). Here, we report two mutations in the CtIP (RBBP8) gene within this locus that result in expression of C-terminally truncated forms of CtIP. We propose that these mutations are the molecular cause of the disease observed in the previously described SCKL2 family and in an additional unrelated family diagnosed with a similar form of congenital microcephaly termed Jawad syndrome. While an exonic frameshift mutation was found in the Jawad family, the SCKL2 family carries a splicing mutation that yields a dominant-negative form of CtIP. Further characterization of cell lines derived from the SCKL2 family revealed defective DNA damage induced formation of single-stranded DNA, a critical co-factor for ATR activation. Accordingly, SCKL2 cells present a lowered apoptopic threshold and hypersensitivity to DNA damage. Notably, over-expression of a comparable truncated CtIP variant in non-Seckel cells recapitulates SCKL2 cellular phenotypes in a dose-dependent manner. This work thus identifies CtIP as a disease gene for Seckel and Jawad syndromes and defines a new type of genetic disease mechanism in which a dominant negative mutation yields a recessively inherited disorder.
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On the functional anatomy of the urge-for-action.
Cogn Neurosci
PUBLISHED: 07-27-2011
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Several common neuropsychiatric disorders (e.g., obsessive-compulsive disorder, Tourette syndrome (TS), autistic spectrum disorder) are associated with unpleasant bodily sensations that are perceived as an urge for action. Similarly, many of our everyday behaviors are also characterized by bodily sensations that we experience as urges for action. Where do these urges originate? In this paper, we consider the nature and the functional anatomy of "urges-for-action," both in the context of everyday behaviors such as yawning, swallowing, and micturition, and in relation to clinical disorders in which the urge-for-action is considered pathological and substantially interferes with activities of daily living (e.g., TS). We review previous frameworks for thinking about behavioral urges and demonstrate that there is considerable overlap between the functional anatomy of urges associated with everyday behaviors such as swallowing, yawning, and micturition, and those urges associated with the generation of tics in TS. Specifically, we show that the limbic sensory and motor regions-insula and mid-cingulate cortex-are common to all of these behaviors, and we argue that this "motivation-for-action" network should be considered distinct from an "intentional action" network, associated with regions of premotor and parietal cortex, which may be responsible for the perception of "willed intention" during the execution of goal-directed actions.
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Biological applications of gold nanorods.
Wiley Interdiscip Rev Nanomed Nanobiotechnol
PUBLISHED: 07-16-2011
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Gold nanoparticles have been used as an additive for aesthetic purposes for centuries. However, only in the last decade scientists have begun to understand the fundamental concepts that explain the fascinating optical properties nanoscale particles possess. Gold nanoparticles may be tuned to absorb and scatter light in the visible to near-infrared region of the electromagnetic spectrum. These properties result from the collective oscillations of electrons along the metal surface and can be altered by changing the particles shape, size, or environment. Gold nanoparticles having a rod-like morphology are of particular interest because of their anisotropic shape. The absorption profile of gold nanorods includes two absorption bands: one due to light absorbed along the short axis (transverse) and the other due to absorption along the long axis (longitudinal). As the rod length increases, so does the longitudinal band red shift together with an increase in the extinction coefficient. As a result of this optical control and sensitivity to changes in local environment, gold nanorods are useful materials for sensing, photothermal therapy, and imaging. This article highlights established and emerging applications of gold nanorods as a platform for viable biological tools.
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Paleoecoinformatics: applying geohistorical data to ecological questions.
Trends Ecol. Evol. (Amst.)
PUBLISHED: 07-08-2011
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Paleoecoinformatics, the development and use of paleoecological databases and tools, has a strong tradition of community support, and is rapidly growing as new tools bring new opportunities to advance understanding of ecological and evolutionary dynamics, from regional to global scales, and across the entire history of life on earth. Paleoecoinformatics occupies the intersection of ecoinformatics and geoinformatics. All face shared challenges, including developing frameworks to store heterogeneous and dynamic datasets, facilitating data contributions, linking heterogeneous data, and tracking improvements in data quality and scientific understanding. The three communities will benefit from increased engagement and exchange.
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Mobile FT mRNA contributes to the systemic florigen signalling in floral induction.
Sci Rep
PUBLISHED: 07-04-2011
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In inducing photoperiodic conditions, plants produce a signal dubbed "florigen" in leaves. Florigen moves through the phloem to the shoot apical meristem (SAM) where it induces flowering. In Arabidopsis, the FLOWERING LOCUS T (FT) protein acts as a component of this phloem-mobile signal. However whether the transportable FT mRNA also contributes to systemic florigen signalling remains to be elucidated. Using non-conventional approaches that exploit virus-induced RNA silencing and meristem exclusion of virus infection, we demonstrated that the ArabidopsisFT mRNA, independent of the FT protein, can move into the SAM. Viral ectopic expression of a non-translatable FT mRNA promoted earlier flowering in the short-day (SD) Nicotiana tabacum Maryland Mammoth tobacco in SD. These data suggest a possible role for FT mRNA in systemic floral signalling, and also demonstrate that cis-transportation of cellular mRNA into SAM and meristem exclusion of pathogenic RNAs are two mechanistically distinct processes.
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A phospho-proteomic screen identifies substrates of the checkpoint kinase Chk1.
Genome Biol.
PUBLISHED: 06-21-2011
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The cell-cycle checkpoint kinase Chk1 is essential in mammalian cells due to its roles in controlling processes such as DNA replication, mitosis and DNA-damage responses. Despite its paramount importance, how Chk1 controls these functions remains unclear, mainly because very few Chk1 substrates have hitherto been identified.
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Structure-specific DNA endonuclease Mus81/Eme1 generates DNA damage caused by Chk1 inactivation.
PLoS ONE
PUBLISHED: 05-13-2011
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The DNA-damage checkpoint kinase Chk1 is essential in higher eukaryotes due to its role in maintaining genome stability in proliferating cells. CHK1 gene deletion is embryonically lethal, and Chk1 inhibition in replicating cells causes cell-cycle defects that eventually lead to perturbed replication and replication-fork collapse, thus generating endogenous DNA damage. What is the cause of replication-fork collapse when Chk1 is inactivated, however, remains poorly understood. Here, we show that generation of DNA double-strand breaks at replication forks when Chk1 activity is compromised relies on the DNA endonuclease complex Mus81/Eme1. Importantly, we show that Mus81/Eme1-dependent DNA damage--rather than a global increase in replication-fork stalling--is the cause of incomplete replication in Chk1-deficient cells. Consequently, Mus81/Eme1 depletion alleviates the S-phase progression defects associated with Chk1 deficiency, thereby increasing cell survival. Chk1-mediated protection of replication forks from Mus81/Eme1 even under otherwise unchallenged conditions is therefore vital to prevent uncontrolled fork collapse and ensure proper S-phase progression in human cells.
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Regulation of Rad51 function by phosphorylation.
EMBO Rep.
PUBLISHED: 05-07-2011
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Rad51 is a key enzyme involved in DNA double-strand break repair by homologous recombination. Here, we show that in response to DNA damage, budding yeast Rad51 is phosphorylated on Ser 192 in a manner that is primarily mediated by the DNA-damage-responsive protein kinase Mec1. We show that mutating Rad51 Ser 192 to Ala or Glu confers hypersensitivity to DNA damage and homologous-recombination defects. Furthermore, biochemical analyses indicate that Ser 192 is required for Rad51 adenosine triphosphate hydrolysis and DNA-binding activity in vitro, whereas mutation of Ser 192 does not interfere with Rad51 multimer formation. These data suggest a model in which Mec1-mediated phosphorylation of Rad51 Ser 192 in response to DNA damage controls Rad51 activity and DNA repair by homologous recombination.
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Give me a break, but not in mitosis: the mitotic DNA damage response marks DNA double-strand breaks with early signaling events.
Cell Cycle
PUBLISHED: 04-15-2011
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: DNA double-strand breaks (DSBs) are extremely cytotoxic with a single unrepaired DSB being sufficient to induce cell death. A complex signalling cascade, termed the DNA damage response (DDR), is in place to deal with such DNA lesions and maintain genome stability. Recent work by us and others has found that the signalling cascade activated by DSBs in mitosis is truncated, displaying apical, but not downstream, components of the DDR. The E3 Ubiquitin ligases RNF8, RNF168 and BRCA1, along with the DDR mediator 53BP1, are not recruited to DSB sites in mitosis, and activation of downstream checkpoint kinases is also impaired. Here, we show that RNF8 and RNF168 are recruited to DNA damage foci in late mitosis, presumably to prime sites for 53BP1 recruitment in early G1. Interestingly, we show that, although RNF8, RNF168 and 53BP1 are excluded from DSB sites during most of mitosis, they associate with mitotic structures such as the kinetochore, suggesting roles for these DDR factors during mitotic cell division. We discuss these and other recent findings and suggest how these novel data collectively contribute to our understanding of mitosis and how cells deal with DNA damage during this crucial cell cycle stage.
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Beyond predictions: biodiversity conservation in a changing climate.
Science
PUBLISHED: 04-02-2011
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Climate change is predicted to become a major threat to biodiversity in the 21st century, but accurate predictions and effective solutions have proved difficult to formulate. Alarming predictions have come from a rather narrow methodological base, but a new, integrated science of climate-change biodiversity assessment is emerging, based on multiple sources and approaches. Drawing on evidence from paleoecological observations, recent phenological and microevolutionary responses, experiments, and computational models, we review the insights that different approaches bring to anticipating and managing the biodiversity consequences of climate change, including the extent of species natural resilience. We introduce a framework that uses information from different sources to identify vulnerability and to support the design of conservation responses. Although much of the information reviewed is on species, our framework and conclusions are also applicable to ecosystems, habitats, ecological communities, and genetic diversity, whether terrestrial, marine, or fresh water.
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High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.
Plant Cell
PUBLISHED: 03-29-2011
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Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a high-resolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence.
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Replication stress induces 53BP1-containing OPT domains in G1 cells.
J. Cell Biol.
PUBLISHED: 03-28-2011
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Chromosomal deletions and rearrangements in tumors are often associated with common fragile sites, which are specific genomic loci prone to gaps and breaks in metaphase chromosomes. Common fragile sites appear to arise through incomplete DNA replication because they are induced after partial replication inhibition by agents such as aphidicolin. Here, we show that in G1 cells, large nuclear bodies arise that contain p53 binding protein 1 (53BP1), phosphorylated H2AX (?H2AX), and mediator of DNA damage checkpoint 1 (MDC1), as well as components of previously characterized OPT (Oct-1, PTF, transcription) domains. Notably, we find that incubating cells with low aphidicolin doses increases the incidence and number of 53BP1-OPT domains in G1 cells, and by chromatin immunoprecipitation and massively parallel sequencing analysis of ?H2AX, we demonstrate that OPT domains are enriched at common fragile sites. These findings invoke a model wherein incomplete DNA synthesis during S phase leads to a DNA damage response and formation of 53BP1-OPT domains in the subsequent G1.
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Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications.
Genes Dev.
PUBLISHED: 03-03-2011
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Genome integrity is constantly monitored by sophisticated cellular networks, collectively termed the DNA damage response (DDR). A common feature of DDR proteins is their mobilization in response to genotoxic stress. Here, we outline how the development of various complementary methodologies has provided valuable insights into the spatiotemporal dynamics of DDR protein assembly/disassembly at sites of DNA strand breaks in eukaryotic cells. Considerable advances have also been made in understanding the underlying molecular mechanisms for these events, with post-translational modifications of DDR factors being shown to play prominent roles in controlling the formation of foci in response to DNA-damaging agents. We review these regulatory mechanisms and discuss their biological significance to the DDR.
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Modulation of somatosensory perception by motor intention.
Cogn Neurosci
PUBLISHED: 03-01-2011
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The intention to execute a movement can modulate our perception of sensory events; however, theoretical accounts of these effects, and also empirical data, are often contradictory. We investigated how perception of a somatosensory stimulus differed according to whether it was delivered to a limb being prepared for movement or to a nonmoving limb. Our results demonstrate that individuals perceive a somatosensory stimulus delivered to the "moving" limb as occurring significantly later than when an identical stimulus is delivered to a "nonmoving" limb. Furthermore, human brain imaging (fMRI) analyses demonstrate that this modulation is accompanied by a significant decrease in BOLD signal in the right parietal operculum (SII) for stimuli delivered to the moving limb. These results indicate that during movement preparation a network of premotor brain areas may facilitate movement execution by attenuating the processing of behaviorally irrelevant signals within higher-order secondary somatosensory (SII) areas.
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Ancient DNA from lake sediments: bridging the gap between paleoecology and genetics.
BMC Evol. Biol.
PUBLISHED: 01-27-2011
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Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes.
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Compensatory neural reorganization in Tourette syndrome.
Curr. Biol.
PUBLISHED: 01-17-2011
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Children with neurological disorders may follow unique developmental trajectories whereby they undergo compensatory neuroplastic changes in brain structure and function that help them gain control over their symptoms. We used behavioral and brain imaging techniques to investigate this conjecture in children with Tourette syndrome (TS). Using a behavioral task that induces high levels of intermanual conflict, we show that individuals with TS exhibit enhanced control of motor output. Then, using structural (diffusion-weighted imaging) brain imaging techniques, we demonstrate widespread differences in the white matter (WM) microstructure of the TS brain that include alterations in the corpus callosum and forceps minor (FM) WM that significantly predict tic severity in TS. Most importantly, we show that task performance for the TS group (but not for controls) is strongly predicted by the WM microstructure of the FM pathways that lead to the prefrontal cortex and by the functional magnetic resonance imaging blood oxygen level-dependent response in prefrontal areas connected by these tracts. These results provide evidence for compensatory brain reorganization that may underlie the increased self-regulation mechanisms that have been hypothesized to bring about the control of tics during adolescence.
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Effects of motor intention on the perception of somatosensory events: a behavioural and functional magnetic resonance imaging study.
Q J Exp Psychol (Hove)
PUBLISHED: 01-06-2011
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The intention to execute a movement can modulate our perception of sensory events, and this modulation is observed ahead of both ocular and upper limb movements. However, theoretical accounts of these effects, and also the empirical data, are often contradictory. Accounts of "active touch", and the premotor theory of attention, have emphasized how movement intention leads to enhanced perceptual processing at the target of a movement, or on the to-be-moved effector. By contrast, recent theories of motor control emphasize how internal "forward" model (FM) estimates may be used to cancel or attenuate sensory signals that arise as a result of self-generated movements. We used behavioural and functional brain imaging (functional magnetic resonance imaging, fMRI) to investigate how perception of a somatosensory stimulus differed according to whether it was delivered to a hand that was about to execute a reaching movement or the alternative, nonmoving, hand. The results of our study demonstrate that a somatosensory stimulus delivered to a hand that is being prepared for movement is perceived to have occurred later than when that same stimulus is delivered to a nonmoving hand. This result indicates that it takes longer for a tactile stimulus to be detected when it is delivered to a moving limb and may correspond to a change in perceptual threshold. Our behavioural results are paralleled by the results of our fMRI study that demonstrated that there were significantly reduced blood-oxygen-level-dependent (BOLD) responses within the parietal operculum and insula following somatosensory stimulation of the hand being prepared for movement, compared to when an identical stimulus was delivered to a nonmoving hand. These findings are consistent with the prediction of FM accounts of motor control that postulate that central sensory suppression of somatosensation accompanies self-generated limb movements, and with previous reports indicating that effects of sensory suppression are observed in higher order somatosensory regions.
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Human SIRT6 promotes DNA end resection through CtIP deacetylation.
Science
PUBLISHED: 09-11-2010
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SIRT6 belongs to the sirtuin family of protein lysine deacetylases, which regulate aging and genome stability. We found that human SIRT6 has a role in promoting DNA end resection, a crucial step in DNA double-strand break (DSB) repair by homologous recombination. SIRT6 depletion impaired the accumulation of replication protein A and single-stranded DNA at DNA damage sites, reduced rates of homologous recombination, and sensitized cells to DSB-inducing agents. We identified the DSB resection protein CtIP [C-terminal binding protein (CtBP) interacting protein] as a SIRT6 interaction partner and showed that SIRT6-dependent CtIP deacetylation promotes resection. A nonacetylatable CtIP mutant alleviated the effect of SIRT6 depletion on resection, thus identifying CtIP as a key substrate by which SIRT6 facilitates DSB processing and homologous recombination. These findings further clarify how SIRT6 promotes genome stability.
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DAY NEUTRAL FLOWERING does not act through GIGANTEA and FKF1 to regulate CONSTANS expression and flowering time.
Plant Signal Behav
PUBLISHED: 09-01-2010
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The regulation of CONSTANS (CO) gene expression and protein levels is the critical factor in determining a plants response to photoperiod, flowering is induced when high levels of CO protein are present in the light. The regulation of CO transcription is mediated in part by GIGANTEA (GI), FKF1 and the CYCLING DOF FACTORS (CDFs) and factors affecting the levels of these proteins will also affect CO expression. The DAY NEUTRAL FLOWERING (DNF) protein is an E3 ligase involved in repressing CO expression in the early part of the day. In this article we present evidence to support the argument that DNF is not acting through the GI/FKF1/CDF regulatory mechanism to repress CO expression, but that it acts on another transcriptional activator of CO.
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DNA damage signaling in response to double-strand breaks during mitosis.
J. Cell Biol.
PUBLISHED: 07-28-2010
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The signaling cascade initiated in response to DNA double-strand breaks (DSBs) has been extensively investigated in interphase cells. Here, we show that mitotic cells treated with DSB-inducing agents activate a "primary" DNA damage response (DDR) comprised of early signaling events, including activation of the protein kinases ataxia telangiectasia mutated (ATM) and DNA-dependent protein kinase (DNA-PK), histone H2AX phosphorylation together with recruitment of mediator of DNA damage checkpoint 1 (MDC1), and the Mre11-Rad50-Nbs1 (MRN) complex to damage sites. However, mitotic cells display no detectable recruitment of the E3 ubiquitin ligases RNF8 and RNF168, or accumulation of 53BP1 and BRCA1, at DSB sites. Accordingly, we found that DNA-damage signaling is attenuated in mitotic cells, with full DDR activation only ensuing when a DSB-containing mitotic cell enters G1. Finally, we present data suggesting that induction of a primary DDR in mitosis is important because transient inactivation of ATM and DNA-PK renders mitotic cells hypersensitive to DSB-inducing agents.
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Genome-wide reprogramming in the mouse germ line entails the base excision repair pathway.
Science
PUBLISHED: 07-03-2010
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Genome-wide active DNA demethylation in primordial germ cells (PGCs), which reprograms the epigenome for totipotency, is linked to changes in nuclear architecture, loss of histone modifications, and widespread histone replacement. Here, we show that DNA demethylation in the mouse PGCs is mechanistically linked to the appearance of single-stranded DNA (ssDNA) breaks and the activation of the base excision repair (BER) pathway, as is the case in the zygote where the paternal pronucleus undergoes active DNA demethylation shortly after fertilization. Whereas BER might be triggered by deamination of a methylcytosine (5mC), cumulative evidence indicates other mechanisms in germ cells. We demonstrate that DNA repair through BER represents a core component of genome-wide DNA demethylation in vivo and provides a mechanistic link to the extensive chromatin remodeling in developing PGCs.
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Human HDAC1 and HDAC2 function in the DNA-damage response to promote DNA nonhomologous end-joining.
Nat. Struct. Mol. Biol.
PUBLISHED: 06-07-2010
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DNA double-strand break (DSB) repair occurs within chromatin and can be modulated by chromatin-modifying enzymes. Here we identify the related human histone deacetylases HDAC1 and HDAC2 as two participants in the DNA-damage response. We show that acetylation of histone H3 Lys56 (H3K56) was regulated by HDAC1 and HDAC2 and that HDAC1 and HDAC2 were rapidly recruited to DNA-damage sites to promote hypoacetylation of H3K56. Furthermore, HDAC1- and 2-depleted cells were hypersensitive to DNA-damaging agents and showed sustained DNA-damage signaling, phenotypes that reflect defective DSB repair, particularly by nonhomologous end-joining (NHEJ). Collectively, these results show that HDAC1 and HDAC2 function in the DNA-damage response by promoting DSB repair and thus provide important insights into the radio-sensitizing effects of HDAC inhibitors that are being developed as cancer therapies.
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Regulation of DNA-damage responses and cell-cycle progression by the chromatin remodelling factor CHD4.
EMBO J.
PUBLISHED: 05-28-2010
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The chromatin remodelling factor chromodomain helicase DNA-binding protein 4 (CHD4) is a catalytic subunit of the NuRD transcriptional repressor complex. Here, we reveal novel functions for CHD4 in the DNA-damage response (DDR) and cell-cycle control. We show that CHD4 mediates rapid poly(ADP-ribose)-dependent recruitment of the NuRD complex to DNA-damage sites, and we identify CHD4 as a phosphorylation target for the apical DDR kinase ataxia-telangiectasia mutated. Functionally, we show that CHD4 promotes repair of DNA double-strand breaks and cell survival after DNA damage. In addition, we show that CHD4 acts as an important regulator of the G1/S cell-cycle transition by controlling p53 deacetylation. These results provide new insights into how the chromatin remodelling complex NuRD contributes to maintaining genome stability.
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Mitochondrial dysfunction in NnaD mutant flies and Purkinje cell degeneration mice reveals a role for Nna proteins in neuronal bioenergetics.
Neuron
PUBLISHED: 05-19-2010
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The Purkinje cell degeneration (pcd) mouse is a recessive model of neurodegeneration, involving cerebellum and retina. Purkinje cell death in pcd is dramatic, as >99% of Purkinje neurons are lost in 3 weeks. Loss of function of Nna1 causes pcd, and Nna1 is a highly conserved zinc carboxypeptidase. To determine the basis of pcd, we implemented a two-pronged approach, combining characterization of loss-of-function phenotypes of the Drosophila Nna1 ortholog (NnaD) with proteomics analysis of pcd mice. Reduced NnaD function yielded larval lethality, with survivors displaying phenotypes that mirror disease in pcd. Quantitative proteomics revealed expression alterations for glycolytic and oxidative phosphorylation enzymes. Nna proteins localize to mitochondria, loss of NnaD/Nna1 produces mitochondrial abnormalities, and pcd mice display altered proteolytic processing of Nna1 interacting proteins. Our studies indicate that Nna1 loss of function results in altered bioenergetics and mitochondrial dysfunction.
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DAY NEUTRAL FLOWERING represses CONSTANS to prevent Arabidopsis flowering early in short days.
Plant Cell
PUBLISHED: 04-30-2010
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The photoperiodic response in Arabidopsis thaliana requires the precise regulation of CONSTANS (CO) expression in relation to the light period during the day. In short days (SDs) levels of CO expression are normally low during the light period, and this results in delayed flowering compared with long days (LDs) when CO expression rises to high levels before the end of the light period. We identified a novel flowering time gene called DAY NEUTRAL FLOWERING (DNF) that acts in the same flowering pathway as CO. DNF is a membrane-bound E3 ligase that represses CO expression and plays an important role in maintaining low levels of CO expression in SDs. The effect of DNF on the rhythm of CO expression is essential for the photoperiodic response of Arabidopsis, enabling it to have a different flowering response in LDs and SDs.
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Parietal cortex coding of limb posture: in search of the body-schema.
Neuropsychologia
PUBLISHED: 04-13-2010
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Computational theories of motor control propose that the brain uses forward models of the body to ensure accurate control of movements. Forward dynamic models are thought to generate an estimate of the next motor state for an upcoming movement: thereby providing a dynamic representation of the current postural configuration of the body that can be utilised during movement planning and execution. We used event-related functional magnetic resonance imaging [fMRI] to investigate brain areas involved in maintaining and updating the postural representations of the upper limb that participate in the control of reaching movements. We demonstrate that the neural correlates for executing memory-guided reaching movements to unseen target locations that were defined by arm posture, are primarily within regions of the superior parietal lobule [SPL]: including an area of the medial SPL identified as the human homologue of the parietal reach region [PRR]. Using effective connectivity analyses we show that signals that influence the BOLD response within this area originate within premotor areas of the frontal lobe, including premotor cortex and the supplementary motor area. These data are consistent with the view that the SPL maintains an up-to-date estimate of the current postural configuration of the arm that is used during the planning and execution of reaching movements.
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Is the visual dorsal stream really very visual after all?
Cogn Neurosci
PUBLISHED: 03-01-2010
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Abstract The perception-action model (PAM) provides a misleading account of the core function of the dorsal stream: which is the integration of sensory signals to create dynamic representations of corporeal and extrapersonal space. Recent evidence suggests that the parietal-occipital cortex plays a key role in integrating multimodal spatial signals that relate to the direction of gaze and the direction of reaching movements. I suggest that a core deficit of the dorsal stream-optic ataxia-arises because of an inability to simultaneously represent different multimodal spatial representations.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.