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1.  Transcriptionally active chromatin recruits homologous recombination at DNA double strand breaks 
While both Homologous recombination (HR) and Non Homologous End Joining (NHEJ) can repair DNA double Strand Breaks (DSB), the mechanisms by which one or other of these pathways is chosen remain unclear. Here we show that transcriptionally active chromatin is preferentially repaired by HR. Using chromatin immunoprecipitation-sequencing (ChIP-seq), to analyse 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 targeted to HR repair via the transcription-elongation associated histone mark, histone H3 lysine 36 trimethylation (H3K36me3). In agreement, depletion of SETD2, the main H3K36 tri-methyltransferase, severely impedes HR at such DSBs. Our study thereby demonstrates a primary role of the chromatin context, in which a break occurs, in DSB repair.
PMCID: PMC4300393  PMID: 24658350
DSB repair; NHEJ; HR; chromatin; transcription; ChIP-seq; H3K36me3
3.  Observational study of subclinical diabetic macular edema 
Eye  2012;26(6):833-840.
To determine the rate of progression of eyes with subclinical diabetic macular edema (DME) to clinically apparent DME or DME necessitating treatment during a 2-year period.
In all, 43 eyes from 39 study participants with subclinical DME, defined as absence of foveal center edema as determined with slit lamp biomicroscopy but a center point thickness (CPT) between 225 and 299 μm on time domain (Stratus, Carl Zeiss Meditec) optical coherence tomography (OCT) scan, were enrolled from 891 eyes of 582 subjects screened. Eyes were evaluated annually for up to 2 years for the primary outcome, which was an increase in OCT CPT of at least 50 μm from baseline and a CPT of at least 300 μm, or treatment for DME (performed at the discretion of the investigator).
The cumulative probability of meeting an increase in OCT CPT of at least 50 μm from baseline and a CPT of at least 300 μm, or treatment for DME was 27% (95% confidence interval (CI): 14%, 38%) by 1 year and 38% (95% CI: 23%, 50%) by 2 years.
Although subclinical DME may be uncommon, this study suggests that between approximately one-quarter and one-half of eyes with subclinical DME will progress to more definite thickening or be judged to need treatment for DME within 2 years after its identification.
PMCID: PMC3376297  PMID: 22441027
diabetic macular edema; optical coherence tomography; subclinical diabetic macular edema
4.  Is the N-Back Task a Valid Neuropsychological Measure for Assessing Working Memory? 
The n-back is a putative working memory task frequently used in neuroimaging research; however, literature addressing n-back use in clinical neuropsychological evaluation is sparse. We examined convergent validity of the n-back with an established measure of working memory, digit span backward. The relationship between n-back performance and scores on measures of processing speed was also examined, as was the ability of the n-back to detect potential between-groups differences in control and Parkinson's disease (PD) groups. Results revealed no correlation between n-back performance and digit span backward. N-back accuracy significantly correlated with a measure of processing speed (Trail Making Test Part A) at the 2-back load. Relative to controls, PD patients performed less accurately on the n-back and showed a trend toward slower reaction times, but did not differ on any of the neuropsychological measures. Results suggest the n-back is not a pure measure of working memory, but may be able to detect subtle differences in cognitive functioning between PD patients and controls.
PMCID: PMC2770861  PMID: 19767297
Working memory; Executive function; Information processing speed; Parkinson's disease; Neuropsychology
5.  Startle reflex hyporeactivity in Parkinson's disease: an emotion-specific or arousal-modulated deficit? 
Neuropsychologia  2009;47(8-9):1917-1927.
We previously reported that patients with Parkinson's disease (PD) demonstrate reduced psychophysiologic reactivity to unpleasant pictures as indexed by diminished startle eyeblink magnitude (Bowers et al., 2006). In the present study, we tested the hypothesis that this hyporeactivity was primarily driven by diminished reactivity to fear-eliciting stimuli as opposed to other types of aversive pictures. This hypothesis was based on previous evidence suggesting amygdalar abnormalities in PD patients coupled with the known role of the amygdala in fear processing. To test this hypothesis, 24 patients with Parkinson's disease and 24 controls viewed standardized sets of emotional pictures that depicted fear, disgust (mutilations, contaminations), pleasant, and neutral contents. Startle eyeblinks were elicited while subjects viewed these emotional pictures. Results did not support the hypothesis of a specific deficit to fear pictures. Instead, the PD patients had reduced reactivity to mutilation pictures relative to other types of negative pictures in the context of normal subjective ratings. Further analyses revealed that controls displayed a pattern of increased startle eyeblink magnitude for “high arousal” versus “low arousal” negative pictures, regardless of picture category, whereas startle eyeblink magnitude in the PD group did not vary by arousal level. These results suggest that previous findings of decreased aversion-modulated startle is driven by reduced reactivity to highly arousing negative stimuli rather than to a specific category (i.e., fear or disgust) of emotion stimuli.
PMCID: PMC2709833  PMID: 19428424
basal ganglia; emotion; neurophysiology; neurological disorders; neurodegenerative disorders
7.  Extracellular matrix-mediated chemotaxis can impede cell migration 
Cells use a combination of changes in adhesion, proteolysis and motility (directed and random) during the process of migration. Proteolysis of the extracellular matrix (ECM) results in thecreation of haptotactic gradients which cells use to move in a directed fashion. The proteolytic creation of these gradients also results in the production of digested fragments of ECM. In this study we show that in the human fibrosarcoma cell line HT1080, matrix metalloproteinase-2(MMP-2)-digested fragments of fibronectin exert a chemotactic pull stronger than that of undigested fibronectin. During invasion, this gradient of ECM fragments is established in the wake of an invading cell, running counter to the direction of invasion. The resultant chemotactic pull is anti-invasive, contrary to the traditional view of the role of chemotaxis in invasion. Uncontrolled ECM degradation by high concentrations of MMP can thus result in steep gradients of ECM fragments, which run against the direction of invasion. Consequently, the invasive potential of a cell depends on MMP production in a biphasic mannerimplying that MMP inhibitors will upregulate invasion in high-MMPexpressing cells. Hence the therapeutic use of protease inhibitors against tumours expressing high levels of MMP could produce an augmentation of invasion.
PMCID: PMC1689540
8.  Changing protective and risky behaviors to prevent child-to-parent transmission of cytomegalovirus. 
Child-to-parent transmission of cytomegalovirus may be reduced by increasing protective behaviors (handwashing and glove use) and decreasing risky behaviors (intimate contact between child and parent). This study showed that an educational intervention resulted in increases in reported and objective measures of protective behaviors and decreases in reported risky behaviors. Further study must determine if changes in protective and risky behavior are maintained and prevent cytomegalovirus transmission.
PMCID: PMC1297873  PMID: 8307832
9.  Occult glove perforation during ophthalmic surgery. 
We examined the latex surgical gloves used by 56 primary surgeons in 454 ophthalmic surgical procedures performed over a 7-month period. Of five techniques used to detect pinholes, air inflation with water submersion and compression was found to be the most sensitive, yielding a 6.80% prevalence in control glove pairs and a 21.8% prevalence in postoperative study glove pairs, for a 15.0% incidence of surgically induced perforations (P = 0.000459). The lowest postoperative perforation rate was 11.4% for cataract and intraocular lens surgery, and the highest was 41.7% for oculoplastic procedures. Factors that correlated significantly with the presence of glove perforations as determined by multiple logistic regression analysis were oculoplastic and pediatric ophthalmology and strabismus surgical procedures, surgeon's status as a fellow in training, operating time, and glove size. The thumb and index finger of the nondominant hand contained the largest numbers of pinholes. These data suggest strategies for reducing the risk of cross-infection during ophthalmic surgery.
PMCID: PMC1298427  PMID: 1494836
10.  In vitro effect of synthetic pyocyanine on neutrophil superoxide production. 
Infection and Immunity  1987;55(3):559-563.
Pyocyanine, a low-molecular-weight phenazine pigment produced by Pseudomonas aeruginosa, has previously been shown to strongly inhibit human lymphocyte blastogenesis. We now report that synthetic pyocyanine can also affect the generation of superoxide by human peripheral blood polymorphonuclear leukocytes (PMNs) in a dose-dependent manner. Superoxide production by PMNs stimulated with phorbol myristate acetate (PMA) was measured in the presence and absence of pyocyanine, phenazine, and trifluoperazine, a phenothiazine of similar chemical structure to the phenazine pigments. Pyocyanine at 50 microM inhibited superoxide production to 28.9 +/- 2.8% of PMA control values, whereas at the lower concentration of 1 microM, the production of superoxide was significantly enhanced (203 +/- 31.7% of PMA control values). Phenazine, the tricyclic parent compound of pyocyanine, had only a minor effect. Trifluoperazine had a marked inhibitory effect on superoxide generation at concentrations above 1 microM. None of the compounds induced superoxide generation in the absence of PMA. Pyocyanine at all concentrations, unlike phenothiazines, had very little effect on the release of neutrophil granule enzymes. The effect of P. aeruginosa phenazine pigments on polymorphonuclear phagocytes is of significance, since inhibition of host PMN function at sites of infection could result in ineffective bacterial killing, whereas enhanced PMN function could lead to greater tissue damage. These two possibilities are not mutually exclusive and may coexist depending on local pyocyanine concentrations.
PMCID: PMC260373  PMID: 3028961

Results 1-10 (10)