Book Reviews

Book reviews by Roger Paul Peters, Stanley J. Parry, George W. Hazlett, Charles E. Sheedy, and Lawrence J. Latto

Common data elements to standardize genomics studies in cerebral palsy

Aim To define clinical common data elements (CDEs) and a mandatory minimum data set (MDS) for genomic studies of cerebral palsy (CP). Method Candidate data elements were collated following a review of the literature and existing CDEs. An online, three-round Delphi survey was used to rate each data element as either ‘core’, ‘recommended’, ‘exploratory’, or ‘not required’. Members of the International Cerebral Palsy Genomics Consortium (ICPGC) rated the core CDEs as either mandatory or not, to form the MDS. For both the CDEs and the MDS, a data element was considered to have reached consensus if more than 75% of respondents agreed. Results Forty-six individuals from around the world formed the Delphi panel: consumers (n=2), scientists/researchers (n=17), medical (n=19), and allied health professionals (n=8). The CDEs include 107 data elements across six categories: demographics, diagnostics, family history, antenatal and neonatal details, clinical traits, and CP-specific assessments. Of these, 10 are mandatory, 42 core, 41 recommended, and 14 are exploratory. Interpretation The ICPGC CDEs provide a foundation for the standardization of phenotype data captured in CP genomic studies and will benefit international collaborations and pooling of data, particularly in rare conditions

Predicting prescribed magnification

Aim: To determine the best method of estimating the optimum magnification needed by visually impaired patients. Methods: The magnification of low vision aids prescribed to 187 presbyopic visually impaired patients for reading newspapers or books was compared with logMAR distance and near acuity (at 25 cm) and magnification predicted by +4 D step near additions. Results: Distance letter (r = 0.58) and near word visual acuity (r = 0.67) were strongly correlated to the prescribed magnification as were predictive formulae based on these measures. Prediction using the effect of proximal magnification resulted in a similar correlation (r = 0.67) and prediction was poorer in those who did not benefit from proximal magnification. The difference between prescribed and predicted magnification was found to be unrelated to the condition causing visual impairment (F = 2.57, p = 0.08), the central visual field status (F = 0.57, p = 0.57) and patient psychology (F = 0.44, p = 0.51), but was higher in those prescribed stand magnifiers than high near additions (F = 5.99, p < 0.01). Conclusions: The magnification necessary to perform normal visual tasks can be predicted in the majority of cases using visual acuity measures, although measuring the effect of proximal magnification demonstrates the effect of stronger glasses and identifies those in whom prescribed magnification is more difficult to predict

Smc5/6: a link between DNA repair and unidirectional replication?

Of the three structural maintenance of chromosome (SMC) complexes, two directly regulate chromosome dynamics. The third, Smc5/6, functions mainly in homologous recombination and in completing DNA replication. The literature suggests that Smc5/6 coordinates DNA repair, in part through post-translational modification of uncharacterized target proteins that can dictate their subcellular localization, and that Smc5/6 also functions to establish DNA-damage-dependent cohesion. A nucleolar-specific Smc5/6 function has been proposed because Smc5/6 yeast mutants display penetrant phenotypes of ribosomal DNA (rDNA) instability. rDNA repeats are replicated unidirectionally. Here, we propose that unidirectional replication, combined with global Smc5/6 functions, can explain the apparent rDNA specificity

CD36 coordinates NLRP3 inflammasome activation by facilitating the intracellular nucleation from soluble to particulate ligands in sterile inflammation

Particulate ligands including cholesterol crystals and amyloid fibrils induce NLRP3-dependent production of interleukin-1β (IL-1β) in atherosclerosis, Alzheimer's disease and diabetes. Soluble endogenous ligands including oxidized-LDL, amyloid-β and amylin peptides accumulate in these diseases. Here we identify a CD36-mediated endocytic pathway that coordinates the intracellular conversion of these soluble ligands to crystals or fibrils, resulting in lysosomal disruption and NLRP3-inflammasome activation. Consequently, macrophages lacking CD36 failed to elicit IL-1β production in response to these ligands and targeting CD36 in atherosclerotic mice reduced serum IL-1β and plaque cholesterol crystal accumulation. Collectively, these findings highlight the importance of CD36 in the accrual and nucleation of NLRP3 ligands from within the macrophage and position CD36 as a central regulator of inflammasome activation in sterile inflammation

Pattern of reading eye movements during monovision contact lens wear in presbyopes

Monovision can be used as a method to correct presbyopia with contact lenses (CL) but its effect on reading behavior is still poorly understood. In this study eye movements (EM) were recorded in fifteen presbyopic participants, naïve to monovision, whilst they read arrays of words, non-words, and text passages to assess whether monovision affected their reading. Three conditions were compared, using daily disposable CLs: baseline (near correction in both eyes), conventional monovision (distance correction in the dominant eye, near correction in the non-dominant eye), and crossed monovision (the reversal of conventional monovision). Behavioral measures (reading speed and accuracy) and EM parameters (single fixation duration, number of fixations, dwell time per item, percentage of regressions, and percentage of skipped items) were analyzed. When reading passages, no differences in behavioral and EM measures were seen in any comparison of the three conditions. The number of fixations and dwell time significantly increased for both monovision and crossed monovision with respect to baseline only with word and non-word arrays. It appears that monovision did not appreciably alter visual processing when reading meaningful texts but some limited stress of the EM pattern was observed only with arrays of unrelated or meaningless items under monovision, which require the reader to have more in-depth controlled visual processing

Smc5/6 coordinates formation and resolution of joint molecules with chromosome morphology to ensure meiotic divisions

During meiosis, Structural Maintenance of Chromosome (SMC) complexes underpin two fundamental features of meiosis: homologous recombination and chromosome segregation. While meiotic functions of the cohesin and condensin complexes have been delineated, the role of the third SMC complex, Smc5/6, remains enigmatic. Here we identify specific, essential meiotic functions for the Smc5/6 complex in homologous recombination and the regulation of cohesin. We show that Smc5/6 is enriched at centromeres and cohesin-association sites where it regulates sister-chromatid cohesion and the timely removal of cohesin from chromosomal arms, respectively. Smc5/6 also localizes to recombination hotspots, where it promotes normal formation and resolution of a subset of joint-molecule intermediates. In this regard, Smc5/6 functions independently of the major crossover pathway defined by the MutLγ complex. Furthermore, we show that Smc5/6 is required for stable chromosomal localization of the XPF-family endonuclease, Mus81-Mms4Eme1. Our data suggest that the Smc5/6 complex is required for specific recombination and chromosomal processes throughout meiosis and that in its absence, attempts at cell division with unresolved joint molecules and residual cohesin lead to severe recombination-induced meiotic catastroph

'Physical activity at home (PAAH)', evaluation of a group versus home based physical activity program in community dwelling middle aged adults: rationale and study design

<p>Abstract</p> <p>Background</p> <p>It is well recognised that the adoption and longer term adherence to physical activity by adults to reduce the risk of chronic disease is a challenge. Interventions, such as group and home based physical activity programs, have been widely reported upon. However few studies have directly compared these interventions over the longer term to determine their adherence and effectiveness. Participant preference for home based or group interventions is important. Some evidence suggests that home based physical activity programs are preferred by middle aged adults and provide better long term physical activity adherence. Physiotherapists may also be useful in increasing physical activity adherence, with limited research on their impact.</p> <p>Methods</p> <p>'Physical Activity at Home' is a 2 year pragmatic randomised control trial, with a non-randomised comparison to group exercise. Middle-aged adults not interested in, or unable to attend, a group exercise program will be targeted. Sedentary community dwelling 50-65 year olds with no serious medical conditions or functional impairments will be recruited via two mail outs using the Australian federal electoral roll. The first mail out will invite participants to a 6 month community group exercise program. The second mail out will be sent to those not interested in the group exercise program inviting them to take part in a home based intervention. Eligible home based participants will be randomised into a 6 month physiotherapy-led home based physical activity program or usual care. Outcome measures will be taken at baseline, 6, 12, 18 and 24 months. The primary outcome is physical activity adherence via exercise diaries. Secondary outcomes include the Active Australia Survey, accelerometry, aerobic capacity (step test), quality of life (SF-12v2), blood pressure, waist circumference, waist-to-hip ratio and body mass index. Costs will be recorded prospectively and qualitative data will be collected.</p> <p>Discussion</p> <p>The planned 18 month follow-up post intervention will provide an indication of the effectiveness of the group and home based interventions in terms of adherence to physical activity, health benefits and cost. If the physiotherapy-led home based physical activity program is successful it could provide an alternative option for physical activity program delivery across a number of settings.</p> <p>Trial registration</p> <p>Australia and New Zealand Clinical Trials Register (ANZCTR): <a href="http://www.anzctr.org.au/ACTRN12611000890932.aspx">ACTRN12611000890932</a></p

Rtt107 Phosphorylation Promotes Localisation to DNA Double-Stranded Breaks (DSBs) and Recombinational Repair between Sister Chromatids

Efficient repair of DNA double-stranded breaks (DSB) requires a coordinated response at the site of lesion. Nucleolytic resection commits repair towards homologous recombination, which preferentially occurs between sister chromatids. DSB resection promotes recruitment of the Mec1 checkpoint kinase to the break. Rtt107 is a target of Mec1 and serves as a scaffold during repair. Rtt107 plays an important role during rescue of damaged replication forks, however whether Rtt107 contributes to the repair of DSBs is unknown. Here we show that Rtt107 is recruited to DSBs induced by the HO endonuclease. Rtt107 phosphorylation by Mec1 and its interaction with the Smc5–Smc6 complex are both required for Rtt107 loading to breaks, while Rtt107 regulators Slx4 and Rtt101 are not. We demonstrate that Rtt107 has an effect on the efficiency of sister chromatid recombination (SCR) and propose that its recruitment to DSBs, together with the Smc5–Smc6 complex is important for repair through the SCR pathway

Rad3ATR Decorates Critical Chromosomal Domains with γH2A to Protect Genome Integrity during S-Phase in Fission Yeast

Schizosaccharomyces pombe Rad3 checkpoint kinase and its human ortholog ATR are essential for maintaining genome integrity in cells treated with genotoxins that damage DNA or arrest replication forks. Rad3 and ATR also function during unperturbed growth, although the events triggering their activation and their critical functions are largely unknown. Here, we use ChIP-on-chip analysis to map genomic loci decorated by phosphorylated histone H2A (γH2A), a Rad3 substrate that establishes a chromatin-based recruitment platform for Crb2 and Brc1 DNA repair/checkpoint proteins. Unexpectedly, γH2A marks a diverse array of genomic features during S-phase, including natural replication fork barriers and a fork breakage site, retrotransposons, heterochromatin in the centromeres and telomeres, and ribosomal RNA (rDNA) repeats. γH2A formation at the centromeres and telomeres is associated with heterochromatin establishment by Clr4 histone methyltransferase. We show that γH2A domains recruit Brc1, a factor involved in repair of damaged replication forks. Brc1 C-terminal BRCT domain binding to γH2A is crucial in the absence of Rqh1Sgs1, a RecQ DNA helicase required for rDNA maintenance whose human homologs are mutated in patients with Werner, Bloom, and Rothmund–Thomson syndromes that are characterized by cancer-predisposition or accelerated aging. We conclude that Rad3 phosphorylates histone H2A to mobilize Brc1 to critical genomic domains during S-phase, and this pathway functions in parallel with Rqh1 DNA helicase in maintaining genome integrity