Computational approach for determining the spectrum of DNA damage induced by ionizing radiation

To study the characteristics of molecular damage induced by ionizing radiation at the DNA level, Monte Carlo track simulation of energetic electrons and ions in liquid water, a canonical model of B-DNA, and a comprehensive classification of DNA damage in terms of the origin and complexity of damage were used to calculate the frequencies of simple and complex strand breaks. A threshold energy of 17.5 eV was used to model the damage by direct energy deposition, and a probability of 0.13 was applied to model the induction of a single-strand break produced in DNA by OH radical reactions. For preliminary estimates, base damage was assumed to be induced by the same direct energy threshold deposition or by the reaction of an OH radical with the base, with a probability of 0.8. Computational data are given on the complexity of damage, including base damage by electrons with energies of 100-4500 eV and ions with energies of 0.3-4.0 MeV/nucleon (59-9 keV microm(-1) protons and 170-55 keV microm(-1) alpha particles). Computational data are presented on the frequencies of single- and double-strand breaks induced as a function of the LET of the particles, and on the relative frequencies of complex single- and double-strand breaks for electrons. The modeling and calculations of strand breaks show that: (1) The yield of strand breaks per unit absorbed dose is nearly constant over a wide range of LET. (2) The majority of DNA damage is of a simple type, but the majority of the simple single-strand breaks are accompanied by at least one base damage. (3) For low-energy electrons, nearly 20-30% of the double-strand breaks are of a complex type by virtue of additional breaks. The proportion of this locally clustered damage increases with LET, reaching about 70% for the highest-LET alpha particles modeled, with the complexity of damage increasing further, to about 90%, when base damage is considered. (4) The extent of damage in the local hit region of the DNA duplex is mostly limited to a length of a few base pairs. (5) The frequency of base damage when no strand breaks are present in the hit segment of DNA varies between 20-40% as a function of LET for protons and alpha particles.

Transforming healthcare: a safety imperative

Ten years ago, the Institute of Medicine reported alarming data on the scope and impact of medical errors in the US and called for national efforts to address this problem. While efforts to improve patient safety have proliferated during the past decade, progress toward improvement has been frustratingly slow. Some of this lack of progress may be attributable to the persistence of a medical ethos, institutionalized in the hierarchical structure of academic medicine and healthcare organizations, that discourages teamwork and transparency and undermines the establishment of clear systems of accountability for safe care. The Lucian Leape Institute, established by the US National Patient Safety Foundation to provide vision and strategic direction for the patient safety work, has identified five concepts as fundamental to the endeavor of achieving meaningful improvement in healthcare system safety. These five concepts are transparency, care integration, patient/consumer engagement, restoration of joy and meaning in work, and medical education reform. This paper introduces the five concepts and illustrates the meaning and implications of each as a component of a vision for healthcare safety improvement. In future roundtable sessions, the Institute will further elaborate on the meaning of each concept, identify the challenges to implementation, and issue recommendations for policy makers, organizations, and healthcare professionals.

Computational modelling of low-energy electron-induced DNA damage by early physical and chemical events

Modelling and calculations are presented as a first step towards mechanistic interpretation and prediction of radiation effects based on the spectrum of initial DNA damage produced by low energy electrons (100 eV-4.5 keV) that can be compared with experimental information. Relative yields of single and clustered strand breaks are presented in terms of complexity and source of damage, either by direct energy deposition or by reaction of OH radicals, and dependence on the activation probability of OH radicals and the amount of energy required to give a single strand break (ssb). Data show that the majority of interactions in DNA do not lead to damage in the form of strand breaks and when they do occur, they are most frequently simple ssb. However, for double-strand breaks (dsb), a high proportion (approximately 30%) are of more complex forms, even without considering additional complexity from base damage. The greater contribution is from direct interactions in the DNA but reactions of OH radicals add substantially to this, both in terms of the total number of breaks and in increasing the complexity within a cluster. It has been shown that the lengths of damaged segments of DNA from individual electron tracks tend to be short, indicating that consequent deletion length (simply by loss of a fragment between nearby dsb) would be short, very seldom exceeding a few tens of base pairs.

Quantitative modelling of DNA damage using Monte Carlo track structure method

This paper presents data on modelling of DNA damage induced by electrons, protons and alpha-particles to provide an insight into factors which determine the biological effectiveness of radiations of high and low linear energy transfer (LET). These data include the yield of single- and double-strand breaks (ssb, dsb) and base damage in a cellular environment. We obtain a ratio of 4-15 for ssb:dsb for solid and cellular DNA and a preliminary ratio of about 2 for base damage to strand breakage. Data are also given on specific characteristics of damage at the DNA level in the form of clustered damage of varying complexity, that challenge the repair processes and if not processed adequately could lead to the observed biological effects. It is shown that nearly 30% of dsb are of complex form for low-LET radiation, solely by virtue of additional breaks, rising to about 70% for high-LET radiation. Inclusion of base damage increases the complex proportion to about 60% and 90% for low- and high-LET radiation, respectively. The data show a twofold increase in frequencies of complex dsb from low-LET radiation when base damage is taken into account. It is shown that most ssb induced by high-LET radiation have associated base damages, and also a substantial proportion is induced by low-energy electrons.

Clustered DNA damage, influence on damage excision by XRS5 nuclear extracts and Escherichia coli Nth and Fpg proteins

Ionizing radiation and radiomimetic anticancer agents induce clustered DNA damage, which are thought to reflect the biological severity. Escherichia coli Nth and Fpg and nuclear extracts from XRS5, a Chinese hamster ovary Ku-deficient cell line, have been used to study the influence on their substrate recognition by the presence of a neighboring damage or an abasic site on the opposite strand, as models of clustered DNA damage. These proteins were tested for their efficiency to induce a single-strand break on a (32)P-labeled oligonucleotide containing either an abasic (AP) site, dihydrothymine (DHT), 7,8-dihydro-8-oxo-2'deoxyguanine, or 7, 8-dihydro-8-oxo-2'deoxyadenine at positions 1, 3, or 5 base pairs 5' or 3' to either an AP site or DHT on the labeled strand. DHT excision is much more affected than cleavage of an AP site by the presence of other damage. The effect on DHT excision is greatest with a neighboring AP site, with the effect being asymmetric with Nth and Fpg. Therefore, this large inhibition of the excision of DHT by the presence of an opposite AP site may minimize the formation of double-strand breaks in the processing of DNA clustered damages.

Induction and rejoining of DNA double-strand breaks in V79-4 mammalian cells following gamma- and alpha-irradiation

The induction and rejoining of DNA double-strand breaks (dsbs) in V79-4 mammalian cells following irradiation by 60Co gamma-rays and 238Pu alpha-particles (average LET 120 keV microns-1) under aerobic conditions have been determined using both the sucrose sedimentation and filter elution techniques under non-denaturing conditions. Cellular inactivation was also determined. The dependence of the initial yield of dsbs at 277 K on dose under aerobic conditions is linear with a relative biological effectiveness (RBE) for alpha-particles of 0.85 +/- 0.14 (sedimentation) and 0.68 +/- 0.12 (elution) compared with 60Co gamma-rays. The ability of the cells to rejoin dsbs at 310K is significantly reduced for alpha-irradiations with only 30-50% rejoined for a 3-h incubation period. With low LET radiation, > 90% of the dsbs are rejoined within 3 h at a dose of 20 Gy. The RBE for cellular inactivation was determined to be 4.0 at the 1% survival level. From the cellular dimensions and the D0-value for cellular inactivation by alpha-particles, it is determined that, on average, 4.7 tracks traverse the cell nucleus per lethal lesion. Under hypoxic conditions, the RBE values for induction of dsbs and cellular inactivation (10% level) by alpha-particles are approximately 3.0 and approximately 11.8 respectively. From these findings, it is suggested that the residual DNA damage and not the initial damage is reflected in the cellular inactivation. It is inferred that the difference in repair of the various lesions is a reflection of the differences in the complexity of the clustered damage produced by these radiations.

Seeing the same thing differently: mechanisms that contribute to assessor differences in directly-observed performance assessments

Assessors' scores in performance assessments are known to be highly variable. Attempted improvements through training or rating format have achieved minimal gains. The mechanisms that contribute to variability in assessors' scoring remain unclear. This study investigated these mechanisms. We used a qualitative approach to study assessors' judgements whilst they observed common simulated videoed performances of junior doctors obtaining clinical histories. Assessors commented concurrently and retrospectively on performances, provided scores and follow-up interviews. Data were analysed using principles of grounded theory. We developed three themes that help to explain how variability arises: Differential Salience-assessors paid attention to (or valued) different aspects of the performances to different degrees; Criterion Uncertainty-assessors' criteria were differently constructed, uncertain, and were influenced by recent exemplars; Information Integration-assessors described the valence of their comments in their own unique narrative terms, usually forming global impressions. Our results (whilst not precluding the operation of established biases) describe mechanisms by which assessors' judgements become meaningfully-different or unique. Our results have theoretical relevance to understanding the formative educational messages that performance assessments provide. They give insight relevant to assessor training, assessors' ability to be observationally "objective" and to the educational value of narrative comments (in contrast to numerical ratings).

Why are there eccentricity effects in visual search? Visual and attentional hypotheses

In standard visual search experiments, observers search for a target item among distracting items. The locations of target items are generally random within the display and ignored as a factor in data analysis. Previous work has shown that targets presented near fixation are, in fact, found more efficiently than are targets presented at more peripheral locations. This paper proposes that the primary cause of this "eccentricity effect" (Carrasco, Evert, Chang, & Katz, 1995) is an attentional bias that allocates attention preferentially to central items. The first four experiments dealt with the possibility that visual, and not attentional, factors underlie the eccentricity effect. They showed that the eccentricity effect cannot be accounted for by the peripheral reduction in visual sensitivity, peripheral crowding, or cortical magnification. Experiment 5 tested the attention allocation model and also showed that RT x set size effects can be independent of eccentricity effects. Experiment 6 showed that the effective set size in a search task depends, in part, on the eccentricity of the target because observers search from fixation outward.

The spectrum of hypoxanthine-guanine phosphoribosyltransferase (HPRT) deficiency. Clinical experience based on 22 patients from 18 Spanish families

The enzyme hypoxanthine-guanine phosphoribosyltransferase (HPRT) catalyzes the reutilization of hypoxanthine and guanine to the purine nucleotides IMP and GMP, respectively. HPRT deficiency is an X-linked disorder characterized by uric acid overproduction and variable neurologic impairment. The complete deficiency of HPRT is diagnostic of Lesch-Nyhan syndrome manifested by choreoathetosis, spasticity, mental retardation, and self-injurious behavior. In some HPRT-deficient patients the enzyme defect appeared to be "partial" and the neurologic symptoms mild to severe (Kelley-Seegmiller syndrome). This has prompted the classification of HPRT deficiency in 2 distinct groups: Lesch-Nyhan syndrome and Kelley-Seegmiller syndrome, which has created much confusion. A spectrum of clinical consequences of HPRT deficiency has been recognized in small series of patients, but the complete spectrum of the neurologic disorder has not been described in a single series of patients examined by the same observers. We analyzed our experience with 22 patients belonging to 18 different families with HPRT deficiency diagnosed at "La Paz" University Hospital in Madrid over the past 16 years. The clinical spectrum of these HPRT-deficient Spanish patients was similar to the different phenotypes occasionally reported in the literature, in some cases diagnosed as Lesch-Nyhan "variants." The clinical, biochemical, enzymatic, and molecular genetic studies on these 22 patients allowed us to delineate a new classification of HPRT deficiency. Based on the neurologic symptoms, dependency for personal care, HPRT activity in hemolysate and in intact erythrocytes, and predicted protein size, patients were classified into 4 groups: Group 1 (2 patients), normal development with no neurologic symptoms, HPRT activity was detectable in hemolysates and in intact erythrocytes, and the mutation did not affect the predicted protein size. Group 2 (3 patients) mild neurologic symptoms that did not prevent independent lives, HPRT activity was detectable in intact erythrocytes, and the protein size was normal. Group 3 (2 patients), severe neurologic impairment that precluded an independent life, no residual HPRT activity, and normal protein size. Group 4 (15 patients), clinical characteristics of Lesch-Nyhan syndrome (some may not show self-injurious behavior), no residual HPRT activity, and in most (7 of 8 patients in whom the mutation could be detected) the mutation affected the predicted protein size. This classification of HPRT deficiency into 4 groups may be more useful in terms of accuracy, reproducibility, assessment for treatment trials and prognosis. The study of this Spanish series allows us to conclude that HPRT deficiency may be manifested by a wide spectrum of neurologic symptoms; the overall severity of the disease is associated with mutations permitting some degree of residual enzyme activity; and mutation analysis provides a valuable tool for prognosis, carrier identification, and prenatal diagnosis.

Changes in spinal cord regenerative ability through phylogenesis and development: lessons to be learnt

Lower vertebrates, such as fish and amphibians, and developing higher vertebrates can regenerate complex body structures, including significant portions of their central nervous system. It is still poorly understood why this potential is lost with evolution and development and becomes very limited in adult mammals. In this review, we will discuss the current knowledge on the cellular and molecular changes after spinal cord injury in adult tailed amphibians, where regeneration does take place, and in developing chick and mammalian embryos at different developmental stages. We will focus on the recruitment of progenitor cells to repair the damage and discuss possible roles of changes in early response to injury, such as cell death by apoptosis, and of myelin-associated proteins, such as Nogo, in the transition between regeneration-competent and regeneration-incompetent stages of development. A better understanding of the mechanisms underlying spontaneous regeneration of the spinal cord in vivo in amphibians and in the chick embryo will help to devise strategies for restoring function to damaged or diseased nervous tissues in mammals.

From shared lineage to distinct functions: the development of the inner ear and epibranchial placodes

The inner ear and the epibranchial ganglia constitute much of the sensory system in the caudal vertebrate head. The inner ear consists of mechanosensory hair cells, their neurons, and structures necessary for sound and balance sensation. The epibranchial ganglia are knots of neurons that innervate and relay sensory signals from several visceral organs and the taste buds. Their development was once thought to be independent, in line with their independent functions. However, recent studies indicate that both systems arise from a morphologically distinct common precursor domain: the posterior placodal area. This review summarises recent studies into the induction, morphogenesis and innervation of these systems and discusses lineage restriction and cell specification in the context of their common origin.

Immunofluorescence detection of clustered gamma-H2AX foci induced by HZE-particle radiation

We studied the spatial and temporal distributions of foci of the phosphorylated form of the histone protein H2AX (gamma-H2AX), which is known to be activated by double-strand breaks after irradiation of human fibroblast cells with high-energy silicon (54 keV/microm) and iron (176 keV/microm) ions. Here we present data obtained with the ion path parallel to a monolayer of human fibroblast cells that leads to gamma-H2AX aggregates in the shape of streaks stretching over several micrometers in an x/y plane, thus enabling the analysis of the fluorescence distributions along the ion trajectories. Qualitative analyses of these distributions provide insights into DNA damage processing kinetics for high charge and energy (HZE) ions, including evidence of increased clustering of DNA damage and slower processing with increasing LET.

Evaluations of situational judgement tests to assess non-academic attributes in selection

OBJECTIVES

This paper presents a systematic review of the emerging international research evidence for the use of situational judgement tests (SJTs) for testing important non-academic attributes (such as empathy, integrity and resilience) in selection processes.

METHODS

Several databases (e.g. MEDLINE, PsycINFO, Web of Science) were searched to retrieve empirical studies relating to SJTs published between 1990 and 2010. Personal contact with experts in the field was made to identify any unpublished research or work in progress to obtain the most current material. Finally, reference lists were checked to access other relevant journal articles and further research. All research studies were required to meet specific inclusion criteria selected by two independent reviewers.

RESULTS

Over 1000 citations were identified during the initial literature search; following the review of abstracts, full-text copies of 76 articles were retrieved and evaluated. A total of 39 articles that adequately met the inclusion criteria were included in the final review. The research evidence shows that, compared with personality and IQ tests, SJTs have good levels of reliability, predictive validity and incremental validity for testing a range of professional attributes, such as empathy and integrity.

CONCLUSIONS

SJTs can be designed to test a broad range of non-academic constructs depending on the selection context. As a relatively low-fidelity assessment, SJTs are a cost-efficient methodology compared with high-fidelity assessments of non-academic attributes, such as those used in objective structured clinical examinations. In general, SJTs are found to demonstrate less adverse impact than IQ tests and are positively received by candidates. Further research is required to explore theoretical developments and the underlying construct validity of SJTs.

Securing genome stability by orchestrating DNA repair: removal of radiation-induced clustered lesions in DNA

In addition to double- and single-strand DNA breaks and isolated base modifications, ionizing radiation induces clustered DNA damage, which contains two or more lesions closely spaced within about two helical turns on opposite DNA strands. Post-irradiation repair of single-base lesions is routinely performed by base excision repair and a DNA strand break is involved as an intermediate. Simultaneous processing of lesions on opposite DNA strands may generate double-strand DNA breaks and enhance nonhomologous end joining, which frequently results in the formation of deletions. Recent studies support the possibility that the mechanism of base excision repair contributes to genome stability by diminishing the formation of double-strand DNA breaks during processing of clustered lesions.

Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

Alternative splicing is a post-transcriptional regulatory mechanism producing distinct mRNA molecules from a single pre-mRNA with a prominent role in the development and function of the central nervous system. We used long-read isoform sequencing to generate full-length transcript sequences in the human and mouse cortex. We identify novel transcripts not present in existing genome annotations, including transcripts mapping to putative novel (unannotated) genes and fusion transcripts incorporating exons from multiple genes. Global patterns of transcript diversity are similar between human and mouse cortex, although certain genes are characterized by striking differences between species. We also identify developmental changes in alternative splicing, with differential transcript usage between human fetal and adult cortex. Our data confirm the importance of alternative splicing in the cortex, dramatically increasing transcriptional diversity and representing an important mechanism underpinning gene regulation in the brain. We provide transcript-level data for human and mouse cortex as a resource to the scientific community.

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There is widespread transcript diversity in the cortex and many novel transcripts

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Some genes display big differences in isoform number between human and mouse cortex

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There is evidence of differential transcript usage between human fetal and adult cortex

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There are many novel isoforms of genes associated with human brain disease

Free radicals associated with DNA damage

This short review focuses on the chemical events related to DNA damage induced by free radicals. Diffusible hydroxyl radicals (HO) are able to react with either the sugar units by hydrogen abstraction or with the base moieties by addition. Selectively generated carbon-centred radicals at C1', C4' and C5' in model nucleosides or oligonucleotides and their subsequent fate under aerobic or anoxic condition are discussed by rationalisation of the available kinetic data. Reaction paths for the formation of nucleobase modifications such as 8-oxoG and FapyG, amplification of base damage, and tandem lesions are also discussed. Some types of DNA damage may be poorly repaired leading to deleterious genetic changes with time.

Dependence of the yield of DNA double-strand breaks in Chinese hamster V79-4 cells on the photon energy of ultrasoft X rays

Induction of DNA DSBs by low-LET radiations reflects clustered damage produced predominantly by low-energy, secondary electron "track ends". Cell inactivation and induction of DSBs and their rejoining, assayed using pulsed-field gel electrophoresis, were determined in Chinese hamster V79-4 cells irradiated as a monolayer with characteristic carbon K-shell (CK) (0.28 keV), aluminum K-shell (AlK) (1.49 keV), and titanium K-shell (TiK) (4.55 keV) ultrasoft X rays under aerobic and anaerobic conditions. Relative to (60)Co gamma rays, the relative biological effectiveness (RBE) for cell inactivation at 10% survival and for induction of DSBs increases as the photon energy of the ultrasoft X rays decreases. The RBE values for cell inactivation and for induction of DSBs by CK ultrasoft X rays are 2.8 +/- 0.3 and 2.7 +/- 0.3, respectively, and by TiK ultrasoft X rays are 1.5 +/- 0.1 and 1.4 +/- 0.1, respectively. Oxygen enhancement ratios (OERs) of approximately 2 for cell inactivation and induction of DSBs by ultrasoft X rays are independent of the photon energy. The time scale for rejoining of DNA DSBs is similar for both ultrasoft X rays and 60Co gamma rays. From the size distribution of small DNA fragments down to 0.48 kbp, we concluded that DSBs are induced randomly by CK and AlK ultrasoft X rays. Therefore, ultrasoft X rays are more efficient per unit dose than gamma radiation at inducing DNA DSBs, the yield of which increases with decreasing photon energy.