Gene conversion and deletion frequencies during double-strand break repair in human cells are controlled by the distance between direct repeats

Homologous recombination (HR) repairs DNA double-strand breaks and maintains genome stability. HR between linked, direct repeats can occur by gene conversion without an associated crossover that maintains the gross repeat structure. Alternatively, direct repeat HR can occur by gene conversion with a crossover, or by single-strand annealing (SSA), both of which delete one repeat and the sequences between the repeats. Prior studies of different repeat structures in yeast and mammalian cells revealed disparate conversion:deletion ratios. Here, we show that a key factor controlling this ratio is the distance between the repeats, with conversion frequency increasing linearly with the distances from 850 to 3800 bp. Deletions are thought to arise primarily by SSA, which involves extensive end-processing to reveal complementary single-strands in each repeat. The results can be explained by a model in which strand-invasion leading to gene conversion competes more effectively with SSA as more extensive end-processing is required for SSA. We hypothesized that a transcription unit between repeats would inhibit end-processing and SSA, thereby increasing the fraction of conversions. However, conversion frequencies were identical for direct repeats separated by 3800 bp of transcriptionally silent or active DNA, indicating that end-processing and SSA are not affected by transcription

Myocarditis, disseminated infection, and early viral persistence following experimental coxsackievirus B infection of cynomolgus monkeys.

Coxsackievirus B (CVB) infection is a common cause of acute viral myocarditis. The clinical presentation of myocarditis caused by this enterovirus is highly variable, ranging from mildly symptoms to complete hemodynamic collapse. These variations in initial symptoms and in the immediate and long term outcomes of this disease have impeded development of effective treatment strategies. Nine cynomolgus monkeys were inoculated with myocarditic strains of CVB. Virological studies performed up to 28 days post-inoculation demonstrated the development of neutralizing antibody in all animals, and the presence of CVB in plasma. High dose intravenous inoculation (n = 2) resulted in severe disseminated disease, while low dose intravenous (n = 6) or oral infection (1 animal) resulted in clinically unapparent infection. Transient, minor, echocardiographic abnormalities were noted in several animals, but no animals displayed signs of significant acute cardiac failure. Although viremia rapidly resolved, signs of myocardial inflammation and injury were observed in all animals at the time of necropsy, and CVB was detected in postmortem myocardial specimens up to 28 days PI. This non-human primate system replicates many features of illness in acute coxsackievirus myocarditis and demonstrates that myocardial involvement may be common in enteroviral infection; it may provide a model system for testing of treatment strategies for enteroviral infections and acute coxsackievirus myocarditis

A little goes a long way: Adapting an ethics training program to work for smaller universities

The present project modified an existing ethics intervention aimed at graduate students, which had previously been evaluated and determined to be effective (e.g., Mumford et al., 2008). The existing program was modified to shorten it from a 2-full day training to a 1-full day training. The effectiveness of the modified training program was evaluated using multiple dependent measures: perceptions of ethical dilemmas, ethical decision-making and the using of cognitive strategies for ethical decision-making, and reactions to the training. The results of the present study indicated that there were significant differences from pre-training to post-training on measures of perceptions of ethical problems and markers of the cognitive processes involved in ethical decision-making, including a focus on the ethical elements of the problem, and overall decision ethicality. Finally, participants responded favorably to the program. Implications of these results are discussed

Microbial community analysis of Acropora palamata mucus swabs, water and sediment samples from Hawksnest Bay, St. John, U.S. Virgin Islands

Colonies of the scleractinian coral Acropora palmata, listed as threatened under the US Endangered Species Act in 2006, have been monitored in Hawksnest Bay, within Virgin Islands National Park, St. John, from 2004 through 2010 by scientists with the US Geological Survey, National Park Service, and the University of the Virgin Islands. The focus has been on documenting the prevalence of disease, including white band, white pox (also called patchy necrosis and white patches), and unidentified diseases (Rogers et al., 2008; Muller et al., 2008). In an effort to learn more about the pathologies that might be involved with the diseases that were observed, samples were collected from apparently healthy and diseased colonies in July 2009 for analysis. Two different microbial assays were performed on Epicentre Biotechnologies DNA swabs containing A. palmata coral mucus, and on water and sediment samples collected in Hawksnest Bay. Both assays are based on polymerase chain reaction (PCR) amplification of portions of the small rRNA gene (16S). The objectives were to determine 1) if known coral bacterial pathogens Serratia marcescens (Acroporid Serratiosis), Vibrio coralliilyticus (temperature-dependent bleaching, White Syndrome), Vibrio shiloi (bleaching, necrosis), and Aurantimonas coralicida (White Plague Type II) were present in any samples, and 2) if there were any differences in microbial community profiles of each healthy, unaffected or diseased coral mucus swab. In addition to coral mucus, water and sediment samples were included to show ambient microbial populations. In the first test, PCR was used to separately amplify the unique and diagnostic region of the 16S rRNA gene for each of the coral pathogens being screened. Each pathogen test was designed so that an amplified DNA fragment could be seen only if the specific pathogen was present in a sample. A positive result was indicated by bands of DNA of the appropriate size on an agarose gel, which separates DNA fragments based on the size of the molecule. DNA from pure cultures of each of the pathogens was used as a positive control for each assay

Development and Assessment of a Patient-Centered Care Curriculum

The purpose of this paper is to chronicle the development and implementation of a pilot offering of the patient-centered care (PCC) curriculum sponsored by a partnership of schools of allied health and nursing and a local health care system. The objective of this interdisciplinary track is to increase the competency of allied health and nursing graduates to function in health care teams in both PCC and non-PCC hospital environments, thus improving the effectiveness of patient care. The elective track consists of two courses; a third course is under consideration. Students and faculty participating in the elective track were surveyed to assess their attitudes toward change and patient-centered care. Generally, participants believed that they could work well together but were not convinced of the viability of the PCC. Although the curriculum is still in its implementation stage and the nursing participation became minimal, this study aids in understanding opinions of nursing and allied health faculty and students regarding a new PCC curriculum

The built environment predicts observed physical activity

Background: In order to improve our understanding of the relationship between the built environment and physical activity, it is important to identify associations between specific geographic characteristics and physical activity behaviors. Purpose: Examine relationships between observed physical activity behavior and measures of the built environment collected on 291 street segments in Indianapolis and St. Louis. Methods: Street segments were selected using a stratified geographic sampling design to ensure representation of neighborhoods with different land use and socioeconomic characteristics. Characteristics of the built environment on-street segments were audited using two methods: in-person field audits and audits based on interpretation of Google Street View imagery with each method blinded to results from the other. Segments were dichotomized as having a particular characteristic (e.g., sidewalk present or not) based on the two auditing methods separately. Counts of individuals engaged in different forms of physical activity on each segment were assessed using direct observation. Non-parametric statistics were used to compare counts of physically active individuals on each segment with built environment characteristic. Results: Counts of individuals engaged in physical activity were significantly higher on segments with mixed land use or all non-residential land use, and on segments with pedestrian infrastructure (e.g., crosswalks and sidewalks) and public transit. Conclusion: Several micro-level built environment characteristics were associated with physical activity. These data provide support for theories that suggest changing the built environment and related policies may encourage more physical activity

Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (Oncorhynchus tshawytscha

Abstract: We evaluated the relative importance of "bottom-up" (production-limited) and "top-down" (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined length, mass, and condition index of age-0 juveniles collected in the ocean during June and September across 11 years in relation to conditions in the river, estuary, and coastal ocean and to future adult returns. Characteristics of juveniles in September, but not June, were related to adult returns. During years when coastal waters were relatively cool and productive, juveniles captured in September displayed relatively low condition and reduced otolith growth compared with years when coastal waters were relatively warm and unproductive; this contrast indicates that top-down effects such as selective mortality or competition are important during early marine residence. Key physical (river plume volume during emigration) and biological (condition) variables and their interaction accounted for >95% of the variation in adult returns. Future research should focus on evaluating predators and competitors and understanding how river plume structure influences survival. Résumé : Nous avons évalué l'importance relative des processus ascendants (limités par la production) et descendants (modulés par les prédateurs) au début du séjour en mer dans une population de saumons quinnat (Oncorhynchus tshawytscha) du cours supérieur du fleuve Columbia (États-Unis). Nous avons examiné la longueur, la masse et l'indice d'embonpoint de juvéniles de 0 an prélevés en océan durant les mois de juin et septembre pendant 11 ans, par rapport aux conditions dans le fleuve, l'estuaire et le littoral océanique, ainsi qu'aux retours d'adultes subséquents. Les caractéristiques des juvéniles en septembre, mais non en juin, étaient reliées aux retours d'adultes. Durant les années où les eaux côtières étaient relativement froides et productives, les juvéniles capturés en septembre présentaient des indices d'embonpoint et des taux de croissance des otolites relativement faibles par rapport à ceux des juvéniles capturés durant des années d'eaux côtières relativement chaudes et non productives. Ces différences indiquent que des effets descendants tels qu'une mortalité sélective ou la concurrence sont importants au début du séjour en mer. Des variables physiques (volume du panache fluvial durant l'émigration) et biologiques (embonpoint) clés et leur interaction expliquaient >95 % de la variabilité des retours d'adultes. Les travaux de recherche futurs devraient se pencher sur l'évaluation des prédateurs et des concurrents et la compréhension de l'influence de la structure du panache fluvial sur la survie. [Traduit par la Rédaction

'The world is full of big bad wolves': investigating the experimental therapeutic spaces of R.D. Laing and Aaron Esterson

In conjunction with the recent critical assessments of the life and work of R.D. Laing, this paper seeks to demonstrate what is revealed when Laing’s work on families and created spaces of mental health care are examined through a geographical lens. The paper begins with an exploration of Laing’s time at the Tavistock Clinic in London during the 1960s, and of the co-authored text with Aaron Esterson entitled, Sanity, Madness and the Family (1964). The study then seeks to demonstrate the importance Laing and his colleague placed on the time-space situatedness of patients and their worlds. Finally, an account is provided of Laing’s and Esterson’s spatial thinking in relation to their creation of both real and imagined spaces of therapeutic care

Disentangling bottom-up and top-down effects on survival during early ocean residence in a population of Chinook salmon (Oncorhynchus tshawytscha)

We evaluated the relative importance of "bottom-up" (production-limited) and "top-down" (predator-mediated) processes during early marine residence in a population of Chinook salmon (Oncorhynchus tshawytscha) from the upper Columbia River, USA. We examined length, mass, and condition index of age-0 juveniles collected in the ocean during June and September across 11 years in relation to conditions in the river, estuary, and coastal ocean and to future adult returns. Characteristics of juveniles in September, but not June, were related to adult returns. During years when coastal waters were relatively cool and productive, juveniles captured in September displayed relatively low condition and reduced otolith growth compared with years when coastal waters were relatively warm and unproductive; this contrast indicates that top-down effects such as selective mortality or competition are important during early marine residence. Key physical (river plume volume during emigration) and biological (condition) variables and their interaction accounted for >95% of the variation in adult returns. Future research should focus on evaluating predators and competitors and understanding how river plume structure influences survival.Keywords: Survival, Chinook salmon (Oncorhynchus tshawytscha