Substrate-selective repair and restart of replication forks by DNA translocases

Stalled replication forks are sources of genetic instability. Multiple fork-remodeling enzymes are recruited to stalled forks, but how they work to promote fork restart is poorly understood. By combining ensemble biochemical assays and single-molecule studies with magnetic tweezers, we show that SMARCAL1 branch migration and DNA-annealing activities are directed by the single-stranded DNA-binding protein RPA to selectively regress stalled replication forks caused by blockage to the leading-strand polymerase and to restore normal replication forks with a lagging-strand gap. We unveil the molecular mechanisms by which RPA enforces SMARCAL1 substrate preference. E. coli RecG acts similarly to SMARCAL1 in the presence of E. coli SSB, whereas the highly related human protein ZRANB3 has different substrate preferences. Our findings identify the important substrates of SMARCAL1 in fork repair, suggest that RecG and SMARCAL1 are functional orthologs, and provide a comprehensive model of fork repair by these DNA translocases

History and philosophy of science in Biology teaching

Neste trabalho, buscamos evidenciar a concepção de História da Biologia que é veiculada nos livros didáticos. Para tanto, analisamos três coleções de livros de Biologia destinados ao Ensino Médio, e alguns livros universitários usados em cursos de formação de professores. Ao analisar este material curricular foi possível observar que a história apresentada é desvinculada do contexto cultural de cada período histórico, o que pode levar o aluno a construir uma falsa representação da ciência e do fazer científico.In this work, we search forto evidences the conception of the History of Biology being is propagated in textbooks. We analyze three Biology book collections designed estined forto middle schooledium education, and some university books used in teacher education courses. When analyzing this curricular material it was possible to observe that the history of biology presented is disengaged from entailedofthe cultural context of each historical period, and this what can lead the student to construct a false representation of science and of scientific meaning making

Complementarity, quantum erasure and delayed choice with modified Mach-Zehnder interferometers

Often cited dictums in Quantum Mechanics include "observation disturbance causes loss of interference" and "ignorance is interference". In this paper we propose and describe a series of experiments with modified Mach-Zehnder interferometers showing that one has to be careful when applying such dictums. We are able to show that without interacting in any way with the light quantum (or quanta) expected to behave "wave-like", interference fringes can be lost by simply gaining (or having the potential to gain) the which-path knowledge. Erasing this information may revive the interference fringes. Delayed choice can be added, arriving to an experiment in line with Wheeler's original proposal. We also show that ignorance is not always synonym with having the interference fringes. The often-invoked "collapse of the wavefunction" is found to be a non-necessary ingredient to describe our experiments.Comment: 8 pages, 3 figures; to appear in EPJ

Biochemical Characterization of a Structure-Specific Resolving Enzyme from Sulfolobus islandicus Rod-Shaped Virus 2

Sulfolobus islandicus rod shaped virus 2 (SIRV2) infects the archaeon Sulfolobus islandicus at extreme temperature (70°C–80°C) and acidity (pH 3). SIRV2 encodes a Holliday junction resolving enzyme (SIRV2 Hjr) that has been proposed as a key enzyme in SIRV2 genome replication. The molecular mechanism for SIRV2 Hjr four-way junction cleavage bias, minimal requirements for four-way junction cleavage, and substrate specificity were determined. SIRV2 Hjr cleaves four-way DNA junctions with a preference for cleavage of exchange strand pairs, in contrast to host-derived resolving enzymes, suggesting fundamental differences in substrate recognition and cleavage among closely related Sulfolobus resolving enzymes. Unlike other viral resolving enzymes, such as T4 endonuclease VII or T7 endonuclease I, that cleave branched DNA replication intermediates, SIRV2 Hjr cleavage is specific to four-way DNA junctions and inactive on other branched DNA molecules. In addition, a specific interaction was detected between SIRV2 Hjr and the SIRV2 virion body coat protein (SIRV2gp26). Based on this observation, a model is proposed linking SIRV2 Hjr genome resolution to viral particle assembly

Data publication with the structural biology data grid supports live analysis

Access to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data. sbgrid. org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis

Spatial and temporal analysis of electric wind generation intermittency and dynamics

A spatial and temporal analysis of wind power generation characteristics was conducted in order to determine the implications of intermittent wind generation dynamics on the profile of the electric loads that must be balanced by dispatchable electrical generators on the electric grid. A parametric analysis was conducted to evaluate the sensitivity of the typical magnitudes of wind power fluctuations on different timescales, power variation range, typical daily and seasonal wind profiles to wind farm size and regional distribution. A methodology to evaluate wind dynamics based on power spectral density analyses have been developed. Results indicate that increasing the size of a local wind farm significantly reduced the magnitude of wind power fluctuations on timescales faster than 12 h, with the largest reductions occurring at the fastest timescales. Additional reductions in power fluctuations can be achieved with the implementation of local and regional distribution of wind turbines in disperse high wind areas. In these cases, it was discovered that the timescale band within which the largest reductions in power fluctuations occurred was dependent on regional geographic features, and did not necessarily correspond to the fastest timescales. In addition, it was also discovered that the aggregation of wind power from different regions could produce a more uniform frequency distribution of power fluctuation reductions. © 2011 Elsevier Ltd

Crystal structures of 3-methyladenine DNA glycosylase MagIII and the recognition of alkylated bases

International audienc

Spatial and temporal analysis of electric wind generation intermittency and dynamics

A spatial and temporal analysis of wind power generation characteristics was conducted in order to determine the implications of intermittent wind generation dynamics on the profile of the electric loads that must be balanced by dispatchable electrical generators on the electric grid. A parametric analysis was conducted to evaluate the sensitivity of the typical magnitudes of wind power fluctuations on different timescales, power variation range, typical daily and seasonal wind profiles to wind farm size and regional distribution. A methodology to evaluate wind dynamics based on power spectral density analyses have been developed. Results indicate that increasing the size of a local wind farm significantly reduced the magnitude of wind power fluctuations on timescales faster than 12 h, with the largest reductions occurring at the fastest timescales. Additional reductions in power fluctuations can be achieved with the implementation of local and regional distribution of wind turbines in disperse high wind areas. In these cases, it was discovered that the timescale band within which the largest reductions in power fluctuations occurred was dependent on regional geographic features, and did not necessarily correspond to the fastest timescales. In addition, it was also discovered that the aggregation of wind power from different regions could produce a more uniform frequency distribution of power fluctuation reductions. © 2011 Elsevier Ltd