Reconstitution of the strand invasion step of double-strand break repair using human Rad51 Rad52 and RPA proteins.

The human Rad51 recombinase is essential for the repair of double-strand breaks in DNA that occur in somatic cells after exposure to ionising irradiation, or in germ line cells undergoing meiotic recombination. The initiation of double-strand break repair is thought to involve resection of the double-strand break to produce 3'-ended single-stranded (ss) tails that invade homologous duplex DNA. Here, we have used purified proteins to set up a defined in vitro system for the initial strand invasion step of double-strand break repair. We show that (i) hRad51 binds to the ssDNA of tailed duplex DNA molecules, and (ii) hRad51 catalyses the invasion of tailed duplex DNA into homologous covalently closed DNA. Invasion is stimulated by the single-strand DNA binding protein RPA, and by the hRad52 protein. Strikingly, hRad51 forms terminal nucleoprotein filaments on either 3' or 5'-ssDNA tails and promotes strand invasion without regard for the polarity of the tail. Taken together, these results show that hRad51 is recruited to regions of ssDNA occurring at resected double-strand breaks, and that hRad51 shows no intrinsic polarity preference at the strand invasion step that initiates double-strand break repair.

Cost information in engineering design -Potentials and limitations of activity-based costing

The purpose of this thesis is to analyse activity-based costing (ABC) and possible modified versions ofit in engineering design context. The design engineers need cost information attheir decision-making level and the cost information should also have a strong future orientation. These demands are high because traditional management accounting has concentrated on the direct actual costs of the products. However, cost accounting has progressed as ABC was introduced late 1980s and adopted widely bycompanies in the 1990s. The ABC has been a success, but it has gained also criticism. In some cases the ambitious ABC systems have become too complex to build,use and update. This study can be called an action-oriented case study with some normative features. In this thesis theoretical concepts are assessed and allowed to unfold gradually through interaction with data from three cases. The theoretical starting points are ABC and theory of engineering design process (chapter2). Concepts and research results from these theoretical approaches are summarized in two hypotheses (chapter 2.3). The hypotheses are analysed with two cases (chapter 3). After the two case analyses, the ABC part is extended to cover alsoother modern cost accounting methods, e.g. process costing and feature costing (chapter 4.1). The ideas from this second theoretical part are operationalized with the third case (chapter 4.2). The knowledge from the theory and three cases is summarized in the created framework (chapter 4.3). With the created frameworkit is possible to analyse ABC and its modifications in the engineering design context. The framework collects the factors that guide the choice of the costing method to be used in engineering design. It also illuminates the contents of various ABC-related costing methods. However, the framework needs to be further tested. On the basis of the three cases it can be said that ABC should be used cautiously when formulating cost information for engineering design. It is suitable when the manufacturing can be considered simple, or when the design engineers are not cost conscious, and in the beginning of the design process when doing adaptive or variant design. If the design engineers need cost information for the embodiment or detailed design, or if manufacturing can be considered complex, or when design engineers are cost conscious, the ABC has to be always evaluated critically.

A 3-step therapeutic strategy for severe alveolar proteinosis.

Pulmonary alveolar proteinosis (PAP) is characterized by accumulation of lipoproteinaceous material in the terminal airways. Whole lung lavage (WLL) remains the gold standard treatment but may be particularly challenging in cases of severe hypoxemia. We present a 3-step strategy that was used in a patient with PAP-associated refractory hypoxemia and that combined venovenous extracorporeal membrane oxygenation (vvECMO), double-lumen orotracheal intubation, and bilateral multisegmental sequential lavage (MSL). The procedure was well tolerated and permitted weaning from the ventilator.

Decoding auditory EEG responses in healthy and clinical populations: A comparative study.

BACKGROUND: Analyses of brain responses to external stimuli are typically based on the means computed across conditions. However in many cognitive and clinical applications, taking into account their variability across trials has turned out to be statistically more sensitive than comparing their means. NEW METHOD: In this study we present a novel implementation of a single-trial topographic analysis (STTA) for discriminating auditory evoked potentials at predefined time-windows. This analysis has been previously introduced for extracting spatio-temporal features at the level of the whole neural response. Adapting the STTA on specific time windows is an essential step for comparing its performance to other time-window based algorithms. RESULTS: We analyzed responses to standard vs. deviant sounds and showed that the new implementation of the STTA gives above-chance decoding results in all subjects (in comparison to 7 out of 11 with the original method). In comatose patients, the improvement of the decoding performance was even more pronounced than in healthy controls and doubled the number of significant results. COMPARISON WITH EXISTING METHOD(S): We compared the results obtained with the new STTA to those based on a logistic regression in healthy controls and patients. We showed that the first of these two comparisons provided a better performance of the logistic regression; however only the new STTA provided significant results in comatose patients at group level. CONCLUSIONS: Our results provide quantitative evidence that a systematic investigation of the accuracy of established methods in normal and clinical population is an essential step for optimizing decoding performance.

Perceptions of twelve-step mutual-help groups and their associations with motivation, treatment attendance and alcohol outcomes among chronically homeless individuals with alcohol problems.

BACKGROUND: Twelve-step mutual-help groups (TMGs) are among the most available forms of support for homeless individuals with alcohol problems. Qualitative research, however, has suggested that this population often has negative perceptions of these groups, which has been shown to be associated with low TMG attendance. It is important to understand this population's perceptions of TMGs and their association with alcohol outcomes to provide more appropriate and better tailored programming for this multiply affected population. The aims of this cross-sectional study were to (a) qualitatively examine perception of TMGs in this population and (b) quantitatively evaluate its association with motivation, treatment attendance and alcohol outcomes. METHODS: Participants (N=62) were chronically homeless individuals with alcohol problems who received single-site Housing First within a larger evaluation study. Perceptions of TMGs were captured using an open-ended item. Quantitative outcome variables were created from assessments of motivation, treatment attendance and alcohol outcomes. RESULTS: Findings indicated that perceptions of TMGs were primarily negative followed by positive and neutral perceptions, respectively. There were significant, positive associations between perceptions of TMGs and motivation and treatment attendance, whereas no association was found for alcohol outcomes. CONCLUSIONS: Although some individuals view TMGs positively, alternative forms of help are needed to engage the majority of chronically homeless individuals with alcohol problems.

Diploid males support a two-step mechanism of endosymbiont-induced thelytoky in a parasitoid wasp.

BACKGROUND: Haplodiploidy, where females develop from diploid, fertilized eggs and males from haploid, unfertilized eggs, is abundant in some insect lineages. Some species in these lineages reproduce by thelytoky that is caused by infection with endosymbionts: infected females lay haploid eggs that undergo diploidization and develop into females, while males are very rare or absent. It is generally assumed that in thelytokous wasps, endosymbionts merely diploidize the unfertilized eggs, which would then trigger female development. RESULTS: We found that females in the parasitoid wasp Asobara japonica infected with thelytoky-inducing Wolbachia produce 0.7-1.2 % male offspring. Seven to 39 % of these males are diploid, indicating that diploidization and female development can be uncoupled in A. japonica. Wolbachia titer in adults was correlated with their ploidy and sex: diploids carried much higher Wolbachia titers than haploids, and diploid females carried more Wolbachia than diploid males. Data from introgression lines indicated that the development of diploid individuals into males instead of females is not caused by malfunction-mutations in the host genome but that diploid males are most likely produced when the endosymbiont fails to activate the female sex determination pathway. Our data therefore support a two-step mechanism by which endosymbionts induce thelytoky in A. japonica: diploidization of the unfertilized egg is followed by feminization, whereby each step correlates with a threshold of endosymbiont titer during wasp development. CONCLUSIONS: Our new model of endosymbiont-induced thelytoky overthrows the view that certain sex determination mechanisms constrain the evolution of endosymbiont-induced thelytoky in hymenopteran insects. Endosymbionts can cause parthenogenesis through feminization, even in groups in which endosymbiont-diploidized eggs would develop into males following the hosts' sex determination mechanism. In addition, our model broadens our understanding of the mechanisms by which endosymbionts induce thelytoky to enhance their transmission to the next generation. Importantly, it also provides a novel window to study the yet-poorly known haplodiploid sex determination mechanisms in haplodiploid insects.

The Next Step: Darwin, Brontë, Fowles

The present article proposes Heathcliff and Sarah Woodruff as monstrous beings who reclaim their desire to be agent subjects in a society and a narrative which deny such a possibility. It would be possible to argue, however, that their monstrosity might be that of the unique specimen, the potential first stage towards the improvement of species through natural selection as theorized by Charles Darwin in 1859. The multiple references to Darwin’s study in the novel by JohnFowles demonstrate that such a theory could clarify what Sarah represents in the novel. In a retroactive manner, Darwinian theory might be used to understand what Heathcliff is, who Heathcliff is, and why he is the object of general animosity. It might be concluded that what is really monstrous about these twocharacters is that both are new specimens, avant la lèttre, and they occupy a space to which language has no access.

Three-step pathway engineering results in more incidence rate and higher emission of nerolidol and improved attraction of Diadegma semiclausum

The concentration and ratio of terpenoids in the headspace volatile blend of plants have a fundamental role in the communication of plants and insects. The sesquiterpene (E)-nerolidol is one of the important volatiles with effect on beneficial carnivores for biologic pest management in the field. To optimize de novo biosynthesis and reliable and uniform emission of (E)-nerolidol, we engineered different steps of the (E)-nerolidol biosynthesis pathway in Arabidopsis thaliana. Introduction of a mitochondrial nerolidol synthase gene mediates de novo emission of (E)-nerolidol and linalool. Co-expression of the mitochondrial FPS1 and cytosolic HMGR1 increased the number of emitting transgenic plants (incidence rate) and the emission rate of both volatiles. No association between the emission rate of transgenic volatiles and their growth inhibitory effect could be established. (E)-Nerolidol was to a large extent metabolized to non-volatile conjugates.

From bird to sparrow: Learning-induced modulations in fine-grained semantic discrimination.

Recognition of environmental sounds is believed to proceed through discrimination steps from broad to more narrow categories. Very little is known about the neural processes that underlie fine-grained discrimination within narrow categories or about their plasticity in relation to newly acquired expertise. We investigated how the cortical representation of birdsongs is modulated by brief training to recognize individual species. During a 60-minute session, participants learned to recognize a set of birdsongs; they improved significantly their performance for trained (T) but not control species (C), which were counterbalanced across participants. Auditory evoked potentials (AEPs) were recorded during pre- and post-training sessions. Pre vs. post changes in AEPs were significantly different between T and C i) at 206-232ms post stimulus onset within a cluster on the anterior part of the left superior temporal gyrus; ii) at 246-291ms in the left middle frontal gyrus; and iii) 512-545ms in the left middle temporal gyrus as well as bilaterally in the cingulate cortex. All effects were driven by weaker activity for T than C species. Thus, expertise in discriminating T species modulated early stages of semantic processing, during and immediately after the time window that sustains the discrimination between human vs. animal vocalizations. Moreover, the training-induced plasticity is reflected by the sharpening of a left lateralized semantic network, including the anterior part of the temporal convexity and the frontal cortex. Training to identify birdsongs influenced, however, also the processing of C species, but at a much later stage. Correct discrimination of untrained sounds seems to require an additional step which results from lower-level features analysis such as apperception. We therefore suggest that the access to objects within an auditory semantic category is different and depends on subject's level of expertise. More specifically, correct intra-categorical auditory discrimination for untrained items follows the temporal hierarchy and transpires in a late stage of semantic processing. On the other hand, correct categorization of individually trained stimuli occurs earlier, during a period contemporaneous with human vs. animal vocalization discrimination, and involves a parallel semantic pathway requiring expertise.

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations.

Biocuration has become a cornerstone for analyses in biology, and to meet needs, the amount of annotations has considerably grown in recent years. However, the reliability of these annotations varies; it has thus become necessary to be able to assess the confidence in annotations. Although several resources already provide confidence information about the annotations that they produce, a standard way of providing such information has yet to be defined. This lack of standardization undermines the propagation of knowledge across resources, as well as the credibility of results from high-throughput analyses. Seeded at a workshop during the Biocuration 2012 conference, a working group has been created to address this problem. We present here the elements that were identified as essential for assessing confidence in annotations, as well as a draft ontology--the Confidence Information Ontology--to illustrate how the problems identified could be addressed. We hope that this effort will provide a home for discussing this major issue among the biocuration community. Tracker URL: https://github.com/BgeeDB/confidence-information-ontology Ontology URL: https://raw.githubusercontent.com/BgeeDB/confidence-information-ontology/master/src/ontology/cio-simple.obo