Mre11 dimers coordinate DNA end bridging and nuclease processing in double-strand-break repair.

Mre11 forms the core of the multifunctional Mre11-Rad50-Nbs1 (MRN) complex that detects DNA double-strand breaks (DSBs), activates the ATM checkpoint kinase, and initiates homologous recombination (HR) repair of DSBs. To define the roles of Mre11 in both DNA bridging and nucleolytic processing during initiation of DSB repair, we combined small-angle X-ray scattering (SAXS) and crystal structures of Pyrococcus furiosus Mre11 dimers bound to DNA with mutational analyses of fission yeast Mre11. The Mre11 dimer adopts a four-lobed U-shaped structure that is critical for proper MRN complex assembly and for binding and aligning DNA ends. Further, mutations blocking Mre11 endonuclease activity impair cell survival after DSB induction without compromising MRN complex assembly or Mre11-dependant recruitment of Ctp1, an HR factor, to DSBs. These results show how Mre11 dimerization and nuclease activities initiate repair of DSBs and collapsed replication forks, as well as provide a molecular foundation for understanding cancer-causing Mre11 mutations in ataxia telangiectasia-like disorder (ATLD).

The Lancaster Sensorimotor Norms: multidimensional measures of perceptual and action strength for 40,000 English words.

Sensorimotor information plays a fundamental role in cognition. However, the existing materials that measure the sensorimotor basis of word meanings and concepts have been restricted in terms of their sample size and breadth of sensorimotor experience. Here we present norms of sensorimotor strength for 39,707 concepts across six perceptual modalities (touch, hearing, smell, taste, vision, and interoception) and five action effectors (mouth/throat, hand/arm, foot/leg, head excluding mouth/throat, and torso), gathered from a total of 3,500 individual participants using Amazon's Mechanical Turk platform. The Lancaster Sensorimotor Norms are unique and innovative in a number of respects: They represent the largest-ever set of semantic norms for English, at 40,000 words × 11 dimensions (plus several informative cross-dimensional variables), they extend perceptual strength norming to the new modality of interoception, and they include the first norming of action strength across separate bodily effectors. In the first study, we describe the data collection procedures, provide summary descriptives of the dataset, and interpret the relations observed between sensorimotor dimensions. We then report two further studies, in which we (1) extracted an optimal single-variable composite of the 11-dimension sensorimotor profile (Minkowski 3 strength) and (2) demonstrated the utility of both perceptual and action strength in facilitating lexical decision times and accuracy in two separate datasets. These norms provide a valuable resource to researchers in diverse areas, including psycholinguistics, grounded cognition, cognitive semantics, knowledge representation, machine learning, and big-data approaches to the analysis of language and conceptual representations. The data are accessible via the Open Science Framework (http://osf.io/7emr6/) and an interactive web application (https://www.lancaster.ac.uk/psychology/lsnorms/).

Culture and mood disorders: the effect of abstraction in image, narrative and film on depression and anxiety.

Can cultural representations be used to therapeutic effect in the treatment of mood disorders like depression and anxiety? This article develops a theoretical framework that outlines how this might be achieved by way of mid-level cultural metrics that allow otherwise heterogeneous forms of representation to be grouped together. Its prediction is that abstract representations-as measured by Shannon entropy-will impact positively on anxiety, where concrete representations will positively impact on depression. The background to the prediction comes from construal level theory, a branch of social psychology that deals with the effects of abstraction on psychological distance; the types of cultural representations analysed include image, narrative and film. With a view to evaluating the hypothesis, the article surveys the empirical literature in art therapy, creative bibliotherapy and cinema therapy.

Ethics-testing an eating disorder recovery memoir: a pre-publication experiment.

BACKGROUND: Narratives (including memoirs and novels) about eating disorders (EDs) are typically published with the intention to benefit readers, but survey evidence suggests that reading such narratives with an active ED may more often be harmful than helpful. To reduce the probability of inadvertent harm and learn more about how narrative reading and EDs interact, a pre-publication study was designed to determine whether or not a recovery memoir should be published. METHODS: 64 participants with a self-reported ED read either the experimental text (The Hungry Anorexic [HA]) or a control text (Ten Zen Questions [TZ]) over a roughly two-week period. All participants completed the Eating Disorder Examination Questionnaire (EDE-Q) and the Anorexia Nervosa Stages of Change Questionnaire (ANSOCQ) one week before and two weeks after reading, and answered three recurring open-ended questions at regular timepoints during and after the reading. Computational analysis of the free-text responses assessed text/response similarity and response characteristics on emotional, sensory, and action-effector dimensions. Both rating-scale and free-text data were analysed using mixed ANOVAs to test for effects of time and condition, and the university ethics board was notified in advance of the quantitative threshold for harmful effects that would prohibit the ED memoir from being published. RESULTS: On the two quantitative measures, there was an effect of time but not of condition: Significant improvement was found in both groups on the EDE-Q (with a medium-to-large effect size) and the ANSOCQ (with a very large effect size). In an ANCOVA analysis, no significant mediating effects were found for age, education, duration of professional support for the ED, or pre/post-reading BMI change. For the free-text responses, linguistic similarity measures indicated that HA responses most closely matched the text of HA, with the same being true for TZ. In a word-norm analysis, text condition significantly affected six emotional, sensory, and action-effector variables (interoception, olfaction, gustatory, mouth, torso, and hand/arm), mean scores for all of which were higher in HA responses than TZ responses. Close reading of readers' responses explored two potential mechanisms for the positive effects of time but not condition: engagement with the during-reading prompts as part of the experimental setup and engagement with the texts' dialogical form. CONCLUSIONS: The ED memoir was found not to yield measurably harmful effects for readers with an ED, and will therefore be published. The finding that significant improvement on both quantitative measures was observed irrespective of text condition suggests that positive effects may be attributable to linguistic characteristics shared by the two texts or to elements of the reading and/or reflective processes scaffolded by both. The quantitative results and the free-text testimony have implications for our understanding of bibliotherapy, "triggering", and the practicalities of responsible publishing.

This paper reports on an experiment designed to decide whether a memoir about recovery from an eating disorder (ED) should be published. Previous research suggested that reading books about EDs may have strongly negative effects, especially for individuals with an ED. In this experiment, 64 participants were randomly assigned to read either the memoir under investigation, The Hungry Anorexic (HA), or a book unrelated to EDs, Ten Zen Questions (TZ). Participants completed two questionnaires before and after reading the book over roughly two weeks: the Eating Disorder Examination Questionnaire (EDE-Q), a common measure of eating disorder severity, and the Anorexia Nervosa Stages of Change Questionnaire (ANSOCQ), used to assess attitudes to illness and recovery. Participants also answered three recurring open-ended questions at timepoints during and after their reading. The book would not be published if EDE-Q scores of participants in the HA group worsened significantly, and worsened more than those of participants in the TZ group. Scores on both measures improved significantly between pre- and post-reading for both groups, so the memoir will be published. The positive effects may be due to a feature shared by the two books or a feature of the reading process independent of the books themselves.

Language about the future on social media as a novel marker of anxiety and depression: A big-data and experimental analysis.

Anxiety and depression negatively impact many. Studies suggest depression is associated with future time horizons, or how "far" into the future people tend to think, and anxiety is associated with temporal discounting, or how much people devalue future rewards. Separate studies from linguistics and economics have shown that how people refer to future time predicts temporal discounting. Yet no one-that we know of-has investigated whether future time reference habits are a marker of anxiety and/or depression. We introduce the FTR classifier, a novel classification system researchers can use to analyse linguistic temporal reference. In Study 1, we used the FTR classifier to analyse data from the social-media website Reddit. Users who had previously posted popular contributions to forums about anxiety and depression referenced the future and past more often than controls, had more proximal future and past time horizons, and significantly differed in their linguistic future time reference patterns: They used fewer future tense constructions (e.g. will), fewer high-certainty constructions (certainly), more low-certainty constructions (could), more bouletic modal constructions (hope), and more deontic modal constructions (must). This motivated Study 2, a survey-based mediation analysis. Self-reported anxious participants represented future events as more temporally distal and therefore temporally discounted to a greater degree. The same was not true of depression. We conclude that methods which combine big-data with experimental paradigms can help identify novel markers of mental illness, which can aid in the development of new therapies and diagnostic criteria.

Human Mre11/human Rad50/Nbs1 and DNA ligase IIIalpha/XRCC1 protein complexes act together in an alternative nonhomologous end joining pathway.

Recent studies have implicated a poorly defined alternative pathway of nonhomologous end joining (alt-NHEJ) in the generation of large deletions and chromosomal translocations that are frequently observed in cancer cells. Here, we describe an interaction between two factors, hMre11/hRad50/Nbs1 (MRN) and DNA ligase IIIα/XRCC1, that have been linked with alt-NHEJ. Expression of DNA ligase IIIα and the association between MRN and DNA ligase IIIα/XRCC1 are altered in cell lines defective in the major NHEJ pathway. Most notably, DNA damage induced the association of these factors in DNA ligase IV-deficient cells. MRN interacts with DNA ligase IIIα/XRCC1, stimulating intermolecular ligation, and together these proteins join incompatible DNA ends in a reaction that mimics alt-NHEJ. Thus, our results provide novel mechanistic insights into the alt-NHEJ pathway that not only contributes to genome instability in cancer cells but may also be a therapeutic target.

Five studies evaluating the impact on mental health and mood of recalling, reading, and discussing fiction.

Does reading fiction improve mental health and well-being? We present the results of five studies that evaluated the impact of five forms of exposure to fiction. These included the effects of recalling reading fiction, of being prescribed fiction, of discussing fiction relative to non-fiction, and of discussing literary fiction relative to best-seller fiction. The first three studies directly recruited participants; the final two relied on scraped social media data from Reddit and Twitter. Results show that fiction can have a positive impact on measures of mood and emotion, but that a process of mnemonic or cognitive consolidation is required first: exposure to fiction does not, on its own, have an immediate impact on well-being.

Quantitative methods for group bibliotherapy research: a pilot study.

Background: Bibliotherapy is under-theorized and under-tested: Its purposes and implementations vary widely, and the idea that 'reading is good for you' is often more assumed than demonstrated. One obstacle to developing robust empirical and theoretical foundations for bibliotherapy is the absence of analytical methods capable of providing sensitive yet replicable insights into complex textual material. This pilot study offers a proof-of-concept for new quantitative methods including VAD (valence-arousal-dominance) modelling of emotional variance and doc2vec modelling of linguistic similarity. Methods: VAD and doc2vec modelling were used on conjunction with qualitative coding to analyse transcripts of reading-group discussions plus the literary texts being discussed, from two reading groups each meeting weekly for six weeks (including 9 participants [5 researchers (3 authors, 2 collaborators), 4 others] in Group 1, and 8 participants [2 authors, 6 others] in Group 2). Results: In-text-discussion similarity was inversely correlated with emotional volatility in the group discussions (arousal: r = -0.25; p = ns; dominance: r = 0.21; p = ns; valence: r = -0.28; p = ns). Enjoyment or otherwise of the texts was less significant than other factors in shaping the significance and potential benefits of participation. (Texts with unpleasant or disturbing content that strongly shaped subsequent discussions of these texts were still able to sponsor 'healthy' discussions of this content.). Conclusions: Our methods and findings offer for the field of bibliotherapy research both new possibilities for hypotheses to test, and viable ways of testing them. In particular, the use of natural language processing methods and word norm data offer valuable complements to intuitive human judgement and self-report when assessing the impact of literary materials. We also share observations on facilitation protocols, interpretative practices, and how our group reading model differs from other trials of group reading for wellbeing.

Thinking avant la lettre: A Review of 4E Cognition.

The "4E" approach to cognition argues that cognition does not occur solely in the head, but is also embodied, embedded, enacted, or extended by way of extra-cranial processes and structures. Though very much in vogue, 4E cognition has received relatively few critical evaluations. By reflecting on two recent collections, this article reviews the 4E paradigm with a view to assessing its strengths and weaknesses.

Gene editing and CRISPR in the clinic: current and future perspectives.

Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.

Fictional narrative as a variational Bayesian method for estimating social dispositions in large groups.

Modelling intentions in large groups is cognitively costly. Not alone must first order beliefs be tracked ('what does A think about X?'), but also beliefs about beliefs ('what does A think about B's belief concerning X?'). Thus linear increases in group size impose non-linear increases in cognitive processing resources. At the same time, however, large groups offer coordination advantages relative to smaller groups due to specialisation and increased productive capacity. How might these competing demands be reconciled? We propose that fictional narrative can be understood as a cultural tool for dealing with large groups. Specifically, we argue that prototypical action roles that are removed from real-world interactions function as interpretive priors in a form of variational Bayesian inference, such that they allow estimations can be made of unknown social motives. We offer support for this claim in two ways. Firstly, by evaluating the existing literature on narrative cognition and showing where it anticipates a variational model; and secondly, by simulation, where we show that an agent-based model naturally converges on a set of social categories that resemble narrative across a wide range of starting points.

Defective p53 response and apoptosis associated with an ataxia-telangiectasia-like phenotype.

Ataxia-telangiectasia mutated (ATM), the protein defective in ataxia-telangiectasia, plays a central role in DNA damage response and signaling to cell cycle checkpoints. We describe here a cell line from a patient with an ataxia-telangiectasia-like clinical phenotype defective in the p53 response to radiation but with normal ATM activation and efficient downstream phosphorylation of other ATM substrates. No mutations were detected in ATM cDNA. A normal level of interaction between p53 and peptidyl-prolyl-isomerase Pin1 suggests that posttranslational modification was intact in these cells but operating at reduced level. Defective p53 stabilization was accompanied by defective induction of p53 effector genes and failure to induce apoptosis in response to DNA-damaging agents. Continued association between p53 and murine double minute-2 (Mdm2) occurred in irradiated ATL2ABR cells in response to DNA damage, and incubation with Mdm2 antagonists, nutlins, increased the stabilization of p53 and its transcriptional activity but failed to induce apoptosis. These results suggest that ATM-dependent stabilization of p53 and induction of apoptosis by radiation involve an additional factor(s) that is defective in ATL2ABR cells.

Delivering CRISPR: a review of the challenges and approaches.

Gene therapy has long held promise to correct a variety of human diseases and defects. Discovery of the Clustered Regularly-Interspaced Short Palindromic Repeats (CRISPR), the mechanism of the CRISPR-based prokaryotic adaptive immune system (CRISPR-associated system, Cas), and its repurposing into a potent gene editing tool has revolutionized the field of molecular biology and generated excitement for new and improved gene therapies. Additionally, the simplicity and flexibility of the CRISPR/Cas9 site-specific nuclease system has led to its widespread use in many biological research areas including development of model cell lines, discovering mechanisms of disease, identifying disease targets, development of transgene animals and plants, and transcriptional modulation. In this review, we present the brief history and basic mechanisms of the CRISPR/Cas9 system and its predecessors (ZFNs and TALENs), lessons learned from past human gene therapy efforts, and recent modifications of CRISPR/Cas9 to provide functions beyond gene editing. We introduce several factors that influence CRISPR/Cas9 efficacy which must be addressed before effective in vivo human gene therapy can be realized. The focus then turns to the most difficult barrier to potential in vivo use of CRISPR/Cas9, delivery. We detail the various cargos and delivery vehicles reported for CRISPR/Cas9, including physical delivery methods (e.g. microinjection; electroporation), viral delivery methods (e.g. adeno-associated virus (AAV); full-sized adenovirus and lentivirus), and non-viral delivery methods (e.g. liposomes; polyplexes; gold particles), and discuss their relative merits. We also examine several technologies that, while not currently reported for CRISPR/Cas9 delivery, appear to have promise in this field. The therapeutic potential of CRISPR/Cas9 is vast and will only increase as the technology and its delivery improves.

Radiosensitization of head/neck squamous cell carcinoma by adenovirus-mediated expression of the Nbs1 protein.

PURPOSE: Local failure and toxicity to adjacent critical structures is a significant problem in radiation therapy of cancers of the head and neck. We are developing a gene therapy based method of sensitizing head/neck squamous cell carcinoma (HNSCC) to radiation treatment. As patients with the rare hereditary disorder, Nijmegen breakage syndrome, show radiation sensitivity we hypothesized that tumor-specific disruption of the function of the Nbs1 protein would lead to enhanced cellular sensitivity to ionizing radiation. EXPERIMENTAL PROCEDURES: We constructed two recombinant adenoviruses by cloning the full-length Nbs1 cDNA as well as the C-terminal 300 amino acids of Nbs1 into an adenovirus backbone under the control of a CMV promoter. The resulting adenoviruses were used to infect HNSCC cell line JHU011. These cells were evaluated for expression of the viral based constructs and assayed for clonogenic survival following radiation exposure. RESULTS: Exposure of cells expressing Nbs1-300 to ionizing radiation resulted in a small reduction in survival relative to cells infected with control virus. Surprisingly, expression of full-length Nbs1 protein resulted in markedly enhanced sensitivity to ionizing radiation. Furthermore, the use of a fractionated radiation scheme following virus infection demonstrates that expression of full-length Nbs1 protein results in significant reduction in cell survival. CONCLUSIONS: These results provide a proof of principle that disruption of Nbs1 function may provide a means of enhancing the radiosensitivity of head and neck tumors. Additionally, this work highlights the Mre11 complex as an attractive target for development of radiation sensitizers.

Functional Benefits of (Modest) Alcohol Consumption.

Alcohol use has a long and ubiquitous history. Despite considerable research on the misuse of alcohol, no one has ever asked why it might have become universally adopted, although the conventional view assumes that its only benefit is hedonic. In contrast, we suggest that alcohol consumption was adopted because it has social benefits that relate both to health and social bonding. We combine data from a national survey with data from more detailed behavioural and observational studies to show that social drinkers have more friends on whom they can depend for emotional and other support, and feel more engaged with, and trusting of, their local community. Alcohol is known to trigger the endorphin system, and the social consumption of alcohol may thus have the same effect as the many other social activities such as laughter, singing and dancing that we use as a means of servicing and reinforcing social bonds.

Mechanisms of eukaryotic DNA double strand break repair.

For all cells, a DNA double strand break (DSB) is a dangerous lesion that can have profound consequences for the genome. If a DSB is encountered during mitosis, chromosomal separation may be adversely affected. Alternatively, during S phase a DSB may cause replication fork stalling or collapse. Improperly repaired DSBs can result in chromosomal rearrangements, senescence or activation of apoptotic pathways. Cells have developed sophisticated recombination pathways to metabolize and repair DSBs quickly as well as the capacity to differentiate physiologically occurring breaks from life threatening lesions. The two major pathways of recombination repair are known as non-homologous end-joining (NHEJ) and homologous recombination (HR). In this review, we will discuss the detection, response, and repair of DSBs in eukaryotes.

Structural and functional analysis of Mre11-3.

The Mre11, Rad50 and Nbs1 proteins make up the conserved multi-functional Mre11 (MRN) complex involved in multiple, critical DNA metabolic processes including double-strand break repair and telomere maintenance. The Mre11 protein is a nuclease with broad substrate recognition, but MRN-dependent processes requiring the nuclease activity are not clearly defined. Here, we report the functional and structural characterization of a nuclease-deficient Mre11 protein termed mre11-3. Importantly, the hmre11-3 protein has wild-type ability to bind DNA, Rad50 and Nbs1; however, nuclease activity was completely abrogated. When expressed in cell lines from patients with ataxia telangiectasia-like disorder (ATLD), hmre11-3 restored the formation of ionizing radiation-induced foci. Consistent with the biochemical results, the 2.3 A crystal structure of mre11-3 from Pyrococcus furiosus revealed an active site structure with a wild-type-like metal-binding environment. The structural analysis of the H85L mutation provides a detailed molecular basis for the ability of mre11-3 to bind but not hydrolyze DNA. Together, these results establish that the mre11-3 protein provides an excellent system for dissecting nuclease-dependent and independent functions of the Mre11 complex.

Werner syndrome protein associates with gamma H2AX in a manner that depends upon Nbs1.

The WRN protein is mutated in the chromosomally unstable Werner syndrome (WS) and the Nbs1 protein is mutated in Nijmegen breakage syndrome (NBS). The Nbs1 protein is an integral component of the M/R/N complex. Although WRN is known to interact with this complex in response to gamma-irradiation, the mechanism of action is unclear. Here, we show that WRN co-localizes and associates with gamma H2AX, a marker protein of DNA double strand breaks (DSBs), after cellular exposure to gamma-irradiation. While the DNA damage-inducible Nbs1 foci formation is normal in WS cells, WRN focus formation is defective in NBS cells. Consistent with this, gamma H2AX colocalizes with Nbs1 in WS cells but not with WRN in NBS cells. The defective WRN-gamma H2AX association in NBS cells can be complemented with wild-type Nbs1, but not with an Nbs1 S343A point mutant that lacks an ATM phosphorylation site. WRN associates with H2AX in a manner dependent upon the M/R/N complex. Our results suggest a novel pathway in which Nbs1 may recruit WRN to the site of DNA DSBs in an ATM-dependent manner.

Differential arrangements of conserved building blocks among homologs of the Rad50/Mre11 DNA repair protein complex.

Structural maintenance of chromosomes (SMC) proteins have diverse cellular functions including chromosome segregation, condensation and DNA repair. They are grouped based on a conserved set of distinct structural motifs. All SMC proteins are predicted to have a bipartite ATPase domain that is separated by a long region predicted to form a coiled coil. Recent structural data on a variety of SMC proteins shows them to be arranged as long intramolecular coiled coils with a globular ATPase at one end. SMC proteins function in pairs as heterodimers or as homodimers often in complexes with other proteins. We expect the arrangement of the SMC protein domains in complex assemblies to have important implications for their diverse functions. We used scanning force microscopy imaging to determine the architecture of human, Saccharomyces cerevisiae, and Pyrococcus furiosus Rad50/Mre11, Escherichia coli SbcCD, and S.cerevisiae SMC1/SMC3 cohesin SMC complexes. Two distinct architectural arrangements are described, based on the way their components were connected. The eukaryotic complexes were similar to each other and differed from their prokaryotic and archaeal homologs. These similarities and differences are discussed with respect to their diverse mechanistic roles in chromosome metabolism.

Women favour dyadic relationships, but men prefer clubs: cross-cultural evidence from social networking.

The ability to create lasting, trust-based friendships makes it possible for humans to form large and coherent groups. The recent literature on the evolution of sociality and on the network dynamics of human societies suggests that large human groups have a layered structure generated by emotionally supported social relationships. There are also gender differences in adult social style which may involve different trade-offs between the quantity and quality of friendships. Although many have suggested that females tend to focus on intimate relations with a few other females, while males build larger, more hierarchical coalitions, the existence of such gender differences is disputed and data from adults is scarce. Here, we present cross-cultural evidence for gender differences in the preference for close friendships. We use a sample of ∼112,000 profile pictures from nine world regions posted on a popular social networking site to show that, in self-selected displays of social relationships, women favour dyadic relations, whereas men favour larger, all-male cliques. These apparently different solutions to quality-quantity trade-offs suggest a universal and fundamental difference in the function of close friendships for the two sexes.