bluuebunny/crossref_metadata_2025 huggingface dataset:
The Development of Autonomy in Preschool Mandarin Chinese-Speaking Children's Play Narratives
Authors: Chang Chien-ju
Published: November 2010

This paper aims to examine to what extent preschool Mandarin Chinese-speaking children can create an autonomous replica play narrative. Twenty-four Taiwanese children, 12 four-year-olds and 12 six-year-olds, participated in this study. The focus of investigation is on the linguistic resources (i.e., temporal and referential devices) the children use to maintain story lines and to mark shifts between types of talk in replica play. Developmental shifts are evident in these children's use of temporal and referential devices to build up a coherent play narrative. The four-year-olds exhibit a great difficulty sustaining their narrative talk, making use of temporal devices, and managing reference in their replica play. The six-year-olds, in comparison, use clearer reference and more temporal and causal connectives, but their ability to achieve autonomy in play narratives is limited. Developmental differences found in this study, in general, accord with crosslinguistic results.
Clinicians' Perceptions of Children's Oral Personal Narratives
Authors: Perez Carmela , Tager-Flusberg Helen
Published: November 2010

A diverse group of child clinicians (n — 39) rated paragraph-long transcriptions of two Euro-American, two African-American, and two Latino children's oral narratives. Clinicians were asked to rate the logic, cohesion, and comprehensibility of the stories using 6-point scales. They were also asked to give a rough estimate of the children's IQ, to comment on the existence of emotional/behavioral and/or learning/language problems, and to assign possible diagnoses. The results indicated clinicians' ratings of the Latino narratives were significantly different from ratings of the Euro-American and African-American narratives, as confirmed by Scheffe post hoc analysis. Diagnoses revealed a distribution by ethnicity of children. Euro-Americans received 21 diagnoses, African-Americans received 33 diagnoses, and Latinos received 53 diagnoses. Further, clinicians' ethnicity and gender did not account for any group differences. The implications of these findings are twofold. First, clinicians seem to be unaware of the differences in Latino children's narrative structure, and seem to be penalizing them for not conforming to the Euro-American structure. Second, it appears that clinicians training and practicing in the U.S. tend to adopt a Euro-American perspective which may desensitize them as to the narrative intricacies of their own culture.
Transferring and Transforming Cultural Norms
Authors: Dills Vivian Lee
Published: November 2010

In this essay, I describe moments in my mother's life and examine them as living narratives or "lifestories" and apply critical theory and analysis that has traditionally been reserved for written narratives. I argue that these moments are teaching tools that reinforce and sometimes challenge cultural norms and discuss how her living narratives were revised by me as I began to "tell" them to my own children. I apply performance narrative, fiction, and Native American literature theories to these narratives. I point out the cultural and generational differences in me and my mother, and discuss the influence of the different regions where we spent our childhoods. This essay is a comparative literary study of a multigenerational living text in process. (Literature, Critical Theory)
Young Adults' Relationship Memories and the Life Story
Authors: Thorne Avril , Cutting Linda , Skaw Danielle
Published: November 2010

Personal memories increasingly have been implicated in the process of identity-making, but systematic study of stability and change in memory telling is rare. Comparisons of relationship memories told by 46 young adults during two interviews separated by about 6 months found moderate thematic consistency across the two sets of memories. The similarity obtained despite a high turnover in the specific events that were selected for telling each time. These findings, paired with ancillary data indicating a similarly high turnover for earliest memories, high points, and low points, suggest that relationship memories for young adults serve more as examples of enduring concerns than as essential landmarks for the life story. Twice-told tales showed quite stable storylines, and were most dense for memories of intimate encounters in late adolescence, suggesting the centrality of this period for the development of relationship identity. {Development, Narrative, Memory, Identity)
Things We Can Learn From Repeated Tellings of the Same Experience
Authors: Chafe Wallace
Published: November 2010

The study of repeated tellings of the same experience by the same speaker has been a neglected source of insights into the human mind. The content of the mind (here termed underlying experience) cannot be equated with any particular verbalization of it. Language, mental imagery, and emotions provide different windows on it, but the very fact that repeated tellings differ shows that language is not in any one-to-one relation with it. The comparison of such tellings can, however, allow us to zero in on the nature of underlying experience by showing what is constant and what variable. Such comparisons suggest that experience is stored in terms of relatively large topics and relatively small foci that are activated, one at a time, as a topic is scanned. They suggest, too, that decisions regarding sentence boundaries are made as one is talking, so that sentences appear not to reflect units of memory. Whereas ideas of events and their participants show stability, the orientations to such ideas that are expressed by the inflectional elements of language are free to vary. The relative importance of ideas may be inferred from their constancy across repetitions. Chronology appears to be important when it is a relevant relation between ideas, but when it is not relevant there is room for random ordering. These points will be illustrated with a comparison of two tellings that were produced fifteen months apart. (Narrative Structure, Memory)
Politeness Markers and Psychological Complements
Authors: Minami Masahiko
Published: November 2010

Frames are not only universal cognitive categories to explain the narrator's consciousness, they are also a socioculturally determined concept. Using verse/stanza analysis, which is widely accepted as an effective means of analyzing narrative structure, this study examines how narrative discourse markers and linguistic strategies contribute to the culturally specific framing of Japanese oral personal narratives. Japanese adult narrators were found to employ particular linguistic markers: (1) the formal verb-ending patterns that are often pointed out as politeness markers indicating the insider-outsider distinction, and (2) psychological complements that are generally assumed to express a greater degree of hesitation and softness. It was found, however, that in narrative contexts, these two markers are more likely to appear at the end of a stanza than in any other position. In other words, in contrast to the general belief that these markers serve as devices to show politeness, when investigated from the viewpoint of narrative discourse, they have turned out to possess multiple functions, such as a psychologically effective means for cultural and contextual framing. These findings also call for an awareness on the part of Japanese language instructors to emphasize such multiple functions in the class-room, so that they may help prevent learners from making subtle but potentially critical mistakes.
Telling Tales
Authors: Cavallaro Johnson Greer
Published: November 2010

This paper presents a progressive understanding of the shifting power relations that are constructed in the telling of a courtship and marriage narrative by an Australian-Italian couple who have been married for well over thirty years. The focus on relations of power is pursued through attention to aspects of the sequenced talk to show how the couple work together to tell the interviewer a newsworthy story that is "old news" to each other. The use of two analytical frames derived from different combinations of narrative analysis (NA), conversational analysis (CA) and critical discourse analysis (CDA) facilitates two readings of the same data. The two frames provide different means of showing how the story tellers negotiate and happily survive specific threats to produce a congenially delivered story in the end. The use of first, a "bottom-up" approach to the data followed by a "top-down" approach enables power relations first at the local level between husband and wife to be inserted later into a wider ideological and discursive context. Overall the paper shows how the application of multiple perspectives to narrative analysis can deepen our understanding of storytelling practices. (Narrative analysis, Conversation analysis, Critical discourse analysis)
The Function of Self-Aggrandizement in Storytelling
Authors: Oliveira Miguel
Published: November 2010

It has often been pointed out that narratives (of personal experience, specifically) are ordinarily told with the prime intent of revealing the narrator's meritous qualities (Labov & Waletzky, 1967; Labov, 1972; Møler, 1996; Quasthoff & Nikolaus, 1982). Although this claim has often been criticized, the debate on this issue is still remarkably peripheral. The hypothesis of this paper is that the function of self-aggrandizement is always at work in the process of storytelling, even if this doesn't seem to be the case. In an attempt to test this hypothesis, two narratives told in Portuguese by different Brazilian speakers are analyzed using a discourse analytic approach.
Life Story Coherence and its Relation to Psychological Well-Being
Authors: Baerger Dana Royce , McAdams Dan P.
Published: November 2010

Over the past few years, the concept of coherence as it applies to people's storied accounts of their lives has become an increasingly popular topic. However, theories of coherence have been slow to appear, and a comprehensive definition of the construct has yet to be presented by researchers. Moreover, almost no work has been done relating the concept of coherence to the particular form of the life story. Thus, the aims of the present study were twofold: first, to investigate whether it is possible to construct a reliable coding scheme for life story coherence, and second, to examine the relationships between life story coherence and mental health. The results of the study indicate that the life story coherence coding system is a reliable measure, and that the coherence construct is therefore amenable to quantitative analysis. The most important finding of this study was that, as predicted, life story coherence demonstrated a statistically significant relationship to psychological well-being. This finding thus lends statistical credibility to the claims of narrative psychologists, who argue that mental well-being is related to, if not the result of, a well-integrated and coherent life story.
Remembering as Social Practice
Authors: Middleton David , Hewitt Helen L.
Published: November 2010

This work represents the development of two lines of interest, one in the study of social practices of remembering and the other concerning issues of identity in the care of people with profound learning difficulties. We examine of the way life story work is used as a resource in providing for continuities in the experience of people with profound learning difficulties when moved from hospital to community based care. Our concern is the way carers attend to issues of identity in their relationships with people who are unable to speak on their own behalf. We discuss how identities are accomplished as part of the social practice of remembering in the construction of life story books designed to resource continuities of identities across changes in the provision of care. Identities are not examined in terms of some subjective representation of coherence across time and space. We examine the way social organisation of remembering in life story work makes visible identities in terms of continuities of participation in the social practices that make up the conditions of living of the recipients of care and the working practices of those who provide it.
The Transformation of Narrative Syntax into Institutional Memory
Authors: Linde Charlotte
Published: November 2010

Narrative has been analyzed as a way of recounting the memory of the past and negotiating current group membership. But in an institutional context, it crucially functions to project the future, in constructing a record which can serve as an institutional memory available in case of possible challenges. Using as data an extended oral narrative from a social service agency about an incident of violence by a client, this study shows that the strongest structural constraints on the discourse and syntactic structure of the narrative are the requirements for a bureaucratically adequate written record. This analysis serves as a case study of how the larger social structure of legal requirements for adequate records serves to shape the structure of oral narrative, as well as a demonstration of the work oral narrative does in producing and reproducing institutional memory. (Discourse, Narrative, Memory, Bureaucratic Language, Language of Violence)
Telling It How It Was
Authors: Aldridge Michelle , Wood Joanne
Published: November 2010

While a number of weaknesses have been identified in children's eyewitness, or evidential narrative accounts (e.g., Aldridge & Wood, 1998; Richardson, 1993; Walker & Warren, 1995), analyses of children's non-evidential narratives indicate that children as young as two years can be competent narrators (e.g., Fivush, Gray & Fromhoff, 1987). A variety of factors might contribute to the child's reported poorer performance in the evidential setting. For example, the interview topic (and associated consequences) is likely to be more stressful, the child is less likely to be familiar with the interview setting and the interviewer, and the child is less likely to be prompted for an answer in the evidential setting.
This study examines young children's narrative performance in an evidential and in a non-evidential (experimental) setting to investigate which factors might contribute to differences in narrative performance. Findings suggest that, while children's narrative competence develops with age, situational factors largely account for the differences in performance in children's evidential and non-evidential narratives. However, we do suggest that interviewers could do more to facilitate, in a non-leading fashion, children's evidential narratives. More specifically, we propose that children should be offered a 'second chance' to tell their story before the interviewer moves on to specific questioning.
Modality and Tense in Children's Autobiographical Accounts
Authors: Quigley Jean
Published: November 2010

This is a study of modal time in the autobiographical narratives of a group of five, eight and twelve year old children. Specifically, it is a description of the discourse functions associated with the English modal auxiliaries in conjunction with tense markings in the narratives. The auxiliaries {can, could, will, would, may, must, might, shall, should, ought) are a set of grammatical functors that express a range of related concepts such as ability, permission, possibility, desire, intention and obligation. The narratives are discussed based on a form of variation analysis focusing on both the grammatical and the discursive shape of the stories. It is part of a wider exploration of the role played by language and grammar in the construction of self and identity.
{Child language, Narrative development, Tense and modality, Functional linguistics, Grammatical analysis)
A Sense of the Sacred
Authors: Black Helen K.
Published: November 2010

Fifty white and 12 African-American elderly, middle class women were interviewed regarding their life history, self-concept and financial circumstances. The middle class women were a contrast group to women living in poverty. The latter was the focus group for the research project, "Chronic Poverty and the Self in Later Life." Using two case studies (1 from each middle class group), the women's spirituality was explored through their narratives. The study shows that aspiration to middle class norms, such as financial security and acquiring the accouterments of success, holds a complex relationship to a spiritual worldview. Spirituality meshed with the family, work and volunteer oriented lives of the women. Themes of gender were complexly interwoven into women's spirituality. Material acquisitions and financial success remained important to the women interviewed. Age did not lessen a need for, or enjoyment of "things" in the women's lives. (Ethnographic narration, Older women's identity, "Middle-class" spirituality)
Narratives and Lives
Authors: Bell Susan E.
Published: November 2010

This paper considers how social structure and available cultural discourses are connected to and reflected in narratives by two DES cancer daughters—women who have had vaginal cancer as a result of their prenatal exposure to DES, a drug prescribed to their mothers to prevent miscarriage. In a narrative analysis of in-depth interviews, it shows how the construction of scientific knowledge about DES, and social/political knowledge produced by women's health activists, shaped relationships between DES daughters and their doctors when they were diagnosed with cancer. It locates terrains of power and resistance in their lives, placing them in historically and culturally specific medical and feminist contexts, in order to highlight the presence and play of power in their relationships with and responses to the news of cancer given to them by their doctors. It also explores the joint production of narratives by interviewer and subject, as well as the influence of dominant and emerging discourses on the researcher's and subject's sense making strategies and knowledge production.
Narrative Identity
Authors: Kyratzis Amy
Published: November 2010

Recently, researchers have been interested in narrative as a conversational point-making activity. Some of the features of narrative (e.g., its "objectivity", Benveniste, 1971) render it ideally suited for self-exploration and positioning of the self with respect to societal institutions (Polanyi, 1989), especially in the context of conversations within friendship groups (Coates, 1996). While past research has often focused on self-constructing and political uses of narratives of personal experience, the present study examines such uses with respect to narratives produced during preschoolers' dramatic play in friendship groups. An ethnographic-sociolinguistic study that followed friendship groups in two preschool classrooms of a California university children's center was conducted. Children were videotaped in their two most representative friendship groups each academic quarter. Narrative was coded when children used explicit proposals of irrealis in one of three forms: the marked subjunctive (past tense irrealis marking in English, e.g., "they were hiding"); the paraphrastic subjunctive (unmarked irrealis proposals such as "and I'm shy"); and pretend directives such as "pretend" ("pretend we're Shy Wizards"). Also, instances of character speech were counted as narrative. Children used con-trastive forms (subjunctive, coherence markers vs. absence of subjunctive; pitch variation) to mark different phases within narrative. Collaborative self-construction was seen in the linguistic forms they used (pretend statements; tag questions; "and-elaborations") and in the identities the children constructed for their protagonists. Girls' protagonists suggested they valued qualities of lovingness, graciousness, and attractiveness. The protagonists the boys constructed suggested they valued physical power. Girls had a greater reliance on story for self-construction than boys did. It is notable that the dramatic play narratives produced during children's play in friendship groups serve some of the same functions in positioning participants with respect to one another and exploring possible selves collaboratively with one another that personal experience narratives serve in adult intimate social groups.
The state of the nation in CPD: a literature review
Authors: McCormick Robert
Published: December 2010

A recent literature review in support of the ‘State of the Nation’ (SoN) investigation into CPD in England indicated a number of limitations both in how researchers see CPD and how schools themselves participate and register this participation in such activities. The SoN review was conducted in the period from late 2007 to early 2008, but was subsequently updated during 2009, to form a starting point for this article. The initial review focused only on the UK literature and was confined to the period 2004–2007. Although the focus was the UK, there was a considerable amount of international literature collected at the time and used subsequently to place this picture in a broader perspective. This broader perspective was an examination of how teachers create and share professional practice, and hence develop that practice within their schools. This work was based on looking at the importance of networks, drawing not only on an extensive consideration of relevant literature, but also on a major study of how schools create and share practice associated with the introduction of assessment for learning practices in classrooms and schools. The SoN study indicates that the CPD literature has not served the field well, in terms of a paucity of literature on what happens in ordinary schools and under‐theorised work, particularly in terms of teacherlearning. The study of networks indicates that there is potential to open up new areas of research and indeed practice in schools. However, there are a number of approaches based either on networks as communities or on electronic metaphors of networks that pay insufficient attention to the thriving network theory literature. This article examines some of the contributions that network thinking can make.
Planning and organisation of teachers' Continuous Professional Development in schools in England
Authors: Pedder David , Opfer V. Darleen
Published: December 2010

This article focuses on the planning and organisation of teachers' continuous professional development as part of the nationally representative Schools and Continuing Professional Development in England – State of the Nation research study (SoNS), commissioned by the Training and Development Agency for Schools (TDA). Thematic analysis of data developed from the literature review, qualitative research, and survey strands of the SoN study led to the identification of four issues related to the planning and organisation of CPD in schools in England: (1) there is a lack of strategic planning of CPD provision to balance effectively between individual and organisational learning needs and national policy priorities; (2) organisational choices made in schools about roles and responsibilities do not always support or help to develop effective CPD planning and provision; (3) little progress has been made in the promotion of the New Professionalism in schools through developing closer alignment between Professional Standards, Performance Management and CPD; (4) school systems and processes for evaluating the effectiveness of CPD provision tend to be developed without reference to planned outcomes, specific criteria or value for money judgements. The article concludes with a number of recommendations for policy and practice.
One Thousand Endoscopic Skull Base Surgical Procedures Demystifying the Infection Potential: Incidence and Description of Postoperative Meningitis and Brain Abscesses
Authors: Kono Yuriko , Prevedello Daniel M. , Snyderman Carl H. , Gardner Paul A. , Kassam Amin B. , Carrau Ricardo L. , Byers Karin E.
Published: December 2010

Background.

Endonasal endoscopic skull base surgery (ESBS) is perceived as having a high risk of infection because it is performed through the sinuses, which are not sterile.

Objective.

To identify the bacteriological characteristics, incidence, mortality, and risk factors for intracranial infection after ESBS.

Methods.

A retrospective analysis of the first 1,000 ESBS procedures performed at the University of Pittsburgh Medical Center from 1998 to 2008.

Results.

In 18 cases (1.8%), the patient developed meningitis. In 2 cases, the patient died within 2 months after surgery, of noninfectious causes. In 11 cases, cerebrospinal fluid (CSF) cultures had positive results. There were no predominant pathogens. Male sex (odds ratio [OR], 3.97 [95% confidence interval {CI}, 1.21-13.03]; P = .02), history of a craniotomy or endonasal surgery (OR, 4.77 [95% CI, 1.68-13.56];P = .003), surgerywith higher levels of complexity (OR, 6.60 [95% CI, 1.77-24.70];P = .005), the presence of an external ventricular drain or ventriculoperitoneal shunt at the time of surgery (OR, 6.38 [95% CI, 1.07-38.09]; P = .04), and postoperative CSF leak (OR, 12.99 [95% CI, 4.24-39.82]; P<.001) were risk factors for infection.

Conclusion.

The incidence of infection of 1.8% in ESBS is comparable to that in open craniotomy. The most important risk factor was a postoperative CSF leak. All patients recovered from their infection.
Gab2 regulates cytoskeletal organization and migration of mammary epithelial cells by modulating RhoA activation
Authors: Abreu Maria Teresa Herrera , Hughes William E. , Mele Katarina , Lyons Ruth J. , Rickwood Danny , Browne Brigid C. , Bennett Haley L. , Vallotton Pascal , Brummer Tilman , Daly Roger J.
Published: December 2010

The docking protein Gab2 is overexpressed in several human malignancies, including breast cancer, and is associated with increased metastatic potential. Here we report that Gab2 overexpression in MCF-10A mammary epithelial cells led to delayed cell spreading, a decrease in stress fibers and mature focal adhesions, and enhanced cell migration. Expression of a Gab2 mutant uncoupled from 14-3-3-mediated negative feedback (Gab22×A) led to a more mesenchymal morphology and acquisition of invasive potential. Expression of either Gab2 or Gab22×Aled to decreased activation of RhoA, but only the latter increased levels of Rac-GTP. Expression of constitutively active RhoA in MCF-10A/Gab2 cells restored stress fibers and focal adhesions, indicating that Gab2 signals upstream of RhoA to suppress these structures. Mutation of the two Shp2-binding sites to phenylalanine (Gab2ΔShp2) markedly reduced the effects of Gab2 on cellular phenotype and RhoA activation. Expression of Gab2 or Gab22×A, but not Gab2ΔShp2, promoted Vav2 phosphorylation and plasma membrane recruitment of p190A RhoGAP. Knockdown of p190A RhoGAP reversed Gab2-mediated effects on stress fibers and focal adhesions. The identification of a novel pathway downstream of Gab2 involving negative regulation of RhoA by p190A RhoGAP sheds new light on the role of Gab2 in cancer progression.
The EDD E3 ubiquitin ligase ubiquitinates and up-regulates β-catenin
Authors: Hay-Koren Avital , Caspi Michal , Zilberberg Alona , Rosin-Arbesfeld Rina
Published: December 2010

Wnt/β-catenin signaling plays a central role in development and is also involved in a diverse array of diseases. β-Catenin activity is tightly regulated via a multiprotein complex that includes the kinase glycogen synthase kinase-3β (GSK-3β). GSK-3β phosphorylates β-catenin, marking it for ubiquitination and degradation via the proteasome. Thus in regulation of the Wnt pathway, the ubiquitin system is known to be involved mostly in mediating the turnover of β-catenin, resulting in reduced Wnt signaling levels. Here we report that an arm of the ubiquitin system increases β-catenin protein levels. We show that GSK-3β directly interacts with the E3 ubiquitin ligase identified by differential display (EDD) that also binds β-catenin. Expression of EDD leads to enhanced nuclear accumulation of both GSK-3β and β-catenin and results in up-regulation of β-catenin expression levels and activity. Importantly, EDD ubiquitinates β-catenin through Lys29- or Lys11-linked ubiquitin chains, leading to enhanced stability of β-catenin. Our results demonstrate a role for the ubiquitin system in up-regulation of the Wnt signaling pathway, suggesting that EDD could function as a colorectal oncogene.
NOA1 is an essential GTPase required for mitochondrial protein synthesis
Authors: Kolanczyk Mateusz , Pech Markus , Zemojtel Tomasz , Yamamoto Hiroshi , Mikula Ivan , Calvaruso Maria-Antonietta , van den Brand Mariël , Richter Ricarda , Fischer Bjoern , Ritz Anita , Kossler Nadine , Thurisch Boris , Spoerle Ralf , Smeitink Jan , Kornak Uwe , Chan Danny , Vingron Martin , Martasek Pavel , Lightowlers Robert N. , Nijtmans Leo , Schuelke Markus , Nierhaus Knud H. , Mundlos Stefan
Published: December 2010

Nitric oxide associated-1 (NOA1) is an evolutionarily conserved guanosine triphosphate (GTP) binding protein that localizes predominantly to mitochondria in mammalian cells. On the basis of bioinformatic analysis, we predicted its possible involvement in ribosomal biogenesis, although this had not been supported by any experimental evidence. Here we determine NOA1 function through generation of knockout mice and in vitro assays. NOA1-deficient mice exhibit midgestation lethality associated with a severe developmental defect of the embryo and trophoblast. Primary embryonic fibroblasts isolated from NOA1 knockout embryos show deficient mitochondrial protein synthesis and a global defect of oxidative phosphorylation (OXPHOS). Additionally, Noa1–/– cells are impaired in staurosporine-induced apoptosis. The analysis of mitochondrial ribosomal subunits from Noa1–/– cells by sucrose gradient centrifugation and Western blotting showed anomalous sedimentation, consistent with a defect in mitochondrial ribosome assembly. Furthermore, in vitro experiments revealed that intrinsic NOA1 GTPase activity was stimulated by bacterial ribosomal constituents. Taken together, our data show that NOA1 is required for mitochondrial protein synthesis, likely due to its yet unidentified role in mitoribosomal biogenesis. Thus, NOA1 is required for such basal mitochondrial functions as adenosine triphosphate (ATP) synthesis and apoptosis.
PAIR3, an axis-associated protein, is essential for the recruitment of recombination elements onto meiotic chromosomes in rice
Authors: Wang Kejian , Wang Mo , Tang Ding , Shen Yi , Qin Baoxiang , Li Ming , Cheng Zhukuan
Published: December 2010

During meiosis, the paired homologous chromosomes are tightly held together by the synaptonemal complex (SC). This complex consists of two parallel axial/lateral elements (AEs/LEs) and one central element. Here, we observed that PAIR3 localized to the chromosome core during prophase I and associated with both unsynapsed AEs and synapsed LEs. Analyses of the severe pair3 mutant demonstrated that PAIR3 was essential for bouquet formation, homologous pairing and normal recombination, and SC assembly. In addition, we showed that although PAIR3 was not required for the initial recruitment of PAIR2, it was required for the proper association of PAIR2 with chromosomes. Dual immunostaining revealed that PAIR3 highly colocalized with REC8. Moreover, studies using a rec8 mutant indicated that PAIR3 localized to chromosomes in a REC8-dependent manner.
High-quality annotation of promoter regions for 913 bacterial genomes
Authors: Rangannan Vetriselvi , Bansal Manju
Published: December 2010

Motivation: The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms.

Results: Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset.

Availability: The binary executable for ‘PromPredict’ algorithm (implemented in PERL and supported on Linux and MS Windows) and the predicted promoter data for all 913 microbial genomes are available at http://nucleix.mbu.iisc.ernet.in/prombase/.

Contact:  mb@mbu.iisc.ernet.in

Supplementary information:  Supplementary data are available at Bioinformatics online.
Flapjack—graphical genotype visualization
Authors: Milne Iain , Shaw Paul , Stephen Gordon , Bayer Micha , Cardle Linda , Thomas William T. B. , Flavell Andrew J. , Marshall David
Published: December 2010

Summary: New software tools for graphical genotyping are required that can routinely handle the large data volumes generated by the high-throughput single-nucleotide polymorphism (SNP) platforms, genotyping-by-sequencing and other comparable genotyping technologies. Flapjack has been developed to facilitate analysis of these data, providing real time rendering with rapid navigation and comparisons between lines, markers and chromosomes, with visualization, sorting and querying based on associated data, such as phenotypes, quantitative trait loci or other mappable features.

Availability: Flapjack is freely available for Microsoft Windows, Mac OS X, Linux and Solaris, and can be downloaded from http://bioinf.scri.ac.uk/flapjack

Contact:  flapjack@scri.ac.uk
HiTEC: accurate error correction in high-throughput sequencing data
Authors: Ilie Lucian , Fazayeli Farideh , Ilie Silvana
Published: November 2010

Motivation: High-throughput sequencing technologies produce very large amounts of data and sequencing errors constitute one of the major problems in analyzing such data. Current algorithms for correcting these errors are not very accurate and do not automatically adapt to the given data.

Results: We present HiTEC, an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods. Our approach provides significantly higher accuracy than previous methods. It is time and space efficient and works very well for all read lengths, genome sizes and coverage levels.

Availability: The source code of HiTEC is freely available at www.csd.uwo.ca/~ilie/HiTEC/.

Contact:  ilie@csd.uwo.ca
Inhibition of RIP2's tyrosine kinase activity limits NOD2-driven cytokine responses
Authors: Tigno-Aranjuez Justine T. , Asara John M. , Abbott Derek W.
Published: December 2010

Upon intracellular bacterial exposure, the Crohn's disease and sarcoidosis susceptibility protein NOD2 (nucleotide oligomerization domain protein 2) binds to the protein kinase RIP2 (receptor-interacting protein 2) to coordinate NF-κB (nuclear factor κ B)-mediated cytokine responses. While RIP2 clearly has kinase activity, the function of its kinase domain has been enigmatic. Although originally classified as a serine–threonine kinase based on homology scans, we find that RIP2 also has tyrosine kinase activity. RIP2 undergoes autophosphorylation on Tyr 474 (Y474). This phosphorylation event is necessary for effective NOD2 signaling and does not occur in the presence of the most common Crohn's disease-associatedNOD2allele. Given this tyrosine kinase activity, a small-molecule inhibitor screen designed to identify pharmacologic agents that inhibit RIP2's tyrosine kinase activity was performed. At nanomolar concentrations, the EGFR (epidermal growth factor receptor) tyrosine kinase inhibitors gefitinib (Iressa) and erlotinib (Tarceva) were found to inhibit both RIP2 tyrosine phosphorylation and MDP (muramyl dipeptide)-induced cytokine release in a variety of NOD2 hyperactivation states. This effect is specific for RIP2 and does not depend on EGFR. The finding that RIP2 has tyrosine kinase activity and the finding that gefitinib and erlotinib, two agents already used clinically for cancer chemotherapy, can inhibit this activity suggest that RIP2's tyrosine kinase activity could be targeted specifically in the treatment of inflammatory diseases.
Break-induced ATR and Ddb1–Cul4Cdt2 ubiquitin ligase-dependent nucleotide synthesis promotes homologous recombination repair in fission yeast
Authors: Moss Jennifer , Tinline-Purvis Helen , Walker Carol A. , Folkes Lisa K. , Stratford Michael R. , Hayles Jacqueline , Hoe Kwang-Lae , Kim Dong-Uk , Park Han-Oh , Kearsey Stephen E. , Fleck Oliver , Holmberg Christian , Nielsen Olaf , Humphrey Timothy C.
Published: December 2010

Nucleotide synthesis is a universal response to DNA damage, but how this response facilitates DNA repair and cell survival is unclear. Here we establish a role for DNA damage-induced nucleotide synthesis in homologous recombination (HR) repair in fission yeast. Using a genetic screen, we found the Ddb1–Cul4Cdt2 ubiquitin ligase complex and ribonucleotide reductase (RNR) to be required for HR repair of a DNA double-strand break (DSB). The Ddb1–Cul4Cdt2 ubiquitin ligase complex is required for degradation of Spd1, an inhibitor of RNR in fission yeast. Accordingly, deleting spd1+ suppressed the DNA damage sensitivity and the reduced HR efficiency associated with loss of ddb1+ or cdt2+. Furthermore, we demonstrate a role for nucleotide synthesis in postsynaptic gap filling of resected ssDNA ends during HR repair. Finally, we define a role for Rad3 (ATR) in nucleotide synthesis and HR through increasing Cdt2 nuclear levels in response to DNA damage. Our findings support a model in which break-induced Rad3 and Ddb1–Cul4Cdt2 ubiquitin ligase-dependent Spd1 degradation and RNR activation promotes postsynaptic ssDNA gap filling during HR repair.
Constitutive mTORC1 activation by a herpesvirus Akt surrogate stimulates mRNA translation and viral replication
Authors: Chuluunbaatar Uyanga , Roller Richard , Feldman Morris E. , Brown Stuart , Shokat Kevan M. , Mohr Ian
Published: December 2010

All viruses require cellular ribosomes to translate their mRNAs. Viruses producing methyl-7 (m7) GTP-capped mRNAs, like Herpes Simplex Virus-1 (HSV-1), stimulate cap-dependent translation by activating mTORC1 to inhibit the translational repressor 4E-binding protein 1 (4E-BP1). Here, we establish that the HSV-1 kinase Us3 masquerades as Akt to activate mTORC1. Remarkably, Us3 displays no sequence homology with the cellular kinase Akt, yet directly phosphorylates tuberous sclerosis complex 2 (TSC2) on the same sites as Akt. TSC2 depletion rescued Us3-deficient virus replication, establishing that Us3 enhances replication by phosphorylating TSC2 to constitutively activate mTORC1, effectively bypassing S6K-mediated feedback inhibition. Moreover, Us3 stimulated Akt substrate phosphorylation in infected cells, including FOXO1 and GSK3. Thus, HSV-1 encodes an Akt surrogate with overlapping substrate specificity to activate mTORC1, stimulating translation and virus replication. This establishes Us3 as a unique viral kinase with promising drug development potential.
Dynamics in the mixed microbial concourse
Authors: Wintermute Edwin H. , Silver Pamela A.
Published: December 2010

Isolated, clonal populations of cells are rarely found in nature. The emergent properties of microbial consortia present a challenge for the systems approach to biology, as chances for competition, communication, or collaboration multiply with the number of interacting agents. This review focuses on recent work on intercourse within biofilms, among quorum-sensing populations, and between cross-feeding metabolic cooperators. New tools from synthetic biology allow microbial interactions to be designed and tightly controlled, creating valuable model systems. We address both natural and synthetic partnerships, with an emphasis on how system behaviors derive from the properties of their components. Essential features of microbial biology arose in the context of a very mixed culture and cannot be understood without unscrambling it.
MicroRNAs prevent precocious gene expression and enable pattern formation during plant embryogenesis
Authors: Nodine Michael D. , Bartel David P.
Published: December 2010

Arabidopsis embryos lacking DICER-LIKE1 (DCL1), which is required for microRNA (miRNA) biogenesis, arrest early in development. To assess the functions of embryonic miRNAs, we determined the developmental and molecular consequences of DCL1 loss. We found that DCL1 is required for cell differentiation events as early as the eight-cell stage and soon thereafter for proper division of the hypophysis and subprotoderm cells. By the early globular (∼32-cell) stage, dcl1-null mutant embryos overexpress ∼50 miRNA targets. In dcl1 eight-cell embryos, the two most up-regulated targets are those of miR156 and encode SPL10 and SPL11 transcription factors. SPL10 and SPL11 are derepressed >150-fold in dcl1 embryos and are redundantly required for the dcl1 early patterning defects. Moreover, as early as the eight-cell stage, miR156-mediated repression of zygotic SPL transcripts prevents premature accumulation of transcripts from genes normally induced during the embryonic maturation phase. Thus, the first perceptible molecular function of plant embryonic miRNAs is the opposite of that in vertebrates; in vertebrates, miRNAs sharpen the first developmental transition, whereas in plants, they forestall developmental transitions by repressing mRNAs that act later. We propose that, by preventing precocious expression of differentiation-promoting transcription factors, miRNAs enable proper embryonic patterning.
Deterioration without replenishment—the misery of oocyte cohesin: Figure 1.
Authors: Jessberger Rolf
Published: December 2010

Humans suffer a steep increase in aneuploidies when oocytes age, and deterioration of cohesin was suggested recently as a prominent cause. In the November 15, 2010, issue of Genes & Development, Tachibana-Konwalski and colleagues (pp. 2505–2516) answered a question central to this hypothesis: Can cohesin be reloaded onto mouse oocyte chromosomes long after birth? They found that it cannot, or at least not with an efficiency adequate to rescue cohesin deficiency. With no chance for sufficient replenishment, age-related loss of sister chromatid cohesion seems unavoidable.
Purification of Arabidopsis DNA for Genotyping in 96-Well Plates Using the Puregene DNA Purification System
Authors: Li Yan
Published: December 2010

INTRODUCTION

This protocol describes the purification of Arabidopsis DNA in high-throughput format using the Puregene DNA purification system adapted to 96-well plates.
Defolliculation of Xenopus Oocytes
Authors: Sive Hazel L. , Grainger Robert M. , Harland Richard M.
Published: December 2010

INTRODUCTION

It is possible to microinject Xenopus oocytes that are still contained within their ovarian follicles, but most researchers find it more convenient to work with defolliculated oocytes. Defolliculation can be carried out enzymatically by treatment with collagenase, or it can be performed manually. Enzymatic treatment is recommended for preparation of large numbers of oocytes (more than 1000); however, this treatment causes complications because it often damages the quality of the oocytes. The manual procedure, which requires some practice, is recommended for experiments requiring only a few hundred oocytes. This protocol details both the enzymatic and manual procedures for defolliculation of Xenopus oocytes.
An Agar Mount for Observation of Caenorhabditis elegans Embryos
Authors: Walston Timothy , Hardin Jeff
Published: December 2010

INTRODUCTION

The Caenorhabditis elegans embryo is particularly amenable to microscopy and embryological studies because of its short developmental time, transparent shell, and nonpigmented cells. The agar mount described in this protocol is an easy way to prepare live C. elegans embryos for microscopic visualization. The mount slightly embeds the embryo in agar to hold it in place. The mount also slightly compresses the embryo to provide consistent orientation such that every embryo will be positioned with either its right side or its left side facing the objective. Other techniques can result in random orientations that complicate analysis and make identification of individual blastomeres more challenging.
Laser Killing of Blastomeres in Caenorhabditis elegans
Authors: Walston Timothy , Hardin Jeff
Published: December 2010

INTRODUCTION

The Caenorhabditis elegans embryo is particularly amenable to microscopy and embryological studies because of its short developmental time, transparent shell, and nonpigmented cells. Within the embryo, contacts between cells often establish the polarization of neighboring cells. Blastomere isolation and recombination experiments have led to a wealth of understanding of the events in the four-cell C. elegans embryo. However, identifying individual blastomeres after isolation at stages past the four-cell stage is limited. In addition, removal of blastomeres from their native surroundings can interfere with many cell contacts besides the contacts of interest. An alternative approach for studying cell interactions within the C. elegans embryo is to use laser ablation of individual cells. Laser ablation can be used to kill one of two cells in contact with each other to understand what happens when a cell no longer signals to its neighbor. Additionally, killing a cell that is between two cells that will eventually contact each other can result in the corpse of the cell forming a steric barrier between the cells, preventing the contact. This protocol describes laser ablation of embryos mounted on an agar mount.
Molecular Evolution and Selection Patterns of Plant F-Box Proteins with C-Terminal Kelch Repeats
Authors: Schumann Nadine , Navarro-Quezada Aura , Ullrich Kristian , Kuhl Carsten , Quint Marcel
Published: December 2010

The F-box protein superfamily represents one of the largest families in the plant kingdom. F-box proteins phylogenetically organize into numerous subfamilies characterized by their carboxyl (C)-terminal protein-protein interaction domain. Among the largest F-box protein subfamilies in plant genomes are those with C-terminal kelch repeats. In this study, we analyzed the phylogeny and evolution of F-box kelch proteins/genes (FBKs) in seven completely sequenced land plant genomes including a bryophyte, a lycophyte, monocots, and eudicots. While absent in prokaryotes, F-box kelch proteins are widespread in eukaryotes. Nonplant eukaryotes usually contain only a single FBK gene. In land plant genomes, however, FBKs expanded dramatically. Arabidopsis thaliana, for example, contains at least 103 F-box genes with well-conserved C-terminal kelch repeats. The construction of a phylogenetic tree based on the full-length amino acid sequences of the FBKs that we identified in the seven species enabled us to classify FBK genes into unstable/stable/superstable categories. In contrast to superstable genes, which are conserved across all seven species, kelch domains of unstable genes, which are defined as lineage specific, showed strong signatures of positive selection, indicating adaptational potential. We found evidence for conserved protein features such as binding affinities toward A. thaliana SKP1-like adaptor proteins and subcellular localization among closely related FBKs. Pseudogenization seems to occur only rarely, but differential transcriptional regulation of close relatives may result in subfunctionalization.