Three attempts to replicate the moral licensing effect

NARCIS (Netherlands)

Blanken, I.; van de Ven, N.; Zeelenberg, M.; Meijers, Marijn H. C.

2014-01-01

The present work includes three attempts to replicate the moral licensing effect by Sachdeva, Iliev, and Medin (2009). The original authors found that writing about positive traits led to lower donations to charity and decreased cooperative behavior. The first two replication attempts (student

A Successful Test of Parallel Replication Teams in Teaching Research Methods

Science.gov (United States)

Standing, Lionel G.; Astrologo, Lisa; Benbow, Felecia F.; Cyr-Gauthier, Chelsea S.; Williams, Charlotte A.

2016-01-01

This paper describes the novel use of parallel student teams from a research methods course to perform a replication study, and suggests that this approach offers pedagogical benefits for both students and teachers, as well as potentially contributing to a resolution of the replication crisis in psychology today. Four teams, of five undergraduates…

Making Connections: Replicating and Extending the Utility Value Intervention in the Classroom

Science.gov (United States)

Hulleman, Chris S.; Kosovich, Jeff J.; Barron, Kenneth E.; Daniel, David B.

2017-01-01

We replicated and extended prior research investigating a theoretically guided intervention based on expectancy-value theory designed to enhance student learning outcomes (e.g., Hulleman & Harackiewicz, 2009). First, we replicated prior work by demonstrating that the utility value intervention, which manipulated whether students made…

Going Online to Make Learning Count

Directory of Open Access Journals (Sweden)

Cathy Brigham

2011-01-01

Full Text Available Adult students often come to higher education with college-level learning that they have acquired outside of the classroom – from the workplace, military service, self-study, or hobbies. For decades, many forward-thinking colleges and universities have been offering services to evaluate that learning and award it college credit that counts towards a degree. However, for a range of reasons, not every institution can offer prior learning assessment (PLA in every discipline or for every student. With funding from several U.S. philanthropic organizations, the Council for Adult and Experiential Learning (CAEL is launching Learning Counts, a national online service that will offer students a range of opportunities to have their learning evaluated for college credit. This online service will expand the capacity of institutions offering PLA to students and provide an efficient and scalable delivery mechanism for the awarding of credit through PLA.

Perfectionism in Gifted Adolescents: A Replication and Extension

Science.gov (United States)

Margot, Kelly C.; Rinn, Anne N.

2016-01-01

To provide further generalizability for the results garnered by two previous studies, the authors conducted a methodological replication. In addition to adding to the body of replication research done with gifted students, the purpose of this study was to examine perfectionism differences among gifted adolescents in regards to gender, birth order,…

An Evaluation of Copy Cover and Compare Spelling Intervention for an Elementary Student with Learning Disabilities: A Replication

Science.gov (United States)

Breach, Celena; McLaughlin, T. F.; Derby, K. Mark

2016-01-01

The purpose of this study was to increase the spelling performance for a 4th grade student with learning disabilities. The second objective was to replicate the document with the efficacy of Copy, Cover, and Compare (CCC) in spelling. The study was conducted in a resource room in a low socio-economic school in the Pacific Northwest. The skill…

Greenness and school-wide test scores are not always positively associated – A replication of "linking student performance in Massachusetts elementary schools with the 'greenness' of school surroundings using remote sensing"

Science.gov (United States)

Matthew H.E.M. Browning; Ming Kuo; Sonya Sachdeva; Kangjae Lee; Lynne Westphal

2018-01-01

Recent studies find vegetation around schools correlates positively with student test scores. To test this relationship in schools with less green cover and more disadvantaged students, we replicated a leading study, using six years of NDVI-derived greenness data to predict school-level math and reading achievement in 404 Chicago public schools. A direct replication...

Immunoregulatory T Cells May Be Involved in Preserving CD4 T Cell Counts in HIV-Infected Long-Term Nonprogressors and Controllers

DEFF Research Database (Denmark)

Gaardbo, Julie C; Ronit, Andreas; Hartling, Hans J

2014-01-01

BACKGROUND: HIV-infected controllers control viral replication and maintain normal CD4 T cell counts. Long-term nonprogressors (LTNPs) also maintain normal CD4 T cell counts but have ongoing viral replication. We hypothesized that immunoregulatory mechanisms are involved in preserved CD4 T cell...... of patients and controls. However, both ECs and LTNPs displayed a large proportion of activated Tregs suggesting immunoregulatory mechanisms to be involved in preserving CD4 T cell counts in HIV-infected nonprogressors....... counts in controllers and in LTNPs. METHODS: Twenty HIV-infected viremic controllers, 5 elite controllers (ECs), and 14 LTNPs were included in this cross-sectional study. For comparison, 25 progressors and 34 healthy controls were included. Regulatory T cells (Tregs), Treg subpopulations, CD161+Th17...

77 FR 13304 - Application for New Awards; Charter Schools Program (CSP); Grants for Replication and Expansion...

Science.gov (United States)

2012-03-06

... Replication and Expansion of High-Quality Charter Schools AGENCY: Office of Innovation and Improvement... Replication and Expansion of High-Quality Charter Schools Notice inviting applications for new awards for... effects on students, student academic achievement, staff, and parents. The purpose of the Replication and...

Is It Counting, or Is It Adding?

Science.gov (United States)

Eisenhardt, Sara; Fisher, Molly H.; Thomas, Jonathan; Schack, Edna O.; Tassell, Janet; Yoder, Margaret

2014-01-01

The Common Core State Standards for Mathematics (CCSSI 2010) expect second grade students to "fluently add and subtract within 20 using mental strategies" (2.OA.B.2). Most children begin with number word sequences and counting approximations and then develop greater skill with counting. But do all teachers really understand how this…

Studies on the Pulse Rate, Pedometer Count and Satisfactoin Degree at Various Exercise

OpenAIRE

小原, 史朗

2004-01-01

This investigation examined whether free exercise of students became good stimulation of breathing circulation function from relation of pulse rate and pedometer count. And, I examined it on satisfaction degree after exercise. Object person was 432 man students (total of 1391) and 94 woman students (total of 472). As for relation of pulse rate and pedometer count, statistical meaning was recognized by man and women. The exercise that a pulse rate and pedometer count were high together seemed ...

Evaluating the reproducibility of environmental radioactivity monitoring data through replicate sample analysis

International Nuclear Information System (INIS)

Lindeken, C.L.; White, J.H.; Silver, W.J.

1978-01-01

At the Lawrence Livermore Laboratory, about 10% of the sampling effort in the environmental monitoring program represents replicate sample collection. Replication of field samples was initiated as part of the quality assurance program for environmental monitoring to determine the reproducibility of environmental measurements. In the laboratory these replicates are processed along with routine samples. As all components of variance are included in analysis of such field samples, comparison of the analytical data from replicate analyses provides a basis for estimating the overall reproducibility of the measurements. The replication study indicates that the reproducibility of environmental radioactivity monitoring data is subject to considerably more variability than is indicated by the accompanying counting errors. The data are also compared with analyses of duplicate aliquots from a well mixed sample or with duplicate aliquots of samples with known radionuclide content. These comparisons show that most of the variability is associated with the collection and preparation of the sample rather than with the analytical procedures

Tutorial on Using Regression Models with Count Outcomes Using R

Directory of Open Access Journals (Sweden)

A. Alexander Beaujean

2016-02-01

Full Text Available Education researchers often study count variables, such as times a student reached a goal, discipline referrals, and absences. Most researchers that study these variables use typical regression methods (i.e., ordinary least-squares either with or without transforming the count variables. In either case, using typical regression for count data can produce parameter estimates that are biased, thus diminishing any inferences made from such data. As count-variable regression models are seldom taught in training programs, we present a tutorial to help educational researchers use such methods in their own research. We demonstrate analyzing and interpreting count data using Poisson, negative binomial, zero-inflated Poisson, and zero-inflated negative binomial regression models. The count regression methods are introduced through an example using the number of times students skipped class. The data for this example are freely available and the R syntax used run the example analyses are included in the Appendix.

How many bootstrap replicates are necessary?

Science.gov (United States)

Pattengale, Nicholas D; Alipour, Masoud; Bininda-Emonds, Olaf R P; Moret, Bernard M E; Stamatakis, Alexandros

2010-03-01

stopping criteria. Practitioners will no longer have to enter a guess nor worry about the quality of support values; moreover, with most counts of replicates in the 100-500 range, robust BS under ML inference becomes computationally practical for most datasets. The complete test suite is available at http://lcbb.epfl.ch/BS.tar.bz2, and BS with our stopping criteria is included in the latest release of RAxML v7.2.5, available at http://wwwkramer.in.tum.de/exelixis/software.html.

High Reproducibility of ELISPOT Counts from Nine Different Laboratories

Directory of Open Access Journals (Sweden)

Srividya Sundararaman

2015-01-01

Full Text Available The primary goal of immune monitoring with ELISPOT is to measure the number of T cells, specific for any antigen, accurately and reproducibly between different laboratories. In ELISPOT assays, antigen-specific T cells secrete cytokines, forming spots of different sizes on a membrane with variable background intensities. Due to the subjective nature of judging maximal and minimal spot sizes, different investigators come up with different numbers. This study aims to determine whether statistics-based, automated size-gating can harmonize the number of spot counts calculated between different laboratories. We plated PBMC at four different concentrations, 24 replicates each, in an IFN-γ ELISPOT assay with HCMV pp65 antigen. The ELISPOT plate, and an image file of the plate was counted in nine different laboratories using ImmunoSpot® Analyzers by (A Basic Count™ relying on subjective counting parameters set by the respective investigators and (B SmartCount™, an automated counting protocol by the ImmunoSpot® Software that uses statistics-based spot size auto-gating with spot intensity auto-thresholding. The average coefficient of variation (CV for the mean values between independent laboratories was 26.7% when counting with Basic Count™, and 6.7% when counting with SmartCount™. Our data indicates that SmartCount™ allows harmonization of counting ELISPOT results between different laboratories and investigators.

Looking Is Not Seeing and Listening Is Not Hearing: A Replication Study With Accelerated BSN Students.

Science.gov (United States)

Honan, Linda; Shealy, Sarah; Fennie, Kristopher; Duffy, Thomas C; Friedlaender, Linda; Del Vecchio, Megan

2016-01-01

Development of perceptual aptitude is a critical yet complex skill that requires the effective organization and interpretation of data using visual and auditory clinical observation. Educators face challenges in creating pedagogy that consistently demonstrates reliability and validity in fostering clinical skills. We have dependably used the arts as a means to improve students' auditory and visual skills, and this article will describe replication of our work with accelerated nursing students in a bachelor's program in their last semester of nursing school (n=23). Our results reveal that auscultative and observational abilities of soon-to-be registered nurses are in need of improvement. The use of art in a museum improves observational and assessment abilities, and music training increases auscultative interpretive skills significantly. Copyright © 2016 Elsevier Inc. All rights reserved.

Cross-Cultural and Intra-Cultural Differences in Finger-Counting Habits and Number Magnitude Processing: Embodied Numerosity in Canadian and Chinese University Students

Directory of Open Access Journals (Sweden)

Kyle Richard Morrissey

2016-04-01

Full Text Available Recent work in numerical cognition has shown-that number magnitude is not entirely abstract, and at least partly rooted in embodied and situated experiences, including finger-counting. The current study extends previous cross-cultural research to address within-culture individual differences in finger counting habits. Results indicated that Canadian participants demonstrated an additional cognitive load when comparing numbers that require more than one hand to represent, and this pattern of performance is further modulated by whether they typically start counting on their left hand or their right hand. Chinese students typically count on only one hand and so show no such effect, except for an increase in errors, similar to that seen in Canadians, for those whom self-identify as predominantly two-hand counters. Results suggest that the impact of finger counting habits extend beyond cultural experience and concord in predictable ways with differences in number magnitude processing for specific number-digits. We conclude that symbolic number magnitude processing is partially rooted in learned finger-counting habits, consistent with a motor simulation account of embodied numeracy and that argument is supported by both cross-cultural and within-culture differences in finger-counting habits.

Chameleon Chasing II: A Replication.

Science.gov (United States)

Newsom, Doug A.; And Others

1993-01-01

Replicates a 1972 survey of students, educators, and Public Relations Society of America members regarding who the public relations counselor really serves. Finds that, in 1992, most respondents thought primary responsibility was to the client, then to the client's relevant publics, then to self, then to society, and finally to media. Compares…

Psychological type and attitude toward Christianity: a replication.

Science.gov (United States)

Francis, Leslie J; Robbins, Mandy; Boxer, Anna; Lewis, Christopher Alan; McGuckin, Conor; McDaid, Charles J

2003-02-01

A sample of 149 university students completed the Francis Psychological Type Scales together with the Francis Scale of Attitude Toward Christianity. The data indicated that university students classified as Feeling Types hold a more positive attitude toward Christianity than those classified as Thinking Types. These findings replicate the 1999 report of Jones and Francis.

A Replication of the Internal Validity Structure of Three Major Teaching Rating Scales

Science.gov (United States)

Peters, Scott J.; Pereira, Nielsen

2017-01-01

Even as the importance of replication research has become more widely understood, the field of gifted education is almost completely devoid of replication studies. An area in which replication is a particular problem is in student identification research, since instrument validity is a necessary prerequisite for any sound psychometric decision. To…

Education: DNA replication using microscale natural convection.

Science.gov (United States)

Priye, Aashish; Hassan, Yassin A; Ugaz, Victor M

2012-12-07

There is a need for innovative educational experiences that unify and reinforce fundamental principles at the interface between the physical, chemical, and life sciences. These experiences empower and excite students by helping them recognize how interdisciplinary knowledge can be applied to develop new products and technologies that benefit society. Microfluidics offers an incredibly versatile tool to address this need. Here we describe our efforts to create innovative hands-on activities that introduce chemical engineering students to molecular biology by challenging them to harness microscale natural convection phenomena to perform DNA replication via the polymerase chain reaction (PCR). Experimentally, we have constructed convective PCR stations incorporating a simple design for loading and mounting cylindrical microfluidic reactors between independently controlled thermal plates. A portable motion analysis microscope enables flow patterns inside the convective reactors to be directly visualized using fluorescent bead tracers. We have also developed a hands-on computational fluid dynamics (CFD) exercise based on modeling microscale thermal convection to identify optimal geometries for DNA replication. A cognitive assessment reveals that these activities strongly impact student learning in a positive way.

Radiation-induced inhibition of human endothelial cells replicating in culture

International Nuclear Information System (INIS)

DeGowin, R.L.; Lewis, L.J.; Mason, R.E.; Borke, M.K.; Hoak, J.C.

1976-01-01

The radiosensitivity of some tumors may depend upon the sensitivity of their microvasculature to radiation. Heretofore, the dose-response of human endothelial cells replicating in tissue culture has not been published. In studies reported here, we exposed flasks containing 4 to 7 x 10 4 genetically identical human endothelial cells to doses of x irradiation from 125 to 1000 rad. During the phase of logarithmic growth, cell counts were compared to those of an unirradiated control to construct a dose--response curve. Similar studies were performed with normal fibroblasts. We found that 160 rad suppressed endothelial cell replication by 37 percent. Although recovery was evident with doses of 500 rad, no net increase in cell number occurred in 3 weeks in flasks of endothelial cells that received 750 or 1000 rad. Fibroblasts were slightly less sensitive under these conditions. To our knowledge, this is the first report of a radiation dose--response curve for human endothelial cells replicating in culture

Replication Rate, Framing, and Format Affect Attitudes and Decisions about Science Claims.

Science.gov (United States)

Barnes, Ralph M; Tobin, Stephanie J; Johnston, Heather M; MacKenzie, Noah; Taglang, Chelsea M

2016-01-01

A series of five experiments examined how the evaluation of a scientific finding was influenced by information about the number of studies that had successfully replicated the initial finding. The experiments also tested the impact of frame (negative, positive) and numeric format (percentage, natural frequency) on the evaluation of scientific findings. In Experiments 1 through 4, an attitude difference score served as the dependent measure, while a measure of choice served as the dependent measure in Experiment 5. Results from a diverse sample of 188 non-institutionalized U.S. adults (Experiment 2) and 730 undergraduate college students (Experiments 1, 3, and 4) indicated that attitudes became more positive as the replication rate increased and attitudes were more positive when the replication information was framed positively. The results also indicate that the manner in which replication rate was framed had a greater impact on attitude than the replication rate itself. The large effect for frame was attenuated somewhat when information about replication was presented in the form of natural frequencies rather than percentages. A fifth study employing 662 undergraduate college students in a task in which choice served as the dependent measure confirmed the framing effect and replicated the replication rate effect in the positive frame condition, but provided no evidence that the use of natural frequencies diminished the effect.

Replication Rate, Framing, and Format Affect Attitudes and Decisions about Science Claims

Directory of Open Access Journals (Sweden)

Ralph M. Barnes

2016-11-01

Full Text Available A series of five experiments examined how the evaluation of a scientific finding was influenced by information about the number of studies that had successfully replicated the initial finding. The experiments also tested the impact of frame (negative, positive and numeric format (percentage, natural frequency on the evaluation of scientific findings. In Experiments 1 through 4, an attitude difference score served as the dependent measure, while a measure of choice served as the dependent measure in Experiment 5. Results from a diverse sample of 188 non-institutionalized U.S. adults (Experiment 2 and 730 undergraduate college students (Experiments 1, 3, and 4 indicated that attitudes became more positive as the replication rate increased and attitudes were more positive when the replication information was framed positively. The results also indicate that the manner in which replication rate was framed had a greater impact on attitude than the replication rate itself. The large effect for frame was attenuated somewhat when information about replication was presented in the form of natural frequencies rather than percentages. A fifth study employing 662 undergraduate college students in a task in which choice served as the dependent measure confirmed the framing effect and replicated the replication rate effect in the positive frame condition, but provided no evidence that the use of natural frequencies diminished the effect.

Replication Rate, Framing, and Format Affect Attitudes and Decisions about Science Claims

Science.gov (United States)

Barnes, Ralph M.; Tobin, Stephanie J.; Johnston, Heather M.; MacKenzie, Noah; Taglang, Chelsea M.

2016-01-01

A series of five experiments examined how the evaluation of a scientific finding was influenced by information about the number of studies that had successfully replicated the initial finding. The experiments also tested the impact of frame (negative, positive) and numeric format (percentage, natural frequency) on the evaluation of scientific findings. In Experiments 1 through 4, an attitude difference score served as the dependent measure, while a measure of choice served as the dependent measure in Experiment 5. Results from a diverse sample of 188 non-institutionalized U.S. adults (Experiment 2) and 730 undergraduate college students (Experiments 1, 3, and 4) indicated that attitudes became more positive as the replication rate increased and attitudes were more positive when the replication information was framed positively. The results also indicate that the manner in which replication rate was framed had a greater impact on attitude than the replication rate itself. The large effect for frame was attenuated somewhat when information about replication was presented in the form of natural frequencies rather than percentages. A fifth study employing 662 undergraduate college students in a task in which choice served as the dependent measure confirmed the framing effect and replicated the replication rate effect in the positive frame condition, but provided no evidence that the use of natural frequencies diminished the effect. PMID:27920743

Tracking replicability as a method of post-publication open evaluation

Directory of Open Access Journals (Sweden)

Joshua eHartshorne

2012-03-01

Full Text Available Recent reports have suggested that many published results are unreliable. To increase the reliability and accuracy of published papers, multiple changes have been proposed, such as changes in statistical methods. We support such reforms. However, we believe that the incentive structure of scientific publishing must change for such reforms to be successful. Under the current system, the quality of individual scientists is judged on the basis of their number of publications and citations, with journals similarly judged via numbers of citations. Neither of these measures takes into account the replicability of the published findings, as false or controversial results are often particularly widely cited. We propose tracking replications as a means of post-publication evaluation, both to help researchers identify reliable findings and to incentivize the publication of reliable results.Tracking replications requires a database linking published studies that replicate one another. As any such database is limited by the number of replication attempts published, we propose establishing an open-access journal dedicated to publishing replication attempts. Data quality of both the database and the affiliated journal would be ensured through a combination of crowd-sourcing and peer review. As reports in the database are aggregated, ultimately it will be possible to calculate replicability scores, which may be used alongside citation counts to evaluate the quality of work published in individual journals. In this paper, we lay out a detailed description of how this system could be implemented, including mechanisms for compiling the information, ensuring data quality, and incentivizing the research community to participate.

The Impact of Teacher Study Groups in Vocabulary on Teaching Practice, Teacher Knowledge, and Student Vocabulary Knowledge: A Large-Scale Replication Study

Science.gov (United States)

Jayanthi, Madhavi; Dimino, Joseph; Gersten, Russell; Taylor, Mary Jo; Haymond, Kelly; Smolkowski, Keith; Newman-Gonchar, Rebecca

2018-01-01

The purpose of this replication study was to examine the impact of the Teacher Study Group (TSG) professional development in vocabulary on first-grade teachers' knowledge of vocabulary instruction and observed teaching practice, and on students' vocabulary knowledge. Sixty-two schools from 16 districts in four states were randomly assigned to…

Effects of morphine on replication of herpes simplex virus type 1 and 2

African Journals Online (AJOL)

USER

2009-05-17

May 17, 2009 ... virus genome has a double strand DNA which codes over. 70 gene products. HSV infection is the most ... essential for viral replication, unlike viral DNA poly- merase. It seems that an alternative method of ... tral red was used and plaques were counted after 12 h. Determination of morphine cytotoxicity.

Replicating a self-affirmation intervention to address gender differences: Successes and challenges

Science.gov (United States)

Kost-Smith, Lauren E.; Pollock, Steven J.; Finkelstein, Noah D.; Cohen, Geoffrey L.; Ito, Tiffany A.; Miyake, Akira

2012-02-01

We previously reported on the success of a psychological intervention implemented to reduce gender differences in achievement in an introductory college physics course. In this prior study, we found that the gender gap on exams and the FMCE among students who completed two 15-minute self-affirmation writing exercises was significantly reduced compared to the gender gap among students who completed neutral writing exercises. In a follow-up study we replicated the self-affirmation intervention in a later semester of the same course, with the same instructor. In this paper, we report the details and preliminary results of the replication study, where we find similar patterns along exams and course grades, but do not observe these patterns along the FMCE. We begin to investigate the critical features of replicating educational interventions, finding that replicating educational interventions is challenging, complex, and involves potentially subtle factors, some of which we explore and others that require further research.

A word-count approach to analyze linguistic patterns in the reflective writings of medical students

Directory of Open Access Journals (Sweden)

Chi-Wei Lin

2016-02-01

Full Text Available Background: Teaching reflection and administering reflective writing assignments to students are widely practiced and discussed in medical education and health professional education. However, little is known about how medical students use language to construct their narratives. Exploring students’ linguistic patterns in their reflective writings can facilitate understanding the scope and facets of their reflections and their representational or communication approaches to share their experiences. Moreover, research findings regarding gender differences in language use are inconsistent. Therefore, we attempted to examine how females and males differ in their use of words in reflective writing within our research circumstance to detect the unique and gender-specific approaches to learning and their applications. Methods: We analyzed the linguistic profiles of psychological process categories in the reflective writings of medical students and examined the difference in word usage between male and female medical students. During the first year of a clinical rotation, 60 fifth-year medical students wrote reflective narratives regarding pediatric patients and the psychosocial challenges faced by the patients and their family members. The narratives were analyzed using the Chinese version of Linguistic Inquiry and Word Count (CLIWC, a text analysis software program. Multivariate procedures were applied for statistical analysis. Results: Cognitive words were most pervasive, averaging 22.16%, whereas perceptual words (2.86% were least pervasive. Female students used more words related to positive emotions and sadness than did male students. The male students exceeded the female students only in the space category. The major limitation of this study is that CLIWC cannot directly acquire contextual text meanings; therefore, depending on the research topic, further qualitative study of the given texts might be necessary. Conclusions: To enhance students�

Dedicated education unit: implementing an innovation in replication sites.

Science.gov (United States)

Moscato, Susan R; Nishioka, Vicki M; Coe, Michael T

2013-05-01

An important measure of an innovation is the ease of replication and achievement of the same positive outcomes. The dedicated education unit (DEU) clinical education model uses a collaborative academic-service partnership to develop an optimal learning environment for students. The University of Portland adapted this model from Flinders University, Australia, to increase the teaching capacity and quality of nursing education. This article identifies DEU implementation essentials and reports on the outcomes of two replication sites that received consultation support from the University of Portland. Program operation information, including education requirements for clinician instructors, types of patient care units, and clinical faculty-to-student ratios is presented. Case studies of the three programs suggest the DEU model is adaptable to a range of different clinical settings and continues to show promise as one strategy for addressing the nurse faculty shortage and strengthening academic-clinical collaborations while maintaining quality clinical education for students. Copyright 2013, SLACK Incorporated.

Multiculturalism in Four Teacher Education Programs: For Replication or Transformation

Science.gov (United States)

Ensign, Jacque

2009-01-01

This article describes four teacher education programs and their student teachers' responses to why some students in their classrooms were not doing well. The responses and programs fell into two categories: education for replication of inequities and education for transformation. If teacher education programs want their prospective teachers to be…

Discussing the Need of Experimental Replication with 5th Grade Students Conducting a Mealworm Experiment

Science.gov (United States)

Asshoff, Roman

2017-01-01

Scientific inquiry requires the replication of results in experimental studies. Recent studies draw a severe picture on the need of replication and the difficulties in replicating already published studies. As replicated confirmation of results is the basis of scientific and medical research, there may be a need to introduce the topic of…

Institutional Ethos: Replicating the Student Experience

Science.gov (United States)

Wood, Cynthia Howman

2011-01-01

International branch campuses (IBCs) have been established in significant numbers over the past ten years. A common criticism of IBCs is that they cannot recreate the student culture of the home campus. While this is true, some IBCs have gone to great lengths not only to create a comparable culture for their students, but also to integrate their…

Counting and Surveying Homeless Youth: Recommendations from YouthCount 2.0!, a Community-Academic Partnership.

Science.gov (United States)

Narendorf, Sarah C; Santa Maria, Diane M; Ha, Yoonsook; Cooper, Jenna; Schieszler, Christine

2016-12-01

Communities across the United States are increasing efforts to find and count homeless youth. This paper presents findings and lessons learned from a community/academic partnership to count homeless youth and conduct an in depth research survey focused on the health needs of this population. Over a 4 week recruitment period, 632 youth were counted and 420 surveyed. Methodological successes included an extended counting period, broader inclusion criteria to capture those in unstable housing, use of student volunteers in health training programs, recruiting from magnet events for high risk youth, and partnering with community agencies to disseminate findings. Strategies that did not facilitate recruitment included respondent driven sampling, street canvassing beyond known hotspots, and having community agencies lead data collection. Surveying was successful in gathering data on reasons for homelessness, history in public systems of care, mental health history and needs, sexual risk behaviors, health status, and substance use. Youth were successfully surveyed across housing types including shelters or transitional housing (n = 205), those in unstable housing such as doubled up with friends or acquaintances (n = 75), and those who were literally on the streets or living in a place not meant for human habitation (n = 140). Most youth completed the self-report survey and provided detailed information about risk behaviors. Recommendations to combine research data collection with counting are presented.

The Money/Counting Kit. The Prospectus Series, Paper No. 6.

Science.gov (United States)

Musumeci, Judith

The Money/Counting Kit for Handicapped Children and Youth, frees the teacher from lessons in money and counting concepts and enables a student to learn at his own rate with immediate feedback from activity cards, name cards, thermoformed coin cards (optional), and self-instructional booklets. The activity cards, which may be used individually or…

Selection bias, vote counting, and money-priming effects: A comment on Rohrer, Pashler, and Harris (2015) and Vohs (2015).

Science.gov (United States)

Vadillo, Miguel A; Hardwicke, Tom E; Shanks, David R

2016-05-01

When a series of studies fails to replicate a well-documented effect, researchers might be tempted to use a "vote counting" approach to decide whether the effect is reliable-that is, simply comparing the number of successful and unsuccessful replications. Vohs's (2015) response to the absence of money priming effects reported by Rohrer, Pashler, and Harris (2015) provides an example of this approach. Unfortunately, vote counting is a poor strategy to assess the reliability of psychological findings because it neglects the impact of selection bias and questionable research practices. In the present comment, we show that a range of meta-analytic tools indicate irregularities in the money priming literature discussed by Rohrer et al. and Vohs, which all point to the conclusion that these effects are distorted by selection bias, reporting biases, or p-hacking. This could help to explain why money-priming effects have proven unreliable in a number of direct replication attempts in which biases have been minimized through preregistration or transparent reporting. Our major conclusion is that the simple proportion of significant findings is a poor guide to the reliability of research and that preregistered replications are an essential means to assess the reliability of money-priming effects. (c) 2016 APA, all rights reserved).

A Paper Model of DNA Structure and Replication.

Science.gov (United States)

Sigismondi, Linda A.

1989-01-01

A paper model which is designed to give students a hands-on experience during lecture and blackboard instruction on DNA structure is provided. A list of materials, paper patterns, and procedures for using the models to teach DNA structure and replication are given. (CW)

On Counting the Rational Numbers

Science.gov (United States)

Almada, Carlos

2010-01-01

In this study, we show how to construct a function from the set N of natural numbers that explicitly counts the set Q[superscript +] of all positive rational numbers using a very intuitive approach. The function has the appeal of Cantor's function and it has the advantage that any high school student can understand the main idea at a glance…

Temporal aggregation of migration counts can improve accuracy and precision of trends

Directory of Open Access Journals (Sweden)

Tara L. Crewe

2016-12-01

Full Text Available Temporal replicate counts are often aggregated to improve model fit by reducing zero-inflation and count variability, and in the case of migration counts collected hourly throughout a migration, allows one to ignore nonindependence. However, aggregation can represent a loss of potentially useful information on the hourly or seasonal distribution of counts, which might impact our ability to estimate reliable trends. We simulated 20-year hourly raptor migration count datasets with known rate of change to test the effect of aggregating hourly counts to daily or annual totals on our ability to recover known trend. We simulated data for three types of species, to test whether results varied with species abundance or migration strategy: a commonly detected species, e.g., Northern Harrier, Circus cyaneus; a rarely detected species, e.g., Peregrine Falcon, Falco peregrinus; and a species typically counted in large aggregations with overdispersed counts, e.g., Broad-winged Hawk, Buteo platypterus. We compared accuracy and precision of estimated trends across species and count types (hourly/daily/annual using hierarchical models that assumed a Poisson, negative binomial (NB or zero-inflated negative binomial (ZINB count distribution. We found little benefit of modeling zero-inflation or of modeling the hourly distribution of migration counts. For the rare species, trends analyzed using daily totals and an NB or ZINB data distribution resulted in a higher probability of detecting an accurate and precise trend. In contrast, trends of the common and overdispersed species benefited from aggregation to annual totals, and for the overdispersed species in particular, trends estimating using annual totals were more precise, and resulted in lower probabilities of estimating a trend (1 in the wrong direction, or (2 with credible intervals that excluded the true trend, as compared with hourly and daily counts.

Students’ Learning Obstacles and Alternative Solution in Counting Rules Learning Levels Senior High School

Directory of Open Access Journals (Sweden)

M A Jatmiko

2017-12-01

Full Text Available The counting rules is a topic in mathematics senior high school. In the learning process, teachers often find students who have difficulties in learning this topic. Knowing the characteristics of students' learning difficulties and analyzing the causes is important for the teacher, as an effort in trying to reflect the learning process and as a reference in constructing alternative learning solutions which appropriate to anticipate students’ learning obstacles. This study uses qualitative methods and involves 70 students of class XII as research subjects. The data collection techniques used in this study is diagnostic test instrument about learning difficulties in counting rules, observation, and interview. The data used to know the learning difficulties experienced by students, the causes of learning difficulties, and to develop alternative learning solutions. From the results of data analysis, the results of diagnostic tests researcher found some obstacles faced by students, such as students get confused in describing the definition, students difficulties in understanding the procedure of solving multiplication rules. Based on those problems, researcher analyzed the causes of these difficulties and make hypothetical learning trajectory as an alternative solution in counting rules learning.

Distributional Replication

OpenAIRE

Beare, Brendan K.

2009-01-01

Suppose that X and Y are random variables. We define a replicating function to be a function f such that f(X) and Y have the same distribution. In general, the set of replicating functions for a given pair of random variables may be infinite. Suppose we have some objective function, or cost function, defined over the set of replicating functions, and we seek to estimate the replicating function with the lowest cost. We develop an approach to estimating the cheapest replicating function that i...

Chromatin Immunoprecipitation of Replication Factors Moving with the Replication Fork

OpenAIRE

Rapp, Jordan B.; Ansbach, Alison B.; Noguchi, Chiaki; Noguchi, Eishi

2009-01-01

Replication of chromosomes involves a variety of replication proteins including DNA polymerases, DNA helicases, and other accessory factors. Many of these proteins are known to localize at replication forks and travel with them as components of the replisome complex. Other proteins do not move with replication forks but still play an essential role in DNA replication. Therefore, in order to understand the mechanisms of DNA replication and its controls, it is important to examine localization ...

Collaborative Strategic Reading: Replications with Consideration of the Role of Fidelity

Science.gov (United States)

Vaughn, Sharon; Roberts, Greg; Reutebuch, Colleen

2013-01-01

Collaborative Strategic Reading (CSR) is a multicomponent reading intervention aimed at improving students' text comprehension. Two 1-year randomized controlled trials were conducted to determine the efficacy of CSR with seventh and eighth grade students. The Year 2 replication study was identical to the original Year 1 study except that the…

Generalized estimators of avian abundance from count survey data

Directory of Open Access Journals (Sweden)

Royle, J. A.

2004-01-01

Full Text Available I consider modeling avian abundance from spatially referenced bird count data collected according to common protocols such as capture-recapture, multiple observer, removal sampling and simple point counts. Small sample sizes and large numbers of parameters have motivated many analyses that disregard the spatial indexing of the data, and thus do not provide an adequate treatment of spatial structure. I describe a general framework for modeling spatially replicated data that regards local abundance as a random process, motivated by the view that the set of spatially referenced local populations (at the sample locations constitute a metapopulation. Under this view, attention can be focused on developing a model for the variation in local abundance independent of the sampling protocol being considered. The metapopulation model structure, when combined with the data generating model, define a simple hierarchical model that can be analyzed using conventional methods. The proposed modeling framework is completely general in the sense that broad classes of metapopulation models may be considered, site level covariates on detection and abundance may be considered, and estimates of abundance and related quantities may be obtained for sample locations, groups of locations, unsampled locations. Two brief examples are given, the first involving simple point counts, and the second based on temporary removal counts. Extension of these models to open systems is briefly discussed.

Going Online to Make Learning Count

Science.gov (United States)

Brigham, Cathy; Klein-Collins, Rebecca

2011-01-01

Adult students often come to higher education with college-level learning that they have acquired outside of the classroom--from the workplace, military service, self-study, or hobbies. For decades, many forward-thinking colleges and universities have been offering services to evaluate that learning and award it college credit that counts towards…

Replication Catastrophe

DEFF Research Database (Denmark)

Toledo, Luis; Neelsen, Kai John; Lukas, Jiri

2017-01-01

Proliferating cells rely on the so-called DNA replication checkpoint to ensure orderly completion of genome duplication, and its malfunction may lead to catastrophic genome disruption, including unscheduled firing of replication origins, stalling and collapse of replication forks, massive DNA...... breakage, and, ultimately, cell death. Despite many years of intensive research into the molecular underpinnings of the eukaryotic replication checkpoint, the mechanisms underlying the dismal consequences of its failure remain enigmatic. A recent development offers a unifying model in which the replication...... checkpoint guards against global exhaustion of rate-limiting replication regulators. Here we discuss how such a mechanism can prevent catastrophic genome disruption and suggest how to harness this knowledge to advance therapeutic strategies to eliminate cancer cells that inherently proliferate under...

Development of a mobile application for manual traffic counts

Directory of Open Access Journals (Sweden)

Ghanim Mohammad

2017-01-01

Full Text Available The use of technology in performing traffic counts has become widely used by many transportation agencies and private sectors. Different technologies have been employed to perform such counts, such as inductive loops, image processing, Bluetooth technologies, and laser and infrared technologies. However, the use of these advanced technologies come with extra cost to develop, install, and maintain. While the use of advanced technologies provide reliable traffic counts and vehicle classifications data, the use of manual traffic is an inevitable task. Manual traffic counts can serve different purposes, such as performing quality control or conducting short-term traffic survey. Manual traffic counts are usually conducted with the use of the traditional paper-and-pencil approach or the use of hand-held devices that are specifically developed to assess performing manual traffic counts. In this paper, the development of a mobile app that can be used to assist those who need to perform manual traffic counts. The app can be used by many public agencies, private sectors, and college students to collect their traffic data. It also provides users with the capabilities of sharing their traffic counts instantly, where traffic counts can be extracted and processed quickly by other parties.

Database Replication Prototype

OpenAIRE

Vandewall, R.

2000-01-01

This report describes the design of a Replication Framework that facilitates the implementation and com-parison of database replication techniques. Furthermore, it discusses the implementation of a Database Replication Prototype and compares the performance measurements of two replication techniques based on the Atomic Broadcast communication primitive: pessimistic active replication and optimistic active replication. The main contributions of this report can be split into four parts....

Fear of AIDS : are there replicable, invariant questionnaire dimensions?

NARCIS (Netherlands)

Arrindell, W.A.; Ross, M.W.; Bridges, K.Robert; van Hout, W.; Hofman, A.; Sanderman, R.

1989-01-01

Explored the dimensional structure of the 38-item Fear of acquired immune deficiency syndrome (AIDS) Schedule with 684 American students. Principal components analysis with VARIMAX rotation revealed 2 separate but related, internally consistent, and replicable dimensions of AIDS fear. These were (1)

The Persuasiveness of Metaphor: A Replication and Extension.

Science.gov (United States)

Siltanen, Susan A.

A study was conducted to replicate and extend an earlier investigation of the persuasive effects of extended, intense concluding sex and death metaphors by using a more controlled design and by mixing metaphors. Fifty-eight high school students completed pretests assessing their attitudes toward a speech topic (legalization of marijuana). Two…

Modeling time-series count data: the unique challenges facing political communication studies.

Science.gov (United States)

Fogarty, Brian J; Monogan, James E

2014-05-01

This paper demonstrates the importance of proper model specification when analyzing time-series count data in political communication studies. It is common for scholars of media and politics to investigate counts of coverage of an issue as it evolves over time. Many scholars rightly consider the issues of time dependence and dynamic causality to be the most important when crafting a model. However, to ignore the count features of the outcome variable overlooks an important feature of the data. This is particularly the case when modeling data with a low number of counts. In this paper, we argue that the Poisson autoregressive model (Brandt and Williams, 2001) accurately meets the needs of many media studies. We replicate the analyses of Flemming et al. (1997), Peake and Eshbaugh-Soha (2008), and Ura (2009) and demonstrate that models missing some of the assumptions of the Poisson autoregressive model often yield invalid inferences. We also demonstrate that the effect of any of these models can be illustrated dynamically with estimates of uncertainty through a simulation procedure. The paper concludes with implications of these findings for the practical researcher. Copyright © 2013 Elsevier Inc. All rights reserved.

The Replication Recipe: What makes for a convincing replication?

NARCIS (Netherlands)

Brandt, M.J.; IJzerman, H.; Dijksterhuis, A.J.; Farach, F.J.; Geller, J.; Giner-Sorolla, R.; Grange, J.A.; Perugini, M.; Spies, J.R.; Veer, A. van 't

2014-01-01

Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

The replication recipe : What makes for a convincing replication?

NARCIS (Netherlands)

Brandt, M.J.; IJzerman, H.; Dijksterhuis, Ap; Farach, Frank J.; Geller, Jason; Giner-Sorolla, Roger; Grange, James A.; Perugini, Marco; Spies, Jeffrey R.; van 't Veer, Anna

Psychological scientists have recently started to reconsider the importance of close replications in building a cumulative knowledge base; however, there is no consensus about what constitutes a convincing close replication study. To facilitate convincing close replication attempts we have developed

The influence of mortality and socioeconomic status on risk and delayed rewards: a replication with British participants

Directory of Open Access Journals (Sweden)

Gillian V. Pepper

2017-07-01

Full Text Available Here, we report three attempts to replicate a finding from an influential psychological study (Griskevicius et al., 2011b. The original study found interactions between childhood SES and experimental mortality-priming condition in predicting risk acceptance and delay discounting outcomes. The original study used US student samples. We used British university students (replication 1 and British online samples (replications 2 and 3 with a modified version of the original priming material, which was tailored to make it more credible to a British audience. We did not replicate the interaction between childhood SES and mortality-priming condition in any of our three experiments. The only consistent trend of note was an interaction between sex and priming condition for delay discounting. We note that psychological priming effects are considered fragile and often fail to replicate. Our failure to replicate the original finding could be due to demographic differences in study participants, alterations made to the prime, or other study limitations. However, it is also possible that the previously reported interaction is not a robust or generalizable finding.

Teaching Preschoolers to Count: Effective Strategies for Achieving Early Mathematics Milestones

Science.gov (United States)

Jacobi-Vessels, Jill L.; Brown, E. Todd; Molfese, Victoria J.; Do, Ahn

2016-01-01

Attention to early childhood mathematics instructional strategies has sharpened due to the relatively poor mathematics performance of U.S. students in comparison to students from other countries and research evidence that early mathematics skills impact later achievement. Early Childhood counting skills form the foundation for subsequent…

Calibration of a liquid scintillation counter for alpha, beta and Cerenkov counting

International Nuclear Information System (INIS)

Scarpitta, S.C.; Fisenne, I.M.

1996-07-01

Calibration data are presented for 25 radionuclides that were individually measured in a Packard Tri-Carb 2250CA liquid scintillation (LS) counter by both conventional and Cerenkov detection techniques. The relationships and regression data between the quench indicating parameters and the LS counting efficiencies were determined using microliter amounts of tracer added to low 40 K borosilicate glass vials containing 15 mL of Insta-Gel XF scintillation cocktail. Using 40 K, the detection efficiencies were linear over a three order of magnitude range (10 - 10,000 mBq) in beta activity for both LS and Cerenkov counting. The Cerenkov counting efficiency (CCE) increased linearly (42% per MeV) from 0.30 to 2.0 MeV, whereas the LS efficiency was >90% for betas with energy in excess of 0.30 MeV. The CCE was 20 - 50% less than the LS counting efficiency for beta particles with maximum energies in excess of 1 MeV. Based on replicate background measurements, the lower limit of detection (LLD) for a 1-h count at the 95% confidence level, using water as a solvent, was 0.024 counts sec- -1 and 0.028 counts sec-1 for plastic and glass vials, respectively. The LLD for a 1-h-count ranged from 46 to 56 mBq (2.8 - 3.4 dpm) for both Cerenkov and conventional LS counting. This assumes: (1) a 100% counting efficiency, (2) a 50% yield of the nuclide of interest, (3) a 1-h measurement time using low background plastic vials, and (4) a 0-50 keV region of interest. The LLD is reduced an order of magnitude when the yield recovery exceeds 90% and a lower background region is used (i.e., 100 - 500 keV alpha region of interest). Examples and applications of both Cerenkov and LS counting techniques are given in the text and appendices

Fast automatic quantitative cell replication with fluorescent live cell imaging

Directory of Open Access Journals (Sweden)

Wang Ching-Wei

2012-01-01

Full Text Available Abstract Background live cell imaging is a useful tool to monitor cellular activities in living systems. It is often necessary in cancer research or experimental research to quantify the dividing capabilities of cells or the cell proliferation level when investigating manipulations of the cells or their environment. Manual quantification of fluorescence microscopic image is difficult because human is neither sensitive to fine differences in color intensity nor effective to count and average fluorescence level among cells. However, auto-quantification is not a straightforward problem to solve. As the sampling location of the microscopy changes, the amount of cells in individual microscopic images varies, which makes simple measurement methods such as the sum of stain intensity values or the total number of positive stain within each image inapplicable. Thus, automated quantification with robust cell segmentation techniques is required. Results An automated quantification system with robust cell segmentation technique are presented. The experimental results in application to monitor cellular replication activities show that the quantitative score is promising to represent the cell replication level, and scores for images from different cell replication groups are demonstrated to be statistically significantly different using ANOVA, LSD and Tukey HSD tests (p-value Conclusion A robust automated quantification method of live cell imaging is built to measure the cell replication level, providing a robust quantitative analysis system in fluorescent live cell imaging. In addition, the presented unsupervised entropy based cell segmentation for live cell images is demonstrated to be also applicable for nuclear segmentation of IHC tissue images.

Replicative Intermediates of Human Papillomavirus Type 11 in Laryngeal Papillomas: Site of Replication Initiation and Direction of Replication

Science.gov (United States)

Auborn, K. J.; Little, R. D.; Platt, T. H. K.; Vaccariello, M. A.; Schildkraut, C. L.

1994-07-01

We have examined the structures of replication intermediates from the human papillomavirus type 11 genome in DNA extracted from papilloma lesions (laryngeal papillomas). The sites of replication initiation and termination utilized in vivo were mapped by using neutral/neutral and neutral/alkaline two-dimensional agarose gel electrophoresis methods. Initiation of replication was detected in or very close to the upstream regulatory region (URR; the noncoding, regulatory sequences upstream of the open reading frames in the papillomavirus genome). We also show that replication forks proceed bidirectionally from the origin and converge 180circ opposite the URR. These results demonstrate the feasibility of analysis of replication of viral genomes directly from infected tissue.

DNA replication and cancer: From dysfunctional replication origin activities to therapeutic opportunities.

Science.gov (United States)

Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

2016-06-01

A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways to promote genome integrity during DNA replication. This includes suppressing new replication origin firing, stabilization of replicating forks, and the safe restart of forks to prevent any loss of genetic information. Here, we describe mechanisms by which oncogenes can interfere with DNA replication thereby causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy. Copyright © 2016 Elsevier Ltd. All rights reserved.

Undergraduate Students' Initial Conceptions of Factorials

Science.gov (United States)

Lockwood, Elise; Erickson, Sarah

2017-01-01

Counting problems offer rich opportunities for students to engage in mathematical thinking, but they can be difficult for students to solve. In this paper, we present a study that examines student thinking about one concept within counting, factorials, which are a key aspect of many combinatorial ideas. In an effort to better understand students'…

Diplomas Count 2013: Second Chances--Turning Dropouts into Graduates

Science.gov (United States)

Education Week, 2013

2013-01-01

The 2013 edition of "Diplomas Count," entitled "Second Chances: Turning Dropouts into Graduates," examines dropout recovery and innovative strategies for returning to the educational fold the 1 million students who leave school without a diploma each year. "Education Week's" journalists investigate interventions that…

Neural Mechanisms of the Transformation from Objective Value to Subjective Utility: Converting from Count to Worth

Science.gov (United States)

Kurnianingsih, Yoanna A.; Mullette-Gillman, O'Dhaniel A.

2016-01-01

When deciding, we aim to choose the “best” possible outcome. This is not just selection of the option that is the most numerous or physically largest, as options are translated from objective value (count) to subjective value (worth or utility). We localized the neural instantiation of the value-to-utility transformation to the dorsal anterior midcingulate cortex (daMCC), with independent replication. The daMCC encodes the context-specific information necessary to convert from count to worth. This encoding is not simply a representation of utility or preference, but the interaction of the two. Specifically, the relationship of brain activation to value is dependent on individual preference, with both positive and negative slopes across the population depending on whether each individual's preference results in enhancement or diminishment of the valuation. For a given value, across participants, enhanced daMCC activation corresponds to diminished subjective valuation, deactivation to enhanced subjective valuation, and non-modulated activation with non-modulated subjective valuation. Further, functional connectivity analyses identified brain regions (positive connectivity with the inferior frontal gyrus and negative connectivity with the nucleus accumbens) through which contextual information may be integrated into the daMCC and allow for outputs to modulate valuation signals. All analyses were replicated through an independent within-study replication, with initial testing in the gains domain and replication in the intermixed and mirrored losses trials. We also present and discuss an ancillary finding: we were unable to identify parametric value signals for losses through whole-brain analyses, and ROI analyses of the vmPFC presented non-modulation across loss value levels. These results identify the neural locus of the value-to-utility transformation, and provide a specific computational function for the daMCC in the production of subjective valuation through

The power of statistical tests using field trial count data of non-target organisms in enviromental risk assessment of genetically modified plants

NARCIS (Netherlands)

Voet, van der H.; Goedhart, P.W.

2015-01-01

Publications on power analyses for field trial count data comparing transgenic and conventional crops have reported widely varying requirements for the replication needed to obtain statistical tests with adequate power. These studies are critically reviewed and complemented with a new simulation

Teachability of collocations: The role of word frequency counts ...

African Journals Online (AJOL)

... beginner/low-intermediate students and only exceed the 2 000-word band from the upper-intermediate learning stage onwards, a suggestion in line with Nation's (2006) discussion on how to teach vocabulary. Keywords: collocation size, controlled productive knowledge, teachability of collocations, word frequency counts, ...

Repair replication in replicating and nonreplicating DNA after irradiation with uv light

Energy Technology Data Exchange (ETDEWEB)

Slor, H.; Cleaver, J.E.

1978-06-01

Ultraviolet light induces more pyrimidine dimers and more repair replication in DNA that replicates within 2 to 3 h of irradiation than in DNA that does not replicate during this period. This difference may be due to special conformational changes in DNA and chromatin that might be associated with semiconservative DNA replication.

Compton suppression gamma-counting: The effect of count rate

Science.gov (United States)

Millard, H.T.

1984-01-01

Past research has shown that anti-coincidence shielded Ge(Li) spectrometers enhanced the signal-to-background ratios for gamma-photopeaks, which are situated on high Compton backgrounds. Ordinarily, an anti- or non-coincidence spectrum (A) and a coincidence spectrum (C) are collected simultaneously with these systems. To be useful in neutron activation analysis (NAA), the fractions of the photopeak counts routed to the two spectra must be constant from sample to sample to variations must be corrected quantitatively. Most Compton suppression counting has been done at low count rate, but in NAA applications, count rates may be much higher. To operate over the wider dynamic range, the effect of count rate on the ratio of the photopeak counts in the two spectra (A/C) was studied. It was found that as the count rate increases, A/C decreases for gammas not coincident with other gammas from the same decay. For gammas coincident with other gammas, A/C increases to a maximum and then decreases. These results suggest that calibration curves are required to correct photopeak areas so quantitative data can be obtained at higher count rates. ?? 1984.

EcoCount

Directory of Open Access Journals (Sweden)

Phillip P. Allen

2014-05-01

Full Text Available Techniques that analyze biological remains from sediment sequences for environmental reconstructions are well established and widely used. Yet, identifying, counting, and recording biological evidence such as pollen grains remain a highly skilled, demanding, and time-consuming task. Standard procedure requires the classification and recording of between 300 and 500 pollen grains from each representative sample. Recording the data from a pollen count requires significant effort and focused resources from the palynologist. However, when an adaptation to the recording procedure is utilized, efficiency and time economy improve. We describe EcoCount, which represents a development in environmental data recording procedure. EcoCount is a voice activated fully customizable digital count sheet that allows the investigator to continuously interact with a field of view during the data recording. Continuous viewing allows the palynologist the opportunity to remain engaged with the essential task, identification, for longer, making pollen counting more efficient and economical. EcoCount is a versatile software package that can be used to record a variety of environmental evidence and can be installed onto different computer platforms, making the adoption by users and laboratories simple and inexpensive. The user-friendly format of EcoCount allows any novice to be competent and functional in a very short time.

Human Parvovirus B19 Utilizes Cellular DNA Replication Machinery for Viral DNA Replication.

Science.gov (United States)

Zou, Wei; Wang, Zekun; Xiong, Min; Chen, Aaron Yun; Xu, Peng; Ganaie, Safder S; Badawi, Yomna; Kleiboeker, Steve; Nishimune, Hiroshi; Ye, Shui Qing; Qiu, Jianming

2018-03-01

Human parvovirus B19 (B19V) infection of human erythroid progenitor cells (EPCs) induces a DNA damage response and cell cycle arrest at late S phase, which facilitates viral DNA replication. However, it is not clear exactly which cellular factors are employed by this single-stranded DNA virus. Here, we used microarrays to systematically analyze the dynamic transcriptome of EPCs infected with B19V. We found that DNA metabolism, DNA replication, DNA repair, DNA damage response, cell cycle, and cell cycle arrest pathways were significantly regulated after B19V infection. Confocal microscopy analyses revealed that most cellular DNA replication proteins were recruited to the centers of viral DNA replication, but not the DNA repair DNA polymerases. Our results suggest that DNA replication polymerase δ and polymerase α are responsible for B19V DNA replication by knocking down its expression in EPCs. We further showed that although RPA32 is essential for B19V DNA replication and the phosphorylated forms of RPA32 colocalized with the replicating viral genomes, RPA32 phosphorylation was not necessary for B19V DNA replication. Thus, this report provides evidence that B19V uses the cellular DNA replication machinery for viral DNA replication. IMPORTANCE Human parvovirus B19 (B19V) infection can cause transient aplastic crisis, persistent viremia, and pure red cell aplasia. In fetuses, B19V infection can result in nonimmune hydrops fetalis and fetal death. These clinical manifestations of B19V infection are a direct outcome of the death of human erythroid progenitors that host B19V replication. B19V infection induces a DNA damage response that is important for cell cycle arrest at late S phase. Here, we analyzed dynamic changes in cellular gene expression and found that DNA metabolic processes are tightly regulated during B19V infection. Although genes involved in cellular DNA replication were downregulated overall, the cellular DNA replication machinery was tightly

MOF Suppresses Replication Stress and Contributes to Resolution of Stalled Replication Forks.

Science.gov (United States)

Singh, Dharmendra Kumar; Pandita, Raj K; Singh, Mayank; Chakraborty, Sharmistha; Hambarde, Shashank; Ramnarain, Deepti; Charaka, Vijaya; Ahmed, Kazi Mokim; Hunt, Clayton R; Pandita, Tej K

2018-03-15

The human MOF (hMOF) protein belongs to the MYST family of histone acetyltransferases and plays a critical role in transcription and the DNA damage response. MOF is essential for cell proliferation; however, its role during replication and replicative stress is unknown. Here we demonstrate that cells depleted of MOF and under replicative stress induced by cisplatin, hydroxyurea, or camptothecin have reduced survival, a higher frequency of S-phase-specific chromosome damage, and increased R-loop formation. MOF depletion decreased replication fork speed and, when combined with replicative stress, also increased stalled replication forks as well as new origin firing. MOF interacted with PCNA, a key coordinator of replication and repair machinery at replication forks, and affected its ubiquitination and recruitment to the DNA damage site. Depletion of MOF, therefore, compromised the DNA damage repair response as evidenced by decreased Mre11, RPA70, Rad51, and PCNA focus formation, reduced DNA end resection, and decreased CHK1 phosphorylation in cells after exposure to hydroxyurea or cisplatin. These results support the argument that MOF plays an important role in suppressing replication stress induced by genotoxic agents at several stages during the DNA damage response. Copyright © 2018 American Society for Microbiology.

RBC count

Science.gov (United States)

... by kidney disease) RBC destruction ( hemolysis ) due to transfusion, blood vessel injury, or other cause Leukemia Malnutrition Bone ... slight risk any time the skin is broken) Alternative Names Erythrocyte count; Red blood cell count; Anemia - RBC count Images Blood test ...

Database Replication

CERN Document Server

Kemme, Bettina

2010-01-01

Database replication is widely used for fault-tolerance, scalability and performance. The failure of one database replica does not stop the system from working as available replicas can take over the tasks of the failed replica. Scalability can be achieved by distributing the load across all replicas, and adding new replicas should the load increase. Finally, database replication can provide fast local access, even if clients are geographically distributed clients, if data copies are located close to clients. Despite its advantages, replication is not a straightforward technique to apply, and

Right and Wrong and Cultural Diversity: Replication of the 2002 NAS/Zogby Poll on Business Ethics

Science.gov (United States)

Ludlum, Marty; Mascaloinov, Sergei

2004-01-01

In April 2002, a NAS/Zogby poll found that only a quarter of sampled students perceived uniform standards of "right and wrong" and that most students felt that ethical behavior depends on cultural diversity. In this effort to replicate those findings in a larger sample of American college students, the authors obtained results that…

Sperm counts may have declined in young university students in Southern Spain

DEFF Research Database (Denmark)

Mendiola, Jaime; Jørgensen, Niels; Mínguez-Alarcón, Lidia

2013-01-01

Several studies have investigated temporal trends in semen quality in Northern Europe, but none has examined this question in Southern Europe. A prior study conducted in Almeria Province (Southern Spain) reported higher sperm count and concentration among Spanish young men recruited from 2001......, Body mass index (BMI), presence of varicocoele and prenatal exposure to tobacco) to look for a birth-cohort effect over the combined study period (2001-2011). Sperm concentration and total sperm count declined significantly with year of birth in the pooled analysis (β = -0.04 and β = -0...

X-irradiation affects all DNA replication intermediates when inhibiting replication initiation

International Nuclear Information System (INIS)

Loenn, U.; Karolinska Hospital, Stockholm

1982-01-01

When a human melanoma line was irradiated with 10 Gy, there was, after 30 to 60 min, a gradual reduction in the DNA replication rate. Ten to twelve hours after the irradiation, the DNA replication had returned to near normal rate. The results showed tht low dose-rate X-irradiation inhibits preferentially the formation of small DNA replication intermediates. There is no difference between the inhibition of these replication intermediates formed only in the irradiated cells and those formed also in untreated cells. (U.K.)

Chromatin Structure and Replication Origins: Determinants Of Chromosome Replication And Nuclear Organization

Science.gov (United States)

Smith, Owen K.; Aladjem, Mirit I.

2014-01-01

The DNA replication program is, in part, determined by the epigenetic landscape that governs local chromosome architecture and directs chromosome duplication. Replication must coordinate with other biochemical processes occurring concomitantly on chromatin, such as transcription and remodeling, to insure accurate duplication of both genetic and epigenetic features and to preserve genomic stability. The importance of genome architecture and chromatin looping in coordinating cellular processes on chromatin is illustrated by two recent sets of discoveries. First, chromatin-associated proteins that are not part of the core replication machinery were shown to affect the timing of DNA replication. These chromatin-associated proteins could be working in concert, or perhaps in competition, with the transcriptional machinery and with chromatin modifiers to determine the spatial and temporal organization of replication initiation events. Second, epigenetic interactions are mediated by DNA sequences that determine chromosomal replication. In this review we summarize recent findings and current models linking spatial and temporal regulation of the replication program with epigenetic signaling. We discuss these issues in the context of the genome’s three-dimensional structure with an emphasis on events occurring during the initiation of DNA replication. PMID:24905010

Prelife catalysts and replicators

OpenAIRE

Ohtsuki, Hisashi; Nowak, Martin A.

2009-01-01

Life is based on replication and evolution. But replication cannot be taken for granted. We must ask what there was prior to replication and evolution. How does evolution begin? We have proposed prelife as a generative system that produces information and diversity in the absence of replication. We model prelife as a binary soup of active monomers that form random polymers. ‘Prevolutionary’ dynamics can have mutation and selection prior to replication. Some sequences might have catalytic acti...

Data from Investigating Variation in Replicability: A “Many Labs” Replication Project

Directory of Open Access Journals (Sweden)

Richard A. Klein

2014-04-01

Full Text Available This dataset is from the Many Labs Replication Project in which 13 effects were replicated across 36 samples and over 6,000 participants. Data from the replications are included, along with demographic variables about the participants and contextual information about the environment in which the replication was conducted. Data were collected in-lab and online through a standardized procedure administered via an online link. The dataset is stored on the Open Science Framework website. These data could be used to further investigate the results of the included 13 effects or to study replication and generalizability more broadly.

Comparing distribution models for small samples of overdispersed counts of freshwater fish

Science.gov (United States)

Vaudor, Lise; Lamouroux, Nicolas; Olivier, Jean-Michel

2011-05-01

The study of species abundance often relies on repeated abundance counts whose number is limited by logistic or financial constraints. The distribution of abundance counts is generally right-skewed (i.e. with many zeros and few high values) and needs to be modelled for statistical inference. We used an extensive dataset involving about 100,000 fish individuals of 12 freshwater fish species collected in electrofishing points (7 m 2) during 350 field surveys made in 25 stream sites, in order to compare the performance and the generality of four distribution models of counts (Poisson, negative binomial and their zero-inflated counterparts). The negative binomial distribution was the best model (Bayesian Information Criterion) for 58% of the samples (species-survey combinations) and was suitable for a variety of life histories, habitat, and sample characteristics. The performance of the models was closely related to samples' statistics such as total abundance and variance. Finally, we illustrated the consequences of a distribution assumption by calculating confidence intervals around the mean abundance, either based on the most suitable distribution assumption or on an asymptotical, distribution-free (Student's) method. Student's method generally corresponded to narrower confidence intervals, especially when there were few (≤3) non-null counts in the samples.

Functions of Ubiquitin and SUMO in DNA Replication and Replication Stress

Science.gov (United States)

García-Rodríguez, Néstor; Wong, Ronald P.; Ulrich, Helle D.

2016-01-01

Complete and faithful duplication of its entire genetic material is one of the essential prerequisites for a proliferating cell to maintain genome stability. Yet, during replication DNA is particularly vulnerable to insults. On the one hand, lesions in replicating DNA frequently cause a stalling of the replication machinery, as most DNA polymerases cannot cope with defective templates. This situation is aggravated by the fact that strand separation in preparation for DNA synthesis prevents common repair mechanisms relying on strand complementarity, such as base and nucleotide excision repair, from working properly. On the other hand, the replication process itself subjects the DNA to a series of hazardous transformations, ranging from the exposure of single-stranded DNA to topological contortions and the generation of nicks and fragments, which all bear the risk of inducing genomic instability. Dealing with these problems requires rapid and flexible responses, for which posttranslational protein modifications that act independently of protein synthesis are particularly well suited. Hence, it is not surprising that members of the ubiquitin family, particularly ubiquitin itself and SUMO, feature prominently in controlling many of the defensive and restorative measures involved in the protection of DNA during replication. In this review we will discuss the contributions of ubiquitin and SUMO to genome maintenance specifically as they relate to DNA replication. We will consider cases where the modifiers act during regular, i.e., unperturbed stages of replication, such as initiation, fork progression, and termination, but also give an account of their functions in dealing with lesions, replication stalling and fork collapse. PMID:27242895

Counting statistics in low level radioactivity measurements fluctuating counting efficiency

International Nuclear Information System (INIS)

Pazdur, M.F.

1976-01-01

A divergence between the probability distribution of the number of nuclear disintegrations and the number of observed counts, caused by counting efficiency fluctuation, is discussed. The negative binominal distribution is proposed to describe the probability distribution of the number of counts, instead of Poisson distribution, which is assumed to hold for the number of nuclear disintegrations only. From actual measurements the r.m.s. amplitude of counting efficiency fluctuation is estimated. Some consequences of counting efficiency fluctuation are investigated and the corresponding formulae are derived: (1) for detection limit as a function of the number of partial measurements and the relative amplitude of counting efficiency fluctuation, and (2) for optimum allocation of the number of partial measurements between sample and background. (author)

Homeless High School Students in America: Who Counts?

Science.gov (United States)

Cumming, John M.; Gloeckner, Gene W.

2012-01-01

After interviewing homeless high school students, the research team in a Colorado school district discovered that many students had not revealed their true living conditions (homelessness) to anyone in the school district. This research team developed an anonymous survey written around the homeless categories identified in the McKinney-Vento…

Up or down? Reading direction influences vertical counting direction in the horizontal plane – a cross-cultural comparison

Directory of Open Access Journals (Sweden)

Silke Melanie Goebel

2015-03-01

Full Text Available Most adults and children in cultures where reading text progresses from left to right also count objects from the left to the right side of space. The reverse is found in cultures with a right-to-left reading direction. The current set of experiments investigated whether vertical counting in the horizontal plane is also influenced by reading direction. In experiment 1, native English-speaking children and adults and native Cantonese-speaking children and adults performed three object counting tasks. Objects were presented flat on a table in a horizontal, vertical and square display. Independent of culture, the horizontal array was mostly counted from left to right. While the majority of English-speaking children counted the vertical display from bottom to top, the majority of the Cantonese-speaking children as well as both Cantonese- and English-speaking adults counted the vertical display from top to bottom. This pattern was replicated in the counting pattern for squares: all groups except the English-speaking children started counting with the top left coin. In experiment 2, Cantonese-speaking adults counted a square array of objects after they read a text presented to them either in left to right or in top to bottom reading direction. Most Cantonese-speaking adults starting counting the array by moving horizontally from left to right. However, significantly more Cantonese-speaking adults started counting with a top-to-bottom movement after reading the text presented in a top-to-bottom reading direction than in a left-to-right reading direction. Our results show clearly that vertical counting in the horizontal plane is influenced by longstanding as well as more recent experience of reading direction.

Up or down? Reading direction influences vertical counting direction in the horizontal plane - a cross-cultural comparison.

Science.gov (United States)

Göbel, Silke M

2015-01-01

Most adults and children in cultures where reading text progresses from left to right also count objects from the left to the right side of space. The reverse is found in cultures with a right-to-left reading direction. The current set of experiments investigated whether vertical counting in the horizontal plane is also influenced by reading direction. Participants were either from a left-to-right reading culture (UK) or from a mixed (left-to-right and top-to-bottom) reading culture (Hong Kong). In Experiment 1, native English-speaking children and adults and native Cantonese-speaking children and adults performed three object counting tasks. Objects were presented flat on a table in a horizontal, vertical, and square display. Independent of culture, the horizontal array was mostly counted from left to right. While the majority of English-speaking children counted the vertical display from bottom to top, the majority of the Cantonese-speaking children as well as both Cantonese- and English-speaking adults counted the vertical display from top to bottom. This pattern was replicated in the counting pattern for squares: all groups except the English-speaking children started counting with the top left coin. In Experiment 2, Cantonese-speaking adults counted a square array of objects after they read a text presented to them either in left-to-right or in top-to-bottom reading direction. Most Cantonese-speaking adults started counting the array by moving horizontally from left to right. However, significantly more Cantonese-speaking adults started counting with a top-to-bottom movement after reading the text presented in a top-to-bottom reading direction than in a left-to-right reading direction. Our results show clearly that vertical counting in the horizontal plane is influenced by longstanding as well as more recent experience of reading direction.

DNA Replication in Engineered Escherichia coli Genomes with Extra Replication Origins.

Science.gov (United States)

Milbredt, Sarah; Farmani, Neda; Sobetzko, Patrick; Waldminghaus, Torsten

2016-10-21

The standard outline of bacterial genomes is a single circular chromosome with a single replication origin. From the bioengineering perspective, it appears attractive to extend this basic setup. Bacteria with split chromosomes or multiple replication origins have been successfully constructed in the last few years. The characteristics of these engineered strains will largely depend on the respective DNA replication patterns. However, the DNA replication has not been investigated systematically in engineered bacteria with multiple origins or split replicons. Here we fill this gap by studying a set of strains consisting of (i) E. coli strains with an extra copy of the native replication origin (oriC), (ii) E. coli strains with an extra copy of the replication origin from the secondary chromosome of Vibrio cholerae (oriII), and (iii) a strain in which the E. coli chromosome is split into two linear replicons. A combination of flow cytometry, microarray-based comparative genomic hybridization (CGH), and modeling revealed silencing of extra oriC copies and differential timing of ectopic oriII copies compared to the native oriC. The results were used to derive construction rules for future multiorigin and multireplicon projects.

Hydroxyurea-Induced Replication Stress

Directory of Open Access Journals (Sweden)

Kenza Lahkim Bennani-Belhaj

2010-01-01

Full Text Available Bloom's syndrome (BS displays one of the strongest known correlations between chromosomal instability and a high risk of cancer at an early age. BS cells combine a reduced average fork velocity with constitutive endogenous replication stress. However, the response of BS cells to replication stress induced by hydroxyurea (HU, which strongly slows the progression of replication forks, remains unclear due to publication of conflicting results. Using two different cellular models of BS, we showed that BLM deficiency is not associated with sensitivity to HU, in terms of clonogenic survival, DSB generation, and SCE induction. We suggest that surviving BLM-deficient cells are selected on the basis of their ability to deal with an endogenous replication stress induced by replication fork slowing, resulting in insensitivity to HU-induced replication stress.

Evaluation of a standardized procedure for [corrected] microscopic cell counts [corrected] in body fluids.

Science.gov (United States)

Emerson, Jane F; Emerson, Scott S

2005-01-01

A standardized urinalysis and manual microscopic cell counting system was evaluated for its potential to reduce intra- and interoperator variability in urine and cerebrospinal fluid (CSF) cell counts. Replicate aliquots of pooled specimens were submitted blindly to technologists who were instructed to use either the Kova system with the disposable Glasstic slide (Hycor Biomedical, Inc., Garden Grove, CA) or the standard operating procedure of the University of California-Irvine (UCI), which uses plain glass slides for urine sediments and hemacytometers for CSF. The Hycor system provides a mechanical means of obtaining a fixed volume of fluid in which to resuspend the sediment, and fixes the volume of specimen to be microscopically examined by using capillary filling of a chamber containing in-plane counting grids. Ninety aliquots of pooled specimens of each type of body fluid were used to assess the inter- and intraoperator reproducibility of the measurements. The variability of replicate Hycor measurements made on a single specimen by the same or different observers was compared with that predicted by a Poisson distribution. The Hycor methods generally resulted in test statistics that were slightly lower than those obtained with the laboratory standard methods, indicating a trend toward decreasing the effects of various sources of variability. For 15 paired aliquots of each body fluid, tests for systematically higher or lower measurements with the Hycor methods were performed using the Wilcoxon signed-rank test. Also examined was the average difference between the Hycor and current laboratory standard measurements, along with a 95% confidence interval (CI) for the true average difference. Without increasing labor or the requirement for attention to detail, the Hycor method provides slightly better interrater comparisons than the current method used at UCI. Copyright 2005 Wiley-Liss, Inc.

Determining random counts in liquid scintillation counting

International Nuclear Information System (INIS)

Horrocks, D.L.

1979-01-01

During measurements involving coincidence counting techniques, errors can arise due to the detection of chance or random coincidences in the multiple detectors used. A method and the electronic circuits necessary are here described for eliminating this source of error in liquid scintillation detectors used in coincidence counting. (UK)

Replicating animal mitochondrial DNA

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Emily A. McKinney

2013-01-01

Full Text Available The field of mitochondrial DNA (mtDNA replication has been experiencing incredible progress in recent years, and yet little is certain about the mechanism(s used by animal cells to replicate this plasmid-like genome. The long-standing strand-displacement model of mammalian mtDNA replication (for which single-stranded DNA intermediates are a hallmark has been intensively challenged by a new set of data, which suggests that replication proceeds via coupled leading-and lagging-strand synthesis (resembling bacterial genome replication and/or via long stretches of RNA intermediates laid on the mtDNA lagging-strand (the so called RITOLS. The set of proteins required for mtDNA replication is small and includes the catalytic and accessory subunits of DNA polymerase y, the mtDNA helicase Twinkle, the mitochondrial single-stranded DNA-binding protein, and the mitochondrial RNA polymerase (which most likely functions as the mtDNA primase. Mutations in the genes coding for the first three proteins are associated with human diseases and premature aging, justifying the research interest in the genetic, biochemical and structural properties of the mtDNA replication machinery. Here we summarize these properties and discuss the current models of mtDNA replication in animal cells.

Radiation counting statistics

Energy Technology Data Exchange (ETDEWEB)

Suh, M. Y.; Jee, K. Y.; Park, K. K.; Park, Y. J.; Kim, W. H

1999-08-01

This report is intended to describe the statistical methods necessary to design and conduct radiation counting experiments and evaluate the data from the experiment. The methods are described for the evaluation of the stability of a counting system and the estimation of the precision of counting data by application of probability distribution models. The methods for the determination of the uncertainty of the results calculated from the number of counts, as well as various statistical methods for the reduction of counting error are also described. (Author). 11 refs., 8 tabs., 8 figs.

Radiation counting statistics

Energy Technology Data Exchange (ETDEWEB)

Suh, M. Y.; Jee, K. Y.; Park, K. K. [Korea Atomic Energy Research Institute, Taejon (Korea)

1999-08-01

This report is intended to describe the statistical methods necessary to design and conduct radiation counting experiments and evaluate the data from the experiments. The methods are described for the evaluation of the stability of a counting system and the estimation of the precision of counting data by application of probability distribution models. The methods for the determination of the uncertainty of the results calculated from the number of counts, as well as various statistical methods for the reduction of counting error are also described. 11 refs., 6 figs., 8 tabs. (Author)

Radiation counting statistics

International Nuclear Information System (INIS)

Suh, M. Y.; Jee, K. Y.; Park, K. K.; Park, Y. J.; Kim, W. H.

1999-08-01

This report is intended to describe the statistical methods necessary to design and conduct radiation counting experiments and evaluate the data from the experiment. The methods are described for the evaluation of the stability of a counting system and the estimation of the precision of counting data by application of probability distribution models. The methods for the determination of the uncertainty of the results calculated from the number of counts, as well as various statistical methods for the reduction of counting error are also described. (Author). 11 refs., 8 tabs., 8 figs

Chromatin Controls DNA Replication Origin Selection, Lagging-Strand Synthesis, and Replication Fork Rates.

Science.gov (United States)

Kurat, Christoph F; Yeeles, Joseph T P; Patel, Harshil; Early, Anne; Diffley, John F X

2017-01-05

The integrity of eukaryotic genomes requires rapid and regulated chromatin replication. How this is accomplished is still poorly understood. Using purified yeast replication proteins and fully chromatinized templates, we have reconstituted this process in vitro. We show that chromatin enforces DNA replication origin specificity by preventing non-specific MCM helicase loading. Helicase activation occurs efficiently in the context of chromatin, but subsequent replisome progression requires the histone chaperone FACT (facilitates chromatin transcription). The FACT-associated Nhp6 protein, the nucleosome remodelers INO80 or ISW1A, and the lysine acetyltransferases Gcn5 and Esa1 each contribute separately to maximum DNA synthesis rates. Chromatin promotes the regular priming of lagging-strand DNA synthesis by facilitating DNA polymerase α function at replication forks. Finally, nucleosomes disrupted during replication are efficiently re-assembled into regular arrays on nascent DNA. Our work defines the minimum requirements for chromatin replication in vitro and shows how multiple chromatin factors might modulate replication fork rates in vivo. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Modeling inhomogeneous DNA replication kinetics.

Directory of Open Access Journals (Sweden)

Michel G Gauthier

Full Text Available In eukaryotic organisms, DNA replication is initiated at a series of chromosomal locations called origins, where replication forks are assembled proceeding bidirectionally to replicate the genome. The distribution and firing rate of these origins, in conjunction with the velocity at which forks progress, dictate the program of the replication process. Previous attempts at modeling DNA replication in eukaryotes have focused on cases where the firing rate and the velocity of replication forks are homogeneous, or uniform, across the genome. However, it is now known that there are large variations in origin activity along the genome and variations in fork velocities can also take place. Here, we generalize previous approaches to modeling replication, to allow for arbitrary spatial variation of initiation rates and fork velocities. We derive rate equations for left- and right-moving forks and for replication probability over time that can be solved numerically to obtain the mean-field replication program. This method accurately reproduces the results of DNA replication simulation. We also successfully adapted our approach to the inverse problem of fitting measurements of DNA replication performed on single DNA molecules. Since such measurements are performed on specified portion of the genome, the examined DNA molecules may be replicated by forks that originate either within the studied molecule or outside of it. This problem was solved by using an effective flux of incoming replication forks at the model boundaries to represent the origin activity outside the studied region. Using this approach, we show that reliable inferences can be made about the replication of specific portions of the genome even if the amount of data that can be obtained from single-molecule experiments is generally limited.

Personal and Interpersonal Motivation for Group Projects: Replications of an Attributional Analysis

Science.gov (United States)

Peterson, Sarah E.; Schreiber, James B.

2012-01-01

We report the results of two replication studies using attribution theory to analyze personal and interpersonal motivation for collaborative projects. Undergraduate students responded to questionnaires containing hypothetical vignettes depicting success or failure outcomes due to ability or effort for dyads working on a group project. Dependent…

Mechanisms of DNA replication termination.

Science.gov (United States)

Dewar, James M; Walter, Johannes C

2017-08-01

Genome duplication is carried out by pairs of replication forks that assemble at origins of replication and then move in opposite directions. DNA replication ends when converging replication forks meet. During this process, which is known as replication termination, DNA synthesis is completed, the replication machinery is disassembled and daughter molecules are resolved. In this Review, we outline the steps that are likely to be common to replication termination in most organisms, namely, fork convergence, synthesis completion, replisome disassembly and decatenation. We briefly review the mechanism of termination in the bacterium Escherichia coli and in simian virus 40 (SV40) and also focus on recent advances in eukaryotic replication termination. In particular, we discuss the recently discovered E3 ubiquitin ligases that control replisome disassembly in yeast and higher eukaryotes, and how their activity is regulated to avoid genome instability.

Tower counts

Science.gov (United States)

Woody, Carol Ann; Johnson, D.H.; Shrier, Brianna M.; O'Neal, Jennifer S.; Knutzen, John A.; Augerot, Xanthippe; O'Neal, Thomas A.; Pearsons, Todd N.

2007-01-01

Counting towers provide an accurate, low-cost, low-maintenance, low-technology, and easily mobilized escapement estimation program compared to other methods (e.g., weirs, hydroacoustics, mark-recapture, and aerial surveys) (Thompson 1962; Siebel 1967; Cousens et al. 1982; Symons and Waldichuk 1984; Anderson 2000; Alaska Department of Fish and Game 2003). Counting tower data has been found to be consistent with that of digital video counts (Edwards 2005). Counting towers do not interfere with natural fish migration patterns, nor are fish handled or stressed; however, their use is generally limited to clear rivers that meet specific site selection criteria. The data provided by counting tower sampling allow fishery managers to determine reproductive population size, estimate total return (escapement + catch) and its uncertainty, evaluate population productivity and trends, set harvest rates, determine spawning escapement goals, and forecast future returns (Alaska Department of Fish and Game 1974-2000 and 1975-2004). The number of spawning fish is determined by subtracting subsistence, sport-caught fish, and prespawn mortality from the total estimated escapement. The methods outlined in this protocol for tower counts can be used to provide reasonable estimates ( plus or minus 6%-10%) of reproductive salmon population size and run timing in clear rivers. 

Students classified as LD who received course substitutions for the college foreign language requirement: a replication study.

Science.gov (United States)

Sparks, Richard L; Philips, Lois G; Javorsky, James

2002-01-01

This replication study examined whether 158 college students classified as learning disabled (LD) who were granted course substitutions for the foreign language (FL) requirement would display significant cognitive and academic achievement differences when grouped by levels of IQ-achievement and achievement-achievement discrepancy and by level of performance on an FL aptitude test (Modern Language Aptitude Test; MLAT), phonological/orthographic processing measures, and in FL courses. The results showed that there were few differences among groups with differing levels of IQ-achievement or achievement-achievement discrepancy (i.e., 1.50 SD) on MLAT and American College Testing (ACT) scores, graduating grade point average (GPA), or college FL GPA. The results also showed that between groups who scored at or above versus below the 15th percentile (i.e., or = 1.0 SD) for classification as LD. These findings suggest that many traditional assumptions about LD and FL learning are likely to be false.

Rolling replication of UV-irradiated duplex DNA in the phi X174 replicative-form----single-strand replication system in vitro

International Nuclear Information System (INIS)

Shavitt, O.; Livneh, Z.

1989-01-01

Cloning of the phi X174 viral origin of replication into phage M13mp8 produced an M13-phi X174 chimera, the DNA of which directed efficient replicative-form----single-strand rolling replication in vitro. This replication assay was performed with purified phi X174-encoded gene A protein, Escherichia coli rep helicase, single-stranded DNA-binding protein, and DNA polymerase III holoenzyme. The nicking of replicative-form I (RFI) DNA by gene A protein was essentially unaffected by the presence of UV lesions in the DNA. However, unwinding of UV-irradiated DNA by the rep helicase was inhibited twofold as compared with unwinding of the unirradiated substrate. UV irradiation of the substrate DNA caused a strong inhibition in its ability to direct DNA synthesis. However, even DNA preparations that contained as many as 10 photodimers per molecule still supported the synthesis of progeny full-length single-stranded DNA. The appearance of full-length radiolabeled products implied at least two full rounds of replication, since the first round released the unlabeled plus viral strand of the duplex DNA. Pretreatment of the UV-irradiated DNA substrate with purified pyrimidine dimer endonuclease from Micrococcus luteus, which converted photodimer-containing supercoiled RFI DNA into relaxed, nicked RFII DNA and thus prevented its replication, reduced DNA synthesis by 70%. Analysis of radiolabeled replication products by agarose gel electrophoresis followed by autoradiography revealed that this decrease was due to a reduction in the synthesis of progeny full-length single-stranded DNA. This implies that 70 to 80% of the full-length DNA products produced in this system were synthesized on molecules that carried photodimers

Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks

DEFF Research Database (Denmark)

Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia

2016-01-01

Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose...... RAD52 facilitates repair of collapsed DNA replication forks in cancer cells....

Kids Count: The State of the Child in Tennessee, 1994.

Science.gov (United States)

Tennessee State Commission on Children and Youth, Nashville.

This Kids Count report examines trends in the well being of Tennessee's children. The statistical portrait is based on 23 indicators of child well being: (1) single-parent families; (2) family income/poverty; (3) children receiving Aid to Families with Dependent Children; (4) students participating in school nutrition programs; (5) teen…

A comparison of different ways of including baseline counts in negative binomial models for data from falls prevention trials.

Science.gov (United States)

Zheng, Han; Kimber, Alan; Goodwin, Victoria A; Pickering, Ruth M

2018-01-01

A common design for a falls prevention trial is to assess falling at baseline, randomize participants into an intervention or control group, and ask them to record the number of falls they experience during a follow-up period of time. This paper addresses how best to include the baseline count in the analysis of the follow-up count of falls in negative binomial (NB) regression. We examine the performance of various approaches in simulated datasets where both counts are generated from a mixed Poisson distribution with shared random subject effect. Including the baseline count after log-transformation as a regressor in NB regression (NB-logged) or as an offset (NB-offset) resulted in greater power than including the untransformed baseline count (NB-unlogged). Cook and Wei's conditional negative binomial (CNB) model replicates the underlying process generating the data. In our motivating dataset, a statistically significant intervention effect resulted from the NB-logged, NB-offset, and CNB models, but not from NB-unlogged, and large, outlying baseline counts were overly influential in NB-unlogged but not in NB-logged. We conclude that there is little to lose by including the log-transformed baseline count in standard NB regression compared to CNB for moderate to larger sized datasets. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

REPLICATION TOOL AND METHOD OF PROVIDING A REPLICATION TOOL

DEFF Research Database (Denmark)

2016-01-01

The invention relates to a replication tool (1, 1a, 1b) for producing a part (4) with a microscale textured replica surface (5a, 5b, 5c, 5d). The replication tool (1, 1a, 1b) comprises a tool surface (2a, 2b) defining a general shape of the item. The tool surface (2a, 2b) comprises a microscale...... energy directors on flange portions thereof uses the replication tool (1, 1a, 1b) to form an item (4) with a general shape as defined by the tool surface (2a, 2b). The formed item (4) comprises a microscale textured replica surface (5a, 5b, 5c, 5d) with a lateral arrangement of polydisperse microscale...

Recommendations for Replication Research in Special Education: A Framework of Systematic, Conceptual Replications

Science.gov (United States)

Coyne, Michael D.; Cook, Bryan G.; Therrien, William J.

2016-01-01

Special education researchers conduct studies that can be considered replications. However, they do not often refer to them as replication studies. The purpose of this article is to consider the potential benefits of conceptualizing special education intervention research within a framework of systematic, conceptual replication. Specifically, we…

Counting carbohydrates

Science.gov (United States)

Carb counting; Carbohydrate-controlled diet; Diabetic diet; Diabetes-counting carbohydrates ... Many foods contain carbohydrates (carbs), including: Fruit and fruit juice Cereal, bread, pasta, and rice Milk and milk products, soy milk Beans, legumes, ...

DNA replication and cancer

DEFF Research Database (Denmark)

Boyer, Anne-Sophie; Walter, David; Sørensen, Claus Storgaard

2016-01-01

A dividing cell has to duplicate its DNA precisely once during the cell cycle to preserve genome integrity avoiding the accumulation of genetic aberrations that promote diseases such as cancer. A large number of endogenous impacts can challenge DNA replication and cells harbor a battery of pathways...... causing DNA replication stress and genome instability. Further, we describe cellular and systemic responses to these insults with a focus on DNA replication restart pathways. Finally, we discuss the therapeutic potential of exploiting intrinsic replicative stress in cancer cells for targeted therapy....

Late-replicating X-chromosome: replication patterns in mammalian females

Directory of Open Access Journals (Sweden)

Tunin Karen

2002-01-01

Full Text Available The GTG-banding and 5-BrdU incorporation patterns of the late-replicating X-chromosome were studied in female dogs and cattle, and compared to human female patterns. The replication patterns of the short arm of the X-chromosomes did not show any difference between human, dog and cattle females. As to the long arm, some bands showed differences among the three studied species regarding the replication kinetics pattern. These differences were observed in a restricted region of the X-chromosome, delimited by Xq11 -> q25 in humans, by Xq1 -> q8 in dogs, and by Xq12 -> q32 in cattle. In an attempt to find out if these differences in the replication kinetics could be a reflection of differences in the localization of genes in that region of the X-chromosome, we used the probe for the human androgen receptor gene (AR localized at Xq12, which is in the region where we observed differences among the three studied species. We did not, however, observe hybridization signals. Our study goes on, using other human probes for genes located in the region Xq11 -> Xq25.

Repeatability of differential goat bulk milk culture and associations with somatic cell count, total bacterial count, and standard plate count

OpenAIRE

Koop, G.; Dik, N.; Nielen, M.; Lipman, L.J.A.

2010-01-01

The aims of this study were to assess how different bacterial groups in bulk milk are related to bulk milk somatic cell count (SCC), bulk milk total bacterial count (TBC), and bulk milk standard plate count (SPC) and to measure the repeatability of bulk milk culturing. On 53 Dutch dairy goat farms, 3 bulk milk samples were collected at intervals of 2 wk. The samples were cultured for SPC, coliform count, and staphylococcal count and for the presence of Staphylococcus aureus. Furthermore, SCC ...

A Replication by Any Other Name: A Systematic Review of Replicative Intervention Studies

Science.gov (United States)

Cook, Bryan G.; Collins, Lauren W.; Cook, Sara C.; Cook, Lysandra

2016-01-01

Replication research is essential to scientific knowledge. Reviews of replication studies often electronically search for "replicat*" as a textword, which does not identify studies that replicate previous research but do not self-identify as such. We examined whether the 83 intervention studies published in six non-categorical research…

Registered Replication Report

DEFF Research Database (Denmark)

Bouwmeester, S.; Verkoeijen, P. P.J.L.; Aczel, B.

2017-01-01

and colleagues. The results of studies using time pressure have been mixed, with some replication attempts observing similar patterns (e.g., Rand et al., 2014) and others observing null effects (e.g., Tinghög et al., 2013; Verkoeijen & Bouwmeester, 2014). This Registered Replication Report (RRR) assessed...... the size and variability of the effect of time pressure on cooperative decisions by combining 21 separate, preregistered replications of the critical conditions from Study 7 of the original article (Rand et al., 2012). The primary planned analysis used data from all participants who were randomly assigned...

Students Serving Christ: Understanding the Role of Student Subcultures on a College Campus

Science.gov (United States)

Magolda, Peter; Ebben, Kelsey

2007-01-01

This article uses the Students Serving Christ student organization to examine the role of student subcultures in higher education. Using subculture theories, this article examines the origins of student subcultures, explores how subcultures are formed and sustained, reveals what counts as normal within and among student subcultures, investigates…

International Expansion through Flexible Replication

DEFF Research Database (Denmark)

Jonsson, Anna; Foss, Nicolai Juul

2011-01-01

Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to ada......, etc.) are replicated in a uniform manner across stores, and change only very slowly (if at all) in response to learning (“flexible replication”). We conclude by discussing the factors that influence the approach to replication adopted by an international replicator.......Business organizations may expand internationally by replicating a part of their value chain, such as a sales and marketing format, in other countries. However, little is known regarding how such “international replicators” build a format for replication, or how they can adjust it in order to adapt...

Sterol Binding by the Tombusviral Replication Proteins Is Essential for Replication in Yeast and Plants.

Science.gov (United States)

Xu, Kai; Nagy, Peter D

2017-04-01

Membranous structures derived from various organelles are important for replication of plus-stranded RNA viruses. Although the important roles of co-opted host proteins in RNA virus replication have been appreciated for a decade, the equally important functions of cellular lipids in virus replication have been gaining full attention only recently. Previous work with Tomato bushy stunt tombusvirus (TBSV) in model host yeast has revealed essential roles for phosphatidylethanolamine and sterols in viral replication. To further our understanding of the role of sterols in tombusvirus replication, in this work we showed that the TBSV p33 and p92 replication proteins could bind to sterols in vitro The sterol binding by p33 is supported by cholesterol recognition/interaction amino acid consensus (CRAC) and CARC-like sequences within the two transmembrane domains of p33. Mutagenesis of the critical Y amino acids within the CRAC and CARC sequences blocked TBSV replication in yeast and plant cells. We also showed the enrichment of sterols in the detergent-resistant membrane (DRM) fractions obtained from yeast and plant cells replicating TBSV. The DRMs could support viral RNA synthesis on both the endogenous and exogenous templates. A lipidomic approach showed the lack of enhancement of sterol levels in yeast and plant cells replicating TBSV. The data support the notion that the TBSV replication proteins are associated with sterol-rich detergent-resistant membranes in yeast and plant cells. Together, the results obtained in this study and the previously published results support the local enrichment of sterols around the viral replication proteins that is critical for TBSV replication. IMPORTANCE One intriguing aspect of viral infections is their dependence on efficient subcellular assembly platforms serving replication, virion assembly, or virus egress via budding out of infected cells. These assembly platforms might involve sterol-rich membrane microdomains, which are

Mcm10 regulates DNA replication elongation by stimulating the CMG replicative helicase.

Science.gov (United States)

Lõoke, Marko; Maloney, Michael F; Bell, Stephen P

2017-02-01

Activation of the Mcm2-7 replicative DNA helicase is the committed step in eukaryotic DNA replication initiation. Although Mcm2-7 activation requires binding of the helicase-activating proteins Cdc45 and GINS (forming the CMG complex), an additional protein, Mcm10, drives initial origin DNA unwinding by an unknown mechanism. We show that Mcm10 binds a conserved motif located between the oligonucleotide/oligosaccharide fold (OB-fold) and A subdomain of Mcm2. Although buried in the interface between these domains in Mcm2-7 structures, mutations predicted to separate the domains and expose this motif restore growth to conditional-lethal MCM10 mutant cells. We found that, in addition to stimulating initial DNA unwinding, Mcm10 stabilizes Cdc45 and GINS association with Mcm2-7 and stimulates replication elongation in vivo and in vitro. Furthermore, we identified a lethal allele of MCM10 that stimulates initial DNA unwinding but is defective in replication elongation and CMG binding. Our findings expand the roles of Mcm10 during DNA replication and suggest a new model for Mcm10 function as an activator of the CMG complex throughout DNA replication. © 2017 Lõoke et al.; Published by Cold Spring Harbor Laboratory Press.

Predictors of trend in CD4-positive T-cell count and mortality among HIV-1-infected individuals with virological failure to all three antiretroviral-drug classes

DEFF Research Database (Denmark)

Ledergerber, Bruno; Lundgren, Jens D; Walker, A Sarah

2014-01-01

Treatment strategies for patients in whom HIV replication is not suppressed after exposure to several drug classes remain unclear. We aimed to assess the inter-relations between viral load, CD4-cell count, and clinical outcome in patients who had experienced three-class virological failure....

Standardization of 241Am by digital coincidence counting, liquid scintillation counting and defined solid angle counting

International Nuclear Information System (INIS)

Balpardo, C.; Capoulat, M.E.; Rodrigues, D.; Arenillas, P.

2010-01-01

The nuclide 241 Am decays by alpha emission to 237 Np. Most of the decays (84.6%) populate the excited level of 237 Np with energy of 59.54 keV. Digital coincidence counting was applied to standardize a solution of 241 Am by alpha-gamma coincidence counting with efficiency extrapolation. Electronic discrimination was implemented with a pressurized proportional counter and the results were compared with two other independent techniques: Liquid scintillation counting using the logical sum of double coincidences in a TDCR array and defined solid angle counting taking into account activity inhomogeneity in the active deposit. The results show consistency between the three methods within a limit of a 0.3%. An ampoule of this solution will be sent to the International Reference System (SIR) during 2009. Uncertainties were analysed and compared in detail for the three applied methods.

Who Needs Replication?

Science.gov (United States)

Porte, Graeme

2013-01-01

In this paper, the editor of a recent Cambridge University Press book on research methods discusses replicating previous key studies to throw more light on their reliability and generalizability. Replication research is presented as an accepted method of validating previous research by providing comparability between the original and replicated…

Feelings Count: Conceptualizing and Measuring Students' Happiness in Schools

Science.gov (United States)

Huebner, Scott

2010-01-01

The importance of positive subjective well-being (SWB) is supported by the wide-ranging network of relations between students' SWB and crucial school processes and outcomes, such as positive student engagement behavior, interpersonal relationships, coping skills, and academic achievement. Some studies have revealed that not only is positive SWB a…

Mechanisms of bacterial DNA replication restart

Science.gov (United States)

Windgassen, Tricia A; Wessel, Sarah R; Bhattacharyya, Basudeb

2018-01-01

Abstract Multi-protein DNA replication complexes called replisomes perform the essential process of copying cellular genetic information prior to cell division. Under ideal conditions, replisomes dissociate only after the entire genome has been duplicated. However, DNA replication rarely occurs without interruptions that can dislodge replisomes from DNA. Such events produce incompletely replicated chromosomes that, if left unrepaired, prevent the segregation of full genomes to daughter cells. To mitigate this threat, cells have evolved ‘DNA replication restart’ pathways that have been best defined in bacteria. Replication restart requires recognition and remodeling of abandoned replication forks by DNA replication restart proteins followed by reloading of the replicative DNA helicase, which subsequently directs assembly of the remaining replisome subunits. This review summarizes our current understanding of the mechanisms underlying replication restart and the proteins that drive the process in Escherichia coli (PriA, PriB, PriC and DnaT). PMID:29202195

20 CFR 416.1112 - Earned income we do not count.

Science.gov (United States)

2010-04-01

... AGED, BLIND, AND DISABLED Income Earned Income § 416.1112 Earned income we do not count. (a) General... receive it. (3) If you are under age 22 and a student who is regularly attending school as described in... not blind) and under age 65 or you are disabled (but not blind) and received SSI as a disabled...

Benjamin Thompson, Count Rumford Count Rumford on the nature of heat

CERN Document Server

Brown, Sanborn C

1967-01-01

Men of Physics: Benjamin Thompson - Count Rumford: Count Rumford on the Nature of Heat covers the significant contributions of Count Rumford in the fields of physics. Count Rumford was born with the name Benjamin Thompson on March 23, 1753, in Woburn, Massachusetts. This book is composed of two parts encompassing 11 chapters, and begins with a presentation of Benjamin Thompson's biography and his interest in physics, particularly as an advocate of an """"anti-caloric"""" theory of heat. The subsequent chapters are devoted to his many discoveries that profoundly affected the physical thought

What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science.

Science.gov (United States)

Patil, Prasad; Peng, Roger D; Leek, Jeffrey T

2016-07-01

A recent study of the replicability of key psychological findings is a major contribution toward understanding the human side of the scientific process. Despite the careful and nuanced analysis reported, the simple narrative disseminated by the mass, social, and scientific media was that in only 36% of the studies were the original results replicated. In the current study, however, we showed that 77% of the replication effect sizes reported were within a 95% prediction interval calculated using the original effect size. Our analysis suggests two critical issues in understanding replication of psychological studies. First, researchers' intuitive expectations for what a replication should show do not always match with statistical estimates of replication. Second, when the results of original studies are very imprecise, they create wide prediction intervals-and a broad range of replication effects that are consistent with the original estimates. This may lead to effects that replicate successfully, in that replication results are consistent with statistical expectations, but do not provide much information about the size (or existence) of the true effect. In this light, the results of the Reproducibility Project: Psychology can be viewed as statistically consistent with what one might expect when performing a large-scale replication experiment. © The Author(s) 2016.

Teenage Mutant Ninja Turtles Counting Pizza Toppings: A Creative Writing Learning Strategy.

Science.gov (United States)

Buchan, Laura; And Others

1996-01-01

This article describes the application of a proofreading mnemonic learning strategy for proofreading creative writing assignments. The mnemonic--Ninja Turtles Counting Pizza Toppings--reminds students to check their work for name, title, capitalization, punctuation, and transition words. Application of the strategy, possible pitfalls, and…

Counting cormorants

DEFF Research Database (Denmark)

Bregnballe, Thomas; Carss, David N; Lorentsen, Svein-Håkon

2013-01-01

This chapter focuses on Cormorant population counts for both summer (i.e. breeding) and winter (i.e. migration, winter roosts) seasons. It also explains differences in the data collected from undertaking ‘day’ versus ‘roost’ counts, gives some definitions of the term ‘numbers’, and presents two...

DNA Replication Profiling Using Deep Sequencing.

Science.gov (United States)

Saayman, Xanita; Ramos-Pérez, Cristina; Brown, Grant W

2018-01-01

Profiling of DNA replication during progression through S phase allows a quantitative snap-shot of replication origin usage and DNA replication fork progression. We present a method for using deep sequencing data to profile DNA replication in S. cerevisiae.

Short communication: Repeatability of differential goat bulk milk culture and associations with somatic cell count, total bacterial count, and standard plate count.

Science.gov (United States)

Koop, G; Dik, N; Nielen, M; Lipman, L J A

2010-06-01

The aims of this study were to assess how different bacterial groups in bulk milk are related to bulk milk somatic cell count (SCC), bulk milk total bacterial count (TBC), and bulk milk standard plate count (SPC) and to measure the repeatability of bulk milk culturing. On 53 Dutch dairy goat farms, 3 bulk milk samples were collected at intervals of 2 wk. The samples were cultured for SPC, coliform count, and staphylococcal count and for the presence of Staphylococcus aureus. Furthermore, SCC (Fossomatic 5000, Foss, Hillerød, Denmark) and TBC (BactoScan FC 150, Foss) were measured. Staphylococcal count was correlated to SCC (r=0.40), TBC (r=0.51), and SPC (r=0.53). Coliform count was correlated to TBC (r=0.33), but not to any of the other variables. Staphylococcus aureus did not correlate to SCC. The contribution of the staphylococcal count to the SPC was 31%, whereas the coliform count comprised only 1% of the SPC. The agreement of the repeated measurements was low. This study indicates that staphylococci in goat bulk milk are related to SCC and make a significant contribution to SPC. Because of the high variation in bacterial counts, repeated sampling is necessary to draw valid conclusions from bulk milk culturing. 2010 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Metrology and statistical analysis for the precise standardisation of cobalt-60 by 4πβ-γ coincidence counting

International Nuclear Information System (INIS)

Buckman, S.M.

1995-03-01

The major part of the thesis is devoted to the theoretical development of a comprehensive PC-based statistical package for the analysis of data from coincidence-counting experiments. This analysis is applied to primary standardizations of Co performed in Australia and Japan. The Australian standardisation, the accuracy of which is confirmed through international comparison, is used to re-calibrate the ionisation chamber. Both Australian and Japanese coincidence-counting systems are interfaced to personal computers to enable replicated sets of measurements to be made under computer control. Further research to confirm the validity of the statistical model includes an experimental investigation into the non-Poisson behaviour of radiation detectors due to the effect of deadtime. Experimental investigation is conducted to determine which areas are most likely to limit the ultimate accuracy achievable with coincidence counting. The thesis concludes by discussing the possibilities of digital coincidence counting and outlines the design of a prototype system presently under development. The accuracy of the Australian standardisation is confirmed by international comparison. From this result a more accurate Co calibration is obtained for the Australian working standard. Based on the work of this thesis, uncertainties in coincidence counting experiments can be better handled with resulting improvements in measurement reliability. The concept and benefits of digital coincidence counting are discussed and a proposed design is given for such a system. All of the data and software associated with this thesis is provided on computer discs. 237 refs., figs., tabs

Induction of UV-resistant DNA replication in Escherichia coli: Induced stable DNA replication as an SOS function

International Nuclear Information System (INIS)

Kogoma, T.; Torrey, T.A.; Connaughton, M.J.

1979-01-01

The striking similarity between the treatments that induce SOS functions and those that result in stable DNA replication (continuous DNA replication in the absence of protein synthesis) prompted us to examine the possibility of stable DNA replication being a recA + lexA + -dependent SOS function. In addition to the treatments previously reported, ultraviolet (UV) irradiation or treatment with mitomycin C was also found to induce stable DNA replication. The thermal treatment of tif-1 strains did not result in detectable levels of stable DNA replication, but nalidixic acid readily induced the activity in these strains. The induction of stable DNA replication with nalidixic acid was severely suppressed in tif-1 lex A mutant strains. The inhibitory activity of lexA3 was negated by the presence of the spr-5l mutation, an intragenic suppressor of lexA3. Induced stable DNA replication was found to be considerably more resistant to UV irradiation than normal replication both in a uvr A6 strain and a uvr + strain. The UV-resistant replication occurred mostly in the semiconservative manner. The possible roles of stable DNA replication in repair of damaged DNA are discussed. (orig.)

Chromatin replication and epigenome maintenance

DEFF Research Database (Denmark)

Alabert, Constance; Groth, Anja

2012-01-01

Stability and function of eukaryotic genomes are closely linked to chromatin structure and organization. During cell division the entire genome must be accurately replicated and the chromatin landscape reproduced on new DNA. Chromatin and nuclear structure influence where and when DNA replication...... initiates, whereas the replication process itself disrupts chromatin and challenges established patterns of genome regulation. Specialized replication-coupled mechanisms assemble new DNA into chromatin, but epigenome maintenance is a continuous process taking place throughout the cell cycle. If DNA...

36 CFR 910.64 - Replication.

Science.gov (United States)

2010-07-01

... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Replication. 910.64 Section 910.64 Parks, Forests, and Public Property PENNSYLVANIA AVENUE DEVELOPMENT CORPORATION GENERAL... DEVELOPMENT AREA Glossary of Terms § 910.64 Replication. Replication means the process of using modern methods...

Replication stress-induced chromosome breakage is correlated with replication fork progression and is preceded by single-stranded DNA formation.

Science.gov (United States)

Feng, Wenyi; Di Rienzi, Sara C; Raghuraman, M K; Brewer, Bonita J

2011-10-01

Chromosome breakage as a result of replication stress has been hypothesized to be the direct consequence of defective replication fork progression, or "collapsed" replication forks. However, direct and genome-wide evidence that collapsed replication forks give rise to chromosome breakage is still lacking. Previously we showed that a yeast replication checkpoint mutant mec1-1, after transient exposure to replication impediment imposed by hydroxyurea (HU), failed to complete DNA replication, accumulated single-stranded DNA (ssDNA) at the replication forks, and fragmented its chromosomes. In this study, by following replication fork progression genome-wide via ssDNA detection and by direct mapping of chromosome breakage after HU exposure, we have tested the hypothesis that the chromosome breakage in mec1 cells occurs at collapsed replication forks. We demonstrate that sites of chromosome breakage indeed correlate with replication fork locations. Moreover, ssDNA can be detected prior to chromosome breakage, suggesting that ssDNA accumulation is the common precursor to double strand breaks at collapsed replication forks.

Replication Research and Special Education

Science.gov (United States)

Travers, Jason C.; Cook, Bryan G.; Therrien, William J.; Coyne, Michael D.

2016-01-01

Replicating previously reported empirical research is a necessary aspect of an evidence-based field of special education, but little formal investigation into the prevalence of replication research in the special education research literature has been conducted. Various factors may explain the lack of attention to replication of special education…

Repeatability of differential goat bulk milk culture and associations with somatic cell count, total bacterial count, and standard plate count

NARCIS (Netherlands)

Koop, G.; Dik, N.; Nielen, M.; Lipman, L.J.A.

2010-01-01

The aims of this study were to assess how different bacterial groups in bulk milk are related to bulk milk somatic cell count (SCC), bulk milk total bacterial count (TBC), and bulk milk standard plate count (SPC) and to measure the repeatability of bulk milk culturing. On 53 Dutch dairy goat farms,

Eukaryotic DNA Replication Fork.

Science.gov (United States)

Burgers, Peter M J; Kunkel, Thomas A

2017-06-20

This review focuses on the biogenesis and composition of the eukaryotic DNA replication fork, with an emphasis on the enzymes that synthesize DNA and repair discontinuities on the lagging strand of the replication fork. Physical and genetic methodologies aimed at understanding these processes are discussed. The preponderance of evidence supports a model in which DNA polymerase ε (Pol ε) carries out the bulk of leading strand DNA synthesis at an undisturbed replication fork. DNA polymerases α and δ carry out the initiation of Okazaki fragment synthesis and its elongation and maturation, respectively. This review also discusses alternative proposals, including cellular processes during which alternative forks may be utilized, and new biochemical studies with purified proteins that are aimed at reconstituting leading and lagging strand DNA synthesis separately and as an integrated replication fork.

The progression of replication forks at natural replication barriers in live bacteria

NARCIS (Netherlands)

Moolman, M.C.; Tiruvadi Krishnan, S; Kerssemakers, J.W.J.; de Leeuw, R.; Lorent, V.J.F.; Sherratt, David J.; Dekker, N.H.

2016-01-01

Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these

Flock House virus subgenomic RNA3 is replicated and its replication correlates with transactivation of RNA2

International Nuclear Information System (INIS)

Eckerle, Lance D.; Albarino, Cesar G.; Ball, L. Andrew.

2003-01-01

The nodavirus Flock House virus has a bipartite genome composed of RNAs 1 and 2, which encode the catalytic component of the RNA-dependent RNA polymerase (RdRp) and the capsid protein precursor, respectively. In addition to catalyzing replication of the viral genome, the RdRp also transcribes from RNA1 a subgenomic RNA3, which is both required for and suppressed by RNA2 replication. Here, we show that in the absence of RNA1 replication, FHV RdRp replicated positive-sense RNA3 transcripts fully and copied negative-sense RNA3 transcripts into positive strands. The two nonstructural proteins encoded by RNA3 were dispensable for replication, but sequences in the 3'-terminal 58 nucleotides were required. RNA3 variants that failed to replicate also failed to transactivate RNA2. These results imply that RNA3 is naturally produced both by transcription from RNA1 and by subsequent RNA1-independent replication and that RNA3 replication may be necessary for transactivation of RNA2

Standardization of {sup 241}Am by digital coincidence counting, liquid scintillation counting and defined solid angle counting

Energy Technology Data Exchange (ETDEWEB)

Balpardo, C., E-mail: balpardo@cae.cnea.gov.a [Laboratorio de Metrologia de Radioisotopos, CNEA, Buenos Aires (Argentina); Capoulat, M.E.; Rodrigues, D.; Arenillas, P. [Laboratorio de Metrologia de Radioisotopos, CNEA, Buenos Aires (Argentina)

2010-07-15

The nuclide {sup 241}Am decays by alpha emission to {sup 237}Np. Most of the decays (84.6%) populate the excited level of {sup 237}Np with energy of 59.54 keV. Digital coincidence counting was applied to standardize a solution of {sup 241}Am by alpha-gamma coincidence counting with efficiency extrapolation. Electronic discrimination was implemented with a pressurized proportional counter and the results were compared with two other independent techniques: Liquid scintillation counting using the logical sum of double coincidences in a TDCR array and defined solid angle counting taking into account activity inhomogeneity in the active deposit. The results show consistency between the three methods within a limit of a 0.3%. An ampoule of this solution will be sent to the International Reference System (SIR) during 2009. Uncertainties were analysed and compared in detail for the three applied methods.

Teaching about Prejudice with a Bogardus Social Distance Scale Activity: Replication and Extension

Science.gov (United States)

Maurer, Trent W.; Keim, Cassidy

2018-01-01

This study presents a three-year replication and extension of Maurer's (2013) evaluation of a classroom activity to reduce prejudice and discrimination. Students in six sections of an introductory family science course were assigned to one of three conditions and one of two target marginalized groups for a 3x2 design. Results differed…

The effect of topic selection on writing fluency among Japanese high school students

Directory of Open Access Journals (Sweden)

Sarah Lin Lubold

2016-01-01

Full Text Available Written fluency and fluency building activities have been shown to promote linguistic choice and student voice development, increased ability to express ideas using complex grammatical structures and greater intrinsic motivation in English language learners. Since the 1970’s, process-oriented writing has been emphasized, yielding an amplified focus on meaning of student content over linguistic form precision. Current research of writing fluency must delve deeper into questions of student ownership of topic and the outcomes for low-risk activities that support fluency practice and encourage confidence building in students. The purpose of this replication study is to further explore previous findings on the effects of topic selection on writing fluency for high school English as foreign language learners. Building off of the work of Bonzo (2008, this study focused on a timed, non-graded writing activity administered to groups of Japanese engineering students in three departments: mechanical, electrical, and global engineering. The six subsequent samples for each participating student were analyzed using online text-analysis for total and unique word counts, providing data used to perform a t-test. Responses to bi-lingual student questionnaires, with prompts on self-perceived written English ability, self-efficacy and strategies for success while writing, provided additional insight into the facets of fluency. The results of these writing sessions offer both confirmation of and contrast to Bonzo’s original work, demonstrate increased student meaning making, and support the use of free writing activities in English language classrooms as a means by which student written fluency may be improved.

Comparison of visual-based helicopter and fixed-wing forward-looking infrared surveys for counting white-tailed deer Odocoileus virginianus

Science.gov (United States)

Storm, Daniel J.; Samuel, Michael D.; Van Deelen, Timothy R.; Malcolm, Karl D.; Rolley, Robert E.; Frost, Nancy A.; Bates, Donald P.; Richards, Bryan J.

2011-01-01

Aerial surveys using direct counts of animals are commonly used to estimate deer abundance. Forward-looking infrared (FLIR) technology is increasingly replacing traditional methods such as visual observation from helicopters. Our goals were to compare fixed-wing FLIR and visual, helicopter-based counts in terms of relative bias, influence of snow cover and cost. We surveyed five plots: four 41.4 km2 plots with free-ranging white-tailed deer Odocoileus virginianus populations in Wisconsin and a 5.3 km2 plot with a white-tailed deer population contained by a high fence in Michigan. We surveyed plots using both fixed-wing FLIR and helicopters, both with snow cover and without snow. None of the methods counted more deer than the other when snow was present. Helicopter counts were lower in the absence of snow, but lack of snow cover did not apparently affect FLIR. Group sizes of observed deer were similar regardless of survey method or season. We found that FLIR counts were generally precise (CV = 0.089) when two or three replicate surveys were conducted within a few hours. However, at the plot level, FLIR counts differed greatly between seasons, suggesting that detection rates vary over larger time scales. Fixed-wing FLIR was more costly than visual observers in helicopters and was more restrictive in terms of acceptable survey conditions. Further research is needed to understand what factors influence the detection of deer during FLIR surveys.

DNA Replication Control During Drosophila Development: Insights into the Onset of S Phase, Replication Initiation, and Fork Progression

Science.gov (United States)

Hua, Brian L.; Orr-Weaver, Terry L.

2017-01-01

Proper control of DNA replication is critical to ensure genomic integrity during cell proliferation. In addition, differential regulation of the DNA replication program during development can change gene copy number to influence cell size and gene expression. Drosophila melanogaster serves as a powerful organism to study the developmental control of DNA replication in various cell cycle contexts in a variety of differentiated cell and tissue types. Additionally, Drosophila has provided several developmentally regulated replication models to dissect the molecular mechanisms that underlie replication-based copy number changes in the genome, which include differential underreplication and gene amplification. Here, we review key findings and our current understanding of the developmental control of DNA replication in the contexts of the archetypal replication program as well as of underreplication and differential gene amplification. We focus on the use of these latter two replication systems to delineate many of the molecular mechanisms that underlie the developmental control of replication initiation and fork elongation. PMID:28874453

The progression of replication forks at natural replication barriers in live bacteria.

Science.gov (United States)

Moolman, M Charl; Tiruvadi Krishnan, Sriram; Kerssemakers, Jacob W J; de Leeuw, Roy; Lorent, Vincent; Sherratt, David J; Dekker, Nynke H

2016-07-27

Protein-DNA complexes are one of the principal barriers the replisome encounters during replication. One such barrier is the Tus-ter complex, which is a direction dependent barrier for replication fork progression. The details concerning the dynamics of the replisome when encountering these Tus-ter barriers in the cell are poorly understood. By performing quantitative fluorescence microscopy with microfuidics, we investigate the effect on the replisome when encountering these barriers in live Escherichia coli cells. We make use of an E. coli variant that includes only an ectopic origin of replication that is positioned such that one of the two replisomes encounters a Tus-ter barrier before the other replisome. This enables us to single out the effect of encountering a Tus-ter roadblock on an individual replisome. We demonstrate that the replisome remains stably bound after encountering a Tus-ter complex from the non-permissive direction. Furthermore, the replisome is only transiently blocked, and continues replication beyond the barrier. Additionally, we demonstrate that these barriers affect sister chromosome segregation by visualizing specific chromosomal loci in the presence and absence of the Tus protein. These observations demonstrate the resilience of the replication fork to natural barriers and the sensitivity of chromosome alignment to fork progression. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Salivary cariogenic bacteria counts are associated with obesity in student women at a Malaysian university.

Science.gov (United States)

Yeo, Wey-Zheng; Lim, Sheng-Pei; Say, Yee-How

2018-01-01

The counts of cariogenic bacteria lactobacilli and mutans streptococci have been studied and correlated with sugar intake. This study was to investigate the association between salivary lactobacilli and mutans streptococci counts with sweet food eating behavior and sweet sensitivity among 120 Malaysian women (101 ethnic Chinese, 19 ethnic Indians), while taking into account anthropometric and menstruation variables. Demographics, anthropometric measurements and menstrual history were taken. Hedonic preference, intake frequency of a list of sweet foods, intensity perception and pleasantness ratings of sweet stimuli were assessed. Saliva was collected for lactobacilli and mutans streptococci culture. We found that centrally obese subjects (high waist circumference and waist-hip ratio) had significantly higher salivary lactobacilli and mutans streptococci counts (all pMalaysian women are associated with central obesity, but not sweet food eating behaviour, sweet sensitivity and menstruation variables. Salivary microbiome analysis could be useful as a potential diagnostic indicator of diseases such as obesity.

Clean Hands Count

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Replication of micro and nano surface geometries

DEFF Research Database (Denmark)

Hansen, Hans Nørgaard; Hocken, R.J.; Tosello, Guido

2011-01-01

The paper describes the state-of-the-art in replication of surface texture and topography at micro and nano scale. The description includes replication of surfaces in polymers, metals and glass. Three different main technological areas enabled by surface replication processes are presented......: manufacture of net-shape micro/nano surfaces, tooling (i.e. master making), and surface quality control (metrology, inspection). Replication processes and methods as well as the metrology of surfaces to determine the degree of replication are presented and classified. Examples from various application areas...... are given including replication for surface texture measurements, surface roughness standards, manufacture of micro and nano structured functional surfaces, replicated surfaces for optical applications (e.g. optical gratings), and process chains based on combinations of repeated surface replication steps....

A New Replication Norm for Psychology

Directory of Open Access Journals (Sweden)

Etienne P LeBel

2015-10-01

Full Text Available In recent years, there has been a growing concern regarding the replicability of findings in psychology, including a mounting number of prominent findings that have failed to replicate via high-powered independent replication attempts. In the face of this replicability “crisis of confidence”, several initiatives have been implemented to increase the reliability of empirical findings. In the current article, I propose a new replication norm that aims to further boost the dependability of findings in psychology. Paralleling the extant social norm that researchers should peer review about three times as many articles that they themselves publish per year, the new replication norm states that researchers should aim to independently replicate important findings in their own research areas in proportion to the number of original studies they themselves publish per year (e.g., a 4:1 original-to-replication studies ratio. I argue this simple approach could significantly advance our science by increasing the reliability and cumulative nature of our empirical knowledge base, accelerating our theoretical understanding of psychological phenomena, instilling a focus on quality rather than quantity, and by facilitating our transformation toward a research culture where executing and reporting independent direct replications is viewed as an ordinary part of the research process. To help promote the new norm, I delineate (1 how each of the major constituencies of the research process (i.e., funders, journals, professional societies, departments, and individual researchers can incentivize replications and promote the new norm and (2 any obstacles each constituency faces in supporting the new norm.

Starting Points and Pathways in Aboriginal Students' Learning of Number: Recognising Different World Views

Science.gov (United States)

Treacy, Kaye; Frid, Sandra; Jacob, Lorraine

2015-01-01

This research was designed to investigate the conceptualisations and thinking strategies Indigenous Australian students use in counting tasks. Eighteen Aboriginal students, in years 1 to 11 at a remote community school, were interviewed using standard counting tasks and a "counting" task that involved fetching "maku" (witchetty…

HIV-infected viremic long-term non-progressors and controllers display different immunological mechanisms for preserved CD4+cell counts

DEFF Research Database (Denmark)

Gaardbo, J; Ronit, A; Hartling, H

2012-01-01

of viral replication cannot explain non-progression in LTNP. Therefore we hypothesized that the immunological mechanism responsible for preserved CD4 counts in LTNP is different from that in VC. Methods: 69 treatment naïve HIV-infected patients were included in a cross-sectional study. A total of 14 LTNP...... ratio in LTNP compared to VC were found (3.8 vs. 5.5, P=0.068) while ratios in LTNP and PR were similar (4.0, P>0.05). Conclusion: LTNP displayed high levels of immune activation, apoptotic cells and reduced Th17/Treg ratio compared to VC, while LTNP were similar to PR. Thus, the immunological mechanism...... responsible for preserved CD4 counts in LTNP is still unclear but seems to be different from that in VC....

Noun Countability; Count Nouns and Non-count Nouns, What are the Syntactic Differences Between them?

Directory of Open Access Journals (Sweden)

Azhar A. Alkazwini

2016-11-01

Full Text Available Words that function as the subjects of verbs, objects of verbs or prepositions and which can have a plural form and possessive ending are known as nouns. They are described as referring to persons, places, things, states, or qualities and might also be used as an attributive modifier. In this paper, classes and subclasses of nouns shall be presented, then, noun countability branching into count and non-count nous shall be discussed. A number of present examples illustrating differences between count and non-count nouns and this includes determiner-head-co-occurrence restrictions of number, subject-verb agreement, in addition to some exceptions to this agreement rule shall be discussed. Also, the lexically inherent number in nouns and how inherently plural nouns are classified in terms of (+/- count are illustrated. This research will discuss partitive construction of count and non-count nouns, nouns as attributive modifier and, finally, conclude with the fact that there are syntactic difference between count and non-count in the English Language.

Centromere replication timing determines different forms of genomic instability in Saccharomyces cerevisiae checkpoint mutants during replication stress.

Science.gov (United States)

Feng, Wenyi; Bachant, Jeff; Collingwood, David; Raghuraman, M K; Brewer, Bonita J

2009-12-01

Yeast replication checkpoint mutants lose viability following transient exposure to hydroxyurea, a replication-impeding drug. In an effort to understand the basis for this lethality, we discovered that different events are responsible for inviability in checkpoint-deficient cells harboring mutations in the mec1 and rad53 genes. By monitoring genomewide replication dynamics of cells exposed to hydroxyurea, we show that cells with a checkpoint deficient allele of RAD53, rad53K227A, fail to duplicate centromeres. Following removal of the drug, however, rad53K227A cells recover substantial DNA replication, including replication through centromeres. Despite this recovery, the rad53K227A mutant fails to achieve biorientation of sister centromeres during recovery from hydroxyurea, leading to secondary activation of the spindle assembly checkpoint (SAC), aneuploidy, and lethal chromosome segregation errors. We demonstrate that cell lethality from this segregation defect could be partially remedied by reinforcing bipolar attachment. In contrast, cells with the mec1-1 sml1-1 mutations suffer from severely impaired replication resumption upon removal of hydroxyurea. mec1-1 sml1-1 cells can, however, duplicate at least some of their centromeres and achieve bipolar attachment, leading to abortive segregation and fragmentation of incompletely replicated chromosomes. Our results highlight the importance of replicating yeast centromeres early and reveal different mechanisms of cell death due to differences in replication fork progression.

Clean Hands Count

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Starting points and pathways in Aboriginal students' learning of number: recognising different world views

Science.gov (United States)

Treacy, Kaye; Frid, Sandra; Jacob, Lorraine

2015-09-01

This research was designed to investigate the conceptualisations and thinking strategies Indigenous Australian students use in counting tasks. Eighteen Aboriginal students, in years 1 to 11 at a remote community school, were interviewed using standard counting tasks and a `counting' task that involved fetching `maku' (witchetty grubs) to have enough to give a maku to each person in a picture. The tasks were developed with, and the interviews conducted by, an Aboriginal research assistant, to ensure appropriate cultural and language contexts. A main finding was that most of the students did not see the need to use counting to make equivalent sets, even though they were able to demonstrate standard counting skills. The findings highlight a need to further examine the world views, orientations and related mathematical concepts and processes that Indigenous students bring to school.

The Inherent Asymmetry of DNA Replication.

Science.gov (United States)

Snedeker, Jonathan; Wooten, Matthew; Chen, Xin

2017-10-06

Semiconservative DNA replication has provided an elegant solution to the fundamental problem of how life is able to proliferate in a way that allows cells, organisms, and populations to survive and replicate many times over. Somewhat lost, however, in our admiration for this mechanism is an appreciation for the asymmetries that occur in the process of DNA replication. As we discuss in this review, these asymmetries arise as a consequence of the structure of the DNA molecule and the enzymatic mechanism of DNA synthesis. Increasing evidence suggests that asymmetries in DNA replication are able to play a central role in the processes of adaptation and evolution by shaping the mutagenic landscape of cells. Additionally, in eukaryotes, recent work has demonstrated that the inherent asymmetries in DNA replication may play an important role in the process of chromatin replication. As chromatin plays an essential role in defining cell identity, asymmetries generated during the process of DNA replication may play critical roles in cell fate decisions related to patterning and development.

Replication dynamics of the yeast genome.

Science.gov (United States)

Raghuraman, M K; Winzeler, E A; Collingwood, D; Hunt, S; Wodicka, L; Conway, A; Lockhart, D J; Davis, R W; Brewer, B J; Fangman, W L

2001-10-05

Oligonucleotide microarrays were used to map the detailed topography of chromosome replication in the budding yeast Saccharomyces cerevisiae. The times of replication of thousands of sites across the genome were determined by hybridizing replicated and unreplicated DNAs, isolated at different times in S phase, to the microarrays. Origin activations take place continuously throughout S phase but with most firings near mid-S phase. Rates of replication fork movement vary greatly from region to region in the genome. The two ends of each of the 16 chromosomes are highly correlated in their times of replication. This microarray approach is readily applicable to other organisms, including humans.

LHCb experience with LFC replication

CERN Document Server

Bonifazi, F; Perez, E D; D'Apice, A; dell'Agnello, L; Düllmann, D; Girone, M; Re, G L; Martelli, B; Peco, G; Ricci, P P; Sapunenko, V; Vagnoni, V; Vitlacil, D

2008-01-01

Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements.

LHCb experience with LFC replication

International Nuclear Information System (INIS)

Bonifazi, F; Carbone, A; D'Apice, A; Dell'Agnello, L; Re, G L; Martelli, B; Ricci, P P; Sapunenko, V; Vitlacil, D; Perez, E D; Duellmann, D; Girone, M; Peco, G; Vagnoni, V

2008-01-01

Database replication is a key topic in the framework of the LHC Computing Grid to allow processing of data in a distributed environment. In particular, the LHCb computing model relies on the LHC File Catalog, i.e. a database which stores information about files spread across the GRID, their logical names and the physical locations of all the replicas. The LHCb computing model requires the LFC to be replicated at Tier-1s. The LCG 3D project deals with the database replication issue and provides a replication service based on Oracle Streams technology. This paper describes the deployment of the LHC File Catalog replication to the INFN National Center for Telematics and Informatics (CNAF) and to other LHCb Tier-1 sites. We performed stress tests designed to evaluate any delay in the propagation of the streams and the scalability of the system. The tests show the robustness of the replica implementation with performance going much beyond the LHCb requirements

Replication capacity in relation to immunologic and virologic outcomes in HIV-1-infected treatment-naive subjects.

Science.gov (United States)

Skowron, Gail; Spritzler, John G; Weidler, Jodi; Robbins, Gregory K; Johnson, Victoria A; Chan, Ellen S; Asmuth, David M; Gandhi, Rajesh T; Lie, Yolanda; Bates, Michael; Pollard, Richard B

2009-03-01

To evaluate the association between baseline (BL) replication capacity (RC) (RCBL) and immunologic/virologic parameters (at BL and after 48 weeks on therapy) in HIV-1-infected subjects initiating antiretroviral therapy. RCBL was determined using a modified Monogram PhenoSense HIV drug susceptibility assay on plasma HIV-1 from 321 treatment-naive subjects from AIDS Clinical Trials Group 384. Univariate and multivariable analyses were performed to determine the association of RCBL with BL and on-therapy virologic and immunologic outcomes. Higher RCBL was associated with lower baseline CD4 (CD4BL) (r = -0.23, P < 0.0001), higher baseline HIV-1 RNA (r = 0.25, P < 0.0001), higher CD4BL activation percent (r = 0.23, P < 0.0001), and lower CD4BL memory count (r = -0.21, P = 0.0002). In a multivariable model, week 48 CD4 increase (DeltaCD448) was associated with lower CD4BL memory count and higher CD4BL-naive percent (P = 0.004, P = 0.015, respectively). The interaction between CD4BL and RCBL was significant (P = 0.018), with a positive association between RCBL and DeltaCD448 in subjects with higher CD4BL and a negative association at lower absCD4BL. At baseline, higher RC was significantly associated with higher HIV-1 RNA, higher CD4 cell activation, lower CD4 cell count, and lower CD4 memory cell count. These factors may interact, directly or indirectly, to modify the extent to which CD4 recovery occurs in patients starting antiretroviral therapy at different CD4BL counts.

Count-to-count time interval distribution analysis in a fast reactor

International Nuclear Information System (INIS)

Perez-Navarro Gomez, A.

1973-01-01

The most important kinetic parameters have been measured at the zero power fast reactor CORAL-I by means of the reactor noise analysis in the time domain, using measurements of the count-to-count time intervals. (Author) 69 refs

Voice of the Researcher: Extending the Limits of What Counts as Research

Directory of Open Access Journals (Sweden)

Stephen John Quaye

2007-01-01

Full Text Available Social sciences research is entrenched with particular values, beliefs, norms, and practices that students, faculty, and researchers reproduce over time. In this article, the author argues for extending what counts as research within the social sciences to be more inclusive of differing methodologies and writing genres. Using personal narrative, diaries, and poetry, the author demonstrates unconventional ways of thinking about, doing, and writing research. He situates his personal experiences as a Ghanaian/American student within relevant literature to illuminate the merging of his home cultural values with those of the academic community and the contradictions and struggles associated with this process. Ultimately, the story portrays the journey of a graduate student as he challenges traditional research norms to open up spaces for underrepresented students to feel more at home within academe.

High-Resolution Replication Profiles Define the Stochastic Nature of Genome Replication Initiation and Termination

Directory of Open Access Journals (Sweden)

Michelle Hawkins

2013-11-01

Full Text Available Eukaryotic genome replication is stochastic, and each cell uses a different cohort of replication origins. We demonstrate that interpreting high-resolution Saccharomyces cerevisiae genome replication data with a mathematical model allows quantification of the stochastic nature of genome replication, including the efficiency of each origin and the distribution of termination events. Single-cell measurements support the inferred values for stochastic origin activation time. A strain, in which three origins were inactivated, confirmed that the distribution of termination events is primarily dictated by the stochastic activation time of origins. Cell-to-cell variability in origin activity ensures that termination events are widely distributed across virtually the whole genome. We propose that the heterogeneity in origin usage contributes to genome stability by limiting potentially deleterious events from accumulating at particular loci.

Platelet count kinetics following interruption of antiretroviral treatment.

Science.gov (United States)

Zetterberg, Eva; Neuhaus, Jacqueline; Baker, Jason V; Somboonwit, Charurut; Llibre, Josep M; Palfreeman, Adrian; Chini, Maria; Lundgren, Jens D

2013-01-02

To investigate the mechanisms of platelet kinetics in the Strategies for Management of Antiretroviral Therapy (SMART) study that demonstrated excess mortality with CD4 guided episodic antiretroviral therapy (ART) drug conservation compared with continuous treatment viral suppression. Follow-up analyses of stored plasma samples demonstrated increased activation of both inflammatory and coagulation pathways after stopping ART. SMART patients from sites that determined platelets routinely. Platelet counts were retrospectively collected from 2206 patients from visits at study entry, and during follow-up. D-dimer levels were measured at study entry, month 1, and 2. Platelet levels decreased in the drug conservation group following randomization, but remained stable in the viral suppression group [median (IQR) decline from study entry to month 4: -24 000/μl (-54 000 to 4000) vs. 3000 (-22 000 to 24 000), respectively, P conservation vs. the viral suppression arm (unadjusted drug conservation/viral suppression [HR (95%CI) = 1.8 (1.2-2.7)]. The decline in platelet count among drug conservation participants on fully suppressive ART correlated with the rise in D-dimer from study entry to either month 1 or 2 (r = -0.41; P = 0.02). Among drug conservation participants who resumed ART 74% recovered to their study entry platelet levels. Interrupting ART increases the risk of thrombocytopenia, but reinitiation of ART typically reverses it. Factors contributing to declines in platelets after interrupting ART may include activation of coagulation pathways or HIV-1 replication itself. The contribution of platelets in HIV-related procoagulant activity requires further study.

DNA replication and post-replication repair in U.V.-sensitive mouse neuroblastoma cells

International Nuclear Information System (INIS)

Lavin, M.F.; McCombe, P.; Kidson, C.

1976-01-01

Mouse neuroblastoma cells differentiated when grown in the absence of serum; differentiation was reversed on the addition of serum. Differentiated cells were more sensitive to U.V.-radiation than proliferating cells. Whereas addition of serum to differentiated neuroblastoma cells normally resulted in immediate, synchronous entry into S phase, irradiation just before the addition of serum resulted in a long delay in the onset of DNA replication. During this lag period, incorporated 3 H-thymidine appeared in the light density region of CsCl gradients, reflecting either repair synthesis or abortive replication. Post-replication repair (gap-filling) was found to be present in proliferating cells and at certain times in differentiated cells. It is suggested that the sensitivity of differentiated neuroblastoma cells to U.V.-radiation may have been due to ineffective post-replication repair or to deficiencies in more than one repair mechanism, with reduction in repair capacity beyond a critical threshold. (author)

DATABASE REPLICATION IN HETEROGENOUS PLATFORM

OpenAIRE

Hendro Nindito; Evaristus Didik Madyatmadja; Albert Verasius Dian Sano

2014-01-01

The application of diverse database technologies in enterprises today is increasingly a common practice. To provide high availability and survavibality of real-time information, a database replication technology that has capability to replicate databases under heterogenous platforms is required. The purpose of this research is to find the technology with such capability. In this research, the data source is stored in MSSQL database server running on Windows. The data will be replicated to MyS...

Overcoming natural replication barriers: differential helicase requirements.

Science.gov (United States)

Anand, Ranjith P; Shah, Kartik A; Niu, Hengyao; Sung, Patrick; Mirkin, Sergei M; Freudenreich, Catherine H

2012-02-01

DNA sequences that form secondary structures or bind protein complexes are known barriers to replication and potential inducers of genome instability. In order to determine which helicases facilitate DNA replication across these barriers, we analyzed fork progression through them in wild-type and mutant yeast cells, using 2-dimensional gel-electrophoretic analysis of the replication intermediates. We show that the Srs2 protein facilitates replication of hairpin-forming CGG/CCG repeats and prevents chromosome fragility at the repeat, whereas it does not affect replication of G-quadruplex forming sequences or a protein-bound repeat. Srs2 helicase activity is required for hairpin unwinding and fork progression. Also, the PCNA binding domain of Srs2 is required for its in vivo role of replication through hairpins. In contrast, the absence of Sgs1 or Pif1 helicases did not inhibit replication through structural barriers, though Pif1 did facilitate replication of a telomeric protein barrier. Interestingly, replication through a protein barrier but not a DNA structure barrier was modulated by nucleotide pool levels, illuminating a different mechanism by which cells can regulate fork progression through protein-mediated stall sites. Our analyses reveal fundamental differences in the replication of DNA structural versus protein barriers, with Srs2 helicase activity exclusively required for fork progression through hairpin structures.

Exploiting replicative stress to treat cancer

DEFF Research Database (Denmark)

Dobbelstein, Matthias; Sørensen, Claus Storgaard

2015-01-01

DNA replication in cancer cells is accompanied by stalling and collapse of the replication fork and signalling in response to DNA damage and/or premature mitosis; these processes are collectively known as 'replicative stress'. Progress is being made to increase our understanding of the mechanisms...

Chromatin maturation depends on continued DNA-replication

International Nuclear Information System (INIS)

Schlaeger, E.J.; Puelm, W.; Knippers, R.

1983-01-01

The structure of [ 3 H]thymidine pulse-labeled chromatin in lymphocytes differs from that of non-replicating chromatin by several operational criteria which are related to the higher nuclease sensitivity of replicating chromatin. These structural features of replicating chromatin rapidly disappear when the [ 3 H]thymidine pulse is followed by a chase in the presence of an excess of non-radioactive thymidine. However, when the rate of DNA replication is reduced, as in cycloheximide-treated lymphocytes, chromatin maturation is retarded. No chromatin maturation is observed when nuclei from pulse-labeled lymphocytes are incubated in vitro in the absence of DNA precursors. In contrast, when these nuclei are incubated under conditions known to be optimal for DNA replication, the structure of replicating chromatin is efficiently converted to that of 'mature', non-replicating chromatin. The authors conclude that the properties of nascent DNA and/or the distance from the replication fork are important factors in chromatin maturation. (Auth.)

The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast

DEFF Research Database (Denmark)

Larsen, Nicolai B; Sass, Ehud; Suski, Catherine

2014-01-01

Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus...... as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications....

The effect of volume and quenching on estimation of counting efficiencies in liquid scintillation counting

International Nuclear Information System (INIS)

Knoche, H.W.; Parkhurst, A.M.; Tam, S.W.

1979-01-01

The effect of volume on the liquid scintillation counting performance of 14 C-samples has been investigated. A decrease in counting efficiency was observed for samples with volumes below about 6 ml and those above about 18 ml when unquenched samples were assayed. Two quench-correction methods, sample channels ratio and external standard channels ratio, and three different liquid scintillation counters, were used in an investigation to determine the magnitude of the error in predicting counting efficiencies when small volume samples (2 ml) with different levels of quenching were assayed. The 2 ml samples exhibited slightly greater standard deviations of the difference between predicted and determined counting efficiencies than did 15 ml samples. Nevertheless, the magnitude of the errors indicate that if the sample channels ratio method of quench correction is employed, 2 ml samples may be counted in conventional counting vials with little loss in counting precision. (author)

TasselNet: counting maize tassels in the wild via local counts regression network.

Science.gov (United States)

Lu, Hao; Cao, Zhiguo; Xiao, Yang; Zhuang, Bohan; Shen, Chunhua

2017-01-01

Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources. Naturally image-based approaches have also received much attention in plant-related studies. Yet a fact is that most image-based systems for plant phenotyping are deployed under controlled laboratory environment. When transferring the application scenario to unconstrained in-field conditions, intrinsic and extrinsic variations in the wild pose great challenges for accurate counting of maize tassels, which goes beyond the ability of conventional image processing techniques. This calls for further robust computer vision approaches to address in-field variations. This paper studies the in-field counting problem of maize tassels. To our knowledge, this is the first time that a plant-related counting problem is considered using computer vision technologies under unconstrained field-based environment. With 361 field images collected in four experimental fields across China between 2010 and 2015 and corresponding manually-labelled dotted annotations, a novel Maize Tassels Counting ( MTC ) dataset is created and will be released with this paper. To alleviate the in-field challenges, a deep convolutional neural network-based approach termed TasselNet is proposed. TasselNet can achieve good adaptability to in-field variations via modelling the local visual characteristics of field images and regressing the local counts of maize tassels. Extensive results on the MTC dataset demonstrate that TasselNet outperforms other state-of-the-art approaches by large margins and achieves the overall best counting

TasselNet: counting maize tassels in the wild via local counts regression network

Directory of Open Access Journals (Sweden)

Hao Lu

2017-11-01

Full Text Available Abstract Background Accurately counting maize tassels is important for monitoring the growth status of maize plants. This tedious task, however, is still mainly done by manual efforts. In the context of modern plant phenotyping, automating this task is required to meet the need of large-scale analysis of genotype and phenotype. In recent years, computer vision technologies have experienced a significant breakthrough due to the emergence of large-scale datasets and increased computational resources. Naturally image-based approaches have also received much attention in plant-related studies. Yet a fact is that most image-based systems for plant phenotyping are deployed under controlled laboratory environment. When transferring the application scenario to unconstrained in-field conditions, intrinsic and extrinsic variations in the wild pose great challenges for accurate counting of maize tassels, which goes beyond the ability of conventional image processing techniques. This calls for further robust computer vision approaches to address in-field variations. Results This paper studies the in-field counting problem of maize tassels. To our knowledge, this is the first time that a plant-related counting problem is considered using computer vision technologies under unconstrained field-based environment. With 361 field images collected in four experimental fields across China between 2010 and 2015 and corresponding manually-labelled dotted annotations, a novel Maize Tassels Counting (MTC dataset is created and will be released with this paper. To alleviate the in-field challenges, a deep convolutional neural network-based approach termed TasselNet is proposed. TasselNet can achieve good adaptability to in-field variations via modelling the local visual characteristics of field images and regressing the local counts of maize tassels. Extensive results on the MTC dataset demonstrate that TasselNet outperforms other state-of-the-art approaches by large

Enzymatic recognition of DNA replication origins

International Nuclear Information System (INIS)

Stayton, M.M.; Bertsch, L.; Biswas, S.

1983-01-01

In this paper we discuss the process of recognition of the complementary-strand origin with emphasis on RNA polymerase action in priming M13 DNA replication, the role of primase in G4 DNA replication, and the function of protein n, a priming protein, during primosome assembly. These phage systems do not require several of the bacterial DNA replication enzymes, particularly those involved in the regulation of chromosome copy number of the initiatiion of replication of duplex DNA. 51 references, 13 figures, 1 table

Surface Microstructure Replication in Injection Moulding

DEFF Research Database (Denmark)

Hansen, Hans Nørgaard; Arlø, Uffe Rolf

2005-01-01

topography is transcribed onto the plastic part through complex mechanisms. This replication however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... moulding of surface microstructures. Emphasis is put on the ability to replicate surface microstructures under normal injection moulding conditions, notably with low cost materials at low mould temperatures. The replication of surface microstructures in injection moulding has been explored...... for Polypropylene at low mould temperatures. The process conditions were varied over the recommended process window for the material. The geometry of the obtained structures was analyzed. Evidence suggests that step height replication quality depends linearly on structure width in a certain range. Further...

Replication Protein A (RPA) Phosphorylation Prevents RPA Association with Replication Centers

OpenAIRE

Vassin, Vitaly M.; Wold, Marc S.; Borowiec, James A.

2004-01-01

Mammalian replication protein A (RPA) undergoes DNA damage-dependent phosphorylation at numerous sites on the N terminus of the RPA2 subunit. To understand the functional significance of RPA phosphorylation, we expressed RPA2 variants in which the phosphorylation sites were converted to aspartate (RPA2D) or alanine (RPA2A). Although RPA2D was incorporated into RPA heterotrimers and supported simian virus 40 DNA replication in vitro, the RPA2D mutant was selectively unable to associate with re...

Isospectral discrete and quantum graphs with the same flip counts and nodal counts

Science.gov (United States)

Juul, Jonas S.; Joyner, Christopher H.

2018-06-01

The existence of non-isomorphic graphs which share the same Laplace spectrum (to be referred to as isospectral graphs) leads naturally to the following question: what additional information is required in order to resolve isospectral graphs? It was suggested by Band, Shapira and Smilansky that this might be achieved by either counting the number of nodal domains or the number of times the eigenfunctions change sign (the so-called flip count) (Band et al 2006 J. Phys. A: Math. Gen. 39 13999–4014 Band and Smilansky 2007 Eur. Phys. J. Spec. Top. 145 171–9). Recent examples of (discrete) isospectral graphs with the same flip count and nodal count have been constructed by Ammann by utilising Godsil–McKay switching (Ammann private communication). Here, we provide a simple alternative mechanism that produces systematic examples of both discrete and quantum isospectral graphs with the same flip and nodal counts.

Variance Swap Replication: Discrete or Continuous?

Directory of Open Access Journals (Sweden)

Fabien Le Floc’h

2018-02-01

Full Text Available The popular replication formula to price variance swaps assumes continuity of traded option strikes. In practice, however, there is only a discrete set of option strikes traded on the market. We present here different discrete replication strategies and explain why the continuous replication price is more relevant.

Counting It Twice.

Science.gov (United States)

Schattschneider, Doris

1991-01-01

Provided are examples from many domains of mathematics that illustrate the Fubini Principle in its discrete version: the value of a summation over a rectangular array is independent of the order of summation. Included are: counting using partitions as in proof by pictures, combinatorial arguments, indirect counting as in the inclusion-exclusion…

Low White Blood Cell Count

Science.gov (United States)

Symptoms Low white blood cell count By Mayo Clinic Staff A low white blood cell count (leukopenia) is a decrease ... of white blood cell (neutrophil). The definition of low white blood cell count varies from one medical ...

Surface microstructure replication in injection molding

DEFF Research Database (Denmark)

Theilade, Uffe Arlø; Hansen, Hans Nørgaard

2006-01-01

topography is transcribed onto the plastic part through complex mechanisms. This replication, however, is not perfect, and the replication quality depends on the plastic material properties, the topography itself, and the process conditions. This paper describes and discusses an investigation of injection...... molding of surface microstructures. The fundamental problem of surface microstructure replication has been studied. The research is based on specific microstructures as found in lab-on-a-chip products and on rough surfaces generated from EDM (electro discharge machining) mold cavities. Emphasis is put...... on the ability to replicate surface microstructures under normal injection-molding conditions, i.e., with commodity materials within typical process windows. It was found that within typical process windows the replication quality depends significantly on several process parameters, and especially the mold...

Activation of human herpesvirus replication by apoptosis.

Science.gov (United States)

Prasad, Alka; Remick, Jill; Zeichner, Steven L

2013-10-01

A central feature of herpesvirus biology is the ability of herpesviruses to remain latent within host cells. Classically, exposure to inducing agents, like activating cytokines or phorbol esters that stimulate host cell signal transduction events, and epigenetic agents (e.g., butyrate) was thought to end latency. We recently showed that Kaposi's sarcoma-associated herpesvirus (KSHV, or human herpesvirus-8 [HHV-8]) has another, alternative emergency escape replication pathway that is triggered when KSHV's host cell undergoes apoptosis, characterized by the lack of a requirement for the replication and transcription activator (RTA) protein, accelerated late gene kinetics, and production of virus with decreased infectivity. Caspase-3 is necessary and sufficient to initiate the alternative replication program. HSV-1 was also recently shown to initiate replication in response to host cell apoptosis. These observations suggested that an alternative apoptosis-triggered replication program might be a general feature of herpesvirus biology and that apoptosis-initiated herpesvirus replication may have clinical implications, particularly for herpesviruses that almost universally infect humans. To explore whether an alternative apoptosis-initiated replication program is a common feature of herpesvirus biology, we studied cell lines latently infected with Epstein-Barr virus/HHV-4, HHV-6A, HHV-6B, HHV-7, and KSHV. We found that apoptosis triggers replication for each HHV studied, with caspase-3 being necessary and sufficient for HHV replication. An alternative apoptosis-initiated replication program appears to be a common feature of HHV biology. We also found that commonly used cytotoxic chemotherapeutic agents activate HHV replication, which suggests that treatments that promote apoptosis may lead to activation of latent herpesviruses, with potential clinical significance.

Evolution of Replication Machines

Science.gov (United States)

Yao, Nina Y.; O'Donnell, Mike E.

2016-01-01

The machines that decode and regulate genetic information require the translation, transcription and replication pathways essential to all living cells. Thus, it might be expected that all cells share the same basic machinery for these pathways that were inherited from the primordial ancestor cell from which they evolved. A clear example of this is found in the translation machinery that converts RNA sequence to protein. The translation process requires numerous structural and catalytic RNAs and proteins, the central factors of which are homologous in all three domains of life, bacteria, archaea and eukarya. Likewise, the central actor in transcription, RNA polymerase, shows homology among the catalytic subunits in bacteria, archaea and eukarya. In contrast, while some “gears” of the genome replication machinery are homologous in all domains of life, most components of the replication machine appear to be unrelated between bacteria and those of archaea and eukarya. This review will compare and contrast the central proteins of the “replisome” machines that duplicate DNA in bacteria, archaea and eukarya, with an eye to understanding the issues surrounding the evolution of the DNA replication apparatus. PMID:27160337

DNA replication origins—where do we begin?

Science.gov (United States)

Prioleau, Marie-Noëlle; MacAlpine, David M.

2016-01-01

For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. PMID:27542827

Hanford whole body counting manual

International Nuclear Information System (INIS)

Palmer, H.E.; Brim, C.P.; Rieksts, G.A.; Rhoads, M.C.

1987-05-01

This document, a reprint of the Whole Body Counting Manual, was compiled to train personnel, document operation procedures, and outline quality assurance procedures. The current manual contains information on: the location, availability, and scope of services of Hanford's whole body counting facilities; the administrative aspect of the whole body counting operation; Hanford's whole body counting facilities; the step-by-step procedure involved in the different types of in vivo measurements; the detectors, preamplifiers and amplifiers, and spectroscopy equipment; the quality assurance aspect of equipment calibration and recordkeeping; data processing, record storage, results verification, report preparation, count summaries, and unit cost accounting; and the topics of minimum detectable amount and measurement accuracy and precision. 12 refs., 13 tabs

Validy and Reliability of two Working Memory Tests: Aritmetic Amplitude and Counting

Directory of Open Access Journals (Sweden)

Burin, Débora I.

2013-04-01

Full Text Available Working Memory is a memory system involved in the storage and concurrent processing of information (Baddeley, 2000. Arithmetic Span (Conway et al., 2005 and Counting Span (Conway, et al. 2005 are two traditional verbal working memory capacity tasks. The aim of this article is to present reliability and validity data of Arithmetic and Counting Span Tasks. They were administered, along with Reading Span task, to 88 university students with a mean age of 23.10 years. The reliability analysis showed an excellent internal consistency, and a one factor model with a very good fit to the data was observed using a confirmatory factor analysis. These results indicate that both tasks are reliable and valid measures to assess verbal working memory capacity.

Women's Stereotypic Roles: A Replication and Standardization of the AWS and PAQ for Selected Ethnic Groups.

Science.gov (United States)

Wheeler, Edwin E.; And Others

A replication of two previous studies, this study examined the effect of both sex and ethnicity on attitudes toward women, self-reported masculinity-femininity, and masculine-feminine stereotypic attitudes. The Attitudes Toward Women Scale (AWS) and the Personal Attributes Questionnaire (PAQ) were administered to 367 college students (112 Anglos,…

Chromosomal DNA replication of Vicia faba cells

International Nuclear Information System (INIS)

Ikushima, Takaji

1976-01-01

The chromosomal DNA replication of higher plant cells has been investigated by DNA fiber autoradiography. The nuclear DNA fibers of Vicia root meristematic cells are organized into many tandem arrays of replication units or replicons which exist as clusters with respect to replication. DNA is replicated bidirectionally from the initiation points at the average rate of 0.15 μm/min at 20 0 C, and the average interinitiation interval is about 16 μm. The manner of chromosomal DNA replication in this higher plant is similar to that found in other eukaryotic cells at a subchromosomal level. (auth.)

Surface micro topography replication in injection moulding

DEFF Research Database (Denmark)

Arlø, Uffe Rolf

Thermoplastic injection moulding is a widely used industrial process that involves surface generation by replication. The surface topography of injection moulded plastic parts can be important for aesthetical or technical reasons. With the emergence of microengineering and nanotechnology additional...... importance of surface topography follows. In general the replication is not perfect and the topography of the plastic part differs from the inverse topography of the mould cavity. It is desirable to be able to control the degree of replication perfection or replication quality. This requires an understanding...... of the physical mechanisms of replication. Such understanding can lead to improved process design and facilitate in-line process quality control with respect to surface properties. The purpose of the project is to identify critical factors that affect topography replication quality and to obtain an understanding...

DNA replication in ultraviolet light irradiated Chinese hamster cells: the nature of replicon inhibition and post-replication repair

International Nuclear Information System (INIS)

Doniger, J.

1978-01-01

DNA replication in ultraviolet light irradiated Chinese hamster cells was studied using techniques of DNA fiber autoradiography and alkaline sucrose sedimentation. Bidirectionally growing replicons were observed in the autoradiograms independent of the irradiation conditions. After a dose of 5 J/m 2 at 254 nm the rate of fork progression was the same as in unirradiated cells, while the rate of replication was reduced by 50%. After a dose of 10J/m 2 the rate of fork progression was reduced 40%, while the replication rate was only 25% of normal. Therefore, at low doses of ultraviolet light irradiation, the inhibition of DNA replication is due to reduction in the number of functioning replicons, while at higher doses the rate of fork progression is also slowed. Those replicons which no longer function after irradiation are blocked in fork movement rather than replicon initiation. After irradiation, pulse label was first incorporated into short nascent strands, the average size of which was approximately equal to the distance between pyrimidine dimers. Under conditions where post-replication repair occurs these short strands were eventually joined into larger pieces. Finally, the data show that slowing post-replication repair with caffeine does not slow fork movement. The results presented here support the post-replication repair model of 'gapped synthesis' and rule out a major role for 'replicative bypass'. (author)

Platelet count evolution as a predictor of outcome after splenectomy for immune thrombocytopenic purpura.

Science.gov (United States)

Kim, Moonhwan; Park, Keun Myoung; Shin, Woo Young; Choe, Yun-Mee; Lee, Keon-Young; Ahn, Seung-Ik

2017-04-01

Splenectomy is the definitive second-line therapy for refractory immune thrombocytopenic purpura (ITP), and has a reported response rate of 50-80%. Medical attention should be reconsidered when there is no evidence of accessory spleen in refractory ITP patients after splenectomy. The purpose of this study was to determine whether platelet count evolution differs between patients with a successful or unsuccessful result after splenectomy for ITP. Archived records of 104 consecutive patients that underwent splenectomy for ITP were reviewed. Patients were divided into two groups (failures and successes) using a final follow-up platelet count of 100,000/μL as a cut-off. Platelet count evolutions in these two groups were compared using the Student's t test. Successes and failures were found to have significantly different platelet counts from two days postoperatively (P = 0.016). The area under the receiver operating characteristic curve was 0.630 (95% confidence interval, 0.518-0.741, P = 0.030), and when a cut-off value of 100,000/μL was used, sensitivity and specificity were 68.2 and 51.2%, respectively. To obtain positive and negative predictive values exceeding 50%, additional platelet counts were required at one week and one month after splenectomy. We propose a protocol for ITP follow-up after splenectomy.

CalCOFI Egg Counts

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Fish egg counts and standardized counts for eggs captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and...

Implementing the Bounce Back Trauma Intervention in Urban Elementary Schools: A Real-World Replication Trial

Science.gov (United States)

Santiago, Catherine DeCarlo; Raviv, Tali; Ros, Anna Maria; Brewer, Stephanie K.; Distel, Laura M. L.; Torres, Stephanie A.; Fuller, Anne K.; Lewis, Krystal M.; Coyne, Claire A.; Cicchetti, Colleen; Langley, Audra K.

2018-01-01

The current study provides the first replication trial of Bounce Back, a school-based intervention for elementary students exposed to trauma, in a different school district and geographical area. Participants in this study were 52 1st through 4th graders (M[subscript age] = 7.76 years; 65% male) who were predominately Latino (82%). Schools were…

Dynamics of Escherichia coli Chromosome Segregation during Multifork Replication

DEFF Research Database (Denmark)

Nielsen, Henrik Jørck; Youngren, Brenda; Hansen, Flemming G.

2007-01-01

Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division, the chro......Slowly growing Escherichia coli cells have a simple cell cycle, with replication and progressive segregation of the chromosome completed before cell division. In rapidly growing cells, initiation of replication occurs before the previous replication rounds are complete. At cell division......, the chromosomes contain multiple replication forks and must be segregated while this complex pattern of replication is still ongoing. Here, we show that replication and segregation continue in step, starting at the origin and progressing to the replication terminus. Thus, early-replicated markers on the multiple......-branched chromosomes continue to separate soon after replication to form separate protonucleoids, even though they are not segregated into different daughter cells until later generations. The segregation pattern follows the pattern of chromosome replication and does not follow the cell division cycle. No extensive...

Nonequilibrium Entropic Bounds for Darwinian Replicators

Directory of Open Access Journals (Sweden)

Jordi Piñero

2018-01-01

Full Text Available Life evolved on our planet by means of a combination of Darwinian selection and innovations leading to higher levels of complexity. The emergence and selection of replicating entities is a central problem in prebiotic evolution. Theoretical models have shown how populations of different types of replicating entities exclude or coexist with other classes of replicators. Models are typically kinetic, based on standard replicator equations. On the other hand, the presence of thermodynamical constraints for these systems remain an open question. This is largely due to the lack of a general theory of statistical methods for systems far from equilibrium. Nonetheless, a first approach to this problem has been put forward in a series of novel developements falling under the rubric of the extended second law of thermodynamics. The work presented here is twofold: firstly, we review this theoretical framework and provide a brief description of the three fundamental replicator types in prebiotic evolution: parabolic, malthusian and hyperbolic. Secondly, we employ these previously mentioned techinques to explore how replicators are constrained by thermodynamics. Finally, we comment and discuss where further research should be focused on.

Count-doubling time safety circuit

International Nuclear Information System (INIS)

Keefe, D.J.; McDowell, W.P.; Rusch, G.K.

1981-01-01

There is provided a nuclear reactor count-factor-increase time monitoring circuit which includes a pulse-type neutron detector, and means for counting the number of detected pulses during specific time periods. Counts are compared and the comparison is utilized to develop a reactor scram signal, if necessary

Count-doubling time safety circuit

Science.gov (United States)

Rusch, Gordon K.; Keefe, Donald J.; McDowell, William P.

1981-01-01

There is provided a nuclear reactor count-factor-increase time monitoring circuit which includes a pulse-type neutron detector, and means for counting the number of detected pulses during specific time periods. Counts are compared and the comparison is utilized to develop a reactor scram signal, if necessary.

Rescue from replication stress during mitosis.

Science.gov (United States)

Fragkos, Michalis; Naim, Valeria

2017-04-03

Genomic instability is a hallmark of cancer and a common feature of human disorders, characterized by growth defects, neurodegeneration, cancer predisposition, and aging. Recent evidence has shown that DNA replication stress is a major driver of genomic instability and tumorigenesis. Cells can undergo mitosis with under-replicated DNA or unresolved DNA structures, and specific pathways are dedicated to resolving these structures during mitosis, suggesting that mitotic rescue from replication stress (MRRS) is a key process influencing genome stability and cellular homeostasis. Deregulation of MRRS following oncogene activation or loss-of-function of caretaker genes may be the cause of chromosomal aberrations that promote cancer initiation and progression. In this review, we discuss the causes and consequences of replication stress, focusing on its persistence in mitosis as well as the mechanisms and factors involved in its resolution, and the potential impact of incomplete replication or aberrant MRRS on tumorigenesis, aging and disease.

Personality and Academic Motivation: Replication, Extension, and Replication

Science.gov (United States)

Jones, Martin H.; McMichael, Stephanie N.

2015-01-01

Previous work examines the relationships between personality traits and intrinsic/extrinsic motivation. We replicate and extend previous work to examine how personality may relate to achievement goals, efficacious beliefs, and mindset about intelligence. Approximately 200 undergraduates responded to the survey with a 150 participants replicating…

DNA replication origins-where do we begin?

Science.gov (United States)

Prioleau, Marie-Noëlle; MacAlpine, David M

2016-08-01

For more than three decades, investigators have sought to identify the precise locations where DNA replication initiates in mammalian genomes. The development of molecular and biochemical approaches to identify start sites of DNA replication (origins) based on the presence of defining and characteristic replication intermediates at specific loci led to the identification of only a handful of mammalian replication origins. The limited number of identified origins prevented a comprehensive and exhaustive search for conserved genomic features that were capable of specifying origins of DNA replication. More recently, the adaptation of origin-mapping assays to genome-wide approaches has led to the identification of tens of thousands of replication origins throughout mammalian genomes, providing an unprecedented opportunity to identify both genetic and epigenetic features that define and regulate their distribution and utilization. Here we summarize recent advances in our understanding of how primary sequence, chromatin environment, and nuclear architecture contribute to the dynamic selection and activation of replication origins across diverse cell types and developmental stages. © 2016 Prioleau and MacAlpine; Published by Cold Spring Harbor Laboratory Press.

Pattern replication by confined dewetting

NARCIS (Netherlands)

Harkema, S.; Schäffer, E.; Morariu, M.D.; Steiner, U

2003-01-01

The dewetting of a polymer film in a confined geometry was employed in a pattern-replication process. The instability of dewetting films is pinned by a structured confining surface, thereby replicating its topographic pattern. Depending on the surface energy of the confining surface, two different

Parametrised Constants and Replication for Spatial Mobility

DEFF Research Database (Denmark)

Hüttel, Hans; Haagensen, Bjørn

2009-01-01

Parametrised replication and replication are common ways of expressing infinite computation in process calculi. While parametrised constants can be encoded using replication in the π-calculus, this changes in the presence of spatial mobility as found in e.g. the distributed π- calculus...... of the distributed π-calculus with parametrised constants and replication are incomparable. On the other hand, we shall see that there exists a simple encoding of recursion in mobile ambients....

Adenovirus sequences required for replication in vivo.

OpenAIRE

Wang, K; Pearson, G D

1985-01-01

We have studied the in vivo replication properties of plasmids carrying deletion mutations within cloned adenovirus terminal sequences. Deletion mapping located the adenovirus DNA replication origin entirely within the first 67 bp of the adenovirus inverted terminal repeat. This region could be further subdivided into two functional domains: a minimal replication origin and an adjacent auxillary region which boosted the efficiency of replication by more than 100-fold. The minimal origin occup...

Mammalian RAD52 Functions in Break-Induced Replication Repair of Collapsed DNA Replication Forks.

Science.gov (United States)

Sotiriou, Sotirios K; Kamileri, Irene; Lugli, Natalia; Evangelou, Konstantinos; Da-Ré, Caterina; Huber, Florian; Padayachy, Laura; Tardy, Sebastien; Nicati, Noemie L; Barriot, Samia; Ochs, Fena; Lukas, Claudia; Lukas, Jiri; Gorgoulis, Vassilis G; Scapozza, Leonardo; Halazonetis, Thanos D

2016-12-15

Human cancers are characterized by the presence of oncogene-induced DNA replication stress (DRS), making them dependent on repair pathways such as break-induced replication (BIR) for damaged DNA replication forks. To better understand BIR, we performed a targeted siRNA screen for genes whose depletion inhibited G1 to S phase progression when oncogenic cyclin E was overexpressed. RAD52, a gene dispensable for normal development in mice, was among the top hits. In cells in which fork collapse was induced by oncogenes or chemicals, the Rad52 protein localized to DRS foci. Depletion of Rad52 by siRNA or knockout of the gene by CRISPR/Cas9 compromised restart of collapsed forks and led to DNA damage in cells experiencing DRS. Furthermore, in cancer-prone, heterozygous APC mutant mice, homozygous deletion of the Rad52 gene suppressed tumor growth and prolonged lifespan. We therefore propose that mammalian RAD52 facilitates repair of collapsed DNA replication forks in cancer cells. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Replication Capacity in Relation to Immunologic and Virologic Outcomes in HIV-1 infected, Treatment-Naïve Subjects

Science.gov (United States)

Skowron, Gail; Spritzler, John G.; Weidler, Jodi; Robbins, Gregory K.; Johnson, Victoria A.; Chan, Ellen S.; Asmuth, David M.; Gandhi, Rajesh T.; Lie, Yolanda; Bates, Michael; Pollard, Richard B.

2012-01-01

Objectives To evaluate the association between baseline (BL) replication capacity (RC) [RCBL] and immunologic/virologic parameters (at BL and after 48 weeks on therapy) in HIV-1 infected subjects initiating antiretroviral therapy. Methods RCBL was determined using a modified Monogram PhenoSense HIV drug susceptibility assay on plasma HIV-1 from 321 treatment-naïve subjects from ACTG384. Univariate and multivariable analyses were performed to determine the association of RCBL with BL and on-therapy virologic and immunologic outcomes. Results Higher RCBL was associated with lower baseline CD4 (CD4BL) (r=−0.23, p<0.0001), higher baseline HIV-1 (RNABL) (r=0.25, p<0.0001), higher CD4BL activation percent (r=0.23, p<0.0001) and lower CD4BL memory count (r=−0.21, p=0.0002). In a multivariable model, week 48 CD4 increase (ΔCD448) was associated with lower CD4BL memory count and higher CD4BL naive percent (p=0.004, p=0.015, respectively). The interaction between CD4BL and RCBL was significant (p=0.018), with a positive association between RCBL and ΔCD448 in subjects with higher CD4BL, and a negative association at lower absCD4BL. Conclusions At baseline, higher RC was significantly associated with higher HIV-1 RNA, higher CD4 cell activation, lower CD4 cell count, and lower CD4 memory cell count. These factors may interact, directly or indirectly, to modify the extent to which CD4 recovery occurs in patients starting antiretroviral therapy at different baseline CD4 counts. PMID:19194319

Suppression of Poxvirus Replication by Resveratrol.

Science.gov (United States)

Cao, Shuai; Realegeno, Susan; Pant, Anil; Satheshkumar, Panayampalli S; Yang, Zhilong

2017-01-01

Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV), the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

Suppression of Poxvirus Replication by Resveratrol

Directory of Open Access Journals (Sweden)

Shuai Cao

2017-11-01

Full Text Available Poxviruses continue to cause serious diseases even after eradication of the historically deadly infectious human disease, smallpox. Poxviruses are currently being developed as vaccine vectors and cancer therapeutic agents. Resveratrol is a natural polyphenol stilbenoid found in plants that has been shown to inhibit or enhance replication of a number of viruses, but the effect of resveratrol on poxvirus replication is unknown. In the present study, we found that resveratrol dramatically suppressed the replication of vaccinia virus (VACV, the prototypic member of poxviruses, in various cell types. Resveratrol also significantly reduced the replication of monkeypox virus, a zoonotic virus that is endemic in Western and Central Africa and causes human mortality. The inhibitory effect of resveratrol on poxviruses is independent of VACV N1 protein, a potential resveratrol binding target. Further experiments demonstrated that resveratrol had little effect on VACV early gene expression, while it suppressed VACV DNA synthesis, and subsequently post-replicative gene expression.

Summative Self-Assessment in Higher Education: Implications of Its Counting towards the Final Mark

Science.gov (United States)

Tejeiro, Ricardo A.; Gomez-Vallecillo, Jorge L.; Romero, Antonio F.; Pelegrina, Manuel; Wallace, Agustin; Emberley, Enrique

2012-01-01

Introduction: Our study aims at assessing the validity of summative criteria-referenced self-assessment in higher education, and in particular, if that validity varies when the professor counts self-assessment toward the final mark. Method: One hundred and twenty-two first year students from two groups in Teacher Education at the Universidad de…

Galaxy number counts: Pt. 2

International Nuclear Information System (INIS)

Metcalfe, N.; Shanks, T.; Fong, R.; Jones, L.R.

1991-01-01

Using the Prime Focus CCD Camera at the Isaac Newton Telescope we have determined the form of the B and R galaxy number-magnitude count relations in 12 independent fields for 21 m ccd m and 19 m ccd m 5. The average galaxy count relations lie in the middle of the wide range previously encompassed by photographic data. The field-to-field variation of the counts is small enough to define the faint (B m 5) galaxy count to ±10 per cent and this variation is consistent with that expected from galaxy clustering considerations. Our new data confirm that the B, and also the R, galaxy counts show evidence for strong galaxy luminosity evolution, and that the majority of the evolving galaxies are of moderately blue colour. (author)

Crinivirus replication and host interactions

Directory of Open Access Journals (Sweden)

Zsofia A Kiss

2013-05-01

Full Text Available Criniviruses comprise one of the genera within the family Closteroviridae. Members in this family are restricted to the phloem and rely on whitefly vectors of the genera Bemisia and/or Trialeurodes for plant-to-plant transmission. All criniviruses have bipartite, positive-sense ssRNA genomes, although there is an unconfirmed report of one having a tripartite genome. Lettuce infectious yellows virus (LIYV is the type species of the genus, the best studied so far of the criniviruses and the first for which a reverse genetics system was available. LIYV RNA 1 encodes for proteins predicted to be involved in replication, and alone is competent for replication in protoplasts. Replication results in accumulation of cytoplasmic vesiculated membranous structures which are characteristic of most studied members of the Closteroviridae. These membranous structures, often referred to as BYV-type vesicles, are likely sites of RNA replication. LIYV RNA 2 is replicated in trans when co-infecting cells with RNA 1, but is temporally delayed relative to RNA1. Efficient RNA 2 replication also is dependent on the RNA 1-encoded RNA binding protein, P34. No LIYV RNA 2-encoded proteins have been shown to affect RNA replication, but at least four, CP, CPm, Hsp70h, and p59 are virion structural components and CPm is a determinant of whitefly transmissibility. Roles of other LIYV RNA 2-encoded proteins are largely as yet unknown, but P26 is a non-virion protein that accumulates in cells as characteristic plasmalemma deposits which in plants are localized within phloem parenchyma and companion cells over plasmodesmata connections to sieve elements. The two remaining crinivirus-conserved RNA 2-encoded proteins are P5 and P9. P5 is 39 amino acid protein and is encoded at the 5’ end of RNA 2 as ORF1 and is part of the hallmark closterovirus gene array. The orthologous gene in BYV has been shown to play a role in cell-to-cell movement and indicated to be localized to the

Effector-Triggered Self-Replication in Coupled Subsystems.

Science.gov (United States)

Komáromy, Dávid; Tezcan, Meniz; Schaeffer, Gaël; Marić, Ivana; Otto, Sijbren

2017-11-13

In living systems processes like genome duplication and cell division are carefully synchronized through subsystem coupling. If we are to create life de novo, similar control over essential processes such as self-replication need to be developed. Here we report that coupling two dynamic combinatorial subsystems, featuring two separate building blocks, enables effector-mediated control over self-replication. The subsystem based on the first building block shows only self-replication, whereas that based on the second one is solely responsive toward a specific external effector molecule. Mixing the subsystems arrests replication until the effector molecule is added, resulting in the formation of a host-effector complex and the liberation of the building block that subsequently engages in self-replication. The onset, rate and extent of self-replication is controlled by the amount of effector present. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Addressing the "Replication Crisis": Using Original Studies to Design Replication Studies with Appropriate Statistical Power.

Science.gov (United States)

Anderson, Samantha F; Maxwell, Scott E

2017-01-01

Psychology is undergoing a replication crisis. The discussion surrounding this crisis has centered on mistrust of previous findings. Researchers planning replication studies often use the original study sample effect size as the basis for sample size planning. However, this strategy ignores uncertainty and publication bias in estimated effect sizes, resulting in overly optimistic calculations. A psychologist who intends to obtain power of .80 in the replication study, and performs calculations accordingly, may have an actual power lower than .80. We performed simulations to reveal the magnitude of the difference between actual and intended power based on common sample size planning strategies and assessed the performance of methods that aim to correct for effect size uncertainty and/or bias. Our results imply that even if original studies reflect actual phenomena and were conducted in the absence of questionable research practices, popular approaches to designing replication studies may result in a low success rate, especially if the original study is underpowered. Methods correcting for bias and/or uncertainty generally had higher actual power, but were not a panacea for an underpowered original study. Thus, it becomes imperative that 1) original studies are adequately powered and 2) replication studies are designed with methods that are more likely to yield the intended level of power.

Replication and robustness in developmental research.

Science.gov (United States)

Duncan, Greg J; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J

2014-11-01

Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key results are robust across estimation methods, data sets, and demographic subgroups. This article makes the case for prioritizing both explicit replications and, especially, within-study robustness checks in developmental psychology. It provides evidence on variation in effect sizes in developmental studies and documents strikingly different replication and robustness-checking practices in a sample of journals in developmental psychology and a sister behavioral science-applied economics. Our goal is not to show that any one behavioral science has a monopoly on best practices, but rather to show how journals from a related discipline address vital concerns of replication and generalizability shared by all social and behavioral sciences. We provide recommendations for promoting graduate training in replication and robustness-checking methods and for editorial policies that encourage these practices. Although some of our recommendations may shift the form and substance of developmental research articles, we argue that they would generate considerable scientific benefits for the field. (PsycINFO Database Record (c) 2014 APA, all rights reserved).

Counting statistics in radioactivity measurements

International Nuclear Information System (INIS)

Martin, J.

1975-01-01

The application of statistical methods to radioactivity measurement problems is analyzed in several chapters devoted successively to: the statistical nature of radioactivity counts; the application to radioactive counting of two theoretical probability distributions, Poisson's distribution law and the Laplace-Gauss law; true counting laws; corrections related to the nature of the apparatus; statistical techniques in gamma spectrometry [fr

Weighted Student Formula: Putting Funds Where They Count in Education Reform

Science.gov (United States)

Cooper, Bruce S.; DeRoche, Timothy R.; Ouchi, William G.; Segal, Lydia G.; Brown, Carolyn

2006-01-01

Ever since the publication of "A Nation At Risk" in 1983, Americans have been preoccupied with two problems regarding public education: (1) student performance is unsatisfactory to most Americans despite large increases in real spending per student; and despite several attempts at reforming curricula, teacher training, testing, and other…

Correlation between total lymphocyte count, hemoglobin, hematocrit and CD4 count in HIV patients in Nigeria.

Science.gov (United States)

Emuchay, Charles Iheanyichi; Okeniyi, Shemaiah Olufemi; Okeniyi, Joshua Olusegun

2014-04-01

The expensive and technology limited setting of CD4 count testing is a major setback to the initiation of HAART in a resource limited country like Nigeria. Simple and inexpensive tools such as Hemoglobin (Hb) measurement and Total Lymphocyte Count (TLC) are recommended as substitute marker. In order to assess the correlations of these parameters with CD4 count, 100 "apparently healthy" male volunteers tested HIV positive aged ≥ 20 years but ≤ 40 years were recruited and from whom Hb, Hct, TLC and CD4 count were obtained. The correlation coefficients, R, the Nash-Sutcliffe Coefficient of Efficiency (CoE) and the p-values of the ANOVA model of Hb, Hct and TLC with CD4 count were assessed. The assessments show that there is no significant relationship of any of these parameters with CD4 count and the correlation coefficients are very weak. This study shows that Hb, Hct and TLC cannot be substitute for CD4 count as this might lead to certain individuals' deprivation of required treatment.

It counts who counts: an experimental evaluation of the importance of observer effects on spotlight count estimates

DEFF Research Database (Denmark)

Sunde, Peter; Jessen, Lonnie

2013-01-01

observers with respect to their ability to detect and estimate distance to realistic animal silhouettes at different distances. Detection probabilities were higher for observers experienced in spotlighting mammals than for inexperienced observers, higher for observers with a hunting background compared...... with non-hunters and decreased as function of age but were independent of sex or educational background. If observer-specific detection probabilities were applied to real counting routes, point count estimates from inexperienced observers without a hunting background would only be 43 % (95 % CI, 39...

Non‐Canonical Replication Initiation: You’re Fired!

Directory of Open Access Journals (Sweden)

Bazilė Ravoitytė

2017-01-01

Full Text Available The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis‐acting DNA sequences, the so‐called origins of replication (ori, with trans‐acting factors involved in the onset of DNA synthesis. The interplay of cis‐acting elements and trans‐acting factors ensures that cells initiate replication at sequence‐specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause breakinduced (BIR or transcription‐initiated replication (TIR, respectively. These non‐canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non‐canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.

Factors influencing microinjection molding replication quality

Science.gov (United States)

Vera, Julie; Brulez, Anne-Catherine; Contraires, Elise; Larochette, Mathieu; Trannoy-Orban, Nathalie; Pignon, Maxime; Mauclair, Cyril; Valette, Stéphane; Benayoun, Stéphane

2018-01-01

In recent years, there has been increased interest in producing and providing high-precision plastic parts that can be manufactured by microinjection molding: gears, pumps, optical grating elements, and so on. For all of these applications, the replication quality is essential. This study has two goals: (1) fabrication of high-precision parts using the conventional injection molding machine; (2) identification of robust parameters that ensure production quality. Thus, different technological solutions have been used: cavity vacuuming and the use of a mold coated with DLC or CrN deposits. AFM and SEM analyses were carried out to characterize the replication profile. The replication quality was studied in terms of the process parameters, coated and uncoated molds and crystallinity of the polymer. Specific studies were processed to quantify the replicability of injection molded parts (ABS, PC and PP). Analysis of the Taguchi experimental designs permits prioritization of the impact of each parameter on the replication quality. A discussion taking into account these new parameters and the thermal and spreading properties on the coatings is proposed. It appeared that, in general, increasing the mold temperature improves the molten polymer fill in submicron features except for the steel insert (for which the presence of a vacuum is the most important factor). Moreover, the DLC coating was the best coating to increase the quality of the replication. This result could be explained by the lower thermal diffusivity of this coating. We noted that the viscosity of the polymers is not a primordial factor of the replication quality.

Realistic Vascular Replicator for TAVR Procedures.

Science.gov (United States)

Rotman, Oren M; Kovarovic, Brandon; Sadasivan, Chander; Gruberg, Luis; Lieber, Baruch B; Bluestein, Danny

2018-04-13

Transcatheter aortic valve replacement (TAVR) is an over-the-wire procedure for treatment of severe aortic stenosis (AS). TAVR valves are conventionally tested using simplified left heart simulators (LHS). While those provide baseline performance reliably, their aortic root geometries are far from the anatomical in situ configuration, often overestimating the valves' performance. We report on a novel benchtop patient-specific arterial replicator designed for testing TAVR and training interventional cardiologists in the procedure. The Replicator is an accurate model of the human upper body vasculature for training physicians in percutaneous interventions. It comprises of fully-automated Windkessel mechanism to recreate physiological flow conditions. Calcified aortic valve models were fabricated and incorporated into the Replicator, then tested for performing TAVR procedure by an experienced cardiologist using the Inovare valve. EOA, pressures, and angiograms were monitored pre- and post-TAVR. A St. Jude mechanical valve was tested as a reference that is less affected by the AS anatomy. Results in the Replicator of both valves were compared to the performance in a commercial ISO-compliant LHS. The AS anatomy in the Replicator resulted in a significant decrease of the TAVR valve performance relative to the simplified LHS, with EOA and transvalvular pressures comparable to clinical data. Minor change was seen in the mechanical valve performance. The Replicator showed to be an effective platform for TAVR testing. Unlike a simplified geometric anatomy LHS, it conservatively provides clinically-relevant outcomes and complement it. The Replicator can be most valuable for testing new valves under challenging patient anatomies, physicians training, and procedural planning.

You can count on the motor cortex: Finger counting habits modulate motor cortex activation evoked by numbers

Science.gov (United States)

Tschentscher, Nadja; Hauk, Olaf; Fischer, Martin H.; Pulvermüller, Friedemann

2012-01-01

The embodied cognition framework suggests that neural systems for perception and action are engaged during higher cognitive processes. In an event-related fMRI study, we tested this claim for the abstract domain of numerical symbol processing: is the human cortical motor system part of the representation of numbers, and is organization of numerical knowledge influenced by individual finger counting habits? Developmental studies suggest a link between numerals and finger counting habits due to the acquisition of numerical skills through finger counting in childhood. In the present study, digits 1 to 9 and the corresponding number words were presented visually to adults with different finger counting habits, i.e. left- and right-starters who reported that they usually start counting small numbers with their left and right hand, respectively. Despite the absence of overt hand movements, the hemisphere contralateral to the hand used for counting small numbers was activated when small numbers were presented. The correspondence between finger counting habits and hemispheric motor activation is consistent with an intrinsic functional link between finger counting and number processing. PMID:22133748

Total lymphocyte count and subpopulation lymphocyte counts in relation to dietary intake and nutritional status of peritoneal dialysis patients.

Science.gov (United States)

Grzegorzewska, Alicja E; Leander, Magdalena

2005-01-01

Dietary deficiency causes abnormalities in circulating lymphocyte counts. For the present paper, we evaluated correlations between total and subpopulation lymphocyte counts (TLC, SLCs) and parameters of nutrition in peritoneal dialysis (PD) patients. Studies were carried out in 55 patients treated with PD for 22.2 +/- 11.4 months. Parameters of nutritional status included total body mass, lean body mass (LBM), body mass index (BMI), and laboratory indices [total protein, albumin, iron, ferritin, and total iron binding capacity (TIBC)]. The SLCs were evaluated using flow cytometry. Positive correlations were seen between TLC and dietary intake of niacin; TLC and CD8 and CD16+56 counts and energy delivered from protein; CD4 count and beta-carotene and monounsaturated fatty acids 17:1 intake; and CD19 count and potassium, copper, vitamin A, and beta-carotene intake. Anorexia negatively influenced CD19 count. Serum albumin showed correlations with CD4 and CD19 counts, and LBM with CD19 count. A higher CD19 count was connected with a higher red blood cell count, hemoglobin, and hematocrit. Correlations were observed between TIBC and TLC and CD3 and CD8 counts, and between serum Fe and TLC and CD3 and CD4 counts. Patients with a higher CD19 count showed a better clinical-laboratory score, especially less weakness. Patients with a higher CD4 count had less expressed insomnia. Quantities of ingested vitamins and minerals influence lymphocyte counts in the peripheral blood of PD patients. Evaluation of TLC and SLCs is helpful in monitoring the effectiveness of nutrition in these patients.

Factors Related to Students' Learning of Biomechanics Concepts

Science.gov (United States)

Hsieh, ChengTu; Smith, Jeremy D.; Bohne, Michael; Knudson, Duane

2012-01-01

The purpose of this study was to replicate and expand a previous study to identify the factors that affect students' learning of biomechanical concepts. Students were recruited from three universities (N = 149) located in the central and western regions of the United States. Data from 142 students completing the Biomechanics Concept Inventory…

Replicating chromatin: a tale of histones

DEFF Research Database (Denmark)

Groth, Anja

2009-01-01

Chromatin serves structural and functional roles crucial for genome stability and correct gene expression. This organization must be reproduced on daughter strands during replication to maintain proper overlay of epigenetic fabric onto genetic sequence. Nucleosomes constitute the structural...... framework of chromatin and carry information to specify higher-order organization and gene expression. When replication forks traverse the chromosomes, nucleosomes are transiently disrupted, allowing the replication machinery to gain access to DNA. Histone recycling, together with new deposition, ensures...

Steps Counts among Middle School Students Vary with Aerobic Fitness Level

Science.gov (United States)

Le Masurier, Guy C.; Corbin, Charles B.

2006-01-01

The purpose of this study was to examine if steps/day taken by middle school students varied based on aerobic fitness classification. Middle school students (N = 223; 112 girls, 111 boys) were assigned to three aerobic fitness categories (HIGH, MOD, LOW) based on results of the FITNESSGRAM PACER test. Four weekdays of pedometer monitoring…

Building counting by traditional game: Mathematics Program for Young Children

OpenAIRE

Nasrullah Nasrullah; Zulkardi Zulkardi

2011-01-01

In line with design research, the use of Bermain Satu Rumah (BSR) as traditional  game to support children’s counting classroom wherein students are encouraged to construct mathematical understanding. Number in traditional games is an interesting aspect that is helpful for children to encounter numerous situations that bring them into contact with sounds, symbols and meanings that relate to numbers. Bermain satu rumah as starting activity would be media to enhance student’s sense of number as...

Varicella-zoster virus (VZV) origin of DNA replication oriS influences origin-dependent DNA replication and flanking gene transcription.

Science.gov (United States)

Khalil, Mohamed I; Sommer, Marvin H; Hay, John; Ruyechan, William T; Arvin, Ann M

2015-07-01

The VZV genome has two origins of DNA replication (oriS), each of which consists of an AT-rich sequence and three origin binding protein (OBP) sites called Box A, C and B. In these experiments, the mutation in the core sequence CGC of the Box A and C not only inhibited DNA replication but also inhibited both ORF62 and ORF63 expression in reporter gene assays. In contrast the Box B mutation did not influence DNA replication or flanking gene transcription. These results suggest that efficient DNA replication enhances ORF62 and ORF63 transcription. Recombinant viruses carrying these mutations in both sites and one with a deletion of the whole oriS were constructed. Surprisingly, the recombinant virus lacking both copies of oriS retained the capacity to replicate in melanoma and HELF cells suggesting that VZV has another origin of DNA replication. Copyright © 2015 Elsevier Inc. All rights reserved.

Heterogeneous counting on filter support media

International Nuclear Information System (INIS)

Long, E.; Kohler, V.; Kelly, M.J.

1976-01-01

Many investigators in the biomedical research area have used filter paper as the support for radioactive samples. This means that a heterogeneous counting of sample sometimes results. The count rate of a sample on a filter will be affected by positioning, degree of dryness, sample application procedure, the type of filter, and the type of cocktail used. Positioning of the filter (up or down) in the counting vial can cause a variation of 35% or more when counting tritiated samples on filter paper. Samples of varying degrees of dryness when added to the counting cocktail can cause nonreproducible counts if handled improperly. Count rates starting at 2400 CPM initially can become 10,000 CPM in 24 hours for 3 H-DNA (deoxyribonucleic acid) samples dried on standard cellulose acetate membrane filters. Data on cellulose nitrate filters show a similar trend. Sample application procedures in which the sample is applied to the filter in a small spot or on a large amount of the surface area can cause nonreproducible or very low counting rates. A tritiated DNA sample, when applied topically, gives a count rate of 4,000 CPM. When the sample is spread over the whole filter, 13,400 CPM are obtained with a much better coefficient of variation (5% versus 20%). Adding protein carrier (bovine serum albumin-BSA) to the sample to trap more of the tritiated DNA on the filter during the filtration process causes a serious beta absorption problem. Count rates which are one-fourth the count rate applied to the filter are obtained on calibrated runs. Many of the problems encountered can be alleviated by a proper choice of filter and the use of a liquid scintillation cocktail which dissolves the filter. Filter-Solv has been used to dissolve cellulose nitrate filters and filters which are a combination of cellulose nitrate and cellulose acetate. Count rates obtained for these dissolved samples are very reproducible and highly efficient

Modes of DNA repair and replication

International Nuclear Information System (INIS)

Hanawalt, P.; Kondo, S.

1979-01-01

Modes of DNA repair and replication require close coordination as well as some overlap of enzyme functions. Some classes of recovery deficient mutants may have defects in replication rather than repair modes. Lesions such as the pyrimidine dimers produced by ultraviolet light irradiation are the blocks to normal DNA replication in vivo and in vitro. The DNA synthesis by the DNA polymerase 1 of E. coli is blocked at one nucleotide away from the dimerized pyrimidines in template strands. Thus, some DNA polymerases seem to be unable to incorporate nucleotides opposite to the non-pairing lesions in template DNA strands. The lesions in template DNA strands may block the sequential addition of nucleotides in the synthesis of daughter strands. Normal replication utilizes a constitutive ''error-free'' mode that copies DNA templates with high fidelity, but which may be totally blocked at a lesion that obscures the appropriate base pairing specificity. It might be expected that modified replication system exhibits generally high error frequency. The error rate of DNA polymerases may be controlled by the degree of phosphorylation of the enzyme. Inducible SOS system is controlled by recA genes that also control the pathways for recombination. It is possible that SOS system involves some process other than the modification of a blocked replication apparatus to permit error-prone transdimer synthesis. (Yamashita, S.)

Charter School Replication. Policy Guide

Science.gov (United States)

Rhim, Lauren Morando

2009-01-01

"Replication" is the practice of a single charter school board or management organization opening several more schools that are each based on the same school model. The most rapid strategy to increase the number of new high-quality charter schools available to children is to encourage the replication of existing quality schools. This policy guide…

Replication of kinetoplast minicircle DNA

International Nuclear Information System (INIS)

Sheline, C.T.

1989-01-01

These studies describe the isolation and characterization of early minicircle replication intermediates from Crithidia fasciculata, and Leishmania tarentolae, the mitochondrial localization of a type II topoisomerase (TIImt) in C. fasciculata, and the implication of the aforementioned TIImt in minicircle replication in L. tarentolae. Early minicircle replication intermediates from C. fasciculata were identified and characterized using isolated kinetoplasts to incorporate radiolabeled nucleotides into its DNA. The pulse-label in an apparent theta-type intermediate chase into two daughter molecules. A uniquely gapped, ribonucleotide primed, knotted molecule represents the leading strand in the model proposed, and a highly gapped molecule represents the lagging strand. This theta intermediate is repaired in vitro to a doubly nicked catenated dimer which was shown to result from the replication of a single parental molecule. Very similar intermediates were found in the heterogeneous population of minicircles of L. tarentolae. The sites of the Leishmania specific discontinuities were mapped and shown to lie within the universally conserved sequence blocks in identical positions as compared to C. fasciculata and Trypanosoma equiperdum

Manual of Cupule Replication Technology

Directory of Open Access Journals (Sweden)

Giriraj Kumar

2015-09-01

Full Text Available Throughout the world, iconic rock art is preceded by non-iconic rock art. Cupules (manmade, roughly semi-hemispherical depressions on rocks form the major bulk of the early non-iconic rock art globally. The antiquity of cupules extends back to the Lower Paleolithic in Asia and Africa, hundreds of thousand years ago. When one observes these cupules, the inquisitive mind poses so many questions with regard to understanding their technology, reasons for selecting the site, which rocks were used to make the hammer stones used, the skill and cognitive abilities employed to create the different types of cupules, the objective of their creation, their age, and so on. Replication of the cupules can provide satisfactory answers to some of these questions. Comparison of the hammer stones and cupules produced by the replication process with those obtained from excavation can provide support to observations. This paper presents a manual of cupule replication technology based on our experience of cupule replication on hard quartzite rock near Daraki-Chattan in the Chambal Basin, India.

Targeting DNA Replication Stress for Cancer Therapy

Directory of Open Access Journals (Sweden)

Jun Zhang

2016-08-01

Full Text Available The human cellular genome is under constant stress from extrinsic and intrinsic factors, which can lead to DNA damage and defective replication. In normal cells, DNA damage response (DDR mediated by various checkpoints will either activate the DNA repair system or induce cellular apoptosis/senescence, therefore maintaining overall genomic integrity. Cancer cells, however, due to constitutive growth signaling and defective DDR, may exhibit “replication stress” —a phenomenon unique to cancer cells that is described as the perturbation of error-free DNA replication and slow-down of DNA synthesis. Although replication stress has been proven to induce genomic instability and tumorigenesis, recent studies have counterintuitively shown that enhancing replicative stress through further loosening of the remaining checkpoints in cancer cells to induce their catastrophic failure of proliferation may provide an alternative therapeutic approach. In this review, we discuss the rationale to enhance replicative stress in cancer cells, past approaches using traditional radiation and chemotherapy, and emerging approaches targeting the signaling cascades induced by DNA damage. We also summarize current clinical trials exploring these strategies and propose future research directions including the use of combination therapies, and the identification of potential new targets and biomarkers to track and predict treatment responses to targeting DNA replication stress.

Global profiling of DNA replication timing and efficiency reveals that efficient replication/firing occurs late during S-phase in S. pombe.

Directory of Open Access Journals (Sweden)

Majid Eshaghi

Full Text Available BACKGROUND: During S. pombe S-phase, initiation of DNA replication occurs at multiple sites (origins that are enriched with AT-rich sequences, at various times. Current studies of genome-wide DNA replication profiles have focused on the DNA replication timing and origin location. However, the replication and/or firing efficiency of the individual origins on the genomic scale remain unclear. METHODOLOGY/PRINCIPAL FINDINGS: Using the genome-wide ORF-specific DNA microarray analysis, we show that in S. pombe, individual origins fire with varying efficiencies and at different times during S-phase. The increase in DNA copy number plotted as a function of time is approximated to the near-sigmoidal model, when considering the replication start and end timings at individual loci in cells released from HU-arrest. Replication efficiencies differ from origin to origin, depending on the origin's firing efficiency. We have found that DNA replication is inefficient early in S-phase, due to inefficient firing at origins. Efficient replication occurs later, attributed to efficient but late-firing origins. Furthermore, profiles of replication timing in cds1Delta cells are abnormal, due to the failure in resuming replication at the collapsed forks. The majority of the inefficient origins, but not the efficient ones, are found to fire in cds1Delta cells after HU removal, owing to the firing at the remaining unused (inefficient origins during HU treatment. CONCLUSIONS/SIGNIFICANCE: Taken together, our results indicate that efficient DNA replication/firing occurs late in S-phase progression in cells after HU removal, due to efficient late-firing origins. Additionally, checkpoint kinase Cds1p is required for maintaining the efficient replication/firing late in S-phase. We further propose that efficient late-firing origins are essential for ensuring completion of DNA duplication by the end of S-phase.

Replicated Data Management for Mobile Computing

CERN Document Server

Douglas, Terry

2008-01-01

Managing data in a mobile computing environment invariably involves caching or replication. In many cases, a mobile device has access only to data that is stored locally, and much of that data arrives via replication from other devices, PCs, and services. Given portable devices with limited resources, weak or intermittent connectivity, and security vulnerabilities, data replication serves to increase availability, reduce communication costs, foster sharing, and enhance survivability of critical information. Mobile systems have employed a variety of distributed architectures from client-server

pUL34 binding near the human cytomegalovirus origin of lytic replication enhances DNA replication and viral growth.

Science.gov (United States)

Slayton, Mark; Hossain, Tanvir; Biegalke, Bonita J

2018-05-01

The human cytomegalovirus (HCMV) UL34 gene encodes sequence-specific DNA-binding proteins (pUL34) which are required for viral replication. Interactions of pUL34 with DNA binding sites represses transcription of two viral immune evasion genes, US3 and US9. 12 additional predicted pUL34-binding sites are present in the HCMV genome (strain AD169) with three binding sites concentrated near the HCMV origin of lytic replication (oriLyt). We used ChIP-seq analysis of pUL34-DNA interactions to confirm that pUL34 binds to the oriLyt region during infection. Mutagenesis of the UL34-binding sites in an oriLyt-containing plasmid significantly reduced viral-mediated oriLyt-dependent DNA replication. Mutagenesis of these sites in the HCMV genome reduced the replication efficiencies of the resulting viruses. Protein-protein interaction analyses demonstrated that pUL34 interacts with the viral proteins IE2, UL44, and UL84, that are essential for viral DNA replication, suggesting that pUL34-DNA interactions in the oriLyt region are involved in the DNA replication cascade. Copyright © 2018 Elsevier Inc. All rights reserved.

Regression models for categorical, count, and related variables an applied approach

CERN Document Server

Hoffmann, John P

2016-01-01

Social science and behavioral science students and researchers are often confronted with data that are categorical, count a phenomenon, or have been collected over time. Sociologists examining the likelihood of interracial marriage, political scientists studying voting behavior, criminologists counting the number of offenses people commit, health scientists studying the number of suicides across neighborhoods, and psychologists modeling mental health treatment success are all interested in outcomes that are not continuous. Instead, they must measure and analyze these events and phenomena in a discrete manner.   This book provides an introduction and overview of several statistical models designed for these types of outcomes--all presented with the assumption that the reader has only a good working knowledge of elementary algebra and has taken introductory statistics and linear regression analysis.   Numerous examples from the social sciences demonstrate the practical applications of these models. The chapte...

Replication of urban innovations - prioritization of strategies for the replication of Dhaka's community-based decentralized composting model.

Science.gov (United States)

Yedla, Sudhakar

2012-01-01

Dhaka's community-based decentralized composting (DCDC) is a successful demonstration of solid waste management by adopting low-cost technology, local resources community participation and partnerships among the various actors involved. This paper attempts to understand the model, necessary conditions, strategies and their priorities to replicate DCDC in the other developing cities of Asia. Thirteen strategies required for its replication are identified and assessed based on various criteria, namely transferability, longevity, economic viability, adaptation and also overall replication. Priority setting by multi-criteria analysis by applying analytic hierarchy process revealed that immediate transferability without long-term and economic viability consideration is not advisable as this would result in unsustainable replication of DCDC. Based on the analysis, measures to ensure the product quality control; partnership among stakeholders (public-private-community); strategies to achieve better involvement of the private sector in solid waste management (entrepreneurship in approach); simple and low-cost technology; and strategies to provide an effective interface among the complementing sectors are identified as important strategies for its replication.

Replication of bacteriophage lambda DNA

International Nuclear Information System (INIS)

Tsurimoto, T.; Matsubara, K.

1983-01-01

In this paper results of studies on the mechanism of bacteriophage lambda replication using molecular biological and biochemical approaches are reported. The purification of the initiator proteins, O and P, and the role of the O and P proteins in the initiation of lambda DNA replication through interactions with specific DNA sequences are described. 47 references, 15 figures

Direct Visualization of DNA Replication Dynamics in Zebrafish Cells.

Science.gov (United States)

Kuriya, Kenji; Higashiyama, Eriko; Avşar-Ban, Eriko; Tamaru, Yutaka; Ogata, Shin; Takebayashi, Shin-ichiro; Ogata, Masato; Okumura, Katsuzumi

2015-12-01

Spatiotemporal regulation of DNA replication in the S-phase nucleus has been extensively studied in mammalian cells because it is tightly coupled with the regulation of other nuclear processes such as transcription. However, little is known about the replication dynamics in nonmammalian cells. Here, we analyzed the DNA replication processes of zebrafish (Danio rerio) cells through the direct visualization of replicating DNA in the nucleus and on DNA fiber molecules isolated from the nucleus. We found that zebrafish chromosomal DNA at the nuclear interior was replicated first, followed by replication of DNA at the nuclear periphery, which is reminiscent of the spatiotemporal regulation of mammalian DNA replication. However, the relative duration of interior DNA replication in zebrafish cells was longer compared to mammalian cells, possibly reflecting zebrafish-specific genomic organization. The rate of replication fork progression and ori-to-ori distance measured by the DNA combing technique were ∼ 1.4 kb/min and 100 kb, respectively, which are comparable to those in mammalian cells. To our knowledge, this is a first report that measures replication dynamics in zebrafish cells.

LAWRENCE RADIATION LABORATORY COUNTING HANDBOOK

Energy Technology Data Exchange (ETDEWEB)

Group, Nuclear Instrumentation

1966-10-01

The Counting Handbook is a compilation of operational techniques and performance specifications on counting equipment in use at the Lawrence Radiation Laboratory, Berkeley. Counting notes have been written from the viewpoint of the user rather than that of the designer or maintenance man. The only maintenance instructions that have been included are those that can easily be performed by the experimenter to assure that the equipment is operating properly.

Insulated hsp70B' promoter: stringent heat-inducible activity in replication-deficient, but not replication-competent adenoviruses.

Science.gov (United States)

Rohmer, Stanimira; Mainka, Astrid; Knippertz, Ilka; Hesse, Andrea; Nettelbeck, Dirk M

2008-04-01

Key to the realization of gene therapy is the development of efficient and targeted gene transfer vectors. Therapeutic gene transfer by replication-deficient or more recently by conditionally replication-competent/oncolytic adenoviruses has shown much promise. For specific applications, however, it will be advantageous to provide vectors that allow for external control of gene expression. The efficient cellular heat shock system in combination with available technology for focused and controlled hyperthermia suggests heat-regulated transcription control as a promising tool for this purpose. We investigated the feasibility of a short fragment of the human hsp70B' promoter, with and without upstream insulator elements, for the regulation of transgene expression by replication-deficient or oncolytic adenoviruses. Two novel adenoviral vectors with an insulated hsp70B' promoter were developed and showed stringent heat-inducible gene expression with induction ratios up to 8000-fold. In contrast, regulation of gene expression from the hsp70B' promoter without insulation was suboptimal. In replication-competent/oncolytic adenoviruses regulation of the hsp70B' promoter was lost specifically during late replication in permissive cells and could not be restored by the insulators. We developed novel adenovirus gene transfer vectors that feature improved and stringent regulation of transgene expression from the hsp70B' promoter using promoter insulation. These vectors have potential for gene therapy applications that benefit from external modulation of therapeutic gene expression or for combination therapy with hyperthermia. Furthermore, our study reveals that vector replication can deregulate inserted cellular promoters, an observation which is of relevance for the development of replication-competent/oncolytic gene transfer vectors. (c) 2008 John Wiley & Sons, Ltd.

Does platelet count in platelet-rich plasma influence slope, maximal amplitude and lag phase in healthy individuals? Results of light transmission aggregometry.

Science.gov (United States)

Chandrashekar, Vani

2015-01-01

Light transmission aggregometry lacks in standardisation and normal reference values are not widely available. The aims of our study were to establish reference ranges for aggregation, slope and lag phase in healthy controls with platelet counts between 150 and 450 × 10(9)/l in platelet-rich plasma (PRP) as well as evaluate the influence of platelet count. Ninety-nine subjects were evaluated with four agonists and divided into two groups based on platelet count and the groups were compared by Student's t-test. There was no difference between the means of the two groups for amplitude and slope barring the lag phase for collagen. Platelet counts between 150 and 450 × 10(9)/l have no effects on light transmission aggregometry and hence adjustment of platelet count is not necessary.

Replication assessment of surface texture at sub-micrometre scale

DEFF Research Database (Denmark)

Quagliotti, Danilo; Tosello, Guido; Hansen, Hans Nørgaard

2017-01-01

[2]. A replication process requires reproducing a master geometry by conveying it to a substrate material. It is typically induced by means of different energy sources (usually heat and force) and a direct physical contact between the master and the substrate. Furthermore, concepts of advanced......, because of the replication nature of molding processes, the required specifications for the manufacture of micro molded components must be ensured by means of a metrological approach to surface replication and dimensional control of both master geometry and replicated substrate [3]-[4]. Therefore...... replication was assessed by the replication fidelity, i.e., comparing the produced parts with the tool used to replicate the geometry. Furthermore, the uncertainty of the replication fidelity was achieved by propagating the uncertainties evaluated for both masters and replicas. Finally, despite the specimens...

Mechanisms and regulation of DNA replication initiation in eukaryotes.

Science.gov (United States)

Parker, Matthew W; Botchan, Michael R; Berger, James M

2017-04-01

Cellular DNA replication is initiated through the action of multiprotein complexes that recognize replication start sites in the chromosome (termed origins) and facilitate duplex DNA melting within these regions. In a typical cell cycle, initiation occurs only once per origin and each round of replication is tightly coupled to cell division. To avoid aberrant origin firing and re-replication, eukaryotes tightly regulate two events in the initiation process: loading of the replicative helicase, MCM2-7, onto chromatin by the origin recognition complex (ORC), and subsequent activation of the helicase by its incorporation into a complex known as the CMG. Recent work has begun to reveal the details of an orchestrated and sequential exchange of initiation factors on DNA that give rise to a replication-competent complex, the replisome. Here, we review the molecular mechanisms that underpin eukaryotic DNA replication initiation - from selecting replication start sites to replicative helicase loading and activation - and describe how these events are often distinctly regulated across different eukaryotic model organisms.

Discrete calculus methods for counting

CERN Document Server

Mariconda, Carlo

2016-01-01

This book provides an introduction to combinatorics, finite calculus, formal series, recurrences, and approximations of sums. Readers will find not only coverage of the basic elements of the subjects but also deep insights into a range of less common topics rarely considered within a single book, such as counting with occupancy constraints, a clear distinction between algebraic and analytical properties of formal power series, an introduction to discrete dynamical systems with a thorough description of Sarkovskii’s theorem, symbolic calculus, and a complete description of the Euler-Maclaurin formulas and their applications. Although several books touch on one or more of these aspects, precious few cover all of them. The authors, both pure mathematicians, have attempted to develop methods that will allow the student to formulate a given problem in a precise mathematical framework. The aim is to equip readers with a sound strategy for classifying and solving problems by pursuing a mathematically rigorous yet ...

Comparing MapReduce and Pipeline Implementations for Counting Triangles

Directory of Open Access Journals (Sweden)

Edelmira Pasarella

2017-01-01

Full Text Available A common method to define a parallel solution for a computational problem consists in finding a way to use the Divide and Conquer paradigm in order to have processors acting on its own data and scheduled in a parallel fashion. MapReduce is a programming model that follows this paradigm, and allows for the definition of efficient solutions by both decomposing a problem into steps on subsets of the input data and combining the results of each step to produce final results. Albeit used for the implementation of a wide variety of computational problems, MapReduce performance can be negatively affected whenever the replication factor grows or the size of the input is larger than the resources available at each processor. In this paper we show an alternative approach to implement the Divide and Conquer paradigm, named dynamic pipeline. The main features of dynamic pipelines are illustrated on a parallel implementation of the well-known problem of counting triangles in a graph. This problem is especially interesting either when the input graph does not fit in memory or is dynamically generated. To evaluate the properties of pipeline, a dynamic pipeline of processes and an ad-hoc version of MapReduce are implemented in the language Go, exploiting its ability to deal with channels and spawned processes. An empirical evaluation is conducted on graphs of different topologies, sizes, and densities. Observed results suggest that dynamic pipelines allows for an efficient implementation of the problem of counting triangles in a graph, particularly, in dense and large graphs, drastically reducing the execution time with respect to the MapReduce implementation.

The Kruskal Count

OpenAIRE

Lagarias, Jeffrey C.; Rains, Eric; Vanderbei, Robert J.

2001-01-01

The Kruskal Count is a card trick invented by Martin J. Kruskal in which a magician "guesses" a card selected by a subject according to a certain counting procedure. With high probability the magician can correctly "guess" the card. The success of the trick is based on a mathematical principle related to coupling methods for Markov chains. This paper analyzes in detail two simplified variants of the trick and estimates the probability of success. The model predictions are compared with simula...

Commercial Building Partnerships Replication and Diffusion

Energy Technology Data Exchange (ETDEWEB)

Antonopoulos, Chrissi A.; Dillon, Heather E.; Baechler, Michael C.

2013-09-16

This study presents findings from survey and interview data investigating replication efforts of Commercial Building Partnership (CBP) partners that worked directly with the Pacific Northwest National Laboratory (PNNL). PNNL partnered directly with 12 organizations on new and retrofit construction projects, which represented approximately 28 percent of the entire U.S. Department of Energy (DOE) CBP program. Through a feedback survey mechanism, along with personal interviews, PNNL gathered quantitative and qualitative data relating to replication efforts by each organization. These data were analyzed to provide insight into two primary research areas: 1) CBP partners’ replication efforts of technologies and approaches used in the CBP project to the rest of the organization’s building portfolio (including replication verification), and, 2) the market potential for technology diffusion into the total U.S. commercial building stock, as a direct result of the CBP program. The first area of this research focused specifically on replication efforts underway or planned by each CBP program participant. Factors that impact replication include motivation, organizational structure and objectives firms have for implementation of energy efficient technologies. Comparing these factors between different CBP partners revealed patterns in motivation for constructing energy efficient buildings, along with better insight into market trends for green building practices. The second area of this research develops a diffusion of innovations model to analyze potential broad market impacts of the CBP program on the commercial building industry in the United States.

SPERM COUNT DISTRIBUTIONS IN FERTILE MEN

Science.gov (United States)

Sperm concentration and count are often used as indicators of environmental impacts on male reproductive health. Existing clinical databases may be biased towards subfertile men with low sperm counts and less is known about expected sperm count distributions in cohorts of fertil...

Extremal dynamics in random replicator ecosystems

Energy Technology Data Exchange (ETDEWEB)

Kärenlampi, Petri P., E-mail: petri.karenlampi@uef.fi

2015-10-02

The seminal numerical experiment by Bak and Sneppen (BS) is repeated, along with computations with replicator models, including a greater amount of features. Both types of models do self-organize, and do obey power-law scaling for the size distribution of activity cycles. However species extinction within the replicator models interferes with the BS self-organized critical (SOC) activity. Speciation–extinction dynamics ruins any stationary state which might contain a steady size distribution of activity cycles. The BS-type activity appears as a dissimilar phenomenon in comparison to speciation–extinction dynamics in the replicator system. No criticality is found from the speciation–extinction dynamics. Neither are speciations and extinctions in real biological macroevolution known to contain any diverging distributions, or self-organization towards any critical state. Consequently, biological macroevolution probably is not a self-organized critical phenomenon. - Highlights: • Extremal Dynamics organizes random replicator ecosystems to two phases in fitness space. • Replicator systems show power-law scaling of activity. • Species extinction interferes with Bak–Sneppen type mutation activity. • Speciation–extinction dynamics does not show any critical phase transition. • Biological macroevolution probably is not a self-organized critical phenomenon.

Combinatorial Tasks and Outcome Listing: Examining Productive Listing among Undergraduate Students

Science.gov (United States)

Lockwood, Elise; Gibson, Bryan R.

2016-01-01

Although counting problems are easy to state and provide rich, accessible problem-solving situations, there is much evidence that students struggle with solving counting problems correctly. With combinatorics (and the study of counting problems) becoming increasingly prevalent in K-12 and undergraduate curricula, there is a need for researchers to…

Bayesian analysis of energy and count rate data for detection of low count rate radioactive sources.

Science.gov (United States)

Klumpp, John; Brandl, Alexander

2015-03-01

A particle counting and detection system is proposed that searches for elevated count rates in multiple energy regions simultaneously. The system analyzes time-interval data (e.g., time between counts), as this was shown to be a more sensitive technique for detecting low count rate sources compared to analyzing counts per unit interval (Luo et al. 2013). Two distinct versions of the detection system are developed. The first is intended for situations in which the sample is fixed and can be measured for an unlimited amount of time. The second version is intended to detect sources that are physically moving relative to the detector, such as a truck moving past a fixed roadside detector or a waste storage facility under an airplane. In both cases, the detection system is expected to be active indefinitely; i.e., it is an online detection system. Both versions of the multi-energy detection systems are compared to their respective gross count rate detection systems in terms of Type I and Type II error rates and sensitivity.

A Model of Students' Combinatorial Thinking

Science.gov (United States)

Lockwood, Elise

2013-01-01

Combinatorial topics have become increasingly prevalent in K-12 and undergraduate curricula, yet research on combinatorics education indicates that students face difficulties when solving counting problems. The research community has not yet addressed students' ways of thinking at a level that facilitates deeper understanding of how students…

Total bacterial count and somatic cell count in refrigerated raw milk stored in communal tanks

Directory of Open Access Journals (Sweden)

Edmar da Costa Alves

2014-09-01

Full Text Available The current industry demand for dairy products with extended shelf life has resulted in new challenges for milk quality maintenance. The processing of milk with high bacterial counts compromises the quality and performance of industrial products. The study aimed to evaluate the total bacteria counts (TBC and somatic cell count (SCC in 768 samples of refrigerated raw milk, from 32 communal tanks. Samples were collected in the first quarter of 2010, 2011, 2012 and 2013 and analyzed by the Laboratory of Milk Quality - LQL. Results showed that 62.5%, 37.5%, 15.6% and 27.1% of the means for TBC in 2010, 2011, 2012 and 2013, respectively, were above the values established by legislation. However, we observed a significant reduction in the levels of total bacterial count (TBC in the studied periods. For somatic cell count, 100% of the means indicated values below 600.000 cells/mL, complying with the actual Brazilian legislation. The values found for the somatic cell count suggests the adoption of effective measures for the sanitary control of the herd. However, the results must be considered with caution as it highlights the need for quality improvements of the raw material until it achieves reliable results effectively.

The Genomic Replication of the Crenarchaeal Virus SIRV2

DEFF Research Database (Denmark)

Martinez Alvarez, Laura

reinitiation events may partially explain the branched topology of the viral replication intermediates. We also analyzed the intracellular location of viral replication, showing the formation of viral peripheral replication centers in SIRV2-infected cells, where viral DNA synthesis and replication...

People counting in classroom based on video surveillance

Science.gov (United States)

Zhang, Quanbin; Huang, Xiang; Su, Juan

2014-11-01

Currently, the switches of the lights and other electronic devices in the classroom are mainly relied on manual control, as a result, many lights are on while no one or only few people in the classroom. It is important to change the current situation and control the electronic devices intelligently according to the number and the distribution of the students in the classroom, so as to reduce the considerable waste of electronic resources. This paper studies the problem of people counting in classroom based on video surveillance. As the camera in the classroom can not get the full shape contour information of bodies and the clear features information of faces, most of the classical algorithms such as the pedestrian detection method based on HOG (histograms of oriented gradient) feature and the face detection method based on machine learning are unable to obtain a satisfied result. A new kind of dual background updating model based on sparse and low-rank matrix decomposition is proposed in this paper, according to the fact that most of the students in the classroom are almost in stationary state and there are body movement occasionally. Firstly, combining the frame difference with the sparse and low-rank matrix decomposition to predict the moving areas, and updating the background model with different parameters according to the positional relationship between the pixels of current video frame and the predicted motion regions. Secondly, the regions of moving objects are determined based on the updated background using the background subtraction method. Finally, some operations including binarization, median filtering and morphology processing, connected component detection, etc. are performed on the regions acquired by the background subtraction, in order to induce the effects of the noise and obtain the number of people in the classroom. The experiment results show the validity of the algorithm of people counting.

Rainflow counting revisited

Energy Technology Data Exchange (ETDEWEB)

Soeker, H [Deutsches Windenergie-Institut (Germany)

1996-09-01

As state of the art method the rainflow counting technique is presently applied everywhere in fatigue analysis. However, the author feels that the potential of the technique is not fully recognized in wind energy industries as it is used, most of the times, as a mere data reduction technique disregarding some of the inherent information of the rainflow counting results. The ideas described in the following aim at exploitation of this information and making it available for use in the design and verification process. (au)

The Role of the Transcriptional Response to DNA Replication Stress.

Science.gov (United States)

Herlihy, Anna E; de Bruin, Robertus A M

2017-03-02

During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage.

The Role of the Transcriptional Response to DNA Replication Stress

Science.gov (United States)

Herlihy, Anna E.; de Bruin, Robertus A.M.

2017-01-01

During DNA replication many factors can result in DNA replication stress. The DNA replication stress checkpoint prevents the accumulation of replication stress-induced DNA damage and the potential ensuing genome instability. A critical role for post-translational modifications, such as phosphorylation, in the replication stress checkpoint response has been well established. However, recent work has revealed an important role for transcription in the cellular response to DNA replication stress. In this review, we will provide an overview of current knowledge of the cellular response to DNA replication stress with a specific focus on the DNA replication stress checkpoint transcriptional response and its role in the prevention of replication stress-induced DNA damage. PMID:28257104

Radon counting statistics - a Monte Carlo investigation

International Nuclear Information System (INIS)

Scott, A.G.

1996-01-01

Radioactive decay is a Poisson process, and so the Coefficient of Variation (COV) of open-quotes nclose quotes counts of a single nuclide is usually estimated as 1/√n. This is only true if the count duration is much shorter than the half-life of the nuclide. At longer count durations, the COV is smaller than the Poisson estimate. Most radon measurement methods count the alpha decays of 222 Rn, plus the progeny 218 Po and 214 Po, and estimate the 222 Rn activity from the sum of the counts. At long count durations, the chain decay of these nuclides means that every 222 Rn decay must be followed by two other alpha decays. The total number of decays is open-quotes 3Nclose quotes, where N is the number of radon decays, and the true COV of the radon concentration estimate is 1/√(N), √3 larger than the Poisson total count estimate of 1/√3N. Most count periods are comparable to the half lives of the progeny, so the relationship between COV and count time is complex. A Monte-Carlo estimate of the ratio of true COV to Poisson estimate was carried out for a range of count periods from 1 min to 16 h and three common radon measurement methods: liquid scintillation, scintillation cell, and electrostatic precipitation of progeny. The Poisson approximation underestimates COV by less than 20% for count durations of less than 60 min

Hanford whole body counting manual

International Nuclear Information System (INIS)

Palmer, H.E.; Rieksts, G.A.; Lynch, T.P.

1990-06-01

This document describes the Hanford Whole Body Counting Program as it is administered by Pacific Northwest Laboratory (PNL) in support of the US Department of Energy--Richland Operations Office (DOE-RL) and its Hanford contractors. Program services include providing in vivo measurements of internally deposited radioactivity in Hanford employees (or visitors). Specific chapters of this manual deal with the following subjects: program operational charter, authority, administration, and practices, including interpreting applicable DOE Orders, regulations, and guidance into criteria for in vivo measurement frequency, etc., for the plant-wide whole body counting services; state-of-the-art facilities and equipment used to provide the best in vivo measurement results possible for the approximately 11,000 measurements made annually; procedures for performing the various in vivo measurements at the Whole Body Counter (WBC) and related facilities including whole body counts; operation and maintenance of counting equipment, quality assurance provisions of the program, WBC data processing functions, statistical aspects of in vivo measurements, and whole body counting records and associated guidance documents. 16 refs., 48 figs., 22 tabs

DNA Copy-Number Control through Inhibition of Replication Fork Progression

Directory of Open Access Journals (Sweden)

Jared T. Nordman

2014-11-01

Full Text Available Proper control of DNA replication is essential to ensure faithful transmission of genetic material and prevent chromosomal aberrations that can drive cancer progression and developmental disorders. DNA replication is regulated primarily at the level of initiation and is under strict cell-cycle regulation. Importantly, DNA replication is highly influenced by developmental cues. In Drosophila, specific regions of the genome are repressed for DNA replication during differentiation by the SNF2 domain-containing protein SUUR through an unknown mechanism. We demonstrate that SUUR is recruited to active replication forks and mediates the repression of DNA replication by directly inhibiting replication fork progression instead of functioning as a replication fork barrier. Mass spectrometry identification of SUUR-associated proteins identified the replicative helicase member CDC45 as a SUUR-associated protein, supporting a role for SUUR directly at replication forks. Our results reveal that control of eukaryotic DNA copy number can occur through the inhibition of replication fork progression.

Platelet Count and Plateletcrit

African Journals Online (AJOL)

strated that neonates with late onset sepsis (bacteremia after 3 days of age) had a dramatic increase in MPV and. PDW18. We hypothesize that as the MPV and PDW increase and platelet count and PCT decrease in sick children, intui- tively, the ratio of MPV to PCT; MPV to Platelet count,. PDW to PCT, PDW to platelet ...

Impact of Simulation Based Education on Biology Student's Academic Achievement in DNA Replication

Science.gov (United States)

Reddy, M. Vijaya Bhaskara; Mint, Phyu Phyu

2017-01-01

The aim of this study is to determine the effect of simulation methods in teaching Science on education students' academic achievement. 70 students (35 control, 35 experimental) who studied at Srinivasa College of education, SV University in the Department of Education. 2015-2016 academic year students were participated in this simulation based…

Initiation of Replication in Escherichia coli

DEFF Research Database (Denmark)

Frimodt-Møller, Jakob

The circular chromosome of Escherichia coli is replicated by two replisomes assembled at the unique origin and moving in the opposite direction until they meet in the less well defined terminus. The key protein in initiation of replication, DnaA, facilitates the unwinding of double-stranded DNA...... to single-stranded DNA in oriC. Although DnaA is able to bind both ADP and ATP, DnaA is only active in initiation when bound to ATP. Although initiation of replication, and the regulation of this, is thoroughly investigated it is still not fully understood. The overall aim of the thesis was to investigate...... the regulation of initiation, the effect on the cell when regulation fails, and if regulation was interlinked to chromosomal organization. This thesis uncovers that there exists a subtle balance between chromosome replication and reactive oxygen species (ROS) inflicted DNA damage. Thus, failure in regulation...

LHCb Data Replication During SC3

CERN Multimedia

Smith, A

2006-01-01

LHCb's participation in LCG's Service Challenge 3 involves testing the bulk data transfer infrastructure developed to allow high bandwidth distribution of data across the grid in accordance with the computing model. To enable reliable bulk replication of data, LHCb's DIRAC system has been integrated with gLite's File Transfer Service middleware component to make use of dedicated network links between LHCb computing centres. DIRAC's Data Management tools previously allowed the replication, registration and deletion of files on the grid. For SC3 supplementary functionality has been added to allow bulk replication of data (using FTS) and efficient mass registration to the LFC replica catalog.Provisional performance results have shown that the system developed can meet the expected data replication rate required by the computing model in 2007. This paper details the experience and results of integration and utilisation of DIRAC with the SC3 transfer machinery.

An Adaptive Smoother for Counting Measurements

International Nuclear Information System (INIS)

Kondrasovs Vladimir; Coulon Romain; Normand Stephane

2013-06-01

Counting measurements associated with nuclear instruments are tricky to carry out due to the stochastic process of the radioactivity. Indeed events counting have to be processed and filtered in order to display a stable count rate value and to allow variations monitoring in the measured activity. Smoothers (as the moving average) are adjusted by a time constant defined as a compromise between stability and response time. A new approach has been developed and consists in improving the response time while maintaining count rate stability. It uses the combination of a smoother together with a detection filter. A memory of counting data is processed to calculate several count rate estimates using several integration times. These estimates are then sorted into the memory from short to long integration times. A measurement position, in terms of integration time, is then chosen into this memory after a detection test. An inhomogeneity into the Poisson counting process is detected by comparison between current position estimate and the other estimates contained into the memory in respect with the associated statistical variance calculated with homogeneous assumption. The measurement position (historical time) and the ability to forget an obsolete data or to keep in memory a useful data are managed using the detection test result. The proposed smoother is then an adaptive and a learning algorithm allowing an optimization of the response time while maintaining measurement counting stability and converging efficiently to the best counting estimate after an effective change in activity. This algorithm has also the specificity to be low recursive and thus easily embedded into DSP electronics based on FPGA or micro-controllers meeting 'real life' time requirements. (authors)

Change in platelet count in patients with hypersplenism subjected to liver transplantation

Directory of Open Access Journals (Sweden)

Júlio Cezar Uili Coelho

2011-09-01

Full Text Available CONTEXT: Most patients subjected to liver transplantation presents hypersplenism, which is reversed after the operation. However, some patients remain with moderate to intense hypersplenism. OBJECTIVES: To study the effect of liver transplantation on platelet count in patients with hypersplenism. METHOD: Of a total of 233 patients who underwent liver transplantation, 162 were excluded from the present study because of occurrence of steroid-resistant rejection, absence of hypersplenism before the transplantation, absence of follow-up for at least 2 years or incomplete exams data. The electronic study protocols of the remaining 71 patients were reviewed to determine the demographics, etiology of cirrhosis, and results of pathologic examination of the explanted liver. Serial platelet count was obtained from the study protocol on the day before liver transplantation and 1, 2, 4, and 6 months and 1 year after liver transplantation. Statistical analysis was performed using the Student's t-test, chi-square test, and Spearman's correlation test. RESULTS: Posttransplant platelet count at all time intervals was significantly higher than the pretransplant value (P100,000/mm³ in 58 patients (81.7% 1 month after liver transplantation. Twelve patients (16.9% remained with thrombocytopenia 1 year after liver transplantation. Three patients (4.2% had recurrence of thrombocytopenia within 1 year after liver transplantation. There was no correlation between pretransplant platelet count and the Child-Pugh class or the MELD score. CONCLUSION: Liver transplantation reverses hypersplenism in most patients.

Ultrastructural Characterization of Zika Virus Replication Factories

Directory of Open Access Journals (Sweden)

Mirko Cortese

2017-02-01

Full Text Available Summary: A global concern has emerged with the pandemic spread of Zika virus (ZIKV infections that can cause severe neurological symptoms in adults and newborns. ZIKV is a positive-strand RNA virus replicating in virus-induced membranous replication factories (RFs. Here we used various imaging techniques to investigate the ultrastructural details of ZIKV RFs and their relationship with host cell organelles. Analyses of human hepatic cells and neural progenitor cells infected with ZIKV revealed endoplasmic reticulum (ER membrane invaginations containing pore-like openings toward the cytosol, reminiscent to RFs in Dengue virus-infected cells. Both the MR766 African strain and the H/PF/2013 Asian strain, the latter linked to neurological diseases, induce RFs of similar architecture. Importantly, ZIKV infection causes a drastic reorganization of microtubules and intermediate filaments forming cage-like structures surrounding the viral RF. Consistently, ZIKV replication is suppressed by cytoskeleton-targeting drugs. Thus, ZIKV RFs are tightly linked to rearrangements of the host cell cytoskeleton. : Cortese et al. show that ZIKV infection in both human hepatoma and neuronal progenitor cells induces drastic structural modification of the cellular architecture. Microtubules and intermediate filaments surround the viral replication factory composed of vesicles corresponding to ER membrane invagination toward the ER lumen. Importantly, alteration of microtubule flexibility impairs ZIKV replication. Keywords: Zika virus, flavivirus, human neural progenitor cells, replication factories, replication organelles, microtubules, intermediate filaments, electron microscopy, electron tomography, live-cell imaging

Tombusviruses upregulate phospholipid biosynthesis via interaction between p33 replication protein and yeast lipid sensor proteins during virus replication in yeast

International Nuclear Information System (INIS)

Barajas, Daniel; Xu, Kai; Sharma, Monika; Wu, Cheng-Yu; Nagy, Peter D.

2014-01-01

Positive-stranded RNA viruses induce new membranous structures and promote membrane proliferation in infected cells to facilitate viral replication. In this paper, the authors show that a plant-infecting tombusvirus upregulates transcription of phospholipid biosynthesis genes, such as INO1, OPI3 and CHO1, and increases phospholipid levels in yeast model host. This is accomplished by the viral p33 replication protein, which interacts with Opi1p FFAT domain protein and Scs2p VAP protein. Opi1p and Scs2p are phospholipid sensor proteins and they repress the expression of phospholipid genes. Accordingly, deletion of OPI1 transcription repressor in yeast has a stimulatory effect on TBSV RNA accumulation and enhanced tombusvirus replicase activity in an in vitro assay. Altogether, the presented data convincingly demonstrate that de novo lipid biosynthesis is required for optimal TBSV replication. Overall, this work reveals that a (+)RNA virus reprograms the phospholipid biosynthesis pathway in a unique way to facilitate its replication in yeast cells. - Highlights: • Tombusvirus p33 replication protein interacts with FFAT-domain host protein. • Tombusvirus replication leads to upregulation of phospholipids. • Tombusvirus replication depends on de novo lipid synthesis. • Deletion of FFAT-domain host protein enhances TBSV replication. • TBSV rewires host phospholipid synthesis

Regulation of beta cell replication

DEFF Research Database (Denmark)

Lee, Ying C; Nielsen, Jens Høiriis

2008-01-01

Beta cell mass, at any given time, is governed by cell differentiation, neogenesis, increased or decreased cell size (cell hypertrophy or atrophy), cell death (apoptosis), and beta cell proliferation. Nutrients, hormones and growth factors coupled with their signalling intermediates have been...... suggested to play a role in beta cell mass regulation. In addition, genetic mouse model studies have indicated that cyclins and cyclin-dependent kinases that determine cell cycle progression are involved in beta cell replication, and more recently, menin in association with cyclin-dependent kinase...... inhibitors has been demonstrated to be important in beta cell growth. In this review, we consider and highlight some aspects of cell cycle regulation in relation to beta cell replication. The role of cell cycle regulation in beta cell replication is mostly from studies in rodent models, but whether...

Phosphorylation of NS5A Serine-235 is essential to hepatitis C virus RNA replication and normal replication compartment formation

Energy Technology Data Exchange (ETDEWEB)

Eyre, Nicholas S., E-mail: nicholas.eyre@adelaide.edu.au [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia); Hampton-Smith, Rachel J.; Aloia, Amanda L. [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia); Eddes, James S. [Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide (Australia); Simpson, Kaylene J. [Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, East Melbourne (Australia); The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville (Australia); Hoffmann, Peter [Adelaide Proteomics Centre, School of Biological Sciences, University of Adelaide, Adelaide (Australia); Institute for Photonics and Advanced Sensing (IPAS), University of Adelaide, Adelaide (Australia); Beard, Michael R. [School of Biological Sciences and Research Centre for Infectious Diseases, University of Adelaide, Adelaide (Australia); Centre for Cancer Biology, SA Pathology, Adelaide (Australia)

2016-04-15

Hepatitis C virus (HCV) NS5A protein is essential for HCV RNA replication and virus assembly. Here we report the identification of NS5A phosphorylation sites Ser-222, Ser-235 and Thr-348 during an infectious HCV replication cycle and demonstrate that Ser-235 phosphorylation is essential for HCV RNA replication. Confocal microscopy revealed that both phosphoablatant (S235A) and phosphomimetic (S235D) mutants redistribute NS5A to large juxta-nuclear foci that display altered colocalization with known replication complex components. Using electron microscopy (EM) we found that S235D alters virus-induced membrane rearrangements while EM using ‘APEX2’-tagged viruses demonstrated S235D-mediated enrichment of NS5A in irregular membranous foci. Finally, using a customized siRNA screen of candidate NS5A kinases and subsequent analysis using a phospho-specific antibody, we show that phosphatidylinositol-4 kinase III alpha (PI4KIIIα) is important for Ser-235 phosphorylation. We conclude that Ser-235 phosphorylation of NS5A is essential for HCV RNA replication and normal replication complex formation and is regulated by PI4KIIIα. - Highlights: • NS5A residues Ser-222, Ser-235 and Thr-348 are phosphorylated during HCV infection. • Phosphorylation of Ser-235 is essential to HCV RNA replication. • Mutation of Ser-235 alters replication compartment localization and morphology. • Phosphatidylinositol-4 kinase III alpha is important for Ser-235 phosphorylation.

Uncoupling of Sister Replisomes during Eukaryotic DNA Replication

NARCIS (Netherlands)

Yardimci, Hasan; Loveland, Anna B.; Habuchi, Satoshi; van Oijen, Antoine M.; Walter, Johannes C.

2010-01-01

The duplication of eukaryotic genomes involves the replication of DNA from multiple origins of replication. In S phase, two sister replisomes assemble at each active origin, and they replicate DNA in opposite directions. Little is known about the functional relationship between sister replisomes.

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

NARCIS (Netherlands)

Tanner, Nathan A.; Loparo, Joseph J.; Oijen, Antoine M. van

2009-01-01

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides. The

Dynamic behavior of DNA replication domains

NARCIS (Netherlands)

Manders, E. M.; Stap, J.; Strackee, J.; van Driel, R.; Aten, J. A.

1996-01-01

Like many nuclear processes, DNA replication takes place in distinct domains that are scattered throughout the S-phase nucleus. Recently we have developed a fluorescent double-labeling procedure that allows us to visualize nascent DNA simultaneously with "newborn" DNA that had replicated earlier in

Counting probe

International Nuclear Information System (INIS)

Matsumoto, Haruya; Kaya, Nobuyuki; Yuasa, Kazuhiro; Hayashi, Tomoaki

1976-01-01

Electron counting method has been devised and experimented for the purpose of measuring electron temperature and density, the most fundamental quantities to represent plasma conditions. Electron counting is a method to count the electrons in plasma directly by equipping a probe with the secondary electron multiplier. It has three advantages of adjustable sensitivity, high sensitivity of the secondary electron multiplier, and directional property. Sensitivity adjustment is performed by changing the size of collecting hole (pin hole) on the incident front of the multiplier. The probe is usable as a direct reading thermometer of electron temperature because it requires to collect very small amount of electrons, thus it doesn't disturb the surrounding plasma, and the narrow sweep width of the probe voltage is enough. Therefore it can measure anisotropy more sensitively than a Langmuir probe, and it can be used for very low density plasma. Though many problems remain on anisotropy, computer simulation has been carried out. Also it is planned to provide a Helmholtz coil in the vacuum chamber to eliminate the effect of earth magnetic field. In practical experiments, the measurement with a Langmuir probe and an emission probe mounted to the movable structure, the comparison with the results obtained in reverse magnetic field by using a Helmholtz coil, and the measurement of ionic sound wave are scheduled. (Wakatsuki, Y.)

A mind you can count on: validating breath counting as a behavioral measure of mindfulness

Directory of Open Access Journals (Sweden)

Daniel B Levinson

2014-10-01

Full Text Available Mindfulness practice of present moment awareness promises many benefits, but has eluded rigorous behavioral measurement. To date, research has relied on self-reported mindfulness or heterogeneous mindfulness trainings to infer skillful mindfulness practice and its effects. In four independent studies with over 400 total participants, we present the first construct validation of a behavioral measure of mindfulness, breath counting. We found it was reliable, correlated with self-reported mindfulness, differentiated long-term meditators from age-matched controls, and was distinct from sustained attention and working memory measures. In addition, we employed breath counting to test the nomological network of mindfulness. As theorized, we found skill in breath counting associated with more meta-awareness, less mind wandering, better mood, and greater nonattachment (i.e. less attentional capture by distractors formerly paired with reward. We also found in a randomized online training study that 4 weeks of breath counting training improved mindfulness and decreased mind wandering relative to working memory training and no training controls. Together, these findings provide the first evidence for breath counting as a behavioral measure of mindfulness.

Building and Activating Students' Background Knowledge: It's What They Already Know That Counts

Science.gov (United States)

Fisher, Douglas; Frey, Nancy; Lapp, Diane

2012-01-01

Students enter the middle grades with varying amounts of background knowledge. Teachers must assess student background knowledge for gaps or misconceptions and then provide instruction to build on that base. This article discusses effective strategies for assessing and developing students' background knowledge so they can become independent…

The evolutionary ecology of molecular replicators.

Science.gov (United States)

Nee, Sean

2016-08-01

By reasonable criteria, life on the Earth consists mainly of molecular replicators. These include viruses, transposons, transpovirons, coviruses and many more, with continuous new discoveries like Sputnik Virophage. Their study is inherently multidisciplinary, spanning microbiology, genetics, immunology and evolutionary theory, and the current view is that taking a unified approach has great power and promise. We support this with a new, unified, model of their evolutionary ecology, using contemporary evolutionary theory coupling the Price equation with game theory, studying the consequences of the molecular replicators' promiscuous use of each others' gene products for their natural history and evolutionary ecology. Even at this simple expository level, we can make a firm prediction of a new class of replicators exploiting viruses such as lentiviruses like SIVs, a family which includes HIV: these have been explicitly stated in the primary literature to be non-existent. Closely connected to this departure is the view that multicellular organism immunology is more about the management of chronic infections rather than the elimination of acute ones and new understandings emerging are changing our view of the kind of theatre we ourselves provide for the evolutionary play of molecular replicators. This study adds molecular replicators to bacteria in the emerging field of sociomicrobiology.

Principles of correlation counting

International Nuclear Information System (INIS)

Mueller, J.W.

1975-01-01

A review is given of the various applications which have been made of correlation techniques in the field of nuclear physics, in particular for absolute counting. Whereas in most cases the usual coincidence method will be preferable for its simplicity, correlation counting may be the only possible approach in such cases where the two radiations of the cascade cannot be well separated or when there is a longliving intermediate state. The measurement of half-lives and of count rates of spurious pulses is also briefly discussed. The various experimental situations lead to different ways the correlation method is best applied (covariance technique with one or with two detectors, application of correlation functions, etc.). Formulae are given for some simple model cases, neglecting dead-time corrections

Development of a single-photon-counting camera with use of a triple-stacked micro-channel plate.

Science.gov (United States)

Yasuda, Naruomi; Suzuki, Hitoshi; Katafuchi, Tetsuro

2016-01-01

At the quantum-mechanical level, all substances (not merely electromagnetic waves such as light and X-rays) exhibit wave–particle duality. Whereas students of radiation science can easily understand the wave nature of electromagnetic waves, the particle (photon) nature may elude them. Therefore, to assist students in understanding the wave–particle duality of electromagnetic waves, we have developed a photon-counting camera that captures single photons in two-dimensional images. As an image intensifier, this camera has a triple-stacked micro-channel plate (MCP) with an amplification factor of 10(6). The ultra-low light of a single photon entering the camera is first converted to an electron through the photoelectric effect on the photocathode. The electron is intensified by the triple-stacked MCP and then converted to a visible light distribution, which is measured by a high-sensitivity complementary metal oxide semiconductor image sensor. Because it detects individual photons, the photon-counting camera is expected to provide students with a complete understanding of the particle nature of electromagnetic waves. Moreover, it measures ultra-weak light that cannot be detected by ordinary low-sensitivity cameras. Therefore, it is suitable for experimental research on scintillator luminescence, biophoton detection, and similar topics.

A Fuzzy Modeling Approach for Replicated Response Measures Based on Fuzzification of Replications with Descriptive Statistics and Golden Ratio

Directory of Open Access Journals (Sweden)

Özlem TÜRKŞEN

2018-03-01

Full Text Available Some of the experimental designs can be composed of replicated response measures in which the replications cannot be identified exactly and may have uncertainty different than randomness. Then, the classical regression analysis may not be proper to model the designed data because of the violation of probabilistic modeling assumptions. In this case, fuzzy regression analysis can be used as a modeling tool. In this study, the replicated response values are newly formed to fuzzy numbers by using descriptive statistics of replications and golden ratio. The main aim of the study is obtaining the most suitable fuzzy model for replicated response measures through fuzzification of the replicated values by taking into account the data structure of the replications in statistical framework. Here, the response and unknown model coefficients are considered as triangular type-1 fuzzy numbers (TT1FNs whereas the inputs are crisp. Predicted fuzzy models are obtained according to the proposed fuzzification rules by using Fuzzy Least Squares (FLS approach. The performances of the predicted fuzzy models are compared by using Root Mean Squared Error (RMSE criteria. A data set from the literature, called wheel cover component data set, is used to illustrate the performance of the proposed approach and the obtained results are discussed. The calculation results show that the combined formulation of the descriptive statistics and the golden ratio is the most preferable fuzzification rule according to the well-known decision making method, called TOPSIS, for the data set.

Rapid transient production in plants by replicating and non-replicating vectors yields high quality functional anti-HIV antibody.

Directory of Open Access Journals (Sweden)

Frank Sainsbury

2010-11-01

Full Text Available The capacity of plants and plant cells to produce large amounts of recombinant protein has been well established. Due to advantages in terms of speed and yield, attention has recently turned towards the use of transient expression systems, including viral vectors, to produce proteins of pharmaceutical interest in plants. However, the effects of such high level expression from viral vectors and concomitant effects on host cells may affect the quality of the recombinant product.To assess the quality of antibodies transiently expressed to high levels in plants, we have expressed and characterised the human anti-HIV monoclonal antibody, 2G12, using both replicating and non-replicating systems based on deleted versions of Cowpea mosaic virus (CPMV RNA-2. The highest yield (approximately 100 mg/kg wet weight leaf tissue of affinity purified 2G12 was obtained when the non-replicating CPMV-HT system was used and the antibody was retained in the endoplasmic reticulum (ER. Glycan analysis by mass-spectrometry showed that the glycosylation pattern was determined exclusively by whether the antibody was retained in the ER and did not depend on whether a replicating or non-replicating system was used. Characterisation of the binding and neutralisation properties of all the purified 2G12 variants from plants showed that these were generally similar to those of the Chinese hamster ovary (CHO cell-produced 2G12.Overall, the results demonstrate that replicating and non-replicating CPMV-based vectors are able to direct the production of a recombinant IgG similar in activity to the CHO-produced control. Thus, a complex recombinant protein was produced with no apparent effect on its biochemical properties using either high-level expression or viral replication. The speed with which a recombinant pharmaceutical with excellent biochemical characteristics can be produced transiently in plants makes CPMV-based expression vectors an attractive option for

Dynamics of picornavirus RNA replication within infected cells

DEFF Research Database (Denmark)

Belsham, Graham; Normann, Preben

2008-01-01

Replication of many picornaviruses is inhibited by low concentrations of guanidine. Guanidine-resistant mutants are readily isolated and the mutations map to the coding region for the 2C protein. Using in vitro replication assays it has been determined previously that guanidine blocks the initiat......Replication of many picornaviruses is inhibited by low concentrations of guanidine. Guanidine-resistant mutants are readily isolated and the mutations map to the coding region for the 2C protein. Using in vitro replication assays it has been determined previously that guanidine blocks...... the initiation of negative-strand synthesis. We have now examined the dynamics of RNA replication, measured by quantitative RT-PCR, within cells infected with either swine vesicular disease virus (an enterovirus) or foot-and-mouth disease virus as regulated by the presence or absence of guanidine. Following...... the removal of guanidine from the infected cells, RNA replication occurs after a significant lag phase. This restoration of RNA synthesis requires de novo protein synthesis. Viral RNA can be maintained for at least 72 h within cells in the absence of apparent replication but guanidine-resistant virus can...

Pyrimidine dimers block simian virus 40 replication forks

International Nuclear Information System (INIS)

Berger, C.A.; Edenberg, H.J.

1986-01-01

UV light produces lesions, predominantly pyrimidine dimers, which inhibit DNA replication in mammalian cells. The mechanism of inhibition is controversial: is synthesis of a daughter strand halted at a lesion while the replication fork moves on and reinitiates downstream, or is fork progression itself blocked for some time at the site of a lesion? We directly addressed this question by using electron microscopy to examine the distances of replication forks from the origin in unirradiated and UV-irradiated simian virus 40 chromosomes. If UV lesions block replication fork progression, the forks should be asymmetrically located in a large fraction of the irradiated molecules; if replication forks move rapidly past lesions, the forks should be symmetrically located. A large fraction of the simian virus 40 replication forks in irradiated molecules were asymmetrically located, demonstrating that UV lesions present at the frequency of pyrimidine dimers block replication forks. As a mechanism for this fork blockage, we propose that polymerization of the leading strand makes a significant contribution to the energetics of fork movement, so any lesion in the template for the leading strand which blocks polymerization should also block fork movement

Autonomous model protocell division driven by molecular replication.

Science.gov (United States)

Taylor, J W; Eghtesadi, S A; Points, L J; Liu, T; Cronin, L

2017-08-10

The coupling of compartmentalisation with molecular replication is thought to be crucial for the emergence of the first evolvable chemical systems. Minimal artificial replicators have been designed based on molecular recognition, inspired by the template copying of DNA, but none yet have been coupled to compartmentalisation. Here, we present an oil-in-water droplet system comprising an amphiphilic imine dissolved in chloroform that catalyses its own formation by bringing together a hydrophilic and a hydrophobic precursor, which leads to repeated droplet division. We demonstrate that the presence of the amphiphilic replicator, by lowering the interfacial tension between droplets of the reaction mixture and the aqueous phase, causes them to divide. Periodic sampling by a droplet-robot demonstrates that the extent of fission is increased as the reaction progresses, producing more compartments with increased self-replication. This bridges a divide, showing how replication at the molecular level can be used to drive macroscale droplet fission.Coupling compartmentalisation and molecular replication is essential for the development of evolving chemical systems. Here the authors show an oil-in-water droplet containing a self-replicating amphiphilic imine that can undergo repeated droplet division.

Initiation preference at a yeast origin of replication.

Science.gov (United States)

Brewer, B J; Fangman, W L

1994-04-12

Replication origins in the yeast Saccharomyces cerevisiae are identified as autonomous replication sequence (ARS) elements. To examine the effect of origin density on replication initiation, we have analyzed the replication of a plasmid that contains two copies of the same origin, ARS1. The activation of origins and the direction that replication forks move through flanking sequences can be physically determined by analyzing replication intermediates on two-dimensional agarose gels. We find that only one of the two identical ARSs on the plasmid initiates replication on any given plasmid molecule; that is, this close spacing of ARSs results in an apparent interference between the potential origins. Moreover, in the particular plasmid that we constructed, one of the two identical copies of ARS1 is used four times more frequently than the other one. These results show that the plasmid context is critical for determining the preferred origin. This origin preference is also exhibited when the tandem copies of ARS1 are introduced into a yeast chromosome. The sequences responsible for establishing the origin preference have been identified by deletion analysis and are found to reside in a portion of the yeast URA3 gene.

Gene organization inside replication domains in mammalian genomes

Science.gov (United States)

Zaghloul, Lamia; Baker, Antoine; Audit, Benjamin; Arneodo, Alain

2012-11-01

We investigate the large-scale organization of human genes with respect to "master" replication origins that were previously identified as bordering nucleotide compositional skew domains. We separate genes in two categories depending on their CpG enrichment at the promoter which can be considered as a marker of germline DNA methylation. Using expression data in mouse, we confirm that CpG-rich genes are highly expressed in germline whereas CpG-poor genes are in a silent state. We further show that, whether tissue-specific or broadly expressed (housekeeping genes), the CpG-rich genes are over-represented close to the replication skew domain borders suggesting some coordination of replication and transcription. We also reveal that the transcription of the longest CpG-rich genes is co-oriented with replication fork progression so that the promoter of these transcriptionally active genes be located into the accessible open chromatin environment surrounding the master replication origins that border the replication skew domains. The observation of a similar gene organization in the mouse genome confirms the interplay of replication, transcription and chromatin structure as the cornerstone of mammalian genome architecture.

Mapping replication origins in yeast chromosomes.

Science.gov (United States)

Brewer, B J; Fangman, W L

1991-07-01

The replicon hypothesis, first proposed in 1963 by Jacob and Brenner, states that DNA replication is controlled at sites called origins. Replication origins have been well studied in prokaryotes. However, the study of eukaryotic chromosomal origins has lagged behind, because until recently there has been no method for reliably determining the identity and location of origins from eukaryotic chromosomes. Here, we review a technique we developed with the yeast Saccharomyces cerevisiae that allows both the mapping of replication origins and an assessment of their activity. Two-dimensional agarose gel electrophoresis and Southern hybridization with total genomic DNA are used to determine whether a particular restriction fragment acquires the branched structure diagnostic of replication initiation. The technique has been used to localize origins in yeast chromosomes and assess their initiation efficiency. In some cases, origin activation is dependent upon the surrounding context. The technique is also being applied to a variety of eukaryotic organisms.

Assembly of Slx4 signaling complexes behind DNA replication forks.

Science.gov (United States)

Balint, Attila; Kim, TaeHyung; Gallo, David; Cussiol, Jose Renato; Bastos de Oliveira, Francisco M; Yimit, Askar; Ou, Jiongwen; Nakato, Ryuichiro; Gurevich, Alexey; Shirahige, Katsuhiko; Smolka, Marcus B; Zhang, Zhaolei; Brown, Grant W

2015-08-13

Obstructions to replication fork progression, referred to collectively as DNA replication stress, challenge genome stability. In Saccharomyces cerevisiae, cells lacking RTT107 or SLX4 show genome instability and sensitivity to DNA replication stress and are defective in the completion of DNA replication during recovery from replication stress. We demonstrate that Slx4 is recruited to chromatin behind stressed replication forks, in a region that is spatially distinct from that occupied by the replication machinery. Slx4 complex formation is nucleated by Mec1 phosphorylation of histone H2A, which is recognized by the constitutive Slx4 binding partner Rtt107. Slx4 is essential for recruiting the Mec1 activator Dpb11 behind stressed replication forks, and Slx4 complexes are important for full activity of Mec1. We propose that Slx4 complexes promote robust checkpoint signaling by Mec1 by stably recruiting Dpb11 within a discrete domain behind the replication fork, during DNA replication stress. © 2015 The Authors.

Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Kai, Mihoko; Wang, Teresa S.-F

2003-11-27

Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Pol{kappa}). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development.

Checkpoint responses to replication stalling: inducing tolerance and preventing mutagenesis

International Nuclear Information System (INIS)

Kai, Mihoko; Wang, Teresa S.-F.

2003-01-01

Replication mutants often exhibit a mutator phenotype characterized by point mutations, single base frameshifts, and the deletion or duplication of sequences flanked by homologous repeats. Mutation in genes encoding checkpoint proteins can significantly affect the mutator phenotype. Here, we use fission yeast (Schizosaccharomyces pombe) as a model system to discuss the checkpoint responses to replication perturbations induced by replication mutants. Checkpoint activation induced by a DNA polymerase mutant, aside from delay of mitotic entry, up-regulates the translesion polymerase DinB (Polκ). Checkpoint Rad9-Rad1-Hus1 (9-1-1) complex, which is loaded onto chromatin by the Rad17-Rfc2-5 checkpoint complex in response to replication perturbation, recruits DinB onto chromatin to generate the point mutations and single nucleotide frameshifts in the replication mutator. This chain of events reveals a novel checkpoint-induced tolerance mechanism that allows cells to cope with replication perturbation, presumably to make possible restarting stalled replication forks. Fission yeast Cds1 kinase plays an essential role in maintaining DNA replication fork stability in the face of DNA damage and replication fork stalling. Cds1 kinase is known to regulate three proteins that are implicated in maintaining replication fork stability: Mus81-Eme1, a hetero-dimeric structure-specific endonuclease complex; Rqh1, a RecQ-family helicase involved in suppressing inappropriate recombination during replication; and Rad60, a protein required for recombinational repair during replication. These Cds1-regulated proteins are thought to cooperatively prevent mutagenesis and maintain replication fork stability in cells under replication stress. These checkpoint-regulated processes allow cells to survive replication perturbation by preventing stalled replication forks from degenerating into deleterious DNA structures resulting in genomic instability and cancer development

Delta count-rate monitoring system

International Nuclear Information System (INIS)

Van Etten, D.; Olsen, W.A.

1985-01-01

A need for a more effective way to rapidly search for gamma-ray contamination over large areas led to the design and construction of a very sensitive gamma detection system. The delta count-rate monitoring system was installed in a four-wheel-drive van instrumented for environmental surveillance and accident response. The system consists of four main sections: (1) two scintillation detectors, (2) high-voltage power supply amplifier and single-channel analyzer, (3) delta count-rate monitor, and (4) count-rate meter and recorder. The van's 6.5-kW generator powers the standard nuclear instrument modular design system. The two detectors are mounted in the rear corners of the van and can be run singly or jointly. A solid-state bar-graph count-rate meter mounted on the dashboard can be read easily by both the driver and passenger. A solid-state strip chart recorder shows trends and provides a permanent record of the data. An audible alarm is sounded at the delta monitor and at the dashboard count-rate meter if a detected radiation level exceeds the set background level by a predetermined amount

Hyperthermia stimulates HIV-1 replication.

Directory of Open Access Journals (Sweden)

Ferdinand Roesch

Full Text Available HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42-45°C and Heat Shock Proteins (HSPs modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38-40°C on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.

Replication and Robustness in Developmental Research

Science.gov (United States)

Duncan, Greg J.; Engel, Mimi; Claessens, Amy; Dowsett, Chantelle J.

2014-01-01

Replications and robustness checks are key elements of the scientific method and a staple in many disciplines. However, leading journals in developmental psychology rarely include explicit replications of prior research conducted by different investigators, and few require authors to establish in their articles or online appendices that their key…

DC KIDS COUNT e-Databook Indicators

Science.gov (United States)

DC Action for Children, 2012

2012-01-01

This report presents indicators that are included in DC Action for Children's 2012 KIDS COUNT e-databook, their definitions and sources and the rationale for their selection. The indicators for DC KIDS COUNT represent a mix of traditional KIDS COUNT indicators of child well-being, such as the number of children living in poverty, and indicators of…

Biomarkers of replicative senescence revisited

DEFF Research Database (Denmark)

Nehlin, Jan

2016-01-01

Biomarkers of replicative senescence can be defined as those ultrastructural and physiological variations as well as molecules whose changes in expression, activity or function correlate with aging, as a result of the gradual exhaustion of replicative potential and a state of permanent cell cycle...... arrest. The biomarkers that characterize the path to an irreversible state of cell cycle arrest due to proliferative exhaustion may also be shared by other forms of senescence-inducing mechanisms. Validation of senescence markers is crucial in circumstances where quiescence or temporary growth arrest may...... be triggered or is thought to be induced. Pre-senescence biomarkers are also important to consider as their presence indicate that induction of aging processes is taking place. The bona fide pathway leading to replicative senescence that has been extensively characterized is a consequence of gradual reduction...

Replication of an Experimental Study Investigating the Efficacy of a Multisyllabic Word Reading Intervention With and Without Motivational Beliefs Training for Struggling Readers.

Science.gov (United States)

Toste, Jessica R; Capin, Philip; Williams, Kelly J; Cho, Eunsoo; Vaughn, Sharon

2018-05-01

This randomized control trial examined the efficacy of an intervention aimed at improving multisyllabic word reading (MWR) skills among fourth- and fifth-grade struggling readers ( n = 109, 48.6% male), as well as the relative effects of an embedded motivational beliefs training component. This study was a closely aligned replication of our earlier work. The intervention was replicated with a three-condition design: MWR only, MWR with a motivational beliefs component, and business-as-usual control. Students were tutored in small groups for 40 lessons (four 40-min lessons each week). When we combined performance of students in both MWR conditions, intervention students significantly outperformed controls on proximal measures of affix reading and MWR, as well as standardized measures of decoding, spelling, and text comprehension. Furthermore, there was a noted interaction between English learner status and treatment on spelling performance. There were no statistically significant main effects between the MWR groups on proximal or standardized measures of interest. Findings are discussed in terms of their relevance to MWR instruction for students with persistent reading difficulties and considerations for future research related to the malleability of motivation.

In vivo counting of uranium

International Nuclear Information System (INIS)

Palmer, H.E.

1985-03-01

A state-of-the-art radiation detector system consisting of six individually mounted intrinsic germanium planar detectors, each 20 cm 2 by 13 mm thick, mounted together such that the angle of the whole system can be changed to match the slope of the chest of the person being counted, is described. The sensitivity of the system for counting uranium and plutonium in vivo and the precedures used in calibrating the system are also described. Some results of counts done on uranium mill workers are presented. 15 figs., 2 tabs

Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.

Science.gov (United States)

Moriyama, Takashi; Sato, Naoki

2014-01-01

Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

Viral hijacking of a replicative helicase loader and its implications for helicase loading control and phage replication

Energy Technology Data Exchange (ETDEWEB)

Hood, Iris V.; Berger, James M.

2016-05-31

Replisome assembly requires the loading of replicative hexameric helicases onto origins by AAA+ ATPases. How loader activity is appropriately controlled remains unclear. Here, we use structural and biochemical analyses to establish how an antimicrobial phage protein interferes with the function of theStaphylococcus aureusreplicative helicase loader, DnaI. The viral protein binds to the loader’s AAA+ ATPase domain, allowing binding of the host replicative helicase but impeding loader self-assembly and ATPase activity. Close inspection of the complex highlights an unexpected locus for the binding of an interdomain linker element in DnaI/DnaC-family proteins. We find that the inhibitor protein is genetically coupled to a phage-encoded homolog of the bacterial helicase loader, which we show binds to the host helicase but not to the inhibitor itself. These findings establish a new approach by which viruses can hijack host replication processes and explain how loader activity is internally regulated to prevent aberrant auto-association.

The transcription elongation factor Bur1-Bur2 interacts with replication protein A and maintains genome stability during replication stress

DEFF Research Database (Denmark)

Clausing, Emanuel; Mayer, Andreas; Chanarat, Sittinan

2010-01-01

Multiple DNA-associated processes such as DNA repair, replication, and recombination are crucial for the maintenance of genome integrity. Here, we show a novel interaction between the transcription elongation factor Bur1-Bur2 and replication protein A (RPA), the eukaryotic single-stranded DNA......-binding protein with functions in DNA repair, recombination, and replication. Bur1 interacted via its C-terminal domain with RPA, and bur1-¿C mutants showed a deregulated DNA damage response accompanied by increased sensitivity to DNA damage and replication stress as well as increased levels of persisting Rad52...... foci. Interestingly, the DNA damage sensitivity of an rfa1 mutant was suppressed by bur1 mutation, further underscoring a functional link between these two protein complexes. The transcription elongation factor Bur1-Bur2 interacts with RPA and maintains genome integrity during DNA replication stress....

Distinct functions of human RecQ helicases during DNA replication.

Science.gov (United States)

Urban, Vaclav; Dobrovolna, Jana; Janscak, Pavel

2017-06-01

DNA replication is the most vulnerable process of DNA metabolism in proliferating cells and therefore it is tightly controlled and coordinated with processes that maintain genomic stability. Human RecQ helicases are among the most important factors involved in the maintenance of replication fork integrity, especially under conditions of replication stress. RecQ helicases promote recovery of replication forks being stalled due to different replication roadblocks of either exogenous or endogenous source. They prevent generation of aberrant replication fork structures and replication fork collapse, and are involved in proper checkpoint signaling. The essential role of human RecQ helicases in the genome maintenance during DNA replication is underlined by association of defects in their function with cancer predisposition. Copyright © 2016 Elsevier B.V. All rights reserved.

Evolution of complexity in RNA-like replicator systems

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Hogeweg Paulien

2008-03-01

Full Text Available Abstract Background The evolution of complexity is among the most important questions in biology. The evolution of complexity is often observed as the increase of genetic information or that of the organizational complexity of a system. It is well recognized that the formation of biological organization – be it of molecules or ecosystems – is ultimately instructed by the genetic information, whereas it is also true that the genetic information is functional only in the context of the organization. Therefore, to obtain a more complete picture of the evolution of complexity, we must study the evolution of both information and organization. Results Here we investigate the evolution of complexity in a simulated RNA-like replicator system. The simplicity of the system allows us to explicitly model the genotype-phenotype-interaction mapping of individual replicators, whereby we avoid preconceiving the functionality of genotypes (information or the ecological organization of replicators in the model. In particular, the model assumes that interactions among replicators – to replicate or to be replicated – depend on their secondary structures and base-pair matching. The results showed that a population of replicators, originally consisting of one genotype, evolves to form a complex ecosystem of up to four species. During this diversification, the species evolve through acquiring unique genotypes with distinct ecological functionality. The analysis of this diversification reveals that parasitic replicators, which have been thought to destabilize the replicator's diversity, actually promote the evolution of diversity through generating a novel "niche" for catalytic replicators. This also makes the current replicator system extremely stable upon the evolution of parasites. The results also show that the stability of the system crucially depends on the spatial pattern formation of replicators. Finally, the evolutionary dynamics is shown to

Molecular Mechanisms of DNA Replication Checkpoint Activation

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Bénédicte Recolin

2014-03-01

Full Text Available The major challenge of the cell cycle is to deliver an intact, and fully duplicated, genetic material to the daughter cells. To this end, progression of DNA synthesis is monitored by a feedback mechanism known as replication checkpoint that is untimely linked to DNA replication. This signaling pathway ensures coordination of DNA synthesis with cell cycle progression. Failure to activate this checkpoint in response to perturbation of DNA synthesis (replication stress results in forced cell division leading to chromosome fragmentation, aneuploidy, and genomic instability. In this review, we will describe current knowledge of the molecular determinants of the DNA replication checkpoint in eukaryotic cells and discuss a model of activation of this signaling pathway crucial for maintenance of genomic stability.

Alpha scintillation radon counting

International Nuclear Information System (INIS)

Lucas, H.F. Jr.

1977-01-01

Radon counting chambers which utilize the alpha-scintillation properties of silver activated zinc sulfide are simple to construct, have a high efficiency, and, with proper design, may be relatively insensitive to variations in the pressure or purity of the counter filling. Chambers which were constructed from glass, metal, or plastic in a wide variety of shapes and sizes were evaluated for the accuracy and the precision of the radon counting. The principles affecting the alpha-scintillation radon counting chamber design and an analytic system suitable for a large scale study of the 222 Rn and 226 Ra content of either air or other environmental samples are described. Particular note is taken of those factors which affect the accuracy and the precision of the method for monitoring radioactivity around uranium mines

A new MCM modification cycle regulates DNA replication initiation.

Science.gov (United States)

Wei, Lei; Zhao, Xiaolan

2016-03-01

The MCM DNA helicase is a central regulatory target during genome replication. MCM is kept inactive during G1, and it initiates replication after being activated in S phase. During this transition, the only known chemical change to MCM is the gain of multisite phosphorylation that promotes cofactor recruitment. Because replication initiation is intimately linked to multiple biological cues, additional changes to MCM can provide further regulatory points. Here, we describe a yeast MCM SUMOylation cycle that regulates replication. MCM subunits undergo SUMOylation upon loading at origins in G1 before MCM phosphorylation. MCM SUMOylation levels then decline as MCM phosphorylation levels rise, thus suggesting an inhibitory role of MCM SUMOylation during replication. Indeed, increasing MCM SUMOylation impairs replication initiation, partly through promoting the recruitment of a phosphatase that decreases MCM phosphorylation and activation. We propose that MCM SUMOylation counterbalances kinase-based regulation, thus ensuring accurate control of replication initiation.

Equivalence of truncated count mixture distributions and mixtures of truncated count distributions.

Science.gov (United States)

Böhning, Dankmar; Kuhnert, Ronny

2006-12-01

This article is about modeling count data with zero truncation. A parametric count density family is considered. The truncated mixture of densities from this family is different from the mixture of truncated densities from the same family. Whereas the former model is more natural to formulate and to interpret, the latter model is theoretically easier to treat. It is shown that for any mixing distribution leading to a truncated mixture, a (usually different) mixing distribution can be found so that the associated mixture of truncated densities equals the truncated mixture, and vice versa. This implies that the likelihood surfaces for both situations agree, and in this sense both models are equivalent. Zero-truncated count data models are used frequently in the capture-recapture setting to estimate population size, and it can be shown that the two Horvitz-Thompson estimators, associated with the two models, agree. In particular, it is possible to achieve strong results for mixtures of truncated Poisson densities, including reliable, global construction of the unique NPMLE (nonparametric maximum likelihood estimator) of the mixing distribution, implying a unique estimator for the population size. The benefit of these results lies in the fact that it is valid to work with the mixture of truncated count densities, which is less appealing for the practitioner but theoretically easier. Mixtures of truncated count densities form a convex linear model, for which a developed theory exists, including global maximum likelihood theory as well as algorithmic approaches. Once the problem has been solved in this class, it might readily be transformed back to the original problem by means of an explicitly given mapping. Applications of these ideas are given, particularly in the case of the truncated Poisson family.

A CI-Independent Form of Replicative Inhibition: Turn Off of Early Replication of Bacteriophage Lambda

Science.gov (United States)

Hayes, Sidney; Horbay, Monique A.; Hayes, Connie

2012-01-01

Several earlier studies have described an unusual exclusion phenotype exhibited by cells with plasmids carrying a portion of the replication region of phage lambda. Cells exhibiting this inhibition phenotype (IP) prevent the plating of homo-immune and hybrid hetero-immune lambdoid phages. We have attempted to define aspects of IP, and show that it is directed to repλ phages. IP was observed in cells with plasmids containing a λ DNA fragment including oop, encoding a short OOP micro RNA, and part of the lambda origin of replication, oriλ, defined by iteron sequences ITN1-4 and an adjacent high AT-rich sequence. Transcription of the intact oop sequence from its promoter, pO is required for IP, as are iterons ITN3–4, but not the high AT-rich portion of oriλ. The results suggest that IP silencing is directed to theta mode replication initiation from an infecting repλ genome, or an induced repλ prophage. Phage mutations suppressing IP, i.e., Sip, map within, or adjacent to cro or in O, or both. Our results for plasmid based IP suggest the hypothesis that there is a natural mechanism for silencing early theta-mode replication initiation, i.e. the buildup of λ genomes with oop + oriλ+ sequence. PMID:22590552

College Students' Beliefs About Domestic Violence: A Replication and Extension.

Science.gov (United States)

Wagers, Shelly M; Wareham, Jennifer; Boots, Denise Paquette

2017-12-01

In recent decades, significant effort and money have been spent to change social and legal responses to domestic violence and affect public perceptions. A small body of research has examined individuals' opinions about what behaviors are considered domestic violence. Using a sample of college students, the present study examined a modified version of a somewhat popular instrument used to measure beliefs about domestic violence, extending previous work done by Carlson and Worden. Results indicated beliefs about domestic violence are multidimensional, depending on the nature of the behavior and, in part, the gender of the perpetrator. Opinions about the lawfulness of these behaviors fit the same factor structure as beliefs about domestic violence. Demographic characteristics, current relationship status, secondhand experiences with domestic violence, and perceived prevalence of domestic violence in the community are generally not related to beliefs about domestic violence or the lawfulness of these behaviors. However, attributions of blame on the victim are negatively related to domestic violence beliefs and lawfulness. Moreover, lawfulness is a key covariate for domestic violence beliefs. In addition, results also indicate that the gender of the perpetrator is an important variable affecting student's beliefs about sexual assault behaviors. Results from this study support the prevailing ideas behind the Battered Women's Movement that enacting policies and educational programs deeming domestic violence socially, morally, and legally wrong could shift long-standing sociocultural beliefs about men's use of violence against women. Implications of this study for research and policy specific to college students are discussed.

Spacetime replication of continuous variable quantum information

International Nuclear Information System (INIS)

Hayden, Patrick; Nezami, Sepehr; Salton, Grant; Sanders, Barry C

2016-01-01

The theory of relativity requires that no information travel faster than light, whereas the unitarity of quantum mechanics ensures that quantum information cannot be cloned. These conditions provide the basic constraints that appear in information replication tasks, which formalize aspects of the behavior of information in relativistic quantum mechanics. In this article, we provide continuous variable (CV) strategies for spacetime quantum information replication that are directly amenable to optical or mechanical implementation. We use a new class of homologically constructed CV quantum error correcting codes to provide efficient solutions for the general case of information replication. As compared to schemes encoding qubits, our CV solution requires half as many shares per encoded system. We also provide an optimized five-mode strategy for replicating quantum information in a particular configuration of four spacetime regions designed not to be reducible to previously performed experiments. For this optimized strategy, we provide detailed encoding and decoding procedures using standard optical apparatus and calculate the recovery fidelity when finite squeezing is used. As such we provide a scheme for experimentally realizing quantum information replication using quantum optics. (paper)

COPI is required for enterovirus 71 replication.

Directory of Open Access Journals (Sweden)

Jianmin Wang

Full Text Available Enterovirus 71 (EV71, a member of the Picornaviridae family, is found in Asian countries where it causes a wide range of human diseases. No effective therapy is available for the treatment of these infections. Picornaviruses undergo RNA replication in association with membranes of infected cells. COPI and COPII have been shown to be involved in the formation of picornavirus-induced vesicles. Replication of several picornaviruses, including poliovirus and Echovirus 11 (EV11, is dependent on COPI or COPII. Here, we report that COPI, but not COPII, is required for EV71 replication. Replication of EV71 was inhibited by brefeldin A and golgicide A, inhibitors of COPI activity. Furthermore, we found EV71 2C protein interacted with COPI subunits by co-immunoprecipitation and GST pull-down assay, indicating that COPI coatomer might be directed to the viral replication complex through viral 2C protein. Additionally, because the pathway is conserved among different species of enteroviruses, it may represent a novel target for antiviral therapies.

DNA replication after mutagenic treatment in Hordeum vulgare.

Science.gov (United States)

Kwasniewska, Jolanta; Kus, Arita; Swoboda, Monika; Braszewska-Zalewska, Agnieszka

2016-12-01

The temporal and spatial properties of DNA replication in plants related to DNA damage and mutagenesis is poorly understood. Experiments were carried out to explore the relationships between DNA replication, chromatin structure and DNA damage in nuclei from barley root tips. We quantitavely analysed the topological organisation of replication foci using pulse EdU labelling during the S phase and its relationship with the DNA damage induced by mutagenic treatment with maleic hydrazide (MH), nitroso-N-methyl-urea (MNU) and gamma ray. Treatment with mutagens did not change the characteristic S-phase patterns in the nuclei; however, the frequencies of the S-phase-labelled cells after treatment differed from those observed in the control cells. The analyses of DNA replication in barley nuclei were extended to the micronuclei induced by mutagens. Replication in the chromatin of the micronuclei was rare. The results of simultanous TUNEL reaction to identify cells with DNA strand breaks and the labelling of the S-phase cells with EdU revealed the possibility of DNA replication occurring in damaged nuclei. For the first time, the intensity of EdU fluorescence to study the rate of DNA replication was analysed. Copyright © 2016 Elsevier B.V. All rights reserved.

Prediction of Optimal Daily Step Count Achievement from Segmented School Physical Activity

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Ryan D. Burns

2015-01-01

Full Text Available Optimizing physical activity in childhood is needed for prevention of disease and for healthy social and psychological development. There is limited research examining how segmented school physical activity patterns relate to a child achieving optimal physical activity levels. The purpose of this study was to examine the predictive relationship between step counts during specific school segments and achieving optimal school (6,000 steps/day and daily (12,000 steps/day step counts in children. Participants included 1,714 school-aged children (mean age = 9.7±1.0 years recruited across six elementary schools. Physical activity was monitored for one week using pedometers. Generalized linear mixed effects models were used to determine the adjusted odds ratios (ORs of achieving both school and daily step count standards for every 1,000 steps taken during each school segment. The school segment that related in strongest way to a student achieving 6,000 steps during school hours was afternoon recess (OR = 40.03; P<0.001 and for achieving 12,000 steps for the entire day was lunch recess (OR = 5.03; P<0.001. School segments including lunch and afternoon recess play an important role for optimizing daily physical activity in children.

The Design of Finite State Machine for Asynchronous Replication Protocol

Science.gov (United States)

Wang, Yanlong; Li, Zhanhuai; Lin, Wei; Hei, Minglei; Hao, Jianhua

Data replication is a key way to design a disaster tolerance system and to achieve reliability and availability. It is difficult for a replication protocol to deal with the diverse and complex environment. This means that data is less well replicated than it ought to be. To reduce data loss and to optimize replication protocols, we (1) present a finite state machine, (2) run it to manage an asynchronous replication protocol and (3) report a simple evaluation of the asynchronous replication protocol based on our state machine. It's proved that our state machine is applicable to guarantee the asynchronous replication protocol running in the proper state to the largest extent in the event of various possible events. It also can helpful to build up replication-based disaster tolerance systems to ensure the business continuity.

Blood Count Tests: MedlinePlus Health Topic

Science.gov (United States)

... Spanish WBC count (Medical Encyclopedia) Also in Spanish Topic Image MedlinePlus Email Updates Get Blood Count Tests ... WBC count Show More Show Less Related Health Topics Bleeding Disorders Blood Laboratory Tests National Institutes of ...

Evaluation of lactate, white blood cell count, neutrophil count, procalcitonin and immature granulocyte count as biomarkers for sepsis in emergency department patients.

Science.gov (United States)

Karon, Brad S; Tolan, Nicole V; Wockenfus, Amy M; Block, Darci R; Baumann, Nikola A; Bryant, Sandra C; Clements, Casey M

2017-11-01

Lactate, white blood cell (WBC) and neutrophil count, procalcitonin and immature granulocyte (IG) count were compared for the prediction of sepsis, and severe sepsis or septic shock, in patients presenting to the emergency department (ED). We prospectively enrolled 501 ED patients with a sepsis panel ordered for suspicion of sepsis. WBC, neutrophil, and IG counts were measured on a Sysmex XT-2000i analyzer. Lactate was measured by i-STAT, and procalcitonin by Brahms Kryptor. We classified patients as having sepsis using a simplification of the 1992 consensus conference sepsis definitions. Patients with sepsis were further classified as having severe sepsis or septic shock using established criteria. Univariate receiver operating characteristic (ROC) analysis was performed to determine odds ratio (OR), area under the ROC curve (AUC), and sensitivity/specificity at optimal cut-off for prediction of sepsis (vs. no sepsis), and prediction of severe sepsis or septic shock (vs. no sepsis). There were 267 patients without sepsis; and 234 with sepsis, including 35 patients with severe sepsis or septic shock. Lactate had the highest OR (1.44, 95th% CI 1.20-1.73) for the prediction of sepsis; while WBC, neutrophil count and percent (neutrophil/WBC) had OR>1.00 (psepsis or septic shock, with an odds ratio (95th% CI) of 2.70 (2.02-3.61) and AUC 0.89 (0.82-0.96). Traditional biomarkers (lactate, WBC, neutrophil count, procalcitonin, IG) have limited utility in the prediction of sepsis. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Serum Copper Level Significantly Influences Platelet Count, Lymphocyte Count and Mean Cell Hemoglobin in Sickle Cell Anemia

Directory of Open Access Journals (Sweden)

Okocha Chide

2015-12-01

Full Text Available Background Changes in serum micro nutrients levels affect a number of critically important metabolic processes; these could potentially influence blood counts and ultimately disease presentation in patients with sickle cell anemia (SCA. Objectives To evaluate the influence of serum micro-nutrients levels; zinc, copper, selenium and magnesium on blood counts in steady state SCA patients. Methods A cross sectional study that involved 28 steady state adult SCA subjects. Seven milliliters (mls of blood was collected; 3 mls was for hemoglobin electrophoresis and full blood count determination while 4 mls was for measurement of serum micro nutrients levels, by the atomic absorption spectrophotometry. Correlation between serum micro-nutrient levels and blood counts was done by the Pearson’s linear regression. Ethical approval was obtained from the institutional review board and each participant gave informed consent. All data was analyzed by SPSS software version 20. Results There was a significant correlation between serum copper levels and mean cell hemoglobin (MCH, platelet and lymphocyte counts (r = 0.418; P = 0.02, r = -0.376; P = 0.04 and r = -0.383; P = 0.04, respectively. There were no significant correlations between serum levels of other micro nutrients (selenium, zinc and magnesium and blood counts. Conclusions Copper influences blood count in SCA patients probably by inducing red cell haemolysis, oxidant tissue damage and stimulating the immune system.

Assessment of the effect of probiotic curd consumption on salivary pH and streptococcus mutans counts.

Science.gov (United States)

Sudhir, R; Praveen, P; Anantharaj, A; Venkataraghavan, Karthik

2012-07-01

Antimicrobial methods of controlling dental caries that include probiotic agents can play a valuable role in establishing caries control in children at moderate to high risk for developing dental caries. Several studies have demonstrated the beneficial effects of use of various Probiotic products including curd. The objective of this study was to compare the effect of short-term consumption of probiotic curd containing Lactobacillus acidophilus and normal curd on salivary Streptococcus Mutans counts, as well as salivary pH. Forty, caries-free, 10-12 years old children were selected and randomly allocated to two groups. Test Group consisted of 20 children who consumed 200ml of probiotic curd daily for 30 days. Control Group consisted of 20 children who were given 200ml of regular curd for 30 days. Salivary pH and salivary Streptococcus Mutans counts were recorded at baseline and after 30 days and statistically compared using the Student's t-test. Consumption of probiotic curd resulted in a statistically significant reduction in S. Mutans colony counts (PpH (P>0.05) in both the groups. Short-term consumption of probiotic curds can reduce oral S. Mutans counts. However, this caused a slight reduction in salivary pH.

The Alleged Crisis and the Illusion of Exact Replication.

Science.gov (United States)

Stroebe, Wolfgang; Strack, Fritz

2014-01-01

There has been increasing criticism of the way psychologists conduct and analyze studies. These critiques as well as failures to replicate several high-profile studies have been used as justification to proclaim a "replication crisis" in psychology. Psychologists are encouraged to conduct more "exact" replications of published studies to assess the reproducibility of psychological research. This article argues that the alleged "crisis of replicability" is primarily due to an epistemological misunderstanding that emphasizes the phenomenon instead of its underlying mechanisms. As a consequence, a replicated phenomenon may not serve as a rigorous test of a theoretical hypothesis because identical operationalizations of variables in studies conducted at different times and with different subject populations might test different theoretical constructs. Therefore, we propose that for meaningful replications, attempts at reinstating the original circumstances are not sufficient. Instead, replicators must ascertain that conditions are realized that reflect the theoretical variable(s) manipulated (and/or measured) in the original study. © The Author(s) 2013.

DNA replication stress restricts ribosomal DNA copy number.

Science.gov (United States)

Salim, Devika; Bradford, William D; Freeland, Amy; Cady, Gillian; Wang, Jianmin; Pruitt, Steven C; Gerton, Jennifer L

2017-09-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

DNA replication stress restricts ribosomal DNA copy number

Science.gov (United States)

Salim, Devika; Bradford, William D.; Freeland, Amy; Cady, Gillian; Wang, Jianmin

2017-01-01

Ribosomal RNAs (rRNAs) in budding yeast are encoded by ~100–200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA) locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how “normal” copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2)-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a “normal” rDNA copy number. PMID:28915237

DNA replication stress restricts ribosomal DNA copy number.

Directory of Open Access Journals (Sweden)

Devika Salim

2017-09-01

Full Text Available Ribosomal RNAs (rRNAs in budding yeast are encoded by ~100-200 repeats of a 9.1kb sequence arranged in tandem on chromosome XII, the ribosomal DNA (rDNA locus. Copy number of rDNA repeat units in eukaryotic cells is maintained far in excess of the requirement for ribosome biogenesis. Despite the importance of the repeats for both ribosomal and non-ribosomal functions, it is currently not known how "normal" copy number is determined or maintained. To identify essential genes involved in the maintenance of rDNA copy number, we developed a droplet digital PCR based assay to measure rDNA copy number in yeast and used it to screen a yeast conditional temperature-sensitive mutant collection of essential genes. Our screen revealed that low rDNA copy number is associated with compromised DNA replication. Further, subculturing yeast under two separate conditions of DNA replication stress selected for a contraction of the rDNA array independent of the replication fork blocking protein, Fob1. Interestingly, cells with a contracted array grew better than their counterparts with normal copy number under conditions of DNA replication stress. Our data indicate that DNA replication stresses select for a smaller rDNA array. We speculate that this liberates scarce replication factors for use by the rest of the genome, which in turn helps cells complete DNA replication and continue to propagate. Interestingly, tumors from mini chromosome maintenance 2 (MCM2-deficient mice also show a loss of rDNA repeats. Our data suggest that a reduction in rDNA copy number may indicate a history of DNA replication stress, and that rDNA array size could serve as a diagnostic marker for replication stress. Taken together, these data begin to suggest the selective pressures that combine to yield a "normal" rDNA copy number.

Replication and Characterization of Association between ABO SNPs and Red Blood Cell Traits by Meta-Analysis in Europeans.

Directory of Open Access Journals (Sweden)

Stela McLachlan

Full Text Available Red blood cell (RBC traits are routinely measured in clinical practice as important markers of health. Deviations from the physiological ranges are usually a sign of disease, although variation between healthy individuals also occurs, at least partly due to genetic factors. Recent large scale genetic studies identified loci associated with one or more of these traits; further characterization of known loci and identification of new loci is necessary to better understand their role in health and disease and to identify potential molecular mechanisms. We performed meta-analysis of Metabochip association results for six RBC traits-hemoglobin concentration (Hb, hematocrit (Hct, mean corpuscular hemoglobin (MCH, mean corpuscular hemoglobin concentration (MCHC, mean corpuscular volume (MCV and red blood cell count (RCC-in 11 093 Europeans from seven studies of the UCL-LSHTM-Edinburgh-Bristol (UCLEB Consortium. We identified 394 non-overlapping SNPs in five loci at genome-wide significance: 6p22.1-6p21.33 (with HFE among others, 6q23.2 (with HBS1L among others, 6q23.3 (contains no genes, 9q34.3 (only ABO gene and 22q13.1 (with TMPRSS6 among others, replicating previous findings of association with RBC traits at these loci and extending them by imputation to 1000 Genomes. We further characterized associations between ABO SNPs and three traits: hemoglobin, hematocrit and red blood cell count, replicating them in an independent cohort. Conditional analyses indicated the independent association of each of these traits with ABO SNPs and a role for blood group O in mediating the association. The 15 most significant RBC-associated ABO SNPs were also associated with five cardiometabolic traits, with discordance in the direction of effect between groups of traits, suggesting that ABO may act through more than one mechanism to influence cardiometabolic risk.

Chaotic interactions of self-replicating RNA.

Science.gov (United States)

Forst, C V

1996-03-01

A general system of high-order differential equations describing complex dynamics of replicating biomolecules is given. Symmetry relations and coordinate transformations of general replication systems leading to topologically equivalent systems are derived. Three chaotic attractors observed in Lotka-Volterra equations of dimension n = 3 are shown to represent three cross-sections of one and the same chaotic regime. Also a fractal torus in a generalized three-dimensional Lotka-Volterra Model has been linked to one of the chaotic attractors. The strange attractors are studied in the equivalent four-dimensional catalytic replicator network. The fractal torus has been examined in adapted Lotka-Volterra equations. Analytic expressions are derived for the Lyapunov exponents of the flow in the replicator system. Lyapunov spectra for different pathways into chaos has been calculated. In the generalized Lotka-Volterra system a second inner rest point--coexisting with (quasi)-periodic orbits--can be observed; with an abundance of different bifurcations. Pathways from chaotic tori, via quasi-periodic tori, via limit cycles, via multi-periodic orbits--emerging out of periodic doubling bifurcations--to "simple" chaotic attractors can be found.

Correction for decay during counting in gamma spectrometry

International Nuclear Information System (INIS)

Nir-El, Y.

2013-01-01

A basic result in gamma spectrometry is the count rate of a relevant peak. Correction for decay during counting and expressing the count rate at the beginning of the measurement can be done by a multiplicative factor that is derived from integrating the count rate over time. The counting time substituted in this factor must be the live time, whereas the use of the real-time is an error that underestimates the count rate by about the dead-time (DT) (in percentage). This error of underestimation of the count rate is corroborated in the measurement of a nuclide with a high DT. The present methodology is not applicable in systems that include a zero DT correction function. (authors)

Insights into the Initiation of Eukaryotic DNA Replication.

Science.gov (United States)

Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

2015-01-01

The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

Interpretation of galaxy counts

International Nuclear Information System (INIS)

Tinsely, B.M.

1980-01-01

New models are presented for the interpretation of recent counts of galaxies to 24th magnitude, and predictions are shown to 28th magnitude for future comparison with data from the Space Telescope. The results supersede earlier, more schematic models by the author. Tyson and Jarvis found in their counts a ''local'' density enhancement at 17th magnitude, on comparison with the earlier models; the excess is no longer significant when a more realistic mixture of galaxy colors is used. Bruzual and Kron's conclusion that Kron's counts show evidence for evolution at faint magnitudes is confirmed, and it is predicted that some 23d magnitude galaxies have redshifts greater than unity. These may include spheroidal systems, elliptical galaxies, and the bulges of early-type spirals and S0's, seen during their primeval rapid star formation

Autonomous replication of plasmids bearing monkey DNA origin-enriched sequences

International Nuclear Information System (INIS)

Frappier, L.; Zannis-Hadjopoulos, M.

1987-01-01

Twelve clones of origin-enriched sequences (ORS) isolated from early replicating monkey (CV-1) DNA were examined for transient episomal replication in transfected CV-1, COS-7, and HeLa cells. Plasmid DNA was isolated at time intervals after transfection and screened by the Dpn I resistance assay or by the bromodeoxyuridine substitution assay to differentiate between input and replicated DNA. The authors have identified four monkey ORS (ORS3, -8, -9, and -12) that can support plasmid replication in mammalian cells. This replication is carried out in a controlled and semiconservative manner characteristic of mammalian replicons. ORS replication was most efficient in HeLa cells. Electron microscopy showed ORS8 and ORS12 plasmids of the correct size with replication bubbles. Using a unique restriction site in ORS12, we have mapped the replication bubble within the monkey DNA sequence

TakeCARE, a Video to Promote Bystander Behavior on College Campuses: Replication and Extension.

Science.gov (United States)

Jouriles, Ernest N; Sargent, Kelli S; Salis, Katie Lee; Caiozzo, Christina; Rosenfield, David; Cascardi, Michele; Grych, John H; O'Leary, K Daniel; McDonald, Renee

2017-08-01

Previous research has demonstrated that college students who view TakeCARE, a video bystander program designed to encourage students to take action to prevent sexual and relationship violence (i.e., bystander behavior), display more bystander behavior relative to students who view a control video. The current study aimed to replicate and extend these findings by testing two different methods of administering TakeCARE and examining moderators of TakeCARE's effects on bystander behavior. Students at four universities ( n = 557) were randomly assigned to one of three conditions: (a) view TakeCARE in a monitored computer lab, (b) view TakeCARE at their own convenience after receiving an email link to the video, or (c) view a video about study skills (control group). Participants completed measures of bystander behavior at baseline and at a 1-month follow-up. Participants in both TakeCARE conditions reported more bystander behavior at follow-up assessments, compared with participants in the control condition. The beneficial effect of TakeCARE did not differ significantly across administration methods. However, the effects of TakeCARE on bystander behavior were moderated by students' perceptions of campus responsiveness to sexual violence, with more potent effects when students perceived their institution as responsive to reports of sexual violence.

Materials Chemistry and Performance of Silicone-Based Replicating Compounds.

Energy Technology Data Exchange (ETDEWEB)

Brumbach, Michael T.; Mirabal, Alex James; Kalan, Michael; Trujillo, Ana B; Hale, Kevin

2014-11-01

Replicating compounds are used to cast reproductions of surface features on a variety of materials. Replicas allow for quantitative measurements and recordkeeping on parts that may otherwise be difficult to measure or maintain. In this study, the chemistry and replicating capability of several replicating compounds was investigated. Additionally, the residue remaining on material surfaces upon removal of replicas was quantified. Cleaning practices were tested for several different replicating compounds. For all replicating compounds investigated, a thin silicone residue was left by the replica. For some compounds, additional inorganic species could be identified in the residue. Simple solvent cleaning could remove some residue.

Total lymphocyte count as a substitute to cd4 count in management of hiv infected individuals in resource limited society

International Nuclear Information System (INIS)

Daud, M.Y.; Qazi, R.A.

2015-01-01

Pakistan is a resource limited society and gold standard parameters to monitor HIV disease activity are very costly. The objective of the study was to evaluate total lymphocyte count (TLC) as a surrogate to CD4 count to monitor disease activity in HIV/AIDS in resource limited society. Methods: This cross sectional study was carried out at HIV/AIDS treatment centre, Pakistan Institute of Medical Sciences (PIMS), Islamabad. A total of seven hundred and seventy four (774) HIV positive patients were enrolled in this study, and their CD4 count and total lymphocyte count were checked to find any correlation between the two by using Spearman ranked correlation coefficient. Results: The mean CD4 count was (434.30 ± 269.23), with minimum CD4 count of (9.00), and maximum of (1974.00). The mean total lymphocyte count (TLC) was (6764.0052 ± 2364.02) with minimum TLC (1200.00) and maximum TLC was (20200.00). Using the Pearson's correlation (r) there was a significant and positive correlation between TLC and CD4 count. (r2=0.127 and p=0.000) at 0.01 level. Conclusion: Our study showed a significant positive correlation between CD4 count and total lymphocyte count (TLC), so TLC can be used as a marker of disease activity in HIV infected patients. (author)

Bayesian tests to quantify the result of a replication attempt

NARCIS (Netherlands)

Verhagen, J.; Wagenmakers, E.-J.

2014-01-01

Replication attempts are essential to the empirical sciences. Successful replication attempts increase researchers’ confidence in the presence of an effect, whereas failed replication attempts induce skepticism and doubt. However, it is often unclear to what extent a replication attempt results in

Spatio-temporal re-organization of replication foci accompanies replication domain consolidation during human pluripotent stem cell lineage specification

Science.gov (United States)

Wilson, Korey A.; Elefanty, Andrew G.; Stanley, Edouard G.; Gilbert, David M.

2016-01-01

ABSTRACT Lineage specification of both mouse and human pluripotent stem cells (PSCs) is accompanied by spatial consolidation of chromosome domains and temporal consolidation of their replication timing. Replication timing and chromatin organization are both established during G1 phase at the timing decision point (TDP). Here, we have developed live cell imaging tools to track spatio-temporal replication domain consolidation during differentiation. First, we demonstrate that the fluorescence ubiquitination cell cycle indicator (Fucci) system is incapable of demarcating G1/S or G2/M cell cycle transitions. Instead, we employ a combination of fluorescent PCNA to monitor S phase progression, cytokinesis to demarcate mitosis, and fluorescent nucleotides to label early and late replication foci and track their 3D organization into sub-nuclear chromatin compartments throughout all cell cycle transitions. We find that, as human PSCs differentiate, the length of S phase devoted to replication of spatially clustered replication foci increases, coincident with global compartmentalization of domains into temporally clustered blocks of chromatin. Importantly, re-localization and anchorage of domains was completed prior to the onset of S phase, even in the context of an abbreviated PSC G1 phase. This approach can also be employed to investigate cell fate transitions in single PSCs, which could be seen to differentiate preferentially from G1 phase. Together, our results establish real-time, live-cell imaging methods for tracking cell cycle transitions during human PSC differentiation that can be applied to study chromosome domain consolidation and other aspects of lineage specification. PMID:27433885

A counting-card circuit based on PCI bus

International Nuclear Information System (INIS)

Shi Jing; Li Yong; Chinese Academy of Sciences, Lanzhou; Su Hong; Dong Chengfu; Li Xiaogang; Ma Xiaoli

2004-01-01

A counting-card circuit based on PCI bus that we developed recently used for advanced personal computer will be introduced in this paper briefly. The maximum count capacity of this counting-card is 10 9 -1, ranging from 0 to 999 999 999, the maximum counting time range, 1 x 10 6 s, can be set in 1 cycle, the maximum counting rate is 20 MHz for positive input. (authors)

TU-FG-209-03: Exploring the Maximum Count Rate Capabilities of Photon Counting Arrays Based On Polycrystalline Silicon

Energy Technology Data Exchange (ETDEWEB)

Liang, A K; Koniczek, M; Antonuk, L E; El-Mohri, Y; Zhao, Q [University of Michigan, Ann Arbor, MI (United States)

2016-06-15

Purpose: Photon counting arrays (PCAs) offer several advantages over conventional, fluence-integrating x-ray imagers, such as improved contrast by means of energy windowing. For that reason, we are exploring the feasibility and performance of PCA pixel circuitry based on polycrystalline silicon. This material, unlike the crystalline silicon commonly used in photon counting detectors, lends itself toward the economic manufacture of radiation tolerant, monolithic large area (e.g., ∼43×43 cm2) devices. In this presentation, exploration of maximum count rate, a critical performance parameter for such devices, is reported. Methods: Count rate performance for a variety of pixel circuit designs was explored through detailed circuit simulations over a wide range of parameters (including pixel pitch and operating conditions) with the additional goal of preserving good energy resolution. The count rate simulations assume input events corresponding to a 72 kVp x-ray spectrum with 20 mm Al filtration interacting with a CZT detector at various input flux rates. Output count rates are determined at various photon energy threshold levels, and the percentage of counts lost (e.g., due to deadtime or pile-up) is calculated from the ratio of output to input counts. The energy resolution simulations involve thermal and flicker noise originating from each circuit element in a design. Results: Circuit designs compatible with pixel pitches ranging from 250 to 1000 µm that allow count rates over a megacount per second per pixel appear feasible. Such rates are expected to be suitable for radiographic and fluoroscopic imaging. Results for the analog front-end circuitry of the pixels show that acceptable energy resolution can also be achieved. Conclusion: PCAs created using polycrystalline silicon have the potential to offer monolithic large-area detectors with count rate performance comparable to those of crystalline silicon detectors. Further improvement through detailed circuit

A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation.

Science.gov (United States)

Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

2018-01-01

Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types.

A Molecular Toolbox to Engineer Site-Specific DNA Replication Perturbation

DEFF Research Database (Denmark)

Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

2018-01-01

" impediment to DNA replication. To further develop this system as a versatile tool, we describe a set of reagents and a detailed protocol that can be used to engineer Tus-Ter barriers into any locus in the budding yeast genome. Because the Tus-Ter complex is a bipartite system with intrinsic DNA replication......Site-specific arrest of DNA replication is a useful tool for analyzing cellular responses to DNA replication perturbation. The E. coli Tus-Ter replication barrier can be reconstituted in eukaryotic cells as a system to engineer an unscheduled collision between a replication fork and an "alien......-blocking activity, the reagents and protocols developed and validated in yeast could also be optimized to engineer site-specific replication fork barriers into other eukaryotic cell types....

Effects of Student Pairing and Public Review on Physical Activity during School Recess

Science.gov (United States)

Zerger, Heather M.; Miller, Bryon G.; Valbuena, Diego; Miltenberger, Raymond G.

2017-01-01

The purpose of this study was to evaluate the effects of student pairing and feedback during recess on children's step counts. During baseline, participants wore a sealed pedometer during recess. During intervention, we paired participants with higher step counts with participants with lower step counts. We encouraged teams to compete for the…

Recursive algorithms for phylogenetic tree counting.

Science.gov (United States)

Gavryushkina, Alexandra; Welch, David; Drummond, Alexei J

2013-10-28

In Bayesian phylogenetic inference we are interested in distributions over a space of trees. The number of trees in a tree space is an important characteristic of the space and is useful for specifying prior distributions. When all samples come from the same time point and no prior information available on divergence times, the tree counting problem is easy. However, when fossil evidence is used in the inference to constrain the tree or data are sampled serially, new tree spaces arise and counting the number of trees is more difficult. We describe an algorithm that is polynomial in the number of sampled individuals for counting of resolutions of a constraint tree assuming that the number of constraints is fixed. We generalise this algorithm to counting resolutions of a fully ranked constraint tree. We describe a quadratic algorithm for counting the number of possible fully ranked trees on n sampled individuals. We introduce a new type of tree, called a fully ranked tree with sampled ancestors, and describe a cubic time algorithm for counting the number of such trees on n sampled individuals. These algorithms should be employed for Bayesian Markov chain Monte Carlo inference when fossil data are included or data are serially sampled.

Structural properties of replication origins in yeast DNA sequences

International Nuclear Information System (INIS)

Cao Xiaoqin; Zeng Jia; Yan Hong

2008-01-01

Sequence-dependent DNA flexibility is an important structural property originating from the DNA 3D structure. In this paper, we investigate the DNA flexibility of the budding yeast (S. Cerevisiae) replication origins on a genome-wide scale using flexibility parameters from two different models, the trinucleotide and the tetranucleotide models. Based on analyzing average flexibility profiles of 270 replication origins, we find that yeast replication origins are significantly rigid compared with their surrounding genomic regions. To further understand the highly distinctive property of replication origins, we compare the flexibility patterns between yeast replication origins and promoters, and find that they both contain significantly rigid DNAs. Our results suggest that DNA flexibility is an important factor that helps proteins recognize and bind the target sites in order to initiate DNA replication. Inspired by the role of the rigid region in promoters, we speculate that the rigid replication origins may facilitate binding of proteins, including the origin recognition complex (ORC), Cdc6, Cdt1 and the MCM2-7 complex

From structure to mechanism—understanding initiation of DNA replication

Science.gov (United States)

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L. Maximilian; Schneider, Sarah; Speck, Christian

2017-01-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2–7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. PMID:28717046

MYC and the Control of DNA Replication

Science.gov (United States)

Dominguez-Sola, David; Gautier, Jean

2014-01-01

The MYC oncogene is a multifunctional protein that is aberrantly expressed in a significant fraction of tumors from diverse tissue origins. Because of its multifunctional nature, it has been difficult to delineate the exact contributions of MYC’s diverse roles to tumorigenesis. Here, we review the normal role of MYC in regulating DNA replication as well as its ability to generate DNA replication stress when overexpressed. Finally, we discuss the possible mechanisms by which replication stress induced by aberrant MYC expression could contribute to genomic instability and cancer. PMID:24890833

Organization of Replication of Ribosomal DNA in Saccharomyces cerevisiae

NARCIS (Netherlands)

Linskens, Maarten H.K.; Huberman, Joel A.

1988-01-01

Using recently developed replicon mapping techniques, we have analyzed the replication of the ribosomal DNA in Saccharomyces cerevisiae. The results show that (i) the functional origin of replication colocalizes with an autonomously replicating sequence element previously mapped to the

Photon-counting image sensors

CERN Document Server

Teranishi, Nobukazu; Theuwissen, Albert; Stoppa, David; Charbon, Edoardo

2017-01-01

The field of photon-counting image sensors is advancing rapidly with the development of various solid-state image sensor technologies including single photon avalanche detectors (SPADs) and deep-sub-electron read noise CMOS image sensor pixels. This foundational platform technology will enable opportunities for new imaging modalities and instrumentation for science and industry, as well as new consumer applications. Papers discussing various photon-counting image sensor technologies and selected new applications are presented in this all-invited Special Issue.

Cyclophilin B facilitates the replication of Orf virus.

Science.gov (United States)

Zhao, Kui; Li, Jida; He, Wenqi; Song, Deguang; Zhang, Ximu; Zhang, Di; Zhou, Yanlong; Gao, Feng

2017-06-15

Viruses interact with host cellular factors to construct a more favourable environment for their efficient replication. Expression of cyclophilin B (CypB), a cellular peptidyl-prolyl cis-trans isomerase (PPIase), was found to be significantly up-regulated. Recently, a number of studies have shown that CypB is important in the replication of several viruses, including Japanese encephalitis virus (JEV), hepatitis C virus (HCV) and human papillomavirus type 16 (HPV 16). However, the function of cellular CypB in ORFV replication has not yet been explored. Suppression subtractive hybridization (SSH) technique was applied to identify genes differentially expressed in the ORFV-infected MDBK cells at an early phase of infection. Cellular CypB was confirmed to be significantly up-regulated by quantitative reverse transcription-PCR (qRT-PCR) analysis and Western blotting. The role of CypB in ORFV infection was further determined using Cyclosporin A (CsA) and RNA interference (RNAi). Effect of CypB gene silencing on ORFV replication by 50% tissue culture infectious dose (TCID 50 ) assay and qRT-PCR detection. In the present study, CypB was found to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection. Cyclosporin A (CsA) exhibited suppressive effects on ORFV replication through the inhibition of CypB. Silencing of CypB gene inhibited the replication of ORFV in MDBK cells. In conclusion, these data suggest that CypB is critical for the efficient replication of the ORFV genome. Cellular CypB was confirmed to be significantly up-regulated in the ORFV-infected MDBK cells at an early phase of infection, which could effectively facilitate the replication of ORFV.

Autophagy Facilitates Salmonella Replication in HeLa Cells

Science.gov (United States)

Yu, Hong B.; Croxen, Matthew A.; Marchiando, Amanda M.; Ferreira, Rosana B. R.; Cadwell, Ken; Foster, Leonard J.; Finlay, B. Brett

2014-01-01

ABSTRACT Autophagy is a process whereby a double-membrane structure (autophagosome) engulfs unnecessary cytosolic proteins, organelles, and invading pathogens and delivers them to the lysosome for degradation. We examined the fate of cytosolic Salmonella targeted by autophagy and found that autophagy-targeted Salmonella present in the cytosol of HeLa cells correlates with intracellular bacterial replication. Real-time analyses revealed that a subset of cytosolic Salmonella extensively associates with autophagy components p62 and/or LC3 and replicates quickly, whereas intravacuolar Salmonella shows no or very limited association with p62 or LC3 and replicates much more slowly. Replication of cytosolic Salmonella in HeLa cells is significantly decreased when autophagy components are depleted. Eventually, hyperreplication of cytosolic Salmonella potentiates cell detachment, facilitating the dissemination of Salmonella to neighboring cells. We propose that Salmonella benefits from autophagy for its cytosolic replication in HeLa cells. PMID:24618251

Stabilization of Reversed Replication Forks by Telomerase Drives Telomere Catastrophe.

Science.gov (United States)

Margalef, Pol; Kotsantis, Panagiotis; Borel, Valerie; Bellelli, Roberto; Panier, Stephanie; Boulton, Simon J

2018-01-25

Telomere maintenance critically depends on the distinct activities of telomerase, which adds telomeric repeats to solve the end replication problem, and RTEL1, which dismantles DNA secondary structures at telomeres to facilitate replisome progression. Here, we establish that reversed replication forks are a pathological substrate for telomerase and the source of telomere catastrophe in Rtel1 -/- cells. Inhibiting telomerase recruitment to telomeres, but not its activity, or blocking replication fork reversal through PARP1 inhibition or depleting UBC13 or ZRANB3 prevents the rapid accumulation of dysfunctional telomeres in RTEL1-deficient cells. In this context, we establish that telomerase binding to reversed replication forks inhibits telomere replication, which can be mimicked by preventing replication fork restart through depletion of RECQ1 or PARG. Our results lead us to propose that telomerase inappropriately binds to and inhibits restart of reversed replication forks within telomeres, which compromises replication and leads to critically short telomeres. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Chronic DNA Replication Stress Reduces Replicative Lifespan of Cells by TRP53-Dependent, microRNA-Assisted MCM2-7 Downregulation.

Directory of Open Access Journals (Sweden)

Gongshi Bai

2016-01-01

Full Text Available Circumstances that compromise efficient DNA replication, such as disruptions to replication fork progression, cause a state known as DNA replication stress (RS. Whereas normally proliferating cells experience low levels of RS, excessive RS from intrinsic or extrinsic sources can trigger cell cycle arrest and senescence. Here, we report that a key driver of RS-induced senescence is active downregulation of the Minichromosome Maintenance 2-7 (MCM2-7 factors that are essential for replication origin licensing and which constitute the replicative helicase core. Proliferating cells produce high levels of MCM2-7 that enable formation of dormant origins that can be activated in response to acute, experimentally-induced RS. However, little is known about how physiological RS levels impact MCM2-7 regulation. We found that chronic exposure of primary mouse embryonic fibroblasts (MEFs to either genetically-encoded or environmentally-induced RS triggered gradual MCM2-7 repression, followed by inhibition of replication and senescence that could be accelerated by MCM hemizygosity. The MCM2-7 reduction in response to RS is TRP53-dependent, and involves a group of Trp53-dependent miRNAs, including the miR-34 family, that repress MCM expression in replication-stressed cells before they undergo terminal cell cycle arrest. miR-34 ablation partially rescued MCM2-7 downregulation and genomic instability in mice with endogenous RS. Together, these data demonstrate that active MCM2-7 repression is a physiologically important mechanism for RS-induced cell cycle arrest and genome maintenance on an organismal level.

Hepatitis C Virus Replication Depends on Endosomal Cholesterol Homeostasis.

Science.gov (United States)

Stoeck, Ina Karen; Lee, Ji-Young; Tabata, Keisuke; Romero-Brey, Inés; Paul, David; Schult, Philipp; Lohmann, Volker; Kaderali, Lars; Bartenschlager, Ralf

2018-01-01

Similar to other positive-strand RNA viruses, hepatitis C virus (HCV) causes massive rearrangements of intracellular membranes, resulting in a membranous web (MW) composed of predominantly double-membrane vesicles (DMVs), the presumed sites of RNA replication. DMVs are enriched for cholesterol, but mechanistic details on the source and recruitment of cholesterol to the viral replication organelle are only partially known. Here we focused on selected lipid transfer proteins implicated in direct lipid transfer at various endoplasmic reticulum (ER)-membrane contact sites. RNA interference (RNAi)-mediated knockdown identified several hitherto unknown HCV dependency factors, such as steroidogenic acute regulatory protein-related lipid transfer domain protein 3 (STARD3), oxysterol-binding protein-related protein 1A and -B (OSBPL1A and -B), and Niemann-Pick-type C1 (NPC1), all residing at late endosome and lysosome membranes and required for efficient HCV RNA replication but not for replication of the closely related dengue virus. Focusing on NPC1, we found that knockdown or pharmacological inhibition caused cholesterol entrapment in lysosomal vesicles concomitant with decreased cholesterol abundance at sites containing the viral replicase factor NS5A. In untreated HCV-infected cells, unesterified cholesterol accumulated at the perinuclear region, partially colocalizing with NS5A at DMVs, arguing for NPC1-mediated endosomal cholesterol transport to the viral replication organelle. Consistent with cholesterol being an important structural component of DMVs, reducing NPC1-dependent endosomal cholesterol transport impaired MW integrity. This suggests that HCV usurps lipid transfer proteins, such as NPC1, at ER-late endosome/lysosome membrane contact sites to recruit cholesterol to the viral replication organelle, where it contributes to MW functionality. IMPORTANCE A key feature of the replication of positive-strand RNA viruses is the rearrangement of the host cell

Platelet counting using the Coulter electronic counter.

Science.gov (United States)

Eggleton, M J; Sharp, A A

1963-03-01

A method for counting platelets in dilutions of platelet-rich plasm using the Coulter electronic counter is described.(1) The results obtained show that such platelet counts are at least as accurate as the best methods of visual counting. The various technical difficulties encountered are discussed.

Automated uranium analysis by delayed-neutron counting

International Nuclear Information System (INIS)

Kunzendorf, H.; Loevborg, L.; Christiansen, E.M.

1980-10-01

Automated uranium analysis by fission-induced delayed-neutron counting is described. A short description is given of the instrumentation including transfer system, process control, irradiation and counting sites, and computer operations. Characteristic parameters of the facility (sample preparations, background, and standards) are discussed. A sensitivity of 817 +- 22 counts per 10 -6 g U is found using irradiation, delay, and counting times of 20 s, 5 s, and 10 s, respectively. Presicion is generally less than 1% for normal geological samples. Critical level and detection limits for 7.5 g samples are 8 and 16 ppb, respectively. The importance of some physical and elemental interferences are outlined. Dead-time corrections of measured count rates are necessary and a polynomical expression is used for count rates up to 10 5 . The presence of rare earth elements is regarded as the most important elemental interference. A typical application is given and other areas of application are described. (auther)

Count rate effect in proportional counters

International Nuclear Information System (INIS)

Bednarek, B.

1980-01-01

A new concept is presented explaining changes in spectrometric parameters of proportional counters which occur due to varying count rate. The basic feature of this concept is that the gas gain of the counter remains constant in a wide range of count rate and that the decrease in the pulse amplitude and the detorioration of the energy resolution observed are the results of changes in the shape of original current pulses generated in the active volume of the counter. In order to confirm the validity of this statement, measurements of the gas amplification factor have been made in a wide count rate range. It is shown that above a certain critical value the gas gain depends on both the operating voltage and the count rate. (author)

Geminin: a major DNA replication safeguard in higher eukaryotes

DEFF Research Database (Denmark)

Melixetian, Marina; Helin, Kristian

2004-01-01

Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

Resonance ionization spectroscopy: Counting noble gas atoms

International Nuclear Information System (INIS)

Hurst, G.S.; Payne, M.G.; Chen, C.H.; Willis, R.D.; Lehmann, B.E.; Kramer, S.D.

1981-01-01

The purpose of this paper is to describe new work on the counting of noble gas atoms, using lasers for the selective ionization and detectors for counting individual particles (electrons or positive ions). When positive ions are counted, various kinds of mass analyzers (magnetic, quadrupole, or time-of-flight) can be incorporated to provide A selectivity. We show that a variety of interesting and important applications can be made with atom-counting techniques which are both atomic number (Z) and mass number (A) selective. (orig./FKS)

Optical tweezers reveal how proteins alter replication

Science.gov (United States)

Chaurasiya, Kathy

Single molecule force spectroscopy is a powerful method that explores the DNA interaction properties of proteins involved in a wide range of fundamental biological processes such as DNA replication, transcription, and repair. We use optical tweezers to capture and stretch a single DNA molecule in the presence of proteins that bind DNA and alter its mechanical properties. We quantitatively characterize the DNA binding mechanisms of proteins in order to provide a detailed understanding of their function. In this work, we focus on proteins involved in replication of Escherichia coli (E. coli ), endogenous eukaryotic retrotransposons Ty3 and LINE-1, and human immunodeficiency virus (HIV). DNA polymerases replicate the entire genome of the cell, and bind both double-stranded DNA (dsDNA) and single-stranded DNA (ssDNA) during DNA replication. The replicative DNA polymerase in the widely-studied model system E. coli is the DNA polymerase III subunit alpha (DNA pol III alpha). We use optical tweezers to determine that UmuD, a protein that regulates bacterial mutagenesis through its interactions with DNA polymerases, specifically disrupts alpha binding to ssDNA. This suggests that UmuD removes alpha from its ssDNA template to allow DNA repair proteins access to the damaged DNA, and to facilitate exchange of the replicative polymerase for an error-prone translesion synthesis (TLS) polymerase that inserts nucleotides opposite the lesions, so that bacterial DNA replication may proceed. This work demonstrates a biophysical mechanism by which E. coli cells tolerate DNA damage. Retroviruses and retrotransposons reproduce by copying their RNA genome into the nuclear DNA of their eukaryotic hosts. Retroelements encode proteins called nucleic acid chaperones, which rearrange nucleic acid secondary structure and are therefore required for successful replication. The chaperone activity of these proteins requires strong binding affinity for both single- and double-stranded nucleic

From structure to mechanism-understanding initiation of DNA replication.

Science.gov (United States)

Riera, Alberto; Barbon, Marta; Noguchi, Yasunori; Reuter, L Maximilian; Schneider, Sarah; Speck, Christian

2017-06-01

DNA replication results in the doubling of the genome prior to cell division. This process requires the assembly of 50 or more protein factors into a replication fork. Here, we review recent structural and biochemical insights that start to explain how specific proteins recognize DNA replication origins, load the replicative helicase on DNA, unwind DNA, synthesize new DNA strands, and reassemble chromatin. We focus on the minichromosome maintenance (MCM2-7) proteins, which form the core of the eukaryotic replication fork, as this complex undergoes major structural rearrangements in order to engage with DNA, regulate its DNA-unwinding activity, and maintain genome stability. © 2017 Riera et al.; Published by Cold Spring Harbor Laboratory Press.

Improving the counting efficiency in time-correlated single photon counting experiments by dead-time optimization

Energy Technology Data Exchange (ETDEWEB)

Peronio, P.; Acconcia, G.; Rech, I.; Ghioni, M. [Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano (Italy)

2015-11-15

Time-Correlated Single Photon Counting (TCSPC) has been long recognized as the most sensitive method for fluorescence lifetime measurements, but often requiring “long” data acquisition times. This drawback is related to the limited counting capability of the TCSPC technique, due to pile-up and counting loss effects. In recent years, multi-module TCSPC systems have been introduced to overcome this issue. Splitting the light into several detectors connected to independent TCSPC modules proportionally increases the counting capability. Of course, multi-module operation also increases the system cost and can cause space and power supply problems. In this paper, we propose an alternative approach based on a new detector and processing electronics designed to reduce the overall system dead time, thus enabling efficient photon collection at high excitation rate. We present a fast active quenching circuit for single-photon avalanche diodes which features a minimum dead time of 12.4 ns. We also introduce a new Time-to-Amplitude Converter (TAC) able to attain extra-short dead time thanks to the combination of a scalable array of monolithically integrated TACs and a sequential router. The fast TAC (F-TAC) makes it possible to operate the system towards the upper limit of detector count rate capability (∼80 Mcps) with reduced pile-up losses, addressing one of the historic criticisms of TCSPC. Preliminary measurements on the F-TAC are presented and discussed.

Murine leukemia virus (MLV replication monitored with fluorescent proteins

Directory of Open Access Journals (Sweden)

Bittner Alexandra

2004-12-01

Full Text Available Abstract Background Cancer gene therapy will benefit from vectors that are able to replicate in tumor tissue and cause a bystander effect. Replication-competent murine leukemia virus (MLV has been described to have potential as cancer therapeutics, however, MLV infection does not cause a cytopathic effect in the infected cell and viral replication can only be studied by immunostaining or measurement of reverse transcriptase activity. Results We inserted the coding sequences for green fluorescent protein (GFP into the proline-rich region (PRR of the ecotropic envelope protein (Env and were able to fluorescently label MLV. This allowed us to directly monitor viral replication and attachment to target cells by flow cytometry. We used this method to study viral replication of recombinant MLVs and split viral genomes, which were generated by replacement of the MLV env gene with the red fluorescent protein (RFP and separately cloning GFP-Env into a retroviral vector. Co-transfection of both plasmids into target cells resulted in the generation of semi-replicative vectors, and the two color labeling allowed to determine the distribution of the individual genomes in the target cells and was indicative for the occurrence of recombination events. Conclusions Fluorescently labeled MLVs are excellent tools for the study of factors that influence viral replication and can be used to optimize MLV-based replication-competent viruses or vectors for gene therapy.

Cytoplasmic ATR Activation Promotes Vaccinia Virus Genome Replication

Directory of Open Access Journals (Sweden)

Antonio Postigo

2017-05-01

Full Text Available In contrast to most DNA viruses, poxviruses replicate their genomes in the cytoplasm without host involvement. We find that vaccinia virus induces cytoplasmic activation of ATR early during infection, before genome uncoating, which is unexpected because ATR plays a fundamental nuclear role in maintaining host genome integrity. ATR, RPA, INTS7, and Chk1 are recruited to cytoplasmic DNA viral factories, suggesting canonical ATR pathway activation. Consistent with this, pharmacological and RNAi-mediated inhibition of canonical ATR signaling suppresses genome replication. RPA and the sliding clamp PCNA interact with the viral polymerase E9 and are required for DNA replication. Moreover, the ATR activator TOPBP1 promotes genome replication and associates with the viral replisome component H5. Our study suggests that, in contrast to long-held beliefs, vaccinia recruits conserved components of the eukaryote DNA replication and repair machinery to amplify its genome in the host cytoplasm.

The DNA Replication Stress Hypothesis of Alzheimer’s Disease

Directory of Open Access Journals (Sweden)

Yuri B. Yurov

2011-01-01

Full Text Available A well-recognized theory of Alzheimer’s disease (AD pathogenesis suggests ectopic cell cycle events to mediate neurodegeneration. Vulnerable neurons of the AD brain exhibit biomarkers of cell cycle progression and DNA replication suggesting a reentry into the cell cycle. Chromosome reduplication without proper cell cycle completion and mitotic division probably causes neuronal cell dysfunction and death. However, this theory seems to require some inputs in accordance with the generally recognized amyloid cascade theory as well as to explain causes and consequences of genomic instability (aneuploidy in the AD brain. We propose that unscheduled and incomplete DNA replication (replication stress destabilizes (epigenomic landscape in the brain and leads to DNA replication “catastrophe” causing cell death during the S phase (replicative cell death. DNA replication stress can be a key element of the pathogenetic cascade explaining the interplay between ectopic cell cycle events and genetic instabilities in the AD brain. Abnormal cell cycle reentry and somatic genome variations can be used for updating the cell cycle theory introducing replication stress as a missing link between cell genetics and neurobiology of AD.

On the cross-cultural replicability of the resilient, undercontrolled, and overcontrolled personality types.

Science.gov (United States)

Alessandri, Guido; Vecchione, Michele; Donnellan, Brent M; Eisenberg, Nancy; Caprara, Gian Vittorio; Cieciuch, Jan

2014-08-01

Personality types reflect typical configurations of personality attributes within individuals. Over the last 20 years, researchers have identified a set of three replicable personality types: resilient (R), undercontrolled (U), and overcontrolled (O) types. In this study, we examined the cross-cultural replicability of the RUO types in Italy, Poland, Spain, and the United States. Personality types were identified using cluster analyses of Big Five profiles in large samples of college students from Italy (n = 322), the United States (n = 499), Spain (n = 420), and Poland (n = 235). Prior to clustering the profiles, the measurement invariance of the Big Five measure across samples was tested. We found evidence for the RUO types in all four samples. The three-cluster solution showed a better fit over alternative solutions and had a relatively high degree of cross-cultural generalizability. The RUO types are evident in samples from four countries with distinct linguistic and cultural traditions. Results were discussed in light of the importance of considering how traits are organized within individuals for advancing contemporary personality psychology. © 2013 Wiley Periodicals, Inc.

CalCOFI Larvae Counts Positive Tows

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Fish larvae counts and standardized counts for eggs captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets],...

An automated image analysis system to measure and count organisms in laboratory microcosms.

Directory of Open Access Journals (Sweden)

François Mallard

Full Text Available 1. Because of recent technological improvements in the way computer and digital camera perform, the potential use of imaging for contributing to the study of communities, populations or individuals in laboratory microcosms has risen enormously. However its limited use is due to difficulties in the automation of image analysis. 2. We present an accurate and flexible method of image analysis for detecting, counting and measuring moving particles on a fixed but heterogeneous substrate. This method has been specifically designed to follow individuals, or entire populations, in experimental laboratory microcosms. It can be used in other applications. 3. The method consists in comparing multiple pictures of the same experimental microcosm in order to generate an image of the fixed background. This background is then used to extract, measure and count the moving organisms, leaving out the fixed background and the motionless or dead individuals. 4. We provide different examples (springtails, ants, nematodes, daphnia to show that this non intrusive method is efficient at detecting organisms under a wide variety of conditions even on faintly contrasted and heterogeneous substrates. 5. The repeatability and reliability of this method has been assessed using experimental populations of the Collembola Folsomia candida. 6. We present an ImageJ plugin to automate the analysis of digital pictures of laboratory microcosms. The plugin automates the successive steps of the analysis and recursively analyses multiple sets of images, rapidly producing measurements from a large number of replicated microcosms.

Comparison of the effects of nafenopin, methyl clofenapate, WY-14,643 and clofibric acid on peroxisome proliferation and replicative DNA synthesis in rat liver

International Nuclear Information System (INIS)

Price, R.J.; Evans, J.G.; Lake, B.G.; Gangolli, S.D.

1991-01-01

A wide variety of chemicals have been shown to produce hepatic peroxisome proliferation (PP) in the rat and certain of these compounds are also hepatocarcinogens. In this study the authors have investigated the relationship between PP and cell replication in the rat liver. Male Sprague-Dawley rats were fed control diet or diet containing either 0.0125 and 0.05% nafenopin (NAF), 0.05% methyl clofenapate (MC), 0.025% Wy-14,643 (WY) or 0.5% clofibric acid (CA) for 1 and 15 wk. All four compounds produced marked liver enlargement and a sustained induction of peroxisomal (palmitoyl-CoA oxidation) and microsomal (lauric acid 12-hydroxylase) fatty acid oxidizing enzyme activities. Enzyme induction was less marked with 0.0125% NAF than with 0.05% NAF which was similar to that produced by the other three compounds. Replicative DNA synthesis was studied by implanting 7 day Alzet osmotic pumps containing [ 3 H]thymidine during wk 0-1 and 14-15. After 1 wk replicative DNA synthesis (assessed as radioactivity incorporated into homogenate DNA by scintillation counting) was increased in all treatment groups to 170-325% of control levels. Hepatocyte Labelling Index (determined by autoradiography of liver sections) was increased in all treated groups. After 15 wk hepatic DNA radioactivity levels were 155 and 200% of control in MC and WY treated rats, respectively, whereas NAF and CA had no effect. These results demonstrate that the relationship between the magnitude of PP and induction of cell replication depends on the compound being studied and that some peroxisome proliferators produce sustained stimulation of replicative DNA synthesis in the rat

Set of counts by scintillations for atmospheric samplings

International Nuclear Information System (INIS)

Appriou, D.; Doury, A.

1962-01-01

The author reports the development of a scintillation-based counting assembly with the following characteristics: a photo-multiplier with a wide photo-cathode, a thin plastic scintillator for the counting of beta + alpha (and possibility of mounting an alpha scintillator), a relatively small own motion with respect to activities to be counted, a weakly varying efficiency. The authors discuss the counting objective, present equipment tests (counter, proportional amplifier and pre-amplifier, input drawer). They describe the apparatus operation, discuss the selection of scintillators, report the study of the own movement (electron-based background noise, total background noise, background noise reduction), discuss counts (influence of the external source, sensitivity to alpha radiations, counting homogeneity, minimum detectable activity) and efficiencies

Track counting in radon dosimetry

International Nuclear Information System (INIS)

Fesenbeck, Ingo; Koehler, Bernd; Reichert, Klaus-Martin

2013-01-01

The newly developed, computer-controlled track counting system is capable of imaging and analyzing the entire area of nuclear track detectors. The high optical resolution allows a new analysis approach for the process of automated counting using digital image processing technologies. This way, higher exposed detectors can be evaluated reliably by an automated process as well. (orig.)

Counting and integrating microelectronics development for direct conversion X-ray imaging

Energy Technology Data Exchange (ETDEWEB)

Kraft, E.

2008-02-15

A novel signal processing concept for X-ray imaging with directly converting pixelated semiconductor sensors is presented. The novelty of this approach compared to existing concepts is the combination of charge integration and photon counting in every single pixel. Simultaneous operation of both signal processing chains extends the dynamic range beyond the limits of the individual schemes and allows determination of the mean photon energy. Medical applications such as X-ray computed tomography can benefit from this additional spectral information through improved contrast and the ability to determine the hardening of the tube spectrum due to attenuation by the scanned object. A prototype chip in 0.35-micrometer technology has been successfully tested. The pixel electronics are designed using a low-swing differential current mode logic. Key element is a configurable feedback circuit for the charge sensitive amplifier which provides continuous reset, leakage current compensation and replicates the input signal for the integrator. The thesis focusses on the electronic characterization of a second generation prototype chip and gives a detailed discussion of the circuit design. (orig.)

Counting and integrating microelectronics development for direct conversion X-ray imaging

International Nuclear Information System (INIS)

Kraft, E.

2008-02-01

A novel signal processing concept for X-ray imaging with directly converting pixelated semiconductor sensors is presented. The novelty of this approach compared to existing concepts is the combination of charge integration and photon counting in every single pixel. Simultaneous operation of both signal processing chains extends the dynamic range beyond the limits of the individual schemes and allows determination of the mean photon energy. Medical applications such as X-ray computed tomography can benefit from this additional spectral information through improved contrast and the ability to determine the hardening of the tube spectrum due to attenuation by the scanned object. A prototype chip in 0.35-micrometer technology has been successfully tested. The pixel electronics are designed using a low-swing differential current mode logic. Key element is a configurable feedback circuit for the charge sensitive amplifier which provides continuous reset, leakage current compensation and replicates the input signal for the integrator. The thesis focusses on the electronic characterization of a second generation prototype chip and gives a detailed discussion of the circuit design. (orig.)

Regulated eukaryotic DNA replication origin firing with purified proteins.

Science.gov (United States)

Yeeles, Joseph T P; Deegan, Tom D; Janska, Agnieszka; Early, Anne; Diffley, John F X

2015-03-26

Eukaryotic cells initiate DNA replication from multiple origins, which must be tightly regulated to promote precise genome duplication in every cell cycle. To accomplish this, initiation is partitioned into two temporally discrete steps: a double hexameric minichromosome maintenance (MCM) complex is first loaded at replication origins during G1 phase, and then converted to the active CMG (Cdc45-MCM-GINS) helicase during S phase. Here we describe the reconstitution of budding yeast DNA replication initiation with 16 purified replication factors, made from 42 polypeptides. Origin-dependent initiation recapitulates regulation seen in vivo. Cyclin-dependent kinase (CDK) inhibits MCM loading by phosphorylating the origin recognition complex (ORC) and promotes CMG formation by phosphorylating Sld2 and Sld3. Dbf4-dependent kinase (DDK) promotes replication by phosphorylating MCM, and can act either before or after CDK. These experiments define the minimum complement of proteins, protein kinase substrates and co-factors required for regulated eukaryotic DNA replication.

DNA replication stress and cancer chemotherapy.

Science.gov (United States)

Kitao, Hiroyuki; Iimori, Makoto; Kataoka, Yuki; Wakasa, Takeshi; Tokunaga, Eriko; Saeki, Hiroshi; Oki, Eiji; Maehara, Yoshihiko

2018-02-01

DNA replication is one of the fundamental biological processes in which dysregulation can cause genome instability. This instability is one of the hallmarks of cancer and confers genetic diversity during tumorigenesis. Numerous experimental and clinical studies have indicated that most tumors have experienced and overcome the stresses caused by the perturbation of DNA replication, which is also referred to as DNA replication stress (DRS). When we consider therapeutic approaches for tumors, it is important to exploit the differences in DRS between tumor and normal cells. In this review, we introduce the current understanding of DRS in tumors and discuss the underlying mechanism of cancer therapy from the aspect of DRS. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

CalCOFI Egg Counts Positive Tows

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Fish egg counts and standardized counts for eggs captured in CalCOFI icthyoplankton nets (primarily vertical [Calvet or Pairovet], oblique [bongo or ring nets], and...

Regression Models For Multivariate Count Data.

Science.gov (United States)

Zhang, Yiwen; Zhou, Hua; Zhou, Jin; Sun, Wei

2017-01-01

Data with multivariate count responses frequently occur in modern applications. The commonly used multinomial-logit model is limiting due to its restrictive mean-variance structure. For instance, analyzing count data from the recent RNA-seq technology by the multinomial-logit model leads to serious errors in hypothesis testing. The ubiquity of over-dispersion and complicated correlation structures among multivariate counts calls for more flexible regression models. In this article, we study some generalized linear models that incorporate various correlation structures among the counts. Current literature lacks a treatment of these models, partly due to the fact that they do not belong to the natural exponential family. We study the estimation, testing, and variable selection for these models in a unifying framework. The regression models are compared on both synthetic and real RNA-seq data.

Evaluating the effectiveness of real-time feedback on the bedside hand hygiene behaviors of nursing students.

Science.gov (United States)

Ott, Lora K; Irani, Vida R

2015-05-01

Traditional hand hygiene teaching methods lack long-term effectiveness. A longitudinal, within-subject design explored the influence of real-time hand microbe feedback and a critical-thinking decision exercise on nursing student hand hygiene behaviors. In three community hospitals, the students' (n = 68) hand swabs were tested for normal flora, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant Enterococcus at three time points. Students completed the Partnering to Heal (PTH) online exercise on hospital-acquired infection prevention decisions. Normal flora colony counts decreased across the semester and MRSA-positive cultures increased in frequency and colony counts. MRSA-positive cultures were not associated with caring for patients in isolation precautions. Significantly higher colony counts were noted in the students who completed the PTH than those who did not complete the PTH. This study explores innovative pedagogy bringing the nonvisible microbial risk to the consciousness of nursing students in an attempt to change hand hygiene behaviors. Copyright 2015, SLACK Incorporated.

Termination of DNA replication forks: "Breaking up is hard to do".

Science.gov (United States)

Bailey, Rachael; Priego Moreno, Sara; Gambus, Agnieszka

2015-01-01

To ensure duplication of the entire genome, eukaryotic DNA replication initiates from thousands of replication origins. The replication forks move through the chromatin until they encounter forks from neighboring origins. During replication fork termination forks converge, the replisomes disassemble and topoisomerase II resolves the daughter DNA molecules. If not resolved efficiently, terminating forks result in genomic instability through the formation of pathogenic structures. Our recent findings shed light onto the mechanism of replisome disassembly upon replication fork termination. We have shown that termination-specific polyubiquitylation of the replicative helicase component - Mcm7, leads to dissolution of the active helicase in a process dependent on the p97/VCP/Cdc48 segregase. The inhibition of terminating helicase disassembly resulted in a replication termination defect. In this extended view we present hypothetical models of replication fork termination and discuss remaining and emerging questions in the DNA replication termination field.

Changes in nucleosome repeat lengths precede replication in the early replicating metallothionein II gene region of cells synchronized in early S phase

International Nuclear Information System (INIS)

D'Anna, J.A.; Tobey, R.A.

1989-01-01

Previous investigations showed that inhibition of DNA synthesis by hydroxyurea, aphidicolin, or 5-fluorodeoxyuridine produced large changes in the composition and nucleosome repeat lengths of bulk chromatin. There the authors report results of investigations to determine whether the changes in nucleosome repeat lengths might be localized in the initiated replicons, as postulated. In most experiments, Chinese hamster (line CHO) cells were synchronized in G1, or they were synchronized in early S phase by allowing G1 cells to enter S phase in medium containing 1 mM hydroxyurea or 5 μg mL -1 aphidicolin, a procedure believed to produce an accumulation of initiated replicons that arise from normally early replicating DNA. Measurements of nucleosome repeat lengths of bulk chromatin, the early replicating unexpressed metallothionein II (MTII) gene region, and a later replicating repeated sequence indicate that the changes in repeat lengths occur preferentially in the early replicating MTII gene region as G1 cells enter and become synchronized in early S phase. During that time, the MTII gene region is not replicated nor is there any evidence for induction of MTII messenger RNA. Thus, the results are consistent with the hypothesis that changes in chromatin structure occur preferentially in the early replicating (presumably initiated) replicons at initiation or that changes in chromatin structure can precede replication during inhibition of DNA synthesis. The shortened repeat lengths that precede MTII replication are, potentially, reversible, because they become elongated when the synchronized early S-phase cells are released to resume cell cycle progression

Validity of total leucocytes count and neutrophil count (differential leucocytes) in diagnosing suspected acute appendicitis

International Nuclear Information System (INIS)

Anwar, M.W.; Abid, I.

2012-01-01

Objective: To compare the diagnostic accuracy of Total Leucocytes Count (TLC) with Neutrophil count; Differential Leucocytes Count (DLC) in diagnosing cases of suspected acute appendicitis. Study design: Validation study. Place and duration of the study: Department of Surgery, Combined Military Hospital (CMH) Rawalpindi, from April 2008 to October 2008. Method: A total of 100 patients of Pain right iliac fossae who underwent appendicectomy were included. Detailed history of all the patients was taken for pain in right lower abdomen, its severity, its nature, relieving or provoking factors. Clinical examination was done in detail. Total and Differential Leucocytes Count was done. Every patient's appendix was examined grossly after appendicectomy for evidence of appendicitis. Diagnostic measures of TLC and DLC were calculated by standard formulas. Results: Sensitivity and specificity of TLC is 86.9% and 81.25% respectively and that of DLC is 82% and 68.75% respectively. Accuracy was 86% for TLC and 80% for DLC. Conclusion: TLC is more sensitive, specific and accurate test as compared to DLC and it should be used as diagnostic aid for suspected acute appendicitis cases. (author)

Chromatin Constrains the Initiation and Elongation of DNA Replication.

Science.gov (United States)

Devbhandari, Sujan; Jiang, Jieqing; Kumar, Charanya; Whitehouse, Iestyn; Remus, Dirk

2017-01-05

Eukaryotic chromosomal DNA is faithfully replicated in a complex series of cell-cycle-regulated events that are incompletely understood. Here we report the reconstitution of DNA replication free in solution with purified proteins from the budding yeast Saccharomyces cerevisiae. The system recapitulates regulated bidirectional origin activation; synthesis of leading and lagging strands by the three replicative DNA polymerases Pol α, Pol δ, and Pol ε; and canonical maturation of Okazaki fragments into continuous daughter strands. We uncover a dual regulatory role for chromatin during DNA replication: promoting origin dependence and determining Okazaki fragment length by restricting Pol δ progression. This system thus provides a functional platform for the detailed mechanistic analysis of eukaryotic chromosome replication. Copyright © 2017 Elsevier Inc. All rights reserved.

Replication, falsification, and the crisis of confidence in social psychology.

Science.gov (United States)

Earp, Brian D; Trafimow, David

2015-01-01

The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt "fails"-does it mean that the original results, or the theory that predicted them, have been falsified? And how should "failed" replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing "failed" replications in terms of how they should affect our confidence in original findings.

Replication, falsification, and the crisis of confidence in social psychology

Science.gov (United States)

Earp, Brian D.; Trafimow, David

2015-01-01

The (latest) crisis in confidence in social psychology has generated much heated discussion about the importance of replication, including how it should be carried out as well as interpreted by scholars in the field. For example, what does it mean if a replication attempt “fails”—does it mean that the original results, or the theory that predicted them, have been falsified? And how should “failed” replications affect our belief in the validity of the original research? In this paper, we consider the replication debate from a historical and philosophical perspective, and provide a conceptual analysis of both replication and falsification as they pertain to this important discussion. Along the way, we highlight the importance of auxiliary assumptions (for both testing theories and attempting replications), and introduce a Bayesian framework for assessing “failed” replications in terms of how they should affect our confidence in original findings. PMID:26042061

Prevalence of plagiarism among medical students.

Science.gov (United States)

Bilić-Zulle, Lidija; Frković, Vedran; Turk, Tamara; Azman, Josip; Petrovecki, Mladen

2005-02-01

To determine the prevalence of plagiarism among medical students in writing essays. During two academic years, 198 second year medical students attending Medical Informatics course wrote an essay on one of four offered articles. Two of the source articles were available in an electronic form and two in printed form. Two (one electronic and one paper article) were considered less complex and the other two more complex. The essays were examined using plagiarism detection software "WCopyfind," which counted the number of matching phrases with six or more words. Plagiarism rate, expressed as the percentage of the plagiarized text, was calculated as a ratio of the absolute number of matching words and the total number of words in the essay. Only 17 (9%) of students did not plagiarize at all and 68 (34%) plagiarized less than 10% of the text. The average plagiarism rate (% of plagiarized text) was 19% (5-95% percentile=0-88). Students who were strictly warned not to plagiarize had a higher total word count in their essays than students who were not warned (P=0.002) but there was no difference between them in the rate of plagiarism. Students with higher grades in Medical Informatics exam plagiarized less than those with lower grades (P=0.015). Gender, subject source, and complexity had no influence on the plagiarism rate. Plagiarism in writing essays is common among medical students. An explicit warning is not enough to deter students from plagiarism. Detection software can be used to trace and evaluate the rate of plagiarism in written student assays.

Effects of Quizzing Methodology on Student Outcomes: Reading Compliance, Retention, and Perceptions

Science.gov (United States)

Dowling, Carey Bernini

2017-01-01

This study set out to replicate and extend research on students' reading compliance and examine the impact of daily quizzing methodology on students' reading compliance and retention. 98 students in two sections of Abnormal Psychology participated (mean age = 21.5, SD = 3.35; 72.4% Caucasian). Using a multiple baseline quasi-experimental design…

Universal Temporal Profile of Replication Origin Activation in Eukaryotes

Science.gov (United States)

Goldar, Arach

2011-03-01

The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

Enhanced counting efficiency of Cerenkov radiation from bismuth-210

International Nuclear Information System (INIS)

Peck, G.A.; Smith, J.D.

1998-01-01

This paper describes the measurement of 210 Bi by Cerenkov counting in a commercial liquid scintillation counter. The counting efficiency in water is 0.17 counts per second per Becquerel (17%). When the enhancers Triton X-100 (15% v/v) and sodium salicylate (1% m/v) are added to the solution the counting efficiency for 210 Bi increases from 17% to 75%. The 210 Po daughter of 210 Bi causes interference of 0.85 counts per second per Becquerel in the presence of the enhancers but not in water. When 210 Bi and 210 Po are present in secular equilibrium the total counting efficiency is 160%. When 210 Bi and 210 Po are not in secular equilibrium the 210 Po can be removed immediately before counting by plating onto silver foil. The use of the enhancers gives a substantial increase in counting efficiency compared to counting in water. Compared with solutions used in liquid scintillation counting the enhancer solution is inexpensive and can be disposed of without environmental hazard. (author)

Clean Hands Count

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Design and development of multiple sample counting setup

International Nuclear Information System (INIS)

Rath, D.P.; Murali, S.; Babu, D.A.R.

2010-01-01

Full text: The analysis of active samples on regular basis for ambient air activity and floor contamination from radio chemical lab accounts for major chunk of the operational activity in Health Physicist's responsibility. The requirement for daily air sample analysis on immediate counting and delayed counting from various labs in addition to samples of smear swipe check of lab led to the urge for development of system that could cater multiple sample analysis in a time programmed manner on a single sample loading. A multiple alpha/beta counting system for counting was designed and fabricated. It has arrangements for loading 10 samples in slots in order, get counted in a time programmed manner with results displayed and records maintained in PC. The paper describes the design and development of multiple sample counting setup presently in use at the facility has resulted in reduction of man-hour consumption in counting and recording of the results

Automated vehicle counting using image processing and machine learning

Science.gov (United States)

Meany, Sean; Eskew, Edward; Martinez-Castro, Rosana; Jang, Shinae

2017-04-01

Vehicle counting is used by the government to improve roadways and the flow of traffic, and by private businesses for purposes such as determining the value of locating a new store in an area. A vehicle count can be performed manually or automatically. Manual counting requires an individual to be on-site and tally the traffic electronically or by hand. However, this can lead to miscounts due to factors such as human error A common form of automatic counting involves pneumatic tubes, but pneumatic tubes disrupt traffic during installation and removal, and can be damaged by passing vehicles. Vehicle counting can also be performed via the use of a camera at the count site recording video of the traffic, with counting being performed manually post-recording or using automatic algorithms. This paper presents a low-cost procedure to perform automatic vehicle counting using remote video cameras with an automatic counting algorithm. The procedure would utilize a Raspberry Pi micro-computer to detect when a car is in a lane, and generate an accurate count of vehicle movements. The method utilized in this paper would use background subtraction to process the images and a machine learning algorithm to provide the count. This method avoids fatigue issues that are encountered in manual video counting and prevents the disruption of roadways that occurs when installing pneumatic tubes

RAD52 Facilitates Mitotic DNA Synthesis Following Replication Stress

DEFF Research Database (Denmark)

Bhowmick, Rahul; Minocherhomji, Sheroy; Hickson, Ian D

2016-01-01

Homologous recombination (HR) is necessary to counteract DNA replication stress. Common fragile site (CFS) loci are particularly sensitive to replication stress and undergo pathological rearrangements in tumors. At these loci, replication stress frequently activates DNA repair synthesis in mitosis...... replication stress at CFS loci during S-phase. In contrast, MiDAS is RAD52 dependent, and RAD52 is required for the timely recruitment of MUS81 and POLD3 to CFSs in early mitosis. Our results provide further mechanistic insight into MiDAS and define a specific function for human RAD52. Furthermore, selective...

Laying a Solid Foundation: Strategies for Effective Program Replication

Science.gov (United States)

Summerville, Geri

2009-01-01

The replication of proven social programs is a cost-effective and efficient way to achieve large-scale, positive social change. Yet there has been little guidance available about how to approach program replication and limited development of systems--at local, state or federal levels--to support replication efforts. "Laying a Solid Foundation:…

Mapping autonomously replicating sequence elements in a 73-kb ...

Indian Academy of Sciences (India)

Autonomously replicating sequence (ARS) elements are the genetic determinants of replication origin function in yeasts. They can be easily identified as the plasmids containing them transform yeast cells at a high frequency. As the first step towards identifying all potential replication origins in a 73-kb region of the long arm ...

Calculating concentration of inhaled radiolabeled particles from external gamma counting: External counting efficiency and attenuation coefficient of thorax

International Nuclear Information System (INIS)

Langenback, E.G.; Foster, W.M.; Bergofsky, E.H.

1989-01-01

We determined the overall external counting efficiency of radiolabeled particles deposited in the sheep lung. This efficiency permits the noninvasive calculation of the number of particles and microcuries from gamma-scintillation lung images of the live sheep. Additionally, we have calculated the attenuation of gamma radiation (120 keV) by the posterior chest wall and the gamma-scintillation camera collection efficiency of radiation emitted from the lung. Four methods were employed in our experiments: (1) by light microscopic counting of discrete carbonized polystyrene particles with a count median diameter (CMD) of 2.85 microns and tagged with cobalt-57, we delineated a linear relationship between the number of particles and the emitted counts per minute (cpm) detected by well scintillation counting; (2) from this conversion relationship we determined the number of particles inhaled and deposited in the lungs by scintillation counting fragments of dissected lung at autopsy; (3) we defined a linear association between the number of particles or microcuries contained in the lung and the emitted radiation as cpm detected by a gamma scintillation camera in the live sheep prior to autopsy; and (4) we compared the emitted radiation from the lungs of the live sheep to that of whole excised lungs in order to calculate the attenuation coefficient (ac) of the chest wall. The mean external counting efficiency was 4.00 X 10(4) particles/cpm (5.1 X 10(-3) microCi/cpm), the camera collection efficiency was 1 cpm/10(4) disintegrations per minute (dpm), and the ac had a mean of 0.178/cm. The external counting efficiency remained relatively constant over a range of particles and microcuries, permitting a more general use of this ratio to estimate number of particles or microcuries depositing after inhalation in a large mammalian lung if a similarly collimated gamma camera system is used

Checkpoint-dependent RNR induction promotes fork restart after replicative stress.

Science.gov (United States)

Morafraile, Esther C; Diffley, John F X; Tercero, José Antonio; Segurado, Mónica

2015-01-20

The checkpoint kinase Rad53 is crucial to regulate DNA replication in the presence of replicative stress. Under conditions that interfere with the progression of replication forks, Rad53 prevents Exo1-dependent fork degradation. However, although EXO1 deletion avoids fork degradation in rad53 mutants, it does not suppress their sensitivity to the ribonucleotide reductase (RNR) inhibitor hydroxyurea (HU). In this case, the inability to restart stalled forks is likely to account for the lethality of rad53 mutant cells after replication blocks. Here we show that Rad53 regulates replication restart through the checkpoint-dependent transcriptional response, and more specifically, through RNR induction. Thus, in addition to preventing fork degradation, Rad53 prevents cell death in the presence of HU by regulating RNR-expression and localization. When RNR is induced in the absence of Exo1 and RNR negative regulators, cell viability of rad53 mutants treated with HU is increased and the ability of replication forks to restart after replicative stress is restored.

Clean Hands Count

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Full Text Available ... Clean Hands Count Centers for Disease Control and Prevention (CDC) Loading... Unsubscribe from Centers for Disease Control and Prevention (CDC)? Cancel Unsubscribe Working... Subscribe Subscribed Unsubscribe 65K ...

Clean Hands Count

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Full Text Available ... Clean Hands Count Centers for Disease Control and Prevention (CDC) Loading... Unsubscribe from Centers for Disease Control and Prevention (CDC)? Cancel Unsubscribe Working... Subscribe Subscribed Unsubscribe 66K ...

Identification of the determinants of efficient Pestivirus replication

OpenAIRE

Risager, Peter Christian; Belsham, Graham; Rasmussen, Thomas Bruun

2013-01-01

The key for the survival of a virus is to copy its own genome into progeny genomes that allows continued reproduction. The mechanism behind this "copy function" or "replication" is a wellorganized process that involves the formation of a replication complex in the cell and interactions between the viral proteins. The replication process in single-stranded RNA viruses of positive polarity requires a particular enzyme, an RNA dependent RNA polymerase, that has no direct counterpart elsewhere in...

Algorithm for counting large directed loops

Energy Technology Data Exchange (ETDEWEB)

Bianconi, Ginestra [Abdus Salam International Center for Theoretical Physics, Strada Costiera 11, 34014 Trieste (Italy); Gulbahce, Natali [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, NM 87545 (United States)

2008-06-06

We derive a Belief-Propagation algorithm for counting large loops in a directed network. We evaluate the distribution of the number of small loops in a directed random network with given degree sequence. We apply the algorithm to a few characteristic directed networks of various network sizes and loop structures and compare the algorithm with exhaustive counting results when possible. The algorithm is adequate in estimating loop counts for large directed networks and can be used to compare the loop structure of directed networks and their randomized counterparts.

The Reputational Consequences of Failed Replications and Wrongness Admission among Scientists.

Directory of Open Access Journals (Sweden)

Adam K Fetterman

Full Text Available Scientists are dedicating more attention to replication efforts. While the scientific utility of replications is unquestionable, the impact of failed replication efforts and the discussions surrounding them deserve more attention. Specifically, the debates about failed replications on social media have led to worry, in some scientists, regarding reputation. In order to gain data-informed insights into these issues, we collected data from 281 published scientists. We assessed whether scientists overestimate the negative reputational effects of a failed replication in a scenario-based study. Second, we assessed the reputational consequences of admitting wrongness (versus not as an original scientist of an effect that has failed to replicate. Our data suggests that scientists overestimate the negative reputational impact of a hypothetical failed replication effort. We also show that admitting wrongness about a non-replicated finding is less harmful to one's reputation than not admitting. Finally, we discovered a hint of evidence that feelings about the replication movement can be affected by whether replication efforts are aimed one's own work versus the work of another. Given these findings, we then present potential ways forward in these discussions.

The Reputational Consequences of Failed Replications and Wrongness Admission among Scientists.

Science.gov (United States)

Fetterman, Adam K; Sassenberg, Kai

2015-01-01

Scientists are dedicating more attention to replication efforts. While the scientific utility of replications is unquestionable, the impact of failed replication efforts and the discussions surrounding them deserve more attention. Specifically, the debates about failed replications on social media have led to worry, in some scientists, regarding reputation. In order to gain data-informed insights into these issues, we collected data from 281 published scientists. We assessed whether scientists overestimate the negative reputational effects of a failed replication in a scenario-based study. Second, we assessed the reputational consequences of admitting wrongness (versus not) as an original scientist of an effect that has failed to replicate. Our data suggests that scientists overestimate the negative reputational impact of a hypothetical failed replication effort. We also show that admitting wrongness about a non-replicated finding is less harmful to one's reputation than not admitting. Finally, we discovered a hint of evidence that feelings about the replication movement can be affected by whether replication efforts are aimed one's own work versus the work of another. Given these findings, we then present potential ways forward in these discussions.

Nuclear mitochondrial DNA activates replication in Saccharomyces cerevisiae.

Directory of Open Access Journals (Sweden)

Laurent Chatre

Full Text Available The nuclear genome of eukaryotes is colonized by DNA fragments of mitochondrial origin, called NUMTs. These insertions have been associated with a variety of germ-line diseases in humans. The significance of this uptake of potentially dangerous sequences into the nuclear genome is unclear. Here we provide functional evidence that sequences of mitochondrial origin promote nuclear DNA replication in Saccharomyces cerevisiae. We show that NUMTs are rich in key autonomously replicating sequence (ARS consensus motifs, whose mutation results in the reduction or loss of DNA replication activity. Furthermore, 2D-gel analysis of the mrc1 mutant exposed to hydroxyurea shows that several NUMTs function as late chromosomal origins. We also show that NUMTs located close to or within ARS provide key sequence elements for replication. Thus NUMTs can act as independent origins, when inserted in an appropriate genomic context or affect the efficiency of pre-existing origins. These findings show that migratory mitochondrial DNAs can impact on the replication of the nuclear region they are inserted in.

Logistic regression for dichotomized counts.

Science.gov (United States)

Preisser, John S; Das, Kalyan; Benecha, Habtamu; Stamm, John W

2016-12-01

Sometimes there is interest in a dichotomized outcome indicating whether a count variable is positive or zero. Under this scenario, the application of ordinary logistic regression may result in efficiency loss, which is quantifiable under an assumed model for the counts. In such situations, a shared-parameter hurdle model is investigated for more efficient estimation of regression parameters relating to overall effects of covariates on the dichotomous outcome, while handling count data with many zeroes. One model part provides a logistic regression containing marginal log odds ratio effects of primary interest, while an ancillary model part describes the mean count of a Poisson or negative binomial process in terms of nuisance regression parameters. Asymptotic efficiency of the logistic model parameter estimators of the two-part models is evaluated with respect to ordinary logistic regression. Simulations are used to assess the properties of the models with respect to power and Type I error, the latter investigated under both misspecified and correctly specified models. The methods are applied to data from a randomized clinical trial of three toothpaste formulations to prevent incident dental caries in a large population of Scottish schoolchildren. © The Author(s) 2014.

Housing Inventory Count

Data.gov (United States)

Department of Housing and Urban Development — This report displays the data communities reported to HUD about the nature of their dedicated homeless inventory, referred to as their Housing Inventory Count (HIC)....

Checkpoint independence of most DNA replication origins in fission yeast.

Science.gov (United States)

Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

2007-12-19

In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleoside triphosphates (dNTPs) and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR) or cds1 (which encodes the fission yeast homologue of Chk2). Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation) that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (approximately 3%) behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild-type cells as in checkpoint

Checkpoint independence of most DNA replication origins in fission yeast

Science.gov (United States)

Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

2007-01-01

Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleoside triphosphates (dNTPs) and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR) or cds1 (which encodes the fission yeast homologue of Chk2). Results Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation) that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (~3%) behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild-type cells as in

Checkpoint independence of most DNA replication origins in fission yeast

Directory of Open Access Journals (Sweden)

Scott Donna

2007-12-01

Full Text Available Abstract Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU, which limits the pool of deoxyribonucleoside triphosphates (dNTPs and activates the replication checkpoint. The checkpoint-mutant cells carried deletions either of rad3 (which encodes the fission yeast homologue of ATR or cds1 (which encodes the fission yeast homologue of Chk2. Results Our microarray results proved to be largely consistent with those independently obtained and recently published by three other laboratories. However, we were able to reconcile differences between the previous studies regarding the extent to which fission yeast replication origins are affected by the replication checkpoint. We found (consistent with the three previous studies after appropriate interpretation that, in surprising contrast to budding yeast, most fission yeast origins, including both early- and late-firing origins, are not significantly affected by checkpoint mutations during replication in the presence of HU. A few origins (~3% behaved like those in budding yeast: they replicated earlier in the checkpoint mutants than in wild type. These were located primarily in the heterochromatic subtelomeric regions of chromosomes 1 and 2. Indeed, the subtelomeric regions defined by the strongest checkpoint restraint correspond precisely to previously mapped subtelomeric heterochromatin. This observation implies that subtelomeric heterochromatin in fission yeast differs from heterochromatin at centromeres, in the mating type region, and in ribosomal DNA, since these regions replicated at least as efficiently in wild

Regulation of replication fork progression through histone supply and demand

DEFF Research Database (Denmark)

Groth, Anja; Corpet, Armelle; Cook, Adam J L

2007-01-01

DNA replication in eukaryotes requires nucleosome disruption ahead of the replication fork and reassembly behind. An unresolved issue concerns how histone dynamics are coordinated with fork progression to maintain chromosomal stability. Here, we characterize a complex in which the human histone c...... progression and histone supply and demand.......1 chaperone function, histone supply, and replicative unwinding of DNA in chromatin. We propose that Asf1, as a histone acceptor and donor, handles parental and new histones at the replication fork via an Asf1-(H3-H4)-MCM2-7 intermediate and thus provides a means to fine-tune replication fork...

The Escherichia coli Tus-Ter replication fork barrier causes site-specific DNA replication perturbation in yeast.

Science.gov (United States)

Larsen, Nicolai B; Sass, Ehud; Suski, Catherine; Mankouri, Hocine W; Hickson, Ian D

2014-04-07

Replication fork (RF) pausing occurs at both 'programmed' sites and non-physiological barriers (for example, DNA adducts). Programmed RF pausing is required for site-specific DNA replication termination in Escherichia coli, and this process requires the binding of the polar terminator protein, Tus, to specific DNA sequences called Ter. Here, we demonstrate that Tus-Ter modules also induce polar RF pausing when engineered into the Saccharomyces cerevisiae genome. This heterologous RF barrier is distinct from a number of previously characterized, protein-mediated, RF pause sites in yeast, as it is neither Tof1-dependent nor counteracted by the Rrm3 helicase. Although the yeast replisome can overcome RF pausing at Tus-Ter modules, this event triggers site-specific homologous recombination that requires the RecQ helicase, Sgs1, for its timely resolution. We propose that Tus-Ter can be utilized as a versatile, site-specific, heterologous DNA replication-perturbing system, with a variety of potential applications.

Chromosome biology: conflict management for replication and transcription.

Science.gov (United States)

Dewar, James M; Walter, Johannes C

2013-03-04

A recent study has uncovered a new mechanism that attenuates DNA replication during periods of heightened gene expression to avoid collisions between replication and transcription. Copyright © 2013 Elsevier Ltd. All rights reserved.

Distribution of DNA replication proteins in Drosophila cells

Science.gov (United States)

Easwaran, Hariharan P; Leonhardt, Heinrich; Cardoso, M Cristina

2007-01-01

Background DNA replication in higher eukaryotic cells is organized in discrete subnuclear sites called replication foci (RF). During the S phase, most replication proteins assemble at the RF by interacting with PCNA via a PCNA binding domain (PBD). This has been shown to occur for many mammalian replication proteins, but it is not known whether this mechanism is conserved in evolution. Results Fluorescent fusions of mammalian replication proteins, Dnmt1, HsDNA Lig I and HsPCNA were analyzed for their ability to target to RF in Drosophila cells. Except for HsPCNA, none of the other proteins and their deletions showed any accumulation at RF in Drosophila cells. We hypothesized that in Drosophila cells there might be some other peptide sequence responsible for targeting proteins to RF. To test this, we identified the DmDNA Lig I and compared the protein sequence with HsDNA Lig I. The two orthologs shared the PBD suggesting a functionally conserved role for this domain in the Drosophila counterpart. A series of deletions of DmDNA Lig I were analyzed for their ability to accumulate at RF in Drosophila and mammalian cells. Surprisingly, no accumulation at RF was observed in Drosophila cells, while in mammalian cells DmDNA Lig I accumulated at RF via its PBD. Further, GFP fusions with the PBD domains from Dnmt1, HsDNA Lig I and DmDNA Lig I, were able to target to RF only in mammalian cells but not in Drosophila cells. Conclusion We show that S phase in Drosophila cells is characterized by formation of RF marked by PCNA like in mammalian cells. However, other than PCNA none of the replication proteins and their deletions tested here showed accumulation at RF in Drosophila cells while the same proteins and deletions are capable of accumulating at RF in mammalian cells. We hypothesize that unlike mammalian cells, in Drosophila cells, replication proteins do not form long-lasting interactions with the replication machinery, and rather perform their functions via very

Multiple-Event, Single-Photon Counting Imaging Sensor

Science.gov (United States)

Zheng, Xinyu; Cunningham, Thomas J.; Sun, Chao; Wang, Kang L.

2011-01-01

The single-photon counting imaging sensor is typically an array of silicon Geiger-mode avalanche photodiodes that are monolithically integrated with CMOS (complementary metal oxide semiconductor) readout, signal processing, and addressing circuits located in each pixel and the peripheral area of the chip. The major problem is its single-event method for photon count number registration. A single-event single-photon counting imaging array only allows registration of up to one photon count in each of its pixels during a frame time, i.e., the interval between two successive pixel reset operations. Since the frame time can t be too short, this will lead to very low dynamic range and make the sensor merely useful for very low flux environments. The second problem of the prior technique is a limited fill factor resulting from consumption of chip area by the monolithically integrated CMOS readout in pixels. The resulting low photon collection efficiency will substantially ruin any benefit gained from the very sensitive single-photon counting detection. The single-photon counting imaging sensor developed in this work has a novel multiple-event architecture, which allows each of its pixels to register as more than one million (or more) photon-counting events during a frame time. Because of a consequently boosted dynamic range, the imaging array of the invention is capable of performing single-photon counting under ultra-low light through high-flux environments. On the other hand, since the multiple-event architecture is implemented in a hybrid structure, back-illumination and close-to-unity fill factor can be realized, and maximized quantum efficiency can also be achieved in the detector array.

Parasites Sustain and Enhance RNA-Like Replicators through Spatial Self-Organisation.

Directory of Open Access Journals (Sweden)

Enrico Sandro Colizzi

2016-04-01

Full Text Available In a prebiotic RNA world, parasitic behaviour may be favoured because template dependent replication happens in trans, thus being altruistic. Spatially extended systems are known to reduce harmful effects of parasites. Here we present a spatial system to show that evolution of replication is (indirectly enhanced by strong parasites, and we characterise the phase transition that leads to this mode of evolution. Building on the insights of this analysis, we identify two scenarios, namely periodic disruptions and longer replication time-span, in which speciation occurs and an evolved parasite-like lineage enables the evolutionary increase of replication rates in replicators. Finally, we show that parasites co-evolving with replicators are selected to become weaker, i.e. worse templates for replication when the duration of replication is increased. We conclude that parasites may not be considered a problem for evolution in a prebiotic system, but a degree of freedom that can be exploited by evolution to enhance the evolvability of replicators, by means of emergent levels of selection.

A Model for Forecasting Enlisted Student IA Billet Requirements

Science.gov (United States)

2016-03-01

IA execution ........................................... 4   Figure 2.   Learning center to resource sponsor alignment...initial entry training” [3]. 4 Figure 1. Training that counts as student IA execution The second type of chargeable training is the...Reference [ 4 ] describes the process the Navy uses to build the student IA program. It comprises three steps. The first is to forecast student IA E

Lazy reference counting for the Microgrid

NARCIS (Netherlands)

Poss, R.; Grelck, C.; Herhut, S.; Scholz, S.-B.

2012-01-01

This papers revisits non-deferred reference counting, a common technique to ensure that potentially shared large heap objects can be reused safely when they are both input and output to computations. Traditionally, thread-safe reference counting exploit implicit memory-based communication of counter

Replication stress activates DNA repair synthesis in mitosis

DEFF Research Database (Denmark)

Minocherhomji, Sheroy; Ying, Songmin; Bjerregaard, Victoria A

2015-01-01

Oncogene-induced DNA replication stress has been implicated as a driver of tumorigenesis. Many chromosomal rearrangements characteristic of human cancers originate from specific regions of the genome called common fragile sites (CFSs). CFSs are difficult-to-replicate loci that manifest as gaps...... into mitotic prophase triggers the recruitment of MUS81 to CFSs. The nuclease activity of MUS81 then promotes POLD3-dependent DNA synthesis at CFSs, which serves to minimize chromosome mis-segregation and non-disjunction. We propose that the attempted condensation of incompletely duplicated loci in early...... mitosis serves as the trigger for completion of DNA replication at CFS loci in human cells. Given that this POLD3-dependent mitotic DNA synthesis is enhanced in aneuploid cancer cells that exhibit intrinsically high levels of chromosomal instability (CIN(+)) and replicative stress, we suggest...

Specificity and function of Archaeal DNA replication initiator proteins

DEFF Research Database (Denmark)

Samson, Rachel Y.; Xu, Yanqun; Gadelha, Catarina

2013-01-01

Chromosomes with multiple DNA replication origins are a hallmark of Eukaryotes and some Archaea. All eukaryal nuclear replication origins are defined by the origin recognition complex (ORC) that recruits the replicative helicase MCM(2-7) via Cdc6 and Cdt1. We find that the three origins...... to investigate the role of ATP binding and hydrolysis in initiator function in vivo and in vitro. We find that the ATP-bound form of Orc1-1 is proficient for replication and implicates hydrolysis of ATP in downregulation of origin activity. Finally, we reveal that ATP and DNA binding by Orc1-1 remodels...

Structure of replicating intermediates of human herpesvirus type 6

International Nuclear Information System (INIS)

Severini, Alberto; Sevenhuysen, Claire; Garbutt, Michael; Tipples, Graham A.

2003-01-01

We have studied the structure of the replicative intermediates of human herpesvirus 6 (HHV-6) using pulsed-field gel electrophoresis, partial digestion, two-dimensional gel electrophoresis, and sedimentation centrifugation. The results show that DNA replication of HHV-6 produces head-to-tail concatemeric intermediates as well as approximately equal amounts of circular monomers or oligomers. Unlike the situation in herpes simplex virus, the intermediates of human herpesvirus 6 replication are not highly branched, suggesting a difference in the mechanism of replication or a lower frequency of homologous recombination in human herpesvirus 6 compared to herpes simplex virus

Transgene Expression and Host Cell Responses to Replication-Defective, Single-Cycle, and Replication-Competent Adenovirus Vectors

Directory of Open Access Journals (Sweden)

Catherine M. Crosby

2017-02-01

Full Text Available Most adenovirus (Ad vectors are E1 gene deleted replication defective (RD-Ad vectors that deliver one transgene to the cell and all expression is based on that one gene. In contrast, E1-intact replication-competent Ad (RC-Ad vectors replicate their DNA and their transgenes up to 10,000-fold, amplifying transgene expression markedly higher than RD-Ad vectors. While RC-Ad are more potent, they run the real risk of causing adenovirus infections in vector recipients and those that administer them. To gain the benefits of transgene amplification, but avoid the risk of Ad infections, we developed “single cycle” Ad (SC-Ad vectors. SC-Ads amplify transgene expression and generated markedly stronger and more persistent immune responses than RD-Ad as expected. However, they also unexpectedly generated stronger immune responses than RC-Ad vectors. To explore the basis of this potency here, we compared gene expression and the cellular responses to infection to these vectors in vitro and in vivo. In vitro, in primary human lung epithelial cells, SC- and RC-Ad amplified their genomes more than 400-fold relative to RD-Ad with higher replication by SC-Ad. This replication translated into higher green fluorescent protein (GFP expression for 48 h by SC- and RC-Ad than by RD-Ad. In vitro, in the absence of an immune system, RD-Ad expression became higher by 72 h coincident with cell death mediated by SC- and RC-Ad and release of transgene product from the dying cells. When the vectors were compared in human THP-1 Lucia- interferon-stimulated gene (ISG cells, which are a human monocyte cell line that have been modified to quantify ISG activity, RC-Ad6 provoked significantly stronger ISG responses than RD- or SC-Ad. In mice, intravenous or intranasal injection produced up to 100-fold genome replication. Under these in vivo conditions in the presence of the immune system, luciferase expression by RC and SC-Ad was markedly higher than that by RD-Ad. In

Are Psychology Journals Anti-replication? A Snapshot of Editorial Practices

OpenAIRE

Martin, G. N.; Clarke, Richard M.

2017-01-01

Recent research in psychology has highlighted a number of replication problems in the discipline, with publication bias – the preference for publishing original and positive results, and a resistance to publishing negative results and replications- identified as one reason for replication failure. However, little empirical research exists to demonstrate that journals explicitly refuse to publish replications. We reviewed the instructions to authors and the published aims of 1151 psychology jo...

Clean Hands Count

Medline Plus

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On Scalability and Replicability of Smart Grid Projects—A Case Study

Directory of Open Access Journals (Sweden)

Lukas Sigrist

2016-03-01

Full Text Available This paper studies the scalability and replicability of smart grid projects. Currently, most smart grid projects are still in the R&D or demonstration phases. The full roll-out of the tested solutions requires a suitable degree of scalability and replicability to prevent project demonstrators from remaining local experimental exercises. Scalability and replicability are the preliminary requisites to perform scaling-up and replication successfully; therefore, scalability and replicability allow for or at least reduce barriers for the growth and reuse of the results of project demonstrators. The paper proposes factors that influence and condition a project’s scalability and replicability. These factors involve technical, economic, regulatory and stakeholder acceptance related aspects, and they describe requirements for scalability and replicability. In order to assess and evaluate the identified scalability and replicability factors, data has been collected from European and national smart grid projects by means of a survey, reflecting the projects’ view and results. The evaluation of the factors allows quantifying the status quo of on-going projects with respect to the scalability and replicability, i.e., they provide a feedback on to what extent projects take into account these factors and on whether the projects’ results and solutions are actually scalable and replicable.

Preverbal and verbal counting and computation.

Science.gov (United States)

Gallistel, C R; Gelman, R

1992-08-01

We describe the preverbal system of counting and arithmetic reasoning revealed by experiments on numerical representations in animals. In this system, numerosities are represented by magnitudes, which are rapidly but inaccurately generated by the Meck and Church (1983) preverbal counting mechanism. We suggest the following. (1) The preverbal counting mechanism is the source of the implicit principles that guide the acquisition of verbal counting. (2) The preverbal system of arithmetic computation provides the framework for the assimilation of the verbal system. (3) Learning to count involves, in part, learning a mapping from the preverbal numerical magnitudes to the verbal and written number symbols and the inverse mappings from these symbols to the preverbal magnitudes. (4) Subitizing is the use of the preverbal counting process and the mapping from the resulting magnitudes to number words in order to generate rapidly the number words for small numerosities. (5) The retrieval of the number facts, which plays a central role in verbal computation, is mediated via the inverse mappings from verbal and written numbers to the preverbal magnitudes and the use of these magnitudes to find the appropriate cells in tabular arrangements of the answers. (6) This model of the fact retrieval process accounts for the salient features of the reaction time differences and error patterns revealed by experiments on mental arithmetic. (7) The application of verbal and written computational algorithms goes on in parallel with, and is to some extent guided by, preverbal computations, both in the child and in the adult.

Determining Gate Count Reliability in a Library Setting

OpenAIRE

Jeffrey Phillips

2016-01-01

Objective – Patron counts are a common form of measurement for library assessment. To develop accurate library statistics, it is necessary to determine any differences between various counting devices. A yearlong comparison between card reader turnstiles and laser gate counters in a university library sought to offer a standard percentage of variance and provide suggestions to increase the precision of counts. Methods – The collection of library exit counts identified the differences be...

CRISPR-mediated control of the bacterial initiation of replication.

Science.gov (United States)

Wiktor, Jakub; Lesterlin, Christian; Sherratt, David J; Dekker, Cees

2016-05-05

Programmable control of the cell cycle has been shown to be a powerful tool in cell-biology studies. Here, we develop a novel system for controlling the bacterial cell cycle, based on binding of CRISPR/dCas9 to the origin-of-replication locus. Initiation of replication of bacterial chromosomes is accurately regulated by the DnaA protein, which promotes the unwinding of DNA at oriC We demonstrate that the binding of CRISPR/dCas9 to any position within origin or replication blocks the initiation of replication. Serial-dilution plating, single-cell fluorescence microscopy, and flow-cytometry experiments show that ongoing rounds of chromosome replication are finished upon CRISPR/dCas9 binding, but no new rounds are initiated. Upon arrest, cells stay metabolically active and accumulate cell mass. We find that elevating the temperature from 37 to 42°C releases the CRISR/dCas9 replication inhibition, and we use this feature to recover cells from the arrest. Our simple and robust method of controlling the bacterial cell cycle is a useful asset for synthetic biology and DNA-replication studies in particular. The inactivation of CRISPR/dCas9 binding at elevated temperatures may furthermore be of wide interest for CRISPR/Cas9 applications in genomic engineering. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Replication and Inhibitors of Enteroviruses and Parechoviruses

Directory of Open Access Journals (Sweden)

Lonneke van der Linden

2015-08-01

Full Text Available The Enterovirus (EV and Parechovirus genera of the picornavirus family include many important human pathogens, including poliovirus, rhinovirus, EV-A71, EV-D68, and human parechoviruses (HPeV. They cause a wide variety of diseases, ranging from a simple common cold to life-threatening diseases such as encephalitis and myocarditis. At the moment, no antiviral therapy is available against these viruses and it is not feasible to develop vaccines against all EVs and HPeVs due to the great number of serotypes. Therefore, a lot of effort is being invested in the development of antiviral drugs. Both viral proteins and host proteins essential for virus replication can be used as targets for virus inhibitors. As such, a good understanding of the complex process of virus replication is pivotal in the design of antiviral strategies goes hand in hand with a good understanding of the complex process of virus replication. In this review, we will give an overview of the current state of knowledge of EV and HPeV replication and how this can be inhibited by small-molecule inhibitors.

Attenuation of Replication-Competent Adenovirus Serotype 26 Vaccines by Vectorization.

Science.gov (United States)

Maxfield, Lori F; Abbink, Peter; Stephenson, Kathryn E; Borducchi, Erica N; Ng'ang'a, David; Kirilova, Marinela M; Paulino, Noelix; Boyd, Michael; Shabram, Paul; Ruan, Qian; Patel, Mayank; Barouch, Dan H

2015-11-01

Replication-competent adenovirus (rcAd)-based vaccine vectors may theoretically provide immunological advantages over replication-incompetent Ad vectors, but they also raise additional potential clinical and regulatory issues. We produced replication-competent Ad serotype 26 (rcAd26) vectors by adding the E1 region back into a replication-incompetent Ad26 vector backbone with the E3 or E3/E4 regions deleted. We assessed the effect of vectorization on the replicative capacity of the rcAd26 vaccines. Attenuation occurred in a stepwise fashion, with E3 deletion, E4 deletion, and human immunodeficiency virus type 1 (HIV-1) envelope (Env) gene insertion all contributing to reduced replicative capacity compared to that with the wild-type Ad26 vector. The rcAd26 vector with E3 and E4 deleted and containing the Env transgene exhibited 2.7- to 4.4-log-lower replicative capacity than that of the wild-type Ad26 in vitro. This rcAd26 vector is currently being evaluated in a phase 1 clinical trial. Attenuation as a result of vectorization and transgene insertion has implications for the clinical development of replication-competent vaccine vectors. Copyright © 2015, Maxfield et al.

Using Replicates in Information Retrieval Evaluation.

Science.gov (United States)

Voorhees, Ellen M; Samarov, Daniel; Soboroff, Ian

2017-09-01

This article explores a method for more accurately estimating the main effect of the system in a typical test-collection-based evaluation of information retrieval systems, thus increasing the sensitivity of system comparisons. Randomly partitioning the test document collection allows for multiple tests of a given system and topic (replicates). Bootstrap ANOVA can use these replicates to extract system-topic interactions-something not possible without replicates-yielding a more precise value for the system effect and a narrower confidence interval around that value. Experiments using multiple TREC collections demonstrate that removing the topic-system interactions substantially reduces the confidence intervals around the system effect as well as increases the number of significant pairwise differences found. Further, the method is robust against small changes in the number of partitions used, against variability in the documents that constitute the partitions, and the measure of effectiveness used to quantify system effectiveness.

Synchronization of DNA array replication kinetics

Science.gov (United States)

Manturov, Alexey O.; Grigoryev, Anton V.

2016-04-01

In the present work we discuss the features of the DNA replication kinetics at the case of multiplicity of simultaneously elongated DNA fragments. The interaction between replicated DNA fragments is carried out by free protons that appears at the every nucleotide attachment at the free end of elongated DNA fragment. So there is feedback between free protons concentration and DNA-polymerase activity that appears as elongation rate dependence. We develop the numerical model based on a cellular automaton, which can simulate the elongation stage (growth of DNA strands) for DNA elongation process with conditions pointed above and we study the possibility of the DNA polymerases movement synchronization. The results obtained numerically can be useful for DNA polymerase movement detection and visualization of the elongation process in the case of massive DNA replication, eg, under PCR condition or for DNA "sequencing by synthesis" sequencing devices evaluation.

Are Psychology Journals Anti-replication? A Snapshot of Editorial Practices.

Science.gov (United States)

Martin, G N; Clarke, Richard M

2017-01-01

Recent research in psychology has highlighted a number of replication problems in the discipline, with publication bias - the preference for publishing original and positive results, and a resistance to publishing negative results and replications- identified as one reason for replication failure. However, little empirical research exists to demonstrate that journals explicitly refuse to publish replications. We reviewed the instructions to authors and the published aims of 1151 psychology journals and examined whether they indicated that replications were permitted and accepted. We also examined whether journal practices differed across branches of the discipline, and whether editorial practices differed between low and high impact journals. Thirty three journals (3%) stated in their aims or instructions to authors that they accepted replications. There was no difference between high and low impact journals. The implications of these findings for psychology are discussed.

The rolling-circle melting-pot model for porcine circovirus DNA replication

Science.gov (United States)

A stem-loop structure, formed by a pair of inverted repeats during DNA replication, is a conserved feature at the origin of DNA replication (Ori) among plant and animal viruses, bacteriophages and plasmids that replicate their genomes via the rolling-circle replication (RCR) mechanism. Porcine circo...

Molecular analysis of the replication program in unicellular model organisms.

Science.gov (United States)

Raghuraman, M K; Brewer, Bonita J

2010-01-01

Eukaryotes have long been reported to show temporal programs of replication, different portions of the genome being replicated at different times in S phase, with the added possibility of developmentally regulated changes in this pattern depending on species and cell type. Unicellular model organisms, primarily the budding yeast Saccharomyces cerevisiae, have been central to our current understanding of the mechanisms underlying the regulation of replication origins and the temporal program of replication in particular. But what exactly is a temporal program of replication, and how might it arise? In this article, we explore this question, drawing again on the wealth of experimental information in unicellular model organisms.

Counting Word Frequencies with Python

Directory of Open Access Journals (Sweden)

William J. Turkel

2012-07-01

Full Text Available Your list is now clean enough that you can begin analyzing its contents in meaningful ways. Counting the frequency of specific words in the list can provide illustrative data. Python has an easy way to count frequencies, but it requires the use of a new type of variable: the dictionary. Before you begin working with a dictionary, consider the processes used to calculate frequencies in a list.

Regulation of DNA replication in irradiated cells by trans-acting factors

International Nuclear Information System (INIS)

Wang, Y.; Huq, M.S.; Cheng, X.; Iliakis, G.

1995-01-01

We compared DNA replication activity in cytoplasmic extracts prepared from irradiated and nonirradiated HeLa cells using a simian virus 40 (SV40)-based in vitro replication assay. The assay measures semi-conservative DNA replication in a plasmid carrying the SV40 origin of replication and requires SV40 T antigen as the sole noncellular protein. The plasmid DNA used in the replication reaction is never exposed to radiation. We find that replication of plasmid DNA is significantly reduced when cytoplasmic extracts from irradiated cells are used. Since plasmid replication proceeds to completion in extracts from irradiated cells, the observed reduction in the overall replication activity is probably due to a reduction in the efficiency of initiation events. The degree of inhibition of DNA replication after exposure to 10, 30 and 50 Gy X rays as measured in vitro using this assay is similar to that measured in intact cells immediately before processing for extract preparation. These observations are compatible with the induction or activation by ionizing radiation of a factor(s) that inhibits in trans DNA replication. The results contribute to our understanding of the mechanism(s) developed by the cells to regulate DNA replication when exposed to clastogenic agents. Such processes may be of significance in the restoration of DNA integrity, and may define yet another checkpoint operating during S at the level of clusters of replicons. 26 refs., 4 figs

Genome-wide alterations of the DNA replication program during tumor progression

Science.gov (United States)

Arneodo, A.; Goldar, A.; Argoul, F.; Hyrien, O.; Audit, B.

2016-08-01

Oncogenic stress is a major driving force in the early stages of cancer development. Recent experimental findings reveal that, in precancerous lesions and cancers, activated oncogenes may induce stalling and dissociation of DNA replication forks resulting in DNA damage. Replication timing is emerging as an important epigenetic feature that recapitulates several genomic, epigenetic and functional specificities of even closely related cell types. There is increasing evidence that chromosome rearrangements, the hallmark of many cancer genomes, are intimately associated with the DNA replication program and that epigenetic replication timing changes often precede chromosomic rearrangements. The recent development of a novel methodology to map replication fork polarity using deep sequencing of Okazaki fragments has provided new and complementary genome-wide replication profiling data. We review the results of a wavelet-based multi-scale analysis of genomic and epigenetic data including replication profiles along human chromosomes. These results provide new insight into the spatio-temporal replication program and its dynamics during differentiation. Here our goal is to bring to cancer research, the experimental protocols and computational methodologies for replication program profiling, and also the modeling of the spatio-temporal replication program. To illustrate our purpose, we report very preliminary results obtained for the chronic myelogeneous leukemia, the archetype model of cancer. Finally, we discuss promising perspectives on using genome-wide DNA replication profiling as a novel efficient tool for cancer diagnosis, prognosis and personalized treatment.

Computerized radioautographic grain counting

International Nuclear Information System (INIS)

McKanna, J.A.; Casagrande, V.A.

1985-01-01

In recent years, radiolabeling techniques have become fundamental assays in physiology and biochemistry experiments. They also have assumed increasingly important roles in morphologic studies. Characteristically, radioautographic analysis of structure has been qualitative rather than quantitative, however, microcomputers have opened the door to several methods for quantifying grain counts and density. The overall goal of this chapter is to describe grain counting using the Bioquant, an image analysis package based originally on the Apple II+, and now available for several popular microcomputers. The authors discuss their image analysis procedures by applying them to a study of development in the central nervous system

Checkpoint independence of most DNA replication origins in fission yeast

OpenAIRE

Mickle, Katie L; Ramanathan, Sunita; Rosebrock, Adam; Oliva, Anna; Chaudari, Amna; Yompakdee, Chulee; Scott, Donna; Leatherwood, Janet; Huberman, Joel A

2007-01-01

Abstract Background In budding yeast, the replication checkpoint slows progress through S phase by inhibiting replication origin firing. In mammals, the replication checkpoint inhibits both origin firing and replication fork movement. To find out which strategy is employed in the fission yeast, Schizosaccharomyces pombe, we used microarrays to investigate the use of origins by wild-type and checkpoint-mutant strains in the presence of hydroxyurea (HU), which limits the pool of deoxyribonucleo...

Replicative intermediates in UV-irradiated Simian virus 40

International Nuclear Information System (INIS)

Clark, J.M.; Hanawalt, P.C.

1984-01-01

The authors have used Simian virus 40 (SV40) as a probe to study the replication of UV-damaged DNA in mammalian cells. Viral DNA replication in infected monkey kidney cells was synchronized by incubating a mutant of SV40 (tsA58) temperature-sensitive for the initiation of DNA synthesis at the restrictive temperature and then adding aphidicolin to temporarily inhibit DNA synthesis at the permissive temperature while permitting pre-replicative events to occur. After removal of the drug, the infected cells were irradiated at 100 J/m 2 (254 nm) to produce 6-7 pyrimidine dimers per SV40 genome, and returned to the restrictive temperature to prevent reinitiation of replication from the SV40 origin. Replicative intermediates (RI) were labeled with [ 3 H]thymidine. The size distribution of daughter DNA strands in RI isolated shortly after irradiation was skewed towards lengths less than the interdimer spacing in parental DNA; this bias persisted for at least 1 h after irradiation, but disappeared within 3 h by which time the size of the newly-synthesized DNA exceeded the interdimer distance. Evidence was obtained for the generation at late times after irradiation, of Form I molecules in which the daughter DNA strand contain dimers. Thus DNA strand exchange as well as trans-dimer synthesis may be involved in the generation of supercoiled Form I DNA from 0V-damaged SV40 replicative intermediates. (Auth.)

Cerenkov counting and Cerenkov-scintillation counting with high refractive index organic liquids using a liquid scintillation counter

International Nuclear Information System (INIS)

Wiebe, L.I.; Helus, F.; Maier-Borst, W.

1978-01-01

18 F and 14 C radioactivity was measured in methyl salicylate (MS), a high refractive index hybrid Cherenkov-scintillation generating medium, using a liquid scintillation counter. At concentrations of up to 21.4%, in MS, dimethyl sulfoxide (DMSO) quenched 14 C fluorescence, and with a 10-fold excess of DMSO over MS, 18 F count rates were reduced below that for DMSO alone, probably as a result of concentration-independent self-quenching due to 'dark-complex' formation. DMSO in lower concentrations did not reduce the counting efficiency of 18 F in MS. Nitrobenzene was a concentration-dependent quencher for both 14 C and 18 F in MS. Chlorobenzene (CB) and DMSO were both found to be weak Cherenkov generators with 18 F. Counting efficiencies for 18 F in MS, CB, and DMSO were 50.3, 7.8 and 4.3% respectively in the coincidence counting mode, and 58.1, 13.0 and 6.8% in the singles mode. 14 C efficiencies were 14.4 and 22.3% for coincidence and singles respectively, and 15.3 and 42.0% using a modern counter designed for coincidence and single photon counting. The high 14 C and 18 F counting efficiency in MS are discussed with respect to excitation mechanism, on the basis of quench and channels ratios changes observed. It is proposed that MS functions as an efficient Cherenkov-scintillation generator for high-energy beta emitters such as 18 F, and as a low-efficiency scintillator for weak beta emitting radionuclides such as 14 C. (author)

Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation

DEFF Research Database (Denmark)

Singhal, Abhishek; Nielsen, Peter E

2014-01-01

We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected...... precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural...

X-ray repair replication in L1210 leukemia cells

International Nuclear Information System (INIS)

Lee, Y.C.; Byfield, J.E.; Bennett, L.R.; Chan, P.Y.M.

1974-01-01

Repair replication has been studied in detail in mouse L1210 leukemia cells. A method of identifying and quantitating repair replication using a pre- and postradiation block of normal replication with cytosine arabinoside is illustrated. The method derived does not require isolation of DNA per se and appears to be satisfactory for screening for inhibitors of repair replication. Repair replication can be demonstrated at doses in the 1000-rad range in bromouridine deoxyriboside-substituted cells and at slightly higher doses in nonsubstituted cells. Drugs that are known to bind to DNA inhibit this x-ray-induced repair replication. Drugs with these properties may be identified by the methods described and compared quantitatively in their ability to inhibit this type of x-ray damage. Since these phenomena can be demonstrated for low radiation doses and at drug concentrations attainable in vivo during human cancer chemotherapy this class of anticancer agent may be worthy of closer study. Application to the L1210 leukemia system should permit comparison of in vitro and in vivo drug effects in the context of the extensive in vivo pharmacological data already available for L1210 cells. (U.S.)