Science.gov

Sample records for alternative gene programs

  1. Alternative Programming for Adults.

    ERIC Educational Resources Information Center

    Flint, Thomas A.; Frey, Ruth

    2003-01-01

    The Council for Adult and Experiential Learning is currently cataloguing alternative programming features that are most effective with adult students in a best practices inventory organized around a framework of high-level descriptive principles of effectiveness. This chapter identifies a few interesting features from a quick survey of this…

  2. Gene expression kinetics in individual plasmodial cells reveal alternative programs of differential regulation during commitment and differentiation.

    PubMed

    Rätzel, Viktoria; Marwan, Wolfgang

    2015-05-26

    During its life cycle, the amoebozoon Physarum polycephalum forms multinucleate plasmodial cells that can grow to macroscopic size while maintaining a naturally synchronous population of nuclei. Sporulation-competent plasmodia were stimulated through photoactivation of the phytochrome photoreceptor and the expression of sporulation marker genes was analyzed quantitatively by repeatedly taking samples of the same plasmodial cell at successive time points after the stimulus pulse. Principal component analysis of the gene expression data revealed that plasmodial cells take different trajectories leading to cell fate decision and differentiation and suggested that averaging over individual cells is inappropriate. Queries for genes with pairwise correlated expression kinetics revealed qualitatively different patterns of co-regulation, indicating that alternative programs of differential regulation are operational in individual plasmodial cells. At the single cell level, the response to stimulation of a non-sporulating mutant was qualitatively different as compared to the wild type with respect to the differentially regulated genes and their patterns of co-regulation. The observation of individual differences during commitment and differentiation supports the concept of a Waddington-type quasipotential landscape for the regulatory control of cell differentiation. Comparison of wild type and sporulation mutant data further supports the idea that mutations may impact the topology of this landscape.

  3. Alternative Work Programs

    ERIC Educational Resources Information Center

    Kuehn, Kerri L.

    2004-01-01

    Employers are feeling the strain of needing to offer alternative work arrangements to retain and recruit employees. Due to a change in demographics, dual-career couples and increased technology; people are demanding a transformation in the workplace environment. Two alternatives, which are being offered by employers, are flextime and…

  4. GATEWAYS: Degree program alternatives

    SciTech Connect

    Strong, K.R.; Thayer, M.M.

    1991-11-01

    Los Alamos National Laboratory is using non-traditional solutions to assist employees in attaining degrees required for essential Laboratory operations. Varieties of distance learning technologies have been implemented to meet some degree needs. While distance learning is not always a perfect solution, it enables the Laboratory to provide education that would otherwise not be practical for full-time employees. The Laboratory has also formed partnerships with local colleges to design programs to fill particular needs. Meeting the challenge of providing cost-effective, viable degree programs in an isolated location requires both patience and innovation.

  5. Integrating alternative splicing detection into gene prediction

    PubMed Central

    Foissac, Sylvain; Schiex, Thomas

    2005-01-01

    Background Alternative splicing (AS) is now considered as a major actor in transcriptome/proteome diversity and it cannot be neglected in the annotation process of a new genome. Despite considerable progresses in term of accuracy in computational gene prediction, the ability to reliably predict AS variants when there is local experimental evidence of it remains an open challenge for gene finders. Results We have used a new integrative approach that allows to incorporate AS detection into ab initio gene prediction. This method relies on the analysis of genomically aligned transcript sequences (ESTs and/or cDNAs), and has been implemented in the dynamic programming algorithm of the graph-based gene finder EuGÈNE. Given a genomic sequence and a set of aligned transcripts, this new version identifies the set of transcripts carrying evidence of alternative splicing events, and provides, in addition to the classical optimal gene prediction, alternative optimal predictions (among those which are consistent with the AS events detected). This allows for multiple annotations of a single gene in a way such that each predicted variant is supported by a transcript evidence (but not necessarily with a full-length coverage). Conclusions This automatic combination of experimental data analysis and ab initio gene finding offers an ideal integration of alternatively spliced gene prediction inside a single annotation pipeline. PMID:15705189

  6. Academic Programs in Alternative Education: An Overview

    ERIC Educational Resources Information Center

    Ruzzi, Betsy Brown; Kraemer, Jacqueline

    2006-01-01

    This paper, second in a series of papers on alternative education, examines the academic programming in alternative education programs by reviewing the literature specifically focused on the academic programs in alternative education and summarizing a survey of fifteen alternative education programs. It suggests options for further research on…

  7. Alcoholism and alternative splicing of candidate genes.

    PubMed

    Sasabe, Toshikazu; Ishiura, Shoichi

    2010-04-01

    Gene expression studies have shown that expression patterns of several genes have changed during the development of alcoholism. Gene expression is regulated not only at the level of transcription but also through alternative splicing of pre-mRNA. In this review, we discuss some of the evidence suggesting that alternative splicing of candidate genes such as DRD2 (encoding dopamine D2 receptor) may form the basis of the mechanisms underlying the pathophysiology of alcoholism. These reports suggest that aberrant expression of splice variants affects alcohol sensitivities, and alcohol consumption also regulates alternative splicing. Thus, investigations of alternative splicing are essential for understanding the molecular events underlying the development of alcoholism.

  8. The Foreign Language Requirement: An Alternative Program.

    ERIC Educational Resources Information Center

    Demuth, Katherine A.; Smith, Nathaniel B.

    1987-01-01

    A new program at Boston University that identifies students who would have great difficulty fulfilling their foreign language requirement is described. This program offers an alternative sequence of courses designed to help these students achieve foreign language learning success. (LMO)

  9. [EDAS, databases of alternatively spliced human genes].

    PubMed

    Nurtdinov, R N; Neverov, A D; Mal'ko, D B; Kosmodem'ianskiĭ, I A; Ermakova, E O; Ramenskiĭ, V E; Mironov, A A; Gel'fand, M S

    2006-01-01

    EDAS, a database of alternatively spliced human genes, contains data on the alignment of proteins, mRNAs, and EST. It contains information on all exons and introns observed, as well as elementary alternatives formed from them. The database makes it possible to filter the output data by changing the cut-off threshold by the significance level. The database is accessible at http://www.gene-bee.msu.ru/edas/.

  10. Alternative Teacher Certification: A Program Theory Analysis

    ERIC Educational Resources Information Center

    Scribner, Jay Paredes; Heinen, Ethan

    2009-01-01

    "Alternative teacher certification program" (ATCP) is widely used as a term for a variety of programs designed to train and credential teachers in expedited fashion. In practice, however, ATCPs consist of a loose confederation of programs and practices ranging from "emergency certification to very sophisticated and well-designed…

  11. An Alternative Professional Development Program: Lessons Learned

    ERIC Educational Resources Information Center

    Erklenz-Watts, Michelle; Westbay, Theresa; Lynd-Balta, Eileen

    2006-01-01

    This article describes how a group of small liberal arts college faculty embraced the opportunity to create a faculty learning circle as an alternative professional development program. We provide a review of the program, discuss the lessons learned, and offer recommendations for future efforts in developing a similar faculty development program.…

  12. Alternative Programs and Desegregation in Flint, Michigan

    ERIC Educational Resources Information Center

    Kugler, Marianne Russell

    1978-01-01

    Discusses the results of the Flint, Michigan Board of Education's decision to include extensive development of alternative programs as part of the Quality Education/Desegregation Plan developed for the Flint schools. (Author/RK)

  13. Alternative Programs and Desegregation in Flint, Michigan

    ERIC Educational Resources Information Center

    Kugler, Marianne Russell

    1978-01-01

    Discusses the results of the Flint, Michigan Board of Education's decision to include extensive development of alternative programs as part of the Quality Education/Desegregation Plan developed for the Flint schools. (Author/RK)

  14. Alternate nozzle ablative materials program

    NASA Technical Reports Server (NTRS)

    Kimmel, N. A.

    1984-01-01

    Four subscale solid rocket motor tests were conducted successfully to evaluate alternate nozzle liner, insulation, and exit cone structural overwrap components for possible application to the Space Shuttle Solid Rocket Motor (SRM) nozzle asasembly. The 10,000 lb propellant motor tests were simulated, as close as practical, the configuration and operational environment of the full scale SRM. Fifteen PAN based and three pitch based materials had no filler in the phenolic resin, four PAN based materials had carbon microballoons in the resin, and the rest of the materials had carbon powder in the resin. Three nozzle insulation materials were evaluated; an aluminum oxide silicon oxide ceramic fiber mat phenolic material with no resin filler and two E-glass fiber mat phenolic materials with no resin filler. It was concluded by MTI/WD (the fabricator and evaluator of the test nozzles) and NASA-MSFC that it was possible to design an alternate material full scale SRM nozzle assembly, which could provide an estimated 360 lb increased payload capability for Space Shuttle launches over that obtainable with the current qualified SRM design.

  15. A Guide for Alternative Certification Program Improvement.

    ERIC Educational Resources Information Center

    McKibbin, Michael; Ray, Lisa

    1994-01-01

    Four conditions for creating or refining alternative teacher certification programs are improving instruction, addressing shortages of qualified teachers, placing teachers in hard-to-staff schools, and measuring teacher competence. Programs should be pragmatic, market sensitive, embedded in the learning context, and performance driven. (SK)

  16. Bridge Program: An Alternative Curricular Model

    ERIC Educational Resources Information Center

    George, Deborah A.

    2012-01-01

    With the motivation for career advancement, many adult learners have chosen to return to graduate education or professional programs. The bridge program is one relatively new alternative curricular model available for adult learners who wish to build on their education within their chosen profession. Evidence on the effectiveness of such programs…

  17. Alternative Learning Programs Evaluation: Part 1 Report.

    ERIC Educational Resources Information Center

    North Carolina State Dept. of Public Instruction, Raleigh. Div. of Accountability Services/Research.

    In North Carolina, Alternative Learning Programs (ALP) is a designation applied to a variety of activities, locations, and student characteristics. This report focuses on descriptive information about the state's ALP efforts, teachers, and the students they serve. Two hundred and fifteen schools and programs met the evaluation criteria as ALPs.…

  18. Alternatives for Revitalizing Student Services Programs.

    ERIC Educational Resources Information Center

    Deegan, William L.

    1984-01-01

    Reviews alternatives for revitalizing the programs and management of community college student services. As program development models, considers Miami-Dade Community College's computer-based instructional management system; entrepreneurial fee-based services; and divestment of situational or special-interest services to student groups. In…

  19. Bridge Program: An Alternative Curricular Model

    ERIC Educational Resources Information Center

    George, Deborah A.

    2012-01-01

    With the motivation for career advancement, many adult learners have chosen to return to graduate education or professional programs. The bridge program is one relatively new alternative curricular model available for adult learners who wish to build on their education within their chosen profession. Evidence on the effectiveness of such programs…

  20. Evaluation of the NYCTF Program as an Alternative Certification Program.

    ERIC Educational Resources Information Center

    Stein, Judith

    The New York City Teaching Fellows (NYCTF) program was established in August 2000 as an alternative certification program to try to fill the void for certified teachers in SURR (Schools Under Registration Review) schools, since a disproportionate number of teachers at SURR schools are not certified. To evaluate the success of the program, a…

  1. Gene and alternative splicing annotation with AIR

    PubMed Central

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V.; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts. PMID:15632090

  2. Gene and alternative splicing annotation with AIR.

    PubMed

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts.

  3. School Counseling in Disciplinary Alternative Education Programs

    ERIC Educational Resources Information Center

    Mullen, Patrick R.; Lambie, Glenn W.

    2013-01-01

    Disciplinary alternative education programs (DAEP) service many students; however, limited literature is published for school counselors working in these schools. Therefore, this manuscript provides a conceptual foundation for counselors working with students attending DAEPs. Specifically, the manuscript (a) reviews the types of alternative…

  4. Grants for Alternative Programs. Research Brief

    ERIC Educational Resources Information Center

    Muir, Mike

    2004-01-01

    There seem to be no grants directly geared toward alternative programs (although the Bill and Melinda Gates Foundation has an interest in funding projects focusing on reforming high schools). This should not be a deterrent, however, as there are plenty of funding sources interested in projects and activities which would support an alternative…

  5. An alternative splicing program promotes adipose tissue thermogenesis

    PubMed Central

    Vernia, Santiago; Edwards, Yvonne JK; Han, Myoung Sook; Cavanagh-Kyros, Julie; Barrett, Tamera; Kim, Jason K; Davis, Roger J

    2016-01-01

    Alternative pre-mRNA splicing expands the complexity of the transcriptome and controls isoform-specific gene expression. Whether alternative splicing contributes to metabolic regulation is largely unknown. Here we investigated the contribution of alternative splicing to the development of diet-induced obesity. We found that obesity-induced changes in adipocyte gene expression include alternative pre-mRNA splicing. Bioinformatics analysis associated part of this alternative splicing program with sequence specific NOVA splicing factors. This conclusion was confirmed by studies of mice with NOVA deficiency in adipocytes. Phenotypic analysis of the NOVA-deficient mice demonstrated increased adipose tissue thermogenesis and improved glycemia. We show that NOVA proteins mediate a splicing program that suppresses adipose tissue thermogenesis. Together, these data provide quantitative analysis of gene expression at exon-level resolution in obesity and identify a novel mechanism that contributes to the regulation of adipose tissue function and the maintenance of normal glycemia. DOI: http://dx.doi.org/10.7554/eLife.17672.001 PMID:27635635

  6. Alternative Learning Programs Evaluation: Part 3 Report. Case Studies of Alternative Schools and Programs.

    ERIC Educational Resources Information Center

    Cobb, Caronly; Brewer, Delores; Bauman, Amy; Groves, Paula; Rayle, Joesph; Noblit, George

    In 1996, North Carolina began a 5-year evaluation of alternative learning programs (ALPs). This report contains in-depth case studies of four ALPs during the 1996-97 school year. The ALPs were selected to represent different types of programs in the state, and include one middle school, two high school, and one elementary school programs. The case…

  7. Alternative promoters of gene MAGE4a

    SciTech Connect

    De Plaen, E.; Naerhuyzen, B.; De Smet, C.

    1997-03-01

    Gene MAGE-4 (HGMW-approved symbol MAGE4) is expressed in several types of tumors, but not in normal tissues, except testis and placenta. The 5{prime} end of this gene contains eight homologous exons spread over a 5.8-kb region. These exons are alternatively spliced to a unique second exon and a unique third exon, which encodes a protein of 317 amino acids. The analysis of transcripts found in testis, placenta, and a sarcoma cell line showed that each of the alternative first exons is used in at least one of these tissues. Various regions of the promoter of the fifth alternative exon (1.5) were cloned in a luciferase reporter plasmid, and the constructs were transfected in a sarcoma cell line that expresses MAGE-4. Two Ets motifs located between positions -70 and -29 relative to the transcription start site were found to drive 55% of the promoter activity. A region containing an Sp1 consensus binding site located upstream of the two Ets motifs was found to be responsible for 44% of the transcriptional activity. MAGE-4a promoters 1.4 and 1.6, which also contain the Sp1 and the two Ets binding motifs, supported a level of transcription comparable to that of promoter 1.5, whereas promoter 1.1, which contains only one Ets binding site, was sixfold less active. In line with observations made with gene MAGE-1 (HGMW-approved symbol MAGE1), we found that promoter 1.5 stimulated a high level of transcription in a melanoma cell line that does not express MAGE-4. This suggests that the tumor-specific expression of MAGE genes is not determined by the presence of specific transcription factors. 26 refs., 7 figs., 2 tabs.

  8. An alternative method on quadratic programming problems

    NASA Astrophysics Data System (ADS)

    Dasril, Y.; Mohd, I. B.; Mustaffa, I.; Aminuddin, MMM.

    2015-05-01

    In this paper we proposed an alternative approach to find the optimum solution of quadratic programming problems (QPP) in its original form without additional information such as slack variable, surplus variable or artificial variable as done in other favourite methods. This approached is based on the violated constraints by the unconstrained optimum. The optimal solution of QPP obtained by searching from initial point to another point alongside of feasible region.

  9. Vials: Visualizing Alternative Splicing of Genes

    PubMed Central

    Strobelt, Hendrik; Alsallakh, Bilal; Botros, Joseph; Peterson, Brant; Borowsky, Mark; Pfister, Hanspeter; Lex, Alexander

    2016-01-01

    Alternative splicing is a process by which the same DNA sequence is used to assemble different proteins, called protein isoforms. Alternative splicing works by selectively omitting some of the coding regions (exons) typically associated with a gene. Detection of alternative splicing is difficult and uses a combination of advanced data acquisition methods and statistical inference. Knowledge about the abundance of isoforms is important for understanding both normal processes and diseases and to eventually improve treatment through targeted therapies. The data, however, is complex and current visualizations for isoforms are neither perceptually efficient nor scalable. To remedy this, we developed Vials, a novel visual analysis tool that enables analysts to explore the various datasets that scientists use to make judgments about isoforms: the abundance of reads associated with the coding regions of the gene, evidence for junctions, i.e., edges connecting the coding regions, and predictions of isoform frequencies. Vials is scalable as it allows for the simultaneous analysis of many samples in multiple groups. Our tool thus enables experts to (a) identify patterns of isoform abundance in groups of samples and (b) evaluate the quality of the data. We demonstrate the value of our tool in case studies using publicly available datasets. PMID:26529712

  10. An Examination of School Climate in Effective Alternative Programs

    ERIC Educational Resources Information Center

    Quinn, Mary Magee; Poirier, Jeffrey M.; Faller, Susan E.; Gable, Robert A.; Tonelson, Steven W.

    2006-01-01

    The alternative education field lacks a common definition and has a major divide between the differing philosophies of alternative programs; little empirical evidence is available to identify the components necessary to create effective alternative educational programs. Tremendous growth in the availability of alternative programs in the United…

  11. Impact of Alternative Programs on an Urban School District.

    ERIC Educational Resources Information Center

    Vincenzi, Harry; Fishman, Roger J.

    The number of secondary alternative programs in the school district of Philadelphia has grown to 75 giving it one of the largest networks of alternative programs in the country. The object of this paper is to report on the impact of those programs. The programs are divided into four categories: (1) disruptive/ truant programs, (2) career programs,…

  12. 33 CFR 101.125 - Approved Alternative Security Programs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Programs. The following have been approved, by the Commandant (CG-54), as Alternative Security Programs... 106 of this subchapter, as applicable: (a) American Gaming Association Alternative Security Program, dated September 11, 2003. (b) American Waterways Operators Alternative Security Program for Tugboats...

  13. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Alternative Security Program. 106... Security Program. An OCS facility owner or operator may use an Alternative Security Program approved under § 101.120 of this subchapter if: (a) The Alternative Security Program is appropriate to that OCS...

  14. 33 CFR 101.125 - Approved Alternative Security Programs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Programs. The following have been approved, by the Commandant (CG-54), as Alternative Security Programs... 106 of this subchapter, as applicable: (a) American Gaming Association Alternative Security Program, dated September 11, 2003. (b) American Waterways Operators Alternative Security Program for Tugboats...

  15. Alternative-splicing-mediated gene expression

    NASA Astrophysics Data System (ADS)

    Wang, Qianliang; Zhou, Tianshou

    2014-01-01

    Alternative splicing (AS) is a fundamental process during gene expression and has been found to be ubiquitous in eukaryotes. However, how AS impacts gene expression levels both quantitatively and qualitatively remains to be fully explored. Here, we analyze two common models of gene expression, each incorporating a simple splice mechanism that a pre-mRNA is spliced into two mature mRNA isoforms in a probabilistic manner. In the constitutive expression case, we show that the steady-state molecular numbers of two mature mRNA isoforms follow mutually independent Poisson distributions. In the bursting expression case, we demonstrate that the tail decay of the steady-state distribution for both mature mRNA isoforms that in general are not mutually independent can be characterized by the product of mean burst size and splicing probability. In both cases, we find that AS can efficiently modulate both the variability (measured by variance) and the noise level of the total mature mRNA, and in particular, the latter is always lower than the noise level of the pre-mRNA, implying that AS always reduces the noise. These results altogether reveal that AS is a mechanism of efficiently controlling the gene expression noise.

  16. 76 FR 11310 - Alternatives Analysis Program Discretionary Funding Allocations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-01

    ... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Transit Administration Alternatives Analysis Program Discretionary Funding Allocations AGENCY: Federal Transit Administration (FTA), DOT. ACTION: Alternatives Analysis Program Announcement of Project...

  17. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Alternative Security Program. 105... MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a) A facility owner or operator may use an Alternative Security Program approved under § 101.120 of this...

  18. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Alternative Security Programs... MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A vessel owner or operator may use an Alternative Security Program as approved under § 101.120 of this subchapter...

  19. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Alternative Security Program. 105... MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a) A facility owner or operator may use an Alternative Security Program approved under § 101.120 of this...

  20. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 33 Navigation and Navigable Waters 1 2011-07-01 2011-07-01 false Alternative Security Programs... MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A vessel owner or operator may use an Alternative Security Program as approved under § 101.120 of this subchapter...

  1. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Alternative Security Program. 105... MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a) A facility owner or operator may use an Alternative Security Program approved under § 101.120 of this...

  2. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Alternative Security Program. 105... MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a) A facility owner or operator may use an Alternative Security Program approved under § 101.120 of this...

  3. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Alternative Security Programs... MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A vessel owner or operator may use an Alternative Security Program as approved under § 101.120 of this subchapter...

  4. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Alternative Security Programs... MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A vessel owner or operator may use an Alternative Security Program as approved under § 101.120 of this subchapter...

  5. Variables Affecting the Success of Alternative School Programs in Mississippi

    ERIC Educational Resources Information Center

    Haley, Sherlyn Williams

    2009-01-01

    This study focused on examining the effect of two alternative school types on student success in Mississippi. To determine alternative school type, alternative program directors self-reported program design, and schools were divided into two groups. Type I schools were defined as "punitive-based" programs in which students receive…

  6. 33 CFR 104.140 - Alternative Security Programs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Alternative Security Programs... MARITIME SECURITY MARITIME SECURITY: VESSELS General § 104.140 Alternative Security Programs. A vessel owner or operator may use an Alternative Security Program as approved under § 101.120 of this subchapter...

  7. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Alternative Security Program. 106... MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135 Alternative Security Program. An OCS facility owner or operator may use an Alternative Security Program approved under...

  8. Alternative Education Guidelines, Model Middle School Alternative Education Program. Workshop II. Prevention Programs & Funding.

    ERIC Educational Resources Information Center

    National Association of School Security Directors, Bellevue, WA.

    These workshop materials are the guidelines Broward County (Florida) has established to carry out the state legislative mandate authorizing school boards to establish educational alternative programs to meet the individual needs and interests of students who are disruptive, unsucessful, or disinterested in the normal school environment. Included…

  9. Alternative Strategies for Gene Therapy of Hemophilia

    PubMed Central

    Montgomery, Robert R.; Shi, Qizhen

    2012-01-01

    Hemophilia A and B are monogenic disorders that were felt to be ideal targets for initiation of gene therapy. Although the first hemophilia gene therapy trial has been over 10 years ago, few trials are currently actively recruiting. Although preclinical studies in animals were promising, levels achieved in humans did not achieve long-term expression at adequate levels to achieve cures. Transplantation as a source of cellular replacement therapy for both hemophilia A and B have been successful following liver transplantation in which the recipient produces normal levels of either factor VIII (FVIII) or factor IX (FIX). Most of these transplants have been conducted for the treatment of liver failure rather than for “curing” hemophilia. There are a variety of new strategies for delivering the missing clotting factor through ectopic expression of the deficient protein. One approach uses hematopoietic stem cells using either a nonspecific promoter or using a lineage-specific promoter. An alternative strategy includes enhanced expression in endothelial cells or blood-outgrowth endothelial cells. An additional approach includes the expression of FVIII or FIX intraarticularly to mitigate the intraarticular bleeding that causes much of the disability for hemophilia patients. Because activated factor VII (FVIIa) can be used to treat patients with inhibitory antibodies to replacement clotting factors, preclinical gene therapy has been performed using platelet- or liver-targeted FVIIa expression. All of these newer approaches are just beginning to be explored in large animal models. Whereas improved recombinant replacement products continue to be the hallmark of hemophilia therapy, the frequency of replacement therapy is beginning to be addressed through longer-acting replacement products. A safe cure of hemophilia is still the desired goal, but many barriers must still be overcome. PMID:21239794

  10. Alternative strategies for gene therapy of hemophilia.

    PubMed

    Montgomery, Robert R; Shi, Qizhen

    2010-01-01

    Hemophilia A and B are monogenic disorders that were felt to be ideal targets for initiation of gene therapy. Although the first hemophilia gene therapy trial has been over 10 years ago, few trials are currently actively recruiting. Although preclinical studies in animals were promising, levels achieved in humans did not achieve long-term expression at adequate levels to achieve cures. Transplantation as a source of cellular replacement therapy for both hemophilia A and B have been successful following liver transplantation in which the recipient produces normal levels of either factor VIII (FVIII) or factor IX (FIX). Most of these transplants have been conducted for the treatment of liver failure rather than for "curing" hemophilia. There are a variety of new strategies for delivering the missing clotting factor through ectopic expression of the deficient protein. One approach uses hematopoietic stem cells using either a nonspecific promoter or using a lineage-specific promoter. An alternative strategy includes enhanced expression in endothelial cells or blood-outgrowth endothelial cells. An additional approach includes the expression of FVIII or FIX intraarticularly to mitigate the intraarticular bleeding that causes much of the disability for hemophilia patients. Because activated factor VII (FVIIa) can be used to treat patients with inhibitory antibodies to replacement clotting factors, preclinical gene therapy has been performed using platelet- or liver-targeted FVIIa expression. All of these newer approaches are just beginning to be explored in large animal models. Whereas improved recombinant replacement products continue to be the hallmark of hemophilia therapy, the frequency of replacement therapy is beginning to be addressed through longer-acting replacement products. A safe cure of hemophilia is still the desired goal, but many barriers must still be overcome.

  11. An Analysis of State Policies Connected with Alternative School Programs

    ERIC Educational Resources Information Center

    Bielefeld, William C.; Stubblefield, Anna; Templeton, Zach

    2009-01-01

    Many school districts offer alternative education programs for their students who do not succeed in the regular classroom. At the high school level, many of these programs are separated from the regular schools. It seemed that many districts were establishing alternative education programs, but there were differences in the types of programs that…

  12. An Analysis of State Policies Connected with Alternative School Programs

    ERIC Educational Resources Information Center

    Bielefeld, William C.; Stubblefield, Anna; Templeton, Zach

    2009-01-01

    Many school districts offer alternative education programs for their students who do not succeed in the regular classroom. At the high school level, many of these programs are separated from the regular schools. It seemed that many districts were establishing alternative education programs, but there were differences in the types of programs that…

  13. Current and Needed Research on Alternative Certification Programs

    ERIC Educational Resources Information Center

    Ham, Edward

    2010-01-01

    With alternative certification programs gaining popularity in teacher education, the need to evaluate these programs has become much more necessary. Without strict guidelines to classify alternative certification programs, it is difficult to make generalizations about these programs because of different requirements for completion and…

  14. Current and Needed Research on Alternative Certification Programs

    ERIC Educational Resources Information Center

    Ham, Edward

    2010-01-01

    With alternative certification programs gaining popularity in teacher education, the need to evaluate these programs has become much more necessary. Without strict guidelines to classify alternative certification programs, it is difficult to make generalizations about these programs because of different requirements for completion and…

  15. Evaluating Organizational Training Programs: Alternatives and Criteria for Selection.

    ERIC Educational Resources Information Center

    Marth, Joseph; And Others

    Managers and program sponsors are often unaware of possible alternatives to costly training evaluation procedures and do not have criteria for selecting alternatives. What is needed is an understanding of the various levels of evaluating training programs, feasible alternatives, and decision criteria for choosing the right system. It is proposed…

  16. 33 CFR 101.125 - Approved Alternative Security Programs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 33 Navigation and Navigable Waters 1 2010-07-01 2010-07-01 false Approved Alternative Security... SECURITY MARITIME SECURITY MARITIME SECURITY: GENERAL General § 101.125 Approved Alternative Security Programs. The following have been approved, by the Commandant (CG-54), as Alternative Security Programs...

  17. Fourth annual report to Congress, Federal Alternative Motor Fuels Programs

    SciTech Connect

    1995-07-01

    This annual report to Congress presents the current status of the alternative fuel vehicle programs being conducted across the country in accordance with the Alternative Motor Fuels Act of 1988. These programs, which represent the most comprehensive data collection effort ever undertaken on alternative fuels, are beginning their fifth year. This report summarizes tests and results from the fourth year.

  18. 33 CFR 154.2180 - Alternative testing program-Generally.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Alternative testing program... Control Systems Alternative Analyzer and Pressure Sensor Reliability Testing § 154.2180 Alternative testing program—Generally. (a) As an alternative to complying with the vapor control system (VCS) analyzer...

  19. The Role of Alternative Programming in College Radio.

    ERIC Educational Resources Information Center

    Sauls, Samuel J.

    College radio is quite often viewed as the true alternative to commercial radio. However, what is alternative radio and how does college radio factor into the ideal? To further understand this concept, this paper focuses on the role of alternative programming in college radio. Areas discussed include alternative radio as a non-mainstream form of…

  20. EPAct Alternative Fuel Transporation Program - State and Alternative Fuel Provider Fleets: Frequently Asked Questions

    SciTech Connect

    2010-03-01

    Factsheet answering frequently asked questions about the U.S. Department of Energy's Alternative Fuel Transportation Program (the Program) that implements provisions of Titles III–V of the Energy Policy Act of 1992 (EPAct). Answers to questions that are frequently asked about the Program by managers of state government and alternative fuel provider fleets are provided in the factsheet.

  1. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Alternative security program. 27.235 Section 27.235 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.235 Alternative security program. (a)...

  2. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 6 Domestic Security 1 2014-01-01 2014-01-01 false Alternative security program. 27.235 Section 27.235 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.235 Alternative security program. (a)...

  3. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by...

  4. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by...

  5. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by...

  6. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by...

  7. 7 CFR 58.141 - Alternate quality control program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Alternate quality control program. 58.141 Section 58... Service 1 Quality Specifications for Raw Milk § 58.141 Alternate quality control program. When a plant has in operation an acceptable quality program, at the producer level, which is approved by the...

  8. An Alternative Program for Pregnant Schoolgirls.

    ERIC Educational Resources Information Center

    Link, Patricia W.

    The paper describes the Lafayette Parish Homebound Program (Louisiana) for students in grades K-12, with particular emphasis on the program's services for pregnant girls. Procedures for admitting students into the program, objectives for the pregnant girls (12-18 years old), and program components are considered. It is explained that the special…

  9. The Compensated Pulsed Alternator Program - A Review

    DTIC Science & Technology

    1981-06-01

    mechanical systems, CEM-UT proposed the compensated pulsed alternator approach in January, lg7s. The basic idea behind the compulsator concept is to...compen- sated, pulsed alternator is shown in Figure 1. STATIONARY FIELD COMPULSATOR Figure 1 Rotor (armature) winding Stator (compensating) winding... Compulsator An engineering prototype compulsator was designed and fabricated under contract to Lawrence Livermore National Laboratory (LLNL) to

  10. Six Powerful Practices for Alternative Education Programs

    ERIC Educational Resources Information Center

    Maillet, Andre L.

    2017-01-01

    Alternative schools can provide all students, especially those with challenging behaviors, low motivation, poor attendance, failing grades, or those afraid to even walk into the school building, with an engaging and enriching educational experience. Through designing, leading, and serving students as an administrator of an alternative middle…

  11. 33 CFR 155.5061 - Alternative Training and Exercise Program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 2 2014-07-01 2014-07-01 false Alternative Training and Exercise... Nontank Vessel Response Plans § 155.5061 Alternative Training and Exercise Program. (a) Owners or... exercise requirements of §§ 155.5055 and 155.5060, may meet an Alternative Training and Exercise...

  12. Toward a New Era: Alternatives for Revitalizing Student Services Programs.

    ERIC Educational Resources Information Center

    Deegan, William L.

    Alternatives for revitalizing the programs and management of student services in community colleges are reviewed in this paper. First, alternatives related to student services programs are considered, including: (1) the increased use of computer-assisted counseling to integrate student services more fully with mainstream academic activities; (2)…

  13. Toward a New Era: Alternatives for Revitalizing Student Services Programs.

    ERIC Educational Resources Information Center

    Deegan, William L.

    Alternatives for revitalizing the programs and management of student services in community colleges are reviewed in this paper. First, alternatives related to student services programs are considered, including: (1) the increased use of computer-assisted counseling to integrate student services more fully with mainstream academic activities; (2)…

  14. Alternative Schools and Programs: Five Descriptions. Technical Assistance Bulletin 37.

    ERIC Educational Resources Information Center

    National School Resource Network, Washington, DC.

    During the past ten years, many school districts have established alternative schools or programs for students who are seriously disruptive and academically unsuccessful. This bulletin describes five different types of alternative programs that have been effective in dealing with disruptive youth. They include the Tri-C Community Centered…

  15. 24 CFR 7.26 - EEO Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 24 Housing and Urban Development 1 2010-04-01 2010-04-01 false EEO Alternative Dispute Resolution...-Complaint Processing § 7.26 EEO Alternative Dispute Resolution Program. (a) The aggrieved person may elect to participate in the EEO ADR Program or the traditional EEO counseling procedures. When ADR is...

  16. Alternative splicing of DNA damage response genes and gastrointestinal cancers.

    PubMed

    Rahmutulla, Bahityar; Matsushita, Kazuyuki; Nomura, Fumio

    2014-12-14

    Alternative splicing, which is a common phenomenon in mammalian genomes, is a fundamental process of gene regulation and contributes to great protein diversity. Alternative splicing events not only occur in the normal gene regulation process but are also closely related to certain diseases including cancer. In this review, we briefly demonstrate the concept of alternative splicing and DNA damage and describe the association of alternative splicing and cancer pathogenesis, focusing on the potential relationship of alternative splicing, DNA damage, and gastrointestinal cancers. We will also discuss whether alternative splicing leads to genetic instability, which is considered to be a driving force for tumorigenesis. Better understanding of the role and mechanism of alternative splicing in tumorigenesis may provide new directions for future cancer studies.

  17. Spaces of Difference: The Contradictions of Alternative Educational Programs

    ERIC Educational Resources Information Center

    Vadeboncoeur, Jennifer A.

    2009-01-01

    Drawing upon the concept of "thirdspace" (Soja 1996), this article extends sociocultural theorizations of space in relation to alternative educational programs: programs designed to re-engage youth who have been pushed out of mainstream schools. Snapshots of educational programs, provided by ethnographic research gathered in the United…

  18. Spaces of Difference: The Contradictions of Alternative Educational Programs

    ERIC Educational Resources Information Center

    Vadeboncoeur, Jennifer A.

    2009-01-01

    Drawing upon the concept of "thirdspace" (Soja 1996), this article extends sociocultural theorizations of space in relation to alternative educational programs: programs designed to re-engage youth who have been pushed out of mainstream schools. Snapshots of educational programs, provided by ethnographic research gathered in the United…

  19. Alternative Strategies for Funding a General Dentistry Residency Program.

    ERIC Educational Resources Information Center

    Kralewski, John E.; Wiggins, Carla

    1987-01-01

    Three alternative program funding approaches used in other professions are examined: (1) the reorientation of selected dental schools toward graduate education, (2) emphasizing and marketing the service aspects of the programs, and (3) developing education programs as in-house training for large organizations. (MSE)

  20. Alternative Living Kidney Donation Programs Boost Genetically Unrelated Donation

    PubMed Central

    Poldervaart, Rosalie A.; Laging, Mirjam; Royaards, Tessa; Kal-van Gestel, Judith A.; van Agteren, Madelon; de Klerk, Marry; Zuidema, Willij; Betjes, Michiel G. H.; Roodnat, Joke I.

    2015-01-01

    Donor-recipient ABO and/or HLA incompatibility used to lead to donor decline. Development of alternative transplantation programs enabled transplantation of incompatible couples. How did that influence couple characteristics? Between 2000 and 2014, 1232 living donor transplantations have been performed. In conventional and ABO-incompatible transplantation the willing donor becomes an actual donor for the intended recipient. In kidney-exchange and domino-donation the donor donates indirectly to the intended recipient. The relationship between the donor and intended recipient was studied. There were 935 conventional and 297 alternative program transplantations. There were 66 ABO-incompatible, 68 domino-paired, 62 kidney-exchange, and 104 altruistic donor transplantations. Waiting list recipients (n = 101) were excluded as they did not bring a living donor. 1131 couples remained of whom 196 participated in alternative programs. Genetically unrelated donors (486) were primarily partners. Genetically related donors (645) were siblings, parents, children, and others. Compared to genetically related couples, almost three times as many genetically unrelated couples were incompatible and participated in alternative programs (P < 0.001). 62% of couples were genetically related in the conventional donation program versus 32% in alternative programs (P < 0.001). Patient and graft survival were not significantly different between recipient programs. Alternative donation programs increase the number of transplantations by enabling genetically unrelated donors to donate. PMID:26421181

  1. A Futuristic Alternative: Campus Fitness Programming.

    ERIC Educational Resources Information Center

    Mueller, C. E.; Oatey, Jennifer Sue

    1980-01-01

    The components of a prescription physical fitness program include a physical examination, fitness and dietary assessment, consultations to determine the fitness and diet prescriptions, instructional sessions, and periodic reviews of the individual's prescription. (CJ)

  2. Alternative mathematical programming formulations for FSS synthesis

    NASA Technical Reports Server (NTRS)

    Reilly, C. H.; Mount-Campbell, C. A.; Gonsalvez, D. J. A.; Levis, C. A.

    1986-01-01

    A variety of mathematical programming models and two solution strategies are suggested for the problem of allocating orbital positions to (synthesizing) satellites in the Fixed Satellite Service. Mixed integer programming and almost linear programming formulations are presented in detail for each of two objectives: (1) positioning satellites as closely as possible to specified desired locations, and (2) minimizing the total length of the geostationary arc allocated to the satellites whose positions are to be determined. Computational results for mixed integer and almost linear programming models, with the objective of positioning satellites as closely as possible to their desired locations, are reported for three six-administration test problems and a thirteen-administration test problem.

  3. 77 FR 32038 - Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-31

    ...; ] DEPARTMENT OF ENERGY 10 CFR Parts 429, 430, and 431 RIN 1904-AC46 Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating Methods AGENCY: Office of Energy Efficiency and Renewable Energy, Department of Energy. ACTION: Notice of proposed rulemaking. SUMMARY: The U.S. Department...

  4. Approval Letter for an Alternative Renewable Biomass Tracking Program

    EPA Pesticide Factsheets

    This January 27, 2015 letter and decision document from EPA approves the Argentine Chamber of Biofuel's (CARBIO) Alternate Biomass Traking Program meeting all the requirements outlined in 40 CFR § 80.1454, including elements determined necessary to achieve

  5. 33 CFR 105.140 - Alternative Security Program.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... a Facility Vulnerability and Security Measures Summary (Form CG-6025) in appendix A to part 105—Facility Vulnerability and Security (CG-6025). ... MARITIME SECURITY MARITIME SECURITY: FACILITIES General § 105.140 Alternative Security Program. (a) A...

  6. Alternatives for Financing School Energy Savings Programs.

    ERIC Educational Resources Information Center

    Esteves, Rich

    1983-01-01

    This report compares shared-savings programs with financing through the use of internal funds, loans, leases, and lease purchase plans for financing energy conservation in nonprofit buildings. The shared savings option was found to offer the greatest benefits to the customer. (MLF)

  7. Degree program alternatives for fulltime employees

    SciTech Connect

    Strong, K.; Thayer, M.

    1992-01-01

    Los Alamos National Laboratory supports and sponsors degree programs for employees in order to help attract and retain the staff required to succeed in its mission. The support for these programs is provided by the Employee and Organization Development Group (HRD-3) which oversees the development, implementation, and delivery. This paper defines successful programs and suggests techniques to achieve a quality product. In order to attract the staff that it needs, the Laboratory has long recognized that educational opportunities must be available to its employees. To meet this need, the University of New Mexico (UNM) Los Alamos Center for Graduate Studies (LACGS) was established in 1956 and represents a unique cooperative venture between the Laboratory and UNM. The LACGS is funded primarily from the Laboratory. Over the years the LACGS has been a primary source of graduate degree programs for Laboratory employees, but until recently most offerings were not systematic or sequential. Nor was there any method to increase the variety of degree options.

  8. Degree program alternatives for fulltime employees

    SciTech Connect

    Strong, K.; Thayer, M.

    1992-03-01

    Los Alamos National Laboratory supports and sponsors degree programs for employees in order to help attract and retain the staff required to succeed in its mission. The support for these programs is provided by the Employee and Organization Development Group (HRD-3) which oversees the development, implementation, and delivery. This paper defines successful programs and suggests techniques to achieve a quality product. In order to attract the staff that it needs, the Laboratory has long recognized that educational opportunities must be available to its employees. To meet this need, the University of New Mexico (UNM) Los Alamos Center for Graduate Studies (LACGS) was established in 1956 and represents a unique cooperative venture between the Laboratory and UNM. The LACGS is funded primarily from the Laboratory. Over the years the LACGS has been a primary source of graduate degree programs for Laboratory employees, but until recently most offerings were not systematic or sequential. Nor was there any method to increase the variety of degree options.

  9. EPAct Alternative Fuel Transportation Program: Success Story (Fact Sheet)

    SciTech Connect

    Not Available

    2010-08-01

    This success story highlights the EPAct Alternative Fuel Transportation Program's series of workshops that bring fleets regulated under the Energy Policy Act of 1992 (EPAct) together with Clean Cities stakeholders and fuel providers to form and strengthen regional partnerships and initiate projects that will deploy more alternative fuel infrastructure.

  10. Evaluation of the Union County Alternative to Suspension Program

    ERIC Educational Resources Information Center

    Dunlap, Joyce Ann

    2010-01-01

    The schools in Union County have undergone a tremendous amount of growth in the past decade. The growth in the county has led to an increase in discipline problems. In order to provide suspended students a second chance, Union County Public Schools implemented an alternative to suspension program, the Union County Alternative to Suspension Program…

  11. Another Alternative: A Ninety-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1976-01-01

    In May, 1974, Fresno County's Narcotic Abuse Treatment Program began a twenty-one-day outpatient methadone detoxification treatment modality. The results of the evaluation suggested an alternative treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the…

  12. Quality Alternative Certification Programs in Special Education Ensure High Retention

    ERIC Educational Resources Information Center

    Karge, Belinda D.; McCabe, Marjorie

    2014-01-01

    Market driven alternative routes to teaching have evolved into a quality program option and not just an answer to the teacher shortage. Alternative certification is a viable means of recruiting, training, and certifying those who have a bachelor's degree and a strong desire to enter the field of teaching. California has been a leader in the…

  13. Evaluating Alternative High Schools: Program Evaluation in Action

    ERIC Educational Resources Information Center

    Hinds, Drew Samuel Wayne

    2013-01-01

    Alternative high schools serve some of the most vulnerable students and their programs present a significant challenge to evaluate. Determining the impact of an alternative high school that serves mostly at-risk students presented a significant research problem. Few studies exist that dig deeper into the characteristics and strategies of…

  14. Another Alternative: A Ninety-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1976-01-01

    In May, 1974, Fresno County's Narcotic Abuse Treatment Program began a twenty-one-day outpatient methadone detoxification treatment modality. The results of the evaluation suggested an alternative treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the…

  15. Evaluation of the Union County Alternative to Suspension Program

    ERIC Educational Resources Information Center

    Dunlap, Joyce Ann

    2010-01-01

    The schools in Union County have undergone a tremendous amount of growth in the past decade. The growth in the county has led to an increase in discipline problems. In order to provide suspended students a second chance, Union County Public Schools implemented an alternative to suspension program, the Union County Alternative to Suspension Program…

  16. Evaluating Alternative High Schools: Program Evaluation in Action

    ERIC Educational Resources Information Center

    Hinds, Drew Samuel Wayne

    2013-01-01

    Alternative high schools serve some of the most vulnerable students and their programs present a significant challenge to evaluate. Determining the impact of an alternative high school that serves mostly at-risk students presented a significant research problem. Few studies exist that dig deeper into the characteristics and strategies of…

  17. Cloning and expression of the potato alternative oxidase gene

    SciTech Connect

    Hiser, C.; McIntosh, L. Michigan State Univ., East Lansing )

    1990-05-01

    Mitochondria from 24-hour-aged potato slices possess an alternative path capacity and a 36kD protein not present in fresh potato mitochondria. This 36kD protein was identified by a monoclonal antibody against the Sauromatum guttatum alternative oxidase. These results suggest de novo synthesis of the 36kD protein during the aging process. To investigate this phenomenon, a clone containing a potato alternative oxidase gene was isolated from a cDNA library using the S. guttatum gene as a probe. This clone shows areas of high homology to the S. guttatum gene. Norther blots of RNA from fresh and 24-hour-aged potato slices are being probed with the potato gene to examine its expression in relation to the appearance of the 36kD protein.

  18. Alternative Education: An Educational Support Program--Union City's Innovative Prototype for Alternative Education.

    ERIC Educational Resources Information Center

    Europa, Eunice

    1982-01-01

    An Alternative Education Program is discussed which uses existing educational personnel and funds to provide determined and persistent identification and intervention for potentially delinquent, nonachieving students in junior high school. Counselor interest and trust are stressed in working with students. Program development, criteria, and…

  19. Alternative Education: An Educational Support Program--Union City's Innovative Prototype for Alternative Education.

    ERIC Educational Resources Information Center

    Europa, Eunice

    1982-01-01

    An Alternative Education Program is discussed which uses existing educational personnel and funds to provide determined and persistent identification and intervention for potentially delinquent, nonachieving students in junior high school. Counselor interest and trust are stressed in working with students. Program development, criteria, and…

  20. Parents' Views of Alternative Public School Programs: Implications for the Use of Alternative Programs to Reduce School Dropout Rates.

    ERIC Educational Resources Information Center

    Collins, Roger L.

    1987-01-01

    Presents results of a survey of Cincinnati, OH, parents' views on alternative school programs (e.g., vocational curricula). Reports that parental approval plays a critical role in choosing particular schools and in a school's ability to retain students. Challenges the degree to which alternative schools act to resegregate school districts by…

  1. Fifth annual report to congress. Federal alternative motor fuels programs

    SciTech Connect

    1996-09-01

    This report presents the status of the US Department of Energy`s alternative fuel vehicle demonstration and performance tracking programs being conducted in accordance with the Energy Policy and Conservation Act. These programs comprise the most comprehensive data collection effort ever undertaken on alternative transportation fuels and alternative fuel vehicles. The report summarizes tests and results from the fifth year. Electric vehicles are not included in these programs, and the annual report does not include information on them. Since the inception of the programs, great strides have been made in developing commercially viable alternative fuel vehicle technologies. However, as is the case in the commercialization of all new technologies, some performance problems have been experienced on vehicles involved in early demonstration efforts. Substantial improvements have been recorded in vehicle practicality, safety, and performance in real-world demonstrations. An aspect of particular interest is emissions output. Results from light duty alternative fuel vehicles have demonstrated superior inservice emissions performance. Heavy duty alternative fuel vehicles have demonstrated dramatic reductions in particulate emissions. However, emissions results from vehicles converted to run on alternative fuel have not been as promising. Although the technologies available today are commercially viable in some markets, further improvements in infrastructure and economics will result in greater market expansion. Information is included in this report on light and heavy duty vehicles, transit buses, vehicle conversions, safety, infrastructure support, vehicle availability, and information dissemination.

  2. Hawaii alternative fuels utilization program. Phase 3, final report

    SciTech Connect

    Kinoshita, C.M.; Staackmann, M.

    1996-08-01

    The Hawaii Alternative Fuels Utilization Program originated as a five-year grant awarded by the US Department of Energy (USDOE) to the Hawaii Natural Energy Institute (HNEI) of the University of Hawaii at Manoa. The overall program included research and demonstration efforts aimed at encouraging and sustaining the use of alternative (i.e., substitutes for gasoline and diesel) ground transportation fuels in Hawaii. Originally, research aimed at overcoming technical impediments to the widespread adoption of alternative fuels was an important facet of this program. Demonstration activities centered on the use of methanol-based fuels in alternative fuel vehicles (AFVs). In the present phase, operations were expanded to include flexible fuel vehicles (FFVs) which can operate on M85 or regular unleaded gasoline or any combination of these two fuels. Additional demonstration work was accomplished in attempting to involve other elements of Hawaii in the promotion and use of alcohol fuels for ground transportation in Hawaii.

  3. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 45 Public Welfare 2 2012-10-01 2012-10-01 false Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  4. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 45 Public Welfare 2 2013-10-01 2012-10-01 true Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  5. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 45 Public Welfare 2 2011-10-01 2011-10-01 false Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  6. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 45 Public Welfare 2 2014-10-01 2012-10-01 true Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  7. Evaluating the Effectiveness of Traditional and Alternative Principal Preparation Programs

    ERIC Educational Resources Information Center

    Pannell, Summer; Peltier-Glaze, Bernnell M.; Haynes, Ingrid; Davis, Delilah; Skelton, Carrie

    2015-01-01

    This study sought to determine the effectiveness on increasing student achievement of principals trained in a traditional principal preparation program and those trained in an alternate route principal preparation program within the same Mississippi university. Sixty-six Mississippi principals and assistant principals participated in the study. Of…

  8. 45 CFR 400.69 - Alternative RCA programs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 2 2010-10-01 2010-10-01 false Alternative RCA programs. 400.69 Section 400.69 Public Welfare Regulations Relating to Public Welfare OFFICE OF REFUGEE RESETTLEMENT, ADMINISTRATION FOR CHILDREN AND FAMILIES, DEPARTMENT OF HEALTH AND HUMAN SERVICES REFUGEE RESETTLEMENT PROGRAM Refugee...

  9. Alternative Program in Small School Stays in the Mainstream.

    ERIC Educational Resources Information Center

    Fazio, Thomas J.; Rossi, Michael J.

    1991-01-01

    The Hastings Alternative School Program (HASP), designed for at-risk students, operates within Hastings-on-Hudson (New York) High School's regular program. Students are given an external structure and set of expectations enforced by an accountability system stressing communication and student responsibility. Nearly half of all HASP students go on…

  10. Therapeutic Nursery Programs: A Survey of Alternative Preschools.

    ERIC Educational Resources Information Center

    Marsh, Pamela T.

    Noting that therapeutic nursery programs (TNPs) offer one alternative to mainstream daycare or preschool settings for young children experiencing severe emotional and behavioral difficulties, this study gathered information about TNPs and their services. Response rate to a survey mailed to a nonrandom nationwide sample of 40 programs was 50…

  11. Selecting forest residue treatment alternatives using goal programming.

    Treesearch

    Bruce B. Bare; Brian F. Anholt

    1976-01-01

    The use of goal programing for selecting forest residue treatment alternatives within a multiple goal framework is described. The basic features of goal programing are reviewed and illustrated with a hypothetical problem involving the selection of residue treatments for 10 cutting units. Twelve residue-regeneration treatment combinations are evaluated by using physical...

  12. Foreign Language Alternative Programs - A Plea for Positive Modification in Foreign Language Programs.

    ERIC Educational Resources Information Center

    Matkovick, Edward

    This paper describes the Foreign Language Alternative Program (FLAP) of Bellevue Community College, in Washington state. The program is designed to provide students with alternative choices best fitted to their individual needs, and is thus individualized and equipped to deal with both academic and vocational programs. The first year of a given…

  13. Conservation of alternative polyadenylation patterns in mammalian genes.

    PubMed

    Ara, Takeshi; Lopez, Fabrice; Ritchie, William; Benech, Philippe; Gautheret, Daniel

    2006-07-26

    Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolution is limited by the lack of a reliable identification of conserved, equivalent poly(A) sites among species. We introduce here a working definition of conserved poly(A) sites as sites that are both (i) properly aligned in human and mouse orthologous 3' untranslated regions (UTRs) and (ii) supported by EST or cDNA data in both species. We identified about 4800 such conserved poly(A) sites covering one third of the orthologous gene set studied. Characteristics of conserved poly(A) sites such as processing efficiency and tissue-specificity were analyzed. Conserved sites show a higher processing efficiency but no difference in tissular distribution when compared to non-conserved sites. In general, alternative poly(A) sites are species-specific and involve minor, non-conserved sites that are unlikely to play essential roles. However, there are about 500 genes with conserved tandem poly(A) sites. A significant fraction of these conserved tandems display a conserved arrangement of major/minor sites in their 3' UTR, suggesting that these alternative 3' ends may be under selection. This analysis allows us to identify potential functional alternative poly(A) sites and provides clues on the selective mechanisms at play in the appearance of multiple poly(A) sites and their maintenance in the 3' UTRs of genes.

  14. Forest gene conservation programs in Alberta, Canada

    Treesearch

    Jodie. Krakowski

    2017-01-01

    Provincial tree improvement programs in Alberta began in 1976. Early gene conservation focused on ex situ measures such as seed and clone banking, and research trials of commercial species with tree improvement programs. The gene conservation program now encompasses representative and unique populations of all native tree species in situ. The ex situ program aims to...

  15. Abnormalities in Alternative Splicing of Apoptotic Genes and Cardiovascular Diseases

    PubMed Central

    Dlamini, Zodwa; Tshidino, Shonisani C.; Hull, Rodney

    2015-01-01

    Apoptosis is required for normal heart development in the embryo, but has also been shown to be an important factor in the occurrence of heart disease. Alternative splicing of apoptotic genes is currently emerging as a diagnostic and therapeutic target for heart disease. This review addresses the involvement of abnormalities in alternative splicing of apoptotic genes in cardiac disorders including cardiomyopathy, myocardial ischemia and heart failure. Many pro-apoptotic members of the Bcl-2 family have alternatively spliced isoforms that lack important active domains. These isoforms can play a negative regulatory role by binding to and inhibiting the pro-apoptotic forms. Alternative splicing is observed to be increased in various cardiovascular diseases with the level of alternate transcripts increasing elevated in diseased hearts compared to healthy subjects. In many cases these isoforms appear to be the underlying cause of the disease, while in others they may be induced in response to cardiovascular pathologies. Regardless of this, the detection of alternate splicing events in the heart can serve as useful diagnostic or prognostic tools, while those splicing events that seem to play a causative role in cardiovascular disease make attractive future drug targets. PMID:26580598

  16. Alternative management and funding options for aeronautics programs, Task 1

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research and technology will be at lower program levels with basic military research for aviation decreasing as fewer aircraft programs are initiated and the present new aircraft programs move into the prototype and production status. The key question is can industry take on the management and financing role and meet the criteria and characteristics considered essential for a viable research and technology program. The criteria for evaluating alternative approaches include an examination of the nature of the product to be provided, responsiveness to changing needs, efficiency in terms of costs, ability to provide leadership, and to provide impartial and independent evaluation of approaches, and to provide technological inputs for regulating functions.

  17. Program Description ModMAP (Modular Multiple Alternatives Program) 1973-1974.

    ERIC Educational Resources Information Center

    Bridgeport Univ., CT. Coll. of Education.

    The Modular Multiple Alternatives Program (ModMAP) is the first competency-based individualized graduate program in teacher education in Connecticut. The program focuses on the training of elementary teachers and includes both Master's and Sixth Year level options. This program deals with creating more flexible and relevant types of teacher…

  18. ModMAP (Modular Multiple Alternatives Program). Program Description 1973-1974.

    ERIC Educational Resources Information Center

    Bridgeport Univ., CT. Coll. of Education.

    The Modular Multiple Alternatives Program (ModMaP), being developed at the University of Bridgeport, is the first competency-based, individualized graduate program in teacher education in the state of Connecticut. The program focuses on elementary teacher training and includes both master's and six-year level options. The program provides the…

  19. Alternative Route Programs for Certification in Special Education: Program Infrastructure Instructional Delivery, and Participant Characteristics

    ERIC Educational Resources Information Center

    Rosenberg, Michael S.; Boyer, K. Lynn; Sindelar, Paul T.; Misra, Sunil K.

    2007-01-01

    This study describes special education alternative route (AR) teacher preparation programs. The authors developed a national database of programs and collected information on program sponsorship, length and intensity, features, and participant demographics. Most of the 235 programs in the database were in states that had significant shortages of…

  20. Alternative Route Programs for Certification in Special Education: Program Infrastructure Instructional Delivery, and Participant Characteristics

    ERIC Educational Resources Information Center

    Rosenberg, Michael S.; Boyer, K. Lynn; Sindelar, Paul T.; Misra, Sunil K.

    2007-01-01

    This study describes special education alternative route (AR) teacher preparation programs. The authors developed a national database of programs and collected information on program sponsorship, length and intensity, features, and participant demographics. Most of the 235 programs in the database were in states that had significant shortages of…

  1. Conservation of alternative polyadenylation patterns in mammalian genes

    PubMed Central

    Ara, Takeshi; Lopez, Fabrice; Ritchie, William; Benech, Philippe; Gautheret, Daniel

    2006-01-01

    Background Alternative polyadenylation is a widespread mechanism contributing to transcript diversity in eukaryotes. Over half of mammalian genes are alternatively polyadenylated. Our understanding of poly(A) site evolution is limited by the lack of a reliable identification of conserved, equivalent poly(A) sites among species. We introduce here a working definition of conserved poly(A) sites as sites that are both (i) properly aligned in human and mouse orthologous 3' untranslated regions (UTRs) and (ii) supported by EST or cDNA data in both species. Results We identified about 4800 such conserved poly(A) sites covering one third of the orthologous gene set studied. Characteristics of conserved poly(A) sites such as processing efficiency and tissue-specificity were analyzed. Conserved sites show a higher processing efficiency but no difference in tissular distribution when compared to non-conserved sites. In general, alternative poly(A) sites are species-specific and involve minor, non-conserved sites that are unlikely to play essential roles. However, there are about 500 genes with conserved tandem poly(A) sites. A significant fraction of these conserved tandems display a conserved arrangement of major/minor sites in their 3' UTR, suggesting that these alternative 3' ends may be under selection. Conclusion This analysis allows us to identify potential functional alternative poly(A) sites and provides clues on the selective mechanisms at play in the appearance of multiple poly(A) sites and their maintenance in the 3' UTRs of genes. PMID:16872498

  2. Detecting alternative gene structures from spliced ESTs: a computational approach.

    PubMed

    Bonizzoni, Paola; Mauri, Giancarlo; Pesole, Graziano; Picardi, Ernesto; Pirola, Yuri; Rizzi, Raffaella

    2009-01-01

    Alternative splicing (AS) is currently considered as one of the main mechanisms able to explain the huge gap between the number of predicted genes and the high complexity of the proteome in humans. The rapid growth of Expressed Sequence Tag (EST) data has encouraged the development of computational methods to predict alternative splicing from the analysis of EST alignment to genome sequences. EST data are also a valuable source to reconstruct the different transcript isoforms that derive from the same gene structure as a consequence of AS, as indeed EST sequences are obtained by fragmenting mRNAs from the same gene. The most recent studies on alternative splice sites detection have revealed that this topic is a quite challenging computational problem, far from a solution. The main computational issues related to the problem of detecting alternative splicing are investigated in this paper, and we analyze algorithmic solutions for this problem. We first formalize an optimization problem related to the prediction of constitutive and alternative splicing sites from EST sequences, the Minimum Exons ESTs Factorization problem (in short, MEF), and show that it is Np-hard, even for restricted instances. This problem leads us to define sets of spliced EST, that is, a set of EST factorized into their constitutive exons with respect to a gene. Then we investigate the computational problem of predicting transcript isoforms from spliced EST sequences. We propose a graph algorithm for the problem that is linear in the number of predicted isoforms and size of the graph. Finally, an experimental analysis of the method is performed to assess the reliability of the predictions.

  3. Portfolios: An Alternative Method of Student and Program Assessment

    PubMed Central

    Hannam, Susan E.

    1995-01-01

    The use of performance-based evaluation and alternative assessment techniques has become essential for curriculum programs seeking Commission of Accreditation of Allied Health Education Programs (CAAHEP) accreditation. In athletic training education, few assessment models exist to assess student performance over the entire course of their educational program. This article describes a model of assessment-a student athletic training portfolio of “best works.” The portfolio can serve as a method to assess student development and to assess program effectiveness. The goals of the program include purposes specific to the five NATA performance domains. In addition, four types of portfolio evidence are described: artifacts, attestations, productions, and reproductions. Quality assignments and projects completed by students as they progress through a six-semester program are identified relative to the type of evidence and the domain(s) they represent. The portfolio assists with student development, provides feedback for curriculum planning, allows for student/faculty collaboration and “coaching” of the student, and assists with job searching. This information will serve as a useful model for those athletic training programs looking for an alternative method of assessing student and program outcomes. PMID:16558359

  4. Portfolios: an alternative method of student and program assessment.

    PubMed

    Hannam, S E

    1995-10-01

    The use of performance-based evaluation and alternative assessment techniques has become essential for curriculum programs seeking Commission of Accreditation of Allied Health Education Programs (CAAHEP) accreditation. In athletic training education, few assessment models exist to assess student performance over the entire course of their educational program. This article describes a model of assessment-a student athletic training portfolio of "best works." The portfolio can serve as a method to assess student development and to assess program effectiveness. The goals of the program include purposes specific to the five NATA performance domains. In addition, four types of portfolio evidence are described: artifacts, attestations, productions, and reproductions. Quality assignments and projects completed by students as they progress through a six-semester program are identified relative to the type of evidence and the domain(s) they represent. The portfolio assists with student development, provides feedback for curriculum planning, allows for student/faculty collaboration and "coaching" of the student, and assists with job searching. This information will serve as a useful model for those athletic training programs looking for an alternative method of assessing student and program outcomes.

  5. Educational Alternatives for Boating Safety Programs. Final Report.

    ERIC Educational Resources Information Center

    Sager, E.; And Others

    The Coast Guard, in efforts to improve the safety of recreational boating, undertook research to identify educational alternatives in boating safety programs. Background research was done to assess materials from areas of boating education and education in comparable recreational areas. Research was also conducted to review educational and mass…

  6. Alternate Learning Center. Abstracts of Inservice Training Programs.

    ERIC Educational Resources Information Center

    Rhode Island State Dept. of Education, Providence. Div. of Development and Operations.

    This booklet is a collection of abstracts describing the 18 programs offered at the Alternate Learning Center of the Rhode Island Teacher Center which has as its Primary function school based inservice training for local teachers and administrators. Each project is described in detail, including course goals, specific objectives, training…

  7. Evaluating the Prevention through Alternative Learning Styles Program

    ERIC Educational Resources Information Center

    Huber, Mary J.; Workman, Judson; Ford, Jo Ann; Moore, Dennis; Mayer, Theresa

    2009-01-01

    This article reports on the evaluation of a two-year alcohol, tobacco and other drug (ATOD) intervention, the Prevention through Alternative Learning Styles ("PALS") program, targeting both teachers and middle-school students. Teachers are taught to recognize students' unique learning styles in the context of the ATOD curriculum and…

  8. Disciplinary Alternative Education Programs in Texas--A 2009 Update

    ERIC Educational Resources Information Center

    Cortez, Albert; Cortez, Josie Danini

    2009-01-01

    This report discusses the issues surrounding the disciplinary alternative education programs (DAEPs) in Texas, its updated findings, and the authors' recommendations on what the state should do to address DAEP problems. DAEPs were supposed to be for criminal offenses--drug-related activities, gun violations and assault--all violations that had…

  9. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 33 Navigation and Navigable Waters 1 2014-07-01 2014-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  10. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 33 Navigation and Navigable Waters 1 2012-07-01 2012-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  11. 33 CFR 106.135 - Alternative Security Program.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 33 Navigation and Navigable Waters 1 2013-07-01 2013-07-01 false Alternative Security Program. 106.135 Section 106.135 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND SECURITY MARITIME SECURITY MARINE SECURITY: OUTER CONTINENTAL SHELF (OCS) FACILITIES General § 106.135...

  12. Another Alternative: A 90-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1978-01-01

    In May 1974, Fresno County's Narcotic Abuse Treatment Program began a 21-day outpatient methadone detoxification treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the rationale for its use. (Author)

  13. Another Alternative: A 90-Day Contractual Detoxification Treatment Program

    ERIC Educational Resources Information Center

    Kahn, Robert B.; And Others

    1978-01-01

    In May 1974, Fresno County's Narcotic Abuse Treatment Program began a 21-day outpatient methadone detoxification treatment modality. The purpose of this paper is to examine this alternative treatment modality, its characteristics, its therapeutic outcomes and the rationale for its use. (Author)

  14. Alternative Learning Programs Evaluation: Part 2 Report. Outcomes.

    ERIC Educational Resources Information Center

    North Carolina State Dept. of Public Instruction, Raleigh. Div. of Accountability Services/Research.

    In 1996, North Carolina began a 5-year evaluation of Alternative Learning Programs (ALPs). This report describes selected outcomes for students who participated in ALPs during 1995-96. These outcomes include performance on North Carolina End-of-Grade tests (elementary school) and performance on the End-of-Course(EOC) tests (high school) for…

  15. Alternate Learning Center. Abstracts of Inservice Training Programs.

    ERIC Educational Resources Information Center

    Rhode Island State Dept. of Education, Providence. Div. of Development and Operations.

    This booklet is a collection of abstracts describing the 18 programs offered at the Alternate Learning Center of the Rhode Island Teacher Center which has as its Primary function school based inservice training for local teachers and administrators. Each project is described in detail, including course goals, specific objectives, training…

  16. Alternative Administrative Certification: Socializing Factors Influencing Program Choice

    ERIC Educational Resources Information Center

    Bickmore, Dana L.; Bickmore, Steven T.; Raines, Sarah

    2013-01-01

    This study used an organizational socialization lens to examine factors influencing participants' decision to pursue the principalship and choice to engage in an alternate administration certification program. Through an analysis of participant focus groups and interviews, factors emerged from the codes that were compared with dimensions of…

  17. 36 CFR 800.14 - Federal agency program alternatives.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Register. (4) Legal effect. Alternate procedures adopted pursuant to this subpart substitute for the... program or the resolution of adverse effects from certain complex project situations or multiple undertakings. (1) Use of programmatic agreements. A programmatic agreement may be used: (i) When effects...

  18. 76 FR 67287 - Alternative Fuel Transportation Program; Alternative Fueled Vehicle Credit Program (Subpart F...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-31

    ... Fuel Transportation Program (AFTP or Program), by including EISA-specified electric drive vehicles and... Fueled Vehicle 3. Automobile 4. Dedicated Vehicle 5. Dual Fueled Vehicle 6. Electric Motor Vehicle and Electric-Hybrid Vehicle 7. Section 133--Identified Vehicles That Already Qualify as AFVs B. New Definitions...

  19. Considerations for the Placement of Youth with EBD in Alternative Education Programs

    ERIC Educational Resources Information Center

    Atkins, Trent; Bartuska, Jamie

    2010-01-01

    Alternative education programs (also called alternative schools) first appeared on the American landscape in the 1960s. Despite the proliferation of these programs, a generic description of what constitutes an alternative education program, historically, has been elusive. Most alternative education programs have the general criteria of serving…

  20. Intrasplicing coordinates alternative first exons with alternative splicing in the protein 4.1R gene

    SciTech Connect

    Conboy, John G.; Parra, Marilyn K.; Tan, Jeff S.; Mohandas, Narla; Conboy, John G.

    2008-11-07

    In the protein 4.1R gene, alternative first exons splice differentially to alternative 3' splice sites far downstream in exon 2'/2 (E2'/2). We describe a novel intrasplicing mechanism by which exon 1A (E1A) splices exclusively to the distal E2'/2 acceptor via two nested splicing reactions regulated by novel properties of exon 1B (E1B). E1B behaves as an exon in the first step, using its consensus 5' donor to splice to the proximal E2'/2 acceptor. A long region of downstream intron is excised, juxtaposing E1B with E2'/2 to generate a new composite acceptor containing the E1B branchpoint/pyrimidine tract and E2 distal 3' AG-dinucleotide. Next, the upstream E1A splices over E1B to this distal acceptor, excising the remaining intron plus E1B and E2' to form mature E1A/E2 product. We mapped branch points for both intrasplicing reactions and demonstrated that mutation of the E1B 5' splice site or branchpoint abrogates intrasplicing. In the 4.1R gene, intrasplicing ultimately determines N-terminal protein structure and function. More generally, intrasplicing represents a new mechanism whereby alternative promoters can be coordinated with downstream alternative splicing.

  1. Evaluation of Clark County School District's Alternative Route to Licensure Program from the Program Participants' Perspectives

    ERIC Educational Resources Information Center

    Kenyon, James J., Jr.

    2013-01-01

    This evaluation assesses the Alternative Route to Licensure (ARL) program of the Clark County School District (CCSD), in Clark County, Nevada from the program participants' perspectives. The program was implemented to reduce teacher shortages in the school district and allow persons with non-education-related Bachelor's Degrees to obtain teaching…

  2. Evaluation of Clark County School District's Alternative Route to Licensure Program from the Program Participants' Perspectives

    ERIC Educational Resources Information Center

    Kenyon, James J., Jr.

    2013-01-01

    This evaluation assesses the Alternative Route to Licensure (ARL) program of the Clark County School District (CCSD), in Clark County, Nevada from the program participants' perspectives. The program was implemented to reduce teacher shortages in the school district and allow persons with non-education-related Bachelor's Degrees to obtain teaching…

  3. The Grimes Alternative School Program and Home Remedies Program. Interim Evaluation Report.

    ERIC Educational Resources Information Center

    Williams, Jay R.

    This report describes and evaluates two programs which deal with chronic status offenders: the Grimes Alternative School Program, a delinquency prevention project which targets intermediate school (grades 4 and 5) students with chronic discipline and/or truant behaviors, and the Home Remedies Program, a short-term crisis intervention and…

  4. Applying genetic programming to the prediction of alternative mRNA splice variants.

    PubMed

    Vukusic, Ivana; Grellscheid, Sushma Nagaraja; Wiehe, Thomas

    2007-04-01

    Genetic programming (GP) can be used to classify a given gene sequence as either constitutively or alternatively spliced. We describe the principles of GP and apply it to a well-defined data set of alternatively spliced genes. A feature matrix of sequence properties, such as nucleotide composition or exon length, was passed to the GP system "Discipulus." To test its performance we concentrated on cassette exons (SCE) and retained introns (SIR). We analyzed 27,519 constitutively spliced and 9641 cassette exons including their neighboring introns; in addition we analyzed 33,316 constitutively spliced introns compared to 2712 retained introns. We find that the classifier yields highly accurate predictions on the SIR data with a sensitivity of 92.1% and a specificity of 79.2%. Prediction accuracies on the SCE data are lower, 47.3% (sensitivity) and 70.9% (specificity), indicating that alternative splicing of introns can be better captured by sequence properties than that of exons.

  5. Alternative epigenetic chromatin states of polycomb target genes.

    PubMed

    Schwartz, Yuri B; Kahn, Tatyana G; Stenberg, Per; Ohno, Katsuhito; Bourgon, Richard; Pirrotta, Vincenzo

    2010-01-01

    Polycomb (PcG) regulation has been thought to produce stable long-term gene silencing. Genomic analyses in Drosophila and mammals, however, have shown that it targets many genes, which can switch state during development. Genetic evidence indicates that critical for the active state of PcG target genes are the histone methyltransferases Trithorax (TRX) and ASH1. Here we analyze the repertoire of alternative states in which PcG target genes are found in different Drosophila cell lines and the role of PcG proteins TRX and ASH1 in controlling these states. Using extensive genome-wide chromatin immunoprecipitation analysis, RNAi knockdowns, and quantitative RT-PCR, we show that, in addition to the known repressed state, PcG targets can reside in a transcriptionally active state characterized by formation of an extended domain enriched in ASH1, the N-terminal, but not C-terminal moiety of TRX and H3K27ac. ASH1/TRX N-ter domains and transcription are not incompatible with repressive marks, sometimes resulting in a "balanced" state modulated by both repressors and activators. Often however, loss of PcG repression results instead in a "void" state, lacking transcription, H3K27ac, or binding of TRX or ASH1. We conclude that PcG repression is dynamic, not static, and that the propensity of a target gene to switch states depends on relative levels of PcG, TRX, and activators. N-ter TRX plays a remarkable role that antagonizes PcG repression and preempts H3K27 methylation by acetylation. This role is distinct from that usually attributed to TRX/MLL proteins at the promoter. These results have important implications for Polycomb gene regulation, the "bivalent" chromatin state of embryonic stem cells, and gene expression in development.

  6. Legislation on Alternative Education Programs. Wisconsin Legislative Council Report No. 1 to the 1993 Legislature.

    ERIC Educational Resources Information Center

    Wisconsin State Legislative Council, Madison.

    Two key pieces of legislation cover changes to Wisconsin's alternative education programs. The first bill is "1993 Senate Bill 88, Relating to Alternative Education Program, Children-At-Risk Programs, Granting Rule-Making Authority and Making an Appropriation." This bill creates an alternative education grant program of $3 million for…

  7. Feelings of Preparedness among Alternatively Certified Teachers: What Is the Role of Program Features?

    ERIC Educational Resources Information Center

    Kee, Ayana N.

    2012-01-01

    In the United States, about one third of new teachers being hired are drawn from alternative certification programs. One way to address controversy about the differences among the training experiences of teachers in traditional certification programs, fast-track alternative programs, and residency alternative programs is to examine teacher reports…

  8. Quality Practices of Alternative Education Learning Environments as Represented in Virginia's Individual Student Alternative Education Plan (ISAEP) Program

    ERIC Educational Resources Information Center

    Feltman, Doris R.

    2013-01-01

    The purpose of this study was to analyze a prominent alternative education practice in the Commonwealth of Virginia through an analysis of the Virginia Department of Education's Individual Student Alternative Education Plan (ISAEP) program and the alternative education environment it provides. This was a descriptive study using non-experimental…

  9. Discovering Successful Elements of Alternative Schools by Studying Student Perspectives in Two Alternative-to-Expulsion Programs

    ERIC Educational Resources Information Center

    Eschen, Eric Thomas

    2013-01-01

    This qualitative study analyzed two alternative-to-expulsion programs for high school students. Both programs, the "Learning with Peers Program" and the "Individualized Online Program", offered students an opportunity to earn credits rather than be expelled, but their philosophies presented an educational dichotomy: Should…

  10. GAP: A computer program for gene assembly

    SciTech Connect

    Eisnstein, J.R.; Uberbacher, E.C.; Guan, X.; Mural, R.J.; Mann, R.C.

    1991-09-01

    A computer program, GAP (Gene Assembly Program), has been written to assemble and score hypothetical genes, given a DNA sequence containing the gene, and the outputs of several other programs which analyze the sequence. These programs include the codign-recognition and splice-junction-recognition modules developed in this laboratory. GAP is a prototype of a planned system in which it will be integrated with an expert system and rule base. Initial tests of GAP have been carried out with four sequences, the exons of which have been determined by biochemcial methods. The highest-scoring hypothetical genes for each of the four sequences had percent correct splice junctions ranging from 50 to 100% (average 81%) and percent correct bases ranging from 92 to 100% (average 96%). 9 refs., 1 tab.

  11. The Evolutionary Relationship between Alternative Splicing and Gene Duplication.

    PubMed

    Iñiguez, Luis P; Hernández, Georgina

    2017-01-01

    The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study.

  12. The Evolutionary Relationship between Alternative Splicing and Gene Duplication

    PubMed Central

    Iñiguez, Luis P.; Hernández, Georgina

    2017-01-01

    The protein diversity that exists today has resulted from various evolutionary processes. It is well known that gene duplication (GD) along with the accumulation of mutations are responsible, among other factors, for an increase in the number of different proteins. The gene structure in eukaryotes requires the removal of non-coding sequences, introns, to produce mature mRNAs. This process, known as cis-splicing, referred to here as splicing, is regulated by several factors which can lead to numerous splicing arrangements, commonly designated as alternative splicing (AS). AS, producing several transcripts isoforms form a single gene, also increases the protein diversity. However, the evolution and manner for increasing protein variation differs between AS and GD. An important question is how are patterns of AS affected after a GD event. Here, we review the current knowledge of AS and GD, focusing on their evolutionary relationship. These two processes are now considered the main contributors to the increasing protein diversity and therefore their relationship is a relevant, yet understudied, area of evolutionary study. PMID:28261262

  13. ISO New England: Results of Ancillary Service Pilot Programs, Alternative Technology Regulation Pilot Program and Demand Response Reserves Pilot Program

    SciTech Connect

    Lowell, Jon; Yoshimura, Henry

    2011-10-26

    This PowerPoint presentation compares performance of pilot program assets and generation resources in alternative technology regulation and demand response reserves for flywheels and residential electric thermal storage.

  14. Alternative pre-mRNA splicing switches modulate gene expression in late erythropoiesis

    SciTech Connect

    Yamamoto, Miki L.; Clark, Tyson A.; Gee, Sherry L.; Kang, Jeong-Ah; Schweitzer, Anthony C.; Wickrema, Amittha; Conboy, John G.

    2009-02-03

    Differentiating erythroid cells execute a unique gene expression program that insures synthesis of the appropriate proteome at each stage of maturation. Standard expression microarrays provide important insight into erythroid gene expression but cannot detect qualitative changes in transcript structure, mediated by RNA processing, that alter structure and function of encoded proteins. We analyzed stage-specific changes in the late erythroid transcriptome via use of high-resolution microarrays that detect altered expression of individual exons. Ten differentiation-associated changes in erythroblast splicing patterns were identified, including the previously known activation of protein 4.1R exon 16 splicing. Six new alternative splicing switches involving enhanced inclusion of internal cassette exons were discovered, as well as 3 changes in use of alternative first exons. All of these erythroid stage-specific splicing events represent activated inclusion of authentic annotated exons, suggesting they represent an active regulatory process rather than a general loss of splicing fidelity. The observation that 3 of the regulated transcripts encode RNA binding proteins (SNRP70, HNRPLL, MBNL2) may indicate significant changes in the RNA processing machinery of late erythroblasts. Together, these results support the existence of a regulated alternative pre-mRNA splicing program that is critical for late erythroid differentiation.

  15. Gene duplication followed by exon structure divergence substitutes for alternative splicing in zebrafish.

    PubMed

    Lambert, Matthew J; Olsen, Kyle G; Cooper, Cynthia D

    2014-08-10

    In this study we report novel findings regarding the evolutionary relationship between gene duplication and alternative splicing, two processes that increase proteomic diversity. By studying teleost fish, we find that gene duplication followed by exon structure divergence between paralogs, but not gene duplication alone, leads to a significant reduction in alternative splicing, as measured by both the proportion of genes that undergo alternative splicing as well as mean number of transcripts per gene. Additionally, we show that this effect is independent of gene family size and gene function. Furthermore, we provide evidence that the reduction in alternative splicing may be due to the partitioning of ancestral splice forms among the duplicate genes - a form of subfunctionalization. Taken together these results indicate that exon structure evolution subsequent to gene duplication may be a common substitute for alternative splicing.

  16. Innovation in two alternative elementary school programs: why it works.

    PubMed

    Dyson, B; O'Sullivan, M

    1998-09-01

    The purpose of this paper was to describe and interpret the factors that supported and maintained curricular innovation at two alternative elementary schools. The two schools have Project Adventure as their curriculum focus and use the concepts of risk, challenge, trust, cooperation, and problem solving; briefing and debriefing; and personal goal-setting contracts as part of their schoolwide curriculum (Project Adventure, 1991). Data were collected through formal interviews with the physical education teachers, the principals, and four classroom teachers at each school. Nonparticipant observation, field notes, informal interviews, and document analysis were also conducted. Inductive analysis and constant comparison were used to analyze and organize the data throughout the research process. Five factors emerged that supported the implementation of this innovative physical education program: a shared vision, external support for the schools' programs, curricula integration, centrality of physical education, and shared decision making. Project Adventure at these schools provides an example of substantive curricular reform where physical education was a critical element in the school programs.

  17. Mitochondrial electron transport regulation of nuclear gene expression. Studies with the alternative oxidase gene of tobacco.

    PubMed Central

    Vanlerberghe, G C; McIntosh, L

    1994-01-01

    We have isolated a cDNA representing the tobacco (Nicotiana tabacum L. cv Bright Yellow) nuclear gene Aox1, which encodes the alternative oxidase of plant mitochondria. The clone contains the complete coding region (1059 base pairs) of a precursor protein of 353 amino acids with a calculated molecular mass of 39.8 kD. A putative transit peptide contains common signals believed to be important for import and processing of mitochondrially localized proteins. We have studied changes in Aox1 gene expression in tobacco in response to changes in cytochrome pathway activity. Inhibition of the cytochrome pathway by antimycin A resulted in a rapid and dramatic accumulation of Aox1 mRNA, whereas the level of mRNAs encoding two proteins of the cytochrome pathway did not change appreciably. This was accompanied by a dramatic increase in alternative pathway capacity and engagement in whole cells. Respiration under these conditions was unaffected by the uncoupler p-trifluoromethoxycarbonylcyanide (FCCP). When inhibition of the cytochrome pathway was relieved, levels of Aox1 mRNA returned to control levels, alternative pathway capacity and engagement declined, and respiration could once again be stimulated by FCCP. The results show that a mechanism involving changes in Aox1 gene expression exists whereby the capacity of the alternative pathway can be adjusted in response to changes in the activity of the cytochrome pathway. PMID:8058837

  18. The Positive Alternative Credit Experience (PACE) Program a Quantitative Comparative Study

    ERIC Educational Resources Information Center

    Warren, Rebecca Anne

    2011-01-01

    The purpose of this quantitative comparative study was to evaluate the Positive Alternative Credit Experience (PACE) Program using an objectives-oriented approach to a formative program evaluation. The PACE Program was a semester-long high school alternative education program designed to serve students at-risk for academic failure or dropping out…

  19. Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

    PubMed Central

    Lianoglou, Steve; Garg, Vidur; Yang, Julie L.; Leslie, Christina S.; Mayr, Christine

    2013-01-01

    More than half of human genes use alternative cleavage and polyadenylation (ApA) to generate mRNA transcripts that differ in the lengths of their 3′ untranslated regions (UTRs), thus altering the post-transcriptional fate of the message and likely the protein output. The extent of 3′ UTR variation across tissues and the functional role of ApA remain poorly understood. We developed a sequencing method called 3′-seq to quantitatively map the 3′ ends of the transcriptome of diverse human tissues and isogenic transformation systems. We found that cell type-specific gene expression is accomplished by two complementary programs. Tissue-restricted genes tend to have single 3′ UTRs, whereas a majority of ubiquitously transcribed genes generate multiple 3′ UTRs. During transformation and differentiation, single-UTR genes change their mRNA abundance levels, while multi-UTR genes mostly change 3′ UTR isoform ratios to achieve tissue specificity. However, both regulation programs target genes that function in the same pathways and processes that characterize the new cell type. Instead of finding global shifts in 3′ UTR length during transformation and differentiation, we identify tissue-specific groups of multi-UTR genes that change their 3′ UTR ratios; these changes in 3′ UTR length are largely independent from changes in mRNA abundance. Finally, tissue-specific usage of ApA sites appears to be a mechanism for changing the landscape targetable by ubiquitously expressed microRNAs. PMID:24145798

  20. Radiopharmaceutical and Gene Therapy Program

    SciTech Connect

    Buchsbaum, Donald J.

    2006-02-09

    The objective of our research program was to determine whether novel receptors can be induced in solid cancers as a target for therapy with radiolabeled unmodified peptides that bind to the receptors. The hypothesis was that induction of a high number of receptors on the surface of these cancer cells would result in an increased uptake of the radiolabeled monomeric peptides as compared to published results with radiolabeled antibodies or peptides to naturally expressed antigens or receptors, and therefore a better therapeutic outcome. The following is a summary of published results.

  1. Alternative RNA processing events in human calcitonin/calcitonin gene-related peptide gene expression.

    PubMed Central

    Jonas, V; Lin, C R; Kawashima, E; Semon, D; Swanson, L W; Mermod, J J; Evans, R M; Rosenfeld, M G

    1985-01-01

    Two mRNAs generated as a consequence of alternative RNA processing events in expression of the human calcitonin gene encode the protein precursors of either calcitonin or calcitonin gene-related peptide (CGRP). Both calcitonin and CGRP RNAs and their encoded peptide products are expressed in the human pituitary and in medullary thyroid tumors. On the basis of sequence comparison, it is suggested that both the calcitonin and CGRP exons arose from a common primordial sequence, suggesting that duplication and rearrangement events are responsible for the generation of this complex transcription unit. Images PMID:3872459

  2. Two alternating motor programs drive navigation in Drosophila larva.

    PubMed

    Lahiri, Subhaneil; Shen, Konlin; Klein, Mason; Tang, Anji; Kane, Elizabeth; Gershow, Marc; Garrity, Paul; Samuel, Aravinthan D T

    2011-01-01

    When placed on a temperature gradient, a Drosophila larva navigates away from excessive cold or heat by regulating the size, frequency, and direction of reorientation maneuvers between successive periods of forward movement. Forward movement is driven by peristalsis waves that travel from tail to head. During each reorientation maneuver, the larva pauses and sweeps its head from side to side until it picks a new direction for forward movement. Here, we characterized the motor programs that underlie the initiation, execution, and completion of reorientation maneuvers by measuring body segment dynamics of freely moving larvae with fluorescent muscle fibers as they were exposed to temporal changes in temperature. We find that reorientation maneuvers are characterized by highly stereotyped spatiotemporal patterns of segment dynamics. Reorientation maneuvers are initiated with head sweeping movement driven by asymmetric contraction of a portion of anterior body segments. The larva attains a new direction for forward movement after head sweeping movement by using peristalsis waves that gradually push posterior body segments out of alignment with the tail (i.e., the previous direction of forward movement) into alignment with the head. Thus, reorientation maneuvers during thermotaxis are carried out by two alternating motor programs: (1) peristalsis for driving forward movement and (2) asymmetric contraction of anterior body segments for driving head sweeping movement.

  3. 46 CFR 8.440 - Vessel enrollment in the Alternate Compliance Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 false Vessel enrollment in the Alternate Compliance Program. 8.440 Section 8.440 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY PROCEDURES APPLICABLE TO THE PUBLIC VESSEL INSPECTION ALTERNATIVES Alternate Compliance Program § 8.440 Vessel enrollment in the...

  4. 78 FR 42159 - Medicaid and Children's Health Insurance Programs: Essential Health Benefits in Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-15

    ... Children's Health Insurance Programs: Essential Health Benefits in Alternative Benefit Plans, Eligibility...-AR04 Medicaid and Children's Health Insurance Programs: Essential Health Benefits in Alternative... sections 1937 of the Social Security Act (which we refer to as ``alternative benefit plans'') to ensure...

  5. Towards a Typology of Alternative Education Programs: A Compilation of Elements from the Literature.

    ERIC Educational Resources Information Center

    Aron, Laudan Y.

    This paper synthesizes existing knowledge, definitions, and themes about alternative education programs, based on a review of literature and reports, focusing on common terminologies to characterize the various kinds of alternative education programs. It seeks to develop a typology of existing alternative education by focusing on certain common…

  6. Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

    PubMed

    Haas, Brian J; Salzberg, Steven L; Zhu, Wei; Pertea, Mihaela; Allen, Jonathan E; Orvis, Joshua; White, Owen; Buell, C Robin; Wortman, Jennifer R

    2008-01-11

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  7. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    SciTech Connect

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  8. [Auto-vaccines: an immunological alternative to gene silencing].

    PubMed

    Uyttenhove, Catherine; van Snick, Jacques

    2013-04-01

    Auto-vaccination is a procedure that recently attracted the interest of a growing number of investigators as an alternative to gene inactivation for functional studies of cytokines or other mediators. It is based on the observation that autologous cytokines cross-linked to a foreign protein or peptide are recognized by self-reactive B cells that present foreign peptides, and by doing so attract illicit help from helper T cells that recognize the foreign peptide on the self-reactive B cell MHC Class II complex. This leads to the production of antibodies reacting with self-proteins and thus to neutralization of the targeted factor. Here, we summarize the different techniques that were successful in breaking this self-tolerance and provide several examples of the functional consequences of these auto-vaccines. An additional output of auto-vaccination is the production of mouse monoclonal antibodies against mouse factors. Such antibodies have obvious advantages for long-term use in vivo. © 2013 médecine/sciences – Inserm / SRMS.

  9. Alternatives Analysis for the Resumption of Transient Testing Program

    SciTech Connect

    Lee Nelson

    2013-11-01

    An alternatives analysis was performed for resumption of transient testing. The analysis considered eleven alternatives – including both US international facilities. A screening process was used to identify two viable alternatives from the original eleven. In addition, the alternatives analysis includes a no action alternative as required by the National Environmental Policy Act (NEPA). The alternatives considered in this analysis included: 1. Restart the Transient Reactor Test Facility (TREAT) 2. Modify the Annular Core Research Reactor (ACRR) which includes construction of a new hot cell and installation of a new hodoscope. 3. No Action

  10. 78 FR 45253 - National Toxicology Program Scientific Advisory Committee on Alternative Toxicological Methods...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-26

    ... HUMAN SERVICES National Institutes of Health National Toxicology Program Scientific Advisory Committee on Alternative Toxicological Methods; Announcement of Meeting; Request for Comments SUMMARY: This notice announces a meeting of the Scientific Advisory Committee on Alternative Toxicological Methods...

  11. Reversion to an embryonic alternative splicing program enhances leukemia stem cell self-renewal

    PubMed Central

    Holm, Frida; Hellqvist, Eva; Mason, Cayla N.; Ali, Shawn A.; Delos-Santos, Nathaniel; Barrett, Christian L.; Chun, Hye-Jung; Minden, Mark D.; Moore, Richard A.; Marra, Marco A.; Runza, Valeria; Frazer, Kelly A.; Sadarangani, Anil; Jamieson, Catriona H. M.

    2015-01-01

    Formative research suggests that a human embryonic stem cell-specific alternative splicing gene regulatory network, which is repressed by Muscleblind-like (MBNL) RNA binding proteins, is involved in cell reprogramming. In this study, RNA sequencing, splice isoform-specific quantitative RT-PCR, lentiviral transduction, and in vivo humanized mouse model studies demonstrated that malignant reprogramming of progenitors into self-renewing blast crisis chronic myeloid leukemia stem cells (BC LSCs) was partially driven by decreased MBNL3. Lentiviral knockdown of MBNL3 resulted in reversion to an embryonic alternative splice isoform program typified by overexpression of CD44 transcript variant 3, containing variant exons 8–10, and BC LSC proliferation. Although isoform-specific lentiviral CD44v3 overexpression enhanced chronic phase chronic myeloid leukemia (CML) progenitor replating capacity, lentiviral shRNA knockdown abrogated these effects. Combined treatment with a humanized pan-CD44 monoclonal antibody and a breakpoint cluster region - ABL proto-oncogene 1, nonreceptor tyrosine kinase (BCR-ABL1) antagonist inhibited LSC maintenance in a niche-dependent manner. In summary, MBNL3 down-regulation–related reversion to an embryonic alternative splicing program, typified by CD44v3 overexpression, represents a previously unidentified mechanism governing malignant progenitor reprogramming in malignant microenvironments and provides a pivotal opportunity for selective BC LSC detection and therapeutic elimination. PMID:26621726

  12. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 7 Agriculture 3 2012-01-01 2012-01-01 false Alternate quality control programs for dairy products... and Grading Service 1 Operations and Operating Procedures § 58.149 Alternate quality control programs for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  13. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 3 2011-01-01 2011-01-01 false Alternate quality control programs for dairy products... and Grading Service 1 Operations and Operating Procedures § 58.149 Alternate quality control programs for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  14. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 7 Agriculture 3 2013-01-01 2013-01-01 false Alternate quality control programs for dairy products... and Grading Service 1 Operations and Operating Procedures § 58.149 Alternate quality control programs for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  15. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 7 Agriculture 3 2014-01-01 2014-01-01 false Alternate quality control programs for dairy products... and Grading Service 1 Operations and Operating Procedures § 58.149 Alternate quality control programs for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  16. Perception of Preparedness of Novice Teachers from Alternative and Traditional Licensing Programs

    ERIC Educational Resources Information Center

    Buchanan, Tenielle; Lang, Nathan; Morin, Laura-Lee

    2013-01-01

    Alternative teacher licensing programs have become very popular; however, very little research has been conducted on the efficacy of the programs. Alternative licensing programs (ALPs) have evolved and multiplied rapidly over the last few decades. The Tennessee Independent Colleges and Universities Association (TICUA) is attempting to determine…

  17. Alternate Route and Traditionally-Trained Teachers' Perceptions of Teaching Preparation Programs

    ERIC Educational Resources Information Center

    Lowery, David C.; Roberts, Jalynn; Roberts, Jessica

    2012-01-01

    The debate about the effectiveness of alternate route teacher preparation programs continues in K-12 schools and institutions of higher learning. As alternate route teacher programs continue to prepare more and more teachers for the K-12 classroom, these programs will continue to face scrutiny regarding their effectiveness. This current study…

  18. Perception of Preparedness of Novice Teachers from Alternative and Traditional Licensing Programs

    ERIC Educational Resources Information Center

    Buchanan, Tenielle; Lang, Nathan; Morin, Laura-Lee

    2013-01-01

    Alternative teacher licensing programs have become very popular; however, very little research has been conducted on the efficacy of the programs. Alternative licensing programs (ALPs) have evolved and multiplied rapidly over the last few decades. The Tennessee Independent Colleges and Universities Association (TICUA) is attempting to determine…

  19. Backgrounds, Teaching Responsibilities, and Motivations of Music Education Candidates Enrolled in Alternative Certification Music Education Programs

    ERIC Educational Resources Information Center

    Hellman, Daniel; McDowell, Carol

    2011-01-01

    The purpose of this study was to examine the factors associated with enrolling, continuing, and completing alternative certification programs in music education. Data were collected via surveys and semi-structured interviews of music teacher candidates from 43 program completers from seven alternative certification programs in three states. In…

  20. Alternate Assessment Manual for the Arizona Student Achievement Program

    ERIC Educational Resources Information Center

    Arizona Department of Education, 2005

    2005-01-01

    The Alternate Assessment Code of Ethics informs school personnel involved in alternate assessments of ethical, nondiscriminatory assessment practices and underscores the diligence necessary to provide accurate assessment data for instructional decision-making. The importance of commitment and adherence to the Alternate Assessment Code of Ethics by…

  1. The evolutionary fate of alternatively spliced homologous exons after gene duplication.

    PubMed

    Abascal, Federico; Tress, Michael L; Valencia, Alfonso

    2015-04-29

    Alternative splicing and gene duplication are the two main processes responsible for expanding protein functional diversity. Although gene duplication can generate new genes and alternative splicing can introduce variation through alternative gene products, the interplay between the two processes is complex and poorly understood. Here, we have carried out a study of the evolution of alternatively spliced exons after gene duplication to better understand the interaction between the two processes. We created a manually curated set of 97 human genes with mutually exclusively spliced homologous exons and analyzed the evolution of these exons across five distantly related vertebrates (lamprey, spotted gar, zebrafish, fugu, and coelacanth). Most of these exons had an ancient origin (more than 400 Ma). We found examples supporting two extreme evolutionary models for the behaviour of homologous axons after gene duplication. We observed 11 events in which gene duplication was accompanied by splice isoform separation, that is, each paralog specifically conserved just one distinct ancestral homologous exon. At other extreme, we identified genes in which the homologous exons were always conserved within paralogs, suggesting that the alternative splicing event cannot easily be separated from the function in these genes. That many homologous exons fall in between these two extremes highlights the diversity of biological systems and suggests that the subtle balance between alternative splicing and gene duplication is adjusted to the specific cellular context of each gene.

  2. An extensive program of periodic alternative splicing linked to cell cycle progression

    PubMed Central

    Dominguez, Daniel; Tsai, Yi-Hsuan; Weatheritt, Robert; Wang, Yang; Blencowe, Benjamin J; Wang, Zefeng

    2016-01-01

    Progression through the mitotic cell cycle requires periodic regulation of gene function at the levels of transcription, translation, protein-protein interactions, post-translational modification and degradation. However, the role of alternative splicing (AS) in the temporal control of cell cycle is not well understood. By sequencing the human transcriptome through two continuous cell cycles, we identify ~1300 genes with cell cycle-dependent AS changes. These genes are significantly enriched in functions linked to cell cycle control, yet they do not significantly overlap genes subject to periodic changes in steady-state transcript levels. Many of the periodically spliced genes are controlled by the SR protein kinase CLK1, whose level undergoes cell cycle-dependent fluctuations via an auto-inhibitory circuit. Disruption of CLK1 causes pleiotropic cell cycle defects and loss of proliferation, whereas CLK1 over-expression is associated with various cancers. These results thus reveal a large program of CLK1-regulated periodic AS intimately associated with cell cycle control. DOI: http://dx.doi.org/10.7554/eLife.10288.001 PMID:27015110

  3. Alternatives for Young Americans: A Catalog of Drug Abuse Prevention Programs.

    ERIC Educational Resources Information Center

    Applied Management Sciences, Inc., Silver Spring, MD.

    This reference book contains resumes of program descriptions geared toward youth and adults who need or want information on drug abuse prevention programs, locally or nationally. Several major entries include: (1) national program models; (2) evaluated alternative programs from all states; and (3) descriptions of prevention programs. All section…

  4. Computational Analysis of an Evolutionarily Conserved VertebrateMuscle Alternative Splicing Program

    SciTech Connect

    Das, Debopriya; Clark, Tyson A.; Schweitzer, Anthony; Marr,Henry; Yamamoto, Miki L.; Parra, Marilyn K.; Arribere, Josh; Minovitsky,Simon; Dubchak, Inna; Blume, John E.; Conboy, John G.

    2006-06-15

    A novel exon microarray format that probes gene expression with single exon resolution was employed to elucidate critical features of a vertebrate muscle alternative splicing program. A dataset of 56 microarray-defined, muscle-enriched exons and their flanking introns were examined computationally in order to investigate coordination of the muscle splicing program. Candidate intron regulatory motifs were required to meet several stringent criteria: significant over-representation near muscle-enriched exons, correlation with muscle expression, and phylogenetic conservation among genomes of several vertebrate orders. Three classes of regulatory motifs were identified in the proximal downstream intron, within 200nt of the target exons: UGCAUG, a specific binding site for Fox-1 related splicing factors; ACUAAC, a novel branchpoint-like element; and UG-/UGC-rich elements characteristic of binding sites for CELF splicing factors. UGCAUG was remarkably enriched, being present in nearly one-half of all cases. These studies suggest that Fox and CELF splicing factors play a major role in enforcing the muscle-specific alternative splicing program, facilitating expression of a set of unique isoforms of cytoskeletal proteins that are critical to muscle cell differentiation. Supplementary materials: There are four supplementary tables and one supplementary figure. The tables provide additional detailed information concerning the muscle-enriched datasets, and about over-represented oligonucleotide sequences in the flanking introns. The supplementary figure shows RT-PCR data confirming the muscle-enriched expression of exons predicted from the microarray analysis.

  5. 75 FR 25913 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... Federal Transit Administration Alternative Transportation in Parks and Public Lands Program AGENCY... Lands (ATPPL)) program, authorized by Section 3021 of the Safe, Accountable, Flexible, Efficient... systems in parks and public lands. Federal land management agencies and State, tribal and local...

  6. Potsdam College Advocate Program: An Alternative to Speech Regulations.

    ERIC Educational Resources Information Center

    Gordon, Anna

    The Potsdam Advocate program is a program designed to aid students who feel they are victims of discrimination or sexual offenses. An analysis of this program and its literature is instructive to students and scholars in the field of organizational communication. Developed in 1991, this program provides a structure and options that students may…

  7. Kindergarten Evaluation Study: Full-Day Alternate Day Programs.

    ERIC Educational Resources Information Center

    Minnesota State Dept. of Education, St. Paul.

    In this evaluation study, two groups of children who attended kindergarten either one-half day every day or full-day on alternate days were compared. An opinion survey was conducted to obtain the observations of parents, kindergarten teachers, and elementary principals in relation to the all-day alternate day schedule in 55 school districts. Data…

  8. Supports and Enhancements Designed for Alternative School Programming

    ERIC Educational Resources Information Center

    Menendez, Anthony L.

    2007-01-01

    In this informational survey, the author briefly explores the needs of professional staff and administrators who serve students in alternative educational settings and special education and provides a listing of helpful Internet resources. Initially, the author provides general information concerning the current state of alternative education…

  9. Alternative filtration testing program: Pre-evaluation of test results

    SciTech Connect

    Georgeton, G.K.; Poirier, M.R.

    1990-09-28

    Based on results of testing eight solids removal technologies and one pretreatment option, it is recommended that a centrifugal ultrafilter and polymeric ultrafilter undergo further testing as possible alternatives to the Norton Ceramic filters. Deep bed filtration should be considered as a third alternative, if a backwashable cartridge filter is shown to be inefficient in separate testing.

  10. Alternative filtration testing program: Pre-evaluation of test results

    SciTech Connect

    Georgeton, G.K.; Poirier, M.R.

    1990-09-28

    Based on results of testing eight solids removal technologies and one pretreatment option, it is recommended that a centrifugal ultrafilter and polymeric ultrafilter undergo further testing as possible alternatives to the Norton Ceramic filters. Deep bed filtration should be considered as a third alternative, if a backwashable cartridge filter is shown to be inefficient in separate testing.

  11. 78 FR 62472 - Energy Conservation Program: Alternative Efficiency Determination Methods, Basic Model Definition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ...; ] DEPARTMENT OF ENERGY 10 CFR Parts 429 and 431 RIN 1904-AC46 Energy Conservation Program: Alternative... alternatives to testing for the purposes of certifying compliance with the applicable energy conservation..., U.S. Department of Energy, Building Technologies Office, Mailstop EE-2J, Alternative Efficiency...

  12. Mixed results in a transitional planning program for alternative school students.

    PubMed

    Wolf, Elaine M; Wolf, Douglas A

    2008-04-01

    Disciplinary alternative schools have a reputation as gateways to the juvenile and criminal justice systems. The authors conducted an evaluation of an intervention (Strategies for Success) designed to divert seventh-, eighth-, and ninth-grade alternative school students from this gateway. They used propensity score matching and a multivariate random effects model to estimate program impacts and found that the program not only increased attendance rates, at least in the short term, but also increased the likelihood of reassignment to alternative schools. The discussion focuses on possible reasons and solutions for high rates of return to alternative school and for the erosion of program effects.

  13. Alternative Education Programs in Pennsylvania. A Continuum of Services for Students.

    ERIC Educational Resources Information Center

    Houck, Terri

    Alternative education programs for disruptive and at-risk students in Pennsylvania were studied to determine the characteristics that make such programs successful. This report presents the results of the analysis and lists model programs and other operating programs in Pennsylvania. Suspension and expulsion are stopgap solutions that relieve the…

  14. Interweaving Teaching and Emotional Support for Novice Special Educators in Alternative Certification Programs

    ERIC Educational Resources Information Center

    Ricci, Leila Ansari; Zetlin, Andrea G.

    2013-01-01

    As the shortage of special education teachers has led to increasing numbers of teacher candidates enrolled in alternative certification programs, there is a need to provide systematic mentoring and coaching. The relationship between support providers and novice teachers enrolled in an alternative certification program in a diverse, urban…

  15. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... the Alternate Compliance Program. 8.420 Section 8.420 Shipping COAST GUARD, DEPARTMENT OF HOMELAND... § 8.420 Classification society authorization to participate in the Alternate Compliance Program. (a... requirements of § 8.430 of this part, which must be accepted by the Coast Guard. (c) A recognized...

  16. Bureaucratic Discretion and Alternative Teacher Certification: Understanding Program Variation in Missouri

    ERIC Educational Resources Information Center

    Heinen, Ethan B.; Scribner, Jay Paredes

    2007-01-01

    Alternative teacher certification literature has contributed significantly to our understanding of this approach to teacher preparation. However, this literature has more often than not treated alternative teacher certification programs (ATCPs) as a black box, thus ignoring program heterogeneity. The present study examines how and why five ATCPs…

  17. Alternative Schools and Programs, Iowa. "Reaching Out to Help People." 1983-84 State Directory.

    ERIC Educational Resources Information Center

    Morley, Raymond E.; Clay, Helen I.

    This directory was developed in response to requests for information on alternative programs for dropouts and potential dropouts. The scope of the dropout problem in Iowa is defined. Presented are definitions of dropout prevention alternative programs as well as a detailed account of useful prevention approaches. The directory includes needs…

  18. 46 CFR 71.50-19 - The Alternative Hull Examination (AHE) Program application.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false The Alternative Hull Examination (AHE) Program...) PASSENGER VESSELS INSPECTION AND CERTIFICATION Drydocking § 71.50-19 The Alternative Hull Examination (AHE... apply to the AHE Program. You must submit an application at least 90 days before the requested hull...

  19. 46 CFR 71.50-31 - Continued participation in the Alternative Hull Examination (AHE) program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Continued participation in the Alternative Hull... the Alternative Hull Examination (AHE) program. (a) To continue to participate in the AHE Program, vessel operators must conduct an annual hull condition assessment. At a minimum, vessel operators must...

  20. 46 CFR 176.650 - Alternative Hull Examination Program options: Divers or underwater ROV.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Alternative Hull Examination Program options: Divers or...) SMALL PASSENGER VESSELS (UNDER 100 GROSS TONS) INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 176.650 Alternative Hull Examination Program options: Divers or underwater ROV. To complete the...

  1. Considerations for Coursework and Mentoring in an Alternative-Route-to- Licensure Program for STEM Teachers

    ERIC Educational Resources Information Center

    Burbank, Mary D.; Shooter, Wynn; Groth, Cori A

    2014-01-01

    The purpose of this project was to investigate stakeholders' perspectives on coursework and the role of mentors within a unique teacher education program for prospective teachers of mathematics in an alternative-route-to-licensure program. The alternative route reflects a partnership between an institution of higher education, a state office of…

  2. Considerations for Coursework and Mentoring in an Alternative-Route-to- Licensure Program for STEM Teachers

    ERIC Educational Resources Information Center

    Burbank, Mary D.; Shooter, Wynn; Groth, Cori A

    2014-01-01

    The purpose of this project was to investigate stakeholders' perspectives on coursework and the role of mentors within a unique teacher education program for prospective teachers of mathematics in an alternative-route-to-licensure program. The alternative route reflects a partnership between an institution of higher education, a state office of…

  3. Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus

    PubMed Central

    Willemsen, Anouk; Zwart, Mark P.; Tromas, Nicolas; Majer, Eszter; Daròs, José-Antonio; Elena, Santiago F.

    2016-01-01

    The order in which genes are organized within a genome is generally not conserved between distantly related species. However, within virus orders and families, strong conservation of gene order is observed. The factors that constrain or promote gene-order diversity are largely unknown, although the regulation of gene expression is one important constraint for viruses. Here we investigate why gene order is conserved for a positive-strand RNA virus encoding a single polyprotein in the context of its authentic multicellular host. Initially, we identified the most plausible trajectory by which alternative gene orders could evolve. Subsequently, we studied the accessibility of key steps along this evolutionary trajectory by constructing two virus intermediates: (1) duplication of a gene followed by (2) loss of the ancestral gene. We identified five barriers to the evolution of alternative gene orders. First, the number of viable positions for reordering is limited. Second, the within-host fitness of viruses with gene duplications is low compared to the wild-type virus. Third, after duplication, the ancestral gene copy is always maintained and never the duplicated one. Fourth, viruses with an alternative gene order have even lower fitness than viruses with gene duplications. Fifth, after more than half a year of evolution in isolation, viruses with an alternative gene order are still vastly inferior to the wild-type virus. Our results show that all steps along plausible evolutionary trajectories to alternative gene orders are highly unlikely. Hence, the inaccessibility of these trajectories probably contributes to the conservation of gene order in present-day viruses. PMID:26868766

  4. Multiple Barriers to the Evolution of Alternative Gene Orders in a Positive-Strand RNA Virus.

    PubMed

    Willemsen, Anouk; Zwart, Mark P; Tromas, Nicolas; Majer, Eszter; Daròs, José-Antonio; Elena, Santiago F

    2016-04-01

    The order in which genes are organized within a genome is generally not conserved between distantly related species. However, within virus orders and families, strong conservation of gene order is observed. The factors that constrain or promote gene-order diversity are largely unknown, although the regulation of gene expression is one important constraint for viruses. Here we investigate why gene order is conserved for a positive-strand RNA virus encoding a single polyprotein in the context of its authentic multicellular host. Initially, we identified the most plausible trajectory by which alternative gene orders could evolve. Subsequently, we studied the accessibility of key steps along this evolutionary trajectory by constructing two virus intermediates: (1) duplication of a gene followed by (2) loss of the ancestral gene. We identified five barriers to the evolution of alternative gene orders. First, the number of viable positions for reordering is limited. Second, the within-host fitness of viruses with gene duplications is low compared to the wild-type virus. Third, after duplication, the ancestral gene copy is always maintained and never the duplicated one. Fourth, viruses with an alternative gene order have even lower fitness than viruses with gene duplications. Fifth, after more than half a year of evolution in isolation, viruses with an alternative gene order are still vastly inferior to the wild-type virus. Our results show that all steps along plausible evolutionary trajectories to alternative gene orders are highly unlikely. Hence, the inaccessibility of these trajectories probably contributes to the conservation of gene order in present-day viruses. Copyright © 2016 by the Genetics Society of America.

  5. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    DOE PAGES

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; ...

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splicemore » site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.« less

  6. A dynamic intron retention program enriched in RNA processing genes regulates gene expression during terminal erythropoiesis

    SciTech Connect

    Pimentel, Harold; Parra, Marilyn; Gee, Sherry L.; Mohandas, Narla; Pachter, Lior; Conboy, John G.

    2015-11-03

    Differentiating erythroblasts execute a dynamic alternative splicing program shown here to include extensive and diverse intron retention (IR) events. Cluster analysis revealed hundreds of developmentallydynamic introns that exhibit increased IR in mature erythroblasts, and are enriched in functions related to RNA processing such as SF3B1 spliceosomal factor. Distinct, developmentally-stable IR clusters are enriched in metal-ion binding functions and include mitoferrin genes SLC25A37 and SLC25A28 that are critical for iron homeostasis. Some IR transcripts are abundant, e.g. comprising ~50% of highly-expressed SLC25A37 and SF3B1 transcripts in late erythroblasts, and thereby limiting functional mRNA levels. IR transcripts tested were predominantly nuclearlocalized. Splice site strength correlated with IR among stable but not dynamic intron clusters, indicating distinct regulation of dynamically-increased IR in late erythroblasts. Retained introns were preferentially associated with alternative exons with premature termination codons (PTCs). High IR was observed in disease-causing genes including SF3B1 and the RNA binding protein FUS. Comparative studies demonstrated that the intron retention program in erythroblasts shares features with other tissues but ultimately is unique to erythropoiesis. Finally, we conclude that IR is a multi-dimensional set of processes that post-transcriptionally regulate diverse gene groups during normal erythropoiesis, misregulation of which could be responsible for human disease.

  7. Terrorism Insurance: Alternative Programs for Protecting Insurance Consumers

    DTIC Science & Technology

    2007-11-02

    insurance in urban areas - Offered federal reinsurance for insured property in urban areas Statement Terrorism Insurance: Alternative Proposals for...and the reinsurers who share the industry’s risks, have indicated that they don’t know how much to charge for this coverage going forward because they...Insurance: Alternative Proposals for Protecting Insurance Consumers Page 2 GAO-02-199T prudent and efficient behavior are not replaced by an attitude

  8. Alternative Summer Educational Programs for Urban Hearing-Impaired Children.

    ERIC Educational Resources Information Center

    Goldfarb, Mark; Israelson, Jo

    The paper describes the summer programs offered by Kendall Demonstration Elementary School, a year-round day school for elementary level hearing impaired students in Washington, D.C. The programs are explained to be based on a three-point philosophy: (1) summer programs should be different from those of the rest of the year; (2) summer programs…

  9. Design and Implementation Considerations for Alternative Teacher Compensation Programs

    ERIC Educational Resources Information Center

    Brodsky, Andrew; DeCesare, Dale; Kramer-Wine, Jennifer

    2010-01-01

    Over the past decade, educators and policymakers have used a variety of approaches to designing and implementing teacher compensation programs. These approaches include federal incentive funds, state-level programs, and district initiatives. This article reviews 6 such programs in order to identify themes and draw conclusions relevant to…

  10. Genomic architecture and functional relationships of intronless, constitutively- and alternatively-spliced genes in Brachypodium distachyon

    PubMed Central

    Mandadi, Kranthi K; Scholthof, Karen-Beth G

    2015-01-01

    Splicing and alternative splicing (AS) are widespread co- and post-transcriptional regulatory processes in plants. Recently, we characterized genome-wide AS landscapes and virus-induced AS patterns in Brachypodium distachyon (Brachypodium), a C3 model grass. Brachypodium plants infected with Panicum mosaic virus (PMV) alone or in mixed infections with its satellite virus (SPMV) were used for high-throughput, paired-end RNA sequencing. Here, using gene attributes of ∼5,655 intronless genes, ∼13,302 constitutively spliced, and ∼7,564 alternatively spliced genes, we analyzed the influence of genomic features on splicing incidence and AS frequency. In Brachypodium, gene length, coding sequence length, and exon and intron number were positively correlated to splicing incidence and AS frequency. In contrast, exon length and the percentage composition of GC (%GC) content were inversely correlated with splicing incidence and AS frequency. Although gene expression status had little correlation with splicing occurrence per se, it negatively correlated to AS frequency: i.e., genes with ≥5 alternatively spliced transcripts were significantly less expressed compared to genes encoding <5 alternative transcripts. Further gene set enrichment analysis uncovered unique functional relationships among nonspliced, constitutively spliced and alternatively spliced genes. PMID:26156297

  11. Analysis of genetic interaction networks shows that alternatively spliced genes are highly versatile.

    PubMed

    Talavera, David; Sheoran, Ritika; Lovell, Simon C

    2013-01-01

    Alternative splicing has the potential to increase the diversity of the transcriptome and proteome. Where more than one transcript arises from a gene they are often so different that they are quite unlikely to have the same function. However, it remains unclear if alternative splicing generally leads to a gene being involved in multiple biological processes or whether it alters the function within a single process. Knowing that genetic interactions occur between functionally related genes, we have used them as a proxy for functional versatility, and have analysed the sets of genes of two well-characterised model organisms: Caenorhabditis elegans and Drosophila melanogaster. Using network analyses we find that few genes are functionally homogenous (only involved in a few functionally-related biological processes). Moreover, there are differences between alternatively spliced genes and genes with a single transcript; specifically, genes with alternatively splicing are, on average, involved in more biological processes. Finally, we suggest that factors other than specific functional classes determine whether a gene is alternatively spliced.

  12. Genomic architecture and functional relationships of intronless, constitutively- and alternatively-spliced genes in Brachypodium distachyon.

    PubMed

    Mandadi, Kranthi K; Scholthof, Karen-Beth G

    2015-01-01

    Splicing and alternative splicing (AS) are widespread co- and post-transcriptional regulatory processes in plants. Recently, we characterized genome-wide AS landscapes and virus-induced AS patterns in Brachypodium distachyon (Brachypodium), a C3 model grass. Brachypodium plants infected with Panicum mosaic virus (PMV) alone or in mixed infections with its satellite virus (SPMV) were used for high-throughput, paired-end RNA sequencing. Here, using gene attributes of ∼5,655 intronless genes, ∼13,302 constitutively spliced, and ∼7,564 alternatively spliced genes, we analyzed the influence of genomic features on splicing incidence and AS frequency. In Brachypodium, gene length, coding sequence length, and exon and intron number were positively correlated to splicing incidence and AS frequency. In contrast, exon length and the percentage composition of GC (%GC) content were inversely correlated with splicing incidence and AS frequency. Although gene expression status had little correlation with splicing occurrence per se, it negatively correlated to AS frequency: i.e., genes with ≥5 alternatively spliced transcripts were significantly less expressed compared to genes encoding <5 alternative transcripts. Further gene set enrichment analysis uncovered unique functional relationships among nonspliced, constitutively spliced and alternatively spliced genes.

  13. Brayton heat exchanger unit development program (alternate design)

    NASA Technical Reports Server (NTRS)

    Duncan, J. D.; Gibson, J. C.; Graves, R. F.; Morse, C. J.; Richard, C. E.

    1973-01-01

    A Brayton Heat Exchanger Unit Alternate Design (BHXU-Alternate) consisting of a recuperator, a heat sink heat exchanger, and a gas ducting system, was designed and fabricated. The design was formulated to provide a high performance unit suitable for use in a long-life Brayton-cycle powerplant. Emphasis was on double containment against external leakage and leakage of the organic coolant into the gas stream. A parametric analysis and design study was performed to establish the optimum component configurations to achieve low weight and size and high reliability, while meeting the requirements of high effectiveness and low pressure drop. Layout studies and detailed mechanical and structural design were performed to obtain a flight-type packaging arrangement, including the close-coupled integration of the BHXU-Alternate with the Brayton Rotating Unit (BRU).

  14. Identification of Krit1B: a novel alternative splicing isoform of cerebral cavernous malformation gene-1.

    PubMed

    Retta, Saverio Francesco; Avolio, Maria; Francalanci, Floriana; Procida, Simone; Balzac, Fiorella; Degani, Simona; Tarone, Guido; Silengo, Lorenzo

    2004-01-21

    Cerebral cavernous malformations (CCM) are vascular malformations, mostly located in the central nervous system, which occur in 0.1-0.5% of the population. They are characterized by abnormally enlarged and often leaking capillary cavities without intervening neural parenchyma. Some are clinically silent, whereas others cause seizures, intracerebral haemorrhage or focal neurological deficits. These vascular malformations can arise sporadically or may be inherited as an autosomal dominant condition with incomplete penetrance. At least 45% of families affected with cerebral cavernous malformations harbour a mutation in Krev interaction trapped-1 (Krit1) gene (cerebral cavernous malformation gene-1, CCM1). This gene contains 16 coding exons which encode a 736-amino acid protein containing three ankyrin repeats and a FERM domain. Neither the CCM1 pathogenetic mechanisms nor the function of the Krit1 protein are understood so far, although several hypotheses have been inferred from the predicted consequences of Krit1 mutations as well as from the identification of Krit1 as a binding partner of Rap1A, ICAP1A and microtubules. Here, we report the identification of Krit1B, a novel Krit1 isoform characterized by the alternative splicing of the 15th coding exon. We show that the Krit1B splice isoform is widely expressed in mouse cell lines and tissues, whereas its expression is highly restricted in human. In addition, we developed a real-time PCR strategy to accurately quantify the relative ratio of the two Krit1 alternative transcripts in different tissues, demonstrating a Krit1B/Krit1A ratio up to 20% in mouse thymus, but significantly lower ratios in other tissues. Bioinformatic analysis using exon/gene-prediction, comparative alignment and structure analysis programs supported the existence of Krit1 alternative transcripts lacking the 15th coding exon and showed that the splicing out of this exon occurs outside of potentially important Krit1 structural domains but in a

  15. An Economic Analysis of Alternative Programs to Finance Higher Education.

    ERIC Educational Resources Information Center

    Mathematica, Inc., Bethesda, MD.

    The Federal government operates several programs that provide money, either as loans or as a combination of grants and loans, to students. This paper attempts to clarify the economic and budgetary implications associated with continuing these existing programs, and discusses the differing economic consequences that would follow if some alternative…

  16. A Special Program for Special Students: The Alternate High School.

    ERIC Educational Resources Information Center

    Cancro, George P.

    1983-01-01

    This program at New York School for the Deaf serves students of average intelligence and slow reading ability between ages 15 and 21. The program gives students both the expertise available in a school for the handicapped and a practical education combined with a mainstreamed vocational setting and appropriate career guidance. (PB)

  17. Development and Delivery of an FCS Alternative Program for License

    ERIC Educational Resources Information Center

    Larson, Marsha L.

    2013-01-01

    When addressing the ongoing shortage of family and consumer sciences (FCS) teachers, it is important to accommodate those unable to follow a traditional college program. This article describes a program that is beneficial to practicing professionals; it utilizes technology to aid in effective communication and efficiency of content delivery.…

  18. Evaluation of Two Alternatives Programs for Junior High School Students.

    ERIC Educational Resources Information Center

    Malvin, Janet; And Others

    Based on the alternatives approach to drug abuse prevention, two service opportunity courses were offered to 8th and 9th grade students. Students in Cross-Age Tutoring were taught tutoring and communication skills and spent one period, 4 days per week tutoring elementary students. Students in School Store (a service opportunity developed for this…

  19. ORNL Research Programs related to chlorofluorocarbon (CFC) alternatives. [Chlorofluorocarbons

    SciTech Connect

    Fairchild, P.D.

    1987-05-13

    Testimony covered: uses and control impacts; federal/Department of Energy role; and relevant DOE research and development (absorption cycle technology, advanced insulation, novel thermodynamic cycles, fluid substitutes and recovery technology, development of replacement chemicals, development of recycling and recovery practices, development of alternative technologies, and resource requirements and schedules for accomplishment). (PSB)

  20. Survey and Analysis of Alternative Education Programs II

    ERIC Educational Resources Information Center

    Hosley, Nathaniel S.; Hosley, Jessica; Thein, Myint

    2009-01-01

    This research is a follow up to a similar study published by the Center for Rural Pennsylvania in 2003 in which researchers examined alternative education policies and practices among Pennsylvania school districts. The current study extended the previous research to include information on the perceptions of administrators and teachers on the…

  1. Digital-computer program for design analysis of salient, wound pole alternators

    NASA Technical Reports Server (NTRS)

    Repas, D. S.

    1973-01-01

    A digital computer program for analyzing the electromagnetic design of salient, wound pole alternators is presented. The program, which is written in FORTRAN 4, calculates the open-circuit saturation curve, the field-current requirements at rated voltage for various loads and losses, efficiency, reactances, time constants, and weights. The methods used to calculate some of these items are presented or appropriate references are cited. Instructions for using the program and typical program input and output for an alternator design are given, and an alphabetical list of most FORTRAN symbols and the complete program listing with flow charts are included.

  2. A bioinformatics analysis of alternative exon usage in human genes coding for extracellular matrix proteins.

    PubMed

    Sakabe, Noboru Jo; Vibranovski, Maria Dulcetti; de Souza, Sandro José

    2004-12-30

    Alternative splicing increases protein diversity through the generation of different mRNA molecules from the same gene. Although alternative splicing seems to be a widespread phenomenon in the human transcriptome, it is possible that different subgroups of genes present different patterns, related to their biological roles. Analysis of a subgroup may enhance common features of its members that would otherwise disappear amidst a heterogeneous population. Extracellular matrix (ECM) proteins are a good set for such analyses since they are structurally and functionally related. This family of proteins is involved in a large variety of functions, probably achieved by the combinatorial use of protein domains through exon shuffling events. To determine if ECM genes have a different pattern of alternative splicing, we compared clusters of expressed sequences of ECM to all other genes regarding features related to the most frequent type of alternative splicing, alternative exon usage (AEU), such as: the number of alternative exon-intron structures per cluster, the number of AEU events per exon-intron structure, the number of exons per event, among others. Although we did not find many differences between the two sets, we observed a higher frequency of AEU events involving entire protein domains in the ECM set, a feature that could be associated with their multi-domain nature. As other subgroups or even the ECM set in different tissues could present distinct patterns of AEU, it may be premature to conclude that alternative splicing is homogeneous among groups of related genes.

  3. EPAct Alternative Fuel Transportation Program: State and Alternative Fuel Provider Fleet Compliance Annual Report; Fleet Compliance Results for MY 2013/FY 2014

    SciTech Connect

    2015-09-01

    Compliance rates for covered state government and alternative fuel provider fleets under the Alternative Fuel Transportation Program (pursuant to the Energy Policy Act or EPAct) are reported for MY 2013/FY 2014 in this publication.

  4. Alternative Transposition Generates New Chimeric Genes and Segmental Duplications at the Maize p1 Locus

    PubMed Central

    Wang, Dafang; Yu, Chuanhe; Zuo, Tao; Zhang, Jianbo; Weber, David F.; Peterson, Thomas

    2015-01-01

    The maize Ac/Ds transposon family was the first transposable element system identified and characterized by Barbara McClintock. Ac/Ds transposons belong to the hAT family of class II DNA transposons. We and others have shown that Ac/Ds elements can undergo a process of alternative transposition in which the Ac/Ds transposase acts on the termini of two separate, nearby transposons. Because these termini are present in different elements, alternative transposition can generate a variety of genome alterations such as inversions, duplications, deletions, and translocations. Moreover, Ac/Ds elements transpose preferentially into genic regions, suggesting that structural changes arising from alternative transposition may potentially generate chimeric genes at the rearrangement breakpoints. Here we identified and characterized 11 independent cases of gene fusion induced by Ac alternative transposition. In each case, a functional chimeric gene was created by fusion of two linked, paralogous genes; moreover, each event was associated with duplication of the ∼70-kb segment located between the two paralogs. An extant gene in the maize B73 genome that contains an internal duplication apparently generated by an alternative transposition event was also identified. Our study demonstrates that alternative transposition-induced duplications may be a source for spontaneous creation of diverse genome structures and novel genes in maize. PMID:26434719

  5. Structure of the human myelin/oligodendrocyte glycoprotein gene and multiple alternative spliced isoforms

    SciTech Connect

    Pham-Dinh, D.; Gaspera, D.B.; Dautigny, A.

    1995-09-20

    Myelin/oligodendrocyte glycoprotein (MOG), a special component of the central nervous system localization on the outermost lamellae of mature myelin, is a member of the immunoglobulin superfamily. We report here the organization of the human MOG gene, which spans approximately 17 kb, and the characterization of six MOG mRNA splicing variants. The intron/exon structure of the human MOG gene confirmed the splicing pattern, supporting the hypothesis that mRNA isoforms could arise by alternative splicing of a single gene. In addition to the eight exons coding for the major MOG isoform, the human MOG gene also contains 3` region, a previously unknown alternatively spliced coding exon, VIA. Alternative utilization of two acceptor splicing sites for exon VIII could produce two different C-termini. The nucleotide sequences presented here may be a useful tool to study further possible involvement if the MOG gene in hereditary neurological disorders. 23 refs., 5 figs.

  6. 77 FR 5617 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-03

    ... Federal Transit Administration Alternative Transportation in Parks and Public Lands Program AGENCY: Federal Transit Administration (FTA), DOT. ACTION: Paul S. Sarbanes Transit in Parks Program Announcement.... Sarbanes Transit in Parks program, as authorized by Section 3021 of the Safe, Accountable, Flexible...

  7. 78 FR 22026 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

    ... Federal Transit Administration Alternative Transportation in Parks and Public Lands Program AGENCY: Federal Transit Administration (FTA), DOT. ACTION: Paul S. Sarbanes Transit in Parks Program Announcement... Administration (FTA) announces the selection of projects for the Paul S. Sarbanes Transit in Parks Program, as...

  8. 76 FR 5244 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-28

    ... Federal Transit Administration Alternative Transportation in Parks and Public Lands Program AGENCY: Federal Transit Administration (FTA), DOT. ACTION: Paul S. Sarbanes Transit in Parks Program Announcement... previously unallocated prior year funds, for the Paul S. Sarbanes Transit in Parks program, as authorized by...

  9. Prevention-Related Research Targeting African American Alternative Education Program Students

    ERIC Educational Resources Information Center

    Carswell, Steven B.; Hanlon, Thomas E.; Watts, Amy M.; O'Grady, Kevin E.

    2014-01-01

    This article reports on a program of research that examined the background, planning, implementation, and evaluation of an after-school preventive intervention program within an ongoing urban alternative education program targeting African American students referred to the school because of their problematic behavior in regular schools. The…

  10. Prevention-Related Research Targeting African American Alternative Education Program Students

    ERIC Educational Resources Information Center

    Carswell, Steven B.; Hanlon, Thomas E.; Watts, Amy M.; O'Grady, Kevin E.

    2014-01-01

    This article reports on a program of research that examined the background, planning, implementation, and evaluation of an after-school preventive intervention program within an ongoing urban alternative education program targeting African American students referred to the school because of their problematic behavior in regular schools. The…

  11. The Effects of an Alternative Spring Break Program on Student Development

    ERIC Educational Resources Information Center

    Beatty, Stephanie Hayne; Meadows, Ken N.; SwamiNathan, Richard; Mulvihill, Catherine

    2016-01-01

    This study examined the potential impact of a week-long cocurricular community service-learning (CSL) program on undergraduate students' psychosocial development. Participants in the Alternative Spring Break program and a matched control group completed surveys assessing a number of psychosocial variables immediately before and after the program,…

  12. What the Research Says about Alternative Teacher Certification Programs. Information Capsule. Volume 1104

    ERIC Educational Resources Information Center

    Blazer, Christie

    2012-01-01

    The shortage of qualified teachers across the U.S. has contributed to the popularity of alternative certification programs. These programs are designed to attract individuals into the teaching profession by allowing candidates to become certified without having to complete a traditional teacher education program. This Information Capsule reviewed…

  13. 76 FR 77716 - Alternate Passenger Rail Service Pilot Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-14

    ... final rules to assess their impact on small entities, unless the Secretary of Transportation certifies... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION... Program AGENCY: Federal Railroad Administration (FRA), Department of Transportation (DOT). ACTION: Final...

  14. FEMP (Federal Energy Management Program) presents alternative financing guidance memoranda

    SciTech Connect

    1998-06-01

    Utility financing of energy efficient measures becomes easier to accomplish with the two new alternative financing guidance memoranda, released April 17, 1998, that address the use of utility incentives for Federal facilities. The memoranda have been approved by the Alternative Financing Guidance Committee on the Interagency Energy Management Task Force. The memoranda include: (1) Policy Statement No. 001: Authority to Sole Source Utility Service Contracts as Referenced in Section 152 of the Energy Policy Act (EPACT) of 1992; and (2) Policy Statement No. 002: Congressional Notification for Utility Projects Under the Authority of Section 152 of the Energy Policy Act (EPACT) of 1992. The purpose for developing the financing memoranda was to address specific issues within current Federal procurement regulations that require clarification or guidance. This new guidance will allow for increased use of utility incentives as a means of financing energy efficient and life cycle cost-effective projects in Federal facilities.

  15. Maternal diet programs embryonic kidney gene expression.

    PubMed

    Welham, Simon J M; Riley, Paul R; Wade, Angie; Hubank, Mike; Woolf, Adrian S

    2005-06-16

    Human epidemiological data associating birth weight with adult disease suggest that organogenesis is "programmed" by maternal diet. In rats, protein restriction in pregnancy produces offspring with fewer renal glomeruli and higher systemic blood pressures than controls. We tested the hypothesis that maternal diet alters gene expression in the metanephros, the precursor of the definitive mammalian kidney. We demonstrated that maternal low-protein diet initiated when pregnancy starts and maintained to embryonic day 13, when the metanephros consists of mesenchyme surrounding a once-branched ureteric bud, is sufficient to significantly reduce glomerular numbers in offspring by about 20%. As assessed by representational difference analyses and real-time quantitative polymerase chain reactions, low-protein diet modulated gene expression in embryonic day 13 metanephroi. In particular, levels of prox-1, the ortholog of Drosophila transcription factor prospero, and cofilin-1, a regulator of the actin cytoskeleton, were reduced. During normal metanephrogenesis, prox-1 protein was first detected in mesenchymal cells around the ureteric tree and thereafter in nascent nephron epithelia, whereas cofilin-1 immunolocalized to bud derivatives and condensing mesenchyme. Previously, we reported that low-protein diets increased mesenchymal apoptosis cells when metanephrogenesis began and thereafter reduced numbers of precursor cells. Collectively, these studies prove that the maternal diet programs the embryonic kidney, altering cell turnover and gene expression at a time when nephrons and glomeruli have yet to form. The human implication is that the maternal diet ingested between conception and 5- 6-wk gestation contributes to the variation in glomerular numbers that are known to occur between healthy and hypertensive populations.

  16. Gene-expression programming for flip-bucket spillway scour.

    PubMed

    Guven, Aytac; Azamathulla, H Md

    2012-01-01

    During the last two decades, researchers have noticed that the use of soft computing techniques as an alternative to conventional statistical methods based on controlled laboratory or field data, gave significantly better results. Gene-expression programming (GEP), which is an extension to genetic programming (GP), has nowadays attracted the attention of researchers in prediction of hydraulic data. This study presents GEP as an alternative tool in the prediction of scour downstream of a flip-bucket spillway. Actual field measurements were used to develop GEP models. The proposed GEP models are compared with the earlier conventional GP results of others (Azamathulla et al. 2008b; RMSE = 2.347, δ = 0.377, R = 0.842) and those of commonly used regression-based formulae. The predictions of GEP models were observed to be in strictly good agreement with measured ones, and quite a bit better than conventional GP and the regression-based formulae. The results are tabulated in terms of statistical error measures (GEP1; RMSE = 1.596, δ = 0.109, R = 0.917) and illustrated via scatter plots.

  17. Gene, Stem Cell, and Alternative Therapies for SCA 1

    PubMed Central

    Wagner, Jacob L.; O'Connor, Deirdre M.; Donsante, Anthony; Boulis, Nicholas M.

    2016-01-01

    Spinocerebellar ataxia 1 is an autosomal dominant disease characterized by neurodegeneration and motor dysfunction. In disease pathogenesis, polyglutamine expansion within Ataxin-1, a gene involved in transcriptional repression, causes protein nuclear inclusions to form. Most notably, neuronal dysfunction presents in Purkinje cells. However, the effect of mutant Ataxin-1 is not entirely understood. Two mouse models are employed to represent spinocerebellar ataxia 1, a B05 transgenic model that specifically expresses mutant Ataxin-1 in Purkinje cells, and a Sca1 154Q/2Q model that inserts the polyglutamine expansion into the mouse Ataxin-1 locus so that the mutant Ataxin-1 is expressed in all cells that express Ataxin-1. This review aims to summarize and evaluate the wide variety of therapies proposed for spinocerebellar ataxia 1, specifically gene and stem cell therapies. PMID:27570504

  18. An Alternative Preparation Program in Early Childhood Education: Description and Comparison of Alternative and Traditional Students.

    ERIC Educational Resources Information Center

    Guyton, Edith; And Others

    1993-01-01

    Students entering traditional and nontraditional early childhood teacher preparation programs completed the Educational Attitudes Inventory, Teacher Certification Test, and Efficacy Scale. Mean personal teaching efficacy scores were significantly higher for traditional students. Nontraditional students tended to be males, minorities, and older,…

  19. An Alternative Preparation Program in Early Childhood Education: Description and Comparison of Alternative and Traditional Students.

    ERIC Educational Resources Information Center

    Guyton, Edith; And Others

    1993-01-01

    Students entering traditional and nontraditional early childhood teacher preparation programs completed the Educational Attitudes Inventory, Teacher Certification Test, and Efficacy Scale. Mean personal teaching efficacy scores were significantly higher for traditional students. Nontraditional students tended to be males, minorities, and older,…

  20. Alternate bearing design fabrication and test program, exhibit B

    NASA Technical Reports Server (NTRS)

    1978-01-01

    A 50 ft-lb-sec (FPS) reaction wheel was modified with an ironless armature brushless dc motor and a magnetic bearing suspension. The purpose was to demonstrate the performance of an alternate bearing concept, i.e., a magnetic bearing suspension, which could be used in Skylab type CMG's to meet the attitude control requirements of long term space stations. A magnetic suspension was built, installed and tested in the 50 FPS reaction wheel. A secondary effort included the build and test of a compatible reaction wheel motor. Performance characteristics of both are presented and discussed.

  1. Alternative splicing of the FMR1 gene in human fetal brain neurons

    SciTech Connect

    Tao Huang; Yan Shen; Xue-bin Qin; Guan-Yun Wu

    1996-08-09

    The alternative splicing expression of the FMR1 gene was reported in several human and mouse tissues. Five regions of FMR1 gene can be alternatively spliced, but the combination of them has not been investigated fully. We reported here the analysis of alternative splicing pattern of the FMR1 gene in cultured fetal human neurons, using a RT-PCR and cloning strategy. Eleven splicing types were cloned and different isoforms were not equally represented. The dominant isoform represents nearly 40%, and the other isoforms were relatively rare. One isoform has a different carboxyl-terminus. Most of the alternative spliced regions appear hydrophilic; thus, they may locate on the surface of the FMR1 protein. 16 refs., 2 figs.

  2. SELENIUM TREATMENT/REMOVAL ALTERNATIVES DEMONSTRATION PROJECT - MINE WASTE TECHNOLOGY PROGRAM ACTIVITY III, PROJECT 20

    EPA Science Inventory

    This document is the final report for EPA's Mine WAste Technology Program (MWTP) Activity III, Project 20--Selenium Treatment/Removal Alternatives Demonstration project. Selenium contamination originates from many sources including mining operations, mineral processing, abandoned...

  3. SELENIUM TREATMENT/REMOVAL ALTERNATIVES DEMONSTRATION PROJECT - MINE WASTE TECHNOLOGY PROGRAM ACTIVITY III, PROJECT 20

    EPA Science Inventory

    This document is the final report for EPA's Mine WAste Technology Program (MWTP) Activity III, Project 20--Selenium Treatment/Removal Alternatives Demonstration project. Selenium contamination originates from many sources including mining operations, mineral processing, abandoned...

  4. Structure of the Minnesota Developmental Programming System Behavioral Scales, Alternate Form C.

    ERIC Educational Resources Information Center

    Silverman, Wayne P.; And Others

    1983-01-01

    The Minnesota Developmental Programming System Behavioral Scales, Alternate Form C, designed to assess adaptive behavior of profoundly developmentally disabled individuals, was evaluated using data from 3,487 individuals. (Author/CL)

  5. An Alternative Avenue to Teacher Certification: A Cost Analysis of the Pathways to Teaching Careers Program.

    ERIC Educational Resources Information Center

    Rice, Jennifer King; Brent, Brian O.

    2002-01-01

    Analyzes cost effectiveness of the Pathways to Teaching Careers, a program that supports an alternative route to university-based teacher certification primarily for noncertified teachers, paraprofessionals, and Peace Corps volunteers. (PKP)

  6. 76 FR 64124 - Implementation of the Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-10-17

    ... on submitting comments and instructions on accessing documents related to this action, see..., and on which the NRC is soliciting public comments are: Questions Related to Pre-investigation ADR... that you believe are effective? Issues Related to Post-investigation ADR 1. Does the program support...

  7. 36 CFR 800.14 - Federal agency program alternatives.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... agency official shall provide summaries of the views, along with copies of any written comments, provided... program or the resolution of adverse effects from certain complex project situations or multiple... projects or multiple undertakings shall follow § 800.6. If consultation pertains to an activity involving...

  8. 36 CFR 800.14 - Federal agency program alternatives.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... agency official shall provide summaries of the views, along with copies of any written comments, provided... program or the resolution of adverse effects from certain complex project situations or multiple... projects or multiple undertakings shall follow § 800.6. If consultation pertains to an activity involving...

  9. 76 FR 55335 - Alternate Passenger Rail Service Pilot Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ... that own infrastructure over which Amtrak operates certain passenger rail service routes to petition FRA to be considered as a passenger rail service provider over such a route in lieu of Amtrak for a... develop a pilot program that permits a rail carrier or rail carriers that own infrastructure over...

  10. Modular Laboratory Courses: An Alternative to a Traditional Laboratory Program

    ERIC Educational Resources Information Center

    Caprette, David R.; Armstrong, Sarah; Beason, K. Beth

    2005-01-01

    Our modular laboratory teaching program is characterized by two major features. First, each course is taught independently and not linked with a particular lecture course. Second, each course is designed to be completed within one-half semester or less. The modular organization has allowed incorporation of the latest technology, reduction of class…

  11. Alternative Strategies for Using Intersection Cuts in Integer Programming.

    DTIC Science & Technology

    In a previous paper the author introduced a new cutting plane for integer programming, generated from the intersection of n halflines originating at...polytope whose interior contains no feasible vertex of K. Hence C can be used to generate intersection cuts that are obviously stronger than the ones considered earlier. (Author)

  12. Alternative Loan Programs: A Comparison of Various Features.

    ERIC Educational Resources Information Center

    New York State Higher Education Services Corp., Albany.

    This report provides comparative data on various features of 36 student loan programs available to undergraduate and/or graduate students in New York. Presented in a table format, the report provides information on loan type, lender, maximum limit, minimum limit, interest rate/payment, fees, repayment guidelines, eligibility, disbursement, and…

  13. Alternatives for Success: One Program’s Unconventional Structure

    DTIC Science & Technology

    2013-12-01

    program. First, the Procurement Contracting Officer ( PCO ) sent a limited stop-work letter for Contract Line-Item Number tasks that were not needed. Based...maintain schedule. To mitigate this risk, the PCO worked with the prime contractor to prepare and award a not-to-exceed (NTE) change order to the

  14. Application of an Alternative Cost Analysis Model to Educational Programs.

    ERIC Educational Resources Information Center

    Beilby, Albert E.

    This paper discusses the development and implementation of a cost analysis model for use by curriculum planners and developers in evaluating educational programs. The paper consists of four major sections that focus in turn on the need to approach educational costs from a nontraditional perspective, development of a cost model, implementation of…

  15. Virginia Alternative Assessment Program: Implementation Manual (Revised 2002).

    ERIC Educational Resources Information Center

    Virginia State Dept. of Education, Richmond.

    The Individuals with Disabilities Education Act requires state programs to adopt standards for all children, including those with disabilities, in state and district-wide assessments with the provision of appropriate and necessary accommodations. For students who cannot participate in state and district-wide assessments, the law requires that…

  16. Clarendon Alternative School Japanese Bilingual Bicultural Program: Curriculum Sampler.

    ERIC Educational Resources Information Center

    San Francisco Unified School District, CA.

    Sample lessons and instructional materials from a Japanese bilingual/bicultural elementary school program are presented. The lessons are designed to integrate Japanese language instruction with content instruction, using thematic units related to the core curriculum. The ten lessons are organized by target grade (K-5), and describe classroom…

  17. Alternative Break Programs: From Isolated Enthusiasm to Best Practices--The Haiti Compact

    ERIC Educational Resources Information Center

    Piacitelli, Jill; Barwick, Molly; Doerr, Elizabeth; Porter, Melody; Sumka, Shoshanna

    2013-01-01

    Alternative break programs, which are short-term service-learning trips, immerse students in direct service and education, resulting in the creation of active citizens who think and act critically around the root causes of social issues. Over the last 20 years, domestic alternative breaks have effectively created strong community partnerships and…

  18. 5 CFR 2424.10 - Collaboration and Alternative Dispute Resolution Program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 5 Administrative Personnel 3 2010-01-01 2010-01-01 false Collaboration and Alternative Dispute... Collaboration and Alternative Dispute Resolution Program. Where an exclusive representative and an agency are unable to resolve disputes that arise under this part, they may request assistance from the...

  19. Alternative Programs for At-Risk Students: Wolves in Sheep's Clothing?

    ERIC Educational Resources Information Center

    Sagor, Richard

    1997-01-01

    Provides a critique of alternative education and details the disadvantages of segregated schooling. Discusses the problems associated with labeling children as "problem students" and outlines ways in which equitable alternative programs can be devised. Gives a case study as an example. (RJM)

  20. Inclusion of Alternative and Complementary Therapies in CACREP Training Programs: A Survey

    ERIC Educational Resources Information Center

    Lumadue, Christine A.; Munk, Melanie; Wooten, H. Ray

    2005-01-01

    Given a heightened focus within the mental health profession on creative, complementary, and alternative practices, the authors surveyed CACREP programs with respect to their inclusion of such approaches in counselor training. For the purpose of this study, these approaches were designated as complementary and alternative methods (CAM) and defined…

  1. Educational Alternatives for Vulnerable Youth: Student Needs, Program Types, and Research Directions

    ERIC Educational Resources Information Center

    Aron, Laudan Y.; Zweig, Janine M.

    2003-01-01

    Chapter 1 of this document examines the need for alternative education among vulnerable youth by reviewing the numbers and characteristics of youth who disconnect from mainstream developmental pathways in various ways. The second chapter examines the question of "what is an alternative education school or program" and draws on a variety…

  2. The Description and Evaluation of the Alternate Day-Full Day Kindergarten Program.

    ERIC Educational Resources Information Center

    Mouw, Annabelle Jean

    This paper describes and evaluates an alternate day-full day kindergarten program. Through the use of Cognitive Abilities Test (CAT) scores and surveys, two kindergarten groups were compared. One group attended school for a half-day daily; the other attended all day on alternate days, but for a comparable length of time. A summary of survey…

  3. Factors Associated with Student Resilience: Perspectives of Graduates of Alternative Education Programs

    ERIC Educational Resources Information Center

    Zolkoski, Staci M.; Bullock, Lyndal M.; Gable, Robert A.

    2016-01-01

    Many students with emotional and behavioral disorders placed in alternative education settings lack resilience and are likely to experience failure in school and beyond without carefully designed intervention programs. Although researchers have examined both resilience in children and youth and their placement in alternative education settings,…

  4. Wellness-Based Group Counseling with Elementary Students in Disciplinary Alternative Education Programs

    ERIC Educational Resources Information Center

    Perepiczka, Michelle

    2009-01-01

    Students in Disciplinary Alternative Education Programs (DAEPs) have a variety of behavior problems. School counselors in DAEPs have the opportunity to address emotional, academic, social, and behavioral concerns of these students. Counselors may use the strengths-based wellness paradigm as an alternative method of addressing students' holistic…

  5. 46 CFR 115.660 - Continued participation in the Alternative Hull Examination (AHE) Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Continued participation in the Alternative Hull... MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.660 Continued participation in the Alternative Hull Examination (AHE) Program. (a) To continue to participate in...

  6. 46 CFR 115.630 - The Alternative Hull Examination (AHE) Program application.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false The Alternative Hull Examination (AHE) Program... PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.630 The Alternative Hull... hull examination date to the Officer in Charge, Marine Inspection (OCMI) who will oversee the survey...

  7. Linking linear programming and spatial simulation models to predict landscape effects of forest management alternatives

    Treesearch

    Eric J. Gustafson; L. Jay Roberts; Larry A. Leefers

    2006-01-01

    Forest management planners require analytical tools to assess the effects of alternative strategies on the sometimes disparate benefits from forests such as timber production and wildlife habitat. We assessed the spatial patterns of alternative management strategies by linking two models that were developed for different purposes. We used a linear programming model (...

  8. Inclusion of Alternative and Complementary Therapies in CACREP Training Programs: A Survey

    ERIC Educational Resources Information Center

    Lumadue, Christine A.; Munk, Melanie; Wooten, H. Ray

    2005-01-01

    Given a heightened focus within the mental health profession on creative, complementary, and alternative practices, the authors surveyed CACREP programs with respect to their inclusion of such approaches in counselor training. For the purpose of this study, these approaches were designated as complementary and alternative methods (CAM) and defined…

  9. Sense of Efficacy in Beginning Teachers Participating in an Alternative Certification Program

    ERIC Educational Resources Information Center

    McKinney, Daniel Lee

    2014-01-01

    Despite the widespread use of alternatively certified personnel by school systems to address shortages of highly qualified teachers, alternative certification programs (ACPs) have appeared largely inconsistent in design and lacked research in effectiveness. Hence, benefit could be gained in evaluating the competency of ACP participants in terms of…

  10. Alternate space shuttle concepts study: Design requirements and phased programs evaluation

    NASA Technical Reports Server (NTRS)

    1971-01-01

    A study to determine program and technical alternatives to the design of the space shuttle orbiter is described. The alternatives include a phased approach, involving orbiter development and operation with an expendable booster for an interim period, as well as design variations to the basic vehicle. The space shuttle orbiter configurations and predicted performance parameters are presented.

  11. Factors Associated with Student Resilience: Perspectives of Graduates of Alternative Education Programs

    ERIC Educational Resources Information Center

    Zolkoski, Staci M.; Bullock, Lyndal M.; Gable, Robert A.

    2016-01-01

    Many students with emotional and behavioral disorders placed in alternative education settings lack resilience and are likely to experience failure in school and beyond without carefully designed intervention programs. Although researchers have examined both resilience in children and youth and their placement in alternative education settings,…

  12. Certification Report: Army Aviation Alternative Fuels Certification Program

    DTIC Science & Technology

    2016-08-01

    mutation test. Screen for possible mutagens and carcinogens using bacteria . 3) In vitro genotoxicity mammalian cell gene mutation test. Screen for...Ames Test. The Ames test is a widely employed method that uses five strains of bacteria to test whether a given chemical can cause mutations...isomerization process. ATJ-SPKs can be produced from bioderived alcohols which are created through traditional fermentation processes using carbohydrate

  13. Alternative Schools/Programs. Proven Exemplary Educational Programs and Practices: A Collection from the National Diffusion Network (NDN).

    ERIC Educational Resources Information Center

    Michigan State Board of Education, Lansing.

    This booklet is a collection of proven exemplary educational programs and practices from the National Diffusion Network (NDN). As part of a two-part series, this publication covers alternative schools and their programs. The NDN facilitates the exchange of information between the developers of successful projects and adopting districts. Many of…

  14. Update from the NREL Alternative Fuel Transit Bus Evaluation Program

    SciTech Connect

    Chandler, K.; Norton, P.; Clark, N.

    1999-05-01

    The object of this project, which is supported by the U.S. Department of Energy (DOE) through the National Renewable Energy Laboratory (NREL), is to provide a comprehensive comparison of heavy-duty urban transit buses operating on alternative fuels and diesel fuel. Final reports from this project were produced in 1996 from data collection and evaluation of 11 transit buses from eight transit sites. With the publication of these final reports, three issues were raised that needed further investigation: (1) the natural gas engines studied were older, open-loop control engines; (2) propane was not included in the original study; and (3) liquefied natural gas (LNG) was found to be in the early stages of deployment in transit applications. In response to these three issues, the project has continued by emissions testing newer natural gas engines and adding two new data collection sites to study the newer natural gas technology and specifically to measure new technology LNG buses.

  15. The Army’s Ground Combat Vehicle Program and Alternatives

    DTIC Science & Technology

    2013-04-01

    Current and Upgraded Bradley Infantry Fighting Vehicle Notional Ground Combat Vehicle Israeli Namer Armored Personnel Carrier German Puma ...19Option 1: Purchase the Israeli Namer APC 21 Option 2: Upgrade the Bradley IFV 26 Option 3: Purchase the German Puma IFV 28 Option 4: Cancel the GCV Program...2008 German Puma IFV 35 to 47 6 6.9 2011 2013 dollars) (Millions of Unit Costb Existing Vehicles Vehicles Requiring Development Into Service Year of

  16. Multidimensional Programming Methods for Energy Facility Siting: Alternative Approaches

    NASA Technical Reports Server (NTRS)

    Solomon, B. D.; Haynes, K. E.

    1982-01-01

    The use of multidimensional optimization methods in solving power plant siting problems, which are characterized by several conflicting, noncommensurable objectives is addressed. After a discussion of data requirements and exclusionary site screening methods for bounding the decision space, classes of multiobjective and goal programming models are discussed in the context of finite site selection. Advantages and limitations of these approaches are highlighted and the linkage of multidimensional methods with the subjective, behavioral components of the power plant siting process is emphasized.

  17. F-35 Alternate Engine Program: Background and Issues for Congress

    DTIC Science & Technology

    2010-03-22

    funding, forcing cuts in future capabilities and force structure . An official from the F-35 program office stated that the reduction in F- 35 procurement... structural failure of an F-15C. The fleet was returned to service on November 21, 2007. (“Entire F-15 Fleet Returning to Flight”, Air Combat Command...fund a second engine.16 Also in July, 2009, DOD created a Joint Assessment Team (JAT) “to investigate and understand Pratt & Whitney’s cost structure

  18. F-35 Alternate Engine Program: Background and Issues for Congress

    DTIC Science & Technology

    2011-01-10

    forcing cuts in future capabilities and force structure . An official from the F-35 program office stated that the reduction in F- 35 procurement over...Defense Report, June 1, 2009, p. 3. 5 For example, the Air Force grounded all of its F-15 aircraft on November 3, 2007, following midair structural ...and understand Pratt & Whitney’s cost structure and help the JSF office in its assessment of the company’s latest … bid. The JAT also will look at

  19. F-35 Alternate Engine Program: Background and Issues for Congress

    DTIC Science & Technology

    2010-09-17

    in future capabilities and force structure . An official from the F-35 program office stated that the reduction in F- 35 procurement over the next...Report, June 1, 2009, p. 3. 5 For example, the Air Force grounded all of its F-15 aircraft on November 3, 2007, following midair structural failure...DOD created a Joint Assessment Team (JAT) “to investigate and understand Pratt & Whitney’s cost structure and help the JSF office in its assessment

  20. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus.

    PubMed

    Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S; Chen, Yidong

    2008-12-01

    The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website.

  1. GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

    PubMed Central

    Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

    2008-01-01

    The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

  2. SKIP Confers Osmotic Tolerance during Salt Stress by Controlling Alternative Gene Splicing in Arabidopsis.

    PubMed

    Feng, Jinlin; Li, Jingjing; Gao, Zhaoxu; Lu, Yaru; Yu, Junya; Zheng, Qian; Yan, Shuning; Zhang, Wenjiao; He, Hang; Ma, Ligeng; Zhu, Zhengge

    2015-07-01

    Deciphering the mechanisms underlying plant responses to abiotic stress is key for improving plant stress resistance. Much is known about the regulation of gene expression in response to salt stress at the transcriptional level; however, little is known about this process at the posttranscriptional level. Recently, we demonstrated that SKIP is a component of spliceosome that interacts with clock gene pre-mRNAs and is essential for regulating their alternative splicing and mRNA maturation. In this study, we found that skip-1 plants are hypersensitive to both salt and osmotic stresses, and that SKIP is required for the alternative splicing and mRNA maturation of several salt-tolerance genes, including NHX1, CBL1, P5CS1, RCI2A, and PAT10. A genome-wide analysis revealed that SKIP mediates the alternative splicing of many genes under salt-stress conditions, and that most of the alternative splicing events in skip-1 involve intron retention and can generate a premature termination codon in the transcribed mRNA. SKIP also controls alternative splicing by modulating the recognition or cleavage of 5' and 3' splice donor and acceptor sites under salt-stress conditions. Therefore, this study addresses the fundamental question of how the mRNA splicing machinery in plants contributes to salt-stress responses at the posttranscriptional level, and provides a link between alternative splicing and salt tolerance.

  3. Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants.

    PubMed

    Verhage, Leonie; Severing, Edouard I; Bucher, Johan; Lammers, Michiel; Busscher-Lange, Jacqueline; Bonnema, Guusje; Rodenburg, Nicole; Proveniers, Marcel C G; Angenent, Gerco C; Immink, Richard G H

    2017-01-01

    Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures.

  4. Changes in cell wall polysaccharide composition, gene transcription and alternative splicing in germinating barley embryos.

    PubMed

    Zhang, Qisen; Zhang, Xiaoqi; Pettolino, Filomena; Zhou, Gaofeng; Li, Chengdao

    2016-02-01

    Barley (Hordeum vulgare L.) seed germination initiates many important biological processes such as DNA, membrane and mitochondrial repairs. However, little is known on cell wall modifications in germinating embryos. We have investigated cell wall polysaccharide composition change, gene transcription and alternative splicing events in four barley varieties at 24h and 48 h germination. Cell wall components in germinating barley embryos changed rapidly, with increases in cellulose and (1,3)(1,4)-β-D-glucan (20-100%) within 24h, but decreases in heteroxylan and arabinan (3-50%). There were also significant changes in the levels of type I arabinogalactans and heteromannans. Alternative splicing played very important roles in cell wall modifications. At least 22 cell wall transcripts were detected to undergo either alternative 3' splicing, alternative 5' splicing or intron retention type of alternative splicing. These genes coded enzymes catalyzing synthesis and degradation of cellulose, heteroxylan, (1,3)(1,4)-β-D-glucan and other cell wall polymers. Furthermore, transcriptional regulation also played very important roles in cell wall modifications. Transcript levels of primary wall cellulase synthase, heteroxylan synthesizing and nucleotide sugar inter-conversion genes were very high in germinating embryos. At least 50 cell wall genes changed transcript levels significantly. Expression patterns of many cell wall genes coincided with changes in polysaccharide composition. Our data showed that cell wall polysaccharide metabolism was very active in germinating barley embryos, which was regulated at both transcriptional and post-transcriptional levels.

  5. Splicing-related genes are alternatively spliced upon changes in ambient temperatures in plants

    PubMed Central

    Bucher, Johan; Lammers, Michiel; Busscher-Lange, Jacqueline; Bonnema, Guusje; Rodenburg, Nicole; Proveniers, Marcel C. G.; Angenent, Gerco C.

    2017-01-01

    Plants adjust their development and architecture to small variations in ambient temperature. In a time in which temperatures are rising world-wide, the mechanism by which plants are able to sense temperature fluctuations and adapt to it, is becoming of special interest. By performing RNA-sequencing on two Arabidopsis accession and one Brassica species exposed to temperature alterations, we showed that alternative splicing is an important mechanism in ambient temperature sensing and adaptation. We found that amongst the differentially alternatively spliced genes, splicing related genes are enriched, suggesting that the splicing machinery itself is targeted for alternative splicing when temperature changes. Moreover, we showed that many different components of the splicing machinery are targeted for ambient temperature regulated alternative splicing. Mutant analysis of a splicing related gene that was differentially spliced in two of the genotypes showed an altered flowering time response to different temperatures. We propose a two-step mechanism where temperature directly influences alternative splicing of the splicing machinery genes, followed by a second step where the altered splicing machinery affects splicing of downstream genes involved in the adaptation to altered temperatures. PMID:28257507

  6. F-35 Alternate Engine Program: Background and Issues for Congress

    DTIC Science & Technology

    2011-04-20

    in future capabilities and force structure . An official from the F-35 program office stated that the reduction in F- 35 procurement over the next five...Report, June 1, 2009, p. 3. 5 For example, the Air Force grounded all of its F-15 aircraft on November 3, 2007, following midair structural failure of...Assessment Team (JAT) “to investigate and understand Pratt & Whitney’s cost structure and help the JSF office in its assessment of the company’s latest

  7. Necroptosis: an alternative cell death program defending against cancer

    PubMed Central

    Chen, Dongshi; Yu, Jian; Zhang, Lin

    2016-01-01

    One of the hallmarks of cancer is resistance to programmed cell death, which maintains the survival of cells en route to oncogenic transformation and underlies therapeutic resistance. Recent studies demonstrate that programmed cell death is not confined to caspase-dependent apoptosis, but includes necroptosis, a form of necrotic death governed by Receptor-Interacting Protein 1 (RIP1), RIP3, and Mixed Lineage Kinase Domain-Like (MLKL). Necroptosis serves as a critical cell-killing mechanism in response to severe stress and blocked apoptosis, and can be induced by inflammatory cytokines or chemotherapeutic drugs. Genetic or epigenetic alterations of necroptosis regulators such as RIP3 and cylindromatosis (CYLD), are frequently found in human tumors. Unlike apoptosis, necroptosis elicits a more robust immune response that may function as a defensive mechanism by eliminating tumor-causing mutations and viruses. Furthermore, several classes of anticancer agents currently under clinical development, such as SMAC and BH3 mimetics, can promote necroptosis in addition to apoptosis. A more complete understanding of the interplay among necroptosis, apoptosis, and other cell death modalities is critical for developing new therapeutic strategies to enhance killing of tumor cells. PMID:26968619

  8. Alternatives in Scheduling Patterns: Practitioner Implementation of Minicourse Programs in Selected Midwestern High Schools.

    ERIC Educational Resources Information Center

    Hansen, Patricia; Guenther, John

    The purposes of the document are to report on the status of social studies minicourse programs in selected midwestern high schools and to provide information to schools regarding obstacles to minicourses as alternatives to traditional programs. A 1976-77 survey of 265 midwestern high schools determined that only 60 (23%) of the schools offered…

  9. Towards a Lakatosian Analysis of the Piagetian and Alternative Conceptions Research Programs.

    ERIC Educational Resources Information Center

    Gilbert, John K.; Swift, David J.

    1985-01-01

    Lakatos's methodology of scientific research programs is summarized and discussed for Piagetian schools and alternative conceptions movement. Commonalities/differences between these two rival programs are presented along with fundamental assumptions, auxiliary hypotheses, and research policy. Suggests that research findings should not be merely…

  10. An Alternative School Teacher Education Program. Teacher Education Forum; Volume 3, Number 7.

    ERIC Educational Resources Information Center

    Barr, Robert D.

    The Alternative School Teacher Education Program, cooperatively developed by participating public schools and Indiana University, is a field-based masters degree program designed for completion in one calendar year. Students spend two summers on campus pursuing graduate course work. During the academic year between these summers, students earn…

  11. A Comparison of Technology Experiences Included in Alternative and Traditional Teacher Education Programs

    ERIC Educational Resources Information Center

    Strycker, Jesse D.

    2011-01-01

    Though an educational technology experience is required as part of a traditional teacher education program student's educational preparation, research has been limited into the experiences had by alternative teacher education program students. Similarly, little research has been done comparing technology experiences between both types of teacher…

  12. Does Teaching Experience Matter? Examining Biology Teachers' Prior Knowledge for Teaching in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Friedrichsen, Patricia J.; Abell, Sandra K.; Pareja, Enrique M.; Brown, Patrick L.; Lankford, Deanna M.; Volkmann, Mark J.

    2009-01-01

    Alternative certification programs (ACPs) have been proposed as a viable way to address teacher shortages, yet we know little about how teacher knowledge develops within such programs. The purpose of this study was to investigate prior knowledge for teaching among students entering an ACP, comparing individuals with teaching experience to those…

  13. Examining Our Career Switching Teachers' First Year of Teaching: Implications for Alternative Teacher Education Program Design

    ERIC Educational Resources Information Center

    Wilcox, Dawn Renee; Samaras, Anastasia P.

    2009-01-01

    This study explores the impact of an alternative teacher preparation program development from the "inside out" or through the voices of second career teachers, known as "Career Switchers," at a mid-size state university. The major objective of this study was to probe into their perceptions to inform program development with reporting framed in…

  14. State-Wide Collaborative Partnerships for Alternative Certification the Kansas Transition to Teaching Program

    ERIC Educational Resources Information Center

    Carroll, Jeri A.; Hayes, Judith L.; Mercer, Debbie; Neuenswander, Bill; Drake, Sheila

    2006-01-01

    Alternative certification programs continue to increase as school districts, institutions of higher education, and commercial companies share common educational expectations. In Kansas, a state-wide collaborative of eleven partner institutions, governed by an advisory board, designed a conceptual framework, a standards-based program, curriculum,…

  15. 19 CFR 101.9 - Test programs or procedures; alternate requirements.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 19 Customs Duties 1 2010-04-01 2010-04-01 false Test programs or procedures; alternate requirements. 101.9 Section 101.9 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND... or procedure designed to evaluate planned components of the National Customs Automation Program...

  16. Program Evaluation of Alternative Schools in North Carolina: A Companion Dissertation

    ERIC Educational Resources Information Center

    Jones, Michael O.

    2013-01-01

    The purpose of the evaluation was to evaluate two alternative programs in a North Carolina (NC) and South Carolina (SC) public school district to determine if they are effective in delivering constructive interventions that modify student behavior once students have left the programs and have returned to their regular learning environments. This…

  17. How Induction Programs Affect the Decision of Alternate Route Urban Teachers to Remain Teaching

    ERIC Educational Resources Information Center

    LoCascio, Steven J.; Smeaton, Patricia S.; Waters, Faith H.

    2016-01-01

    This mixed-methods study analyzes the induction programs for alternate route beginning teachers in low socioeconomic, urban schools. The researcher surveyed 53 teachers at the end of their first year and conducted six in-depth follow-up interviews. The study found that half the teachers did not receive an induction program congruent with state…

  18. A Comparison of the Alternative and Traditional Licensure Programs at Metropolitan State College of Denver.

    ERIC Educational Resources Information Center

    Heyman, Ernest L.

    This study evaluated Metropolitan State College of Denver's Teacher-in-Residence (TiR) alternative licensure program. To participate, teacher candidates must possess a baccalaureate degree, have a teaching contract in a participating local school district, enroll in the TiR program, and pass a state content test. This study examined what Metro…

  19. Does Teaching Experience Matter? Examining Biology Teachers' Prior Knowledge for Teaching in an Alternative Certification Program

    ERIC Educational Resources Information Center

    Friedrichsen, Patricia J.; Abell, Sandra K.; Pareja, Enrique M.; Brown, Patrick L.; Lankford, Deanna M.; Volkmann, Mark J.

    2009-01-01

    Alternative certification programs (ACPs) have been proposed as a viable way to address teacher shortages, yet we know little about how teacher knowledge develops within such programs. The purpose of this study was to investigate prior knowledge for teaching among students entering an ACP, comparing individuals with teaching experience to those…

  20. Alternative Teacher Education Programs: A Review of the Literature and Outcome Studies

    ERIC Educational Resources Information Center

    Suell, Jo Lynn; Piotrowski, Chris

    2007-01-01

    This paper provides an overview on alternative teacher education programs (ATEP). This review covers the formation, development and design of these non-traditional certification approaches over the past 2 decades. The major reasons for the viability of these programs are presented. Moreover, research studies on critical issues such as teacher…

  1. 7 CFR 58.149 - Alternate quality control programs for dairy products.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 3 2010-01-01 2010-01-01 false Alternate quality control programs for dairy products... for dairy products. (a) When a plant has in operation an acceptable quality control program which is... (CONTINUED) REGULATIONS AND STANDARDS UNDER THE AGRICULTURAL MARKETING ACT OF 1946 AND THE EGG PRODUCTS...

  2. Yoga for Stress Management Program as a Complementary Alternative Counseling Resource in a University Counseling Center

    ERIC Educational Resources Information Center

    Milligan, Colleen K.

    2006-01-01

    A Yoga for Stress Management Program (YSMP) that served as a complementary alternative therapy resource was successfully implemented at a midsize, predominantly undergraduate university. It was offered in addition to traditional treatments for student mental health. Counselors, Residence Life staff, and faculty found that the program was useful…

  3. Effectiveness of an Alternative Certification Program for the Preparation of Elementary Teachers

    ERIC Educational Resources Information Center

    Follo, Eric J.; Rivard, James J.

    2009-01-01

    This study focuses on the effectiveness of the alternative elementary teacher certification program at Oakland University in Rochester, Michigan. The program was developed in response to the projected teacher shortage, the need for teachers in subjects such as mathematics and science, the need for teachers in urban schools, and the need for…

  4. Yoga for Stress Management Program as a Complementary Alternative Counseling Resource in a University Counseling Center

    ERIC Educational Resources Information Center

    Milligan, Colleen K.

    2006-01-01

    A Yoga for Stress Management Program (YSMP) that served as a complementary alternative therapy resource was successfully implemented at a midsize, predominantly undergraduate university. It was offered in addition to traditional treatments for student mental health. Counselors, Residence Life staff, and faculty found that the program was useful…

  5. How Induction Programs Affect the Decision of Alternate Route Urban Teachers to Remain Teaching

    ERIC Educational Resources Information Center

    LoCascio, Steven J.; Smeaton, Patricia S.; Waters, Faith H.

    2016-01-01

    This mixed-methods study analyzes the induction programs for alternate route beginning teachers in low socioeconomic, urban schools. The researcher surveyed 53 teachers at the end of their first year and conducted six in-depth follow-up interviews. The study found that half the teachers did not receive an induction program congruent with state…

  6. Evaluation of Treatment Alternatives to Street Crime; National Evaluation Program, Phase 2 Report.

    ERIC Educational Resources Information Center

    System Sciences, Inc., Chapel Hill, NC.

    The National Treatment Alternatives to Street Crime (TASC) Program is assessed in terms of process effectiveness and cost benefits of the program. Major conclusions are: (1) the TASC processes of identification and screening, diagnosis and referral and client monitoring are being effectively performed; (2) TASC is a very positive factor in the…

  7. Towards a Lakatosian Analysis of the Piagetian and Alternative Conceptions Research Programs.

    ERIC Educational Resources Information Center

    Gilbert, John K.; Swift, David J.

    1985-01-01

    Lakatos's methodology of scientific research programs is summarized and discussed for Piagetian schools and alternative conceptions movement. Commonalities/differences between these two rival programs are presented along with fundamental assumptions, auxiliary hypotheses, and research policy. Suggests that research findings should not be merely…

  8. Daemen Alternative Energy/Geothermal Technologies Demonstration Program, Erie County

    SciTech Connect

    Beiswanger, Robert C.

    2013-02-28

    The purpose of the Daemen Alternative Energy/Geothermal Technologies Demonstration Project is to demonstrate the use of geothermal technology as model for energy and environmental efficiency in heating and cooling older, highly inefficient buildings. The former Marian Library building at Daemen College is a 19,000 square foot building located in the center of campus. Through this project, the building was equipped with geothermal technology and results were disseminated. Gold LEED certification for the building was awarded. 1) How the research adds to the understanding of the area investigated. This project is primarily a demonstration project. Information about the installation is available to other companies, organizations, and higher education institutions that may be interested in using geothermal energy for heating and cooling older buildings. 2) The technical effectiveness and economic feasibility of the methods or techniques investigated or demonstrated. According to the modeling and estimates through Stantec, the energy-efficiency cost savings is estimated at 20%, or $24,000 per year. Over 20 years this represents $480,000 in unrestricted revenue available for College operations. See attached technical assistance report. 3) How the project is otherwise of benefit to the public. The Daemen College Geothermal Technologies Ground Source Heat Pumps project sets a standard for retrofitting older, highly inefficient, energy wasting and environmentally irresponsible buildings that are quite typical of many of the buildings on the campuses of regional colleges and universities. As a model, the project serves as an energy-efficient system with significant environmental advantages. Information about the energy-efficiency measures is available to other colleges and universities, organizations and companies, students, and other interested parties. The installation and renovation provided employment for 120 individuals during the award period. Through the new Center

  9. Daemen Alternative Energy/Geothermal Technologies Demonstration Program Erie County

    SciTech Connect

    Beiswanger, Jr, Robert C

    2010-05-20

    The purpose of the Daemen Alternative Energy/Geothermal Technologies Demonstration Project is to demonstrate the use of geothermal technology as model for energy and environmental efficiency in heating and cooling older, highly inefficient buildings. The former Marian Library building at Daemen College is a 19,000 square foot building located in the center of campus. Through this project, the building was equipped with geothermal technology and results were disseminated. Gold LEED certification for the building was awarded. 1) How the research adds to the understanding of the area investigated. This project is primarily a demonstration project. Information about the installation is available to other companies, organizations, and higher education institutions that may be interested in using geothermal energy for heating and cooling older buildings. 2) The technical effectiveness and economic feasibility of the methods or techniques investigated or demonstrated. According to the modeling and estimates through Stantec, the energy-efficiency cost savings is estimated at 20%, or $24,000 per year. Over 20 years this represents $480,000 in unrestricted revenue available for College operations. See attached technical assistance report. 3) How the project is otherwise of benefit to the public. The Daemen College Geothermal Technologies Ground Source Heat Pumps project sets a standard for retrofitting older, highly inefficient, energy wasting and environmentally irresponsible buildings quite typical of many of the buildings on the campuses of regional colleges and universities. As a model, the project serves as an energy-efficient system with significant environmental advantages. Information about the energy-efficiency measures is available to other colleges and universities, organizations and companies, students, and other interested parties. The installation and renovation provided employment for 120 individuals during the award period. Through the new Center, Daemen will

  10. Regulation of Translation Factor EEF1D Gene Function by Alternative Splicing

    PubMed Central

    Kaitsuka, Taku; Matsushita, Masayuki

    2015-01-01

    Alternative splicing is an exquisite mechanism that allows one coding gene to have multiple functions. The alternative splicing machinery is necessary for proper development, differentiation and stress responses in a variety of organisms, and disruption of this machinery is often implicated in human diseases. Previously, we discovered a long form of eukaryotic elongation factor 1Bδ (eEF1Bδ; this long-form eEF1Bδ results from alternative splicing of EEF1D transcripts and regulates the cellular stress response by transcriptional activation, not translational enhancement, of heat-shock responsive genes. In this review, we discuss the molecular function of EEF1D alternative splicing products and the estimated implication of human diseases. PMID:25686034

  11. Evaluation of a training program for nurse supervisors who monitor nurses in an alternative-to-discipline program.

    PubMed

    Cadiz, David; Truxillo, Donald; OʼNeill, Chris

    2012-01-01

    Nurse alternative-to-discipline programs aim to protect the public from the harm of impaired practice and to support nurses in early recovery from substance use disorders. Supervisor observation of work behavior is one key monitoring activity that protects the public. We evaluate a supervisory training called "Fit to Perform" for nurse managers to help them monitor and manage nurses enrolled in an alternative-to-discipline program. We observed significant mean changes in knowledge, training utility, self-efficacy, and substance abuse stigma. The results suggest that the training positively affects knowledge about substance use disorders, confidence to supervise nurses enrolled in an alternative-to-discipline program, and reduces stigma, which may create a supportive workplace for nurses in recovery.

  12. Program Alternatives to Special Education. Interim Report on 1985-86. O.E.A. Evaluation Report.

    ERIC Educational Resources Information Center

    Hebard, Amy J.; And Others

    This interim report on the Program Alternatives to Special Education (PASE) program in New York City: (1) describes strategies offered by 32 districts that provide program alternatives to special education referrals; (2) elucidates the strengths and weaknesses of program designs and highlights factors having positive effects on at-risk children;…

  13. Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.

    PubMed

    Finnegan, Patrick M; Umbach, Ann L; Wilce, Jackie A

    2003-12-18

    The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.

  14. Linking linear programming and spatial simulation models to predict landscape effects of forest management alternatives.

    PubMed

    Gustafson, Eric J; Roberts, L Jay; Leefers, Larry A

    2006-12-01

    Forest management planners require analytical tools to assess the effects of alternative strategies on the sometimes disparate benefits from forests such as timber production and wildlife habitat. We assessed the spatial patterns of alternative management strategies by linking two models that were developed for different purposes. We used a linear programming model (Spectrum) to optimize timber harvest schedules, then a simulation model (HARVEST) to project those schedules in a spatially explicit way and produce maps from which the spatial pattern of habitat could be calculated. We demonstrated the power of this approach by evaluating alternative plans developed for a national forest plan revision in Wisconsin, USA. The amount of forest interior habitat was inversely related to the amount of timber cut, and increased under the alternatives compared to the current plan. The amount of edge habitat was positively related to the amount of timber cut, and increased under all alternatives. The amount of mature northern hardwood interior and edge habitat increased for all alternatives, but mature pine habitat area varied. Mature age classes of all forest types increased, and young classes decreased under all alternatives. The average size of patches (defined by age class) generally decreased. These results are consistent with the design goals of each of the alternatives, but reveal that the spatial differences among the alternatives are modest. These complementary models are valuable for quantifying and comparing the spatial effects of alternative management strategies.

  15. Complementary and alternative medicine education in dietetics programs: existent but not consistent.

    PubMed

    Vickery, Connie E; Cotugna, Nancy

    2006-06-01

    This descriptive survey was undertaken to determine the inclusion of complementary and alternative medicine topics into undergraduate didactic dietetics education. The response rate was 34% (n=92) of all directors (N=273) of didactic and coordinated dietetics programs. Almost all programs (n=81; 88%) include complementary and alternative medicine instruction in some form in their curricula; the majority of content is integrated into already existing nutrition courses. The nutrition courses most often containing complementary and alternative medicine were medical nutrition therapy, advance nutrition, and community nutrition. Topics addressed were varied and included herbal supplements, functional foods, Native-American healing, and quackery in medicine. Most directors indicated that complementary and alternative medicine is an important component of dietetics education, yet many indicated that students are not being adequately prepared in this area. The mean familiarity of program directors with complementary and alternative medicine competencies for dietetics practice was 6 on a scale, with 10 being the most knowledgeable. Respondents also identified whether complementary and alternative medicine and dietary supplement competencies were being addressed at all in their curricula. Lack of time seemed to be the limiting factor to incorporation of complementary and alternative medicine topics into the curricula. Evidence from this study indicates that current curricula are providing some complementary and alternative medicine content, but a core of knowledge is lacking. The complementary and alternative medicine competencies for entry-level dietetics practice anticipated by 2006 will be useful in helping educators adequately meet the needs of future professionals in the area of complementary and alternative medicine.

  16. Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.

    PubMed

    Rodríguez, Sofía A; Grochová, Diana; McKenna, Tomás; Borate, Bhavesh; Trivedi, Niraj S; Erdos, Michael R; Eriksson, Maria

    2016-04-01

    Alternative splicing (AS) is a key regulatory mechanism for the development of different tissues; however, not much is known about changes to alternative splicing during aging. Splicing events may become more frequent and widespread genome-wide as tissues age and the splicing machinery stringency decreases. Using skin, skeletal muscle, bone, thymus, and white adipose tissue from wild-type C57BL6/J male mice (4 and 18 months old), we examined the effect of age on splicing by AS analysis of the differential exon usage of the genome. The results identified a considerable number of AS genes in skeletal muscle, thymus, bone, and white adipose tissue between the different age groups (ranging from 27 to 246 AS genes corresponding to 0.3-3.2% of the total number of genes analyzed). For skin, skeletal muscle, and bone, we included a later age group (28 months old) that showed that the number of alternatively spliced genes increased with age in all three tissues (P < 0.01). Analysis of alternatively spliced genes across all tissues by gene ontology and pathway analysis identified 158 genes involved in RNA processing. Additional analysis of AS in a mouse model for the premature aging disease Hutchinson-Gilford progeria syndrome was performed. The results show that expression of the mutant protein, progerin, is associated with an impaired developmental splicing. As progerin accumulates, the number of genes with AS increases compared to in wild-type skin. Our results indicate the existence of a mechanism for increased AS during aging in several tissues, emphasizing that AS has a more important role in the aging process than previously known.

  17. Global variability in gene expression and alternative splicing is modulated by mitochondrial content.

    PubMed

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J

    2015-05-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype.

  18. Global variability in gene expression and alternative splicing is modulated by mitochondrial content

    PubMed Central

    Guantes, Raul; Rastrojo, Alberto; Neves, Ricardo; Lima, Ana; Aguado, Begoña; Iborra, Francisco J.

    2015-01-01

    Noise in gene expression is a main determinant of phenotypic variability. Increasing experimental evidence suggests that genome-wide cellular constraints largely contribute to the heterogeneity observed in gene products. It is still unclear, however, which global factors affect gene expression noise and to what extent. Since eukaryotic gene expression is an energy demanding process, differences in the energy budget of each cell could determine gene expression differences. Here, we quantify the contribution of mitochondrial variability (a natural source of ATP variation) to global variability in gene expression. We find that changes in mitochondrial content can account for ∼50% of the variability observed in protein levels. This is the combined result of the effect of mitochondria dosage on transcription and translation apparatus content and activities. Moreover, we find that mitochondrial levels have a large impact on alternative splicing, thus modulating both the abundance and type of mRNAs. A simple mathematical model in which mitochondrial content simultaneously affects transcription rate and splicing site choice can explain the alternative splicing data. The results of this study show that mitochondrial content (and/or probably function) influences mRNA abundance, translation, and alternative splicing, which ultimately affects cellular phenotype. PMID:25800673

  19. Processes and Outcomes from a Medical Student Research Training Program in Integrative, Complementary, and Alternative Medicine.

    PubMed

    Dicianno, Brad E; Glick, Ronald M; Sowa, Gwendolyn A; Boninger, Michael L

    2016-10-01

    In response to the growing need to train a new generation of clinician scientists, a research program was developed to train medical students in integrative, complementary, and alternative medicine (ICAM) research early in their careers. A total of 25 students (100%) successfully completed a 10-week program. Students reported significantly increased levels of knowledge in all 7 integrative, complementary, and alternative medicine topics at the conclusion of the program. All students presented their work at one or more local research symposia. In addition, the average number of quality research outputs, which included manuscripts, awards, and abstracts presented at national and international meetings, was 1.5 per student, which exceeded benchmarks based on prior program outcomes. Results from this program may be useful when planning larger or longer-term projects aimed at attracting physicians who will become our next generation of academicians, researchers, and healers.

  20. Misregulation of Gene Expression and Sterility in Interspecies Hybrids: Causal Links and Alternative Hypotheses.

    PubMed

    Civetta, Alberto

    2016-05-01

    Understanding the origin of species is of interest to biologist in general and evolutionary biologist in particular. Hybrid male sterility (HMS) has been a focus in studies of speciation because sterility imposes a barrier to free gene flow between organisms, thus effectively isolating them as distinct species. In this review, I focus on the role of differential gene expression in HMS and speciation. Microarray and qPCR assays have established associations between misregulation of gene expression and sterility in hybrids between closely related species. These studies originally proposed disrupted expression of spermatogenesis genes as a causative of sterility. Alternatively, rapid genetic divergence of regulatory elements, particularly as they relate to the male sex (fast-male evolution), can drive the misregulation of sperm developmental genes in the absence of sterility. The use of fertile hybrids (both backcross and F1 progeny) as controls has lent support to this alternative explanation. Differences in gene expression between fertile and sterile hybrids can also be influenced by a pattern of faster evolution of the sex chromosome (fast-X evolution) than autosomes. In particular, it would be desirable to establish whether known X-chromosome sterility factors can act as trans-regulatory drivers of genome-wide patterns of misregulation. Genome-wide expression studies coupled with assays of proxies of sterility in F1 and BC progeny have identified candidate HMS genes but functional assays, and a better phenotypic characterization of sterility phenotypes, are needed to rigorously test how these genes might contribute to HMS.

  1. The Enforcer Aircraft Program: A Lower-Cost Alternative Weapon System.

    DTIC Science & Technology

    1984-03-01

    BUREAU OF STANDARDS-19o3-A NAVAL POSTGRADUATE SCHOOL Monterey, California In ID THESIS THE ENFORCER AIRCRAFT PROGRAM: A LOWER-COST ALTERNATIVE WEAPON...SYSTEM _by Robert P. Holt and Robert D. Dolan March 1984 Thesis Advisor% P. M. Carrick Approved for public release; distribution unlimited. 04 5 29...Master’s Thesis ; Cost Alternative Weapon System March 1984 6. PERFORMING ORG. REPORT NUMBER 7- AUTHOR() S. CONTRACT ORt GRANT NUNIER-() Robert P. Holt

  2. Effects of hydrogen sulfide on alternative pathway respiration and induction of alternative oxidase gene expression in rice suspension cells.

    PubMed

    Xiao, Man; Ma, Jun; Li, Hongyu; Jin, Han; Feng, Hanqing

    2010-01-01

    The toxic effects of H2S on plants are well documented. However, the molecular mechanisms reponsible for inhibition of plants by H2S are still not completely understood. We determined the effects of NaHS in the range of 0.5-10 mM on the growth of rice suspension culture cells, as well as on the expression of the alternative oxidase (AOX) gene. AOX is the terminal oxidase of the alternative pathway (AP) and exists in plant mitochondria. The results showed that H2S treatment enhanced the AP activity. During the process of H2S treatment for 4 h, the AP activity increased dramatically and achieved the peak value at a concentration of 2 mM NaHS. Then it declined at higher concentrations of NaHS (5-10 mM) and maintained a steady level. The AOX1 gene transcript level also showed a similar change as the AP activity. Interestingly, different NaHS concentrations seemed to have different effects on the expression of AOX1a, AOX1b, and AOX1c. The induction of AOX expression by low concentrations of NaHS was inferred through a reactive oxygen species (ROS)-independent pathway. At the same time, rice cells grown in culture were very sensitive to H2S, different H2S concentrations induced an increase in the cell viability. These results indicate that the H2S-induced AOX induction might play a role in inhibiting the ROS production and have an influence on cell viability.

  3. Cognitive Influences of Students' Alternative Conceptions within a Hands-On Gene Technology Module

    ERIC Educational Resources Information Center

    Franke, Gaitano; Bogner, Franz X.

    2011-01-01

    In a German out-of-school laboratory, 293 medium-achieving 10th-grade students participated in a lesson unit about gene technology. They were divided into two groups (I-1, I-2), both of which followed the same hands-on lesson procedure. Students within I-2 were additionally confronted with alternative conceptions to central issues of the specific…

  4. Cloning and Analysis of the Alternative Oxidase Gene of Neurospora Crassa

    PubMed Central

    Li, Q.; Ritzel, R. G.; McLean, LLT.; McIntosh, L.; Ko, T.; Bertrand, H.; Nargang, F. E.

    1996-01-01

    Mitochondria of Neurospora crassa contain a cyanide-resistant alternative respiratory pathway in addition to the cytochrome pathway. The alternative oxidase is present only when electron flow through the cytochrome chain is restricted. Both genomic and cDNA copies for the alternative oxidase gene have been isolated and analyzed. The sequence of the predicted protein is homologous to that of other species. The mRNA for the alternative oxidase is scarce in wild-type cultures grown under normal conditions, but it is abundant in cultures grown in the presence of chloramphenicol, an inhibitor of mitochondrial protein synthesis, or in mutants deficient in mitochondrial cytochromes. Thus, induction of alternative oxidase appears to be at the transcriptional level. Restriction fragment length polymorphism mapping of the isolated gene demonstrated that it is located in a position corresponding to the aod-1 locus. Sequence analysis of mutant aod-1 alleles reveals mutations affecting the coding sequence of the alternative oxidase. The level of aod-1 mRNA in an aod-2 mutant strain that had been grown in the presence of chloramphenicol was reduced several fold relative to wild-type, supporting the hypothesis that the product of aod-2 is required for optimal expression of aod-1. PMID:8770590

  5. Alternative fuels for vehicles fleet demonstration program. Final report, volume 2: Appendices

    SciTech Connect

    1997-06-01

    The Alternative Fuels for Vehicles Fleet Demonstration Program (AFV-FDP) was a multiyear effort to collect technical data for use in determining the costs and benefits of alternative-fuel vehicles (AFVs) in typical applications in New York State. This report, Volume 2, includes 13 appendices to Volume 1 that expand upon issues raised therein. Volume 1 provides: (1) Information about the purpose and scope of the AFV-FDP; (2) A summary of AFV-FDP findings organized on the basis of vehicle type and fuel type; (3) A short review of the status of AFV technology development, including examples of companies in the State that are active in developing AFVs and AFV components; and (4) A brief overview of the status of AFV deployment in the State. Volume 3 provides expanded reporting of AFV-FDP technical details, including the complete texts of the brochure Garage Guidelines for Alternative Fuels and the technical report Fleet Experience Survey Report, plus an extensive glossary of AFV terminology. The appendices cover a wide range of issues including: emissions regulations in New York State; production and health effects of ozone; vehicle emissions and control systems; emissions from heavy-duty engines; reformulated gasoline; greenhouse gases; production and characteristics of alternative fuels; the Energy Policy Act of 1992; the Clean Fuel Fleet Program; garage design guidelines for alternative fuels; surveys of fleet managers using alternative fuels; taxes on conventional and alternative fuels; and zero-emission vehicle technology.

  6. Expression profiles for macrophage alternative activation genes in AD and in mouse models of AD

    PubMed Central

    Colton, Carol A; Mott, Ryan T; Sharpe, Hayley; Xu, Qing; Van Nostrand, William E; Vitek, Michael P

    2006-01-01

    Background Microglia are associated with neuritic plaques in Alzheimer disease (AD) and serve as a primary component of the innate immune response in the brain. Neuritic plaques are fibrous deposits composed of the amyloid beta-peptide fragments (Abeta) of the amyloid precursor protein (APP). Numerous studies have shown that the immune cells in the vicinity of amyloid deposits in AD express mRNA and proteins for pro-inflammatory cytokines, leading to the hypothesis that microglia demonstrate classical (Th-1) immune activation in AD. Nonetheless, the complex role of microglial activation has yet to be fully explored since recent studies show that peripheral macrophages enter an "alternative" activation state. Methods To study alternative activation of microglia, we used quantitative RT-PCR to identify genes associated with alternative activation in microglia, including arginase I (AGI), mannose receptor (MRC1), found in inflammatory zone 1 (FIZZ1), and chitinase 3-like 3 (YM1). Results Our findings confirmed that treatment of microglia with anti-inflammatory cytokines such as IL-4 and IL-13 induces a gene profile typical of alternative activation similar to that previously observed in peripheral macrophages. We then used this gene expression profile to examine two mouse models of AD, the APPsw (Tg-2576) and Tg-SwDI, models for amyloid deposition and for cerebral amyloid angiopathy (CAA) respectively. AGI, MRC1 and YM1 mRNA levels were significantly increased in the Tg-2576 mouse brains compared to age-matched controls while TNFα and NOS2 mRNA levels, genes commonly associated with classical activation, increased or did not change, respectively. Only TNFα mRNA increased in the Tg-SwDI mouse brain. Alternative activation genes were also identified in brain samples from individuals with AD and were compared to age-matched control individuals. In AD brain, mRNAs for TNFα, AGI, MRC1 and the chitinase-3 like 1 and 2 genes (CHI3L1; CHI3L2) were significantly increased

  7. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

    PubMed Central

    Batut, Philippe; Dobin, Alexander; Plessy, Charles; Carninci, Piero; Gingeras, Thomas R.

    2013-01-01

    Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5′-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes. PMID:22936248

  8. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression.

    PubMed

    Batut, Philippe; Dobin, Alexander; Plessy, Charles; Carninci, Piero; Gingeras, Thomas R

    2013-01-01

    Many eukaryotic genes possess multiple alternative promoters with distinct expression specificities. Therefore, comprehensively annotating promoters and deciphering their individual regulatory dynamics is critical for gene expression profiling applications and for our understanding of regulatory complexity. We introduce RAMPAGE, a novel promoter activity profiling approach that combines extremely specific 5'-complete cDNA sequencing with an integrated data analysis workflow, to address the limitations of current techniques. RAMPAGE features a streamlined protocol for fast and easy generation of highly multiplexed sequencing libraries, offers very high transcription start site specificity, generates accurate and reproducible promoter expression measurements, and yields extensive transcript connectivity information through paired-end cDNA sequencing. We used RAMPAGE in a genome-wide study of promoter activity throughout 36 stages of the life cycle of Drosophila melanogaster, and describe here a comprehensive data set that represents the first available developmental time-course of promoter usage. We found that >40% of developmentally expressed genes have at least two promoters and that alternative promoters generally implement distinct regulatory programs. Transposable elements, long proposed to play a central role in the evolution of their host genomes through their ability to regulate gene expression, contribute at least 1300 promoters shaping the developmental transcriptome of D. melanogaster. Hundreds of these promoters drive the expression of annotated genes, and transposons often impart their own expression specificity upon the genes they regulate. These observations provide support for the theory that transposons may drive regulatory innovation through the distribution of stereotyped cis-regulatory modules throughout their host genomes.

  9. Alternative-fueled truck demonstration natural gas program: Caterpillar G3406LE development and demonstration

    SciTech Connect

    1995-06-01

    In 1990, the California Energy Commission, the South Coast Air Quality Management District, and the Southern California Gas Company joined together to sponsor the development and demonstration of compressed natural gas engines for Class 8 heavy-duty line-haul trucking applications. This program became part of an overall Alternative-Fueled Truck Demonstration Program, with the goal of advancing the technological development of alternative-fueled engines. The demonstration showed natural gas to be a technically viable fuel for Class 8 truck engines.

  10. Hypoxia Regulates Alternative Splicing of HIF and non-HIF Target Genes

    PubMed Central

    Sena, Johnny A.; Wang, Liyi; Heasley, Lynn E.; Hu, Cheng-Jun

    2014-01-01

    Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia-inducible transcription factor 1α (HIF1A) and 2α (HIF2α/EPAS1) to activate gene transcription, which promotes tumor cell survival. The majority of human genes are alternatively spliced, producing RNA isoforms that code for functionally distinct proteins. Thus, an effective hypoxia response requires increased HIF target gene expression as well as proper RNA splicing of these HIF-dependent transcripts. However, it is unclear if and how hypoxia regulates RNA splicing of HIF targets. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in hepatocellular carcinoma (HCC) cells and characterized the role of HIF in regulating AS of HIF induced genes. The results indicate that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF targets including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirm that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of a PDK1 minigene by other transcription factors in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing. PMID:24850901

  11. Data collection plan for Phase 2 Alternative Fuels Bus Data Collection Program. Final report

    SciTech Connect

    Krenelka, T

    1993-07-01

    This document constitutes the plan for collecting and reporting data associated with a special set of transit bus demonstrations to be conducted under the Urban Bus Program of the Alternative Motor Fuels Act (AMFA) of 1988. This program, called the Phase 2 Bus Data Collection Program, serves as an adjunct to the Phase I Bus Data Collection Program, collecting detailed data on just a few buses to augment and enhance the Phase 1 data in fulfilling the urban bus requirements of AMFA. Demonstrations will be conducted at a few transit system locations throughout the US and will use alternative fuels and associated technologies to reduce undesirable transit bus exhaust emissions. Several organizations will be involved in the data collection; NREL will manage the program, analyze and store vehicle data, and make these data available through the Alternative Fuels Data Center. This information will enable transit agencies, equipment manufacturers, fuel suppliers, and government policy makers to make informed decisions about buying and using alternative fuels.

  12. Differential expression and alternative splicing of cell cycle genes in imatinib-treated K562 cells.

    PubMed

    Liu, Jing; Lin, Jin; Huang, Lin-Feng; Huang, Bo; Xu, Yan-Mei; Li, Jing; Wang, Yan; Zhang, Jing; Yang, Wei-Ming; Min, Qing-Hua; Wang, Xiao-Zhong

    2015-09-01

    Cancer progression often involves the disorder of the cell cycle, and a number of effective chemotherapeutic drugs have been shown to induce cell cycle arrest. The purpose of this study was to comprehensively investigate the effects of imatinib on the expression profile of cell cycle genes in the chronic myeloid leukemia (CML) K562 cell line. In addition, we also investigated alternative splicing of the cell cycle genes affected by imatinib, since an important relationship has been shown to exist between RNA splicing and cell cycle progression. Exon array analysis was performed using total RNA purified from normal and imatinib-treated K562 cells. We identified 185 differentially expressed genes and 277 alternative splicing events between the two cell groups. A detailed analysis by reverse transcription-PCR (RT-PCR) of key genes confirmed the experimental results of the exon array. These results suggested that treatment of K562 cells with imatinib shifts the expression and alternative splicing profiles of several cell cycle-related genes. Importantly, these findings may help improve imatinib treatment strategies in patients with CML and may be useful for imatinib resistance research and CML drug development.

  13. Gene set analysis for self-contained tests: complex null and specific alternative hypotheses

    PubMed Central

    Rahmatallah, Y.; Glazko, G.

    2012-01-01

    Motivation: The analysis of differentially expressed gene sets became a routine in the analyses of gene expression data. There is a multitude of tests available, ranging from aggregation tests that summarize gene-level statistics for a gene set to true multivariate tests, accounting for intergene correlations. Most of them detect complex departures from the null hypothesis but when the null hypothesis is rejected, the specific alternative leading to the rejection is not easily identifiable. Results: In this article we compare the power and Type I error rates of minimum-spanning tree (MST)-based non-parametric multivariate tests with several multivariate and aggregation tests, which are frequently used for pathway analyses. In our simulation study, we demonstrate that MST-based tests have power that is for many settings comparable with the power of conventional approaches, but outperform them in specific regions of the parameter space corresponding to biologically relevant configurations. Further, we find for simulated and for gene expression data that MST-based tests discriminate well against shift and scale alternatives. As a general result, we suggest a two-step practical analysis strategy that may increase the interpretability of experimental data: first, apply the most powerful multivariate test to find the subset of pathways for which the null hypothesis is rejected and second, apply MST-based tests to these pathways to select those that support specific alternative hypotheses. Contact: gvglazko@uams.edu or yrahmatallah@uams.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23044539

  14. Using mini-genes to identify factors that modulate alternative splicing.

    PubMed

    Morse, Robert; Todd, Adrian G; Young, Philip J

    2012-01-01

    Many genetic mutations result in the disruption of (alternative) splicing. Prime examples are the SMN1 and SMN2 genes: a silent mutation in SMN2 leads to the skipping of the constitutive exon 7 in the majority of SMN2 transcripts, while this exon is generally included in SMN1 transcripts. Lack of SMN is embryonic lethal and loss of SMN1 genes leads to a severe decrease in SMN protein and is associated with spinal muscular atrophy. There are proteins and drugs that can chance alternative splicing events, e.g. increase the inclusion of exon 7 in SMN2. This chapter describes mini-genes and methods that can be employed to screen for candidate proteins and drugs.

  15. Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants.

    PubMed

    Shang, Xudong; Cao, Ying; Ma, Ligeng

    2017-02-20

    Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism's transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants.

  16. Alternative Splicing of the Amelogenin Gene in a Caudate Amphibian, Plethodoncinereus

    PubMed Central

    Wang, Xinping; Xing, Zeli; Zhang, Xichen; Zhu, Lisai; Diekwisch, Thomas G. H.

    2013-01-01

    As the major enamel matrix protein contributing to tooth development, amelogenin has been demonstrated to play a crucial role in tooth enamel formation. Previous studies have revealed amelogenin alternative splicing as a mechanism for amelogenin heterogeneous expression in mammals. While amelogenin and its splicing forms in mammalian vertebrates have been characterized, splicing variants of amelogenin gene still remains largely unknown in non-mammalian species. Here, using PCR and sequence analysis we discovered two novel amelogenin transcript variants in tooth organ extracts from a caudate amphibian, the salamander Plethodoncinereus. The one was shorter -S- (416 nucleotides including untranslated regions, 5 exons) and the other larger -L- (851 nt, 7 exons) than the previously published “normal” gene in this species -M- (812 nucleotides, 6 exons). This is the first report demonstrating the amelogenin alternative splicing in amphibian, revealing a unique exon 2b and two novel amelogenin gene transcripts in Plethodoncinereus. PMID:23840861

  17. Alternative Splicing in Plant Genes: A Means of Regulating the Environmental Fitness of Plants

    PubMed Central

    Shang, Xudong; Cao, Ying; Ma, Ligeng

    2017-01-01

    Gene expression can be regulated through transcriptional and post-transcriptional mechanisms. Transcription in eukaryotes produces pre-mRNA molecules, which are processed and spliced post-transcriptionally to create translatable mRNAs. More than one mRNA may be produced from a single pre-mRNA by alternative splicing (AS); thus, AS serves to diversify an organism’s transcriptome and proteome. Previous studies of gene expression in plants have focused on the role of transcriptional regulation in response to environmental changes. However, recent data suggest that post-transcriptional regulation, especially AS, is necessary for plants to adapt to a changing environment. In this review, we summarize recent advances in our understanding of AS during plant development in response to environmental changes. We suggest that alternative gene splicing is a novel means of regulating the environmental fitness of plants. PMID:28230724

  18. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons.

    PubMed

    Cusack, Brian P; Wolfe, Kenneth H

    2005-11-01

    Alternative splicing is known to be an important source of protein sequence variation, but its evolutionary impact has not been explored in detail. Studying alternative splicing requires extensive sampling of the transcriptome, but new data sets based on expressed sequence tags aligned to chromosomes make it possible to study alternative splicing on a genome-wide scale. Although genes showing alternative splicing by exon skipping are conserved as compared to the genome as a whole, we find that genes where structural differences between human and mouse result in genome-specific alternatively spliced exons in one species show almost 60% greater nonsynonymous divergence in constitutive exons than genes where exon skipping is conserved. This effect is also seen for genes showing species-specific patterns of alternative splicing where gene structure is conserved. Our observations are not attributable to an inherent difference in rate of evolution between these two sets of proteins or to differences with respect to predictors of evolutionary rate such as expression level, tissue specificity, or genetic redundancy. Where genome-specific alternatively spliced exons are seen in mammals, the vast majority of skipped exons appear to be recent additions to gene structures. Furthermore, among genes with genome-specific alternatively spliced exons, the degree of nonsynonymous divergence in constitutive sequence is a function of the frequency of incorporation of these alternative exons into transcripts. These results suggest that alterations in alternative splicing pattern can have knock-on effects in terms of accelerated sequence evolution in constant regions of the protein.

  19. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony.

    PubMed

    Wehe, André; Bansal, Mukul S; Burleigh, J Gordon; Eulenstein, Oliver

    2008-07-01

    DupTree is a new software program for inferring rooted species trees from collections of gene trees using the gene tree parsimony approach. The program implements a novel algorithm that significantly improves upon the run time of standard search heuristics for gene tree parsimony, and enables the first truly genome-scale phylogenetic analyses. In addition, DupTree allows users to examine alternate rootings and to weight the reconciliation costs for gene trees. DupTree is an open source project written in C++. DupTree for Mac OS X, Windows, and Linux along with a sample dataset and an on-line manual are available at http://genome.cs.iastate.edu/CBL/DupTree

  20. Dispositions and Perceived Preparedness of Teacher Candidates in Traditional Undergraduate Teacher Education, Master's with Licensure, and Alternative Licensure Programs

    ERIC Educational Resources Information Center

    Iyer, Nithya Narayanaswamy; Soled, Suzanne Wegener

    2007-01-01

    This study compares the dispositions and perceived preparedness of three teacher preparation programs: traditional, masters, and alternative licensure. We specifically investigated whether teachers in alternative licensure programs have the dispositions and perceived preparation essential for teaching. Each program was examined to identify…

  1. Programs and Practices for Special Education Students in Alternative Education Settings. Research to Practice Brief. Volume 6, Issue 1

    ERIC Educational Resources Information Center

    Unruh, Deanne; Bullis, Michael; Todis, Bonnie; Waintrup, Miriam; Atkins, Trent

    2007-01-01

    This brief presents a review of alternative education programs targeting students with disabilities. Because there is no clear picture of how alternative education programs operate, specifically regarding youth with disabilities, the U.S. Department of Education's Office of Special Education Programs (OSEP) funded three grants to develop a…

  2. Alternatives to Social Promotion Program at Grades 7 & 8. Final Report.

    ERIC Educational Resources Information Center

    Wircenski, Jerry L.; Sarkees, Michelle D.

    This final report and curriculum guide are products of a project conducted to improve existing at-risk programs through cooperation between vocational and academic personnel by coordinating lesson plans. The following project activities are described: (1) a literature review on the diverse needs of at-risk students enrolled in an alternative to…

  3. Supporting First Year Alternatively Certified Urban and Rural Intern Teachers through a Multicomponent Distance Induction Program

    ERIC Educational Resources Information Center

    Gresko, Jennifer A.

    2013-01-01

    The pathway for entering the K-12 classroom as a teacher varies compared to what was once the traditional model of teacher preparation. In this mixed-methods action research study, I explore supporting first year alternatively certified urban and rural intern teachers through a multicomponent distance induction program. The induction model in this…

  4. Accelerating the commercialization on new technologies. [free market operation of federal alternate energy sources programs

    NASA Technical Reports Server (NTRS)

    Kuehn, T. J.; Nawrocki, P. M.

    1978-01-01

    It is suggested that federal programs for hastening the adoption of alternative energy sources must operate within the free market structure. Five phases of the free market commercialization process are described. Federal role possibilities include information dissemination and funding to stimulate private sector activities within these five phases, and federally sponsored procedures for accelerating commercialization of solar thermal small power systems are considered.

  5. Alternative Education for Disruptive Youth: Recommended Parameters and Best Practices for Effective Programs

    ERIC Educational Resources Information Center

    Pennsylvania Department of Education, 2005

    2005-01-01

    This document was prepared to serve as an aid in the planning, design, implementation, and ongoing evaluation of Alternative Education for Disruptive Youth Programs in Pennsylvania. School Codes and Public Laws are cited for guidance on mandatory issues. The suggestions and implementation strategies provided in this document are not requirements…

  6. Alternative Transportation Program, P.L. 94-142. 1985-86 Evaluation Report.

    ERIC Educational Resources Information Center

    Case, Elizabeth J.; Bouchard, Donald

    Overall effectiveness and impact were evaluated for the Alternative Transportation Program (ATP) of the Albuquerque (New Mexico) Public Schools, funded under Public Law 94-142, the Education for All Handicapped Children Act. Two specialists implemented the ATP, which developed and presented curricula and assemblies tailored to handicapped students…

  7. Clarendon Alternative School. Japanese Bilingual Bicultural Program. Curriculum Sampler II: Science.

    ERIC Educational Resources Information Center

    Choy, V. Kanani, Ed.; And Others

    A sampler of thematic science lessons from the Japanese bilingual/bicultural education program of the Clarendon Alternative School, a California elementary school, is presented. The lessons are designed to integrate Japanese instruction with the core science curriculum. Each lesson contains this information: the grade level, teacher(s), and…

  8. Outcomes from a School-Based Nutrition Education Program Alternating Special Resource Teachers and Classroom Teachers.

    ERIC Educational Resources Information Center

    Auld, Garry W.; Romaniello, Cathy; Heimendinger, Jerianne; Hambridge, Carolyn; Hambridge, Michael

    1999-01-01

    Tested the efficacy of a modified nutrition education program for elementary students. Sixteen nutrition lessons were taught alternately by special resource teachers (SRTs) and classroom teachers (as opposed to 24 lessons taught by SRTs). Surveys, observations, interviews, and plate waste data indicated that treatment students had greater…

  9. Piloting a Dialectical Behavioral Therapy (DBT) Infused Skills Group in a Disciplinary Alternative Education Program (DAEP)

    ERIC Educational Resources Information Center

    Ricard, Richard J.; Lerma, Eunice; Heard, Courtney C. C.

    2013-01-01

    This study explored the impact of a 4-week skills group intervention based on the principles of Dialectical Behavior Therapy (DBT) with a sample of adolescents attending a Disciplinary Alternative Education Program. This article provides a session-by-session overview of activities adapted from DBT-specified training modules of mindfulness,…

  10. 46 CFR 71.50-19 - The Alternative Hull Examination (AHE) Program application.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ...) PASSENGER VESSELS INSPECTION AND CERTIFICATION Drydocking § 71.50-19 The Alternative Hull Examination (AHE) Program application. If your vessel meets the eligibility criteria in § 71.50-17 of this part, you may... examination date to the Officer in Charge, Marine Inspection (OCMI), who will oversee the hull...

  11. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 1 2014-10-01 2014-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program. (a) The Commandant may authorize a recognized classification society to participate in the...

  12. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 1 2010-10-01 2010-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program. (a) The Commandant may authorize a recognized classification society to participate in the...

  13. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 1 2013-10-01 2013-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program. (a) The Commandant may authorize a recognized classification society to participate in the...

  14. 46 CFR 8.420 - Classification society authorization to participate in the Alternate Compliance Program.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 1 2011-10-01 2011-10-01 false Classification society authorization to participate in... § 8.420 Classification society authorization to participate in the Alternate Compliance Program. (a) The Commandant may authorize a recognized classification society to participate in the...

  15. Alternative Break Programs and the Factors that Contribute to Changes in Students' Lives

    ERIC Educational Resources Information Center

    Niehaus, Elizabeth Kathleen

    2012-01-01

    The purpose of this study was to explore the extent to and ways in which student participants in Alternative Break (AB) programs report that their AB experience influenced their intentions or plans to volunteer, engage in advocacy, or study or travel abroad, or their major or career plans. Additional analysis explored the specific program…

  16. Clarendon Alternative School. Japanese Bilingual Bicultural Program. Curriculum Sampler II: Science.

    ERIC Educational Resources Information Center

    Choy, V. Kanani, Ed.; And Others

    A sampler of thematic science lessons from the Japanese bilingual/bicultural education program of the Clarendon Alternative School, a California elementary school, is presented. The lessons are designed to integrate Japanese instruction with the core science curriculum. Each lesson contains this information: the grade level, teacher(s), and…

  17. Implementing a Tier 2 Behavioral Intervention in a Therapeutic Alternative High School Program

    ERIC Educational Resources Information Center

    Fallon, Lindsay M.; Feinberg, Adam B.

    2017-01-01

    The research base for Check-in, Check-out (CICO), a targeted behavioral intervention within a schoolwide positive behavioral interventions and supports framework, is growing. However, little has been written about its application in therapeutic alternative programs. To extend the literature base, the current article describes a study conducted…

  18. Total Program Efficacy: A Comparison of Traditionally and Alternatively Certified Agriculture Teachers

    ERIC Educational Resources Information Center

    Duncan, Dennis W.; Ricketts, John C.

    2008-01-01

    The purpose of this study was to determine agriculture teachers' perceived levels of efficacy as they relate to managing the total program of agricultural education, both for traditionally and alternatively certified teachers. The constructs used in this study were technical content, FFA/leadership development/SAE, teaching and learning, and…

  19. Perceptions of Educators Regarding the Effectiveness of Alternative Programs in a Southern State

    ERIC Educational Resources Information Center

    Roberson, Lydia

    2015-01-01

    At-risk students are engaged in dangerous behaviors that lead them to become involved in the juvenile justice system and cause the feeling of low self-worth. This eventually causes at-risk youths to drop out of school and engage in detrimental behaviors that meddle in their academic success. The alternative education program provides these at-risk…

  20. Piloting a Dialectical Behavioral Therapy (DBT) Infused Skills Group in a Disciplinary Alternative Education Program (DAEP)

    ERIC Educational Resources Information Center

    Ricard, Richard J.; Lerma, Eunice; Heard, Courtney C. C.

    2013-01-01

    This study explored the impact of a 4-week skills group intervention based on the principles of Dialectical Behavior Therapy (DBT) with a sample of adolescents attending a Disciplinary Alternative Education Program. This article provides a session-by-session overview of activities adapted from DBT-specified training modules of mindfulness,…

  1. Responding to Special Education Teacher Shortages in Diverse Urban Settings: An Accelerated Alternative Credential Program

    ERIC Educational Resources Information Center

    Esposito, Mary C.; Lal, Shirley

    2005-01-01

    In an effort to better serve the school districts within its service area and the unique credential candidate population, California State University Dominguez Hills (CSUDH) implemented an accelerated alternative certification program based upon the Professional Development School (PDS) model hereinafter referred to as SPED PDS. During the…

  2. Alternative Break Programs and the Factors that Contribute to Changes in Students' Lives

    ERIC Educational Resources Information Center

    Niehaus, Elizabeth Kathleen

    2012-01-01

    The purpose of this study was to explore the extent to and ways in which student participants in Alternative Break (AB) programs report that their AB experience influenced their intentions or plans to volunteer, engage in advocacy, or study or travel abroad, or their major or career plans. Additional analysis explored the specific program…

  3. Concept Mapping: An Approach for Evaluating a Public Alternative School Program

    ERIC Educational Resources Information Center

    Streeter, Calvin L.; Franklin, Cynthia; Kim, Johnny S.; Tripodi, Stephen J.

    2011-01-01

    This article describes how concept mapping techniques were applied to evaluate the development of a solution-focused, public alternative school program. Concept Systems software was used to create 15 cluster maps based on statements generated from students, teachers, and school staff. In addition, pattern matches were analyzed to examine the…

  4. Infant/Toddler Child Development Program. Forrest City Alternative School, Forrest City, Arkansas. Final Report.

    ERIC Educational Resources Information Center

    Forrest City Public Schools, AR.

    In 1988, the Forrest City Alternative School (Arkansas) began a program to provide care for the preschool children of teen mothers who wanted to obtain their high school diplomas. The children ranged in age from 8 weeks to 3 years in the infant/toddler group and 3-6 years in the child care group. These children were provided with care, preschool…

  5. A Critical Examination of the Process of Modifying the Curriculum of Alternative Secondary Educational Programs

    ERIC Educational Resources Information Center

    Ross, Michael

    2014-01-01

    This study, "A Critical Examination of the Process of Modifying the Curriculum of Alternative Secondary Educational Programs," was done with the use of action research to study (a) whether students currently participating in a continuation school believe their educational and career needs are presently being met; (b) the types of career…

  6. Correlates of Risky Sexual Activity for Urban African American Youth in an Alternative Education Program

    ERIC Educational Resources Information Center

    Carswell, Steven B.; Hanlon, Thomas E.; Watts, Amy M.; O'Grady, Kevin E.

    2014-01-01

    This study examined the link between developmental risk and protective factors and risky sexual activity among 222 urban African American youth attending an alternative education program (AEP) because of problematic behavior. Self-report information provided by these AEP participants revealed that, for the risk and protective factors examined, the…

  7. Concept Mapping: An Approach for Evaluating a Public Alternative School Program

    ERIC Educational Resources Information Center

    Streeter, Calvin L.; Franklin, Cynthia; Kim, Johnny S.; Tripodi, Stephen J.

    2011-01-01

    This article describes how concept mapping techniques were applied to evaluate the development of a solution-focused, public alternative school program. Concept Systems software was used to create 15 cluster maps based on statements generated from students, teachers, and school staff. In addition, pattern matches were analyzed to examine the…

  8. Correlates of Risky Sexual Activity for Urban African American Youth in an Alternative Education Program

    ERIC Educational Resources Information Center

    Carswell, Steven B.; Hanlon, Thomas E.; Watts, Amy M.; O'Grady, Kevin E.

    2014-01-01

    This study examined the link between developmental risk and protective factors and risky sexual activity among 222 urban African American youth attending an alternative education program (AEP) because of problematic behavior. Self-report information provided by these AEP participants revealed that, for the risk and protective factors examined, the…

  9. 77 FR 14587 - FY 2012 Discretionary Livability Funding Opportunity: Alternatives Analysis Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-12

    ... infrastructure investments that enhance the use of transit and other transportation options for the community. On... development, and improving our Nation's environment through investments in clean energy resources, have been... transportation, environmental protection, and housing investments. The Alternatives Analysis program will...

  10. 75 FR 25867 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... HUMAN SERVICES National Institutes of Health National Toxicology Program (NTP) Interagency Center for...), National Institutes of Health (NIH), Department of Health and Human Services. ACTION: Announcement of a... alternative methods that can reduce, refine, and replace the use of animals for human and veterinary...

  11. Closing the Gap: The Effects of Alternative Certification Programs on Intern Self-Efficacy

    ERIC Educational Resources Information Center

    Mitchell, Marianne

    2011-01-01

    The shortage of teachers necessitates systems of certification that quickly provide teachers for the field, especially in hard to staff schools. Alternative certification programs have attempted to address the need by enlisting non-certified college graduates and offering these individuals shortcuts to certification, special assistance, or…

  12. Supporting First Year Alternatively Certified Urban and Rural Intern Teachers through a Multicomponent Distance Induction Program

    ERIC Educational Resources Information Center

    Gresko, Jennifer A.

    2013-01-01

    The pathway for entering the K-12 classroom as a teacher varies compared to what was once the traditional model of teacher preparation. In this mixed-methods action research study, I explore supporting first year alternatively certified urban and rural intern teachers through a multicomponent distance induction program. The induction model in this…

  13. EPAct Alternative Fuel Transportation Program: State and Alternative Fuel Provider Fleet Compliance Annual Report, Fleet Compliance Results for MY 2014/ FY 2015

    SciTech Connect

    2016-04-01

    This annual report of the Alternative Fuel Transportation Program, which ensures compliance with DOE regulations covering state government and alternative fuel provider fleets pursuant to the Energy Policy Act of 1992 (EPAct), as amended, provides fleet compliance results for manufacturing year 2014 / fiscal year 2015.

  14. Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis.

    PubMed

    Kwon, Young-Ju; Park, Mi-Jeong; Kim, Sang-Gyu; Baldwin, Ian T; Park, Chung-Mo

    2014-05-19

    The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5' splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock and environmental stress

  15. Alternative splicing and nonsense-mediated decay of circadian clock genes under environmental stress conditions in Arabidopsis

    PubMed Central

    2014-01-01

    Background The circadian clock enables living organisms to anticipate recurring daily and seasonal fluctuations in their growth habitats and synchronize their biology to the environmental cycle. The plant circadian clock consists of multiple transcription-translation feedback loops that are entrained by environmental signals, such as light and temperature. In recent years, alternative splicing emerges as an important molecular mechanism that modulates the clock function in plants. Several clock genes are known to undergo alternative splicing in response to changes in environmental conditions, suggesting that the clock function is intimately associated with environmental responses via the alternative splicing of the clock genes. However, the alternative splicing events of the clock genes have not been studied at the molecular level. Results We systematically examined whether major clock genes undergo alternative splicing under various environmental conditions in Arabidopsis. We also investigated the fates of the RNA splice variants of the clock genes. It was found that the clock genes, including EARLY FLOWERING 3 (ELF3) and ZEITLUPE (ZTL) that have not been studied in terms of alternative splicing, undergo extensive alternative splicing through diverse modes of splicing events, such as intron retention, exon skipping, and selection of alternative 5′ splice site. Their alternative splicing patterns were differentially influenced by changes in photoperiod, temperature extremes, and salt stress. Notably, the RNA splice variants of TIMING OF CAB EXPRESSION 1 (TOC1) and ELF3 were degraded through the nonsense-mediated decay (NMD) pathway, whereas those of other clock genes were insensitive to NMD. Conclusion Taken together, our observations demonstrate that the major clock genes examined undergo extensive alternative splicing under various environmental conditions, suggesting that alternative splicing is a molecular scheme that underlies the linkage between the clock

  16. The role of alternative Polyadenylation in regulation of rhythmic gene expression.

    PubMed

    Ptitsyna, Natalia; Boughorbel, Sabri; El Anbari, Mohammed; Ptitsyn, Andrey

    2017-08-04

    Alternative transcription is common in eukaryotic cells and plays important role in regulation of cellular processes. Alternative polyadenylation results from ambiguous PolyA signals in 3' untranslated region (UTR) of a gene. Such alternative transcripts share the same coding part, but differ by a stretch of UTR that may contain important functional sites. The methodoogy of this study is based on mathematical modeling, analytical solution, and subsequent validation by datamining in multiple independent experimental data from previously published studies. In this study we propose a mathematical model that describes the population dynamics of alternatively polyadenylated transcripts in conjunction with rhythmic expression such as transcription oscillation driven by circadian or metabolic oscillators. Analysis of the model shows that alternative transcripts with different turnover rates acquire a phase shift if the transcript decay rate is different. Difference in decay rate is one of the consequences of alternative polyadenylation. Phase shift can reach values equal to half the period of oscillation, which makes alternative transcripts oscillate in abundance in counter-phase to each other. Since counter-phased transcripts share the coding part, the rate of translation becomes constant. We have analyzed a few data sets collected in circadian timeline for the occurrence of transcript behavior that fits the mathematical model. Alternative transcripts with different turnover rate create the effect of rectifier. This "molecular diode" moderates or completely eliminates oscillation of individual transcripts and stabilizes overall protein production rate. In our observation this phenomenon is very common in different tissues in plants, mice, and humans. The occurrence of counter-phased alternative transcripts is also tissue-specific and affects functions of multiple biological pathways. Accounting for this mechanism is important for understanding the natural and engineering

  17. Genome-wide cataloging and analysis of alternatively spliced genes in cereal crops.

    PubMed

    Min, Xiang Jia; Powell, Brian; Braessler, Jonathan; Meinken, John; Yu, Feng; Sablok, Gaurav

    2015-09-21

    Protein functional diversity at the post-transcriptional level is regulated through spliceosome mediated pre-mRNA alternative splicing (AS) events and that has been widely demonstrated to be a key player in regulating the functional diversity in plants. Identification and analysis of AS genes in cereal crop plants are critical for crop improvement and understanding regulatory mechanisms. We carried out the comparative analyses of the functional landscapes of the AS using the consensus assembly of expressed sequence tags and available mRNA sequences in four cereal plants. We identified a total of 8,734 in Oryza sativa subspecies (ssp) japonica, 2,657 in O. sativa ssp indica, 3,971 in Sorghum bicolor, and 10,687 in Zea mays AS genes. Among the identified AS events, intron retention remains to be the dominant type accounting for 23.5 % in S. bicolor, and up to 55.8 % in O. sativa ssp indica. We identified a total of 887 AS genes that were conserved among Z. mays, S. bicolor, and O. sativa ssp japonica; and 248 AS genes were found to be conserved among all four studied species or ssp. Furthermore, we identified 53 AS genes conserved with Brachypodium distachyon. Gene Ontology classification of AS genes revealed functional assignment of these genes in many biological processes with diverse molecular functions. AS is common in cereal plants. The AS genes identified in four cereal crops in this work provide the foundation for further studying the roles of AS in regulation of cereal plant growth and development. The data can be accessed at Plant Alternative Splicing Database (http://proteomics.ysu.edu/altsplice/).

  18. Alternative splicing of the tuberous sclerosis 2 (TSC2) gene in human and mouse tissues

    SciTech Connect

    Xu, Lin; Sterner, C.; Maheshwar, M.M.

    1995-06-10

    The recently isolated gene for tuberous sclerosis 2 (TSC2) encodes a 5.5.kb transcript that is widely expressed. The TSC2 gene product, named tuberin, is a 1784-amino-acid protein that shows a small stretch of homology to the GTPase activating protein rap1GAP. We have detected a novel variant of the TSC2 mRNA lacking 129 nucleotides, predicting an in-frame deletion of 43 amino acids spanning codons 946-988 of tuberin. This 129-bp deletion precisely corresponds to exon 25 of the TSC2 gene suggesting that alternative splicing leads to production of two forms of transcripts designated isoforms 1 and 2. Further molecular analysis revealed a third isoform exhibiting a deletion of 44 amino acids spanning codons 946-989 of tuberin. Amino acid 989 is a Ser residue encoded by the first codon of exon 26. The two isoforms also exist in newborn and adult mouse tissues, reinforcing the potential functional importance of these alternatively spliced products. These alternative isoforms should have implications for efforts aimed at identifying mutations in TSC patients. The distinct polypeptides encoded by the TSC2 gene may have different targets as well as functions involved in the regulation of cell growth. 26 refs., 4 figs.

  19. Alternative splicing and genomic structure of the Wilms tumor gene WT1

    SciTech Connect

    Haber, D.A. Massachusetts General Hospital Cancer Center, Charlestown ); Sohn, R.L.; Buckler, A.J.; Pelletier, J.; Call, K.M.; Housman, D.E. )

    1991-11-01

    The chromosome 11p13 Wilms tumor susceptibility gene WT1 appears to play a crucial role in regulating the proliferation and differentiation of nephroblasts and gonadal tissue. The WT1 gene consists of 10 exons, encoding a complex pattern of mRNA species: four distinct transcripts are expressed, reflecting the presence or absence of two alternative splices. Splice I consists of a separate exon, encoding 17 amino acids, which is inserted between the proline-rich amino terminus and the zinc finger domains. Splice II arises from the use of an alternative 5{prime} splice junction and results in the insertion of 3 amino acids between zinc fingers 3 and 4. RNase protection analysis demonstrates that the most prevalent splice variant in both human and mouse is that which contains both alternative splices, whereas the least common is the transcript missing both splices. The relative distribution of splice variants is highly conserved between normal fetal kidney tissue and Wilms tumors that have intact WT1 transcripts. The ratio of these different WT1 mRNA species is also maintained as a function of development in the mouse kidney and in various mouse tissues expressing WT1. The conservation in structure and relative levels of each of the four WT1 mRNA species suggest that each encoded polypeptide makes a significant contribution to normal gene function. The control of cellular proliferation and differentiation exerted by the WT1 gene products may involve interactions between four polypeptides with distinct targets and functions.

  20. Alternative transcripts of the SERPINA1 gene in alpha-1 antitrypsin deficiency.

    PubMed

    Matamala, Nerea; Martínez, Maria Teresa; Lara, Beatriz; Pérez, Laura; Vázquez, Irene; Jimenez, Azucena; Barquín, Miguel; Ferrarotti, Ilaria; Blanco, Ignacio; Janciauskiene, Sabina; Martinez-Delgado, Beatriz

    2015-07-04

    SERPINA1 is the gene for alpha-1 antitrypsin (AAT), an acute phase protein with anti-protease and immunoregulatory activities. Mutations in SERPINA1 gene cause AAT deficiency and predispose individuals to early-onset emphysema and liver diseases. Expression of the SERPINA1 gene is regulated by different promoters and alternative splicing events among non-coding exons 1A, 1B and 1C. We have developed three quantitative PCR (QT-PCR) assays (1A, 1B and 1C). These assays were applied for the analysis of SERPINA1 alternative transcripts in: (1) 16 human tissues and (2) peripheral blood leukocytes from 33 subjects with AAT mutations and 7 controls. Tissue-specific expression was found for the SERPINA1 transcripts. The 1A transcripts were mainly expressed in leukocytes and lung tissue while those detected with the 1B assay were highly restricted to leukocytes. Only 1B transcripts significantly correlated with serum AAT levels. The 1C transcripts were specifically found in lung, liver, kidney and pancreas. Furthermore, the expression of transcripts was related to AAT genotypes. While deficient variants of AAT had no pronounced effect on the transcript expression, null alleles were associated with significant reduction of different transcripts. The possibility to discriminate between SERPINA1 alternative splicing products will help us to understand better the regulation of SERPINA1 gene and its association with SERPINA1 mutations-related diseases.

  1. Alternative polyadenylation in a family of paralogous EPB41 genes generates protein 4.1 diversity.

    PubMed

    Rangel, Laura; Lospitao, Eva; Ruiz-Sáenz, Ana; Alonso, Miguel A; Correas, Isabel

    2017-02-01

    Alternative polyadenylation (APA) is a step in mRNA 3'-end processing that contributes to the complexity of the transcriptome by generating isoforms that differ in either their coding sequence or their 3'-untranslated regions (UTRs). The EPB41 genes, EPB41, EPB41L2, EPB41L3 and EPB41L1, encode an impressively complex array of structural adaptor proteins (designated 4.1R, 4.1G, 4.1B and 4.1N, respectively) by using alternative transcriptional promoters and tissue-specific alternative pre-mRNA splicing. The great variety of 4.1 proteins mainly results from 5'-end and internal processing of the EPB41 pre-mRNAs. Thus, 4.1 proteins can vary in their N-terminal extensions but all contain a highly homologous C-terminal domain (CTD). Here we study a new group of EPB41-related mRNAs that originate by APA and lack the exons encoding the CTD characteristic of prototypical 4.1 proteins, thereby encoding a new type of 4.1 protein. For the EPB41 gene, this type of processing was observed in all 11 human tissues analyzed. Comparative genomic analysis of EPB41 indicates that APA is conserved in various mammals. In addition, we show that APA also functions for the EPB41L2, EPB41L3 and EPB41L1 genes, but in a more restricted manner in the case of the latter 2 than it does for the EPB41 and EPB41L2 genes. Our study shows alternative polyadenylation to be an additional mechanism for the generation of 4.1 protein diversity in the already complex EPB41-related genes. Understanding the diversity of EPB41 RNA processing is essential for a full appreciation of the many 4.1 proteins expressed in normal and pathological tissues.

  2. Reference gene alternatives to Gapdh in rodent and human heart failure gene expression studies

    PubMed Central

    2010-01-01

    Background Quantitative real-time RT-PCR (RT-qPCR) is a highly sensitive method for mRNA quantification, but requires invariant expression of the chosen reference gene(s). In pathological myocardium, there is limited information on suitable reference genes other than the commonly used Gapdh mRNA and 18S ribosomal RNA. Our aim was to evaluate and identify suitable reference genes in human failing myocardium, in rat and mouse post-myocardial infarction (post-MI) heart failure and across developmental stages in fetal and neonatal rat myocardium. Results The abundance of Arbp, Rpl32, Rpl4, Tbp, Polr2a, Hprt1, Pgk1, Ppia and Gapdh mRNA and 18S ribosomal RNA in myocardial samples was quantified by RT-qPCR. The expression variability of these transcripts was evaluated by the geNorm and Normfinder algorithms and by a variance component analysis method. Biological variability was a greater contributor to sample variability than either repeated reverse transcription or PCR reactions. Conclusions The most stable reference genes were Rpl32, Gapdh and Polr2a in mouse post-infarction heart failure, Polr2a, Rpl32 and Tbp in rat post-infarction heart failure and Rpl32 and Pgk1 in human heart failure (ischemic disease and cardiomyopathy). The overall most stable reference genes across all three species was Rpl32 and Polr2a. In rat myocardium, all reference genes tested showed substantial variation with developmental stage, with Rpl4 as was most stable among the tested genes. PMID:20331858

  3. Conserved transcriptional responses to cyanobacterial stressors are mediated by alternate regulation of paralogous genes in Daphnia.

    PubMed

    Asselman, Jana; Pfrender, Michael E; Lopez, Jacqueline A; De Coninck, Dieter I M; Janssen, Colin R; Shaw, Joseph R; De Schamphelaere, Karel A C

    2015-04-01

    Despite a significant increase in genomic data, our knowledge of gene functions and their transcriptional responses to environmental stimuli remains limited. Here, we use the model keystone species Daphnia pulex to study environmental responses of genes in the context of their gene family history to better understand the relationship between genome structure and gene function in response to environmental stimuli. Daphnia were exposed to five different treatments, each consisting of a diet supplemented with one of five cyanobacterial species, and a control treatment consisting of a diet of only green algae. Differential gene expression profiles of Daphnia exposed to each of these five cyanobacterial species showed that genes with known functions are more likely to be shared by different expression profiles, whereas genes specific to the lineage of Daphnia are more likely to be unique to a given expression profile. Furthermore, while only a small number of nonlineage-specific genes were conserved across treatment type, there was a high degree of overlap in expression profiles at the functional level. The conservation of functional responses across the different cyanobacterial treatments can be attributed to the treatment-specific expression of different paralogous genes within the same gene family. Comparison with available gene expression data in the literature suggests differences in nutritional composition in diets with cyanobacterial species compared to diets of green algae as a primary driver for cyanobacterial effects on Daphnia. We conclude that conserved functional responses in Daphnia across different cyanobacterial treatments are mediated through alternate regulation of paralogous gene families. © 2015 John Wiley & Sons Ltd.

  4. Alternative activation deprives macrophages of a coordinated defense program to Mycobacterium tuberculosis.

    PubMed

    Kahnert, Antje; Seiler, Peter; Stein, Maik; Bandermann, Silke; Hahnke, Karin; Mollenkopf, Hans; Kaufmann, Stefan H E

    2006-03-01

    A potent Th1 immune response is critical to the control of tuberculosis. The impact of an additive Th2 response on the course of disease has so far been insufficiently characterized, despite increased morbidity after co-infection with Mycobacterium tuberculosis and Th2-eliciting helminths and possible involvement of Th2 polarization in reactivation of latent tuberculosis. Here, we describe the gene expression profile of murine bone marrow-derived macrophages alternatively activated by IL-4 in response to infection with M. tuberculosis. Comparison of transcriptional profiles of infected IL-4- and IFN-gamma-activated macrophages revealed delayed and partially diminished responses to intracellular bacteria in alternatively activated macrophages, characterized by reduced exposure to nitrosative stress and increased iron availability, respectively. Alternative activation of host macrophages correlated with elevated expression of the M. tuberculosis iron storage protein bacterioferritin as well as reduced expression of the mycobactin synthesis genes mbtI and mbtJ. The extracellular matrix-remodeling enzyme matrix metalloproteinase (MMP)-12 was induced in alternatively activated macrophages in vitro, and MMP-12-expressing macrophages were abundant at late, but not early, stages of tuberculosis in murine lungs. Our findings emphasize that alternative activation deprives macrophages of control mechanisms that limit mycobacterial growth in vivo, thus supporting intracellular persistence of M. tuberculosis.

  5. Crisis intervention program: an alternative to inpatient psychiatric treatment for children.

    PubMed

    Blumberg, Samuel H

    2002-03-01

    This study evaluated the impact of a Crisis Intervention program as an alternative to use of psychiatric treatment beds for young children. A multidisciplinary community-based intervention was utilized, including family therapy, psychiatric intervention, and school consultations. The impact of the service was evaluated in relation to the use of psychiatric treatment beds by the population of children eligible for Medicaid or uninsured. In comparison to an historical control group, the program resulted in a 23% reduction in the use of psychiatric treatment beds. A cost-minimization analysis indicated that in addition to the program reducing the use of psychiatric treatment beds, the cost of treatment was also slightly reduced.

  6. Alternative Splicing of Barley Clock Genes in Response to Low Temperature

    PubMed Central

    Calixto, Cristiane P. G.; Simpson, Craig G.; Waugh, Robbie; Brown, John W. S.

    2016-01-01

    Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement. PMID:27959947

  7. Alternative Splicing of Barley Clock Genes in Response to Low Temperature.

    PubMed

    Calixto, Cristiane P G; Simpson, Craig G; Waugh, Robbie; Brown, John W S

    2016-01-01

    Alternative splicing (AS) is a regulated mechanism that generates multiple transcripts from individual genes. It is widespread in eukaryotic genomes and provides an effective way to control gene expression. At low temperatures, AS regulates Arabidopsis clock genes through dynamic changes in the levels of productive mRNAs. We examined AS in barley clock genes to assess whether temperature-dependent AS responses also occur in a monocotyledonous crop species. We identify changes in AS of various barley core clock genes including the barley orthologues of Arabidopsis AtLHY and AtPRR7 which showed the most pronounced AS changes in response to low temperature. The AS events modulate the levels of functional and translatable mRNAs, and potentially protein levels, upon transition to cold. There is some conservation of AS events and/or splicing behaviour of clock genes between Arabidopsis and barley. In addition, novel temperature-dependent AS of the core clock gene HvPPD-H1 (a major determinant of photoperiod response and AtPRR7 orthologue) is conserved in monocots. HvPPD-H1 showed a rapid, temperature-sensitive isoform switch which resulted in changes in abundance of AS variants encoding different protein isoforms. This novel layer of low temperature control of clock gene expression, observed in two very different species, will help our understanding of plant adaptation to different environments and ultimately offer a new range of targets for plant improvement.

  8. An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype

    PubMed Central

    Flytzanis, Nicholas C.; Balsamo, Michele; Condeelis, John S.; Oktay, Maja H.; Burge, Christopher B.; Gertler, Frank B.

    2011-01-01

    Epithelial-mesenchymal transition (EMT), a mechanism important for embryonic development, plays a critical role during malignant transformation. While much is known about transcriptional regulation of EMT, alternative splicing of several genes has also been correlated with EMT progression, but the extent of splicing changes and their contributions to the morphological conversion accompanying EMT have not been investigated comprehensively. Using an established cell culture model and RNA–Seq analyses, we determined an alternative splicing signature for EMT. Genes encoding key drivers of EMT–dependent changes in cell phenotype, such as actin cytoskeleton remodeling, regulation of cell–cell junction formation, and regulation of cell migration, were enriched among EMT–associated alternatively splicing events. Our analysis suggested that most EMT–associated alternative splicing events are regulated by one or more members of the RBFOX, MBNL, CELF, hnRNP, or ESRP classes of splicing factors. The EMT alternative splicing signature was confirmed in human breast cancer cell lines, which could be classified into basal and luminal subtypes based exclusively on their EMT–associated splicing pattern. Expression of EMT–associated alternative mRNA transcripts was also observed in primary breast cancer samples, indicating that EMT–dependent splicing changes occur commonly in human tumors. The functional significance of EMT–associated alternative splicing was tested by expression of the epithelial-specific splicing factor ESRP1 or by depletion of RBFOX2 in mesenchymal cells, both of which elicited significant changes in cell morphology and motility towards an epithelial phenotype, suggesting that splicing regulation alone can drive critical aspects of EMT–associated phenotypic changes. The molecular description obtained here may aid in the development of new diagnostic and prognostic markers for analysis of breast cancer progression. PMID:21876675

  9. Hypoxia regulates alternative splicing of HIF and non-HIF target genes.

    PubMed

    Sena, Johnny A; Wang, Liyi; Heasley, Lynn E; Hu, Cheng-Jun

    2014-09-01

    Hypoxia is a common characteristic of many solid tumors. The hypoxic microenvironment stabilizes hypoxia-inducible transcription factor 1α (HIF1α) and 2α (HIF2α/EPAS1) to activate gene transcription, which promotes tumor cell survival. The majority of human genes are alternatively spliced, producing RNA isoforms that code for functionally distinct proteins. Thus, an effective hypoxia response requires increased HIF target gene expression as well as proper RNA splicing of these HIF-dependent transcripts. However, it is unclear if and how hypoxia regulates RNA splicing of HIF targets. This study determined the effects of hypoxia on alternative splicing (AS) of HIF and non-HIF target genes in hepatocellular carcinoma cells and characterized the role of HIF in regulating AS of HIF-induced genes. The results indicate that hypoxia generally promotes exon inclusion for hypoxia-induced, but reduces exon inclusion for hypoxia-reduced genes. Mechanistically, HIF activity, but not hypoxia per se is found to be necessary and sufficient to increase exon inclusion of several HIF targets, including pyruvate dehydrogenase kinase 1 (PDK1). PDK1 splicing reporters confirm that transcriptional activation by HIF is sufficient to increase exon inclusion of PDK1 splicing reporter. In contrast, transcriptional activation of a PDK1 minigene by other transcription factors in the absence of endogenous HIF target gene activation fails to alter PDK1 RNA splicing. This study demonstrates a novel function of HIF in regulating RNA splicing of HIF target genes. ©2014 American Association for Cancer Research.

  10. Divergent Functions Through Alternative Splicing: The Drosophila CRMP Gene in Pyrimidine Metabolism, Brain, and Behavior

    PubMed Central

    Morris, Deanna H.; Dubnau, Josh; Park, Jae H.; Rawls, John M.

    2012-01-01

    DHP and CRMP proteins comprise a family of structurally similar proteins that perform divergent functions, DHP in pyrimidine catabolism in most organisms and CRMP in neuronal dynamics in animals. In vertebrates, one DHP and five CRMP proteins are products of six genes; however, Drosophila melanogaster has a single CRMP gene that encodes one DHP and one CRMP protein through tissue-specific, alternative splicing of a pair of paralogous exons. The proteins derived from the fly gene are identical over 90% of their lengths, suggesting that unique, novel functions of these proteins derive from the segment corresponding to the paralogous exons. Functional homologies of the Drosophila and mammalian CRMP proteins are revealed by several types of evidence. Loss-of-function CRMP mutation modifies both Ras and Rac misexpression phenotypes during fly eye development in a manner that is consistent with the roles of CRMP in Ras and Rac signaling pathways in mammalian neurons. In both mice and flies, CRMP mutation impairs learning and memory. CRMP mutant flies are defective in circadian activity rhythm. Thus, DHP and CRMP proteins are derived by different processes in flies (tissue-specific, alternative splicing of paralogous exons of a single gene) and vertebrates (tissue-specific expression of different genes), indicating that diverse genetic mechanisms have mediated the evolution of this protein family in animals. PMID:22649077

  11. Subfunctionalization of duplicate mitf genes associated with differential degeneration of alternative exons in fish.

    PubMed Central

    Altschmied, Joachim; Delfgaauw, Jacqueline; Wilde, Brigitta; Duschl, Jutta; Bouneau, Laurence; Volff, Jean-Nicolas; Schartl, Manfred

    2002-01-01

    The microphthalmia-associated transcription factor (MITF) exists in at least four isoforms. These are generated in higher vertebrates using alternative 5' exons and promoters from a single gene. Two separate genes (mitf-m and mitf-b), however, are present in different teleost fish species including the poeciliid Xiphophorus, the pufferfishes Fugu rubripes and Tetraodon nigroviridis, and the zebrafish Danio rerio. Fish proteins MITF-m and MITF-b correspond at both the structural and the expression levels to one particular bird/mammalian MITF isoform. In the teleost lineage subfunctionalization of mitf genes after duplication at least 100 million years ago is associated with the degeneration of alternative exons and, probably, regulatory elements and promoters. For example, a remnant of the first exon specific for MITF-m is detected within the pufferfish gene encoding MITF-b. Retracing the evolutionary history of mitf genes in vertebrates uncovered the differential recruitment of new introns specific for either the teleost or the bird/mammalian lineage. PMID:12019239

  12. Cloning and expression of an alternative oxidase gene from Lycopersicon esculentum.

    PubMed

    Song, Cong-Feng; Borth, Wayne; Wang, Jin-Sheng; Hu, John-Sheng

    2004-10-01

    A full-length cDNA gene (LeAox1au) was isolated from a cDNA library made from ripening fruit of tomato "UC-82B" (Lycopersicon esculentum), after probing with alternative oxidase (AOX) gene fragments, obtained by degenerate primer PCR. Sequence analysis showed that LeAox1au was 1418 bp long and contained a 1077-bp open reading frame encoding a about 40 kD precursor protein which is processed to a mature protein of 32 kD. Southern blot analysis suggested LeAox1au is present as a single copy in the genome of tomato. RT-PCR analysis indicated LeAox1au was expressed in roots, stems, leaves and cotyledons of tomato plants. A recombinant construct containing the open reading frame sequence of the LeAox1au was transformed into Escherichia coli to express the alternative oxidase precursor protein.

  13. Thrifty genes for obesity, an attractive but flawed idea, and an alternative perspective: the 'drifty gene' hypothesis.

    PubMed

    Speakman, J R

    2008-11-01

    Almost 50 years ago Neel proposed a hypothesis to explain the prevalence of obesity and diabetes in modern society--the 'thrifty gene' hypothesis. The fundamental basis of the hypothesis was that, in our early evolutionary history, genes, that promoted efficient fat deposition would have been advantageous because they allowed their holders to survive at periods of famine. In modern society, such genes are disadvantageous because they promote fat deposition in preparation for a famine that never comes, and the result is widespread obesity and diabetes. In recent years I, and others, have questioned some of the fundamental assumptions of this hypothesis--particularly focusing on whether differential survival of lean against obese in famines provides sufficient selective pressure for the spread of so-called 'thrifty genes'. These arguments have been criticized because famines not only affect survival but also fecundity, and obese people would be expected to sustain fecundity longer in the face of food shortages. In this paper, I show that the reduced fecundity argument is flawed because famines are almost universally followed by periods of enhanced fecundity, which offsets the decline observed during the famine itself. The net effect of famines on fecundity is consequently insufficient to rescue the thrifty gene idea. Elsewhere, I have suggested an alternative scenario that subsections of the population have a genetic predisposition to obesity due to an absence of selection, combined with genetic drift. The scenario presented earlier was based on evidence from prehistory concerning the release of our ancestors from heavy predation pressure around 2 million years ago. I suggest here that this is one of a number of potential scenarios based on random genetic drift that may explain the specific aetiology of the obesity epidemic. Together, these alternatives, based on central notion that genetic drift rather than positive selection was a dominant factor, may be called the

  14. Alternative splicing and gene duplication differentially shaped the regulation of isochorismate synthase in Populus and Arabidopsis

    PubMed Central

    Yuan, Yinan; Chung, Jeng-Der; Fu, Xueyan; Johnson, Virgil E.; Ranjan, Priya; Booth, Sarah L.; Harding, Scott A.; Tsai, Chung-Jui

    2009-01-01

    Isochorismate synthase (ICS) converts chorismate to isochorismate for the biosynthesis of phylloquinone, an essential cofactor for photosynthetic electron transport. ICS is also required for salicylic acid (SA) synthesis during Arabidopsis defense. In several other species, including Populus, SA is derived primarily from the phenylpropanoid pathway. We therefore sought to investigate ICS regulation in Populus to learn the extent of ICS involvement in SA synthesis and defense. Arabidopsis harbors duplicated AtICS genes that differ in their exon-intron structure, basal expression, and stress inducibility. In contrast, we found a single ICS gene in Populus and six other sequenced plant genomes, pointing to the AtICS duplication as a lineage-specific event. The Populus ICS encodes a functional plastidic enzyme, and was not responsive to stresses that stimulated phenylpropanoid accumulation. Populus ICS underwent extensive alternative splicing that was rare for the duplicated AtICSs. Sequencing of 184 RT-PCR Populus clones revealed 37 alternative splice variants, with normal transcripts representing ≈50% of the population. When expressed in Arabidopsis, Populus ICS again underwent alternative splicing, but did not produce normal transcripts to complement AtICS1 function. The splice-site sequences of Populus ICS are unusual, suggesting a causal link between junction sequence, alternative splicing, and ICS function. We propose that gene duplication and alternative splicing of ICS evolved independently in Arabidopsis and Populus in accordance with their distinct defense strategies. AtICS1 represents a divergent isoform for inducible SA synthesis during defense. Populus ICS primarily functions in phylloquinone biosynthesis, a process that can be sustained at low ICS transcript levels. PMID:19996170

  15. Differential Expression of Alternative Oxidase Genes in Soybean Cotyledons during Postgerminative Development1

    PubMed Central

    McCabe, Tulene C.; Finnegan, Patrick M.; Harvey Millar, A.; Day, David A.; Whelan, James

    1998-01-01

    The expression of the alternative oxidase (AOX) was investigated during cotyledon development in soybean (Glycine max [L.] Merr.) seedlings. The total amount of AOX protein increased throughout development, not just in earlier stages as previously thought, and was correlated with the increase in capacity of the alternative pathway. Each AOX isoform (AOX1, AOX2, and AOX3) showed a different developmental trend in mRNA abundance, such that the increase in AOX protein and capacity appears to involve a shift in gene expression from AOX2 to AOX3. As the cotyledons aged, the size of the mitochondrial ubiquinone pool decreased. We discuss how this and other factors may affect the alternative pathway activity that results from the developmental regulation of AOX expression. PMID:9765553

  16. Mammalian Glutaminase Gls2 Gene Encodes Two Functional Alternative Transcripts by a Surrogate Promoter Usage Mechanism

    PubMed Central

    Campos-Sandoval, José A.; Manzanares, Elisa; Lobo, Carolina; Segura, J. A.; Alonso, Francisco J.; Matés, José M.; Márquez, Javier

    2012-01-01

    Background Glutaminase is expressed in most mammalian tissues and cancer cells, but the regulation of its expression is poorly understood. An essential step to accomplish this goal is the characterization of its species- and cell-specific isoenzyme pattern of expression. Our aim was to identify and characterize transcript variants of the mammalian glutaminase Gls2 gene. Methodology/Principal Findings We demonstrate for the first time simultaneous expression of two transcript variants from the Gls2 gene in human, rat and mouse. A combination of RT-PCR, primer-extension analysis, bioinformatics, real-time PCR, in vitro transcription and translation and immunoblot analysis was applied to investigate GLS2 transcripts in mammalian tissues. Short (LGA) and long (GAB) transcript forms were isolated in brain and liver tissue of human, rat and mouse. The short LGA transcript arises by a combination of two mechanisms of transcriptional modulation: alternative transcription initiation and alternative promoter. The LGA variant contains both the transcription start site (TSS) and the alternative promoter in the first intron of the Gls2 gene. The full human LGA transcript has two in-frame ATGs in the first exon, which are missing in orthologous rat and mouse transcripts. In vitro transcription and translation of human LGA yielded two polypeptides of the predicted size, but only the canonical full-length protein displayed catalytic activity. Relative abundance of GAB and LGA transcripts showed marked variations depending on species and tissues analyzed. Conclusions/Significance This is the first report demonstrating expression of alternative transcripts of the mammalian Gls2 gene. Transcriptional mechanisms giving rise to GLS2 variants and isolation of novel GLS2 transcripts in human, rat and mouse are presented. Results were also confirmed at the protein level, where catalytic activity was demonstrated for the human LGA protein. Relative abundance of GAB and LGA transcripts was

  17. Isolation and characterization of alternatively spliced variants of the mouse sigma1 receptor gene, Sigmar1

    PubMed Central

    Pan, Ling; Pasternak, David A.; Xu, Jin; Xu, Mingming; Lu, Zhigang; Pasternak, Gavril W.

    2017-01-01

    The sigma1 receptor acts as a chaperone at the endoplasmic reticulum, associates with multiple proteins in various cellular systems, and involves in a number of diseases, such as addiction, pain, cancer and psychiatric disorders. The sigma1 receptor is encoded by the single copy SIGMAR1 gene. The current study identifies five alternatively spliced variants of the mouse sigma1 receptor gene using a polymerase chain reaction cloning approach. All the splice variants are generated by exon skipping or alternative 3’ or 5’ splicing, producing the truncated sigma1 receptor. Similar alternative splicing has been observed in the human SIGMAR1 gene based on the molecular cloning or genome sequence prediction, suggesting conservation of alternative splicing of SIGMAR1 gene. Using quantitative polymerase chain reactions, we demonstrate differential expression of several splice variants in mouse tissues and brain regions. When expressed in HEK293 cells, all the splice variants fail to bind sigma ligands, implicating that each truncated region in these splice variants is important for ligand binding. However, co-immunoprecipitation (Co-IP) study in HEK293 cells co-transfected with tagged constructs reveals that all the splice variants maintain their ability to physically associate with a mu opioid receptor (mMOR-1), providing useful information to correlate the motifs/sequences necessary for their physical association. Furthermore, a competition Co-IP study showed that all the variants can disrupt in a dose-dependent manner the dimerization of the original sigma1 receptor with mMOR-1, suggesting a potential dominant negative function and providing significant insights into their function. PMID:28350844

  18. Phylogenetic Analysis of Gene Structure and Alternative Splicing in α-Actinins

    PubMed Central

    Lek, Monkol; MacArthur, Daniel G.; Yang, Nan; North, Kathryn N.

    2010-01-01

    The α-actinins are an important family of actin-binding proteins with the ability to cross-link actin filaments when in dimer form. Members of the α-actinin family share a domain topology composed of highly conserved actin-binding and EF-hand domains separated by a rod domain composed of spectrin-like repeats. Functional diversity within this family has arisen through exon duplication and the formation of alternate splice isoforms as well as gene duplications during the evolution of vertebrates. In addition to the known functional domains, α-actinins also contain a consensus PDZ-binding site. The completed genome sequence of over 32 invertebrate species has allowed the analysis of gene structure and exon–gene duplication over a diverse range of phyla. Our analysis shows that relative to early branching metazoans, there has been considerable intron loss especially in arthropods with few cases of intron gains. The C-terminal PDZ-binding site is conserved in nearly all invertebrates but is missing in some nematodes and platyhelminths. Alternative splicing in the actin-binding domain is conserved in chordates, arthropods, and some nematodes and platyhelminths. In contrast, alternative splicing of the EF-hand domain is only observed in chordates. Finally, given the prevalence of exon duplications seen in the actin-binding domain, this may act as a significant mechanism in the modification of actin-binding properties. PMID:19897525

  19. A cell-based in vitro alternative to identify skin sensitizers by gene expression

    SciTech Connect

    Hooyberghs, Jef Schoeters, Elke; Lambrechts, Nathalie; Nelissen, Inge; Witters, Hilda; Schoeters, Greet; Heuvel, Rosette van den

    2008-08-15

    The ethical and economic burden associated with animal testing for assessment of skin sensitization has triggered intensive research effort towards development and validation of alternative methods. In addition, new legislation on the registration and use of cosmetics and chemicals promote the use of suitable alternatives for hazard assessment. Our previous studies demonstrated that human CD34{sup +} progenitor-derived dendritic cells from cord blood express specific gene profiles upon exposure to low molecular weight sensitizing chemicals. This paper presents a classification model based on this cell type which is successful in discriminating sensitizing chemicals from non-sensitizing chemicals based on transcriptome analysis of 13 genes. Expression profiles of a set of 10 sensitizers and 11 non-sensitizers were analyzed by RT-PCR using 9 different exposure conditions and a total of 73 donor samples. Based on these data a predictive dichotomous classifier for skin sensitizers has been constructed, which is referred to as . In a first step the dimensionality of the input data was reduced by selectively rejecting a number of exposure conditions and genes. Next, the generalization of a linear classifier was evaluated by a cross-validation which resulted in a prediction performance with a concordance of 89%, a specificity of 97% and a sensitivity of 82%. These results show that the present model may be a useful human in vitro alternative for further use in a test strategy towards the reduction of animal use for skin sensitization.

  20. A cell-based in vitro alternative to identify skin sensitizers by gene expression.

    PubMed

    Hooyberghs, Jef; Schoeters, Elke; Lambrechts, Nathalie; Nelissen, Inge; Witters, Hilda; Schoeters, Greet; Van Den Heuvel, Rosette

    2008-08-15

    The ethical and economic burden associated with animal testing for assessment of skin sensitization has triggered intensive research effort towards development and validation of alternative methods. In addition, new legislation on the registration and use of cosmetics and chemicals promote the use of suitable alternatives for hazard assessment. Our previous studies demonstrated that human CD34(+) progenitor-derived dendritic cells from cord blood express specific gene profiles upon exposure to low molecular weight sensitizing chemicals. This paper presents a classification model based on this cell type which is successful in discriminating sensitizing chemicals from non-sensitizing chemicals based on transcriptome analysis of 13 genes. Expression profiles of a set of 10 sensitizers and 11 non-sensitizers were analyzed by RT-PCR using 9 different exposure conditions and a total of 73 donor samples. Based on these data a predictive dichotomous classifier for skin sensitizers has been constructed, which is referred to as VITOSENS. In a first step the dimensionality of the input data was reduced by selectively rejecting a number of exposure conditions and genes. Next, the generalization of a linear classifier was evaluated by a cross-validation which resulted in a prediction performance with a concordance of 89%, a specificity of 97% and a sensitivity of 82%. These results show that the present model may be a useful human in vitro alternative for further use in a test strategy towards the reduction of animal use for skin sensitization.

  1. Distinct regulation of alternative polyadenylation and gene expression by nuclear poly(A) polymerases.

    PubMed

    Li, Weimin; Li, Wencheng; Laishram, Rakesh S; Hoque, Mainul; Ji, Zhe; Tian, Bin; Anderson, Richard A

    2017-09-06

    Polyadenylation of nascent RNA by poly(A) polymerase (PAP) is important for 3' end maturation of almost all eukaryotic mRNAs. Most mammalian genes harbor multiple polyadenylation sites (PASs), leading to expression of alternative polyadenylation (APA) isoforms with distinct functions. How poly(A) polymerases may regulate PAS usage and hence gene expression is poorly understood. Here, we show that the nuclear canonical (PAPα and PAPγ) and non-canonical (Star-PAP) PAPs play diverse roles in PAS selection and gene expression. Deficiencies in the PAPs resulted in perturbations of gene expression, with Star-PAP impacting lowly expressed mRNAs and long-noncoding RNAs to the greatest extent. Importantly, different PASs of a gene are distinctly regulated by different PAPs, leading to widespread relative expression changes of APA isoforms. The location and surrounding sequence motifs of a PAS appear to differentiate its regulation by the PAPs. We show Star-PAP-specific PAS usage regulates the expression of the eukaryotic translation initiation factor EIF4A1, the tumor suppressor gene PTEN and the long non-coding RNA NEAT1. The Star-PAP-mediated APA of PTEN is essential for DNA damage-induced increase of PTEN protein levels. Together, our results reveal a PAS-guided and PAP-mediated paradigm for gene expression in response to cellular signaling cues. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  2. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato.

    PubMed

    Wang, Guixiang; Weng, Lin; Li, Meng; Xiao, Han

    2017-03-02

    Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops.

  3. Response of Gene Expression and Alternative Splicing to Distinct Growth Environments in Tomato

    PubMed Central

    Wang, Guixiang; Weng, Lin; Li, Meng; Xiao, Han

    2017-01-01

    Phenotypic plasticity is the phenomenon that one particular genotype produces different phenotypes under different environmental conditions, but its underlying molecular and genetic mechanisms are poorly understood. Plastic traits may be under the control of genes whose expression is modulated by environmental cues. In this study, we investigated phenotypic plasticity in tomato (Solanum lycopersicum) and its ancestral species S. pimpinellifolium by comparing the global gene expression of young seedlings grown under two distinct growth conditions. Our results show that more than 7000 genes exhibited differential expression in response to environmental changes from phytotron to a plastic greenhouse, and 98 environmentally sensitive genes displayed the same patterns of expression response across the two tomato species. We also found that growth conditions had a remarkable impact on transcriptome complexity, attributable to alternative splicing (AS), in which 665 splice variants showed differential expression in response to the environmental changes. Moreover, more splice variants and AS events per gene were detected in plastic greenhouse-grown seedlings than their phytotron counterparts, and these seedlings also had higher percentages of intron retention events. The identification of the conserved environmentally-sensitive genes and the splice variants in this study will be useful for further analysis of gene regulation of environmental response in tomato and other crops. PMID:28257093

  4. A Preventive Intervention Program for Urban African American Youth Attending an Alternative Education Program: Background, Implementation, and Feasibility

    PubMed Central

    Carswell, Steven B.; Hanlon, Thomas E.; O'Grady, Kevin E.; Watts, Amy M.; Pothong, Pattarapan

    2009-01-01

    This paper presents background, implementation, and feasibility findings associated with planning and conducting an after-school intervention program in an alternative education setting designed to prevent the initiation and escalation of violence and substance abuse among urban African American youth at high risk for life-long problem behaviors. Evolving from earlier preventive interventions implemented in clinic and school settings, the program, entitled The Village Model of Care, consisted of structured group mentoring, parental support, and community outreach services administered to alternative education students and their primary caregiver(s) during the school year. Over a two-year intake period, 109 youth participated in the present process evaluation study. Findings from the study not only provided relevant demographic information on the characteristics of youth likely to be included in such programs but also indicated the importance of including the family in the rehabilitation effort and the need for school administrative system support for the underlying alternative education approach. The information presented in this report has a direct bearing on the planning of future prevention efforts conducted in similar settings that are aimed at reducing problem behaviors and promoting positive lifestyles among high-risk youth. PMID:20054423

  5. Alternative Renewable Biomass Tracking Program Document under the Renewable Fuel Standard Program

    EPA Pesticide Factsheets

    The approval letters that EPA approves a company's biomass tracking program meeting all the requirements outlined in 40 CFR part 80.1454, including elements determined necessary to achieve the level of quality assurance required under the regulation list.

  6. Development Of Educational Programs In Renewable And Alternative Energy Processing: The Case Of Russia

    NASA Astrophysics Data System (ADS)

    Svirina, Anna; Shindor, Olga; Tatmyshevsky, Konstantin

    2014-12-01

    The paper deals with the main problems of Russian energy system development that proves necessary to provide educational programs in the field of renewable and alternative energy. In the paper the process of curricula development and defining teaching techniques on the basis of expert opinion evaluation is defined, and the competence model for renewable and alternative energy processing master students is suggested. On the basis of a distributed questionnaire and in-depth interviews, the data for statistical analysis was obtained. On the basis of this data, an optimization of curricula structure was performed, and three models of a structure for optimizing teaching techniques were developed. The suggested educational program structure which was adopted by employers is presented in the paper. The findings include quantitatively estimated importance of systemic thinking and professional skills and knowledge as basic competences of a masters' program graduate; statistically estimated necessity of practice-based learning approach; and optimization models for structuring curricula in renewable and alternative energy processing. These findings allow the establishment of a platform for the development of educational programs.

  7. Alternative splicing of breast cancer associated gene BRCA1 from breast cancer cell line.

    PubMed

    Lixia, Miao; Zhijian, Cao; Chao, Shen; Chaojiang, Gu; Congyi, Zheng

    2007-01-31

    Breast cancer is the most common malignancy among women, and mutations in the BRCA1 gene produce increased susceptibility to these malignancies in certain families. In this study, the forward 1-13 exons of breast cancer associated gene BRCA1 were cloned from breast cancer cell line ZR-75-30 by RT-PCR method. Sequence analysis showed that nine BRCA1 splice forms were isolated and characterized, compared with wild-type BRCA1 gene, five splice forms of which were novel. These splice isoforms were produced from the molecular mechanism of 5' and 3' alternative splicing. All these splice forms deleting exon 11b and the locations of alternative splicing were focused on two parts:one was exons 2 and 3, and the other was exons 9 and 10. These splice forms accorded with GT-AG rule. Most these BRCA1 splice variants still kept the original reading frame. Western blot analysis indicated that some BRCA1 splice variants were expressed in ZR-75-30 cell line at the protein level. In addition, we confirmed the presence of these new transcripts of BRCA1 gene in MDA-MB-435S, K562, Hela, HLA, HIC, H9, Jurkat and human fetus samples by RT-PCR analysis. These results suggested that breast cancer associated gene BRCA1 may have unexpectedly a large number of splice variants. We hypothesized that alternative splicing of BRCA1 possibly plays a major role in the tumorigenesis of breast and/or ovarian cancer. Thus, the identification of cancer-specific splice forms will provide a novel source for the discovery of diagnostic or prognostic biomarkers and tumor antigens suitable as targets for therapeutic intervention.

  8. LPS challenge regulates gene expression and tissue localization of a Ciona intestinalis gene through an alternative polyadenylation mechanism.

    PubMed

    Vizzini, Aiti; Bonura, Angela; Parrinello, Daniela; Sanfratello, Maria Antonietta; Longo, Valeria; Colombo, Paolo

    2013-01-01

    A subtractive hybridization strategy for the identification of differentially expressed genes was performed between LPS-challenged and naive Ciona intestinalis. This strategy allowed the characterization of two transcripts (Ci8short and Ci8long) generated by the use of two Alternative Polyadenylation sites. The Ci8long transcript contains a protein domain with relevant homology to several components of the Receptor Transporting Protein (RTP) family not present in the Ci8short mRNA. By means of Real Time PCR and Northern Blot, the Ci8short and Ci8long transcripts showed a different pattern of gene expression with the Ci8short mRNA being strongly activated after LPS injection in the pharynx. In situ hybridization analysis demonstrated that the activation of the APA site also influenced the tissue localization of the Ci8short transcript. This analysis showed that the Ci8long mRNA was expressed in hemocytes meanwhile the Ci8short mRNA was highly transcribed also in vessel endothelial cells and in the epithelium of pharynx. These findings demonstrated that regulation of gene expression based on different polyadenylation sites is an ancestral powerful strategy influencing both the level of expression and tissue distribution of alternative transcripts.

  9. Alternative programs to presynchronize estrous cycles in dairy cattle before a timed artificial insemination program.

    PubMed

    Stevenson, J S

    2011-01-01

    The objective was to test potential presynchronization programs applied to cows before a timed artificial insemination (TAI) program to increase the percentage of cows ovulating in response to both GnRH injections of a TAI program and having a functional corpus luteum before the first GnRH injection of the TAI program. At calving, cows were blocked by lactation (1 vs. 2+) and assigned randomly to receive 1 of 5 presynchronization treatments. Two variants of the standard Presynch program were tested in which 2 injections of PGF2α were administered 14 d apart with either 14 d (Pre14; n=122), 12 d (Pre12; n=123), or 10 d (Pre10; n=151) intervening before a TAI program was initiated. Two other presynchronization programs consisted of administering a progesterone-releasing controlled internal drug release (CIDR) insert for 7 d plus PGF2α administration at insert removal. Insert removal occurred either 10 d (CIDR10; n=157) or 3 d (CIDR3; n=117) before a TAI program was initiated. The TAI program was a standard Cosynch program [injection of GnRH 7 d before (GnRH-1) and 72 h after (GnRH-2) PGF2α with TAI administered 72 h after PGF2α]. Cosynch served as the control (n=157), and cows were assumed to be starting this program at random stages of the estrous cycle. From a subset of cows per treatment (ranging from 49 to 51 cows each), blood samples were collected from coccygeal vessels by using evacuated tubes at d -28, -14, 0 (onset of TAI program), 7, 9, 14, and 21. Ovarian scans were conducted on d 0, 7, 9, 14, and 21 by transrectal ultrasonography. Diameters of follicles and corpus luteum were measured at each exam, and ovulation was determined on d 7 (response to GnRH-1 on d 0) and d 14 (response to GnRH-2 on d 10). Ovulatory incidence after GnRH-1 (47.1 to 67.3%) and GnRH-2 (78 to 90.2%) varied but did not differ among treatments. Before GnRH-1, progesterone concentrations were less in the CIDR3 treatment than in all other treatments. Before GnRH-2, progesterone was

  10. When One Program Fizzled and Another Flourished, I Discovered What It Takes to Succeed with Alternative Education.

    ERIC Educational Resources Information Center

    Eichinger, Lynn

    1984-01-01

    The histories of two alternative programs are compared. Considered a main factor in one program's success is a high level of administrative support; among problems causing the demise of the other are failure to involve the developing committee in the program's implementation and changing the program's emphasis and the students targeted. (MJL)

  11. Life in the Fast Track: How States Seek to Balance Incentives and Quality in Alternative Teacher Certification Programs

    ERIC Educational Resources Information Center

    Johnson, Susan Moore; Birkeland, Sarah E.; Peske, Heather G.

    2005-01-01

    The prospect of overseeing the rapid preparation of many participants in fast-track alternative certification programs presents several challenges for state education officials who seek to maintain, or even enhance, the quality of the state's teaching force. This study examined a range of fast-track alternative teacher certification programs in 11…

  12. Alternative Programs in Public Secondary Schools in Greater Cleveland: A Descriptive Study. [Summary Report; Detailed Study, Sections 1-9].

    ERIC Educational Resources Information Center

    Wertheim, Sally H.; And Others

    The puposes of the study are: (1) to provide a description of alternative programs within public high schools, (2) to compile a written history of these programs, (3) to provide information necessary to compare innovations in alternative schools within and without public school systems, and (4) to collect and disseminate information about…

  13. Description of the Prometheus Program Alternator/Thruster Integration Laboratory (ATIL)

    NASA Technical Reports Server (NTRS)

    Baez, Anastacio N.; Birchenough, Arthur G.; Lebron-Velilla, Ramon C.; Gonzalez, Marcelo C.

    2005-01-01

    The Project Prometheus Alternator Electric Thruster Integration Laboratory's (ATIL) primary two objectives are to obtain test data to influence the power conversion and electric propulsion systems design, and to assist in developing the primary power quality specifications prior to system Preliminary Design Review (PDR). ATIL is being developed in stages or configurations of increasing fidelity and complexity in order to support the various phases of the Prometheus program. ATIL provides a timely insight of the electrical interactions between a representative Permanent Magnet Generator, its associated control schemes, realistic electric system loads, and an operating electric propulsion thruster. The ATIL main elements are an electrically driven 100 kWe Alternator Test Unit (ATU), an alternator controller using parasitic loads, and a thruster Power Processing Unit (PPU) breadboard. This paper describes the ATIL components, its development approach, preliminary integration test results, and current status.

  14. Alternative splicing and nonsense-mediated decay modulate expression of important regulatory genes in Arabidopsis

    PubMed Central

    Kalyna, Maria; Simpson, Craig G.; Syed, Naeem H.; Lewandowska, Dominika; Marquez, Yamile; Kusenda, Branislav; Marshall, Jacqueline; Fuller, John; Cardle, Linda; McNicol, Jim; Dinh, Huy Q.; Barta, Andrea; Brown, John W. S.

    2012-01-01

    Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used a high-resolution AS RT–PCR panel to identify endogenous AS isoforms which increase in abundance when NMD is impaired in the Arabidopsis NMD factor mutants, upf1-5 and upf3-1. Of 270 AS genes (950 transcripts) on the panel, 102 transcripts from 97 genes (32%) were identified as NMD targets. Extrapolating from these data around 13% of intron-containing genes in the Arabidopsis genome are potentially regulated by AS/NMD. This cohort of naturally occurring NMD-sensitive AS transcripts also allowed the analysis of the signals for NMD in plants. We show the importance of AS in introns in 5′ or 3′UTRs in modulating NMD-sensitivity of mRNA transcripts. In particular, we identified upstream open reading frames overlapping the main start codon as a new trigger for NMD in plants and determined that NMD is induced if 3′-UTRs were >350 nt. Unexpectedly, although many intron retention transcripts possess NMD features, they are not sensitive to NMD. Finally, we have shown that AS/NMD regulates the abundance of transcripts of many genes important for plant development and adaptation including transcription factors, RNA processing factors and stress response genes. PMID:22127866

  15. A Recently Evolved Alternative Splice Site in the BRANCHED1a Gene Controls Potato Plant Architecture.

    PubMed

    Nicolas, Michael; Rodríguez-Buey, María Luisa; Franco-Zorrilla, José Manuel; Cubas, Pilar

    2015-07-20

    Amplification and diversification of transcriptional regulators that control development is a driving force of morphological evolution. A major source of protein diversity is alternative splicing, which leads to the generation of different isoforms from a single gene. The mechanisms and timing of intron evolution nonetheless remain unclear, and the functions of alternative splicing-generated protein isoforms are rarely studied. In Solanum tuberosum, the BRANCHED1a (BRC1a) gene encodes a TCP transcription factor that controls lateral shoot outgrowth. Here, we report the recent evolution in Solanum of an alternative splice site in BRC1a that leads to the generation of two BRC1a protein isoforms with distinct C-terminal regions, BRC1a(Long) and BRC1a(Short), encoded by unspliced and spliced mRNA, respectively. The BRC1a(Long) C-terminal region has a strong activation domain, whereas that of BRC1a(S) lacks an activation domain and is predicted to form an amphipathic helix, the H domain, which prevents protein nuclear targeting. BRC1a(Short) is thus mainly cytoplasmic, while BRC1a(Long) is mainly nuclear. BRC1a(Long) functions as a transcriptional activator, whereas BRC1a(Short) appears to have no transcriptional activity. Moreover, BRC1a(Short) can heterodimerize with BRC1a(Long) and act as a dominant-negative factor; it increases BRC1a(Long) concentration in cytoplasm and reduces its transcriptional activity. This alternative splicing mechanism is regulated by hormones and external stimuli that control branching. The evolution of a new alternative splicing site and a novel protein domain in Solanum BRC1a led to a multi-level mechanism of post-transcriptional and post-translational BRC1a regulation that effectively modulates its branch suppressing activity in response to environmental and endogenous cues. Copyright © 2015 Elsevier Ltd. All rights reserved.

  16. RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum.

    PubMed

    Zhao, Chunzhao; Waalwijk, Cees; de Wit, Pierre J G M; Tang, Dingzhong; van der Lee, Theo

    2013-01-16

    The genome of Fusarium graminearum has been sequenced and annotated previously, but correct gene annotation remains a challenge. In addition, posttranscriptional regulations, such as alternative splicing and RNA editing, are poorly understood in F. graminearum. Here we took advantage of RNA-Seq to improve gene annotations and to identify alternative splicing and RNA editing in F. graminearum. We identified and revised 655 incorrectly predicted gene models, including revisions of intron predictions, intron splice sites and prediction of novel introns. 231 genes were identified with two or more alternative splice variants, mostly due to intron retention. Interestingly, the expression ratios between different transcript isoforms appeared to be developmentally regulated. Surprisingly, no RNA editing was identified in F. graminearum. Moreover, 2459 novel transcriptionally active regions (nTARs) were identified and our analysis indicates that many of these could be missed genes. Finally, we identified the 5' UTR and/or 3' UTR sequences of 7666 genes. A number of representative novel gene models and alternatively spliced genes were validated by reverse transcription polymerase chain reaction and sequencing of the generated amplicons. We have developed novel and efficient strategies to identify alternatively spliced genes and incorrect gene models based on RNA-Seq data. Our study identified hundreds of alternatively spliced genes in F. graminearum and for the first time indicated that alternative splicing is developmentally regulated in filamentous fungi. In addition, hundreds of incorrect predicted gene models were identified and revised and thousands of nTARs were discovered in our study, which will be helpful for the future genomic and transcriptomic studies in F. graminearum.

  17. The Personal Support Worker Program Standard in Ontario: An Alternative to Self-Regulation?

    PubMed Central

    Bourgeault, Ivy Lynn

    2015-01-01

    Personal support workers (PSWs) provide hands-on assistance in a variety of long-term care and community settings. The question of whether PSWs should become regulated similar to other self-regulating health professions is a perennial concern in policy circles, especially because of the intimate nature of their work and the potential for abuse of clients and workers. This article explores a chain of policy decisions around PSWs in Ontario culminating in the creation of a common educational standard for PSW programs, titled the PSW Program Standard. We argue that these policy developments may represent an alternative pathway to self-regulation of an essential workforce. PMID:26742113

  18. The Personal Support Worker Program Standard in Ontario: An Alternative to Self-Regulation?

    PubMed

    Kelly, Christine; Bourgeault, Ivy Lynn

    2015-11-01

    Personal support workers (PSWS) provide hands-on assistance in a variety of long-term care and community settings. The question of whether psws should become regulated similar to other self-regulating health professions is a perennial concern in policy circles, especially because of the intimate nature of their work and the potential for abuse of clients and workers. This article explores a chain of policy decisions around psws in ontario culminating in the creation of a common educational standard for psw programs, titled the psw program standard. We argue that these policy developments may represent an alternative pathway to self-regulation of an essential workforce.

  19. Fusion energy program. The role of TPX and alternate concepts. Background paper

    SciTech Connect

    1995-02-01

    The background paper, responding to a request by the House Committee on Science, focuses on the following two questions for the U.S. fusion energy program. First, what is the role of the Tokamak Physics Experiment (TPX), an approximately $700 million fusion reactor currently awaiting a congressional decision to begin construction. Second, what is the role of alternatives to the tokamak concept in a broad-based fusion energy program. While the focus of the study is on the TPX and alternate concepts, it also provides a history of the overall fusion energy program. With this context, the study identifies (but does not answer) some underlying qeustions that must be addressed. The most pressing of these are: what is the potential role of the fusion energy program in meeting long-term energy needs; what level of research funding is justified by that role; and what are the most reasonable goals and directions for the program under scenarios of flat or declining budgets.

  20. Neural Progenitors Adopt Specific Identities by Directly Repressing All Alternative Progenitor Transcriptional Programs.

    PubMed

    Kutejova, Eva; Sasai, Noriaki; Shah, Ankita; Gouti, Mina; Briscoe, James

    2016-03-21

    In the vertebrate neural tube, a morphogen-induced transcriptional network produces multiple molecularly distinct progenitor domains, each generating different neuronal subtypes. Using an in vitro differentiation system, we defined gene expression signatures of distinct progenitor populations and identified direct gene-regulatory inputs corresponding to locations of specific transcription factor binding. Combined with targeted perturbations of the network, this revealed a mechanism in which a progenitor identity is installed by active repression of the entire transcriptional programs of other neural progenitor fates. In the ventral neural tube, sonic hedgehog (Shh) signaling, together with broadly expressed transcriptional activators, concurrently activates the gene expression programs of several domains. The specific outcome is selected by repressive input provided by Shh-induced transcription factors that act as the key nodes in the network, enabling progenitors to adopt a single definitive identity from several initially permitted options. Together, the data suggest design principles relevant to many developing tissues.

  1. Catalase and alternative oxidase cooperatively regulate programmed cell death induced by beta-glucan elicitor in potato suspension cultures.

    PubMed

    Mizuno, Masashi; Tada, Yasuomi; Uchii, Kimitaka; Kawakami, Sachiko; Mayama, Shigeyuki

    2005-04-01

    In potato (Solanum tuberosum L.) suspension cells, the expression of the gene encoding alternative oxidase (AOX) and H2O2 accumulation were induced by treatment with beta-glucan elicitor. The inhibition of catalase activity enhanced both AOX mRNA expression and the production of H2O2, whereas the ascorbate peroxidase inhibitor did not have any effect on these responses. Simultaneous inhibition of catalase and AOX activities in elicited cells dramatically increased H2O2 accumulation, leading to the disruption of mitochondrial membrane potential (deltapsi(m)) and programmed cell death (PCD). The results demonstrate, for the first time, that not only AOX but also catalase plays a central role in the suppression of mitochondrial deltapsi(m) breakdown and PCD induced by beta-glucan elicitor.

  2. Functions, structure, and read-through alternative splicing of feline APOBEC3 genes

    PubMed Central

    Münk, Carsten; Beck, Thomas; Zielonka, Jörg; Hotz-Wagenblatt, Agnes; Chareza, Sarah; Battenberg, Marion; Thielebein, Jens; Cichutek, Klaus; Bravo, Ignacio G; O'Brien, Stephen J; Lochelt, Martin; Yuhki, Naoya

    2008-01-01

    Background Over the past years a variety of host restriction genes have been identified in human and mammals that modulate retrovirus infectivity, replication, assembly, and/or cross-species transmission. Among these host-encoded restriction factors, the APOBEC3 (A3; apolipoprotein B mRNA-editing catalytic polypeptide 3) proteins are potent inhibitors of retroviruses and retrotransposons. While primates encode seven of these genes (A3A to A3H), rodents carry only a single A3 gene. Results Here we identified and characterized several A3 genes in the genome of domestic cat (Felis catus) by analyzing the genomic A3 locus. The cat genome presents one A3H gene and three very similar A3C genes (a-c), probably generated after two consecutive gene duplications. In addition to these four one-domain A3 proteins, a fifth A3, designated A3CH, is expressed by read-through alternative splicing. Specific feline A3 proteins selectively inactivated only defined genera of feline retroviruses: Bet-deficient feline foamy virus was mainly inactivated by feA3Ca, feA3Cb, and feA3Cc, while feA3H and feA3CH were only weakly active. The infectivity of Vif-deficient feline immunodeficiency virus and feline leukemia virus was reduced only by feA3H and feA3CH, but not by any of the feA3Cs. Within Felidae, A3C sequences show significant adaptive selection, but unexpectedly, the A3H sequences present more sites that are under purifying selection. Conclusion Our data support a complex evolutionary history of expansion, divergence, selection and individual extinction of antiviral A3 genes that parallels the early evolution of Placentalia, becoming more intricate in taxa in which the arms race between host and retroviruses is harsher. PMID:18315870

  3. Sperm is epigenetically programmed to regulate gene transcription in embryos

    PubMed Central

    Teperek, Marta; Simeone, Angela; Gaggioli, Vincent; Miyamoto, Kei; Allen, George E.; Erkek, Serap; Kwon, Taejoon; Marcotte, Edward M.; Zegerman, Philip; Bradshaw, Charles R.; Peters, Antoine H.F.M.; Gurdon, John B.; Jullien, Jerome

    2016-01-01

    For a long time, it has been assumed that the only role of sperm at fertilization is to introduce the male genome into the egg. Recently, ideas have emerged that the epigenetic state of the sperm nucleus could influence transcription in the embryo. However, conflicting reports have challenged the existence of epigenetic marks on sperm genes, and there are no functional tests supporting the role of sperm epigenetic marking on embryonic gene expression. Here, we show that sperm is epigenetically programmed to regulate embryonic gene expression. By comparing the development of sperm- and spermatid-derived frog embryos, we show that the programming of sperm for successful development relates to its ability to regulate transcription of a set of developmentally important genes. During spermatid maturation into sperm, these genes lose H3K4me2/3 and retain H3K27me3 marks. Experimental removal of these epigenetic marks at fertilization de-regulates gene expression in the resulting embryos in a paternal chromatin-dependent manner. This demonstrates that epigenetic instructions delivered by the sperm at fertilization are required for correct regulation of gene expression in the future embryos. The epigenetic mechanisms of developmental programming revealed here are likely to relate to the mechanisms involved in transgenerational transmission of acquired traits. Understanding how parental experience can influence development of the progeny has broad potential for improving human health. PMID:27034506

  4. Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani.

    PubMed

    McNeil, Bonnie A; Simon, Dawn M; Zimmerly, Steven

    2014-02-01

    Group II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5' splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5' exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns.

  5. Alternative splicing of a group II intron in a surface layer protein gene in Clostridium tetani

    PubMed Central

    McNeil, Bonnie A.; Simon, Dawn M.; Zimmerly, Steven

    2014-01-01

    Group II introns are ribozymes and retroelements found in bacteria, and are thought to have been the ancestors of nuclear pre-mRNA introns. Whereas nuclear introns undergo prolific alternative splicing in some species, group II introns are not known to carry out equivalent reactions. Here we report a group II intron in the human pathogen Clostridium tetani, which undergoes four alternative splicing reactions in vivo. Together with unspliced transcript, five mRNAs are produced, each encoding a distinct surface layer protein isoform. Correct fusion of exon reading frames requires a shifted 5′ splice site located 8 nt upstream of the canonical boundary motif. The shifted junction is accomplished by an altered IBS1-EBS1 pairing between the intron and 5′ exon. Growth of C. tetani under a variety of conditions did not result in large changes in alternative splicing levels, raising the possibility that alternative splicing is constitutive. This work demonstrates a novel type of gene organization and regulation in bacteria, and provides an additional parallel between group II and nuclear pre-mRNA introns. PMID:24214997

  6. DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees.

    PubMed

    Foret, Sylvain; Kucharski, Robert; Pellegrini, Matteo; Feng, Suhua; Jacobsen, Steven E; Robinson, Gene E; Maleszka, Ryszard

    2012-03-27

    In honey bees (Apis mellifera), the development of a larva into either a queen or worker depends on differential feeding with royal jelly and involves epigenomic modifications by DNA methyltransferases. To understand the role of DNA methylation in this process we sequenced the larval methylomes in both queens and workers. We show that the number of differentially methylated genes (DMGs) in larval head is significantly increased relative to adult brain (2,399 vs. 560) with more than 80% of DMGs up-methylated in worker larvae. Several highly conserved metabolic and signaling pathways are enriched in methylated genes, underscoring the connection between dietary intake and metabolic flux. This includes genes related to juvenile hormone and insulin, two hormones shown previously to regulate caste determination. We also tie methylation data to expressional profiling and describe a distinct role for one of the DMGs encoding anaplastic lymphoma kinase (ALK), an important regulator of metabolism. We show that alk is not only differentially methylated and alternatively spliced in Apis, but also seems to be regulated by a cis-acting, anti-sense non-protein-coding transcript. The unusually complex regulation of ALK in Apis suggests that this protein could represent a previously unknown node in a process that activates downstream signaling according to a nutritional context. The correlation between methylation and alternative splicing of alk is consistent with the recently described mechanism involving RNA polymerase II pausing. Our study offers insights into diet-controlled development in Apis.

  7. Alternative spliced variants in the pantetheinase family of genes expressed in human neutrophils.

    PubMed

    Nitto, Takeaki; Inoue, Teruo; Node, Koichi

    2008-12-15

    Pantetheinase (EC 3.5.1.92) is an enzyme that hydrolyzes pantetheine, an intermediate metabolite of coenzyme A, into pantothenic acid (vitamin B(5)) and cysteamine, a potent antioxidant. The pantetheinase gene family consists of three independent genes, pantetheinase/vanin-1/VNN1, GPI-80/VNN2 and vanin-3/VNN3 that are each composed of seven exons. We herein report that human neutrophils express transcripts encoding at least nine splice variants of VNN3 and four splice variants of GPI-80/VNN2. Analysis of the DNA sequence of the human VNN3 gene demonstrated that the VNN3 locus in the human genome as well as the sequence of cDNA clones obtained in this study does not encode the complete VNN3 protein, as previously reported due to a frame shift caused by lack of one nucleotide. Moreover, the VNN3 locus indeed encodes smaller peptides compared to the proteins encoded by the mouse orthologous gene, vanin-3. The anti-GPI-80 monoclonal antibody 3H9 recognized amino acids 120-179 of the GPI-80/VNN2 protein as shown by the results of immunoblotting with recombinant GPI-80/VNN2 variant proteins. Immunoblotting with human neutrophil lysate suggests that the GPI-80/VNN2 variants exist in human neutrophils. The existence of splice variants in the pantetheinase gene family suggests the possibility of alternative roles in addition to canonical enzymatic activity in human neutrophils.

  8. Alternative life histories shape brain gene expression profiles in males of the same population.

    PubMed

    Aubin-Horth, Nadia; Landry, Christian R; Letcher, Benjamin H; Hofmann, Hans A

    2005-08-22

    Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker.

  9. Myocardial alternative RNA splicing and gene expression profiling in early stage hypoplastic left heart syndrome.

    PubMed

    Ricci, Marco; Xu, Yanji; Hammond, Harriet L; Willoughby, David A; Nathanson, Lubov; Rodriguez, Maria M; Vatta, Matteo; Lipshultz, Steven E; Lincoln, Joy

    2012-01-01

    Hypoplastic Left Heart Syndrome (HLHS) is a congenital defect characterized by underdevelopment of the left ventricle and pathological compensation of the right ventricle. If untreated, HLHS is invariably lethal due to the extensive increase in right ventricular workload and eventual failure. Despite the clinical significance, little is known about the molecular pathobiological state of HLHS. Splicing of mRNA transcripts is an important regulatory mechanism of gene expression. Tissue specific alterations of this process have been associated with several cardiac diseases, however, transcriptional signature profiles related to HLHS are unknown. In this study, we performed genome-wide exon array analysis to determine differentially expressed genes and alternatively spliced transcripts in the right ventricle (RV) of six neonates with HLHS, compared to the RV and left ventricle (LV) from non-diseased control subjects. In HLHS, over 180 genes were differentially expressed and 1800 were differentially spliced, leading to changes in a variety of biological processes involving cell metabolism, cytoskeleton, and cell adherence. Additional hierarchical clustering analysis revealed that differential gene expression and mRNA splicing patterns identified in HLHS are unique compared to non-diseased tissue. Our findings suggest that gene expression and mRNA splicing are broadly dysregulated in the RV myocardium of HLHS neonates. In addition, our analysis identified transcriptome profiles representative of molecular biomarkers of HLHS that could be used in the future for diagnostic and prognostic stratification to improve patient outcome.

  10. Alternative life histories shape brain gene expression profiles in males of the same population

    USGS Publications Warehouse

    Aubin-Horth, N.; Landry, C.R.; Letcher, B.H.; Hofmann, H.A.

    2005-01-01

    Atlantic salmon (Salmo salar) undergo spectacular marine migrations before homing to spawn in natal rivers. However, males that grow fastest early in life can adopt an alternative 'sneaker' tactic by maturing earlier at greatly reduced size without leaving freshwater. While the ultimate evolutionary causes have been well studied, virtually nothing is known about the molecular bases of this developmental plasticity. We investigate the nature and extent of coordinated molecular changes that accompany such a fundamental transformation by comparing the brain transcription profiles of wild mature sneaker males to age-matched immature males (future large anadromous males) and immature females. Of the ca. 3000 genes surveyed, 15% are differentially expressed in the brains of the two male types. These genes are involved in a wide range of processes, including growth, reproduction and neural plasticity. Interestingly, despite the potential for wide variation in gene expression profiles among individuals sampled in nature, consistent patterns of gene expression were found for individuals of the same reproductive tactic. Notably, gene expression patterns in immature males were different both from immature females and sneakers, indicating that delayed maturation and sea migration by immature males, the 'default' life cycle, may actually result from an active inhibition of development into a sneaker. ?? 2005 The Royal Society.

  11. Regulation of the beta-hydroxyacyl ACP dehydratase gene of Picea mariana by alternative splicing.

    PubMed

    Tai, Helen H; Williams, Martin; Iyengar, Abhinav; Yeates, Jessica; Beardmore, Tannis

    2007-01-01

    The gene for beta-hydroxyacyl ACP dehydratase, a de novo fatty acid biosynthetic enzyme, was cloned from Picea mariana (black spruce) and consists of five exons and four introns. The first intron of the beta-hydroxyacyl ACP dehydratase mRNA is alternatively spliced. Retention of intron 1 in splice variants results in truncation of the beta-hydroxyacyl ACP dehydratase ORF at a premature termination codon. In addition, splicing of intron 1 was found to be associated with cold temperature. mRNAs retaining intron 1 increase with seed imbibition at 22 degrees C but not 4 degrees C, whereas, splicing of intron 1 increases in winter weeks with temperatures below freezing. These results provide evidence that alternative splicing may also contribute to regulation of lipid biosynthesis in Picea mariana.

  12. Family nutrition program assistants' perception of farmers' markets, alternative agricultural practices, and diet quality.

    PubMed

    Misyak, Sarah; Ledlie Johnson, Meredith; McFerren, Mary; Serrano, Elena

    2014-01-01

    To explore Family Nutrition Program assistants' perception of farmers' markets and alternative agricultural practices for themselves and their clients. Cross-section design, survey of Virginia Expanded Food and Nutrition Education Program (NEP) and Supplemental Nutrition Assistance Program-Education Family Nutrition Program assistants (n = 52) working with limited-resource populations. Twenty-one percent to 55% of FNP assistants valued alternative agricultural practices, and only 5% to 8% of FNP assistants perceived that their clients did so. Benefits to shopping at farmers' markets included supporting local economies, and food price, quality, and safety. Barriers included lack of transportation, location/convenience, hours, and food prices. Assistants rated the benefits to shopping at farmers' markets similarly for themselves and their clients, but rated many of the barriers to shopping at farmers' markets as significantly lower (P < .05) for themselves than for their clients. Future assistant trainings should address the connection between agriculture and health, and how to overcome barriers to shopping at farmers' markets for their clients. Copyright © 2014 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  13. Implementation of alternative bio-based fuels in aviation: The Clean Airports Program

    SciTech Connect

    Shauck, M.E.; Zanin, M.G.

    1997-12-31

    The Renewable Aviation Fuels Development Center at Baylor University in Waco, Texas, was designated, in March 1996, by the US Department of Energy (US DOE) as the national coordinator of the Clean Airports Program. This program, a spin-off of the Clean Cities Program, was initiated to increase the use of alternative fuels in aviation. There are two major fuels used in aviation today, the current piston engine aviation gasoline, and the current turbine engine fuel. The environmental impact of each of these fuels is significant. Aviation Gasoline (100LL), currently used in the General Aviation piston engine fleet, contributes 100% of the emissions containing lead in the USA today. In the case of the turbine engine fuel (Jet fuel), there are two major environmental impacts to be considered: the local, in the vicinity of the airports, and the global impact on climate change. The Clean Airports Program was established to promote the use of clean burning fuels in order to achieve and maintain clean air at and in the vicinities of airports through the use of alternative fuel-powered air and ground transportation vehicles.

  14. Study of human dopamine sulfotransferases based on gene expression programming.

    PubMed

    Si, Hongzong; Zhao, Jiangang; Cui, Lianhua; Lian, Ning; Feng, Hanlin; Duan, Yun-Bo; Hu, Zhide

    2011-09-01

    A quantitative model is developed to predict the Km of 47 human dopamine sulfotransferases by gene expression programming. Each kind of compound is represented by several calculated structural descriptors of moment of inertia A, average electrophilic reactivity index for a C atom, relative number of triple bonds, RNCG relative negative charge, HA-dependent HDSA-1, and HBCA H-bonding charged surface area. Eight fitness functions of the gene expression programming method are used to find the best nonlinear model. The best quantitative model with squared standard error and square of correlation coefficient are 0.096 and 0.91 for training data set, and 0.102 and 0.88 for test set, respectively. It is shown that the gene expression programming-predicted results with fitness function are in good agreement with experimental ones. © 2011 John Wiley & Sons A/S.

  15. Structure of the human laminin {gamma}2 chain gene (LAMC2): Alternative splicing with different tissue distribution of two transcripts

    SciTech Connect

    Airenne, T.; Haakana, H.; Kallunki, T.

    1996-02-15

    This article discusses the exon-intron structure and tissue distribution of the laminin {gamma}2 chain (LAMC2) gene, which is mutated in some cases of junctional epidermolysis bullosa. The article also discusses the transcription and splicing of this gene, which result in alternative uses of the last two exons of the gene. The different tissue distributions of the transcripts indicate different functions for the gene in vivo. 36 refs., 8 figs., 3 tabs.

  16. Functional characterization of two alternatively spliced transcripts of tomato ABSCISIC ACID INSENSITIVE3 (ABI3) gene.

    PubMed

    Gao, Yongfeng; Liu, Jikai; Zhang, Zhiguo; Sun, Xiaochun; Zhang, Ni; Fan, Jing; Niu, Xiangli; Xiao, Fangming; Liu, Yongsheng

    2013-05-01

    Alternative splicing can produce transcripts that encode proteins with altered functions. The transcripts of the ABSCISIC ACID INSENSITIVE3 (ABI3)/VIVIPAROUS1 (VP1) gene, which is an important component in abscisic acid (ABA) signaling, are subjected to alternative splicing in both monocotyledons and dicotyledons. We identified two alternatively spliced tomato (Solanum lycopersicum) SlABI3 transcripts, SlABI3-F and SlABI3-T, which encode the nucleus-localized full-length and truncated proteins, respectively. The tissue-specific accumulation of SlABI3-F and SlABI3-T was determined, particularly in seeds at different developmental stages and in response to phytohormonal and abiotic stress. Ectopic over-expression of SlABI3-F and SlABI3-T resulted in the induction of seed-specific genes SlSOM, SlEM1 and SlEM6 in vegetative tissues. However, over-expression of SlABI3-F, but not SlABI3-T, activated expression of the downstream gene SlABI5 and conferred hypersensitivity to exogenous ABA during seed germination and primary root growth. In addition, the SlABI3-F protein interacted with SlABI5 much stronger than SlABI3-T did in the yeast two-hybrid assay. These results suggest that SlABI3-F and SlABI3-T have similar and distinct functionality in the ABA signaling, dependent on which tissue/organ they accumulate in.

  17. Alu-Derived Alternative Splicing Events Specific to Macaca Lineages in CTSF Gene

    PubMed Central

    Lee, Ja-Rang; Park, Sang-Je; Kim, Young-Hyun; Choe, Se-Hee; Cho, Hyeon-Mu; Lee, Sang-Rae; Kim, Sun-Uk; Kim, Ji-Su; Sim, Bo-Woong; Song, Bong-Seok; Jeong, Kang-Jin; Lee, Youngjeon; Jin, Yeung Bae; Kang, Philyong; Huh, Jae-Won; Chang, Kyu-Tae

    2017-01-01

    Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element–AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crab-eating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues. Results demonstrated that AluYRa1 was only integrated into the genome of Macaca species and this lineage-specific integration led to exonization events by producing a conserved 3′ splice site. Six transcript variants (V1–V6) were generated by alternative splicing (AS) events, including intron retention and alternative 5′ splice sites in the 5′ and 3′ flanking regions of CTSF_AluYRa1. Among them, V3–V5 transcripts were ubiquitously expressed in all tissues of rhesus monkey and crab-eating monkey, whereas AluYRa1-exonized V1 was dominantly expressed in the testis of the crab-eating monkey, and V2 was only expressed in the testis of the two monkeys. These five transcript variants also had different amino acid sequences in the C-terminal region of CTSF, as compared to reference sequences. Thus, species-specific Alu-derived exonization by lineage-specific integration of Alu elements and AS events seems to have played an important role during primate evolution by producing transcript variants and gene diversification. PMID:28196413

  18. Alternative haplotypes of antigen processing genes in zebrafish diverged early in vertebrate evolution

    PubMed Central

    McConnell, Sean C.; Hernandez, Kyle M.; Wcisel, Dustin J.; Kettleborough, Ross N.; Stemple, Derek L.; Andrade, Jorge; de Jong, Jill L. O.

    2016-01-01

    Antigen processing and presentation genes found within the MHC are among the most highly polymorphic genes of vertebrate genomes, providing populations with diverse immune responses to a wide array of pathogens. Here, we describe transcriptome, exome, and whole-genome sequencing of clonal zebrafish, uncovering the most extensive diversity within the antigen processing and presentation genes of any species yet examined. Our CG2 clonal zebrafish assembly provides genomic context within a remarkably divergent haplotype of the core MHC region on chromosome 19 for six expressed genes not found in the zebrafish reference genome: mhc1uga, proteasome-β 9b (psmb9b), psmb8f, and previously unknown genes psmb13b, tap2d, and tap2e. We identify ancient lineages for Psmb13 within a proteasome branch previously thought to be monomorphic and provide evidence of substantial lineage diversity within each of three major trifurcations of catalytic-type proteasome subunits in vertebrates: Psmb5/Psmb8/Psmb11, Psmb6/Psmb9/Psmb12, and Psmb7/Psmb10/Psmb13. Strikingly, nearby tap2 and MHC class I genes also retain ancient sequence lineages, indicating that alternative lineages may have been preserved throughout the entire MHC pathway since early diversification of the adaptive immune system ∼500 Mya. Furthermore, polymorphisms within the three MHC pathway steps (antigen cleavage, transport, and presentation) are each predicted to alter peptide specificity. Lastly, comparative analysis shows that antigen processing gene diversity is far more extensive than previously realized (with ancient coelacanth psmb8 lineages, shark psmb13, and tap2t and psmb10 outside the teleost MHC), implying distinct immune functions and conserved roles in shaping MHC pathway evolution throughout vertebrates. PMID:27493218

  19. 'Living stones' reveal alternative petal identity programs within the core eudicots.

    PubMed

    Brockington, Samuel F; Rudall, Paula J; Frohlich, Michael W; Oppenheimer, David G; Soltis, Pamela S; Soltis, Douglas E

    2012-01-01

    Petals, defined as the showy laminar floral organs in the second floral whorl, have been shown to be under similar genetic control in distantly related core eudicot model organisms. On the basis of these findings, it is commonly assumed that the petal identity program regulated by B-class MADS-box gene homologs is invariant across the core eudicot clade. However, the core eudicots, which comprise >70% of angiosperm species, exhibit numerous instances of petal and sepal loss, transference of petal function between floral whorls, and recurrent petal evolution. In the face of these complex patterns of perianth evolution, the concept of a core eudicot petal identity program has not been tested. We therefore examined the petal identity program in the Caryophyllales, a core eudicot clade in which perianth differentiation into sepals and petals has evolved multiple times. Specifically, we analyzed the expression patterns of B- and C-class MADS-box homologs for evidence of a conserved petal identity program between sepal-derived and stamen-derived petaloid organs in the 'living stone' family Aizoaceae. We found that neither sepal-derived nor stamen-derived petaloid organs exhibit gene expression patterns consistent with the core eudicot petal identity program. B-class gene homologs are not expressed during the development of sepal-derived petals and are not implicated in petal identity in stamen-derived petals, as their transient expression coincides with early expression of the C-class homolog. We therefore provide evidence for petal development that is independent of B-class genes and suggest that different genetic control of petal identity has evolved within this lineage of core eudicots. These findings call for a more comprehensive understanding of perianth variation and its genetic causes within the core eudicots--an endeavor that will have broader implications for the interpretation of perianth evolution across angiosperms.

  20. New gene models and alternative splicing in the maize pathogen Colletotrichum graminicola revealed by RNA-Seq analysis.

    PubMed

    Schliebner, Ivo; Becher, Rayko; Hempel, Marcus; Deising, Holger B; Horbach, Ralf

    2014-10-02

    An annotated genomic sequence of the corn anthracnose fungus Colletotrichum graminicola has been published previously, but correct identification of gene models by means of automated gene annotation remains a challenge. RNA-Seq offers the potential for substantially improved gene annotations and for the identification of posttranscriptional RNA modifications, such as alternative splicing and RNA editing. Based on the nucleotide sequence information of transcripts, we identified 819 novel transcriptionally active regions (nTARs) and revised 906 incorrectly predicted gene models, including revisions of exon-intron structure, gene orientation and sequencing errors. Among the nTARs, 146 share significant similarity with proteins that have been identified in other species suggesting that they are hitherto unidentified genes in C. graminicola. Moreover, 5'- and 3'-UTR sequences of 4378 genes have been retrieved and alternatively spliced variants of 69 genes have been identified. Comparative analysis of RNA-Seq data and the genome sequence did not provide evidence for RNA editing in C. graminicola. We successfully employed deep sequencing RNA-Seq data in combination with an elaborate bioinformatics strategy in order to identify novel genes, incorrect gene models and mechanisms of transcript processing in the corn anthracnose fungus C. graminicola. Sequence data of the revised genome annotation including several hundreds of novel transcripts, improved gene models and candidate genes for alternative splicing have been made accessible in a comprehensive database. Our results significantly contribute to both routine laboratory experiments and large-scale genomics or transcriptomic studies in C. graminicola.

  1. Alternatively spliced adenomatous polyposis coli (APC) gene transcripts that delete exons mutated in attenuated APC.

    PubMed

    Samowitz, W S; Thliveris, A; Spirio, L N; White, R

    1995-09-01

    Reverse transcription-PCR combined with either (a) restriction enzyme digestion and repeat PCR or (b) ligase chain reaction has identified two new alternatively spliced transcripts of the adenomatous polyposis coli (APC) gene. In one of these transcripts exons 1-4 and the first 16 bases of exon 5 are deleted; in the other exons 2-4 and the first 16 bases of 5 are deleted. Both transcripts use an intraexonic splice acceptor in exon 5. These transcripts delete exons mutated in attenuated APC (3 and 4) and could account for the reduction in severity of this variant.

  2. Alternatives for management of wastes generated by the formerly utilized sites remedial action program and supplement

    SciTech Connect

    Gilbert, T.L.; Peterson, J.M.; Vocke, R.W.; Alexander, J.K.

    1983-03-01

    Alternatives for disposal or stabilization of the wastes generated by the US Department of Energy's Formerly Utilized Sites Remedial Action Program (FUSRAP) are identified and compared, with emphasis on the long-term aspects. These wastes consist of soil material and rubble containing trace amounts of radionuclides. A detailed pathway analysis for the dose to the maximally exposed individual is carried out using an adaptation of the natural analogue method. Comparisons of the different alternatives, based on the results of the pathway analysis and qualitative cost considerations, indicate that, if the hazard is such that the wastes must be removed and disposed of rather than stabilized in place, disposal by immediate dispersal is preferable to containment, and containment followed by slow planned dispersal is preferable to containment without dispersal. The Supplement presents refinements of work that was reported at the 1982 International Decommissioning Symposium. The new material consists of revisions of the estimates of the predicted potential dose to the maximally exposed individual and a more detailed comparative assessment of the radiological impacts of alternatives for management of wastes generated by the US Department of Energy's Formerly Utilized Sites Remedial Action Program (FUSRAP).

  3. A framework program for the teaching of alternative methods (replacement, reduction, refinement) to animal experimentation.

    PubMed

    Daneshian, Mardas; Akbarsha, Mohammad A; Blaauboer, Bas; Caloni, Francesca; Cosson, Pierre; Curren, Rodger; Goldberg, Alan; Gruber, Franz; Ohl, Frauke; Pfaller, Walter; van der Valk, Jan; Vinardell, Pilar; Zurlo, Joanne; Hartung, Thomas; Leist, Marcel

    2011-01-01

    Development of improved communication and education strategies is important to make alternatives to the use of animals, and the broad range of applications of the 3Rs concept better known and understood by different audiences. For this purpose, the Center for Alternatives to Animal Testing in Europe (CAAT-Europe) together with the Transatlantic Think Tank for Toxicology (t(4)) hosted a three-day workshop on "Teaching Alternative Methods to Animal Experimentation". A compilation of the recommendations by a group of international specialists in the field is summarized in this report. Initially, the workshop participants identified the different audience groups to be addressed and also the communication media that may be used. The main outcome of the workshop was a framework for a comprehensive educational program. The modular structure of the teaching program presented here allows adaptation to different audiences with their specific needs; different time schedules can be easily accommodated on this basis. The topics cover the 3Rs principle, basic research, toxicological applications, method development and validation, regulatory aspects, case studies and ethical aspects of 3Rs approaches. This expert consortium agreed to generating teaching materials covering all modules and providing them in an open access online repository.

  4. Identification of new alternative splice events in the TCIRG1 gene in different human tissues

    SciTech Connect

    Smirnova, Anna S.; Morgun, Andrey . E-mail: anemorgun@hotmail.com; Shulzhenko, Natalia; Silva, Ismael D.C.G.; Gerbase-DeLima, Maria

    2005-05-13

    Two transcript variants (TV) of the T cell immune regulator gene 1 (TCIRG1) have already been characterized. TV1 encodes a subunit of the osteoclast vacuolar proton pump and TV2 encodes a T cell inhibitory receptor. Based on the search in dbEST, we validated by RT-PCR six new alternative splice events in TCIRG1 in most of the 28 human tissues studied. In addition, we observed that transcripts using the TV1 transcription start site and two splice forms previously described in a patient with infantile malignant osteopetrosis are also expressed in various tissues of healthy individuals. Studies of these nine splice forms in cytoplasmic RNA of peripheral blood mononuclear cells showed that at least six of them could be efficiently exported from the nucleus. Since various products with nearly ubiquitous tissue distribution are generated from TCIRG1, this gene may be involved in other processes besides immune response and bone resorption.

  5. Transfer of toxin genes to alternate bacterial hosts for mosquito control.

    PubMed

    Orduz, S; Restrepo, N; Patiño, M M; Rojas, W

    1995-01-01

    Mosquitoes are vector of serious human and animal diseases, such as malaria, dengue, yellow fever, among others. The use of biological control agents has provide an environmentally safe and highly specific alternative to the use of chemical insecticides in the control of vector borne diseases. Bacillus thuringiensis and B. sphaericus produce toxic proteins to mosquito larvae. Great progress has been made on the biochemical and molecular characterization of such proteins and the genes encoding them. Nevertheless, the low residuality of these biological insecticides is one of the major drawbacks. This article present some interesting aspects of the mosquito larvae feeding habits and review the attempts that have been made to genetically engineer microorganisms that while are used by mosquito larvae as a food source should express the Bacillus toxin genes in order to improve the residuality and stability in the mosquito breeding ponds.

  6. 75 FR 34017 - Protection of Stratospheric Ozone: Notice 25 for Significant New Alternatives Policy Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-16

    ...This Determination of Acceptability expands the list of acceptable substitutes for ozone-depleting substances under the U.S. Environmental Protection Agency's Significant New Alternatives Policy program. The substitutes are for use in the following sectors: Refrigeration and air-conditioning, foam blowing, aerosols, and sterilants. The majority of the acceptability decisions find substitutes acceptable as alternatives to the class II ozone depleting substances hydrochlorofluorocarbon (HCFC)-22, HCFC-142b and blends containing one or both of these substances. EPA is also finding one of the alternatives, HFO- 1234ze, acceptable as a substitute for CFC-113 in the heat transfer end use and as a substitute for CFC-11 in the aerosol propellant end use. The listing of additional refrigerant alternatives as acceptable will provide users in the refrigeration and air-conditioning sector with more options for replacing HCFC-22 and HCFC-142b, which, pursuant to EPA's phaseout regulations, may generally be used only as a refrigerant to service equipment manufactured before January 1, 2010.

  7. Evaluation of the Courtlink Auto Crime Prevention Program (CACPP) for Senior Elementary and Alternative School Students in British Columbia.

    ERIC Educational Resources Information Center

    Curtis, Charles K.; Meehan, George

    This study evaluated the Courtlink Auto Crime Prevention Program (CACPP), a 13-hour curriculum for senior elementary school and secondary school alternative program at-risk students in British Columbia, Canada. The program provides students with information about automobile crime and its costs, consequences, and prevention. It promotes positive…

  8. Continued Educational Services to Expelled Students in Texas: A Comparison of Voluntary and Mandated Juvenile Justice Alternative Education Programs.

    ERIC Educational Resources Information Center

    Czaja, Marion D.

    In 1995, the Texas Legislature mandated the formation of Juvenile Justice Alternative Education Programs (JJAEPs) to serve adjudicated youth in counties with a population of 125,000 or more. Some less-populated counties formed their own JJAEPs. This paper presents a comparison of these voluntary programs to the mandated programs. Of the 22…

  9. An Experimental Study of the Effects of an Alternative Work Experience Program in the Middle School. Final Report.

    ERIC Educational Resources Information Center

    Newton, Mark

    Objectives of the study were (1) to develop and implement an alternative work experience program for a middle school; (2) to test the effect of the program on attitudes toward school, career maturity, and vocational interests of the students; and (3) to provide information and procedures for a model work experience program. Western Kentucky…

  10. 46 CFR 176.620 - Description of the Alternative Hull Examination (AHE) Program for certain passenger vessels.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Description of the Alternative Hull Examination (AHE... completed using only divers, this program has four steps: the application process, the preliminary... program, or if a remotely operated vehicle (ROV) is used during the program, the preliminary exam step may...

  11. Molecular structure of the human argininosuccinate synthetase gene: Occurrence of alternative mRNA splicing

    SciTech Connect

    Freytag, S.O.; Beaudet, A.L.; Bock, H.G.O.; O'Brien, W.E.

    1984-10-01

    The human genome contains one expressed argininosuccinate synthetase gene and ca. 14 pseudogenes that are dispersed to at least 11 human chromosomes. Eleven clones isolated from a human genomic DNA library were characterized extensively by restriction mapping, Southern blotting, and nucleotide sequencing. These 11 clones represent the entire expressed argininosuccinate synthetase gene that spans 63 kilobases and contains at least 13 exons. The expressed gene codes for two mRNAs that differ in their 5' untranslated sequences and arise by alternative splicing involving the inclusion or deletion of an entire exon. In normal human liver and cultured fibroblasts, the predominant mature argininosuccinate synthetase mRNA lacks sequences encoded by exon 2 in the expressed gene. In contrast, the predominant argininosuccinate synthetase mRNA in baboon liver contains exon 2 sequences. A transformed canavanine-resistant human cell line in which argininosuccinate synthetase activity is 180-fold higher than that in wild-type cells contains abundant amounts of both forms of the argininosuccinate synthetase mRNA. The mRNA lacking exon 2 sequences is the more abundant mRNA species in the canavanine-resistant cells. These observations show that splicing of the argininosuccinate synthetase mRNA is species specific in primates and varies among different human cell types.

  12. Alternative Polyadenylation of Tumor Suppressor Genes in Small Intestinal Neuroendocrine Tumors

    PubMed Central

    Rehfeld, Anders; Plass, Mireya; Døssing, Kristina; Knigge, Ulrich; Kjær, Andreas; Krogh, Anders; Friis-Hansen, Lennart

    2014-01-01

    The tumorigenesis of small intestinal neuroendocrine tumors (SI-NETs) is poorly understood. Recent studies have associated alternative polyadenylation (APA) with proliferation, cell transformation, and cancer. Polyadenylation is the process in which the pre-messenger RNA is cleaved at a polyA site and a polyA tail is added. Genes with two or more polyA sites can undergo APA. This produces two or more distinct mRNA isoforms with different 3′ untranslated regions. Additionally, APA can also produce mRNAs containing different 3′-terminal coding regions. Therefore, APA alters both the repertoire and the expression level of proteins. Here, we used high-throughput sequencing data to map polyA sites and characterize polyadenylation genome-wide in three SI-NETs and a reference sample. In the tumors, 16 genes showed significant changes of APA pattern, which lead to either the 3′ truncation of mRNA coding regions or 3′ untranslated regions. Among these, 11 genes had been previously associated with cancer, with 4 genes being known tumor suppressors: DCC, PDZD2, MAGI1, and DACT2. We validated the APA in three out of three cases with quantitative real-time-PCR. Our findings suggest that changes of APA pattern in these 16 genes could be involved in the tumorigenesis of SI-NETs. Furthermore, they also point to APA as a new target for both diagnostic and treatment of SI-NETs. The identified genes with APA specific to the SI-NETs could be further tested as diagnostic markers and drug targets for disease prevention and treatment. PMID:24782827

  13. A functional alternative splicing mutation in AIRE gene causes autoimmune polyendocrine syndrome type 1.

    PubMed

    Zhang, Junyu; Liu, Hongbin; Liu, Zhiyuan; Liao, Yong; Guo, Luo; Wang, Honglian; He, Lin; Zhang, Xiaodong; Xing, Qinghe

    2013-01-01

    Autoimmune polyendocrine syndrome type 1 (APS-1) is a rare autosomal recessive disease defined by the presence of two of the three conditions: mucocutaneous candidiasis, hypoparathyroidism, and Addison's disease. Loss-of-function mutations of the autoimmune regulator (AIRE) gene have been linked to APS-1. Here we report mutational analysis and functional characterization of an AIRE mutation in a consanguineous Chinese family with APS-1. All exons of the AIRE gene and adjacent exon-intron sequences were amplified by PCR and subsequently sequenced. We identified a homozygous missense AIRE mutation c.463G>A (p.Gly155Ser) in two siblings with different clinical features of APS-1. In silico splice-site prediction and minigene analysis were carried out to study the potential pathological consequence. Minigene splicing analysis and subsequent cDNA sequencing revealed that the AIRE mutation potentially compromised the recognition of the splice donor of intron 3, causing alternative pre-mRNA splicing by intron 3 retention. Furthermore, the aberrant AIRE transcript was identified in a heterozygous carrier of the c.463G>A mutation. The aberrant intron 3-retaining transcript generated a truncated protein (p.G155fsX203) containing the first 154 AIRE amino acids and followed by 48 aberrant amino acids. Therefore, our study represents the first functional characterization of the alternatively spliced AIRE mutation that may explain the pathogenetic role in APS-1.

  14. Alternative splicing, a new target to block cellular gene expression by poliovirus 2A protease

    SciTech Connect

    Alvarez, Enrique; Castello, Alfredo; Carrasco, Luis; Izquierdo, Jose M.

    2011-10-14

    Highlights: {yields} Novel role for poliovirus 2A protease as splicing modulator. {yields} Poliovirus 2A protease inhibits the alternative splicing of pre-mRNAs. {yields} Poliovirus 2A protease blocks the second catalytic step of splicing. -- Abstract: Viruses have developed multiple strategies to interfere with the gene expression of host cells at different stages to ensure their own survival. Here we report a new role for poliovirus 2A{sup pro} modulating the alternative splicing of pre-mRNAs. Expression of 2A{sup pro} potently inhibits splicing of reporter genes in HeLa cells. Low amounts of 2A{sup pro} abrogate Fas exon 6 skipping, whereas higher levels of protease fully abolish Fas and FGFR2 splicing. In vitro splicing of MINX mRNA using nuclear extracts is also strongly inhibited by 2A{sup pro}, leading to accumulation of the first exon and the lariat product containing the unspliced second exon. These findings reveal that the mechanism of action of 2A{sup pro} on splicing is to selectively block the second catalytic step.

  15. Can Thrifty Gene(s) or Predictive Fetal Programming for Thriftiness Lead to Obesity?

    PubMed

    Baig, Ulfat; Belsare, Prajakta; Watve, Milind; Jog, Maithili

    2011-01-01

    Obesity and related disorders are thought to have their roots in metabolic "thriftiness" that evolved to combat periodic starvation. The association of low birth weight with obesity in later life caused a shift in the concept from thrifty gene to thrifty phenotype or anticipatory fetal programming. The assumption of thriftiness is implicit in obesity research. We examine here, with the help of a mathematical model, the conditions for evolution of thrifty genes or fetal programming for thriftiness. The model suggests that a thrifty gene cannot exist in a stable polymorphic state in a population. The conditions for evolution of thrifty fetal programming are restricted if the correlation between intrauterine and lifetime conditions is poor. Such a correlation is not observed in natural courses of famine. If there is fetal programming for thriftiness, it could have evolved in anticipation of social factors affecting nutrition that can result in a positive correlation.

  16. Functional analysis of alternative splicing of the FLOWERING LOCUS T orthologous gene in Chrysanthemum morifolium

    PubMed Central

    Mao, Yachao; Sun, Jing; Cao, Peipei; Zhang, Rong; Fu, Qike; Chen, Sumei; Chen, Fadi; Jiang, Jiafu

    2016-01-01

    As the junction of floral development pathways, the FLOWERING LOCUS T (FT) protein called ‘florigen’ plays an important role in the process of plant flowering through signal integration. We isolated four transcripts encoding different isoforms of a FT orthologous gene CmFTL1, from Chrysanthemum morifolium cultivar ‘Jimba’. Sequence alignments suggested that the four transcripts are related to the intron 1. Expression analysis showed that four alternative splicing (AS) forms of CmFTL1 varied depending on the developmental stage of the flower. The functional complement experiment using an Arabidopsis mutant ft-10 revealed that the archetypal and AS forms of CmFTL1 had the function of complementing late flower phenotype in different levels. In addition, transgenic confirmation at transcript level showed CmFTL1 and CmFTL1ast coexist in the same tissue type at the same developmental stage, indicating a post-transcriptional modification of CmFTL1 in Arabidopsis. Moreover, ectopic expression of different AS forms in chrysanthemum resulted in the development of multiple altered phenotypes, varying degrees of early flowering. We found that an alternative splicing form (CmFTL1-astE134) without the exon 2 lacked the ability causing the earlier flower phenotype. The evidence in this study indicates that complex alternative processing of CmFTL1 transcripts in C. morifolium may be associated with flowering regulation and hold some potential for biotechnical engineering to create early-flowering phenotypes in ornamental cultivars. PMID:27917290

  17. Alternative Splicing in Adhesion- and Motility-Related Genes in Breast Cancer.

    PubMed

    Aversa, Rosanna; Sorrentino, Anna; Esposito, Roberta; Ambrosio, Maria Rosaria; Amato, Angela; Zambelli, Alberto; Ciccodicola, Alfredo; D'Apice, Luciana; Costa, Valerio

    2016-01-16

    Breast cancer is the most common tumor and the second leading cause of cancer death among woman, mainly caused by the metastatic spread. Tumor invasiveness is due to an altered expression of adhesion molecules. Among them, semaphorins are of peculiar interest. Cancer cells can manipulate alternative splicing patterns to modulate the expression of adhesion- and motility-related molecules, also at the isoform level. In this study, combining RNA-Sequencing on MCF-7 to targeted experimental validations-in human breast cell lines and breast tumor biopsies-we identified 12 new alternative splicing transcripts in genes encoding adhesion- and motility-related molecules, including semaphorins, their receptors and co-receptors. Among them, a new SEMA3F transcript is expressed in all breast cell lines and breast cancer biopsies, and is translated into a new semaphorin 3F isoform. In silico analysis predicted that most of the new putative proteins lack functional domains, potentially missing some functions and acquiring new ones. Our findings better describe the extent of alternative splicing in breast cancer and highlight the need to further investigate adhesion- and motility-related molecules to gain insights into breast cancer progression.

  18. Alternative Education: A Comparative Case Study of the Behavior Modification Programs of Two Upstate South Carolina Alternative Schools for Youth Who Exhibit Behavior That Is Disruptive

    ERIC Educational Resources Information Center

    Scipio, Timothy Lamont

    2013-01-01

    This study examined behavior modification programs in schools designed to focus on discipline and that aim to reform disruptive behavior in students, usually over a limited period of time. This was a comparative case study of two type II alternative schools in the Upstate of South Carolina. The findings contributed to the research base regarding…

  19. Alternative Splicing of Rice WRKY62 and WRKY76 Transcription Factor Genes in Pathogen Defense.

    PubMed

    Liu, Jiqin; Chen, Xujun; Liang, Xiaoxing; Zhou, Xiangui; Yang, Fang; Liu, Jia; He, Sheng Yang; Guo, Zejian

    2016-06-01

    The WRKY family of transcription factors (TFs) functions as transcriptional activators or repressors in various signaling pathways. In this study, we discovered that OsWRKY62 and OsWRKY76, two genes of the WRKY IIa subfamily, undergo constitutive and inducible alternative splicing. The full-length OsWRKY62.1 and OsWRKY76.1 proteins formed homocomplexes and heterocomplexes, and the heterocomplex dominates in the nuclei when analyzed in Nicotiana benthamiana leaves. Transgenic overexpression of OsWRKY62.1 and OsWRKY76.1 in rice (Oryza sativa) enhanced plant susceptibility to the blast fungus Magnaporthe oryzae and the leaf blight bacterium Xanthomonas oryzae pv oryzae, whereas RNA interference and loss-of-function knockout plants exhibited elevated resistance. The dsOW62/76 and knockout lines of OsWRKY62 and OsWRKY76 also showed greatly increased expression of defense-related genes and the accumulation of phytoalexins. The ratio of full-length versus truncated transcripts changed in dsOW62/76 plants as well as in response to pathogen infection. The short alternative OsWRKY62.2 and OsWRKY76.2 isoforms could interact with each other and with full-length proteins. OsWRKY62.2 showed a reduced repressor activity in planta, and two sequence determinants required for the repressor activity were identified in the amino terminus of OsWRKY62.1. The amino termini of OsWRKY62 and OsWRKY76 splice variants also showed reduced binding to the canonical W box motif. These results not only enhance our understanding of the DNA-binding property, the repressor sequence motifs, and the negative feedback regulation of the IIa subfamily of WRKYs but also provide evidence for alternative splicing of WRKY TFs during the plant defense response. © 2016 American Society of Plant Biologists. All Rights Reserved.

  20. Overexpression of ALTERNATIVE OXIDASE1a alleviates mitochondria-dependent programmed cell death induced by aluminium phytotoxicity in Arabidopsis.

    PubMed

    Liu, Jian; Li, Zhe; Wang, Yongqiang; Xing, Da

    2014-08-01

    Alternative oxidase (AOX) is a terminal oxidase found in all plants, and functions to maintain the electron flux and reduce the production of reactive oxygen species (ROS). Our previous study demonstrated that aluminium (Al) treatment could induce increased expression of the AOX1a gene, but the mechanism of how AOX1a participates in the regulation of Al-induced programmed cell death (PCD) is still not clear. To investigate the possible mechanism, mitochondrial ROS production and the behaviour of mitochondria, as well as caspase-3-like activation were monitored under Al treatment in wild-type (WT), AOX1a-lacking (aox1a), and AOX1a-overexpressing (AOX1a-OE) Arabidopsis. Our results showed that Al treatment increased the expression of AOX1a at both the transcriptional and translational levels. Overexpression of AOX1a reduced mitochondrial ROS production by maintaining the mitochondrial electron flux, and alleviated subsequent mitochondrial dysfunction and caspase-3-like activation in Al-induced PCD. Moreover, it was found that a change in AOX1a level could influence the expression levels of downstream functional genes that play protective roles in Al-induced PCD. Experiments using mutants and inhibitors demonstrated that superoxide anion (O2 (-)) derived from mitochondria was involved in Al-induced upregulation of AOX1a gene expression. Taken together, these results indicated that overexpression of AOX1a alleviated Al-induced PCD by maintaining mitochondrial function and promoting the expression of protective functional genes, providing new insights into the signalling cascades that modulate the Al phytotoxicity mechanism.

  1. The Gene Expression Program for the Formation of Wing Cuticle in Drosophila

    PubMed Central

    Adler, Paul N.

    2016-01-01

    The cuticular exoskeleton of insects and other arthropods is a remarkably versatile material with a complex multilayer structure. We made use of the ability to isolate cuticle synthesizing cells in relatively pure form by dissecting pupal wings and we used RNAseq to identify genes expressed during the formation of the adult wing cuticle. We observed dramatic changes in gene expression during cuticle deposition, and combined with transmission electron microscopy, we were able to identify candidate genes for the deposition of the different cuticular layers. Among genes of interest that dramatically change their expression during the cuticle deposition program are ones that encode cuticle proteins, ZP domain proteins, cuticle modifying proteins and transcription factors, as well as genes of unknown function. A striking finding is that mutations in a number of genes that are expressed almost exclusively during the deposition of the envelope (the thin outermost layer that is deposited first) result in gross defects in the procuticle (the thick chitinous layer that is deposited last). An attractive hypothesis to explain this is that the deposition of the different cuticle layers is not independent with the envelope instructing the formation of later layers. Alternatively, some of the genes expressed during the deposition of the envelope could form a platform that is essential for the deposition of all cuticle layers. PMID:27232182

  2. EXCAVATOR: a computer program for efficiently mining gene expression data.

    PubMed

    Xu, Dong; Olman, Victor; Wang, Li; Xu, Ying

    2003-10-01

    Massive amounts of gene expression data are generated using microarrays for functional studies of genes and gene expression data clustering is a useful tool for studying the functional relationship among genes in a biological process. We have developed a computer package EXCAVATOR for clustering gene expression profiles based on our new framework for representing gene expression data as a minimum spanning tree. EXCAVATOR uses a number of rigorous and efficient clustering algorithms. This program has a number of unique features, including capabilities for: (i) data- constrained clustering; (ii) identification of genes with similar expression profiles to pre-specified seed genes; (iii) cluster identification from a noisy background; (iv) computational comparison between different clustering results of the same data set. EXCAVATOR can be run from a Unix/Linux/DOS shell, from a Java interface or from a Web server. The clustering results can be visualized as colored figures and 2-dimensional plots. Moreover, EXCAVATOR provides a wide range of options for data formats, distance measures, objective functions, clustering algorithms, methods to choose number of clusters, etc. The effectiveness of EXCAVATOR has been demonstrated on several experimental data sets. Its performance compares favorably against the popular K-means clustering method in terms of clustering quality and computing time.

  3. T cell receptor V[alpha] gene segment with alternate splicing in the junctional region

    SciTech Connect

    Marche, P.N.; Six, A.; Gahery, H.; Gris-Liebe, C.; Cazenave, P.A.; Jouvin-Marche, E. )

    1993-11-15

    The locus encoding mouse TCR-[alpha] chain includes approximately 100 V[alpha] gene segments that can be organized in about 20 structural subfamilies. Southern blot analysis of a T cell line derived from the BALB/c strain, M5T, has indicated that both [alpha] loci were rearranged, as assessed by the deletion of the [delta] locus, and that the V[alpha] gene-segment involved in one of the rearrangements did not belong to any of the V[alpha] subfamilies already described. Transcripts of TCR-[alpha] chains from the M5T line were cloned after cDNA synthesis and anchored-polymerase chain reaction, revealing a V[alpha] gene segment of an as yet unidentified subfamily, V[alpha]5T. Molecular cloning of germ-line V[alpha]5T gene segments has shown that this subfamily contained two members, one of them being a pseudogene. The two members were located to each extremity of the [alpha] locus associated with a member of the V[alpha]13 and V[alpha]BWB subfamilies. Analysis of transcripts bearing the V[alpha]5T gene segment in the M5T line as well as in thymocytes has revealed that J[alpha] are frequently absent. This is due to an alternate donor splice site generated at the V[alpha]5T-J[alpha] junction that leads to a splicing from the end of V[alpha]5T to C[alpha] instead of the J[alpha] to C[alpha] conventional splicing. The impact of J[alpha] spliced-out transcripts on the allelic exclusion process is discussed. 41 refs., 5 figs.

  4. Advanced Transportation System Studies. Technical Area 3: Alternate Propulsion Subsystems Concepts. Volume 3; Program Cost Estimates

    NASA Technical Reports Server (NTRS)

    Levack, Daniel J. H.

    2000-01-01

    The objective of this contract was to provide definition of alternate propulsion systems for both earth-to-orbit (ETO) and in-space vehicles (upper stages and space transfer vehicles). For such propulsion systems, technical data to describe performance, weight, dimensions, etc. was provided along with programmatic information such as cost, schedule, needed facilities, etc. Advanced technology and advanced development needs were determined and provided. This volume separately presents the various program cost estimates that were generated under three tasks: the F- IA Restart Task, the J-2S Restart Task, and the SSME Upper Stage Use Task. The conclusions, technical results , and the program cost estimates are described in more detail in Volume I - Executive Summary and in individual Final Task Reports.

  5. 46 CFR 115.625 - Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 4 2010-10-01 2010-10-01 false Eligibility requirements for the Alternative Hull... OVERNIGHT ACCOMMODATIONS FOR MORE THAN 49 PASSENGERS INSPECTION AND CERTIFICATION Hull and Tailshaft Examinations § 115.625 Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain...

  6. 46 CFR 71.50-17 - Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 3 2010-10-01 2010-10-01 false Eligibility requirements for the Alternative Hull...-17 Eligibility requirements for the Alternative Hull Examination (AHE) Program for certain passenger... aluminum; (2) It has an effective hull protection system; (3) It has operated exclusively in fresh water...

  7. Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.

    PubMed

    Yang, Xiaozeng; Zhang, Huiyong; Li, Lei

    2012-05-01

    MicroRNAs (miRNAs) represent an important class of sequence-specific, trans-acting endogenous small RNA molecules that modulate gene expression at the post-transcriptional level. They function by binding to partial complementary cis-regulatory sites (miRNA binding sites) in their target mRNAs. Based on two recent observations from plant genome studies, namely that alternative splicing is a common phenomenon and that miRNA regulates a significant proportion of the transcriptome, we hypothesize that there may be a mechanism for gene regulation that involves both processes. In the present study, we performed a systemic search in the model plant Arabidopsis thaliana using annotated gene models as well as publically available high-throughput RNA sequencing data with a total of 570 million reads. Of the 354 high-confidence miRNA binding sites identified in Arabidopsis, at least 44 (12.4%) were affected by alternative splicing such that mRNA isoforms of the same miRNA target gene differ in the sequences encoding the miRNA binding sites. By simulation, we found that the frequency of alternative splicing at miRNA binding sites is significantly higher than at other regions. Comparative and functional analyses further indicated that the alternative splicing events are important for target gene expression and miRNA action. Together our results show that alternative splicing of miRNA binding sites is a plausible mechanism for attenuating miRNA-mediated gene regulation.

  8. Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes.

    PubMed

    Zhang, Chengjun; Gschwend, Andrea R; Ouyang, Yidan; Long, Manyuan

    2014-05-01

    The structure of eukaryotic genes evolves extensively by intron loss or gain. Previous studies have revealed two models for gene structure evolution through the loss of introns: RNA-based gene conversion, dubbed the Fink model and retroposition model. However, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. We detected hundreds of retroduplication-derived genes in human (Homo sapiens), fly (Drosophila melanogaster), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplicated genes that have at least lost one and retained one intron compared with the parental copy (intron-retaining [IR] type). Our new model attributes intron retention alternative splicing to the generation of these IR-type gene pairs. We presented 25 parental genes that have an intron retention isoform and have retained introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis. Our alternative-splicing-based model in conjunction with the retroposition and Fink models can explain the IR-type gene observed. We discovered a greater percentage of IR-type genes in plants than in animals, which may be due to the abundance of intron retention cases in plants. Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures.

  9. Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes1[W

    PubMed Central

    Zhang, Chengjun; Gschwend, Andrea R.; Ouyang, Yidan; Long, Manyuan

    2014-01-01

    The structure of eukaryotic genes evolves extensively by intron loss or gain. Previous studies have revealed two models for gene structure evolution through the loss of introns: RNA-based gene conversion, dubbed the Fink model and retroposition model. However, retrogenes that experienced both intron loss and intron-retaining events have been ignored; evolutionary processes responsible for the variation in complex exon-intron structure were unknown. We detected hundreds of retroduplication-derived genes in human (Homo sapiens), fly (Drosophila melanogaster), rice (Oryza sativa), and Arabidopsis (Arabidopsis thaliana) and categorized them either as duplicated genes that have all introns lost or as duplicated genes that have at least lost one and retained one intron compared with the parental copy (intron-retaining [IR] type). Our new model attributes intron retention alternative splicing to the generation of these IR-type gene pairs. We presented 25 parental genes that have an intron retention isoform and have retained introns in the same locations in the IR-type duplicate genes, which directly support our hypothesis. Our alternative-splicing-based model in conjunction with the retroposition and Fink models can explain the IR-type gene observed. We discovered a greater percentage of IR-type genes in plants than in animals, which may be due to the abundance of intron retention cases in plants. Given the prevalence of intron retention in plants, this new model gives a support that plant genomes have very complex gene structures. PMID:24520158

  10. Differential gene expression and alternative splicing between diploid and tetraploid watermelon

    PubMed Central

    Saminathan, Thangasamy; Nimmakayala, Padma; Manohar, Sumanth; Malkaram, Sridhar; Almeida, Aldo; Cantrell, Robert; Tomason, Yan; Abburi, Lavanya; Rahman, Mohammad A.; Vajja, Venkata G.; Khachane, Amit; Kumar, Brajendra; Rajasimha, Harsha K.; Levi, Amnon; Wehner, Todd; Reddy, Umesh K.

    2015-01-01

    The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits. PMID:25520388

  11. Differential gene expression and alternative splicing between diploid and tetraploid watermelon.

    PubMed

    Saminathan, Thangasamy; Nimmakayala, Padma; Manohar, Sumanth; Malkaram, Sridhar; Almeida, Aldo; Cantrell, Robert; Tomason, Yan; Abburi, Lavanya; Rahman, Mohammad A; Vajja, Venkata G; Khachane, Amit; Kumar, Brajendra; Rajasimha, Harsha K; Levi, Amnon; Wehner, Todd; Reddy, Umesh K

    2015-03-01

    The exploitation of synthetic polyploids for producing seedless fruits is well known in watermelon. Tetraploid progenitors of triploid watermelon plants, compared with their diploid counterparts, exhibit wide phenotypic differences. Although many factors modulate alternative splicing (AS) in plants, the effects of autopolyploidization on AS are still unknown. In this study, we used tissues of leaf, stem, and fruit of diploid and tetraploid sweet watermelon to understand changes in gene expression and the occurrence of AS. RNA-sequencing analysis was performed along with reverse transcription quantitative PCR and rapid amplification of cDNA ends (RACE)-PCR to demonstrate changes in expression and splicing. All vegetative tissues except fruit showed an increased level of AS in the tetraploid watermelon throughout the growth period. The ploidy levels of diploids and the tetraploid were confirmed using a ploidy analyser. We identified 5362 and 1288 genes that were up- and downregulated, respectively, in tetraploid as compared with diploid plants. We further confirmed that 22 genes underwent AS events across tissues, indicating possibilities of generating different protein isoforms with altered functions of important transcription factors and transporters. Arginine biosynthesis, chlorophyllide synthesis, GDP mannose biosynthesis, trehalose biosynthesis, and starch and sucrose degradation pathways were upregulated in autotetraploids. Phloem protein 2, chloroplastic PGR5-like protein, zinc-finger protein, fructokinase-like 2, MYB transcription factor, and nodulin MtN21 showed AS in fruit tissues. These results should help in developing high-quality seedless watermelon and provide additional transcriptomic information related to other cucurbits.

  12. PAX6 maintains β cell identity by repressing genes of alternative islet cell types

    PubMed Central

    Swisa, Avital; Avrahami, Dana; Eden, Noa; Zhang, Jia; Feleke, Eseye; Dahan, Tehila; Cohen-Tayar, Yamit; Stolovich-Rain, Miri; Kaestner, Klaus H.; Glaser, Benjamin; Ashery-Padan, Ruth

    2016-01-01

    Type 2 diabetes is thought to involve a compromised β cell differentiation state, but the mechanisms underlying this dysfunction remain unclear. Here, we report a key role for the TF PAX6 in the maintenance of adult β cell identity and function. PAX6 was downregulated in β cells of diabetic db/db mice and in WT mice treated with an insulin receptor antagonist, revealing metabolic control of expression. Deletion of Pax6 in β cells of adult mice led to lethal hyperglycemia and ketosis that were attributed to loss of β cell function and expansion of α cells. Lineage-tracing, transcriptome, and chromatin analyses showed that PAX6 is a direct activator of β cell genes, thus maintaining mature β cell function and identity. In parallel, we found that PAX6 binds promoters and enhancers to repress alternative islet cell genes including ghrelin, glucagon, and somatostatin. Chromatin analysis and shRNA-mediated gene suppression experiments indicated a similar function of PAX6 in human β cells. We conclude that reduced expression of PAX6 in metabolically stressed β cells may contribute to β cell failure and α cell dysfunction in diabetes. PMID:27941241

  13. Environmental restoration program pollution prevention checklist guide for the evaluation of alternatives project phase

    SciTech Connect

    Not Available

    1993-09-01

    Evaluation of alternative studies determine what decontamination and decommissioning (D&D) alternatives are presented to regulators for facility and site cleanup. A key consideration in this process is the waste to be generated. Minimizing the volume and toxicity of this waste will ultimately contribute to the selection of the best clean-up option. The purpose of this checklist guide is to assist the user with incorporating pollution prevention/waste minimization (PP/WM) in all Evaluation of Alternatives (EV) phase projects of the Environmental Restoration (ER) Program. This guide will assist users with documenting PP/WM activities for technology transfer and reporting requirements. Automated computer screens will be created from the checklist data to help users implement and evaluate waste reduction. Users can then establish numerical performance measures to measure progress in planning, training, self-assessments, field implementation, documentation, and technology transfer. Cost savings result as users train and assess themselves, eliminating expensive process waste assessments and audit teams.

  14. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

    PubMed Central

    Llorian, Miriam; Gooding, Clare; Bellora, Nicolas; Hallegger, Martina; Buckroyd, Adrian; Wang, Xiao; Rajgor, Dipen; Kayikci, Melis; Feltham, Jack; Ule, Jernej; Eyras, Eduardo; Smith, Christopher W.J.

    2016-01-01

    Alternative splicing (AS) is a key component of gene expression programs that drive cellular differentiation. Smooth muscle cells (SMCs) are important in the function of a number of physiological systems; however, investigation of SMC AS has been restricted to a handful of events. We profiled transcriptome changes in mouse de-differentiating SMCs and observed changes in hundreds of AS events. Exons included in differentiated cells were characterized by particularly weak splice sites and by upstream binding sites for Polypyrimidine Tract Binding protein (PTBP1). Consistent with this, knockdown experiments showed that that PTBP1 represses many smooth muscle specific exons. We also observed coordinated splicing changes predicted to downregulate the expression of core components of U1 and U2 snRNPs, splicing regulators and other post-transcriptional factors in differentiated cells. The levels of cognate proteins were lower or similar in differentiated compared to undifferentiated cells. However, levels of snRNAs did not follow the expression of splicing proteins, and in the case of U1 snRNP we saw reciprocal changes in the levels of U1 snRNA and U1 snRNP proteins. Our results suggest that the AS program in differentiated SMCs is orchestrated by the combined influence of auxiliary RNA binding proteins, such as PTBP1, along with altered activity and stoichiometry of the core splicing machinery. PMID:27317697

  15. Biodiesel Drives Florida Power & Light's EPAct Alternative Compliance Strategy; EPAct Alternative Fuel Transportation Program: Success Story (Fact Sheet)

    SciTech Connect

    Not Available

    2010-05-01

    This success story highlights how Florida Power & Light Company has successfully complied with the Energy Policy Act of 1992 (EPAct) through Alternative Compliance using biodiesel technologies and how it has become a biofuel leader, reducing petroleum use and pollutant emissions throughout Florida.

  16. Periodic gene expression program of the fission yeast cell cycle.

    PubMed

    Rustici, Gabriella; Mata, Juan; Kivinen, Katja; Lió, Pietro; Penkett, Christopher J; Burns, Gavin; Hayles, Jacqueline; Brazma, Alvis; Nurse, Paul; Bähler, Jürg

    2004-08-01

    Cell-cycle control of transcription seems to be universal, but little is known about its global conservation and biological significance. We report on the genome-wide transcriptional program of the Schizosaccharomyces pombe cell cycle, identifying 407 periodically expressed genes of which 136 show high-amplitude changes. These genes cluster in four major waves of expression. The forkhead protein Sep1p regulates mitotic genes in the first cluster, including Ace2p, which activates transcription in the second cluster during the M-G1 transition and cytokinesis. Other genes in the second cluster, which are required for G1-S progression, are regulated by the MBF complex independently of Sep1p and Ace2p. The third cluster coincides with S phase and a fourth cluster contains genes weakly regulated during G2 phase. Despite conserved cell-cycle transcription factors, differences in regulatory circuits between fission and budding yeasts are evident, revealing evolutionary plasticity of transcriptional control. Periodic transcription of most genes is not conserved between the two yeasts, except for a core set of approximately 40 genes that seem to be universally regulated during the eukaryotic cell cycle and may have key roles in cell-cycle progression.

  17. Update on a Pharmacokinetic-Centric Alternative Tier II Program for MMT—Part I: Program Implementation and Lessons Learned

    PubMed Central

    Dorman, David C.; Andersen, Melvin E.; Roper, Jerry M.; Taylor, Michael D.

    2012-01-01

    Concerns have been raised regarding environmental manganese exposure since high exposures have been associated with neurological disorders. The USA Environmental Protection Agency most recent human health risk assessment of inhaled manganese conducted in 1993 identified specific areas of uncertainty regarding manganese pharmacokinetics. This led to the development of a test rule under the USA Clean Air Act that required the generation of pharmacokinetic information on the inorganic manganese combustion products of the organometallic fuel additive methylcyclopentadienyl manganese tricarbonyl (MMT). The Alternative Tier 2 testing program for MMT, described in this paper, has yielded substantial pharmacokinetic data and has enabled the generation of physiologically based pharmacokinetic (PBPK) models for manganese. These models are capable of predicting tissue manganese concentrations across a variety of dose routes, levels, and durations while accounting for factors such as age, gender, and reproductive status, enabling the consideration of tissue dosimetry in future risk assessments. PMID:22545047

  18. Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma

    PubMed Central

    Li, Ryan; Ochs, Michael F.; Ahn, Sun Mi; Hennessey, Patrick; Tan, Marietta; Soudry, Ethan; Gaykalova, Daria A.; Uemura, Mamoru; Brait, Mariana; Shao, Chunbo; Westra, William; Bishop, Justin; Fertig, Elana J.; Califano, Joseph A.

    2014-01-01

    Purpose Prior studies have demonstrated tumor-specific alternative splicing events in various solid tumor types. The role of alternative splicing in the development and progression of head and neck squamous cell carcinoma (HNSCC) is unclear. Our study queried exon-level expression to implicate splice variants in HNSCC tumors. Experimental Design We performed a comparative genome-wide analysis of 44 HNSCC tumors and 25 uvulopalatopharyngoplasty (UPPP) tissue samples at an exon expression level. In our comparison we ranked genes based upon a novel score—the Maximum-Minimum Exon Score (MMES) – designed to predict the likelihood of an alternative splicing event occurring. We validated predicted alternative splicing events using quantitative RT-PCR on an independent cohort. Results After MMES scoring of 17,422 genes, the top 900 genes with the highest scores underwent additional manual inspection of expression patterns in a graphical analysis. The genes LAMA3, DST, VEGFC, SDHA, RASIP1, and TP63 were selected for further validation studies because of a high frequency of alternative splicing suggested in our graphical analysis, and literature review showing their biological relevance and known splicing patterns. We confirmed TP63 as having dominant expression of the short DeltaNp63 isoform in HNSCC tumor samples, consistent with prior reports. Two of the six genes (LAMA3 and DST) validated by quantitative RT-PCR for tumor-specific alternative splicing events (Student's t test, P<0.001). Conclusion Alternative splicing events of oncologically relevant proteins occur in HNSCC. The number of genes expressing tumor-specific splice variants needs further elucidation, as does the functional significance of selective isoform expression. PMID:24675808

  19. A sugarcane R2R3-MYB transcription factor gene is alternatively spliced during drought stress

    PubMed Central

    Guo, Jinlong; Ling, Hui; Ma, Jingjing; Chen, Yun; Su, Yachun; Lin, Qingliang; Gao, Shiwu; Wang, Hengbo; Que, Youxiong; Xu, Liping

    2017-01-01

    MYB transcription factors of the R2R3-MYB family have been shown to play important roles in many plant processes. A sugarcane R2R3-MYB gene (ScMYB2) and its two alternative forms of transcript (ScMYB2S1 and ScMYB2S2) were identified in this study. The deduced protein of ScMYB2S1 is a typical plant R2R3-MYB protein, while ScMYB2S2 encodes a truncated protein. Real-time qPCR analysis revealed that ScMYB2S1 is suppressed under PEG-simulated drought stress in sugarcane, while ScMYB2S2 is induced at later treatment stage. A senescence symptom was observed when ScMYB2S1 was injected into tobacco leaves mediated by Agrobacterium, but no symptom for ScMYB2S2. Further investigation showed that the expression levels of 4 senescence-associated genes, NtPR-1a, NtNYC1, NtCAT3 and NtABRE, were markedly induced in tobacco leaves after ScMYB2S1-injection, while they were not sensitive to ScMYB2S2-injection. Moreover, MDA and proline were also investigated after injection. Similarly, MDA and proline levels were induced by ABA and ScMYB2S1, while inhibited by ScMYB2S2. We propose that ScMYB2, by alternatively splicing two transcripts (ScMYB2S1 and ScMYB2S2), is involved in an ABA-mediated leaf senescence signaling pathway and play positive role in respond to drought-induced senescence in sugarcane. The results of this study provide information for further research in sugarcane stress processes. PMID:28167824

  20. High gene flow between alternative morphs and the evolutionary persistence of facultative paedomorphosis

    PubMed Central

    Oromi, Neus; Michaux, Johan; Denoël, Mathieu

    2016-01-01

    Paedomorphosis and metamorphosis are two major developmental processes that characterize the evolution of complex life cycles in many lineages. Whereas these processes were fixed in some taxa, they remained facultative in others, with alternative phenotypes expressed in the same populations. From a genetic perspective, it is still unknown whether such phenotypes form a single population or whether they show some patterns of isolation in syntopy. This has deep implications for understanding the evolution of the phenotypes, i.e. towards their persistence or their fixation and speciation. Newts and salamanders are excellent models to test this hypothesis because they exhibit both developmental processes in their populations: the aquatic paedomorphs retain gills, whereas the metamorphs are able to colonize land. Using microsatellite data of coexisting paedomorphic and metamorphic palmate newts (Lissotriton helveticus), we found that they formed a panmictic population, which evidences sexual compatibility between the two phenotypes. The high gene flow could be understood as an adaptation to unstable habitats in which phenotypic plasticity is favored over the fixation of developmental alternatives. This makes then possible the persistence of a polyphenism: only metamorphosis could be maintained in case of occasional drying whereas paedomorphosis could offer specific advantages in organisms remaining in water. PMID:27534370

  1. Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei

    PubMed Central

    2012-01-01

    Background Alternative sigma factors trigger various adaptive responses. Lactobacillus sakei, a non-sporulating meat-borne bacterium, carries an alternative sigma factor seemingly orthologous to σH of Bacillus subtilis, best known for its contribution to the initiation of a large starvation response ultimately leading to sporulation. As the role of σH-like factors has been little studied in non-sporulating bacteria, we investigated the function of σH in L. sakei. Results Transcription of sigH coding for σH was hardly affected by entry into stationary phase in our laboratory conditions. Twenty-five genes potentially regulated by σH in L. sakei 23 K were revealed by genome-wide transcriptomic profiling of sigH overexpression and/or quantitative PCR analysis. More than half of them are involved in the synthesis of a DNA uptake machinery linked to genetic competence, and in DNA metabolism; however, σH overproduction did not allow detectable genetic transformation. σH was found to be conserved in the L. sakei species. Conclusion Our results are indicative of the existence of a genetic competence state activated by σH in L. sakei, and sustain the hypothesis that σH-like factors in non sporulating Firmicutes share this common function with the well-known ComX of naturally transformable streptococci. PMID:22409597

  2. Alternative promoters regulate transcription of the gene that encodes stem cell surface protein AC133.

    PubMed

    Shmelkov, Sergey V; Jun, Lin; St Clair, Ryan; McGarrigle, Deirdre; Derderian, Christopher A; Usenko, Jaroslav K; Costa, Carla; Zhang, Fan; Guo, Xinzheng; Rafii, Shahin

    2004-03-15

    AC133 is a member of a novel family of cell surface proteins with 5 transmembrane domains. The function of AC133 is unknown. Although AC133 mRNA is detected in different tissues, its expression in the hematopoietic system is restricted to CD34+ stem cells. AC133 is also expressed on stem cells of other tissues, including endothelial progenitor cells. However, despite the potential importance of AC133 to the field of stem cell biology, nothing is known about the transcriptional regulation of AC133 expression. In this report we showed that the human AC133 gene has at least 9 distinctive 5'-untranslated region (UTR) exons, resulting in the formation of at least 7 alternatively spliced 5'-UTR isoforms of AC133 mRNA, which are expressed in a tissue-dependent manner. We found that transcription of these AC133 isoforms is controlled by 5 alternative promoters, and we demonstrated their activity on AC133-expressing cell lines using a luciferase reporter system. We also showed that in vitro methylation of 2 of these AC133 promoters completely suppresses their activity, suggesting that methylation plays a role in their regulation. Identification of tissue-specific AC133 promoters may provide a novel method to isolate tissue-specific stem and progenitor cells.

  3. Association study of the CNR1 gene exon 3 alternative promoter region polymorphisms and substance dependence

    PubMed Central

    Herman, Aryeh I.; Kranzler, Henry R.; Cubells, Joseph F.; Gelernter, Joel; Covault, Jonathan

    2008-01-01

    An alternative promoter producing a novel 5′-untranslated region of cannabinoid receptor mRNA has recently been described in CNR1, the gene encoding the cannabinoid receptor protein. Single nucleotide polymorphisms (SNPs) adjacent to this site were reported to be associated with polysubstance abuse (Zhang et al. 2004). We examined the association of 4 SNPs (rs6928499, rs806379, rs1535255, rs2023239) in the distal region of intron 2 of CNR1 both with individual substance dependence diagnoses (i.e., alcohol, cocaine, and opioids), as well as with polysubstance dependence. The study samples consisted of European American and African American subjects with drug and or alcohol dependence (n=895), and controls (n = 472). Subjects were grouped as polysubstance dependent, opioid dependent, cocaine dependent, cannabis dependent and alcohol dependent. There was a modest association of marker rs1535255 with alcohol dependence, respectively (P=0.04), though with correction for multiple phenotype comparisons, this effect was not considered statistically significant. These findings fail to replicate the original report of an association between SNPs adjacent to an alternative CNR1 exon 3 transcription start site and polysubstance abuse. PMID:16741937

  4. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma

    PubMed Central

    Zhang, Shile; Wei, Jun S.; Li, Samuel Q.; Badgett, Tom C.; Song, Young K.; Agarwal, Saurabh; Coarfa, Cristian; Tolman, Catherine; Hurd, Laura; Liao, Hongling; He, Jianbin; Wen, Xinyu; Liu, Zhihui; Thiele, Carol J.; Westermann, Frank; Asgharzadeh, Shahab; Seeger, Robert C.; Maris, John M.; Auvil, Jamie M Guidry; Smith, Malcolm A; Kolaczyk, Eric D; Shohet, Jason; Khan, Javed

    2016-01-01

    The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p≤0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification. PMID:26683771

  5. MYCN controls an alternative RNA splicing program in high-risk metastatic neuroblastoma.

    PubMed

    Zhang, Shile; Wei, Jun S; Li, Samuel Q; Badgett, Tom C; Song, Young K; Agarwal, Saurabh; Coarfa, Cristian; Tolman, Catherine; Hurd, Laura; Liao, Hongling; He, Jianbin; Wen, Xinyu; Liu, Zhihui; Thiele, Carol J; Westermann, Frank; Asgharzadeh, Shahab; Seeger, Robert C; Maris, John M; Guidry Auvil, Jamie M; Smith, Malcolm A; Kolaczyk, Eric D; Shohet, Jason; Khan, Javed

    2016-02-28

    The molecular mechanisms underlying the aggressive behavior of MYCN driven neuroblastoma (NBL) is under intense investigation; however, little is known about the impact of this family of transcription factors on the splicing program. Here we used high-throughput RNA sequencing to systematically study the expression of RNA isoforms in stage 4 MYCN-amplified NBL, an aggressive subtype of metastatic NBL. We show that MYCN-amplified NBL tumors display a distinct gene splicing pattern affecting multiple cancer hallmark functions. Six splicing factors displayed unique differential expression patterns in MYCN-amplified tumors and cell lines, and the binding motifs for some of these splicing factors are significantly enriched in differentially-spliced genes. Direct binding of MYCN to promoter regions of the splicing factors PTBP1 and HNRNPA1 detected by ChIP-seq demonstrates that MYCN controls the splicing pattern by direct regulation of the expression of these key splicing factors. Furthermore, high expression of PTBP1 and HNRNPA1 was significantly associated with poor overall survival of stage4 NBL patients (p ≤ 0.05). Knocking down PTBP1, HNRNPA1 and their downstream target PKM2, an isoform of pro-tumor-growth, result in repressed growth of NBL cells. Therefore, our study reveals a novel role of MYCN in controlling global splicing program through regulation of splicing factors in addition to its well-known role in the transcription program. These findings suggest a therapeutically potential to target the key splicing factors or gene isoforms in high-risk NBL with MYCN-amplification.

  6. Constructing an Online MCAT Preparation Program as an Alternative to On-Site Preparation for Medical School

    ERIC Educational Resources Information Center

    Navarre, Berengaria; Perez, Norma A.; Smith, Sarah Toombs

    2017-01-01

    Based on a successful five-week summer program, we constructed an online alternative to prepare Hispanic students to take the Medical College Admission Test (MCAT). We used input from student premed advisors, students, a faculty mentor, a Verbal Reasoning coach, and the program administrator. Online activities were provided to support the student…

  7. Comparison of Alternative and Traditional Teacher Preparation Programs for First Year Special Education Teachers in Northwest Ohio

    ERIC Educational Resources Information Center

    Alhamisi, Judy Carol

    2011-01-01

    This study compares knowledge as measured by grade point averages and Praxis II scores between first-year special education teachers who completed one university's alternative teacher preparation program (ATTP) and those who completed the university's traditional teacher preparation program (TTPP). A total of 33 teachers, 15 from the ATTP and 18…

  8. Perspectives on Best Practices for Gene Therapy Programs

    PubMed Central

    Cheever, Thomas R.; Berkley, Dale; Braun, Serge; Brown, Robert H.; Byrne, Barry J.; Chamberlain, Jeffrey S.; Cwik, Valerie; Duan, Dongsheng; Federoff, Howard J.; High, Katherine A.; Kaspar, Brian K.; Klinger, Katherine W.; Larkindale, Jane; Lincecum, John; Mavilio, Fulvio; McDonald, Cheryl L.; McLaughlin, James; Weiss McLeod, Bonnie; Mendell, Jerry R.; Nuckolls, Glen; Stedman, Hansell H.; Tagle, Danilo A.; Vandenberghe, Luk H.; Wang, Hao; Wernett, Pamela J.; Wilson, James M.; Porter, John D.

    2015-01-01

    Abstract With recent successes in gene therapy trials for hemophilia and retinal diseases, the promise and prospects for gene therapy are once again garnering significant attention. To build on this momentum, the National Institute of Neurological Disorders and Stroke and the Muscular Dystrophy Association jointly hosted a workshop in April 2014 on “Best Practices for Gene Therapy Programs,” with a focus on neuromuscular disorders. Workshop participants included researchers from academia and industry as well as representatives from the regulatory, legal, and patient advocacy sectors to cover the gamut from preclinical optimization to intellectual property concerns and regulatory approval. The workshop focused on three key issues in the field: (1) establishing adequate scientific premise for clinical trials in gene therapy, (2) addressing regulatory process issues, and (3) intellectual property and commercialization issues as they relate to gene therapy. The outcomes from the discussions at this workshop are intended to provide guidance for researchers and funders in the gene therapy field. PMID:25654329

  9. Using gene expression programming to infer gene regulatory networks from time-series data.

    PubMed

    Zhang, Yongqing; Pu, Yifei; Zhang, Haisen; Su, Yabo; Zhang, Lifang; Zhou, Jiliu

    2013-12-01

    Gene regulatory networks inference is currently a topic under heavy research in the systems biology field. In this paper, gene regulatory networks are inferred via evolutionary model based on time-series microarray data. A non-linear differential equation model is adopted. Gene expression programming (GEP) is applied to identify the structure of the model and least mean square (LMS) is used to optimize the parameters in ordinary differential equations (ODEs). The proposed work has been first verified by synthetic data with noise-free and noisy time-series data, respectively, and then its effectiveness is confirmed by three real time-series expression datasets. Finally, a gene regulatory network was constructed with 12 Yeast genes. Experimental results demonstrate that our model can improve the prediction accuracy of microarray time-series data effectively. Copyright © 2013 Elsevier Ltd. All rights reserved.

  10. Identification and expression analysis of alternatively spliced new transcript isoform of Bax gene in mouse.

    PubMed

    Husain, Mohammed Amir; Ishqi, Hassan Mubarak; Sarwar, Tarique; Rehman, Sayeed Ur; Tabish, Mohammad

    2017-07-20

    Bax, a pro-apoptotic member of Bcl-2 family regulates apoptosis through homodimerization/heterodimerization with Bcl-2. Bax-α is the only product of the Bax gene that has been extensively studied. Bax-α exists in inactive form and several conformational changes are required during apoptosis to activate it. Here, we have identified a novel transcript variant of Bax gene in mouse which contains alternatively spliced new first exon that is different from the first exon of previously reported transcript. Conceptual translation of new transcript encodes a protein (Bax-α1), having different N-terminus. The existence of the new transcript variant was confirmed by reverse transcriptase-PCR, semi-nested PCR using primers designed for the newly identified transcript variant. The identity of PCR product obtained after semi-nested PCR was confirmed by DNA sequencing. Relative expression of new transcript variant with respect to reported transcript was also studied with the help of real time PCR. The existence of new transcript variant was further supported by the presence of clusters of overlapping ESTs from the database. Bax-α1 possibly displays heterogeneous properties as predicted by post-translational modification analysis tools. The differences in post-translational modifications might play important roles in divergent function of the new isoform. The three dimensional structure was generated by homology modelling to visualize the differences at N termini of known and newly identified variant. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Antisense Oligodeoxynucleotide Inhibition as an Alternative and Convenient Method for Gene Function Analysis in Pollen Tubes

    PubMed Central

    Liao, Fanglei; Wang, Lu; Yang, Li-Bo; Zhang, Liyao; Peng, Xiongbo; Sun, Meng-xiang

    2013-01-01

    Antisense oligodeoxynucleotide (A-ODN) inhibition works well in animal cells. However, there have been few successful examples to date of its application in plants, and more specifically whether the technique can be used in pollen tubes as a model of plant cell growth. NtGNL1 plays an important role in pollen tube development and was thus selected as an indicator to assess the biological effects of A-ODN. An A-ODN inhibition technique was used to down-regulate NtGNL1 expression in tobacco pollen tubes and showed that A-ODNs could quickly enter pollen tubes through the thick wall and cell membrane and effectively block NtGNL1 expression. Phenotype analysis revealed that the down-regulation of NtGNL1 by A-ODNs resulted in abnormalities in endocytosis and subsequent vesicle trafficking, similar to the phenotypes of pollen tubes treated with NtGNL1 RNAi. This investigation confirmed that A-ODNs could specifically inhibit target gene expression, and furthermore demonstrated that A-ODN functioned in a concentration- and duration-dependent manner, because A-ODNs could be degraded when incubated with pollen tubes. Thus, the A-ODN technique was successfully used for gene function analysis in pollen tubes and appears to be an alternative and convenient technique when the in vitro pollen tube is used as the study model. This technique will greatly facilitate investigations on the molecular mechanism(s) underlying pollen tube growth. PMID:23527102

  12. Molecular cloning and functional characterization of a mouse gene upregulated by lipopolysaccharide treatment reveals alternative splicing

    SciTech Connect

    Du, Kejun; Chen, Yaoming; Dai, Zongming; Bi, Yuan; Cai, Tongjian; Hou, Lichao; Chai, Yubo; Song, Qinghe; Chen, Sumin; Luo, Wenjing; Chen, Jingyuan

    2010-01-01

    Treatment of mouse cells with lipopolysaccharide (LPS) potently initiates an inflammatory response, but the underlying mechanisms are unclear. We therefore sought to characterize cDNA sequences of a new mouse LPS-responsive gene, and to evaluate the effects of MLrg. Full-length cDNAs were obtained from LPS-treated NIH3T3 cells. We report that the MLrg gene produces two alternative splice products (GenBank Accession Nos. (DQ316984) and (DQ320011)), respectively, encoding MLrgW and MLrgS polypeptides. Both proteins contain zinc finger and leucine zipper domains and are thus potential regulators of transcription. Expression of MLrgW and MLrgS were robustly upregulated following LPS treatment, and the proteins were localized predominantly in the nuclear membrane and cytoplasm. In stable transfectants over-expressing MLrgW the proportion of cells in G1 phase was significantly reduced, while in cells over-expressing MLrgS the proportion of cells in G2 was significantly increased; both proteins are thus potential regulators of cell cycle progression. Upregulation of MLrgW and MLrgS may be an important component of the LPS inflammatory pathway and of the host response to infection with GNB.

  13. [Alternating hemiplegia of childhood: ATP1A3 gene analysis in 16 patients].

    PubMed

    Ulate-Campos, Adriana; Fons, Carmen; Campistol, Jaume; Martorell, Loreto; Cancho-Candela, Ramón; Eiris, Jesús; López-Laso, Eduardo; Pineda, Mercedes; Sans, Anna; Velázquez, Ramón

    2014-07-07

    Alternating hemiplegia in childhood (AHC) is a disease characterized by recurrent episodes of hemiplegia, tonic or dystonic crisis and abnormal ocular movements. Recently, mutations in the ATP1A3 gene have been identified as the causal mechanism of AHC. The objective is to describe a series of 16 patients with clinical and genetic diagnosis of AHC. It is a descriptive, retrospective, multicenter study of 16 patients with clinical diagnosis of AHC in whom mutations in ATP1A3 were identified. Six heterozygous, de novo mutations were found in the ATP1A3 gene. The most frequent mutation was G2401A in 8 patients (50%) followed by G2443A in 3 patients (18.75%), G2893A in 2 patients (12.50%) and C2781G, G2893C and C2411T in one patient, respectively (6.25% each). In the studied population with AHC, de novo mutations were detected in 100% of patients. The most frequent mutations were D801N y la E815K, as reported in other series. Copyright © 2013 Elsevier España, S.L. All rights reserved.

  14. Conserved Gene Expression Programs in Developing Roots from Diverse Plants

    PubMed Central

    Huang, Ling; Schiefelbein, John

    2015-01-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants. PMID:26265761

  15. Conserved Gene Expression Programs in Developing Roots from Diverse Plants.

    PubMed

    Huang, Ling; Schiefelbein, John

    2015-08-01

    The molecular basis for the origin and diversification of morphological adaptations is a central issue in evolutionary developmental biology. Here, we defined temporal transcript accumulation in developing roots from seven vascular plants, permitting a genome-wide comparative analysis of the molecular programs used by a single organ across diverse species. The resulting gene expression maps uncover significant similarity in the genes employed in roots and their developmental expression profiles. The detailed analysis of a subset of 133 genes known to be associated with root development in Arabidopsis thaliana indicates that most of these are used in all plant species. Strikingly, this was also true for root development in a lycophyte (Selaginella moellendorffii), which forms morphologically different roots and is thought to have evolved roots independently. Thus, despite vast differences in size and anatomy of roots from diverse plants, the basic molecular mechanisms employed during root formation appear to be conserved. This suggests that roots evolved in the two major vascular plant lineages either by parallel recruitment of largely the same developmental program or by elaboration of an existing root program in the common ancestor of vascular plants.

  16. Determination of ligand-binding specificity by alternative splicing: Two distinct growth factor receptors encoded by a single gene

    SciTech Connect

    Miki, T.; Bottaro, D.P.; Fleming, T.P.; Smith, C.L.; Chan, A.M.L.; Aaronson, S.A. ); Burgess, W.H. )

    1992-01-01

    Expression cDNA cloning and structural analysis of the human keratinocyte growth factor receptor (KGFR) revealed identity with one of the fibroblast growth factor (FGF) receptors encoded by the bek gene (FGFR-2), except for a divergent stretch of 49 amino acids in their extracellular domains. Binding assays demonstrated that the KGFR was a high-affinity receptor for both KGF and acidic FGF, while FGFR-2 showed high affinity for basic and acidic FGF but no detectable binding by KGF. Genomic analysis of the bek gene revealed two alternative exons responsible for the region of divergence between the two receptors. The KGFR transcript was specific to epithelial cells, and it appeared to be differentially regulated with respect to the alternative FGFR-2 transcript. Thus, two growth factor receptors with different ligand-binding specificities and expression patterns are encoded by alternative transcripts of the same gene.

  17. Program Evaluation: A Study to Evaluate the Effectiveness of Academic and Behavioral Interventions in an Alternative to out of School Suspension Program

    ERIC Educational Resources Information Center

    Rizzi, Lorenzo

    2011-01-01

    The purpose of this study was to provide insight regarding the impact that the alternative to suspension program Achievement Character Excellence (ACE) has on the students who are placed there. The study utilized four achievement indicators to track the level of improvement of students after they were placed in the ACE program and after they were…

  18. Gene expression in human skeletal muscle: alternative normalization method and effect of repeated biopsies.

    PubMed

    Lundby, Carsten; Nordsborg, Nikolai; Kusuhara, Keiko; Kristensen, Kristina Møller; Neufer, P Darrell; Pilegaard, Henriette

    2005-10-01

    The reverse transcriptase-polymerase chain reaction (RT-PCR) method has lately become widely used to determine transcription and mRNA content in rodent and human muscle samples. However, the common use of endogenous controls for correcting for variance in cDNA between samples is not optimal. Specifically, we investigated (1) a new normalization method based on determining the cDNA content by the flourophores PicoGreen and OliGreen, (2) effect of repeated muscle biopsies on mRNA gene expression, and (3) the spatial heterogeneity in mRNA expression across the muscle. Standard curves using oligo standards revealed a high degree of sensitivity and linearity (2.5-45 ng; R2>0.99) with OliGreen reagent, as was the case for OliGreen analyses with standard curves constructed from serial dilutions of representative RT samples (R2 >0.99 for a ten times dilution range of a representative reversed transcribed (RT) sample). Likewise, PicoGreen reagent detected the RNA:DNA hybrid content in RT samples with great sensitivity. Standard curves constructed from both double-stranded lambda DNA (1-10 ng) and from serial dilutions of representative RT samples consistently resulted in linearity with R2 >0.99. The present determination of cDNA content in reversed transcribed human skeletal muscle RNA samples by both PicoGreen and OliGreen analyses suggests that these fluorophores provide a potential alternative normalization procedure for human gene expression studies. In addition, the present study shows that multiple muscle biopsies obtained from the same muscle do not influence the mRNA response induced by an acute exercise bout for any of the genes examined.

  19. Alternative splicing of the AGAMOUS orthologous gene in double flower of Magnolia stellata (Magnoliaceae).

    PubMed

    Zhang, Bo; Liu, Zhi-Xiong; Ma, Jiang; Song, Yi; Chen, Fa-Ju

    2015-12-01

    Magnolia stellata is a woody ornamental shrub with more petaloid tepals than related plants from family Magnoliaceae. Recent studies revealed that expression changes in an AGAMOUS (AG) orthologous gene could resulted in double flowers with increased numbers of petals. We isolated three transcripts encoding different isoforms of a single AG orthologous gene, MastAG, mastag_2 and mastag_3, from M. stellata. Sequence alignments and Southern blot analyses suggested that MastAG was a single-copy gene in M. stellata genomes, and that mastag_2 and mastag_3 were abnormally spliced isoforms of MastAG. An 144bp exon skipping in MastAG results in the truncated mastag_2 protein lacking the completely I domain and 18 aa of the K1 subdomain, whereas an 165bp exon skipping of MastAG produces a truncated mastag_3 protein lacking 6 aa of the K3 subdomain and the completely C terminal region. Expression analyses showed that three alternative splicing (AS) isoforms expressed only in developing stamens and carpels. Functional analyses revealed that MastAG could mimic the endogenous AG to specify carpel identity, but failed to regulate stamen development in an Arabidopsis ag-1 mutant. Moreover, the key domain or subdomain deletions represented by mastag_2 and mastag_3 resulted in loss of C-function. However, ectopic expression of mastag_2 in Arabidopsis produced flowers with sepals converted into carpeloid organs, but without petals and stamens, whereas ectopic expression of mastag_3 in Arabidopsis could mimic the flower phenotype of the ag mutant and produced double flowers with homeotic transformation of stamens into petals and carpels into another ag flower. Our results also suggest that mastag_3 holds some potential for biotechnical engineering to create multi-petal phenotypes in commercial ornamental cultivars.

  20. Multicriteria decision methodology for selecting technical alternatives in the Mixed Waste Integrated Program

    SciTech Connect

    Ferrada, J.J.; Berry, J.B.

    1993-11-01

    The US Department of Energy (DOE) Mixed Waste Integrated Program (MWIP) has as one of its tasks the identification of a decision methodology and key decision criteria for the selection methodology. The aim of a multicriteria analysis is to provide an instrument for a systematic evaluation of distinct alternative projects. Determination of this methodology will clarify (1) the factors used to evaluate these alternatives, (2) the evaluator`s view of the importance of the factors, and (3) the relative value of each alternative. The selected methodology must consider the Comprehensive Environmental Response Compensation and Liability Act (CERCLA) decision-making criteria for application to the analysis technology subsystems developed by the DOE Office of Technology Development. This report contains a compilation of several decision methodologies developed in various national laboratories, institutions, and universities. The purpose of these methodologies may vary, but the core of the decision attributes are very similar. Six approaches were briefly analyzed; from these six, in addition to recommendations made by the MWIP technical support group leaders and CERCLA, the final decision methodology was extracted. Slight variations are observed in the many methodologies developed by different groups, but most of the analyzed methodologies address similar aspects for the most part. These common aspects were the core of the methodology suggested in this report for use within MWIP for the selection of technologies. The set of criteria compiled and developed for this report have been grouped in five categories: (1) process effectiveness, (2) developmental status, (3) life-cycle cost, (4) implementability, and (5) regulatory compliance.