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. Alternative Programs for Disruptive Youth.

    ERIC Educational Resources Information Center

    Thomas, M. Angele, Ed.; And Others

    The book addresses issues in meeting the educational needs of disruptive students. In the introduction, R. Sarri examines the rise of alternative schools and discusses common elements in their design and operation. D. Sabatino follows with "Issues and Concerns: Problems with Alternative Schools," in which he examines the particular difficulties…

  10. [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/.

  11. 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…

  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. 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.

  14. 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.…

  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. 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

  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

    ...DOE today proposes a rule pursuant to the Energy Independence and Security Act of 2007 (EISA), that would revise the allocation of marketable credits under DOE's Alternative Fuel Transportation Program (AFTP or Program), by including EISA-specified electric drive vehicles and investments in qualified alternative fuel infrastructure, nonroad equipment, and relevant emerging technologies. DOE......

  19. 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…

  20. 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…

  1. 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

  2. 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…

  3. 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.

  4. 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

  5. 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.

  6. 76 FR 11310 - Alternatives Analysis Program Discretionary Funding Allocations

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-03-01

    ...: Federal Transit Administration (FTA), DOT. ACTION: Alternatives Analysis Program Announcement of Project...) announces the selection of projects funded with unallocated Section 5339 Alternatives Analysis Program funds... potential sponsors of major transit capital investments (``New Starts'' and ``Small Starts'' projects)...

  7. 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.

  8. 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…

  9. 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…

  10. 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.

  11. 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…

  12. 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…

  13. 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.

  14. 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...

  15. 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...

  16. 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...

  17. 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...

  18. 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...

  19. 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…

  20. 77 FR 31756 - Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-30

    ... Parts 429, 430, and 431 RIN 1904-AC46 Energy Conservation Program: Alternative Efficiency Determination Methods and Alternative Rating Methods: Public Meeting AGENCY: Office of Energy Efficiency and Renewable... proposed modifications to the regulations authorizing the use of alternative methods of determining...

  1. 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

  2. 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...

  3. 78 FR 31535 - Assistive Technology Alternative Financing Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-24

    ... [Federal Register Volume 78, Number 101 (Friday, May 24, 2013)] [Notices] [Pages 31535-31536] [FR Doc No: 2013-12495] DEPARTMENT OF EDUCATION Assistive Technology Alternative Financing Program AGENCY... slate of applicants developed for the Assistive Technology (AT) Alternative Financing Program (AFP)...

  4. 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)…

  5. 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…

  6. 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

  7. 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.

  8. 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....

  9. 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

  10. 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…

  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. 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…

  14. 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.

  15. 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)

  16. 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.

  17. 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.

  18. 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.

  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, 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...

  4. 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...

  5. 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...

  6. 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...

  7. 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...

  8. 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

  9. 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.

  10. 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…

  11. 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

  12. 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.

  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 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…

  15. 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…

  16. 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…

  17. 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-Generally. 154.2180 Section 154.2180 Navigation and Navigable Waters COAST GUARD, DEPARTMENT OF HOMELAND... difference in the analyzer output readings from the established reference value after a stated period...

  18. The Alternate Route to Certification: Program Information and Application, 2004.

    ERIC Educational Resources Information Center

    Connecticut State Board of Governors for Higher Education, Hartford.

    This document presents information on the Alternate Route to Certification (ARC) program, which prepares talented people from outside of education to enter teaching. It has been offered since 1988 by the Connecticut Department of Higher Education. ARC prepares aspiring teachers by: providing intensive non-credit preparation in teaching methods and…

  19. 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…

  20. 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...

  1. 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...

  2. 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...

  3. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  4. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  5. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  6. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  7. 6 CFR 27.235 - Alternative security program.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... facilities may submit an Alternate Security Program (ASP) pursuant to the requirements of this section. The... submit an ASP in lieu of a Security Vulnerability Assessment, Site Security Plan, or both. (2) Tier 1, Tier 2, or Tier 3 facilities may submit an ASP in lieu of a Site Security Plan. Tier 1, Tier 2,...

  8. 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…

  9. 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...

  10. 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…

  11. 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.

  12. 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…

  13. 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…

  14. 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.

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

    DTIC Science & Technology

    2010-09-17

    1-2. See also Antonie Boessenkool, “Pratt & Whitney’s Costs Parts-Reject Rate Too High: JSF Official,” Defense News, August 3, 2009. 12 Office of...congressionally directed appropriations over the past four years. A February 2010 letter from DOD’s Director of Cost Assessment and Program Evaluation cited the...Alternate Engine Cost/Benefit Analysis,” undated. Press reports and CRS sources indicate that the letter was received by the Congressional defense

  16. 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.

  17. 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…

  18. 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…

  19. 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…

  20. 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…

  1. 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.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. Validation and Interrogation of Differentially Expressed and Alternatively Spliced Genes in African-American Prostate Cancer

    DTIC Science & Technology

    2015-10-01

    RNA and annotated. In addition, we have developed SSOs to manipulate PIK3CD alternative splicing, to correct aberrant splicing leading to production...molecular mechanisms, differential gene expression, alternative RNA splicing, epigenetic alterations, clinical tumor aggressiveness 16. SECURITY...words): Prostate cancer, health disparities among racial groups, molecular mechanisms, differential gene expression, alternative RNA splicing

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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

  15. 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…

  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. 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...

  18. 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...

  19. 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...

  20. 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...

  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. 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…

  3. 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.

  4. 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...

  5. 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…

  6. 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.

  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. 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…

  9. 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…

  10. 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…

  11. 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…

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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

  17. Certification Report: Army Aviation Alternative Fuels Certification Program

    DTIC Science & Technology

    2016-08-01

    Words) The Department of Defense’s primary alternative fuels goal is to ensure operational military readiness, improve battle space effectiveness...Department of Defense’s primary alternative fuels goal is to ensure operational military readiness, improve battle space effectiveness, and further...testing protocols. 4 Table 1. MIL-HDBK-510A Overview of Tasks Chemical Tests (Appendix B) • Properties: • Chemical description of fuel • MSDS

  18. 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.

  19. 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

  20. 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.

  1. 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).

  2. 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

  3. Programming gene expression with combinatorial promoters

    PubMed Central

    Cox, Robert Sidney; Surette, Michael G; Elowitz, Michael B

    2007-01-01

    Promoters control the expression of genes in response to one or more transcription factors (TFs). The architecture of a promoter is the arrangement and type of binding sites within it. To understand natural genetic circuits and to design promoters for synthetic biology, it is essential to understand the relationship between promoter function and architecture. We constructed a combinatorial library of random promoter architectures. We characterized 288 promoters in Escherichia coli, each containing up to three inputs from four different TFs. The library design allowed for multiple −10 and −35 boxes, and we observed varied promoter strength over five decades. To further analyze the functional repertoire, we defined a representation of promoter function in terms of regulatory range, logic type, and symmetry. Using these results, we identified heuristic rules for programming gene expression with combinatorial promoters. PMID:18004278

  4. 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)

  5. 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)

  6. 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…

  7. 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…

  8. 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.

  9. 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.

  10. 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.

  11. 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…

  12. 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,…

  13. 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…

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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

  20. 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,…

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

    DTIC Science & Technology

    2011-04-20

    111-212).7 In a letter , Office of Management and Budget Director Jacob Lew stated that “DoD would be expected to continue funding activities on a pro...discussion. 8 Letter from Jacob J. Lew, Director, Office of Management and Budget, to Senator Sherrod Brown, December 21, 2010. 9 Tony Capaccio...2009, pp. 1-2. See also Antonie Boessenkool, “Pratt & Whitney’s Costs Parts-Reject Rate Too High: JSF Official,” (continued...) F-35 Alternate Engine

  2. 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)

  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. 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.

  5. 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…

  6. 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,…

  7. 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...

  8. 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…

  9. 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…

  10. 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…

  11. 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…

  12. 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…

  13. 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…

  14. 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

  15. 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…

  16. 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…

  17. 76 FR 77716 - Alternate Passenger Rail Service Pilot Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-14

    ... bidder's verifiable cost projections for their proposed service, rather than the historical Amtrak costs... quantitative measurements of the cost and benefit streams expected to result from the adoption of a rule... pay for any such operating subsidy, or any other costs arising from the proposed pilot program;...

  18. 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…

  19. 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.

  20. 76 FR 55335 - Alternate Passenger Rail Service Pilot Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-09-07

    ...This NPRM is in response to a statutory mandate that FRA complete a rulemaking proceeding to develop a pilot program that permits a rail carrier or rail carriers 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 period not to exceed five years......

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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.

  6. 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…

  7. 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…

  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. 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...

  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. 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…

  12. 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…

  13. 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 GRADES OF DAIRY PRODUCTS 1 General Specifications for Dairy Plants Approved for USDA Inspection... for dairy products. (a) When a plant has in operation an acceptable quality control program which...

  14. 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…

  15. 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…

  16. 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

  17. 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

  18. 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;…

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. 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.

  7. 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…

  8. 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.

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. 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

  16. 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.

  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. 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.

  19. 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…

  20. 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…

  1. 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…

  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. 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…

  4. 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…

  5. 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.

  6. 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…

  7. 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…

  8. 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,…

  9. 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...

  10. 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...

  11. 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...

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

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 1 2012-10-01 2012-10-01 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, 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...

  14. 46 CFR 71.50-19 - The Alternative Hull Examination (AHE) Program application.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ...) 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...

  15. 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...

  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. 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…

  18. 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…

  19. 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.

  20. 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.

  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. 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.

  3. 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.

  4. 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

  5. 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

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. 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)

  19. 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.

  20. 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…

  1. 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.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. Perspectives on best practices for gene therapy programs.

    PubMed

    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; Gubitz, Amelie K

    2015-03-01

    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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  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.

  15. 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

  16. '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.

  17. 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

  18. 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.

  19. 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).

  20. 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.

  1. 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…

  2. 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…

  3. 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.

  4. Community-based home-care program for the management of pre-eclampsia: an alternative.

    PubMed Central

    Helewa, M; Heaman, M; Robinson, M A; Thompson, L

    1993-01-01

    OBJECTIVE: To evaluate the safety, acceptability and cost of a community-based home-care program for the management of mild pre-eclampsia. DESIGN: A descriptive study of outcomes between Apr. 1, 1985, and Dec. 31, 1989. SETTING: St. Boniface General Hospital, Winnipeg. PATIENTS: Urban Winnipeg residents between 27 and 40 weeks' gestation with mild pre-eclampsia who demonstrated acceptance and compliance with home-care management; 321 patients of 1330 were enrolled in the program. INTERVENTIONS: Bed rest at home with daily biochemical and biophysical follow-up protocol and weekly clinic visits; patient education; hospital admission for labour, induction, worsening pre-eclampsia or noncompliance with rest at home. OUTCOME MEASURES: Patterns of referral to the program; clinical, biochemical and biophysical profiles; incidence of severe complications; reduction in total hospital stay and cost analysis. RESULTS: As many women were referred from physicians' offices as were referred from the hospital's antepartum unit, the average gestational age at referral being 36 weeks. Most (205 [64%]) of the women were nulliparous. The average length of stay in the program was 11.5 days. The program's availability resulted in a reduction of 2 days (from 5.7 days to 3.7 days) on average in the length of hospital stay when analysed for all 1330 women with pre-eclampsia. Of the 321 patients in the program 137 (43%) were admitted to hospital for worsening pre-eclampsia; severe pre-eclampsia developed 4 days after admission in 9. No patient suffered eclampsia, disseminated intravascular coagulopathy, abruption or fetal loss related to pre-eclampsia while in the program. The estimated cost saving in the management of pre-eclampsia was over $700,000 over the study period. CONCLUSION: The community-based home-care program is a safe, feasible and less costly alternative to hospital admission in the management of mild pre-eclampsia. PMID:8374846

  5. 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.

  6. 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.

  7. 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

  8. 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…

  9. 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.

  10. 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

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. Current status of the Gene-Tox Program.

    PubMed Central

    Auletta, A E; Brown, M; Wassom, J S; Cimino, M C

    1991-01-01

    The U.S. Environmental Protection Agency's Gene-Tox Program is a multiphased effort to review and evaluate the existing literature in assay systems available in the field of genetic toxicology. The first phase of the Gene-Tox Program selected assay systems for evaluation, generated expert panel reviews of the data from the scientific literature, and recommended testing protocols for the systems. Phase II established and evaluated the database of chemical genetic toxicity data for its relevance to identifying human health hazards. The ongoing phase III continues reviewing and updating chemical data in selected assay systems. Currently, data exist on over 4000 chemicals in 27 assay systems; two additional assay systems will be included in phase III. The review data are published in the scientific literature and are also publicly available through the National Library of Medicine TOXNET system. The review and analysis components of Gene-Tox comprise 45 published papers, and several others are in preparation. Differences that have been observed between Gene-Tox and National Toxicology Program databases relative to the sensitivity, specificity, accuracy, and predictivity of genetic toxicity data compared to carcinogenesis data are ascribable to differences between the two databases in chemical selection criteria, testing protocols, and chemical class distributions. PMID:1820273

  20. 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.

  1. 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

  2. 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

  3. 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

  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. 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.

  7. 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

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. MSWT-01, an alternative in combining Production Based Education (PBE) and student CSR program in Polman

    NASA Astrophysics Data System (ADS)

    Ananto, Gamawan; Setiawan, Albertus B.; Z, Darman M.

    2014-06-01

    MSWT-01, Mobile Surface Water Treatment, producing 1m3 per hour, is an alternative for providing clean water in flood disaster areas, and was developed at Bandung State Polytechnic for Manufacturing (Polman) as a part of institution research project. The combination of cartridge or membrane technology such as carbon block, MF, UF and filtration media is used for this machine, instead of coagulation-flocculation with chemical addition, due to emergency purposes related with its treatment processing time. The idea is that MSWT could be combined with Production Based Education (PBE) concept in Polman as a vocational education institution and students 'CSR', students social activities. With the number of implementation trials in real flood area condition, MSWT will be developed further based on the technical output result. The manufacturing process for improving or adding necessary features could be implemented as a student's project in PBE system. This might be an ideal combination alternative for such vocational institution that students get the product media for their PBE program and implement their work as a defined social activity. They will learn and experience related technical matters and more social interactions with the people and other disaster stakeholder as well.

  16. HuR Regulates Alternative Splicing of the TRA2β Gene in Human Colon Cancer Cells under Oxidative Stress

    PubMed Central

    Akaike, Yoko; Kuwano, Yuki; Nishida, Kensei; Kajita, Keisuke; Kurokawa, Ken; Satake, Yuzuru; Shoda, Katsutoshi; Imoto, Issei; Rokutan, Kazuhito

    2014-01-01

    Hu antigen R (HuR) regulates stress responses through stabilizing and/or facilitating the translation of target mRNAs. The human TRA2β gene encodes splicing factor transformer 2β (Tra2β) and generates 5 mRNA isoforms (TRA2β1 to -5) through alternative splicing. Exposure of HCT116 colon cancer cells to sodium arsenite stimulated checkpoint kinase 2 (Chk2)- and mitogen-activated protein kinase p38 (p38MAPK)-mediated phosphorylation of HuR at positions S88 and T118. This induced an association between HuR and the 39-nucleotide (nt) proximal region of TRA2β exon 2, generating a TRA2β4 mRNA that includes exon 2, which has multiple premature stop codons. HuR knockdown or Chk2/p38MAPK double knockdown inhibited the arsenite-stimulated production of TRA2β4 and increased Tra2β protein, facilitating Tra2β-dependent inclusion of exons in target pre-mRNAs. The effects of HuR knockdown or Chk2/p38MAPK double knockdown were also confirmed using a TRA2β minigene spanning exons 1 to 4, and the effects disappeared when the 39-nt region was deleted from the minigene. In endogenous HuR knockdown cells, the overexpression of a HuR mutant that could not be phosphorylated (with changes of serine to alanine at position 88 [S88A], S100A, and T118A) blocked the associated TRA2β4 interaction and TRA2β4 generation, while the overexpression of a phosphomimetic HuR (with mutations S88D, S100D, and T118D) restored the TRA2β4-related activities. Our findings revealed the potential role of nuclear HuR in the regulation of alternative splicing programs under oxidative stress. PMID:24865968

  17. HuR regulates alternative splicing of the TRA2β gene in human colon cancer cells under oxidative stress.

    PubMed

    Akaike, Yoko; Masuda, Kiyoshi; Kuwano, Yuki; Nishida, Kensei; Kajita, Keisuke; Kurokawa, Ken; Satake, Yuzuru; Shoda, Katsutoshi; Imoto, Issei; Rokutan, Kazuhito

    2014-08-01

    Hu antigen R (HuR) regulates stress responses through stabilizing and/or facilitating the translation of target mRNAs. The human TRA2β gene encodes splicing factor transformer 2β (Tra2β) and generates 5 mRNA isoforms (TRA2β1 to -5) through alternative splicing. Exposure of HCT116 colon cancer cells to sodium arsenite stimulated checkpoint kinase 2 (Chk2)- and mitogen-activated protein kinase p38 (p38(MAPK))-mediated phosphorylation of HuR at positions S88 and T118. This induced an association between HuR and the 39-nucleotide (nt) proximal region of TRA2β exon 2, generating a TRA2β4 mRNA that includes exon 2, which has multiple premature stop codons. HuR knockdown or Chk2/p38(MAPK) double knockdown inhibited the arsenite-stimulated production of TRA2β4 and increased Tra2β protein, facilitating Tra2β-dependent inclusion of exons in target pre-mRNAs. The effects of HuR knockdown or Chk2/p38(MAPK) double knockdown were also confirmed using a TRA2β minigene spanning exons 1 to 4, and the effects disappeared when the 39-nt region was deleted from the minigene. In endogenous HuR knockdown cells, the overexpression of a HuR mutant that could not be phosphorylated (with changes of serine to alanine at position 88 [S88A], S100A, and T118A) blocked the associated TRA2β4 interaction and TRA2β4 generation, while the overexpression of a phosphomimetic HuR (with mutations S88D, S100D, and T118D) restored the TRA2β4-related activities. Our findings revealed the potential role of nuclear HuR in the regulation of alternative splicing programs under oxidative stress.

  18. Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine.

    PubMed

    Sheng, Zhen; Sun, Yi; Zhu, Ruixin; Jiao, Na; Tang, Kailin; Cao, Zhiwei; Ma, Chao

    2015-01-01

    Berberine has been identified with anti-proliferative effects on various cancer cells. Many researchers have been trying to elucidate the anti-cancer mechanisms of berberine based on differentially expressed genes. However, differentially alternative splicing genes induced by berberine might also contribute to its pharmacological actions and have not been reported yet. Moreover, the potential functional cross-talking between the two sets of genes deserves further exploration. In this study, RNA-seq technology was used to detect the differentially expressed genes and differentially alternative spliced genes in BEL-7402 cancer cells induced by berberine. Functional enrichment analysis indicated that these genes were mainly enriched in the p53 and cell cycle signalling pathway. In addition, it was statistically proven that the two sets of genes were locally co-enriched along chromosomes, closely connected to each other based on protein-protein interaction and functionally similar on Gene Ontology tree. These results suggested that the two sets of genes regulated by berberine might be functionally cross-talked and jointly contribute to its cell cycle arresting effect. It has provided new clues for further researches on the pharmacological mechanisms of berberine as well as the other botanical drugs.

  19. Characterization of the interferon genes in homozygous rainbow trout reveals two novel genes, alternate splicing and differential regulation of duplicated genes

    USGS Publications Warehouse

    Purcell, M.K.; Laing, K.J.; Woodson, J.C.; Thorgaard, G.H.; Hansen, J.D.

    2009-01-01

    The genes encoding the type I and type II interferons (IFNs) have previously been identified in rainbow trout and their proteins partially characterized. These previous studies reported a single type II IFN (rtIFN-??) and three rainbow trout type I IFN genes that are classified into either group I (rtIFN1, rtIFN2) or group II (rtIFN3). In this present study, we report the identification of a novel IFN-?? gene (rtIFN-??2) and a novel type I group II IFN (rtIFN4) in homozygous rainbow trout and predict that additional IFN genes or pseudogenes exist in the rainbow trout genome. Additionally, we provide evidence that short and long forms of rtIFN1 are actively and differentially transcribed in homozygous trout, and likely arose due to alternate splicing of the first exon. Quantitative reverse transcriptase PCR (qRT-PCR) assays were developed to systematically profile all of the rainbow trout IFN transcripts, with high specificity at an individual gene level, in na??ve fish and after stimulation with virus or viral-related molecules. Cloned PCR products were used to ensure the specificity of the qRT-PCR assays and as absolute standards to assess transcript abundance of each gene. All IFN genes were modulated in response to Infectious hematopoietic necrosis virus (IHNV), a DNA vaccine based on the IHNV glycoprotein, and poly I:C. The most inducible of the type I IFN genes, by all stimuli tested, were rtIFN3 and the short transcript form of rtIFN1. Gene expression of rtIFN-??1 and rtIFN-??2 was highly up-regulated by IHNV infection and DNA vaccination but rtIFN-??2 was induced to a greater magnitude. The specificity of the qRT-PCR assays reported here will be useful for future studies aimed at identifying which cells produce IFNs at early time points after infection. ?? 2008 Elsevier Ltd.

  20. Comparative analysis of alternative splicing, alternative polyadenylation and the expression of the two KIN genes from cytoplasmic male sterility cabbage (Brassica oleracea L. var. capitata L.).

    PubMed

    Tao, Peng; Huang, Xiaoyun; Li, Biyuan; Wang, Wuhong; Yue, Zhichen; Lei, Juanli; Zhong, Xinmin

    2014-06-01

    The KIN genes are crucial members of the cold-regulated gene family. They play exclusive roles during the developmental processes of many organs and respond to various abiotic stresses in plants. However, little is known about the regulation of KIN gene expression in cytoplasmic male sterility (CMS) cabbages (Brassica oleracea L. var. capitata L.). We carried out a genome-wide analysis to identify the KIN genes in the CMS cabbage. Two non-redundant KIN genes, named BoKIN1 (Bol021262) and BoKIN2 (Bol030498), were identified. Reverse transcriptase PCR detected alternative splicing (AS) products of BoKIN1 (four AS products) and BoKIN2 (three AS products). In addition, alternative polyadenylation (APA) was observed for BoKIN1 and BoKIN2 in the CMS cabbage, resulting in variable 3'UTRs in their transcripts. Furthermore, the transcription levels of BoKIN1-0 and BoKIN2-0, the introns of which were spliced completely, were analyzed in various organs and young leaves treated by abiotic stresses. Our data indicated that BoKIN1-0 is highly expressed in various organs, whereas BoKIN2-0 is expressed exclusively in the stamen. Our study also suggested that BoKIN1-0 was upregulated significantly in young leaves of plants exposed to abscisic acid treatment, and cold and heat stress. BoKIN1 and BoKIN2 had differential AS and APA patterns in pre-mRNA processing, and showed differences in their expression patterns and transcript levels. BoKIN1 participates widely in organ development and responds to diverse abiotic stresses, whereas BoKIN2 plays a main role in stamen development in the CMS cabbage.

  1. The Anne Frank Haven: A case of an alternative educational program in an integrative Kibbutz setting

    NASA Astrophysics Data System (ADS)

    Ben-Peretz, Miriam; Giladi, Moshe; Dror, Yuval

    1992-01-01

    The essential features of the programme of the Anne Frank Haven are the complete integration of children from low SES and different cultural backgrounds with Kibbutz children; a holistic approach to education; and the involvement of the whole community in an "open" residential school. After 33 years, it is argued that the experiment has proved successful in absorbing city-born youth in the Kibbutz, enabling at-risk populations to reach significant academic achievements, and ensuring their continued participation in the dominant culture. The basic integration model consists of "layers" of concentric circles, in dynamic interaction. The innermost circle is the class, the learning community. The Kibbutz community and the foster parents form a supportive, enveloping circle, which enables students to become part of the outer community and to intervene in it. A kind of meta-environment, the inter-Kibbutz partnership and the Israeli educational system, influence the program through decision making and guidance. Some of the principles of the Haven — integration, community involvement, a year's induction for all new students, and open residential settings — could be useful for cultures and societies outside the Kibbutz. The real "secret" of success of an alternative educational program is the dedicated, motivated and highly trained staff.

  2. Persistently low transplantation rate of ABO blood type O and highly sensitised patients despite alternative transplantation programs.

    PubMed

    Roodnat, Joke I; van de Wetering, Jacqueline; Claas, Frans H; Ijzermans, Jan; Weimar, Willem

    2012-09-01

    ABO blood type O and highly sensitised patients have the smallest chance to receive kidney transplantation. Do alternative donation programs increase this chance? In the period studied: 2323 patients were enlisted on the Rotterdam waiting list for a renal transplantation: 435 patients still waiting (WL), 464 delisted without transplantation (DWT). 1424 received deceased donor (DD, 535) or living donor (LD, 889, including 204 alternative) transplantation. Alternative LD programs in our centre are: paired kidney-exchange, altruistic with domino-paired donation and ABO-incompatible donation (ABOi). Compared to populations not transplanted, blood type O recipients are significantly underrepresented in DD and all LD transplantation populations, except the ABOi program. Highly sensitised patients are overrepresented in DD, but underrepresented in all LD transplantation populations. The high transplantation rate of highly sensitised patients was the result of Eurotransplant Acceptable mismatch program (AM). The LD ABOi and DD AM programs are the only alternative donation programs favourable for patients with low chances. While the contribution of direct LD transplantations will increase in time, the relative success rate of low-chance patients will decrease. Beside increasing LD ABOi transplantation, a new DD allocation model favouring both highly immunised and blood type O patients is essential.

  3. Regulation of tissue-specific expression of alternative peripheral myelin protein-22 (PMP22) gene transcripts by two promoters

    SciTech Connect

    Patel, P.I.; Schoener-Scott, R.; Lupski, J.R.

    1994-09-01

    Mutations affecting the peripheral myelin protein-22 (PMP22) gene have been shown to be associated with inherited peripheral neuropathies. We have cloned and characterized the human PMP22 gene which spans approximately 40 kilobases and contains four coding exons. Towards developing gene therapy regimens for the associated peripheral neuropathies, we have initiated detailed analysis of the 5{prime} flanking region of the PMP22 gene and identified two alternatively transcribed, but untranslated exons. Mapping of separate PMP22 mRNA transcription initiation sites to each of these exons indicates that PMP22 expression is regulated by two alternatively used promoters. Both putative promoter sequences demonstrated the ability to drive expression of reporter genes in transfection experiments. Furthermore, the structure of the 5{prime} portion of the PMP22 gene appears to be identical in rat and human, supporting the biological significance of the observed arrangement of regulatory regions. The relative expression of the alternative PMP22 transcripts is tissue-specific and high levels of the exon 1A-containing transcript are tightly coupled to myelin formation. In contrast, exon 1B-containing transcripts are predominant in non-neural tissues and in growth-arrested primary fibroblasts. The observed regulation of the PMP22 by a complex molecular mechanism is consistent with the proposed dual role of PMP22 in neural and non-neural tissue.

  4. Alternate serotype adenovector provides long-term therapeutic gene expression in the eye

    PubMed Central

    Hamilton, Melissa M.; Byrnes, Gordon A.; Gall, Jason G.; Brough, Douglas E.; King, C. Richter

    2008-01-01

    Purpose To determine whether the duration of transgene expression from an alternate adenovector serotype, Ad35, can provide advantages over an Ad5 serotype vector following a single intravitreal (IVT) administration. Methods To assess the transgene expression profile, mice received one IVT injection of Ad5- or Ad35-based vectors expressing green fluorescent protein (GFP), luciferase or pigment epithelium-derived factor (PEDF). At specified time points following vector administration, eyes were monitored for GFP expression, or eyes were harvested and assayed for adenovector genomes, luciferase activity or PEDF levels. Ad35-based vector in vivo biologic activity was investigated using a mouse model of laser-induced choroidal neovascularization (CNV). On Day 0, mice received one IVT injection of Ad5.PEDF or Ad35.PEDF (HI-RGD) followed by laser-induced CNV on Day 28. Fourteen days later, animals were perfused with fluorescein-labeled dextran and CNV lesion size quantitated in choroidal flat mounts. Results These studies demonstrate that following a single IVT adenovector administration: 1) gene expression is prolonged following administration of an Ad35 compared to an Ad5-based vector; 2) the amount of vector genomes in the eye remain constant out to 60 days post injection of both Ad5 and Ad35-based vectors; and 3) an Ad35.PEDF (HI-RGD) vector inhibits CNV in a mouse model at 42 days post injection. Conclusions These studies show that transgene and genome levels are prolonged in the eye following 1 IVT injection of an Ad35-based vector. Moreover, therapeutic gene levels from 1 IVT administration of Ad35.PEDF (HI-RGD) vector block abnormal blood vessel growth in a laser-induced CNV mouse model. PMID:19122827

  5. Genes encoding Cher-TPR fusion proteins are predominantly found in gene clusters encoding chemosensory pathways with alternative cellular functions.

    PubMed

    Muñoz-Martínez, Francisco; García-Fontana, Cristina; Rico-Jiménez, Miriam; Alfonso, Carlos; Krell, Tino

    2012-01-01

    Chemosensory pathways correspond to major signal transduction mechanisms and can be classified into the functional families flagellum-mediated taxis, type four pili-mediated taxis or pathways with alternative cellular functions (ACF). CheR methyltransferases are core enzymes in all of these families. CheR proteins fused to tetratricopeptide repeat (TPR) domains have been reported and we present an analysis of this uncharacterized family. We show that CheR-TPRs are widely distributed in GRAM-negative but almost absent from GRAM-positive bacteria. Most strains contain a single CheR-TPR and its abundance does not correlate with the number of chemoreceptors. The TPR domain fused to CheR is comparatively short and frequently composed of 2 repeats. The majority of CheR-TPR genes were found in gene clusters that harbor multidomain response regulators in which the REC domain is fused to different output domains like HK, GGDEF, EAL, HPT, AAA, PAS, GAF, additional REC, HTH, phosphatase or combinations thereof. The response regulator architectures coincide with those reported for the ACF family of pathways. Since the presence of multidomain response regulators is a distinctive feature of this pathway family, we conclude that CheR-TPR proteins form part of ACF type pathways. The diversity of response regulator output domains suggests that the ACF pathways form a superfamily which regroups many different regulatory mechanisms, in which all CheR-TPR proteins appear to participate. In the second part we characterize WspC of Pseudomonas putida, a representative example of CheR-TPR. The affinities of WspC-Pp for S-adenosylmethionine and S-adenosylhomocysteine were comparable to those of prototypal CheR, indicating that WspC-Pp activity is in analogy to prototypal CheRs controlled by product feed-back inhibition. The removal of the TPR domain did not impact significantly on the binding constants and consequently not on the product feed-back inhibition. WspC-Pp was found to be

  6. Extensive divergence in alternative splicing patterns after gene and genome duplication during the evolutionary history of Arabidopsis.

    PubMed

    Zhang, Peter G; Huang, Suzanne Z; Pin, Anne-Laure; Adams, Keith L

    2010-07-01

    Gene duplication at various scales, from single gene duplication to whole-genome (WG) duplication, has occurred throughout eukaryotic evolution and contributed greatly to the large number of duplicated genes in the genomes of many eukaryotes. Previous studies have shown divergence in expression patterns of many duplicated genes at various evolutionary time scales and cases of gain of a new function or expression pattern by one duplicate or partitioning of functions or expression patterns between duplicates. Alternative splicing (AS) is a fundamental aspect of the expression of many genes that can increase gene product diversity and affect gene regulation. However, the evolution of AS patterns of genes duplicated by polyploidy, as well as in a sizable number of duplicated gene pairs in plants, has not been examined. Here, we have characterized conservation and divergence in AS patterns in genes duplicated by a polyploidy event during the evolutionary history of Arabidopsis thaliana. We used reverse transcription-polymerase chain reaction to assay 104 WG duplicates in six organ types and in plants grown under three abiotic stress treatments to detect organ- and stress-specific patterns of AS. Differences in splicing patterns in one or more organs, or under stress conditions, were found between the genes in a large majority of the duplicated pairs. In a few cases, AS patterns were the same between duplicates only under one or more abiotic stress treatments and not under normal growing conditions or vice versa. We also examined AS in 42 tandem duplicates and we found patterns of AS roughly comparable with the genes duplicated by polyploidy. The alternatively spliced forms in some of the genes created premature stop codons that would result in missing or partial functional domains if the transcripts are translated, which could affect gene function and cause functional divergence between duplicates. Our results indicate that AS patterns have diverged considerably after

  7. THE GRK4 SUBFAMILY OF G PROTEIN-COUPLED RECEPTOR KINASES: ALTERNATIVE SPLICING, GENE ORGANIZATION, AND SEQUENCE CONSERVATION

    EPA Science Inventory

    The GRK4 subfamily of G protein-coupled receptor kinases. Alternative splicing, gene organization, and sequence conservation.

    Premont RT, Macrae AD, Aparicio SA, Kendall HE, Welch JE, Lefkowitz RJ.

    Department of Medicine, Howard Hughes Medical Institute, Duke Univer...

  8. Plant Gene and Alternatively Spliced Variant Annotator. A plant genome annotation pipeline for rice gene and alternatively spliced variant identification with cross-species expressed sequence tag conservation from seven plant species.

    PubMed

    Chen, Feng-Chi; Wang, Sheng-Shun; Chaw, Shu-Miaw; Huang, Yao-Ting; Chuang, Trees-Juen

    2007-03-01

    The completion of the rice (Oryza sativa) genome draft has brought unprecedented opportunities for genomic studies of the world's most important food crop. Previous rice gene annotations have relied mainly on ab initio methods, which usually yield a high rate of false-positive predictions and give only limited information regarding alternative splicing in rice genes. Comparative approaches based on expressed sequence tags (ESTs) can compensate for the drawbacks of ab initio methods because they can simultaneously identify experimental data-supported genes and alternatively spliced transcripts. Furthermore, cross-species EST information can be used to not only offset the insufficiency of same-species ESTs but also derive evolutionary implications. In this study, we used ESTs from seven plant species, rice, wheat (Triticum aestivum), maize (Zea mays), barley (Hordeum vulgare), sorghum (Sorghum bicolor), soybean (Glycine max), and Arabidopsis (Arabidopsis thaliana), to annotate the rice genome. We developed a plant genome annotation pipeline, Plant Gene and Alternatively Spliced Variant Annotator (PGAA). Using this approach, we identified 852 genes (931 isoforms) not annotated in other widely used databases (i.e. the Institute for Genomic Research, National Center for Biotechnology Information, and Rice Annotation Project) and found 87% of them supported by both rice and nonrice EST evidence. PGAA also identified more than 44,000 alternatively spliced events, of which approximately 20% are not observed in the other three annotations. These novel annotations represent rich opportunities for rice genome research, because the functions of most of our annotated genes are currently unknown. Also, in the PGAA annotation, the isoforms with non-rice-EST-supported exons are significantly enriched in transporter activity but significantly underrepresented in transcription regulator activity. We have also identified potential lineage-specific and conserved isoforms, which are

  9. More than genes: the advanced fetal programming hypothesis.

    PubMed

    Hocher, Berthold

    2014-10-01

    Many lines of data, initial epidemiologic studies as well as subsequent extensive experimental studies, indicate that early-life events play a powerful role in influencing later suceptibility to certain chronic diseases. Such events might be over- or undernutrition, exposure to environmental toxins, but also changes in hormones, in particular stress hormones. Typically, those events are triggered by the environmental challenges of the mother. However, recent studies have shown that paternal environmental or nutritional factors affect the phenotype of the offspring as well. The maternal and paternal environmental factors act on the phenotype of the offspring via epigenetic modification of its genome. The advanced fetal programming hypothesis proposes an additional non-environmentally driven mechanism: maternal and also paternal genes may influence the maturating sperm, the oocyte, and later the embryo/fetus, leading to their epigenetic alteration. Thus, the observed phenotype of the offspring may be altered by maternal/paternal genes independent of the fetal genome. Meanwhile, several independent association studies in humans dealing with metabolic and neurological traits also suggest that maternal genes might affect the offspring phenotype independent of the transmission of that particular gene to the offspring. Considering the implications of this hypothesis, some conclusions drawn from transgenic or knockout animal models and based on the causality between a genetic alteration and a phenotype, need to be challenged. Possible implications for the development, diagnostic and therapy of human genetic diseases have to be investigated.

  10. Calcitonin gene-related peptide receptor expression in alternatively activated monocytes/macrophages during irreversible pulpitis.

    PubMed

    Caviedes-Bucheli, Javier; Moreno, Gloria Cristina; López, María Paula; Bermeo-Noguera, Ana Milena; Pacheco-Rodríguez, Gloriana; Cuellar, Adriana; Muñoz, Hugo Roberto

    2008-08-01

    The purpose of this study was to quantify the percentage and the mean fluorescence intensity of viable alternatively activated monocytes/macrophages (AAMø) CD163+ positive for calcitonin gene-related peptide receptor (CGRPr) within the total AAMø population in human dental pulp. Pulp tissue samples were collected from teeth with a clinical diagnosis of irreversible pulpitis (n = 13), pulps with induced inflammation (n = 13), and normal pulps (n = 13). All samples were labeled to identify positive cells for CGRPr and CD163 using a flow cytometry assay. Results demonstrated that a high percentage of total viable AAMø CD163+ expressed CGRPr on their membranes (72.12% in healthy pulp, 62.20% in irreversible pulpitis, and 58.01% in induced pulpitis). Significant differences were found between mean AAMø CD163+ fluorescence for CGRPr according to pulp condition, being greater in irreversible pulpitis. It can be concluded that AAMø CD163+ are expressed during normal and inflammatory processes, supporting the hypothesis that they could exercise an anti-inflammatory action that could be controlled by CGRP signaling after its binding.

  11. The dynamics of the alternatively spliced NOL7 gene products and role in nucleolar architecture

    PubMed Central

    Kinor, Noa

    2011-01-01

    Three alternatively spliced forms of the human NOL7 gene coding for relatively small proteins were identified. The two shorter forms were generated by intron retention events, and each isoform was differently localized within the cell. The NOL7-SP1 long form (29 kD) localized to the nucleolus, SP2 was nucleoplasmic, while SP3 was distributed throughout the whole cell. NOL7-SP1 was confined to the nucleolar granular component, and during cell division disassociated from the nucleolus. Knockdown of NOL7-SP1 levels abrogated nucleolar architecture, in particular the internal regions, and reduced cell proliferation. Analysis of the nucleolar dynamics of the SP1 protein during interphase showed nucleolar high binding affinity. Dissection of protein domains showed that nucleolar targeting was mediated by a unique C-terminal nucleolar localization sequence (NoLS). However, this sequence was not sufficient for conferring high binding affinity, which required additional regions of the protein. Our analysis shows that NOL7 is important for maintaining internal nucleolar structure and cell growth rates, and that while specific protein localization can be obtained by specific short localization motifs, nucleolar residency through binding must be mediated by a synergistic combination of protein modules. PMID:21818416

  12. Alternative fuels for vehicles fleet demonstration program final report. Volume 1: Summary

    SciTech Connect

    1997-03-01

    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 in typical applications in New York State. During 3 years of collecting data, 7.3 million miles of driving were accumulated, 1,003 chassis-dynamometer emissions tests were performed, 862,000 gallons of conventional fuel were saved, and unique information was developed about garage safety recommendations, vehicle performance, and other topics. Findings are organized by vehicle and fuel type. For light-duty compressed natural gas (CNG) vehicles, technology has evolved rapidly and closed-loop, electronically-controlled fuel systems provide performance and emissions advantages over open-loop, mechanical systems. The best CNG technology produces consistently low tailpipe emissions versus gasoline, and can eliminate evaporative emissions. Reduced driving range remains the largest physical drawback. Fuel cost is low ($/Btu) but capital costs are high, indicating that economics are best with vehicles that are used intensively. Propane produces impacts similar to CNG and is less expensive to implement, but fuel cost is higher than gasoline and safety codes limit use in urban areas. Light-duty methanol/ethanol vehicles provide performance and emissions benefits over gasoline with little impact on capital costs, but fuel costs are high. Heavy-duty CNG engines are evolving rapidly and provide large reductions in emissions versus diesel. Capital costs are high for CNG buses and fuel efficiency is reduced, but the fuel is less expensive and overall operating costs are about equal to those of diesel buses. Methanol buses provide performance and emissions benefits versus diesel, but fuel costs are high. Other emerging technologies were also evaluated, including electric vehicles, hybrid-electric vehicles, and fuel cells.

  13. Transcriptome analyses and differential gene expression in a non-model fish species with alternative mating tactics

    PubMed Central

    2014-01-01

    Background Social dominance is important for the reproductive success of males in many species. In the black-faced blenny (Tripterygion delaisi) during the reproductive season, some males change color and invest in nest making and defending a territory, whereas others do not change color and ‘sneak’ reproductions when females lay their eggs. Using RNAseq, we profiled differential gene expression between the brains of territorial males, sneaker males, and females to study the molecular signatures of male dimorphism. Results We found that more genes were differentially expressed between the two male phenotypes than between males and females, suggesting that during the reproductive period phenotypic plasticity is a more important factor in differential gene expression than sexual dimorphism. The territorial male overexpresses genes related to synaptic plasticity and the sneaker male overexpresses genes involved in differentiation and development. Conclusions Previously suggested candidate genes for social dominance in the context of alternative mating strategies seem to be predominantly species-specific. We present a list of novel genes which are differentially expressed in Tripterygion delaisi. This is the first genome-wide study for a molecular non-model species in the context of alternative mating strategies and provides essential information for further studies investigating the molecular basis of social dominance. PMID:24581002

  14. Commute alternatives educational outreach. Transportation demand management resource program for the transportation professional. Report for July 1993-December 1994

    SciTech Connect

    Winters, P.L.; Rudge, D.E.

    1995-01-01

    This project is designed to aid in the planning, implementation, evaluation, and improvements of a (TDM) agency of program. Through the use of examples, the TDM professional can review innovative programs and initiatives throughout the United States, and model activities after these exhibits. The equations and benchmarks cited by this publication are other effective tools which offer insights into the relative success of TDM plan components in various environments. This report also introduces many of the traditional and innovative commute alternatives and discusses the benefits, obstacles, and goals of these initiatives. Strategies including carpooling, vanpooling, telecommuting, tax incentives, guaranteed ride home programs, bicycle and pedestrian facilities, transit, telecommuting, alternative work hour programs, and intermodalism are discussed and evaluated in real-world scenarios.

  15. The Development and Implementation of Alternative Teacher Preparation Programs in Maryland: A Cross-Case Study of Montgomery and Prince George's County Public Schools

    ERIC Educational Resources Information Center

    Coffman, Ann Lynette Nutter

    2010-01-01

    Alternative teacher certification programs have become a prominent policy option to address teacher quality issues. Despite recent headway in the analysis of alternative teacher preparation graduates and programs (e.g., Weschler, et al., 2009; Boyd, et al., 2007), the literature has been plagued by incomplete program descriptions, limited research…

  16. Reverse engineering of gene regulatory network using restricted gene expression programming.

    PubMed

    Yang, Bin; Liu, Sanrong; Zhang, Wei

    2016-10-01

    Inference of gene regulatory networks has been becoming a major area of interest in the field of systems biology over the past decade. In this paper, we present a novel representation of S-system model, named restricted gene expression programming (RGEP), to infer gene regulatory network. A new hybrid evolutionary algorithm based on structure-based evolutionary algorithm and cuckoo search (CS) is proposed to optimize the architecture and corresponding parameters of model, respectively. Two synthetic benchmark datasets and one real biological dataset from SOS DNA repair network in E. coli are used to test the validity of our method. Experimental results demonstrate that our proposed method performs better than previously proposed popular methods.

  17. The CAM Education Program of the National Center for Complementary and Alternative Medicine: an overview.

    PubMed

    Pearson, Nancy J; Chesney, Margaret A

    2007-10-01

    The authors provide a historical context and overview of the experience of education projects at 14 health professions schools in the United States and the American Medical Students Association that were funded by the National Center for Complementary and Alternative Medicine at the National Institutes of Health in cohorts of five per year in 2000, 2001, and 2002-2003. These 15 projects were designed to incorporate CAM information into the curricula of conventional health professions schools. A longer-term goal was to accelerate the integration of CAM and conventional medicine. The overall program started in 2000 at a time when discussions about the definition, goals, and value of integrative medicine were already well underway. The efforts specific to each project, as well as the shared challenges, accomplishments, and collaborative efforts of all 15 projects, can provide guidance for the education of conventional health care providers about CAM in an integrative medicine environment. Challenging issues that must be faced include (1) the need to develop successful strategies to incorporate information about CAM into already dense health professions school curricula, (2) the need for conventional health professionals to have authoritative resources to provide their patients information about risks and benefits of CAM practices, and (3) the need to identify appropriate roles for CAM practitioners in educating conventional health professionals about CAM therapies. The authors discuss these issues and others and present some recommendations.

  18. EM-21 ALTERNATIVE ENHANCED CHEMICAL CLEANING PROGRAM FOR SLUDGE HEEL REMOVAL

    SciTech Connect

    Hay, M; King, W; Martino, C

    2009-12-18

    Preliminary studies in the EM-21 Alternative Chemical Cleaning Program have focused on understanding the dissolution of Hematite (a primary sludge heel phase) in oxalic acid, with a focus on minimizing oxalic acid usage. Literature reviews, thermodynamic modeling, and experimental results have all confirmed that pH control, preferably using a supplemental proton source, is critical to oxalate minimization. With pH control, iron concentrations as high as 0.103 M have been obtained in 0.11 M oxalic acid. This is consistent with the formation of a 1:1 (iron:oxalate) complex. The solubility of Hematite in oxalic acid has been confirmed to increase by a factor of 3 when the final solution pH decreases from 5 to below 1. This is consistent with literature predictions of a shift in speciation from a 1:3 to 1:1 as the pH is lowered. Above a solution pH of 6, little Hematite dissolves. These results emphasize the importance of pH control in optimizing Hematite dissolution in oxalic acid.

  19. Capacity Building Special Alternatives Program Community School District 3. Final Evaluation Report, 1993-94. OER Report.

    ERIC Educational Resources Information Center

    Duque, Diana L.

    The Capacity Building Special Alternatives Program, an Elementary and Secondary Education Act Title VII-funded project in its second year of operation, functioned at seven schools in a community school district of Manhattan (New York). The project served 195 students of limited English proficiency (LEP) whose native languages were Albanian,…

  20. Educators' Perceptions of the Effects of School Uniforms on School Climate in a Selected Metropolitan Disciplinary Alternative Education Program

    ERIC Educational Resources Information Center

    Chime, Emmanuel Onoh

    2010-01-01

    The purpose of this study was to examine educators' perceptions regarding the effects of school uniforms on school climate in a selected metropolitan disciplinary alternative education program. More specifically, this study investigated the influence of the variables group status, gender, ethnicity, age and years of experience on the perceptions…

  1. Teacher and Parent Perceptions of Classroom Experiences of African American Male Students in a High School Alternative Program

    ERIC Educational Resources Information Center

    Johnson, Kimberly C.

    2013-01-01

    A major concern in the public schools is the low academic achievement of African American males. This mixed methods study examined the classroom experiences of African American male students in an alternative program. The dual purpose was to investigate the teachers' perceptions and their ability to provide best learning environments for…

  2. An Interactive Microcomputer Program for Teaching the Impacts of Alternative Policy Sets in the Market for a Single Commodity.

    ERIC Educational Resources Information Center

    Li, Elton; Stoecker, Arthur

    1995-01-01

    Describes a computer software program where students define alternative policy sets and compare their effects on the welfare of consumers, producers, and the public sector. Policy sets may be a single tax or quota or a mix of taxes, subsidies, and/or price supports implemented in the marketing chain. (MJP)

  3. 46 CFR 71.50-27 - Alternative Hull Examination (AHE) program options: Divers or underwater remotely operated...

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ...: Divers or underwater remotely operated vehicle (ROV). 71.50-27 Section 71.50-27 Shipping COAST GUARD...-27 Alternative Hull Examination (AHE) program options: Divers or underwater remotely operated vehicle... minimum. Plating thickness gaugings must also be taken along a longitudinal belt at the wind and...

  4. Beginning Mathematics Teachers from Alternative Certification Programs: Their Success in the Classroom and How They Achieved It

    ERIC Educational Resources Information Center

    Ham, Edward

    2011-01-01

    This dissertation focuses on beginning mathematics teachers from alternative certification programs and their perceptions of what is required to be successful. A mixed-methods research study was completed with several goals in mind: (1) identifying how beginning mathematics teachers define success in the classroom during their earliest years, (2)…

  5. Views of Inquiry: Mismatches between Views of Science Education Faculty and Students of an Alternative Certification Program

    ERIC Educational Resources Information Center

    Demir, Abdulkadir; Abell, Sandra K.

    2010-01-01

    The purpose of this phenomenographic study was to: (a) gain an understanding of the meaning of inquiry held by beginning science teachers and their instructors in an Alternative Teacher Certification Program (ATCP); and (b) compare science teachers' views of inquiry with what they learned in their ATCP. Participants were four beginning science…

  6. When There Is No Blueprint: The Provision of Mental Health Services in Alternative School Programs for Suspended and Expelled Youth

    ERIC Educational Resources Information Center

    Goldenson, Julie

    2011-01-01

    A variety of alternative programs are being implemented in Canada and the United States for students who have exhibited conduct problems and who are suspended or expelled from their schools. Given the complexity of issues that these students frequently face, treatment must be multifaceted, wrap-around, delivered by trained professionals and be…

  7. UNESCO Science Programs: Impacts of U.S. Withdrawal and Suggestions for Alternative Interim Arrangements. A Preliminary Assessment.

    ERIC Educational Resources Information Center

    National Academy of Sciences - National Research Council, Washington, DC. Office of International Affairs.

    This study was conducted to provide the U.S. Department of State with an assessment of the potential impacts on science of a United States withdrawal from UNESCO and to suggest possible alternative arrangements to maintain essential U.S. scientific contacts with UNESCO-sponsored programs in case the United States were no longer a member of UNESCO…

  8. An Alternative Undergraduate Teacher Preparation Program: A Comprehensive One-to-One iPad Initiative Model

    ERIC Educational Resources Information Center

    Nguyen, Neal Nghia; Lyons, Catherine; Rogers-Adkinson, Diana; Bohannon, Larry; Fridley, Daryl; Gunn, Sharon; Smith, Shonta

    2016-01-01

    To date little literature has been published on how an alternative undergraduate teacher preparation program infuses mobile devices such as the iPad and its applications, model classrooms, and a high-tech computer lab to prepare teacher candidates. Preparing teacher candidates to generalize technological skills is most effective when it is hands…

  9. Alternatively spliced transcripts of Pi-ta blast resistance gene in Oryza sativa

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The Pi-ta gene in rice (Oryza sativa L.) confers resistance to races of Magnaporthe oryzae containing its cognate avirulence gene AVR-Pita. Pi-ta is a single-copy gene belonging to the nucleotide-binding site leucine-rich repeat (NBS-LRR) class of plant resistance (R) genes. In the present study, w...

  10. Caffeine induces tumor cytotoxicity via the regulation of alternative splicing in subsets of cancer-associated genes.

    PubMed

    Lu, Guan-Yu; Huang, Shih-Ming; Liu, Shu-Ting; Liu, Pei-Yao; Chou, Wei-Yuan; Lin, Wei-Shiang

    2014-02-01

    Caffeine causes a diverse range of pharmacological effects that are time- and concentration-dependent and reversible. The detailed mechanisms of caffeine in tumor suppression via tumor suppressor protein p53 remain unclear. The isoforms of p53 are physiological proteins that are expressed in normal cells and generated via alternative promoters, splicing sites and/or translational initiation sites. In this study, we investigated how caffeine modulated cell cycle arrest and apoptosis via the expression of various alternatively spliced p53 isoforms. Caffeine reduced p53α expression and induced the expression of p53β, which contains an alternatively spliced p53 C-terminus. In HeLa cells, the expression levels of many serine/arginine-rich splicing factors, including serine/arginine-rich splicing factors 2 and 3, were altered by caffeine. Serine/arginine-rich splicing factor 3 was a promising candidate for the serine/arginine-rich splicing factors responsible for the alternative splicing of p53 in response to caffeine treatment. In addition to p53-dependent functions, multiple target genes of serine/arginine-rich splicing factor 3 suggest that caffeine can regulate epithelial-mesenchymal-transition and hypoxic conditions to inhibit the survival of tumor cells. In summary, our data provide a new pathway of caffeine-modulated tumor suppression via the alternative splicing of the target genes of serine/arginine-rich splicing factor 3.

  11. SR proteins and the nonsense-mediated decay mechanism are involved in human GLB1 gene alternative splicing

    PubMed Central

    Santamaria, Raül; Vilageliu, Lluïsa; Grinberg, Daniel

    2008-01-01

    Background The human GLB1 gene is known to give rise to two alternatively spliced mRNAs, which encode two different proteins: lysosomal β-galactosidase (β-gal) and elastin-binding protein (EBP). The β-gal transcript includes the 16 exons of the GLB1 gene. In the EBP transcript, exons 3, 4 and 6 are skipped, while exon 5 has a different reading frame. However, little is known on how this alternative splicing is regulated. Findings Cycloheximide treatment of HeLa cells and human fibroblasts revealed the presence of new transcripts that are otherwise degraded by nonsense-mediated decay (NMD). A minigene carrying the exons involved in the alternative splicing of GLB1 was constructed. Improving the acceptor-site scores of exons 3 or 4 increased the relative inclusion of these exons, but did not stop them being skipped in some transcripts. Overexpression of different SR proteins altered the relative proportion of the different transcripts produced by the minigene, indicating a possible mechanism for the regulation of the alternative splicing of GLB1. Finally, a comparison of this gene among different species was performed. Conclusion In the processing of the GLB1 RNA several transcripts are generated, but only those with a correct reading frame are not degraded. The differential inclusion/exclusion of exons could be partially explained by the relatively weak splice sites in the exons involved. Different SR proteins have an effect on the process of skipping of these exons, at least in the minigene conditions, indicating a possible mechanism for the regulation of the alternative splicing of the GLB1 gene. PMID:19114006

  12. Alternatively spliced products lacking exon 12 dominate the expression of fragile X mental retardation 1 gene in human tissues.

    PubMed

    Fu, Xianguo; Zheng, Dezhu; Liao, Juan; Li, Qingqin; Lin, Yuxiang; Zhang, Duo; Yan, Aizhen; Lan, Fenghua

    2015-08-01

    Fragile X mental retardation 1 gene (FMR1) expression is associated with fragile X syndrome (FXS) and exhibits several splicing products. However, the proportion of spliced isoforms that are expressed in different tissues remains unclear. In the present study, long-chain reverse transcription-polymerase chain reaction with a T cloning-sequencing method was conducted in order to analyze the entire coding region of the FMR1 gene in human tissues. In particular, FXS-associated tissues were analyzed, including the brain and testis. Twenty alternatively spliced isoforms were observed among 271 recombinants, including six novel ones. The isoform that consisted of the entire FMR1 coding region (ISO1) accounted for a small proportion of all isoforms. Isoforms lacking exon 12 were the most abundant. In particular, spliced isoforms ISO7 and ISO17 were the most abundant. However, their relative abundance varied between the peripheral blood cells, and the testis and brain tissues. Bioinformatic analyses suggested that exon 12 may be the sole exon undergoing positive selection. The results of the present study suggested that the mechanisms underlying alternative splicing (AS) of the FMR1 gene may be more complex. Furthermore, the functions of alternatively spliced products lacking exon 12 require further investigation. The results of the present study provide novel insights into the association between AS and the structure and function of the FMR1 gene.

  13. [The teaching and application of alternative medicine in medical education programs].

    PubMed

    Chiang, Han-Sun

    2014-12-01

    The history of alternative medicine is perhaps as long as the history of human medicine. The development of evidence-based medicine has not annihilated alternative medicine. On the contrary, more people turn to alternative medicine because this approach to treatment serves as an effective remedial or supportive treatment when used in conjunction with evidence-based medicine. In contemporary healthcare, alternative medicine is now an essential part of integrated medicine. In Taiwan, most professional medical practitioners have not received proper education about alternative medicine and therefore generally lack comprehensive knowledge on this subject. While alternative medicine may be effective when used with some patients, it may also impart a placebo effect, which helps restore the body and soul of the patients. Medical staff with advanced knowledge of alternative medicine may not only help patients but also improve the doctor-patient relationship. There is great diversity in alternative medicine, with some alternative therapies supported by evidence and covered by insurance. However, there also remain fraudulent medical practices that may be harmful to health. Medical staff must be properly educated so that they can provide patients and their family a proper understanding and attitude toward alternative medicine. Therefore, alternative medicine should be included in the standard medical education curriculum. Offering classes on alternative medicine in university for more than 10 years, the author shares his experiences regarding potential content, lecture subjects, group experience exercises, and in-class activities. This article is intended to provide a reference to professors in university medical education and offer a possible model for alternative medicine education in Taiwan.

  14. Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability

    PubMed Central

    2014-01-01

    Background Resistant cultivars are key elements for pathogen control and pesticide reduction, but their repeated use may lead to the emergence of virulent pathogen populations, able to overcome the resistance. Increased research efforts, mainly based on theoretical studies, explore spatio-temporal deployment strategies of resistance genes in order to maximize their durability. We evaluated experimentally three of these strategies to control root-knot nematodes: cultivar mixtures, alternating and pyramiding resistance genes, under controlled and field conditions over a 3-years period, assessing the efficiency and the durability of resistance in a protected crop rotation system with pepper as summer crop and lettuce as winter crop. Results The choice of the resistance gene and the genetic background in which it is introgressed, affected the frequency of resistance breakdown. The pyramiding of two different resistance genes in one genotype suppressed the emergence of virulent isolates. Alternating different resistance genes in rotation was also efficient to decrease virulent populations in fields due to the specificity of the virulence and the trapping effect of resistant plants. Mixing resistant cultivars together appeared as a less efficient strategy to control nematodes. Conclusions This work provides experimental evidence that, in a cropping system with seasonal sequences of vegetable species, pyramiding or alternating resistance genes benefit yields in the long-term by increasing the durability of resistant cultivars and improving the long-term control of a soil-borne pest. To our knowledge, this result is the first one obtained for a plant-nematode interaction, which helps demonstrate the general applicability of such strategies for breeding and sustainable management of resistant cultivars against pathogens. PMID:24559060

  15. Gene regulation, alternative splicing, and posttranslational modification of troponin subunits in cardiac development and adaptation: a focused review.

    PubMed

    Sheng, Juan-Juan; Jin, Jian-Ping

    2014-01-01

    Troponin plays a central role in regulating the contraction and relaxation of vertebrate striated muscles. This review focuses on the isoform gene regulation, alternative RNA splicing, and posttranslational modifications of troponin subunits in cardiac development and adaptation. Transcriptional and posttranscriptional regulations such as phosphorylation and proteolysis modifications, and structure-function relationships of troponin subunit proteins are summarized. The physiological and pathophysiological significances are discussed for impacts on cardiac muscle contractility, heart function, and adaptations in health and diseases.

  16. Analysis of Minuteman Missile Crew Member Attitudes Toward Present Minuteman Education Program and Possible Alternatives.

    DTIC Science & Technology

    1980-06-01

    WERE NOT FOR COST (Questionnaire Data) .. .......... 95 x La Table Page 29. ENROLL IN OTHER GRADUATE PROGRAMS (x2 One Sample Test) .. .......... .97...30. ENROLL IN OTHER GRADUATE PROGRAMS (Questionnaire Data) .. .......... .97 31. PREFERRED TO ENROLL IN OTHER GRADUATE PROGRAMS IF CONSIDERATION GIVEN...SUPERVISORS ENCOURAGE PARTICIPATION (X2 One Sample Test) . ......... 117 48. ENROLL IN OTHER GRADUATE PROGRAMS (Questionnaire Data) . ......... 118 49

  17. Serving a Higher Power: The Influence of Alternative Break Programs on Students' Religiousness

    ERIC Educational Resources Information Center

    Niehaus, Elizabeth; Rivera, Mark

    2016-01-01

    The purpose of this study was to explore the relationship between students' religiousness and participation in alternative breaks (ABs) using both survey and interview data from the National Survey of Alternative Breaks. Findings from this mixed methods study demonstrate the potential for ABs to facilitate religiousness and help students connect…

  18. Mixed Results in a Transitional Planning Program for Alternative School Students

    ERIC Educational Resources Information Center

    Wolf, Elaine M.; Wolf, Douglas A.

    2008-01-01

    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…

  19. The novel gene Ny-1 on potato chromosome IX confers hypersensitive resistance to Potato virus Y and is an alternative to Ry genes in potato breeding for PVY resistance.

    PubMed

    Szajko, K; Chrzanowska, M; Witek, K; Strzelczyk-Zyta, D; Zagórska, H; Gebhardt, C; Hennig, J; Marczewski, W

    2008-01-01

    Hypersensitive resistance (HR) is an efficient defense strategy in plants that restricts pathogen growth and can be activated during host as well as non-host interactions. HR involves programmed cell death and manifests itself in tissue collapse at the site of pathogen attack. A novel hypersensitivity gene, Ny-1, for resistance to Potato virus Y (PVY) was revealed in potato cultivar Rywal. This is the first gene that confers HR in potato plants both to common and necrotic strains of PVY. The locus Ny-1 mapped on the short arm of potato chromosome IX, where various resistance genes are clustered in Solanaceous genomes. Expression of HR was temperature-dependent in cv. Rywal. Strains PVYO and PVYN, including subgroups PVYNW and PVYNTN, were effectively localized when plants were grown at 20 degrees C. At 28 degrees C, plants were systemically infected but no symptoms were observed. In field trials, PVY was restricted to the inoculated leaves and PVY-free tubers were produced. Therefore, the gene Ny-1 can be useful for potato breeding as an alternative donor of PVY resistance, because it is efficacious in practice-like resistance conferred by Ry genes.

  20. Intron retention as a component of regulated gene expression programs.

    PubMed

    Jacob, Aishwarya G; Smith, Christopher W J

    2017-04-08

    Intron retention has long been an exemplar of regulated splicing with case studies of individual events serving as models that provided key mechanistic insights into the process of splicing control. In organisms such as plants and budding yeast, intron retention is well understood as a major mechanism of gene expression regulation. In contrast, in mammalian systems, the extent and functional significance of intron retention have, until recently, remained greatly underappreciated. Technical challenges to the global detection and quantitation of transcripts with retained introns have often led to intron retention being overlooked or dismissed as "noise". Now, however, with the wealth of information available from high-throughput deep sequencing, combined with focused computational and statistical analyses, we are able to distinguish clear intron retention patterns in various physiological and pathological contexts. Several recent studies have demonstrated intron retention as a central component of gene expression programs during normal development as well as in response to stress and disease. Furthermore, these studies revealed various ways in which intron retention regulates protein isoform production, RNA stability and translation efficiency, and rapid induction of expression via post-transcriptional splicing of retained introns. In this review, we highlight critical findings from these transcriptomic studies and discuss commonalties in the patterns prevalent in intron retention networks at the functional and regulatory levels.

  1. Non-proliferation, safeguards, and security for the fissile materials disposition program immobilization alternatives

    SciTech Connect

    Duggan, R.A.; Jaeger, C.D.; Tolk, K.M.; Moore, L.R.

    1996-05-01

    The Department of Energy is analyzing long-term storage and disposition alternatives for surplus weapons-usable fissile materials. A number of different disposition alternatives are being considered. These include facilities for storage, conversion and stabilization of fissile materials, immobilization in glass or ceramic material, fabrication of fissile material into mixed oxide (MOX) fuel for reactors, use of reactor based technologies to convert material into spent fuel, and disposal of fissile material using geologic alternatives. This paper will focus on how the objectives of reducing security and proliferation risks are being considered, and the possible facility impacts. Some of the areas discussed in this paper include: (1) domestic and international safeguards requirements, (2) non-proliferation criteria and measures, (3) the threats, and (4) potential proliferation, safeguards, and security issues and impacts on the facilities. Issues applicable to all of the possible disposition alternatives will be discussed in this paper. However, particular attention is given to the plutonium immobilization alternatives.

  2. Alternatively Spliced Genes as Biomarkers for Schizophrenia, Bipolar Disorder and Psychosis: A Blood-Based Spliceome-Profiling Exploratory Study.

    PubMed

    Glatt, S J; Chandler, S D; Bousman, C A; Chana, G; Lucero, G R; Tatro, E; May, T; Lohr, J B; Kremen, W S; Everall, I P; Tsuang, M T

    2009-09-01

    OBJECTIVE: Transcriptomic biomarkers of psychiatric diseases obtained from a query of peripheral tissues that are clinically accessible (e.g., blood cells instead of post-mortem brain tissue) have substantial practical appeal to discern the molecular subtypes of common complex diseases such as major psychosis. To this end, spliceome-profiling is a new methodological approach that has considerable conceptual relevance for discovery and clinical translation of novel biomarkers for psychiatric illnesses. Advances in microarray technology now allow for improved sensitivity in measuring the transcriptome while simultaneously querying the "exome" (all exons) and "spliceome" (all alternatively spliced variants). The present study aimed to evaluate the feasibility of spliceome-profiling to discern transcriptomic biomarkers of psychosis. METHODS: We measured exome and spliceome expression in peripheral blood mononuclear cells from 13 schizophrenia patients, nine bipolar disorder patients, and eight healthy control subjects. Each diagnostic group was compared to each other, and the combined group of bipolar disorder and schizophrenia patients was also compared to the control group. Furthermore, we compared subjects with a history of psychosis to subjects without such history. RESULTS: After applying Bonferroni corrections for the 21,866 full-length gene transcripts analyzed, we found significant interactions between diagnostic group and exon identity, consistent with group differences in rates or types of alternative splicing. Relative to the control group, 18 genes in the bipolar disorder group, eight genes in the schizophrenia group, and 15 genes in the combined bipolar disorder and schizophrenia group appeared differentially spliced. Importantly, thirty-three genes showed differential splicing patterns between the bipolar disorder and schizophrenia groups. More frequent exon inclusion and/or over-expression was observed in psychosis. Finally, these observations are

  3. Global transcription analysis of Krebs tricarboxylic acid cycle mutants reveals an alternating pattern of gene expression and effects on hypoxic and oxidative genes.

    PubMed

    McCammon, Mark T; Epstein, Charles B; Przybyla-Zawislak, Beata; McAlister-Henn, Lee; Butow, Ronald A

    2003-03-01

    To understand the many roles of the Krebs tricarboxylic acid (TCA) cycle in cell function, we used DNA microarrays to examine gene expression in response to TCA cycle dysfunction. mRNA was analyzed from yeast strains harboring defects in each of 15 genes that encode subunits of the eight TCA cycle enzymes. The expression of >400 genes changed at least threefold in response to TCA cycle dysfunction. Many genes displayed a common response to TCA cycle dysfunction indicative of a shift away from oxidative metabolism. Another set of genes displayed a pairwise, alternating pattern of expression in response to contiguous TCA cycle enzyme defects: expression was elevated in aconitase and isocitrate dehydrogenase mutants, diminished in alpha-ketoglutarate dehydrogenase and succinyl-CoA ligase mutants, elevated again in succinate dehydrogenase and fumarase mutants, and diminished again in malate dehydrogenase and citrate synthase mutants. This pattern correlated with previously defined TCA cycle growth-enhancing mutations and suggested a novel metabolic signaling pathway monitoring TCA cycle function. Expression of hypoxic/anaerobic genes was elevated in alpha-ketoglutarate dehydrogenase mutants, whereas expression of oxidative genes was diminished, consistent with a heme signaling defect caused by inadequate levels of the heme precursor, succinyl-CoA. These studies have revealed extensive responses to changes in TCA cycle function and have uncovered new and unexpected metabolic networks that are wired into the TCA cycle.

  4. Differential gene expression and alternative splicing between diploid and tetraploid watermelon lines

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Synthetic tetraploid plants have been used for production of seedless triploid watermelon lines being pollinated with diploid plants. When compared to their diploid or triploid counterparts, the tetraploid exhibit wide phenotypic differences. Though many factors, including alternative splicing (AS),...

  5. 20 CFR 411.710 - How will an alternate participant choose to participate as an EN in the Ticket to Work program?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... participate as an EN in the Ticket to Work program? 411.710 Section 411.710 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM The Ticket to Work Program and... will an alternate participant choose to participate as an EN in the Ticket to Work program? (a)...

  6. 20 CFR 411.710 - How will an alternate participant choose to participate as an EN in the Ticket to Work program?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... participate as an EN in the Ticket to Work program? 411.710 Section 411.710 Employees' Benefits SOCIAL SECURITY ADMINISTRATION THE TICKET TO WORK AND SELF-SUFFICIENCY PROGRAM The Ticket to Work Program and... will an alternate participant choose to participate as an EN in the Ticket to Work program? (a)...

  7. A Feasibility Study to Assess Alternative Energy Program Development Potential at the Community College Level, October 1, 1983-June 30, 1984. Final Report.

    ERIC Educational Resources Information Center

    Blair, Brittain A.

    In 1983-84, a feasibility study was conducted to determine the viability of establishing a comprehensive alternative energy technology program at Southeastern Illinois College (SIC). The study involved an examination of a number of exemplary associate degree programs in alternative energy, through on-site visits and telephone surveys; a survey of…

  8. Alternative Schools and Programs for Public School Students at Risk of Educational Failure: 2007-08. First Look. NCES 2010-026

    ERIC Educational Resources Information Center

    Carver, Priscilla Rouse; Lewis, Laurie; Tice, Peter

    2010-01-01

    This report provides national estimates on the availability of alternative schools and programs for students at risk of educational failure in public school districts during the 2007-08 school year. The National Center for Education Statistics (NCES) previously reported results from a similar survey of alternative schools and programs conducted…

  9. Alternative splicing and differential expression of two transcripts of nicotine adenine dinucleotide phosphate oxidase B gene from Zea mays.

    PubMed

    Lin, Fan; Zhang, Yun; Jiang, Ming-Yi

    2009-03-01

    With the exception of rice, little is known about the existence of respiratory burst oxidase homolog (rboh) gene in cereals. The present study reports the cloning and analysis of a novel rboh gene, termed ZmrbohB, from maize (Zea mays L.). The full-length cDNA of ZmrbohB encodes a 942 amino acid protein containing all of the respiratory burst oxidase homolog catalytically critical motifs. Alternative splicing of ZmrbohB has generated two transcript isoforms, ZmrbohB-alpha and -beta. Spliced transcript ZmrbohB-beta retains an unspliced intron 11 that carries a premature termination codon and probably leads to nonsense-mediated mRNA decay. Expression analysis showed that two splice isoforms were differentially expressed in various tissues and at different developmental stages, and the major product was ZmrbohB-alpha. The transcripts of ZmrbohB-alpha accumulated markedly when the maize seedlings were subjected to various abiotic stimuli, such as wounding, cold (4 degrees C), heat (40 degrees C), UV and salinity stress. In addition, several abiotic stimuli also affected the alternative splicing pattern of ZmrbohB except wounding. These results provide new insight into roles in the expression regulation of plant rboh genes and suggest that ZmrbohB gene may play a role in response to environmental stresses.

  10. Ligand-Bound GeneSwitch Causes Developmental Aberrations in Drosophila that Are Alleviated by the Alternative Oxidase

    PubMed Central

    Andjelković, Ana; Kemppainen, Kia K.; Jacobs, Howard T.

    2016-01-01

    Culture of Drosophila expressing the steroid-dependent GeneSwitch transcriptional activator under the control of the ubiquitous α-tubulin promoter was found to produce extensive pupal lethality, as well as a range of dysmorphic adult phenotypes, in the presence of high concentrations of the inducing drug RU486. Prominent among these was cleft thorax, seen previously in flies bearing mutant alleles of the nuclear receptor Ultraspiracle and many other mutants, as well as notched wings, leg malformations, and bristle abnormalities. Neither the α-tubulin-GeneSwitch driver nor the inducing drug on their own produced any of these effects. A second GeneSwitch driver, under the control of the daughterless promoter, which gave much lower and more tissue-restricted transgene expression, exhibited only mild bristle abnormalities in the presence of high levels of RU486. Coexpression of the alternative oxidase (AOX) from Ciona intestinalis produced a substantial shift in the developmental outcome toward a wild-type phenotype, which was dependent on the AOX expression level. Neither an enzymatically inactivated variant of AOX, nor GFP, or the alternative NADH dehydrogenase Ndi1 from yeast gave any such rescue. Users of the GeneSwitch system should be aware of the potential confounding effects of its application in developmental studies. PMID:27412986

  11. Lifeline electric rates and alternative approaches to the problems of low-income ratepayers: ten case studies of rejected programs

    SciTech Connect

    Not Available

    1980-07-01

    This volume, Volume 3, contains ten case studies of non-implemented programs. It is noted that in Volume 2, the implemented lifeline programs, evolved as policy closely after the 1973 oil embargo; in contrast, the rejected programs were initiated about 4 years later and considered in a more-complex policy environment - after which time alternate methods of assisting low-income people had been developed. Specifically presented here are program summary, issue development, governmental process, and impact for the following: (a) Delaware Senate Bill 202; (b) Illinois House Bill 83; (c) Maine Legislative Document No. 1043; (d) Minnesota House File 1243; (e) New York Assembly Bill 12214; (f) New York Senate Bill 7013-A; (g) Rhode Island Resolution 79-H 5770-A; (h) South Dakota Senate Joint Resolution 9; (i) West Virginia House Bill 943; and (j) Wisconsin Assembly Bill 1250. 4 figures, 24 tables.

  12. Population genomics of resource exploitation: insights from gene expression profiles of two Daphnia ecotypes fed alternate resources.

    PubMed

    Dudycha, Jeffry L; Brandon, Christopher S; Deitz, Kevin C

    2012-02-01

    Consumer-resource interactions are a central issue in evolutionary and community ecology because they play important roles in selection and population regulation. Most consumers encounter resource variation at multiple scales, and respond through phenotypic plasticity in the short term or evolutionary divergence in the long term. The key traits for these responses may influence resource acquisition, assimilation, and/or allocation. To identify relevant candidate genes, we experimentally assayed genome-wide gene expression in pond and lake Daphnia ecotypes exposed to alternate resource environments. One was a simple, high-quality laboratory diet, Ankistrodesmus falcatus. The other was the complex natural seston from a large lake. In temporary ponds, Daphnia generally experience high-quality, abundant resources, whereas lakes provide low-quality, seasonally shifting resources that are chronically limiting. For both ecotypes, we used replicate clones drawn from a number of separate populations. Fourteen genes were differentially regulated with respect to resources, including genes involved in gut processes, resource allocation, and activities with no obvious connection to resource exploitation. Three genes were differentially regulated in both ecotypes; the others may play a role in ecological divergence. Genes clearly linked to gut processes include two peritrophic matrix proteins, a Niemann-Pick type C2 gene, and a chymotrypsin. A pancreatic lipase, an epoxide hydrolase, a neuroparsin, and an UDP-dependent glucuronyltransferase are potentially involved in resource allocation through effects on energy processing and storage or hormone pathways. We performed quantitative rt-PCR for eight genes in independent samples of three clones of each of the two ecotypes. Though these largely confirmed observed differential regulation, some genes' expression was highly variable among clones. Our results demonstrate the value of matching the level of biological replication in

  13. 75 FR 32942 - National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-10

    ... Alternative Toxicological Methods (NICEATM): Availability of the Biennial Progress Report of the Interagency... Environmental Health Sciences (NIEHS), National Institutes of Health (NIH) . ACTION: Availability of the ICCVAM Biennial Progress Report. SUMMARY: NICEATM announces the availability of the Biennial Progress Report...

  14. Nuclear proliferation and civilian nuclear power. Report of the Nonproliferation Alternative Systems Assessment Program. Volume IV. Commercial potential

    SciTech Connect

    Not Available

    1980-06-01

    This volume of the Nonproliferation Alternative Systems Assessment Program (NASAP) report provides time and cost estimates for positioning new nuclear power systems for commercial deployment. The assessment also estimates the rates at which the new systems might penetrate the domestic market, assuming the continuing viability of the massive light-water reactor network that now exists worldwide. This assessment does not recommend specific, detailed program plans and budgets for individual systems; however, it is clear from this analysis that any of the systems investigated could be deployed if dictated by national interest.

  15. Lifeline electric rates and alternative approaches to the problems of low-income ratepayers. Ten case studies of implemented programs

    SciTech Connect

    Not Available

    1980-07-01

    Program summaries, issue developments, governmental processes, and impacts are discussed for 10 case studies dealing with lifeline electric rates and alternative approaches to the problems of low-income ratepayers, namely; the Boston Edison rate freeze; the California lifeline; Florida Power and Light conservation rate; the Iowa-Illinois Gas and Electric small-use rate; the Maine demonstration lifeline program; the Massachusetts Electric Company A-65 rate; the Michigan optional senior citizen rate; the Narragansett Electric Company A-65 SSI rate; the Northern States Power Company conservation rate break; and the Potomac Electric Power Company rate freeze. (MCW)

  16. Federal Alternative Fuel Program Light Duty Vehicle Operations. Second annual report to Congress for fiscal year 1992

    SciTech Connect

    Not Available

    1993-07-01

    This annual report to Congress details the second year of the Federal light duty vehicle operations as required by Section 400AA(b)(1)(B) of the Energy Policy and Conservation Act as amended by the Alternative Motor Fuels Act of 1988, Public Law 100-494. In 1992, the Federal alternative fuel vehicle fleet expanded significantly, from the 65 M85 (85 percent methanol and 15 percent unleaded gasoline) vehicles acquired in 1991 to an anticipated total of 3,267 light duty vehicles. Operating data are being collected from slightly over 20 percent, or 666, of these vehicles. The 601 additional vehicles that were added to the data collection program in 1992 include 75 compressed natural gas Dodge full-size (8-passenger) vans, 25 E85 (85 percent denatured ethanol and 15 percent unleaded gasoline) Chevrolet Lumina sedans, 250 M85 Dodge Spirit sedans (planned to begin operation in fiscal year 1993), and 251 compressed natural gas Chevrolet C-20 pickup trucks. Figure ES-1 illustrates the locations where the Federal light duty alternative fuel vehicles that are participating in the data collection program are operating. The primary criteria for placement of vehicles will continue to include air quality attainment status and the availability of an alternative fuel infrastructure to support the vehicles. This report details the second year of the Federal light duty vehicle operations, from October 1991 through September 1992.

  17. The Effectiveness of Adapted Versions of an Evidence-based Prevention Program in Reducing Alcohol Use among Alternative School Students

    PubMed Central

    Hopson, Laura M.; Holleran Steiker, Lori K.

    2010-01-01

    Although there is a strong evidence base for effective substance abuse prevention programs for youth, there is a need to facilitate the implementation and evaluation of these programs in real world settings. This study evaluates the effectiveness of adapted versions of an evidence-based prevention program, keepin’ it REAL (kiR), with alternative school students. Programs are often adapted when used in schools and other community settings for a variety of reasons. The kiR adaptations, developed during an earlier phase of this study, were created to make the curriculum more appropriate for alternative high school youth. The adaptations were evaluated using a quasi-experimental design in which questionnaires were administered at pretest, posttest, and follow-up, and focus groups were conducted at posttest. MANOVA analyses indicate significantly reduced intentions to accept alcohol and, for younger participants, reduced alcohol use. Focus group data support the need for age appropriate prevention content. The authors discuss implications for practitioners implementing prevention programs in schools. PMID:20622971

  18. Presenting an Alternative Source Code Plagiarism Detection Framework for Improving the Teaching and Learning of Programming

    ERIC Educational Resources Information Center

    Hattingh, Frederik; Buitendag, Albertus A. K.; van der Walt, Jacobus S.

    2013-01-01

    The transfer and teaching of programming and programming related skills has become, increasingly difficult on an undergraduate level over the past years. This is partially due to the number of programming languages available as well as access to readily available source code over the Web. Source code plagiarism is common practice amongst many…

  19. Alternative Secondary Mathematics Programs for Migrant Students: Cultural and Linguistic Considerations.

    ERIC Educational Resources Information Center

    Celedon-Pattichis, Sylvia

    This chapter describes various programs providing secondary mathematics curricula to migrant students and discusses some challenges of integrating the cultural and linguistic experiences of migrant students learning mathematics. Among the distance-education programs designed for migrant students, the University of Texas Migrant Program delivers 22…

  20. Predictive Validity of Measures of the Pathfinder Scaling Algorithm on Programming Performance: Alternative Assessment Strategy for Programming Education

    ERIC Educational Resources Information Center

    Lau, Wilfred W. F.; Yuen, Allan H. K.

    2009-01-01

    Recent years have seen a shift in focus from assessment of learning to assessment for learning and the emergence of alternative assessment methods. However, the reliability and validity of these methods as assessment tools are still questionable. In this article, we investigated the predictive validity of measures of the Pathfinder Scaling…

  1. Expression and Alternative Splicing of Classical and Nonclassical MHCI Genes in the Hippocampus and Neuromuscular Junction

    PubMed Central

    Tetruashvily, Mazell M.; Melson, John W.; Park, Joseph J.; Peng, Xiaoyu; Boulanger, Lisa M.

    2016-01-01

    The major histocompatibility complex class I (MHCI) is a large gene family, with over 30 members in mouse. Some MHCIs are well-known for their critical roles in the immune response. Studies in mice which lack stable cell-surface expression of many MHCI proteins suggest that one or more MHCIs also play unexpected, essential roles in the establishment, function, and modification of neuronal synapses in the central nervous system (CNS). However, there is little information about which genes mediate MHCI’s effects in neurons. In this study, RT-PCR was used to simultaneously assess transcription of many MHCI genes in regions of the central and peripheral nervous system where MHCI has a known or suspected role. In the hippocampus, a part of the CNS where MHCI regulates synapse density, synaptic transmission, and plasticity, we found that more than a dozen MHCI genes are transcribed. Single-cell RT-PCR revealed that individual hippocampal neurons can express more than one MHCI gene, and that the MHCI gene expression profile of CA1 pyramidal neurons differs significantly from that of CA3 pyramidal neurons or granule cells of the dentate gyrus. MHCI gene expression was also assessed at the neuromuscular junction (NMJ), a part of the peripheral nervous system (PNS) where MHCI plays a role in neuronal regeneration, and could potentially influence developmental synapse elimination. Four MHCI genes are expressed at the NMJ at an age when synapse elimination is occurring in three different muscles. Several MHCI mRNA splice variants were detected in hippocampus, but not at the NMJ. Together, these results establish the first profile of MHCI gene expression at the developing NMJ, and demonstrate that MHCI gene expression is under tight spatial and temporal regulation in the nervous system. They also identify more than a dozen MHCIs that could play important roles in synaptic transmission and plasticity in the central and peripheral nervous systems. PMID:26802536

  2. LIN28A Modulates Splicing and Gene Expression Programs in Breast Cancer Cells.

    PubMed

    Yang, Jun; Bennett, Brian D; Luo, Shujun; Inoue, Kaoru; Grimm, Sara A; Schroth, Gary P; Bushel, Pierre R; Kinyamu, H Karimi; Archer, Trevor K

    2015-09-01

    LIN28 is an evolutionarily conserved RNA-binding protein with critical functions in developmental timing and cancer. However, the molecular mechanisms underlying LIN28's oncogenic properties are yet to be described. RNA-protein immunoprecipitation coupled with genome-wide sequencing (RIP-Seq) analysis revealed significant LIN28 binding within 843 mRNAs in breast cancer cells. Many of the LIN28-bound mRNAs are implicated in the regulation of RNA and cell metabolism. We identify heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1), a protein with multiple roles in mRNA metabolism, as a LIN28-interacting partner. Subsequently, we used a custom computational method to identify differentially spliced gene isoforms in LIN28 and hnRNP A1 small interfering RNA (siRNA)-treated cells. The results reveal that these proteins regulate alternative splicing and steady-state mRNA expression of genes implicated in aspects of breast cancer biology. Notably, cells lacking LIN28 undergo significant isoform switching of the ENAH gene, resulting in a decrease in the expression of the ENAH exon 11a isoform. The expression of ENAH isoform 11a has been shown to be elevated in breast cancers that express HER2. Intriguingly, analysis of publicly available array data from the Cancer Genome Atlas (TCGA) reveals that LIN28 expression in the HER2 subtype is significantly different from that in other breast cancer subtypes. Collectively, our data suggest that LIN28 may regulate splicing and gene expression programs that drive breast cancer subtype phenotypes.

  3. Benefits and Costs of Aggressive Energy Efficiency Programs and the Impacts of Alternative Sources of Funding: Case Study of Massachusetts

    SciTech Connect

    Cappers, Peter; Satchwell, Andrew; Goldman, Charles; Schlegel, Jeff

    2010-08-06

    Increased interest by state (and federal) policymakers and regulatory agencies in pursuing aggressive energy efficiency efforts could deliver significant utility bill savings for customers while having long-term implications for ratepayers (e.g. potential rate impacts). Equity and distributional concerns associated with the authorized recovery of energy efficiency program costs may necessitate the pursuit of alternative program funding approaches. In 2008, Massachusetts passed the Green Communities Act which directed its energy efficiency (EE) program administrators to obtain all cost-effective EE resources. This goal has translated into achieving annual electric energy savings equivalent to a 2.4% reduction in retail sales from energy efficiency programs in 2012. Representatives of electricity consumer groups supported the new portfolio of EE programs (and the projected bill savings) but raised concerns about the potential rate impacts associated with achieving such aggressive EE goals, leading policymakers to seek out alternative funding sources which can potentially mitigate these effects. Utility administrators have also raised concerns about under-recovery of fixed costs when aggressive energy efficiency programs are pursued and have proposed ratemaking policies (e.g. decoupling) and business models that better align the utility's financial interests with the state's energy efficiency public policy goals. Quantifying these concerns and identifying ways they can be addressed are crucial steps in gaining the support of major stakeholder groups - lessons that can apply to other states looking to significantly increase savings targets that can be achieved from their own ratepayer-funded energy efficiency programs. We use a pro-forma utility financial model to quantify the bill and rate impacts on electricity customers when very aggressive annual energy efficiency savings goals ({approx}2.4%) are achieved over the long-term and also assess the impact of different

  4. Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

    PubMed Central

    Ardell, David H; Lozupone, Catherine A; Landweber, Laura F

    2003-01-01

    DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D. PMID:14704164

  5. NPY family genes respond negatively to alternative feedstuffs in channel catfish diets

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Of considerable importance in fish nutrition is the development of aquafeeds using alternative dietary ingredients which will allow aquaculture to grow globally, without putting excessive pressure on natural fisheries or adding considerable cost to production, while also addressing and maintaining t...

  6. Low Emissions Alternative Power (LEAP) Project Office Business Team of the Aeropropulsion Research Program Office (ARPO) Org. 0140

    NASA Technical Reports Server (NTRS)

    Buttler, Jennifer A.

    2004-01-01

    The program for which I am working at this summer is Propulsion and Power/Low Emissions Alternative Power (P&P/LEAP). It invests in a fundamental TRL 1-6 research and technology portfolio that will enable the future of: Alternative fuels and/or alternative propulsion systems, non-combustion (electric) propulsion systems. P&P/LEAP will identify and capitalize on the highest potential concepts generated both internal and external to the Agency. During my 2004 summer at NASA Glenn Research Center, I worked with my mentor Barbara Mader, in the Project Office with the Business Team completing various tasks for the project and personnel. The LEAP project is a highly matrixed organization. The Project Office is responsible for the goals advocacy and dollar (budget) of the LEAP project. The objectives of the LEAP Project are to discover new energy sources and develop unconventional engines and power systems directed towards greatly reduced emissions, enable new vehicle concepts for public mobility, new science missions and national security. The Propulsion and PowerLow Emissions Alternative Power directly supports the environmental, mobility, national security objectives of the Vehicle Systems Program and the Aeronautics Technology Theme. Technology deliverables include the demonstration through integrated ground tests, a constant volume combustor in an engine system, and UAV/small transport aircraft all electric power system. My mentor serves as a key member of the management team for the Aeropropulsion Research Program Office (ARPO). She has represented the office on numerous occasions, and is a member of a number of center-wide panels/teams, such as the Space management Committee and is chair to the Business Process Consolidation Team. She is responsible for the overall coordination of resources for the Propulsion and Power Project - from advocacy to implementation. The goal for my summer at NASA was to document processes and archive program documents from the past

  7. Network activity-independent coordinated gene expression program for synapse assembly.

    PubMed

    Valor, Luis M; Charlesworth, Paul; Humphreys, Lawrence; Anderson, Chris N G; Grant, Seth G N

    2007-03-13

    Global biological datasets generated by genomics, transcriptomics, and proteomics provide new approaches to understanding the relationship between the genome and the synapse. Combined transcriptome analysis and multielectrode recordings of neuronal network activity were used in mouse embryonic primary neuronal cultures to examine synapse formation and activity-dependent gene regulation. Evidence for a coordinated gene expression program for assembly of synapses was observed in the expression of 642 genes encoding postsynaptic and plasticity proteins. This synaptogenesis gene expression program preceded protein expression of synapse markers and onset of spiking activity. Continued expression was followed by maturation of morphology and electrical neuronal networks, which was then followed by the expression of activity-dependent genes. Thus, two distinct sequentially active gene expression programs underlie the genomic programs of synapse function.

  8. 77 FR 47375 - Applications for New Awards; Assistive Technology Alternative Financing Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-08

    ... build programs that will provide financing for the full array of AT devices and services and ensure that... this program by the CFDA number. Do not include the CFDA number's alpha suffix in your search (e.g... 424 the CFDA number, including suffix letter, if any, of the competition under which you...

  9. Admission to the Master of Business Administration Program: An Alternative for Savannah State University

    ERIC Educational Resources Information Center

    Dowling, Bill

    2009-01-01

    Traditionally, graduate programs in business administration have heavily relied on the Graduate Management Aptitude Test prepared and administered by the Educational Testing Service in the decision to admit a candidate to the program. The purpose of this paper is to review the literature regarding the statistical validity and statistical…

  10. Alternatives to Custody: A Ten-Year Review of a Community-Based Program in Britain.

    ERIC Educational Resources Information Center

    Stevens, Barbara Christine

    1996-01-01

    Describes the development of a community forensic psychology service during its first 10 years of service. Service emphasizes cooperation among psychologists, probation officers, and others in establishing alternatives to custody for sex offenders, shoplifters, drug and alcohol abusers, and young criminals. Discusses theoretical orientation of the…

  11. Identification and Analysis of the Alternatives for Achieving Greater Television Program Diversity in the United States.

    ERIC Educational Resources Information Center

    Dimling, John A., Jr.; And Others

    Several alternatives to the present television industry structure are considered in this study. They are: continuation of present policies, satellite-to-home broadcasting, and cable distribution of television. Trends noted are: the growth of commercial UHF (Ultra High Frequency) stations, the introduction of all-channel sets, population growth,…

  12. Program Evaluation in Alternative Education: An Annotated Bibliography. Teacher Education Forum; Volume 4, Number 17.

    ERIC Educational Resources Information Center

    Esp, Barbara

    The Forum Series is a collection of papers dealing with all phases of teacher education including inservice training and graduate study. This selection is an annotated bibliography in two parts: (1) Evaluation Issues and Methods; and (2) Studies of Alternative Environments. (DMT)

  13. State High School Exit Exams: Trends in Test Programs, Alternate Pathways, and Pass Rates

    ERIC Educational Resources Information Center

    Zhang, Ying

    2009-01-01

    The report draws from Center on Education Policy's eight-year study of high school exit exams to identify long-term trends in state policies and student performance. It highlights a growing trend among states to establish alternate pathways to graduation for students who are struggling to pass exit exams. The report also analyzes exit exam pass…

  14. 78 FR 14843 - Temporary Scope Expansion of the Post-Investigation Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-07

    ... discrimination and other wrongdoing after the NRC's Office of Investigations has completed an investigation... findings of discrimination and other wrongdoing. (see the staff requirements memorandum (SRM) for SECY-03... Alternative Dispute Resolution (ADR) Techniques in the Handling of Discrimination and Other...

  15. 78 FR 62472 - Energy Conservation Program: Alternative Efficiency Determination Methods, Basic Model Definition...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-10-22

    ... assess a unit's performance through third party testing. Under this approach, DOE would begin the... Conditioners.... Sensible Coefficient 5% (0.05) of Performance. Commercial Warm-Air Furnaces...... Thermal..., U.S. Department of Energy, Building Technologies Office, Mailstop EE-2J, Alternative...

  16. 75 FR 25867 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... tests require large numbers of laboratory animals that may experience unrelieved pain and distress, the... accepted for use that can reduce, refine (less pain and distress), and replace animal use in vaccine... Animal Pain and Distress in Vaccine Potency Challenge Testing Reduction Alternatives: Strategies...

  17. Harvesting Alternative Credit Transfer Students: Redefining Selectivity in Your Online Learning Program Enrollment Leads

    ERIC Educational Resources Information Center

    Corlett, Bradly

    2014-01-01

    Several recent issues and trends in online education have resulted in consolidation of efforts for Massive Open Online Courses (MOOCs), increased Open Educational Resources (OER) in the form of asynchronous course repositories, with noticeable increases in governance and policy amplification. These emerging enrollment trends in alternative online…

  18. 75 FR 25866 - National Toxicology Program (NTP); NTP Interagency Center for the Evaluation of Alternative...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... Local Lymph Node Assay, An Alternative Test Method for Assessing the Allergic Contact Dermatitis... safety testing method used to assess the potential of chemicals and products to cause allergic contact...-ps.htm . FOR FURTHER INFORMATION CONTACT: Dr. William S. Stokes, Director, NICEATM, NIEHS, P.O....

  19. The Relationship of Academic Achievement and Duration of Placement in Alternative Education Programming

    ERIC Educational Resources Information Center

    Elias, Janilyn

    2011-01-01

    Education agencies are driven by the need to remove disruptive and dangerous students from classrooms without suspending or expelling them to home or the streets (Bear, 1998). As stated in the National Association of State Boards of Education (1994), the term "alternative education" refers to nontraditional educational services ranging from…

  20. Strange Bedfellows? Title I Funding, Alternative Teacher Certification Programs, and State Teacher Standards.

    ERIC Educational Resources Information Center

    Bales, Barbara L.

    This paper discusses the need to build instructional capacity in high poverty, low performing schools using Title I funding and integrate the corresponding federal policy requirements with state teacher education policies to allow states and districts to develop locally designed partnerships with alternative certification agencies. It recommends…

  1. Sketching Some Postmodern Alternatives: Beyond Paradigms and Research Programs as Referents for Science Education.

    ERIC Educational Resources Information Center

    Geelan, David R.

    2000-01-01

    Suggests that Kuhn's and Lakatos' schemes for the philosophy of science have been pervasive metaphors for conceptual change approaches to the learning and teaching of science, and have been used both implicitly and explicitly to provide an organizing framework and justification matrix for those perspectives. Describes four alternative perspectives…

  2. Disciplinary Alternative Education Programs in Texas--What Is Known; What Is Needed. A Policy Brief.

    ERIC Educational Resources Information Center

    Cortez, Albert; Robledo Montecel, Maria

    In 1995, the Texas legislature established a policy that each school district must have an "alternative educational setting for behavioral management." This policy brief examines the ways in which this idea has been implemented in Texas, using data from the Texas Education Agency. Findings show that, for the most part, these alternative…

  3. Genetic programming as alternative for predicting development effort of individual software projects.

    PubMed

    Chavoya, Arturo; Lopez-Martin, Cuauhtemoc; Andalon-Garcia, Irma R; Meda-Campaña, M E

    2012-01-01

    Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model. A sample of 219 projects developed by 71 practitioners was used for generating the two models, whereas another sample of 130 projects developed by 38 practitioners was used for validating them. The models used two kinds of lines of code as well as programming language experience as independent variables. Accuracy results from the model obtained with genetic programming suggest that it could be used to predict the software development effort of individual projects when these projects have been developed in a disciplined manner within a development-controlled environment.

  4. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences

    PubMed Central

    Laslett, Dean; Canback, Bjorn

    2004-01-01

    A computer program, ARAGORN, identifies tRNA and tmRNA genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with recognized tRNA consensus sequences and ability to form a base-paired cloverleaf. tmRNA genes are identified using a modified version of the BRUCE program. ARAGORN achieves a detection sensitivity of 99% from a set of 1290 eubacterial, eukaryotic and archaeal tRNA genes and detects all complete tmRNA sequences in the tmRNA database, improving on the performance of the BRUCE program. Recently discovered tmRNA genes in the chloroplasts of two species from the ‘green’ algae lineage are detected. The output of the program reports the proposed tRNA secondary structure and, for tmRNA genes, the secondary structure of the tRNA domain, the tmRNA gene sequence, the tag peptide and a list of organisms with matching tmRNA peptide tags. PMID:14704338

  5. Evolutionary effects of alternative artificial propagation programs: implications for viability of endangered anadromous salmonids

    PubMed Central

    McClure, Michelle M; Utter, Fred M; Baldwin, Casey; Carmichael, Richard W; Hassemer, Peter F; Howell, Philip J; Spruell, Paul; Cooney, Thomas D; Schaller, Howard A; Petrosky, Charles E

    2008-01-01

    Most hatchery programs for anadromous salmonids have been initiated to increase the numbers of fish for harvest, to mitigate for habitat losses, or to increase abundance in populations at low abundance. However, the manner in which these programs are implemented can have significant impacts on the evolutionary trajectory and long-term viability of populations. In this paper, we review the potential benefits and risks of hatchery programs relative to the conservation of species listed under the US Endangered Species Act. To illustrate, we present the range of potential effects within a population as well as among populations of Chinook salmon (Oncorhynchus tshawytscha) where changes to major hatchery programs are being considered. We apply evolutionary considerations emerging from these examples to suggest broader principles for hatchery uses that are consistent with conservation goals. We conclude that because of the evolutionary risks posed by artificial propagation programs, they should not be viewed as a substitute for addressing other limiting factors that prevent achieving viability. At the population level, artificial propagation programs that are implemented as a short-term approach to avoid imminent extinction are more likely to achieve long-term population viability than approaches that rely on long-term supplementation. In addition, artificial propagation programs can have out-of-population impacts that should be considered in conservation planning. PMID:25567637

  6. A Longitudinal Comparative Study of Alternative and Traditional Teacher Education Programs in Israel: Initial Training, Induction Period, School Placement, and Retention Rates

    ERIC Educational Resources Information Center

    Weinberger, Yehudith; Donitsa-Schmidt, Smadar

    2016-01-01

    The purpose of this study is to compare alternative teacher education programs in English as a foreign language (EFL), biology, and mathematics to traditional programs in the same subjects. To do this, we analyzed data on all of the students who studied in the aforementioned programs during 2009 and 2010 in the largest college of education in…

  7. Analysis of the First Year of Operation of the Federal Alternative Financing Program for Individuals with Disabilities: Providing Low Cost Loans for the Purchase of Assistive Technology.

    ERIC Educational Resources Information Center

    RESNA: Association for the Advancement of Rehabilitation Technology, Arlington, VA.

    This report analyzes the first year of the Federal Alternative Financing Program (AFP), a program designed to help individuals with disabilities who need to purchase assistive technology (AT) find a way to pay for the equipment. The program receives funding under Title III of the Assistive Technology Act of 1998 and provides low-cost financing for…

  8. Alternative splicing of VEGFA, APP and NUMB genes in colorectal cancer

    PubMed Central

    Zhao, Yi-Jun; Han, Hua-Zhong; Liang, Yong; Shi, Chen-Zhang; Zhu, Qing-Chao; Yang, Jun

    2015-01-01

    AIM: To investigate alternative splicing in vascular endothelial growth factor A (VEGFA), amyloid beta precursor protein (APP), and Numb homolog (NUMB) in colorectal cancer (CRC). METHODS: Real-time quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) and PCR-restriction fragment length polymorphism analyses were performed to detect the expression of VEGFA, APP, and NUMB mRNA in 20 CRC tissues and matched adjacent normal tissues, as well as their alternative splicing variants. RESULTS: qRT-PCR analysis revealed that the expression of APP, NUMB, and VEGFA165b mRNA were significantly downregulated, while VEGFA mRNA was upregulated, in CRC tissues (all P < 0.05). PCR-restriction fragment length polymorphism analysis revealed that the expression of VEGFA165a/b in CRC tissues was significantly higher than in adjacent normal tissues (P < 0.05). Compared with adjacent normal tissues, the expression of NUMB-PRRS in CRC tissues was significantly decreased (P < 0.05), and the expression of NUMB-PRRL was increased (P < 0.05). CONCLUSION: Alternative splicing of VEGFA, APP, and NUMB may regulate the development of CRC, and represent new targets for its diagnosis, prognosis, and treatment. PMID:26074693

  9. The Program of Gene Transcription for a Single Differentiating Cell Type during Sporulation in Bacillus subtilis

    PubMed Central

    Eichenberger, Patrick; Fujita, Masaya; Jensen, Shane T; Conlon, Erin M; Rudner, David Z; Wang, Stephanie T; Ferguson, Caitlin; Haga, Koki; Sato, Tsutomu; Liu, Jun S

    2004-01-01

    Asymmetric division during sporulation by Bacillus subtilis generates a mother cell that undergoes a 5-h program of differentiation. The program is governed by a hierarchical cascade consisting of the transcription factors: σE, σK, GerE, GerR, and SpoIIID. The program consists of the activation and repression of 383 genes. The σE factor turns on 262 genes, including those for GerR and SpoIIID. These DNA-binding proteins downregulate almost half of the genes in the σE regulon. In addition, SpoIIID turns on ten genes, including genes involved in the appearance of σK . Next, σK activates 75 additional genes, including that for GerE. This DNA-binding protein, in turn, represses half of the genes that had been activated by σK while switching on a final set of 36 genes. Evidence is presented that repression and activation contribute to proper morphogenesis. The program of gene expression is driven forward by its hierarchical organization and by the repressive effects of the DNA-binding proteins. The logic of the program is that of a linked series of feed-forward loops, which generate successive pulses of gene transcription. Similar regulatory circuits could be a common feature of other systems of cellular differentiation. PMID:15383836

  10. 78 FR 52116 - Request for Public Comment on a Review Level Alternative Dispute Resolution Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-08-22

    ... From the Federal Register Online via the Government Publishing Office OCCUPATIONAL SAFETY AND... Dispute Resolution Program AGENCY: Occupational Safety and Health Review Commission. ACTION: Request for comment. SUMMARY: The Occupational Safety and Health Review Commission invites the public to comment...

  11. 77 FR 14587 - FY 2012 Discretionary Livability Funding Opportunity: Alternatives Analysis Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-12

    ... and value of such improvements. Livable Communities and Sustainable Development FTA has long fostered livable communities and sustainable development through its various transit ] programs and activities... Maintaining transit assets in a state of good repair, fostering livable communities and promoting...

  12. Alternative splicing mechanisms orchestrating post-transcriptional gene expression: intron retention and the intron-rich genome of apicomplexan parasites.

    PubMed

    Lunghi, Matteo; Spano, Furio; Magini, Alessandro; Emiliani, Carla; Carruthers, Vern B; Di Cristina, Manlio

    2016-02-01

    Apicomplexan parasites including Toxoplasma gondii and Plasmodium species have complex life cycles that include multiple hosts and differentiation through several morphologically distinct stages requiring marked changes in gene expression. This review highlights emerging evidence implicating regulation of mRNA splicing as a mechanism to prime these parasites for rapid gene expression upon differentiation. We summarize the most important insights in alternative splicing including its role in regulating gene expression by decreasing mRNA abundance via 'Regulated Unproductive Splicing and Translation'. As a related but less well-understood mechanism, we discuss also our recent work suggesting a role for intron retention for precluding translation of stage specific isoforms of T. gondii glycolytic enzymes. We additionally provide new evidence that intron retention might be a widespread mechanism during parasite differentiation. Supporting this notion, recent genome-wide analysis of Toxoplasma and Plasmodium suggests intron retention is more pervasive than heretofore thought. These findings parallel recent emergence of intron retention being more prevalent in mammals than previously believed, thereby adding to the established roles in plants, fungi and unicellular eukaryotes. Deeper mechanistic studies of intron retention will provide important insight into its role in regulating gene expression in apicomplexan parasites and more general in eukaryotic organisms.

  13. Space transportation alternatives for large space programs: The International Space University Summer Session, 1992

    NASA Technical Reports Server (NTRS)

    Palaszewski, Bryan A.

    1993-01-01

    In 1992, the International Space University (ISU) held its Summer Session in Kitakyushu, Japan. This paper summarizes and expands upon some aspects of space solar power and space transportation that were considered during that session. The issues discussed in this paper are the result of a 10-week study by the Space Solar Power Program design project members and the Space Transportation Group to investigate new paradigms in space propulsion and how those paradigms might reduce the costs for large space programs. The program plan was to place a series of power satellites in Earth orbit. Several designs were studied where many kW, MW, or GW of power would be transmitted to Earth or to other spacecraft in orbit. During the summer session, a space solar power system was also detailed and analyzed. A high-cost space transportation program is potentially the most crippling barrier to such a space power program. At ISU, the focus of the study was to foster and develop some of the new paradigms that may eliminate the barriers to low cost for space exploration and exploitation. Many international and technical aspects of a large multinational program were studied. Environmental safety, space construction and maintenance, legal and policy issues of frequency allocation, technology transfer and control and many other areas were addressed. Over 120 students from 29 countries participated in this summer session. The results discussed in this paper, therefore, represent the efforts of many nations.

  14. Chitosan-thioglycolic acid conjugate: an alternative carrier for oral nonviral gene delivery?

    PubMed

    Martien, Ronny; Loretz, Brigitta; Thaler, Marlene; Majzoob, Sayeh; Bernkop-Schnürch, Andreas

    2007-07-01

    Regarding safety concerns, nonviral gene delivery vehicles that have the required efficiency and safety for use in human gene therapy are being widely investigated. The aim of this study was to synthesize and evaluate a thiolated chitosan to improve the efficacy of oral gene delivery systems. Thiolated chitosan was synthesized by introducing thioglycolic acid (TGA) to chitosan via amide bond formation mediated by a carbodiimide. Based on this conjugate, nanoparticles with pDNA were generated at pH 4.0 and 5.0. Cytotoxicity of the thiolated chitosan/pDNA nanoparticles on Caco-2 cells was evaluated. The diameter of thiolated chitosan/pDNA nanoparticles was in the range of 100-200 nm. The zeta potential was determined to be 5-6 mV. Due to stability toward nucleases, the transfection rate of thiolated chitosan/pDNA nanoparticles was fivefold higher than that of unmodified chitosan/pDNA nanoparticles. Lactate dehydrogenase tests for thiolated chitosan/pDNA (pH 4.0 and 5.0) showed that (3.79 +/- 0.23)% and (2.9 +/- 0.13)% cell damage. According to these results, thiolated chitosan represents promising excipients for preparation DNA nanoparticles in nonviral gene delivery system.

  15. Alternating tandem array of histone and ribosomal RNA gene blocks in the boll weevil

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Histones are the major protein component of the ncleosome. The histone family is made up of a quintet of proteins, four core histones (H2A, H2B, H3 & H4) and the linker histones (H1). Spacers are found between the coding regions. Among insects this quintet of genes is usually clustered and the clust...

  16. Confirmatory and Competitive Evaluation of Alternative Gene-Environment Interaction Hypotheses

    ERIC Educational Resources Information Center

    Belsky, Jay; Pluess, Michael; Widaman, Keith F.

    2013-01-01

    Background: Most gene-environment interaction (GXE) research, though based on clear, vulnerability-oriented hypotheses, is carried out using exploratory rather than hypothesis-informed statistical tests, limiting power and making formal evaluation of competing GXE propositions difficult. Method: We present and illustrate a new regression technique…

  17. Rethinking gene regulatory networks in light of alternative splicing, intrinsically disordered protein domains, and post-translational modifications

    PubMed Central

    Niklas, Karl J.; Bondos, Sarah E.; Dunker, A. Keith; Newman, Stuart A.

    2015-01-01

    Models for genetic regulation and cell fate specification characteristically assume that gene regulatory networks (GRNs) are essentially deterministic and exhibit multiple stable states specifying alternative, but pre-figured cell fates. Mounting evidence shows, however, that most eukaryotic precursor RNAs undergo alternative splicing (AS) and that the majority of transcription factors contain intrinsically disordered protein (IDP) domains whose functionalities are context dependent as well as subject to post-translational modification (PTM). Consequently, many transcription factors do not have fixed cis-acting regulatory targets, and developmental determination by GRNs alone is untenable. Modeling these phenomena requires a multi-scale approach to explain how GRNs operationally interact with the intra- and intercellular environments. Evidence shows that AS, IDP, and PTM complicate gene expression and act synergistically to facilitate and promote time- and cell-specific protein modifications involved in cell signaling and cell fate specification and thereby disrupt a strict deterministic GRN-phenotype mapping. The combined effects of AS, IDP, and PTM give proteomes physiological plasticity, adaptive responsiveness, and developmental versatility without inefficiently expanding genome size. They also help us understand how protein functionalities can undergo major evolutionary changes by buffering mutational consequences. PMID:25767796

  18. Alternate Bearing in Citrus: Changes in the Expression of Flowering Control Genes and in Global Gene Expression in ON- versus OFF-Crop Trees

    PubMed Central

    Shalom, Liron; Samuels, Sivan; Zur, Naftali; Shlizerman, Lyudmila; Zemach, Hanita; Weissberg, Mira; Ophir, Ron; Blumwald, Eduardo; Sadka, Avi

    2012-01-01

    Alternate bearing (AB) is the process in fruit trees by which cycles of heavy yield (ON crop) one year are followed by a light yield (OFF crop) the next. Heavy yield usually reduces flowering intensity the following year. Despite its agricultural importance, how the developing crop influences the following year's return bloom and yield is not fully understood. It might be assumed that an ‘AB signal’ is generated in the fruit, or in another organ that senses fruit presence, and moves into the bud to determine its fate—flowering or vegetative growth. The bud then responds to fruit presence by altering regulatory and metabolic pathways. Determining these pathways, and when they are altered, might indicate the nature of this putative AB signal. We studied bud morphology, the expression of flowering control genes, and global gene expression in ON- and OFF-crop buds. In May, shortly after flowering and fruit set, OFF-crop buds were already significantly longer than ON-crop buds. The number of differentially expressed genes was higher in May than at the other tested time points. Processes differentially expressed between ON- and OFF-crop trees included key metabolic and regulatory pathways, such as photosynthesis and secondary metabolism. The expression of genes of trehalose metabolism and flavonoid metabolism was validated by nCounter technology, and the latter was confirmed by metabolomic analysis. Among genes induced in OFF-crop trees was one homologous to SQUAMOSA PROMOTER BINDING-LIKE (SPL), which controls juvenile-to-adult and annual phase transitions, regulated by miR156. The expression pattern of SPL-like, miR156 and other flowering control genes suggested that fruit load affects bud fate, and therefore development and metabolism, a relatively long time before the flowering induction period. Results shed light on some of the metabolic and regulatory processes that are altered in ON and OFF buds. PMID:23071667

  19. Alternative fuels

    SciTech Connect

    Not Available

    1991-07-01

    This paper presents the preliminary results of a review, of the experiences of Brazil, Canada, and New Zealand, which have implemented programs to encourage the use of alternative motor fuels. It will also discuss the results of a separate completed review of the Department of Energy's (DOE) progress in implementing the Alternative Motor Fuels Act of 1988. The act calls for, among other things, the federal government to use alternative-fueled vehicles in its fleet. The Persian Gulf War, environmental concerns, and the administration's National Energy Strategy have greatly heightened interest in the use of alternative fuels in this country.

  20. Alternative Splicing of Rice WRKY62 and WRKY76 Transcription Factor Genes in Pathogen Defense1[OPEN

    PubMed Central

    Chen, Xujun; Zhou, Xiangui; Yang, Fang

    2016-01-01

    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. PMID:27208272

  1. Hydrogen peroxide triggers a novel alternative splicing of arsenic (+3 oxidation state) methyltransferase gene.

    PubMed

    Sumi, Daigo; Takeda, Chieri; Yasuoka, Daiki; Himeno, Seiichiro

    2016-11-04

    We previously reported that two splicing variants of human AS3MT mRNA, exon-3 skipping form (Δ3) and exons-4 and -5 skipping form (Δ4,5), were detected in HepG2 cells and that both variants lacked arsenic methylation activity (Sumi et al., 2011). Here we studied whether hydrogen peroxide (H2O2) triggers alternative splicing of AS3MT mRNA. The results showed that exposure of HepG2 cells to H2O2 resulted in increased levels of a novel spliced form skipping exon-3 to exon-10 (Δ3-10) in an H2O2-concentration-dependent manner, although no change was detected in the mRNA levels of Δ3 AS3MT. We found decreased protein levels of serine/arginine-rich 40 (SRp40), which we determined to be a candidate splice factor for controlling the splicing of AS3MT mRNA. We next compared the amounts of methylated arsenic metabolites between control and H2O2-exposed HepG2 cells after the addition of arsenite as a substance. The results showed lower levels of methylated arsenic metabolites in HepG2 cells exposed to H2O2. These data suggest that the splicing of AS3MT pre-mRNA was disconcerted by oxidative stress and that abnormal alternative splicing of AS3MT mRNA may affect arsenic methylation ability.

  2. Gene-specific factors determine mitotic expression and bookmarking via alternate regulatory elements

    PubMed Central

    Arampatzi, Panagiota; Gialitakis, Manolis; Makatounakis, Takis; Papamatheakis, Joseph

    2013-01-01

    Transcriptional silencing during mitosis is caused by inactivation of critical transcriptional regulators and/or chromatin condensation. Inheritance of gene expression patterns through cell division involves various bookmarking mechanisms. In this report, we have examined the mitotic and post-mitotic expression of the DRA major histocompatibility class II (MHCII) gene in different cell types. During mitosis the constitutively MHCII-expressing B lymphoblastoid cells showed sustained occupancy of the proximal promoter by the cognate enhanceosome and general transcription factors. In contrast, although mitotic epithelial cells were depleted of these proteins irrespectively of their MHCII transcriptional activity, a distal enhancer selectively recruited the PP2A phosphatase via NFY and maintained chromatin accessibility. Based on our data, we propose a novel chromatin anti-condensation role for this element in mitotic bookmarking and timing of post-mitotic transcriptional reactivation. PMID:23303784

  3. Successive Losses of Central Immune Genes Characterize the Gadiformes' Alternate Immunity.

    PubMed

    Solbakken, Monica H; Rise, Matthew L; Jakobsen, Kjetill S; Jentoft, Sissel

    2016-12-31

    Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene (Mx) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus, thus predating the loss of Major Histocompatibility Complex class II (MHCII) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time.

  4. Successive Losses of Central Immune Genes Characterize the Gadiformes’ Alternate Immunity

    PubMed Central

    Solbakken, Monica H.; Rise, Matthew L.; Jakobsen, Kjetill S.; Jentoft, Sissel

    2016-01-01

    Great genetic variability among teleost immunomes, with gene losses and expansions of central adaptive and innate components, has been discovered through genome sequencing over the last few years. Here, we demonstrate that the innate Myxovirus resistance gene (Mx) is lost from the ancestor of Gadiformes and the closely related Stylephorus chordatus, thus predating the loss of Major Histocompatibility Complex class II (MHCII) in Gadiformes. Although the functional implication of Mx loss is still unknown, we demonstrate that this loss is one of several ancient events appearing in successive order throughout the evolution of teleost immunity. In particular, we find that the loss of Toll-like receptor 5 predates the loss of Mx involving the entire Paracanthopterygii lineage. Using a time-calibrated phylogeny, we show that loss of MHCII and Mx overlap with major paleoclimatic and geological events indicating that these genetic changes were adaptive responses to the changing environment at the time. PMID:27797950

  5. Comparison of Teaching Attitudes, Teacher Efficacy, and Teacher Performance of First Year Teachers Prepared by Alternative and Traditional Teacher Education Programs.

    ERIC Educational Resources Information Center

    Guyton, Edith; And Others

    1991-01-01

    The findings from this study of Georgia teachers generally support the contention that condensed pedagogical preparation and a supervised internship are a reasonable alternative to traditional teacher preparation programs for persons with degrees in the subject they will teach. (IAH)

  6. Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts.

    PubMed

    Calsa, Tercilio; Figueira, Antonio

    2007-04-01

    Sugarcane (Saccharum spp.) is a highly efficient biomass and sugar producing crop. Leaf reactions have been considered as potential rate-limiting step for sucrose accumulation in sugarcane stalks. To characterize the sugarcane leaf transcriptome, field-grown mature leaves from cultivar "SP80-3280" were analyzed using Serial Analysis of Gene Expression (SAGE). From 480 sequenced clones, 9,482 valid tags were extracted, with 5,227 unique sequences, from which 3,659 (70%) matched at least a sugarcane assembled sequence (SAS) with putative function; while 872 tags (16.7%) matched SAS with unknown function; 523 (10%) matched SAS without a putative annotation; and only 173 (3.3%) did not match any sugarcane ESTs. Based on gene ontology (GO), photosystem (PS) I reaction center was identified as the most frequent gene product location, followed by the remaining sites of PS I, PS II and thylakoid complexes. For metabolic processes, photosynthesis light harvesting complexes; carbon fixation; and chlorophyll biosynthesis were the most enriched GO-terms. Considering the alternative photosynthetic C(4) cycles, tag frequencies related to phosphoenolpyruvate carboxykinase (PEPCK) and aspartate aminotransferase compared to those for NADP(+)-malic enzyme (NADP-ME) and NADP-malate dehydrogenase, suggested that PEPCK-type decarboxylation appeared to predominate over NADP-ME in mature leaves, although both may occur, opposite to currently assumed in sugarcane. From the unique tag set, 894 tags (17.1%) were assigned as potentially derived from antisense transcripts, while 73 tags (1.4%) were assigned to more than one SAS, suggesting the occurrence of alternative processing. The occurrence of antisense was validated by quantitative reverse transcription amplification. Sugarcane leaf transcriptome provided new insights for functional studies associated with sucrose synthesis and accumulation.

  7. Alternative live-attenuated influenza vaccines based on modifications in the polymerase genes protect against epidemic and pandemic flu.

    PubMed

    Solórzano, Alicia; Ye, Jianqiang; Pérez, Daniel R

    2010-05-01

    Human influenza is a seasonal disease associated with significant morbidity and mortality. Influenza vaccination is the most effective means for disease prevention. We have previously shown that mutations in the PB1 and PB2 genes of the live-attenuated influenza vaccine (LAIV) from the cold-adapted (ca) influenza virus A/Ann Arbor/6/60 (H2N2) could be transferred to avian influenza viruses and produce partially attenuated viruses. We also demonstrated that avian influenza viruses carrying the PB1 and PB2 mutations could be further attenuated by stably introducing a hemagglutinin (HA) epitope tag in the PB1 gene. In this work, we wanted to determine whether these modifications would also result in attenuation of a so-called triple reassortant (TR) swine influenza virus (SIV). Thus, the TR influenza A/swine/Wisconsin/14094/99 (H3N2) virus was generated by reverse genetics and subsequently mutated in the PB1 and PB2 genes. Here we show that a combination of mutations in this TR backbone results in an attenuated virus in vitro and in vivo. Furthermore, we show the potential of our TR backbone as a vaccine that provides protection against the 2009 swine-origin pandemic influenza H1N1 virus (S-OIV) when carrying the surface of a classical swine strain. We propose that the availability of alternative backbones to the conventional ca A/Ann Arbor/6/60 LAIV strain could also be useful in epidemic and pandemic influenza and should be considered for influenza vaccine development. In addition, our data provide evidence that the use of these alternative backbones could potentially circumvent the effects of original antigenic sin (OAS) in certain circumstances.

  8. An Exploratory Inquiry of the Outcomes of Adults Who Participated in a Virginia Alternative Education Program: Making Sense of Their Experience

    ERIC Educational Resources Information Center

    Hackney, Melody D.

    2012-01-01

    The purpose of this retrospective study was to develop an understanding of how one group of adults who graduated from a Virginia regional alternative program made sense of their experience in an alternative education setting. Specifically, this study sought to determine if adult participants, several years later, perceived participation in the…

  9. Alternative Education Models--Interim Findings from the Replication of Career Intern Programs. Education and Training Approaches. Youth Knowledge Development Report 5.1.

    ERIC Educational Resources Information Center

    Employment and Training Administration (DOL), Washington, DC. Office of Youth Programs.

    This volume contains four interim reports of the Career Intern Program (CIP) replication portion of the Alternative Education Demonstration operated by Opportunities Industrialization Centers of America and evaluated by the National Institute of Education. (The CIP is an alternative high school serving dropouts and students at a high risk of…

  10. Collected Evaluations on the WCPSS Alternative School Program for Students with Long-Term Suspensions. Executive Summary. Eye on Evaluation. E&R Report.

    ERIC Educational Resources Information Center

    Carruthers, William L.

    The Wake County Public School System (WCPSS) has provided an alternative school program for students with long-term suspensions since the 1995-96 school year. Since 1996-97, the WCPSS has contracted with a private firm to operate the Richard M. Milburn High School (RMHS), as an alternative learning center. This Executive Summary highlights the…

  11. Income and Employment Generation in Rural Areas in Relation to Alternative Farm Programs (with Special Emphasis on the North Central Region).

    ERIC Educational Resources Information Center

    Heady, Earl O.; Sonka, Steven T.

    Four alternative government farm policies were analyzed to determine their effect upon farm income and employment generation in rural areas and agriculturally related industries. A linear programming model of interregional competition was used to determine the impact of alternative farm policies on the quantity of major commodities produced, the…

  12. Giving Literacy Away. Alternative Strategies for Increasing Adult Literacy Development, Training Capacity and Program Participation.

    ERIC Educational Resources Information Center

    Reder, Stephen M.

    The phenomenon of adult functional illiteracy in the United States is examined, and strategies are considered for addressing the problem. Reasons for the failure of existing programs (schools, adult education, and volunteer tutoring) to close the literacy gap are explored; among these factors are the relative growth of underserved populations,…

  13. Intervention Research and Program Evaluation in the School Setting: Issues and Alternative Research Designs

    ERIC Educational Resources Information Center

    de Anda, Diane

    2007-01-01

    This article discusses the difficulties in conducting intervention research or evaluating intervention programs in a school setting. In particular, the problems associated with randomization and obtaining control groups are examined. The use of quasi-experimental designs, specifically a paired comparison design using the individual as his or her…

  14. Space transportation alternatives for large space programs - The International Space University summer session - 1992

    NASA Astrophysics Data System (ADS)

    Palaszewski, Bryan

    1993-06-01

    The issues discussed in this paper are the result of a 10-week study by the Space Solar Power Program design project members and the Space Transportation Group at the International Space University (ISU) summer session of 1992 to investigate new paradigms in space propulsion and how those paradigms might reduce the costs for large space programs. The program plan was to place a series of power satellites in Earth orbit. Several designs were studied where many kW, MW or GW of power would be transmitted to Earth or to other spacecraft in orbit. During the summer session, a space solar power system was also detailed and analyzed. At ISU, the focus of the study was to foster and develop some of the new paradigms that may eliminate the barriers to low cost for space exploration and exploitation. Many international and technical aspects of a large multinational program were studied. Environmental safety, space construction and maintenance, legal and policy issues of frequency allocation, technology transfer and control and many other areas were addressed.

  15. Space transportation alternatives for large space programs - The International Space University summer session - 1992

    NASA Technical Reports Server (NTRS)

    Palaszewski, Bryan

    1993-01-01

    The issues discussed in this paper are the result of a 10-week study by the Space Solar Power Program design project members and the Space Transportation Group at the International Space University (ISU) summer session of 1992 to investigate new paradigms in space propulsion and how those paradigms might reduce the costs for large space programs. The program plan was to place a series of power satellites in Earth orbit. Several designs were studied where many kW, MW or GW of power would be transmitted to Earth or to other spacecraft in orbit. During the summer session, a space solar power system was also detailed and analyzed. At ISU, the focus of the study was to foster and develop some of the new paradigms that may eliminate the barriers to low cost for space exploration and exploitation. Many international and technical aspects of a large multinational program were studied. Environmental safety, space construction and maintenance, legal and policy issues of frequency allocation, technology transfer and control and many other areas were addressed.

  16. Lower East Side Preparatory School: An Alternative to the Conventional High School Program. Final Evaluation Report.

    ERIC Educational Resources Information Center

    Wohl, Seth F.

    In this second year evaluation report of the Lower East Side Preparatory school in New York City's Chinatown, a history of the project is provided as well as information on the characteristics of the program in operation, the evaluation design used for this report, the findings after three trimesters and the recommendations for the recycling of…

  17. Competency-Based Education: A Viable Alternative for Developmental Studies Program Design.

    ERIC Educational Resources Information Center

    Herrscher, Barton R.

    1980-01-01

    Advocates the use of both descriptive and prescriptive approaches to designing developmental studies programs in community colleges. Defines competency-based education (CBE) and examines five critical elements of CBE: educational framework, systematic structure, educational attainment, learning outcomes, and instructional processes. Discusses the…

  18. 78 FR 22026 - Alternative Transportation in Parks and Public Lands Program

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-12

    ... capital and planning projects across the country, ranging from shuttle bus purchases to the construction... of FY 2012 Project Selections. SUMMARY: The U.S. Department of Transportation's (DOT) Federal Transit Administration (FTA) announces the selection of projects for the Paul S. Sarbanes Transit in Parks Program,...

  19. Value-Added Models for Teacher Preparation Programs: Validity and Reliability Threats, and a Manageable Alternative

    ERIC Educational Resources Information Center

    Brady, Michael P.; Heiser, Lawrence A.; McCormick, Jazarae K.; Forgan, James

    2016-01-01

    High-stakes standardized student assessments are increasingly used in value-added evaluation models to connect teacher performance to P-12 student learning. These assessments are also being used to evaluate teacher preparation programs, despite validity and reliability threats. A more rational model linking student performance to candidates who…

  20. Criteria for Evaluating Alternative Network and Link Layer Protocols for the NASA Constellation Program Communication Architecture

    NASA Technical Reports Server (NTRS)

    Benbenek, Daniel; Soloff, Jason; Lieb, Erica

    2010-01-01

    Selecting a communications and network architecture for future manned space flight requires an evaluation of the varying goals and objectives of the program, development of communications and network architecture evaluation criteria, and assessment of critical architecture trades. This paper uses Cx Program proposed exploration activities as a guideline; lunar sortie, outpost, Mars, and flexible path options are described. A set of proposed communications network architecture criteria are proposed and described. They include: interoperability, security, reliability, and ease of automating topology changes. Finally a key set of architecture options are traded including (1) multiplexing data at a common network layer vs. at the data link layer, (2) implementing multiple network layers vs. a single network layer, and (3) the use of a particular network layer protocol, primarily IPv6 vs. Delay Tolerant Networking (DTN). In summary, the protocol options are evaluated against the proposed exploration activities and their relative performance with respect to the criteria are assessed. An architectural approach which includes (a) the capability of multiplexing at both the network layer and the data link layer and (b) a single network layer for operations at each program phase, as these solutions are best suited to respond to the widest array of program needs and meet each of the evaluation criteria.

  1. When Prohibition Works: Alternatives to Violence in the Odyssey House Youth Program and in the Family.

    ERIC Educational Resources Information Center

    King, David F.; Straus, Murray A.

    Physical violence, a factor often associated with drug addiction, must be reduced or eliminated in order for drug dependent individuals to reenter society. To examine the extent to which individual violence associated with drug addiction was controllable by the Odyssey House drug addiction rehabilitation program, the violence potential of 47…

  2. Fighting High School Senior Slump: The Spread of an Alternative Senior Program.

    ERIC Educational Resources Information Center

    Wade, Taron

    1999-01-01

    At several New York State high schools, seniors hold internships in architectural firms, Planned Parenthood, dentists' offices, and television and radio stations. Some make documentaries or pursue independent study in various subjects. These opportunities arise through a program (WISE) allowing second-semester seniors to design and complete their…

  3. New Chemicals Program Review of Alternatives for PFOA and Related Chemicals

    EPA Pesticide Factsheets

    In 2006, EPA and the eight major companies in the industry launched the 2010/15 PFOA Stewardship Program, in which companies committed to reduce global facility emissions and product content of PFOA and related chemicals by 95 percent by 2010, and to work

  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

    ...This final rule implements provisions of the Patient Protection and Affordable Care Act and the Health Care and Education Reconciliation Act of 2010 (collectively referred to as the Affordable Care Act. This final rule finalizes new Medicaid eligibility provisions; finalizes changes related to electronic Medicaid and the Children's Health Insurance Program (CHIP) eligibility notices and......

  5. An Alternative Approach for MBA Mentor Programs: Empower the Protégé

    ERIC Educational Resources Information Center

    Artis, Andrew B.

    2013-01-01

    A new approach is proposed to maximize the benefits of mentor relationships between master of business administration (MBA) students and executives by empowering students to select and recruit their own mentors, and then be responsible for managing those relationships. This mentor program is designed to be short but intensive. First-year MBA…

  6. Assessment of capital requirements for alternative fuels infrastructure under the PNGV program

    SciTech Connect

    Stork, K.; Singh, M.; Wang, M.; Vyas, A.

    1998-12-31

    This paper presents an assessment of the capital requirements of using six different fuels in the vehicles with tripled fuel economy (3X vehicles) that the Partnership for a new Generation of Vehicles is currently investigating. The six fuels include two petroleum-based fuels (reformulated gasoline and low-sulfur diesel) and four alternative fuels (methanol, ethanol, dimethyl ether, and hydrogen). This study develops estimates of cumulative capital needs for establishing fuels production and distribution infrastructure to accommodate 3X vehicle fuel needs. Two levels of fuel volume-70,000 barrels per day and 1.6 million barrels per day-were established for meeting 3X-vehicle fuel demand. As expected, infrastructure capital needs for the high fuel demand level are much higher than for the low fuel demand level. Between fuel production infrastructure and distribution infrastructure, capital needs for the former far exceed those for the latter. Among the four alternative fuels, hydrogen bears the largest capital needs for production and distribution infrastructure.

  7. Offer of rapid testing and alternative biological samples as practical tools to implement HIV screening programs.

    PubMed

    Parisi, Maria Rita; Soldini, Laura; Di Perri, Giovanni; Tiberi, Simon; Lazzarin, Adriano; Lillo, Flavia B

    2009-10-01

    Implementation of HIV testing has the objective to increase screening, identify and counsel persons with infection, link them to clinical services and reduce transmission. Rapid tests and/or alternative biological samples (like oral fluid) give the option for a better general consent in approaching screening, immediate referral of HIV positives to medical treatment and partner notification. We tested the performance characteristics of an oral fluid-based rapid HIV test (Rapidtest HIV lateral flow-Healthchem diag. LLC) in comparison with routinely utilized methods in a selected population of known positive (N = 121) or negative (N = 754) subjects. The sensitivity of the rapid test was 99.1% (one false negative sample) and the specificity 98.8%. Five negatives showed a faint reactivity, 3 of these were reactive also in the reference test, one with a p24 only reaction in Western blot. If these 3 samples were excluded from the analysis the specificity increases to 99.2%. Results from our study confirm that, although a continuous improvement of the test performance is still needed to minimize false negative and positive results, rapid test and alternative biological samples may contribute to HIV prevention strategies by reaching a larger population particularly when and where regular screening procedures are difficult to obtain.

  8. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design

    PubMed Central

    Bissinger, Alexa; Muller, Mundenga Mutendi; Gebreyesus, Alegnta; Geremew, Haimanot; Wendell, Sarah; Azaza, Aklilu; Salumu, Maurice; Benfield, Nerys

    2015-01-01

    This paper describes design of a low cost, ultrasound gel from local products applying aspects of Human Centered Design methodology. A multidisciplinary team worked with clinicians who use ultrasound where commercial gel is cost prohibitive and scarce. The team followed the format outlined in the Ideo Took Kit. Research began by defining the challenge "how to create locally available alternative ultrasound gel for a low-resourced environment? The "End-Users," were identified as clinicians who use ultrasound in Democratic Republic of the Congo and Ethiopia. An expert group was identified and queried for possible alternatives to commercial gel. Responses included shampoo, oils, water and cornstarch. Cornstarch, while a reasonable solution, was either not available or too expensive. We then sought deeper knowledge of locally sources materials from local experts, market vendors, to develop a similar product. Suggested solutions gleaned from these interviews were collected and used to create ultrasound gel accounting for cost, image quality, manufacturing capability. Initial prototypes used cassava root flour from Great Lakes Region (DRC, Rwanda, Uganda, Tanzania) and West Africa, and bula from Ethiopia. Prototypes were tested in the field and resulting images evaluated by our user group. A final prototype was then selected. Cassava and bula at a 32 part water, 8 part flour and 4 part salt, heated, mixed then cooled was the product design of choice. PMID:26252003

  9. Alternative Ultrasound Gel for a Sustainable Ultrasound Program: Application of Human Centered Design.

    PubMed

    Salmon, Margaret; Salmon, Christian; Bissinger, Alexa; Muller, Mundenga Mutendi; Gebreyesus, Alegnta; Geremew, Haimanot; Wendel, Sarah K; Wendell, Sarah; Azaza, Aklilu; Salumu, Maurice; Benfield, Nerys

    2015-01-01

    This paper describes design of a low cost, ultrasound gel from local products applying aspects of Human Centered Design methodology. A multidisciplinary team worked with clinicians who use ultrasound where commercial gel is cost prohibitive and scarce. The team followed the format outlined in the Ideo Took Kit. Research began by defining the challenge "how to create locally available alternative ultrasound gel for a low-resourced environment? The "End-Users," were identified as clinicians who use ultrasound in Democratic Republic of the Congo and Ethiopia. An expert group was identified and queried for possible alternatives to commercial gel. Responses included shampoo, oils, water and cornstarch. Cornstarch, while a reasonable solution, was either not available or too expensive. We then sought deeper knowledge of locally sources materials from local experts, market vendors, to develop a similar product. Suggested solutions gleaned from these interviews were collected and used to create ultrasound gel accounting for cost, image quality, manufacturing capability. Initial prototypes used cassava root flour from Great Lakes Region (DRC, Rwanda, Uganda, Tanzania) and West Africa, and bula from Ethiopia. Prototypes were tested in the field and resulting images evaluated by our user group. A final prototype was then selected. Cassava and bula at a 32 part water, 8 part flour and 4 part salt, heated, mixed then cooled was the product design of choice.

  10. Transcriptome Analysis in Rat Kidneys: Importance of Genes Involved in Programmed Hypertension

    PubMed Central

    Tain, You-Lin; Huang, Li-Tung; Chan, Julie Y. H.; Lee, Chien-Te

    2015-01-01

    Suboptimal conditions in pregnancy can elicit long-term effects on the health of offspring. The most common outcome is programmed hypertension. We examined whether there are common genes and pathways in the kidney are responsible for generating programmed hypertension among three different models using next generation RNA sequencing (RNA-Seq) technology. Pregnant Sprague-Dawley rats received dexamethasone (DEX, 0.1 mg/kg) from gestational day 16 to 22, 60% high-fructose (HF) diet, or NG-nitro-l-arginine-methyester (l-NAME, 60 mg/kg/day) to conduct DEX, HF, or l-NAME model respectively. All three models elicited programmed hypertension in adult male offspring. We observed five shared genes (Bcl6, Dmrtc1c, Egr1, Inmt, and Olr1668) among three different models. The identified differential genes (DEGs) that are related to regulation of blood pressure included Aqp2, Ptgs1, Eph2x, Hba-a2, Apln, Guca2b, Hmox1, and Npy. RNA-Seq identified genes in arachidonic acid metabolism are potentially gatekeeper genes contributing to programmed hypertension. In addition, HF and DEX increased expression and activity of soluble epoxide hydrolase (Ephx2 gene encoding protein). Conclusively, the DEGs in arachidonic acid metabolism are potentially gatekeeper genes in programmed hypertension. The roles of DEGs identified by the RNA-Seq in this study deserve further clarification, to develop the potential interventions in the prevention of programmed hypertension. PMID:25739086

  11. Integrative analyses of RNA editing, alternative splicing, and expression of young genes in human brain transcriptome by deep RNA sequencing.

    PubMed

    Wu, Dong-Dong; Ye, Ling-Qun; Li, Yan; Sun, Yan-Bo; Shao, Yi; Chen, Chunyan; Zhu, Zhu; Zhong, Li; Wang, Lu; Irwin, David M; Zhang, Yong E; Zhang, Ya-Ping

    2015-08-01

    Next-generation RNA sequencing has been successfully used for identification of transcript assembly, evaluation of gene expression levels, and detection of post-transcriptional modifications. Despite these large-scale studies, additional comprehensive RNA-seq data from different subregions of the human brain are required to fully evaluate the evolutionary patterns experienced by the human brain transcriptome. Here, we provide a total of 6.5 billion RNA-seq reads from different subregions of the human brain. A significant correlation was observed between the levels of alternative splicing and RNA editing, which might be explained by a competition between the molecular machineries responsible for the splicing and editing of RNA. Young human protein-coding genes demonstrate biased expression to the neocortical and non-neocortical regions during evolution on the lineage leading to humans. We also found that a significantly greater number of young human protein-coding genes are expressed in the putamen, a tissue that was also observed to have the highest level of RNA-editing activity. The putamen, which previously received little attention, plays an important role in cognitive ability, and our data suggest a potential contribution of the putamen to human evolution.

  12. Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai.

    PubMed

    Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

    2017-03-09

    In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone.

  13. Analysis of mutations and alternative splicing patterns in the CFTR gene using mRNA derived from nasal epithelial cells.

    PubMed

    Hull, J; Shackleton, S; Harris, A

    1994-07-01

    Ten to fifteen percent of CF chromosomes carry mutations which are not detected by routine screening of the CFTR gene for known mutations. Many techniques have been used to screen the CFTR gene for these remaining mutations. Most of the methods use genomic DNA, and since the CFTR gene contains 27 exons, are necessarily labour intensive. We have screened the entire coding region of CFTR, by chemical cleavage of 7 overlapping segments of amplified cDNA. Using this method we have identified 4 sequence changes which had not been detected by screening genomic DNA, and successfully detected 10 out of 13 known mutations. In addition, we have identified 8 alternatively spliced forms of CFTR mRNA, 4 of which have not been described previously. These include transcripts lacking a) exon 3, b) exons 2 + 3, c) exons 9 + 12, and d) the final 357 bp of exon 15 as a result of use of the cryptic splice donor site CA2863/GTTCGT).

  14. The subsidiary GntII system for gluconate metabolism in Escherichia coli: alternative induction of the gntV gene.

    PubMed

    Gómez, Keyla M; Rodríguez, Andrea; Rodriguez, Yesseima; Ramírez, Alvaro H; Istúriz, Tomás

    2011-01-01

    Two systems are involved in the transport and phosphorylation of gluconate in Escherichia coli. GntI, the main system, consists of high and low-affinity gluconate transporters and a thermoresistant gluconokinase for its phosphorylation. The corresponding genes, gntT, gntU and gntK at 76.5 min, are induced by gluconate. GntII, the subsidiary system, includes IdnT and GntV, which duplicate activities of transport and phosphorylation of gluconate, respectively. Gene gntV at 96.8 min is divergently transcribed from the idnDOTR operon involved in L-idonate metabolism. These genetic elements are induced by the substrate or 5-keto-D-gluconate. Because gntV is also induced in cells grown in gluconate, it was of interest to investigate its expression in this condition. E. coli gntK, idnOokan mutants were constructed to study this question. These idnO kan-cassete inserted mutants, unable to convert gluconate to 5-keto-D-gluconate, permitted examining gntV expression in the absence of this inducer and demonstrating that it is not required when the cells grow in gluconate. The results suggest that E. coli gntV gene is alternatively induced by 5-keto-D-gluconate or gluconate in cells cultivated either in idonate or gluconate. In this way, the control of gntV expression would seem to be involved in the efficient utilization of these substrates.

  15. Alternative Splicing Profile and Sex-Preferential Gene Expression in the Female and Male Pacific Abalone Haliotis discus hannai

    PubMed Central

    Kim, Mi Ae; Rhee, Jae-Sung; Kim, Tae Ha; Lee, Jung Sick; Choi, Ah-Young; Choi, Beom-Soon; Choi, Ik-Young; Sohn, Young Chang

    2017-01-01

    In order to characterize the female or male transcriptome of the Pacific abalone and further increase genomic resources, we sequenced the mRNA of full-length complementary DNA (cDNA) libraries derived from pooled tissues of female and male Haliotis discus hannai by employing the Iso-Seq protocol of the PacBio RSII platform. We successfully assembled whole full-length cDNA sequences and constructed a transcriptome database that included isoform information. After clustering, a total of 15,110 and 12,145 genes that coded for proteins were identified in female and male abalones, respectively. A total of 13,057 putative orthologs were retained from each transcriptome in abalones. Overall Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analyzed in each database showed a similar composition between sexes. In addition, a total of 519 and 391 isoforms were genome-widely identified with at least two isoforms from female and male transcriptome databases. We found that the number of isoforms and their alternatively spliced patterns are variable and sex-dependent. This information represents the first significant contribution to sex-preferential genomic resources of the Pacific abalone. The availability of whole female and male transcriptome database and their isoform information will be useful to improve our understanding of molecular responses and also for the analysis of population dynamics in the Pacific abalone. PMID:28282934

  16. Glucocorticoid Effects on the Programming of AT1b Angiotensin Receptor Gene Methylation and Expression in the Rat

    PubMed Central

    Bogdarina, Irina; Haase, Andrea; Langley-Evans, Simon; Clark, Adrian J. L.

    2010-01-01

    Adverse events in pregnancy may ‘programme’ offspring for the later development of cardiovascular disease and hypertension. Previously, using a rodent model of programmed hypertension we have demonstrated the role of the renin-angiotensin system in this process. More recently we showed that a maternal low protein diet resulted in undermethylation of the At1b angiotensin receptor promoter and the early overexpression of this gene in the adrenal of offspring. Here, we investigate the hypothesis that maternal glucocorticoid modulates this effect on fetal DNA methylation and gene expression. We investigated whether treatment of rat dams with the 11β-hydroxylase inhibitor metyrapone, could prevent the epigenetic and gene expression changes we observed. Offspring of mothers subjected to a low protein diet in pregnancy showed reduced adrenal Agtr1b methylation and increased adrenal gene expression as we observed previously. Treatment of mothers with metyrapone for the first 14 days of pregnancy reversed these changes and prevented the appearance of hypertension in the offspring at 4 weeks of age. As a control for non-specific effects of programmed hypertension we studied offspring of mothers treated with dexamethasone from day 15 of pregnancy and showed that, whilst they had raised blood pressure, they failed to show any evidence of Agtr1b methylation or increase in gene expression. We conclude that maternal glucocorticoid in early pregnancy may induce changes in methylation and expression of the Agtr1b gene as these are clearly reversed by an 11 beta-hydroxylase inhibitor. However in later pregnancy a converse effect with dexamethasone could not be demonstrated and this may reflect either an alternative mechanism of this glucocorticoid or a stage-specific influence. PMID:20169056

  17. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    SciTech Connect

    Harmon, Harry D.

    2000-11-30

    In March 2000, DOE-Headquarters (HQ) requested the Tanks Focus Area (TFA) to assume management responsibility for the Salt Processing Project technology development program at Savannah River Site. The TFA was requested to conduct several activities, including review and revision of the technology development roadmaps, development of down-selection criteria, and preparation of a comprehensive Research and Development (R&D) Program Plan for three candidate cesium removal technologies, as well as the Alpha and strontium removal processes that must also be carried out. The three cesium removal candidate technologies are Crystalline Silicotitanate (CST) Non-Elutable Ion Exchange, Caustic Side Solvent Extraction (CSSX), and Small Tank Tetraphenylborate Precipitation (STTP). This plan describes the technology development needs for each process that must be satisfied in order to reach a down-selection decision, as well as continuing technology development required to support conceptual design activities.

  18. Tanks Focus Area Alternative Salt Processing Research and Development Program Plan

    SciTech Connect

    Harmon, Harry D.

    2000-05-15

    In March 2000, DOE-Headquarters (HQ) requested the Tanks Focus Area (TFA)to assume management responsibility for the Salt Processing Project technology development program at Savannah River Site. The TFA was requested to conduct several activities, including review and revision of the technology development roadmaps, development of down-selection criteria, and preparation of a comprehensive Research and Development (R&D) Program Plan for three candidate cesium removal technologies, as well as the Alpha and strontium removal processes that must also be carried out. The three cesium removal candidate technologies are Crystalline Silicotitanate (CST) Non-Elutable Ion Exchange, Caustic Side Solvent Extraction (CSSX), and Small Tank Tetraphenylborate Precipitation (STTP). This plan describes the technology development needs for each process that must be satisfied in order to reach a down-selection decision, as well as continuing technology development required to support conceptual design activities.

  19. From Punishment to Treatment: The "Clinical Alternative to Punitive Segregation" (CAPS) Program in New York City Jails.

    PubMed

    Glowa-Kollisch, Sarah; Kaba, Fatos; Waters, Anthony; Leung, Y Jude; Ford, Elizabeth; Venters, Homer

    2016-02-02

    The proliferation of jails and prisons as places of institutionalization for persons with serious mental illness (SMI) has resulted in many of these patients receiving jail-based punishments, including solitary confinement. Starting in 2013, the New York City (NYC) jail system developed a new treatment unit for persons with SMI who were judged to have violated jail rules (and previously would have been punished with solitary confinement) called the Clinical Alternative to Punitive Segregation (CAPS) unit. CAPS is designed to offer a full range of therapeutic activities and interventions for these patients, including individual and group therapy, art therapy, medication counseling and community meetings. Each CAPS unit requires approximately $1.5 million more investment per year, largely in additional staff as compared to existing mental health units, and can house approximately 30 patients. Patients with less serious mental illness who received infractions were housed on units that combined solitary confinement with some clinical programming, called Restrictive Housing Units (RHU). Between 1 December 2013 and 31 March 2015, a total of 195 and 1433 patients passed through the CAPS and RHU units, respectively. A small cohort of patients experienced both CAPS and RHU (n = 90). For these patients, their rates of self-harm and injury were significantly lower while on the CAPS unit than when on the RHU units. Improvements in clinical outcomes are possible for incarcerated patients with mental illness with investment in new alternatives to solitary confinement. We have started to adapt the CAPS approach to existing mental health units as a means to promote better clinical outcomes and also help prevent jail-based infractions. The cost of these programs and the dramatic differences in length of stay for patients who earn these jail-based infractions highlight the need for alternatives to incarceration, some of which have recently been announced in NYC.

  20. From Punishment to Treatment: The “Clinical Alternative to Punitive Segregation” (CAPS) Program in New York City Jails

    PubMed Central

    Glowa-Kollisch, Sarah; Kaba, Fatos; Waters, Anthony; Leung, Y. Jude; Ford, Elizabeth; Venters, Homer

    2016-01-01

    The proliferation of jails and prisons as places of institutionalization for persons with serious mental illness (SMI) has resulted in many of these patients receiving jail-based punishments, including solitary confinement. Starting in 2013, the New York City (NYC) jail system developed a new treatment unit for persons with SMI who were judged to have violated jail rules (and previously would have been punished with solitary confinement) called the Clinical Alternative to Punitive Segregation (CAPS) unit. CAPS is designed to offer a full range of therapeutic activities and interventions for these patients, including individual and group therapy, art therapy, medication counseling and community meetings. Each CAPS unit requires approximately $1.5 million more investment per year, largely in additional staff as compared to existing mental health units, and can house approximately 30 patients. Patients with less serious mental illness who received infractions were housed on units that combined solitary confinement with some clinical programming, called Restrictive Housing Units (RHU). Between 1 December 2013 and 31 March 2015, a total of 195 and 1433 patients passed through the CAPS and RHU units, respectively. A small cohort of patients experienced both CAPS and RHU (n = 90). For these patients, their rates of self-harm and injury were significantly lower while on the CAPS unit than when on the RHU units. Improvements in clinical outcomes are possible for incarcerated patients with mental illness with investment in new alternatives to solitary confinement. We have started to adapt the CAPS approach to existing mental health units as a means to promote better clinical outcomes and also help prevent jail-based infractions. The cost of these programs and the dramatic differences in length of stay for patients who earn these jail-based infractions highlight the need for alternatives to incarceration, some of which have recently been announced in NYC. PMID:26848667

  1. [Computer simulation programs as an alternative for classical nerve, muscle and heart experiments using frog tissues].

    PubMed

    Breves, G; Schröder, B

    2000-03-01

    Courses in Physiology include different methodical approaches such as exercises with living animals, experiments using organs or tissues from killed or slaughtered animals, application of diagnostic techniques in humans and theoretical seminars. In addition to these classical approaches computer programs for multimedia simulation of nerve, muscle and heart physiology are now a regular component of courses in Physiology at the School of Veterinary Medicine in Hannover. It is the aim of the present paper to give the first experiences about these new components.

  2. Pro-socially shareable entertainment television programmes: a programming alternative in developing countries?

    PubMed

    Singhal, A; Svenkerud, P J

    1994-12-01

    Over the period 1975-82, the Mexican television network created and aired seven entertainment soap operas promoting educational-development themes like adult literacy, smaller family size norms, and an higher social status for women. These emissions earned high ratings in Mexico and in other Latin American countries where they were subsequently broadcast. Evidence suggests that many of the social objectives of the soaps were met. In light of such success, the authors investigated the potential of pro-socially shareable entertainment television programs in developing countries. These programs use entertaining media formats to carry pro-social messages to a wide, yet culturally-proximate audience group. Entertainment television genres such as melodramatic soap operas offer certain advantages for carrying pro-socially shareable messages to audiences. The possibility of using other television genres and media channels, however, also needs to be seriously considered. Pro-socially shareable entertainment programs do have their limitations and problems, with a certain degree of message dilution invariably accompanying the quest for shareability. Targeting specific problems in specific audience groups is difficult and the identity of a relatively small homogeneous group can be threatened in a larger culturally proximate group. The value-laden nature of pro-social content can also be problematic.

  3. The alternative sigma factor B modulates virulence gene expression in a murine Staphylococcus aureus infection model but does not influence kidney gene expression pattern of the host.

    PubMed

    Depke, Maren; Burian, Marc; Schäfer, Tina; Bröker, Barbara M; Ohlsen, Knut; Völker, Uwe

    2012-01-01

    Infections caused by Staphylococcus aureus are associated with significant morbidity and mortality and are an increasing threat not only in hospital settings. The expression of the staphylococcal virulence factor repertoire is known to be affected by the alternative sigma factor B (SigB). However, its impact during infection still is a matter of debate. Kidney tissues of controls or mice infected with S. aureus HG001 or its isogenic sigB mutant were analyzed by transcriptome profiling to monitor the host response, and additionally expression of selected S. aureus genes was monitored by RT-qPCR. Direct transcript analysis by RT-qPCR revealed significant SigB activity in all mice infected with the wild-type strain, but not in its isogenic sigB mutant (p<0.0001). Despite a clear-cut difference in the SigB-dependent transcription pattern of virulence genes (clfA, aur, and hla), the host reaction to infection (either wild type or sigB mutant) was almost identical. Despite its significant activity in vivo, loss of SigB did neither have an effect on the outcome of infection nor on murine kidney gene expression pattern. Thus, these data support the role of SigB as virulence modulator rather than being a virulence determinant by itself.

  4. Control of Gene Expression by RNA Binding Protein Action on Alternative Translation Initiation Sites

    PubMed Central

    Re, Angela; Waldron, Levi; Quattrone, Alessandro

    2016-01-01

    Transcript levels do not faithfully predict protein levels, due to post-transcriptional regulation of gene expression mediated by RNA binding proteins (RBPs) and non-coding RNAs. We developed a multivariate linear regression model integrating RBP levels and predicted RBP-mRNA regulatory interactions from matched transcript and protein datasets. RBPs significantly improved the accuracy in predicting protein abundance of a portion of the total modeled mRNAs in three panels of tissues and cells and for different methods employed in the detection of mRNA and protein. The presence of upstream translation initiation sites (uTISs) at the mRNA 5’ untranslated regions was strongly associated with improvement in predictive accuracy. On the basis of these observations, we propose that the recently discovered widespread uTISs in the human genome can be a previously unappreciated substrate of translational control mediated by RBPs. PMID:27923063

  5. Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy

    PubMed Central

    Du, Hongqing; Cline, Melissa S.; Osborne, Robert J.; Tuttle, Daniel L.; Clark, Tyson A.; Donohue, John Paul; Hall, Megan P.; Shiue, Lily; Swanson, Maurice S.; Thornton, Charles A.; Ares, Manuel

    2009-01-01

    Myotonic dystrophy (DM1) is associated with expression of expanded CTG DNA repeats as RNA (CUGexp RNA). To test whether CUGexp RNA creates a global splicing defect, we compared skeletal muscle of two mouse DM1 models, one expressing a CTGexp transgene, and another homozygous for a defective Mbnl1 gene. Strong correlation in splicing changes for ~100 new Mbnl1-regulated exons indicates loss of Mbnl1 explains >80% of the splicing pathology due to CUGexp RNA. In contrast, only about half of mRNA level changes can be attributed to loss of Mbnl1, indicating CUGexp RNA has Mbnl1-independent effects, particularly on mRNAs for extracellular matrix (ECM) proteins. We propose that CUGexp RNA causes two separate effects: loss of Mbnl1 function, disrupting splicing, and loss of another function that disrupts ECM mRNA regulation, possibly mediated by MBNL2. These findings reveal unanticipated similarities between DM1 and other muscular dystrophies. PMID:20098426

  6. Evidence for alternative candidate genes near RB1 involved in clonal expansion of in situ urothelial neoplasia.

    PubMed

    Kim, Mi-Sook; Jeong, Joon; Majewski, Tadeusz; Kram, Andrzej; Yoon, Dong-Sup; Zhang, Ruo-Dan; Li, Jun-Zhi; Ptaszynski, Konrad; Kuang, Tang C; Zhou, Jain-Hua; Sathyanarayana, Ubaradka G; Tuziak, Tomasz; Johnston, Dennis A; Grossman, Herbert B; Gazdar, Adi F; Scherer, Steven E; Benedict, William F; Czerniak, Bogdan

    2006-02-01

    In this paper, we present whole-organ histologic and genetic mapping studies using hypervariable DNA markers on chromosome 13 and then integrate the recombination- and single-nucleotide polymorphic sites (SNPs)-based deletion maps with the annotated genome sequence. Using bladders resected from patients with invasive urothelial carcinoma, we studied allelic patterns of 40 microsatellite markers mapping to all regions of chromosome 13 and 79 SNPs located within the 13q14 region containing the RB1 gene. A whole-organ histologic and genetic mapping strategy was used to identify the evolution of allelic losses on chromosome 13 during the progression of bladder neoplasia. Markers mapping to chromosomal regions involved in clonal expansion of preneoplastic intraurothelial lesions were subsequently tested in 25 tumors and 21 voided urine samples of patients with bladder cancer. Four clusters of allelic losses mapping to distinct regions of chromosome 13 were identified. Markers mapping to the 13q14 region that is flanked by D13S263 and D13S276, which contains the RB1 gene, showed allelic losses associated with early clonal expansion of intraurothelial neoplasia. Such losses could be identified in approximately 32% bladder tumor tissue samples and 38% of voided urines from patients with bladder cancer. The integration of distribution patterns of clonal allelic losses revealed by the microsatellite markers with those obtained by genotyping of SNPs disclosed that the loss within an approximately 4-Mb segment centered around RB1 may represent an incipient event in bladder neoplasia. However, the inactivation of RB1 occurred later and was associated with the onset of severe dysplasia/carcinoma in situ. Our studies provide evidence for the presence of critical alternative candidate genes mapping to the 13q14 region that are involved in clonal expansion of neoplasia within the bladder antecedent to the inactivation of the RB1 gene.

  7. Mutation in the 5' alternatively spliced region of the XNP/ATR-X gene causes Chudley-Lowry syndrome.

    PubMed

    Abidi, Fatima E; Cardoso, Carlos; Lossi, Anne-Marie; Lowry, Robert Brian; Depetris, Danielle; Mattéi, Marie-Geneviève; Lubs, Herbert A; Stevenson, Roger E; Fontes, Michel; Chudley, Albert E; Schwartz, Charles E

    2005-02-01

    The Chudley-Lowry syndrome (ChLS, MIM 309490) is an X-linked recessive condition characterized by moderate to severe mental retardation, short stature, mild obesity, hypogonadism, and distinctive facial features characterized by depressed nasal bridge, anteverted nares, inverted-V-shaped upper lip, and macrostomia. The original Chudley-Lowry family consists of three affected males in two generations. Linkage analysis had localized the gene to a large interval, Xp21-Xq26 and an obligate carrier was demonstrated to have highly skewed X inactivation. The combination of the clinical phenotype, consistent with that of the patients with ATR-X syndrome, the skewed X-inactivation pattern in a carrier female, as well as the mapping interval including band Xq13.3, prompted us to consider the XNP/ATR-X gene being involved in this syndrome. Using RT-PCR analysis, we screened the entire XNP/ATR-X gene and found a mutation in exon 2 (c.109C > T) giving rise to a stop codon at position 37 (p.R37X). Western blot and immunocytochemical analyses using a specific monoclonal antibody directed against XNP/ATR-X showed the protein to be present in lymphoblastoid cells from one affected male, despite the premature stop codon. To explain these discordant results, we further analyzed the 5' region of the XNP/ATR-X gene and found three alternative transcripts, which differ in the presence or absence of exon 2, and the length of exon 1. Our data suggest that ChLS is allelic to the ATR-X syndrome with its less severe phenotype being due to the presence of some XNP/ATR-X protein.

  8. Differentially expressed three non-coding alternate exons at 5' UTR of regulatory type I beta subunit gene of mouse.

    PubMed

    Banday, Abdul Rouf; Azim, Shafquat; Tabish, Mohammad

    2012-04-01

    Prkar1b gene encodes regulatory type I, beta subunit (RIβ) of cAMP dependent protein kinase A in mouse. Among the various isoforms of regulatory and catalytic subunits that comprise mammalian PKA, RIβ subunit is considered to be one of the important subunits for neuronal functions. This is involved in multiple forms of synaptic plasticity, and influences memory and learning by maintaining hippocampal long-term potentiation (LTP). Deficient expression of this gene has been implicated in autoimmune disease systemic lupus erythematosus (SLE). We have identified two novel non-coding exons of the Prkar1b gene (designated as exon 1A and exon 1B), which are spliced to the canonical exon 2 and constitute the 5' untranslated region giving rise to three alternative transcript isoforms. We have also confirmed the expression of the previously known first exon (designated as exon 1C) with known transcript published earlier. The transcripts containing exons 1A, 1B and 1C are differentially regulated during the development and tissue types. In silico study of more than 20 kb nucleotide sequence upstream of known translational initiation codon revealed three distinct promoter regions named as PA, PB, and PC upstream of the exon 1A, exon 1B and exon 1C respectively. PB is non-CpG related promoter but PA and PC are CpG related promoters, however all three promoters are TATA less. Further analysis showed that these promoters possess potential signature sequences for common as well as different transcription factors suggesting complex regulation of Prkar1b gene.

  9. Alternative splicing interference by xenobiotics.

    PubMed

    Zaharieva, Emanuela; Chipman, J Kevin; Soller, Matthias

    2012-06-14

    The protein coding sequence of most eukaryotic genes (exons) is interrupted by non-coding parts (introns), which are excised in a process termed splicing. To generate a mature messenger RNA (mRNA) hundreds of combinatorial protein-protein and RNA-protein interactions are required to splice out often very large introns with high fidelity and accuracy. Inherent to splicing is the use of alternative splice sites generating immense proteomic diversity from a limited number of genes. In humans, alternative splicing is a major mode of regulating gene expression, occurs in over 90% of genes and is particularly abundant in the brain. Only recently, it has been recognized that the complexity of the splicing process makes it susceptible to interference by various xenobiotics. These compounds include antineoplastic substances, commonly used drugs and food supplements and cause a spectrum of effects ranging from deleterious inhibition of general splicing to highly specific modifications of alternative splicing affecting only certain genes. Alterations in splicing have been implicated in numerous diseases such as cancer and neurodegeneration. Splicing regulation plays an important role in the execution of programmed cell death. The switch between anti- and pro-apoptotic isoforms by alternative splice site selection and misregulation of a number of splicing factors impacts on cell survival and disease. Here, our current knowledge is summarized on compounds interfering with general and alternative splicing and of the current methodology to study changes in these processes relevant to the field of toxicology and future risk assessments.

  10. Cell Cycle Programs of Gene Expression Control Morphogenetic Protein Localization

    PubMed Central

    Lord, Matthew; Yang, Melody C.; Mischke, Michelle; Chant, John

    2000-01-01

    Genomic studies in yeast have revealed that one eighth of genes are cell cycle regulated in their expression. Almost without exception, the significance of cell cycle periodic gene expression has not been tested. Given that many such genes are critical to cellular morphogenesis, we wanted to examine the importance of periodic gene expression to this process. The expression profiles of two genes required for the axial pattern of cell division, BUD3 and BUD10/AXL2/SRO4, are strongly cell cycle regulated. BUD3 is expressed close to the onset of mitosis. BUD10 is expressed in late G1. Through promotor-swap experiments, the expression profile of each gene was altered and the consequences examined. We found that an S/G2 pulse of BUD3 expression controls the timing of Bud3p localization, but that this timing is not critical to Bud3p function. In contrast, a G1 pulse of BUD10 expression plays a direct role in Bud10p localization and function. Bud10p, a membrane protein, relies on the polarized secretory machinery specific to G1 to be delivered to its proper location. Such a secretion-based targeting mechanism for membrane proteins provides cells with flexibility in remodeling their architecture or evolving new forms. PMID:11134078

  11. Investigation of potential alternative hydrogen carrier, Mg supported zeolite with temperature programmed desorption of NH3.

    PubMed

    Cho, Sung June; Kim, Tak Hee; Jang, Young Bae; Lee, Jun

    2007-11-01

    Magnesium ion exchanged zeolite A was subject to the measurement of the temperature programmed desorption of NH3 to explore the possibility of the potential hydrogen carrier. The result suggested that the Mg supported NaA zeolite released a significant amount of ammonia corresponding to 1.4 Hwt% hydrogen at around 373 K. Under the same condition after the NH3 adsorption at ambient temperature, the MgCl2 sample released 1.0 Hwt% hydrogen at around 340 K. The present work suggests that the Mg supported zeolite can also be utilized as hydrogen carrier.

  12. Integrative Gene Regulatory Network Analysis Reveals Light-Induced Regional Gene Expression Phase Shift Programs in the Mouse Suprachiasmatic Nucleus

    PubMed Central

    Zhu, Haisun; Vadigepalli, Rajanikanth; Rafferty, Rachel; Gonye, Gregory E.; Weaver, David R.; Schwaber, James S.

    2012-01-01

    We use the multigenic pattern of gene expression across suprachiasmatic nuclei (SCN) regions and time to understand the dynamics within the SCN in response to a circadian phase-resetting light pulse. Global gene expression studies of the SCN indicate that circadian functions like phase resetting are complex multigenic processes. While the molecular dynamics of phase resetting are not well understood, it is clear they involve a “functional gene expression program”, e.g., the coordinated behavior of functionally related genes in space and time. In the present study we selected a set of 89 of these functionally related genes in order to further understand this multigenic program. By use of high-throughput qPCR we studied 52 small samples taken by anatomically precise laser capture from within the core and shell SCN regions, and taken at time points with and without phase resetting light exposure. The results show striking regional differences in light response to be present in the mouse SCN. By using network-based analyses, we are able to establish a highly specific multigenic correlation between genes expressed in response to light at night and genes normally activated during the day. The light pulse triggers a complex and highly coordinated network of gene regulation. The largest differences marking neuroanatomical location are in transmitter receptors, and the largest time-dependent differences occur in clock-related genes. Nighttime phase resetting appears to recruit transcriptional regulatory processes normally active in the day. This program, or mechanism, causes the pattern of core region gene expression to transiently shift to become more like that of the shell region. PMID:22662235

  13. High efficiency myogenic conversion of human fibroblasts by adenoviral vector-mediated MyoD gene transfer. An alternative strategy for ex vivo gene therapy of primary myopathies.

    PubMed Central

    Lattanzi, L; Salvatori, G; Coletta, M; Sonnino, C; Cusella De Angelis, M G; Gioglio, L; Murry, C E; Kelly, R; Ferrari, G; Molinaro, M; Crescenzi, M; Mavilio, F; Cossu, G

    1998-01-01

    Ex vivo gene therapy of primary myopathies, based on autologous transplantation of genetically modified myogenic cells, is seriously limited by the number of primary myogenic cells that can be isolated, expanded, transduced, and reimplanted into the patient's muscles. We explored the possibility of using the MyoD gene to induce myogenic conversion of nonmuscle, primary cells in a quantitatively relevant fashion. Primary human and murine fibroblasts from skin, muscle, or bone marrow were infected by an E1-deleted adenoviral vector carrying a retroviral long terminal repeat-promoted MyoD cDNA. Expression of MyoD caused irreversible withdrawal from the cell cycle and myogenic differentiation in the majority (from 60 to 90%) of cultured fibroblasts, as defined by activation of muscle-specific genes, fusion into contractile myotubes, and appearance of ultrastructurally normal sarcomagenesis in culture. 24 h after adenoviral exposure, MyoD-converted cultures were injected into regenerating muscle of immunodeficient (severe combined immunodeficiency/beige) mice, where they gave rise to beta-galactosidase positive, centrally nucleated fibers expressing human myosin heavy chains. Fibers originating from converted fibroblasts were indistinguishable from those obtained by injection of control cultures of lacZ-transduced satellite cells. MyoD-converted murine fibroblasts participated to muscle regeneration also in immunocompetent, syngeneic mice. Although antibodies from these mice bound to adenoviral infected cells in vitro, no inflammatory infiltrate was present in the graft site throughout the 3-wk study period. These data support the feasibility of an alternative approach to gene therapy of primary myopathies, based on implantation of large numbers of genetically modified primary fibroblasts massively converted to myogenesis by adenoviral delivery of MyoD ex vivo. PMID:9593768

  14. Profiling the array of Ca(v)3.1 variants from the human T-type calcium channel gene CACNA1G: alternative structures, developmental expression, and biophysical variations.

    PubMed

    Emerick, Mark C; Stein, Rebecca; Kunze, Robin; McNulty, Megan M; Regan, Melissa R; Hanck, Dorothy A; Agnew, William S

    2006-08-01

    We describe the regulated transcriptome of CACNA1G, a human gene for T-type Ca(v)3.1 calcium channels that is subject to extensive alternative RNA splicing. Fifteen sites of transcript variation include 2 alternative 5'-UTR promoter sites, 2 alternative 3'-UTR polyadenylation sites, and 11 sites of alternative splicing within the open reading frame. A survey of 1580 fetal and adult human brain full-length complementary DNAs reveals a family of 30 distinct transcripts, including multiple functional forms that vary in expression with development. Statistical analyses of fetal and adult transcript populations reveal patterns of linkages among intramolecular splice site configurations that change dramatically with development. A shift from nearly independent, biased splicing in fetal transcripts to strongly concerted splicing in adult transcripts suggests progressive activation of multiple "programs" of splicing regulation that reorganize molecular structures in differentiating cells. Patch-clamp studies of nine selected variants help relate splicing regulation to permutations of the gating parameters most likely to modify T-channel physiology in expressing neurons. Gating behavior reflects combinatorial interactions between variable domains so that molecular phenotype depends on ensembles of coselected domains, consistent with the observed emergence of concerted splicing during development. We conclude that the structural gene and networks of splicing regulatory factors define an integrated system for the phenotypic variation of Ca(v)3.1 biophysics during nervous system development.

  15. A Case Study of the Approach to Teaching and to Technology of Three New Teachers in an Alternative Teacher Certification Program

    ERIC Educational Resources Information Center

    O'Connor, Eileen A.

    2007-01-01

    The Master of Arts in Teaching program at Empire State College, a new alternative teacher certification program focused on bringing career-changing adults to high-needs schools, provides a unique opportunity to understand the challenges facing new teachers, in their content area and in their use of technology. This article describes aspects of…

  16. Low-Budget Computer Programming in Your School (An Alternative to the Cost of Large Computers). Illinois Series on Educational Applications of Computers. No. 14.

    ERIC Educational Resources Information Center

    Dennis, J. Richard; Thomson, David

    This paper is concerned with a low cost alternative for providing computer experience to secondary school students. The brief discussion covers the programmable calculator and its relevance for teaching the concepts and the rudiments of computer programming and for computer problem solving. A list of twenty-five programming activities related to…

  17. Development of a Student Mentored Research Program between a Complementary and Alternative Medicine University and a Traditional, Research Intensive University

    PubMed Central

    Sullivan, Barbara M.; Furner, Sylvia E.; Cramer, Gregory D.

    2014-01-01

    The global need to develop clinician-scientists capable of using research in clinical practice, translating research knowledge into practice, and carrying out research that affects the quality, efficacy, and efficiency of health care is well-documented. The complementary and alternative medicine (CAM) professions embrace the call to develop physician-researchers to carry out translational and applied research for CAM modalities. CAM universities face unique challenges when implementing research training compared to traditional, research intensive (TRI) universities and medical centers where the majority of medical research is carried out. The authors present the development and outcomes of a mentored research program (MRP) between a CAM and a TRI institution, the National University of Health Sciences and the University of Illinois at Chicago School of Public Health, between 2006 and 2012. CAM pre-doctoral students engaged in a full-immersion semester at the TRI, including didactic courses and active research with a TRI faculty research mentor. Half of the participating doctor of chiropractic (DC) students continued on to PhD programs and half established integrative medicine, primary care clinical careers. Establishing rigorous criteria for mentors and mentees, communicating expectations, developing solid relationships between the mentor, mentee, and home school advisor, responding quickly to impediments, and providing adequate support from CAM and TRI investigators were key to the MRP success. To sustain research opportunities, coordinated degree programs for the DC and master of public health (DC/MPH) and master of clinical and translational research (DC/MS CTS) were established. PMID:24988423

  18. An event of alternative splicing affects the expression of the NTRC gene, encoding NADPH-thioredoxin reductase C, in seed plants.

    PubMed

    Nájera, Victoria A; González, María Cruz; Pérez-Ruiz, Juan Manuel; Cejudo, Francisco Javier

    2017-05-01

    The NTRC gene encodes a NADPH-dependent thioredoxin reductase with a joint thioredoxin domain, exclusive of photosynthetic organisms. An updated search shows that although most species harbor a single copy of the NTRC gene, two copies were identified in different species of the genus Solanum, Glycine max and the moss Physcomitrella patens. The phylogenetic analysis of NTRCs from different sources produced a tree with the major groups of photosynthetic organisms: cyanobacteria, algae and land plants, indicating the evolutionary success of the NTRC gene among photosynthetic eukaryotes. An event of alternative splicing affecting the expression of the NTRC gene was identified, which is conserved in seed plants but not in algae, bryophytes and lycophytes. The alternative splicing event results in a transcript with premature stop codon, which would produce a truncated form of the enzyme. The standard splicing/alternative splicing (SS/AS) transcripts ratio was higher in photosynthetic tissues from Arabidopsis, Brachypodium and tomato, in line with the higher content of the NTRC polypeptide in these tissues. Moreover, environmental stresses such as cold or high salt affected the SS/AS ratio of the NTRC gene transcripts in Brachypodium seedlings. These results suggest that the alternative splicing of the NTRC gene might be an additional mechanism for modulating the content of NTRC in photosynthetic and non-photosynthetic tissues of seed plants.

  19. Valuation of selected environmental impacts associated with Bonneville Power Administration Resource Program alternatives

    SciTech Connect

    Englin, J E; Gygi, K F

    1992-03-01

    This report documents work undertaken by the Pacific Northwest Laboratory (PNL) and its contractors to assist the Bonneville Power Administration (Bonneville) in assessing the potential environmental consequences of new power resources. A major purpose of this effort is to describe and evaluate the techniques available for economic valuation of environmental costs. Another is to provide estimates of the environmental costs associated with specific power resources called for under Bonneville's Resource Programs. Bonneville's efforts to extend valuation techniques to as many impacts as can be reliably assessed represents a substantial advance in the application of state-of-the-art economic techniques to environmental assessments. This economic analysis evaluates effects on human health, wildlife, crops, and visibility impacts associated with air pollution. This report also discusses river recreation (primarily fishing) which may be affected by fluctuations in water levels. 70 refs.

  20. Mixed Waste Focus Area alternative oxidation technologies development and demonstration program

    SciTech Connect

    Borduin, L.C.; Fewell, T.; Gombert, D.; Priebe, S.

    1998-07-01

    The Mixed Waste Focus Area (MWFA) is currently supporting the development and demonstration of several alternative oxidation technology (AOT) processes for treatment of combustible mixed low-level wastes. The impetus for this support derives from regulatory and political hurdles frequently encountered by traditional thermal techniques, primarily incinerators. AOTs have been defined as technologies that destroy organic material without using open-flame reactions. Whether thermal or nonthermal, the processes have the potential advantages of relatively low-volume gaseous emissions, generation of few or no dioxin/furan compounds, and operation at low enough temperatures that metals (except mercury) and most radionuclides are not volatilized. Technology development and demonstration are needed to confirm and realize the potential of AOTs and to compare them on an equal basis with their fully demonstrated thermal counterparts. AOTs include both thermal and nonthermal processes that oxidize organic wastes but operate under significantly different physical and chemical conditions than incinerators. Nonthermal processes currently being studied include Delphi DETOX and acid digestion at the Savannah River Site, and direct chemical oxidation at Lawrence Livermore National Laboratory. All three technologies are at advanced stages of development or are entering the demonstration phase. Nonflame thermal processes include catalytic chemical oxidation, which is being developed and deployed at Lawrence Berkeley National Laboratory, and team reforming, a commercial process being supported by Department of Energy. Related technologies include two low-flow, secondary oxidation processes (Phoenix and Thermatrix units) that have been tested at MSE, Inc., in Butte, Montana. Although testing is complete on some AOT technologies, most require additional support to complete some or all of the identified development objectives. Brief descriptions, status, and planned paths forward for each

  1. Global Identification of the Full-Length Transcripts and Alternative Splicing Related to Phenolic Acid Biosynthetic Genes in Salvia miltiorrhiza

    PubMed Central

    Xu, Zhichao; Luo, Hongmei; Ji, Aijia; Zhang, Xin; Song, Jingyuan; Chen, Shilin

    2016-01-01

    Salvianolic acids are among the main bioactive components in Salvia miltiorrhiza, and their biosynthesis has attracted widespread interest. However, previous studies on the biosynthesis of phenolic acids using next-generation sequencing platforms are limited with regard to the assembly of full-length transcripts. Based on hybrid-seq (next-generation and single molecular real-time sequencing) of the S. miltiorrhiza root transcriptome, we experimentally identified 15 full-length transcripts and four alternative splicing events of enzyme-coding genes involved in the biosynthesis of rosmarinic acid. Moreover, we herein demonstrate that lithospermic acid B accumulates in the phloem and xylem of roots, in agreement with the expression patterns of the identified key genes related to rosmarinic acid biosynthesis. According to co-expression patterns, we predicted that six candidate cytochrome P450s and five candidate laccases participate in the salvianolic acid pathway. Our results provide a valuable resource for further investigation into the synthetic biology of phenolic acids in S. miltiorrhiza. PMID:26904067

  2. The eyeless mouse mutation (ey1) removes an alternative start codon from the Rx/rax homeobox gene.

    PubMed

    Tucker, P; Laemle, L; Munson, A; Kanekar, S; Oliver, E R; Brown, N; Schlecht, H; Vetter, M; Glaser, T

    2001-09-01

    The eyeless inbred mouse strain ZRDCT has long served as a spontaneous model for human anophthalmia and the evolutionary reduction of eyes that has occurred in some naturally blind mammals. ZRDCT mice have orbits but lack eyes and optic tracts and have hypothalamic abnormalities. Segregation data suggest that a small number of interacting genes are responsible, including at least one major recessive locus, ey1. Although predicted since the 1940s, these loci were never identified. We mapped ey1 to chromosome 18 using an F2 genome scan and there found a Met10-->Leu mutation in Rx/rax, a homeobox gene that is expressed in the anterior headfold, developing retina, pineal, and hypothalamus and is translated via a leaky scanning mechanism. The mutation affects a conserved AUG codon that functions as an alternative translation initiation site and consequently reduces the abundance of Rx protein. In contrast to a targeted Rx null allele, which causes anophthalmia, central nervous system defects, and neonatal death, the hypomorphic M10L allele is fully viable.

  3. PEG-ADA: an alternative to haploidentical bone marrow transplantation and an adjunct to gene therapy for adenosine deaminase deficiency.

    PubMed

    Hershfield, M S

    1995-01-01

    PEG-ADA is a long-circulating form of adenosine deaminase (ADA) that has been in use for > 8 years as replacement therapy for severe combined immunodeficiency disease due to ADA deficiency. Treatment with PEG-ADA almost completely corrects metabolic abnormalities, allowing the recovery of a variable degree of immune function. Although not normal, the level of function achieved has in most cases been sufficient to protect against opportunistic and life-threatening infections. PEG-ADA has been used as an alternative for patients who lack an HLA-identical bone marrow donor, but are judged to be at too high a risk for undergoing HLA-haploidentical marrow transplantation. To date, mortality and morbidity with PEG-ADA have been less than for the latter procedure. PEG-ADA has also been an important adjunct to attempts to develop somatic cell gene therapy for ADA deficiency, although its continued use poses a problem for evaluation of the benefit of gene therapy. As a true "orphan drug" developed to treat a very small patient population, the cost per patient of PEG-ADA is very high.

  4. mRNA leader length and initiation codon context determine alternative AUG selection for the yeast gene MOD5.

    PubMed Central

    Slusher, L B; Gillman, E C; Martin, N C; Hopper, A K

    1991-01-01

    MOD5, a nuclear gene of Saccharomyces cerevisiae, encodes two isozymic forms of a tRNA-modification enzyme. These enzymes modify both cytoplasmic and mitochondrial tRNAs. Two inframe ATGs of the MOD5 gene are used for initiation of translation, and the form of the protein translated from the first AUG is imported into mitochondria. Protein translated from the second AUG functions in the cytoplasm. Since all transcripts contain both of these translational start sites and two proteins are made, the question arises as to the factors that influence the translation start-site choice. Extending the 5' ends of the MOD5 mRNA to include leader sequences of the ADH1 (alcohol dehydrogenase defective) transcript produces significant changes in the choice of AUGs. This suggests that for wild-type MOD5 transcripts, the length or structure of the leader sequence plays a role in AUG choice. The nucleotides surrounding the first ATG of MOD5 also have an effect on translation initiation. Altering these nucleotides changes initiation choice and suggests that ribosomal bypass of a suboptimal AUG is another mechanism controlling the alternate use of two initiation codons. Our data support the model that at least one MOD5 transcript is able to produce two proteins with different N-terminal sequences. Images PMID:1946403

  5. The genes required for heme synthesis in Salmonella typhimurium include those encoding alternative functions for aerobic and anaerobic coproporphyrinogen oxidation.

    PubMed Central

    Xu, K; Delling, J; Elliott, T

    1992-01-01

    Insertion mutagenesis has been used to isolate Salmonella typhimurium strains that are blocked in the conversion of 5-aminolevulinic acid (ALA) to heme. These mutants define the steps of the heme biosynthetic pathway after ALA. Insertions were recovered at five unlinked loci: hemB, hemCD, and hemE, which have been mapped previously in S. typhimurium, and hemG and hemH, which have been described only for Escherichia coli. No other simple hem mutants were found. However, double mutants are described that are auxotrophic for heme during aerobic growth and fail to convert coproporphyrinogen III to protoporphyrinogen IX. These mutant strains are defective in two genes, hemN and hemF. Single mutants defective only in hemN require heme for anaerobic growth on glycerol plus nitrate but not for aerobic growth on glycerol. Mutants defective only in hemF have no apparent growth defect. We suggest that these two genes encode alternative forms of coproporphyrinogen oxidase. Anaerobic heme synthesis requires hemN function, while either hemN or hemF is sufficient for aerobic heme synthesis. These phenotypes are consistent with the requirement of a well-characterized class of coproporphyrinogen oxidase for molecular oxygen. PMID:1317844

  6. Alternative splicing of DENND1A, a PCOS candidate gene, generates variant 2.

    PubMed

    Tee, Meng Kian; Speek, Mart; Legeza, Balázs; Modi, Bhavi; Teves, Maria Eugenia; McAllister, Janette M; Strauss, Jerome F; Miller, Walter L

    2016-10-15

    Polycystic ovary syndrome (PCOS) is a common endocrinopathy characterized by hyperandrogenism and metabolic disorders. The excess androgens may be of both ovarian and adrenal origin. PCOS has a strong genetic component, and genome-wide association studies have identified several candidate genes, notably DENND1A, which encodes connecdenn 1, involved in trafficking of endosomes. DENND1A encodes two principal variants, V1 (1009 amino acids) and V2 (559 amino acids). The androgen-producing ovarian theca cells of PCOS women over-express V2. Knockdown of V2 in these cells reduces androgen production, and overexpression of V2 in normal theca cells confers upon them a PCOS phenotype of increased androgen synthesis. We report that human adrenal NCI-H295A cells express V1 and V2 mRNA and that the V2 isoform is produced by exonization of sequences in intron 20, which generates a unique exon 20A, encoding the C-terminus of V2. As in human theca cells from normal women, forced expression of V2 in NCI-H295A cells resulted in increased abundance of CYP17A1 and CYP11A1 mRNAs. We also found genetic variation in the intronic region 330 bp upstream from exon 20A, which could have the potential to drive the selective expression of V2. There was no clear association with these variants with PCOS when we analyzed genomc DNA from normal women and women with PCOS. Using minigene expression vectors in NCI-H295A cells, this variable region did not consistently favor splicing of the V2 transcript. These findings suggest increased V2 expression in PCOS theca cells is not the result of genomic sequence variation in intron 20.

  7. Alternative Oxidase Gene Family in Hypericum perforatum L.: Characterization and Expression at the Post-germinative Phase.

    PubMed

    Velada, Isabel; Cardoso, Hélia G; Ragonezi, Carla; Nogales, Amaia; Ferreira, Alexandre; Valadas, Vera; Arnholdt-Schmitt, Birgit

    2016-01-01

    Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide. In silico analysis of regulatory elements located at intronic regions identified putative sequences coding for miRNA precursors and trace elements of a transposon. Simple sequence repeats were also identified. Additionally, the mRNA levels for the HpAOX1 and HpAOX2, along with the ones for the HpGAPA (glyceraldehyde-3-phosphate dehydrogenase A subunit) and the HpCAT1 (catalase 1), were evaluated during the post-germinative development. Gene expression analysis was performed by RT-qPCR with accurate data normalization, pointing out HpHYP1 (chamba phenolic oxidative coupling protein 1) and HpH2A (histone 2A) as the most suitable reference genes (RGs) according to GeNorm algorithm. The HpAOX2 transcript demonstrated larger stability during the process with a slight down-regulation in its expression. Contrarily, HpAOX1 and HpGAPA (the corresponding protein is homolog to the chloroplast isoform involved in the photosynthetic carbon assimilation in other plant species) transcripts showed a marked increase, with a similar expression pattern between them, during the post-germinative development. On the other hand, the HpCAT1 (the corresponding protein is homolog to the major H2O2-scavenging enzyme in other plant species) transcripts showed an opposite behavior with a down-regulation during the process. In summary, our findings, although preliminary, highlight the importance to

  8. Alternative splicing: a novel mechanism of regulation identified in the chorismate mutase gene of the potato cyst nematode Globodera rostochiensis.

    PubMed

    Lu, Shun-Wen; Tian, Duanhua; Borchardt-Wier, Harmony B; Wang, Xiaohong

    2008-11-01

    Chorismate mutase (CM) secreted from the stylet of plant-parasitic nematodes plays an important role in plant parasitism. We isolated and characterized a new nematode CM gene (Gr-cm-1) from the potato cyst nematode, Globodera rostochiensis. The Gr-cm-1 gene was found to exist in the nematode genome as a single-copy gene that has two different alleles, Gr-cm-1A and Gr-cm-1B, both of which could give rise to two different mRNA transcripts of Gr-cm-1 and Gr-cm-1-IRII. In situ mRNA hybridization showed that the Gr-cm-1 gene was exclusively expressed within the subventral oesophageal gland cells of the nematode. Gr-cm-1 was demonstrated to encode a functional CM (GR-CM-1) potentially having a dimeric structure as the secreted bacterial *AroQ CMs. Gr-cm-1-IRII, generated by retention of intron 2 of the Gr-cm-1 pre-mRNA through alternative splicing (AS), would encode a truncated protein (GR-CM-1t) lacking the CM domain with no CM activity. The quantitative real-time reverse transcription-PCR assay revealed that splicing of the Gr-cm-1 gene was developmentally regulated; Gr-cm-1 was up-regulated whereas Gr-cm-1-IRII was down-regulated in early nematode parasitic stages compared to the preparasitic juvenile stage. Low-temperature SDS-PAGE analysis revealed that GR-CM-1 could form homodimers when expressed in Escherichia coli and the dimerization domain was retained in the truncated GR-CM-1t protein. The specific interaction between the two proteins was demonstrated in yeast. Our data suggested that the novel splice variant might function as a dominant negative isoform through heterodimerization with the full-length GR-CM-1 protein and that AS may represent an important mechanism for regulating CM activity during nematode parasitism.

  9. Alternative Oxidase Gene Family in Hypericum perforatum L.: Characterization and Expression at the Post-germinative Phase

    PubMed Central

    Velada, Isabel; Cardoso, Hélia G.; Ragonezi, Carla; Nogales, Amaia; Ferreira, Alexandre; Valadas, Vera; Arnholdt-Schmitt, Birgit

    2016-01-01

    Alternative oxidase (AOX) protein is located in the inner mitochondrial membrane and is encoded in the nuclear genome being involved in plant response upon a diversity of environmental stresses and also in normal plant growth and development. Here we report the characterization of the AOX gene family of Hypericum perforatum L. Two AOX genes were identified, both with a structure of four exons (HpAOX1, acc. KU674355 and HpAOX2, acc. KU674356). High variability was found at the N-terminal region of the protein coincident with the high variability identified at the mitochondrial transit peptide. In silico analysis of regulatory elements located at intronic regions identified putative sequences coding for miRNA precursors and trace elements of a transposon. Simple sequence repeats were also identified. Additionally, the mRNA levels for the HpAOX1 and HpAOX2, along with the ones for the HpGAPA (glyceraldehyde-3-phosphate dehydrogenase A subunit) and the HpCAT1 (catalase 1), were evaluated during the post-germinative development. Gene expression analysis was performed by RT-qPCR with accurate data normalization, pointing out HpHYP1 (chamba phenolic oxidative coupling protein 1) and HpH2A (histone 2A) as the most suitable reference genes (RGs) according to GeNorm algorithm. The HpAOX2 transcript demonstrated larger stability during the process with a slight down-regulation in its expression. Contrarily, HpAOX1 and HpGAPA (the corresponding protein is homolog to the chloroplast isoform involved in the photosynthetic carbon assimilation in other plant species) transcripts showed a marked increase, with a similar expression pattern between them, during the post-germinative development. On the other hand, the HpCAT1 (the corresponding protein is homolog to the major H2O2-scavenging enzyme in other plant species) transcripts showed an opposite behavior with a down-regulation during the process. In summary, our findings, although preliminary, highlight the importance to

  10. Evolutionary diversification and characterization of the eubacterial gene family encoding DXR type II, an alternative isoprenoid biosynthetic enzyme

    PubMed Central

    2013-01-01

    Background Isoprenoids constitute a vast family of natural compounds performing diverse and essential functions in all domains of life. In most eubacteria, isoprenoids are synthesized through the methylerythritol 4-phosphate (MEP) pathway. The production of MEP is usually catalyzed by deoxyxylulose 5-phosphate reductoisomerase (DXR-I) but a few organisms use an alternative DXR-like enzyme (DXR-II). Results Searches through 1498 bacterial complete proteomes detected 130 sequences with similarity to DXR-II. Phylogenetic analysis identified three well-resolved clades: the DXR-II family (clustering 53 sequences including eleven experimentally verified as functional enzymes able to produce MEP), and two previously uncharacterized NAD(P)-dependent oxidoreductase families (designated DLO1 and DLO2 for DXR-II-like oxidoreductases 1 and 2). Our analyses identified amino acid changes critical for the acquisition of DXR-II biochemical function through type-I functional divergence, two of them mapping onto key residues for DXR-II activity. DXR-II showed a markedly discontinuous distribution, which was verified at several levels: taxonomic (being predominantly found in Alphaproteobacteria and Firmicutes), metabolic (being mostly found in bacteria with complete functional MEP pathways with or without DXR-I), and phenotypic (as no biological/phenotypic property was found to be preferentially distributed among DXR-II-containing strains, apart from pathogenicity in animals). By performing a thorough comparative sequence analysis of GC content, 3:1 dinucleotide frequencies, codon usage and codon adaptation indexes (CAI) between DXR-II sequences and their corresponding genomes, we examined the role of horizontal gene transfer (HGT), as opposed to an scenario of massive gene loss, in the evolutionary origin and diversification of the DXR-II subfamily in bacteria. Conclusions Our analyses support a single origin of the DXR-II family through functional divergence, in which constitutes

  11. Detecting tissue-specific alternative splicing and disease-associated aberrant splicing of the PTCH gene with exon junction microarrays.

    PubMed

    Nagao, Kazuaki; Togawa, Naoyuki; Fujii, Katsunori; Uchikawa, Hideki; Kohno, Yoichi; Yamada, Masao; Miyashita, Toshiyuki

    2005-11-15

    Mutations in the human ortholog of Drosophila patched (PTCH) have been identified in patients with autosomal dominant nevoid basal cell carcinoma syndrome (NBCCS), characterized by minor developmental anomalies and an increased incidence of cancers such as medulloblastoma and basal cell carcinoma. We identified many isoforms of PTCH mRNA involving exons 1-5, exon 10 and a novel exon, 12b, generated by alternative splicing (AS), most of which have not been deposited in GenBank nor discussed earlier. To monitor splicing events of the PTCH gene, we designed oligonucleotide arrays on which exon probes and exon-exon junction probes as well as a couple of intron probes for the PTCH gene were placed in duplicate. Probe intensities were normalized on the basis of the total expression of PTCH and probe sensitivity. Tissue-specific regulation of AS identified with the microarrays closely correlated with the results obtained by RT-PCR. Of note, the novel exon, exon 12b, was specifically expressed in the brain and heart, especially in the cerebellum. Additionally, using these microarrays, we were able to detect disease-associated aberrant splicings of the PTCH gene in two patients with NBCCS. In both cases, cryptic splice donor sites located either in an exon or in an intron were activated because of the partial disruption of the consensus sequence for the authentic splice donor sites due to point mutations. Taken together, oligonucleotide microarrays containing exon junction probes are demonstrated to be a powerful tool to investigate tissue-specific regulation of AS and aberrant splicing taking place in genetic disorders.

  12. Programmed improvements of the alternating gradient synchrotron complex at Brookhaven National Laboratory, Upton, New York. Environmental assessment

    SciTech Connect

    1994-03-01

    The purpose and need for DOE to undertake the actions described in this document are to improve the efficiency of the Alternating Gradient Synchrotron (AGS) complex. Benefits would include optimization of the AGS scientific program, increased high-energy and nuclear physics experimentation, improved health and safety conditions for workers and users, reduced impact on the environment and the general public, energy conservation, decreased generation of hazardous and radioactive wastes, and completion of actions required to permit the AGS to be the injector to the Relativistic Heavy Ion Collider (RHIC)., Improved efficiency is defined as increasing the AGS`s capabilities to capture and accelerate the proton intensity transferred to the AGS from the AGS booster. Improved capture of beam intensity would reduce the beam losses which equate to lost scientific opportunity for study and increased potential for radiation doses to workers and the general public. The action would also refurbish magnets used in the transfer tunnel which connects the AGS complex to RHIC to permit smooth injection of beam into the RHIC accelerator. These magnets were previously used to direct beam to fixed targets for high energy physics studies but have hot received proper maintenance to be reliable as injectors to RHIC. The document describes alternative actions, the affected environment, and environmental impacts.

  13. Incorporating precision, accuracy and alternative sampling designs into a continental monitoring program for colonial waterbirds

    USGS Publications Warehouse

    Steinkamp, Melanie J.; Peterjohn, B.G.; Keisman, J.L.

    2003-01-01

    A comprehensive monitoring program for colonial waterbirds in North America has never existed. At smaller geographic scales, many states and provinces conduct surveys of colonial waterbird populations. Periodic regional surveys are conducted at varying times during the breeding season using a variety of survey methods, which complicates attempts to estimate population trends for most species. The US Geological Survey Patuxent Wildlife Research Center has recently started to coordinate colonial waterbird monitoring efforts throughout North America. A centralized database has been developed with an Internet-based data entry and retrieval page. The extent of existing colonial waterbird surveys has been defined, allowing gaps in coverage to be identified and basic inventories completed where desirable. To enable analyses of comparable data at regional or larger geographic scales, sampling populations through statistically sound sampling designs should supersede obtaining counts at every colony. Standardized breeding season survey techniques have been agreed upon and documented in a monitoring manual. Each survey in the manual has associated with it recommendations for bias estimation, and includes specific instructions on measuring detectability. The methods proposed in the manual are for developing reliable, comparable indices of population size to establish trend information at multiple spatial and temporal scales, but they will not result in robust estimates of total population numbers.

  14. MLP: A Parallel Programming Alternative to MPI for New Shared Memory Parallel Systems

    NASA Technical Reports Server (NTRS)

    Taft, James R.

    1999-01-01

    Recent developments at the NASA AMES Research Center's NAS Division have demonstrated that the new generation of NUMA based Symmetric Multi-Processing systems (SMPs), such as the Silicon Graphics Origin 2000, can successfully execute legacy vector oriented CFD production codes at sustained rates far exceeding processing rates possible on dedicated 16 CPU Cray C90 systems. This high level of performance is achieved via shared memory based Multi-Level Parallelism (MLP). This programming approach, developed at NAS and outlined below, is distinct from the message passing paradigm of MPI. It offers parallelism at both the fine and coarse grained level, with communication latencies that are approximately 50-100 times lower than typical MPI implementations on the same platform. Such latency reductions offer the promise of performance scaling to very large CPU counts. The method draws on, but is also distinct from, the newly defined OpenMP specification, which uses compiler directives to support a limited subset of multi-level parallel operations. The NAS MLP method is general, and applicable to a large class of NASA CFD codes.

  15. High-throughput sequence analysis of Ciona intestinalis SL trans-spliced mRNAs: alternative expression modes and gene function correlates.

    PubMed

    Matsumoto, Jun; Dewar, Ken; Wasserscheid, Jessica; Wiley, Graham B; Macmil, Simone L; Roe, Bruce A; Zeller, Robert W; Satou, Yutaka; Hastings, Kenneth E M

    2010-05-01

    Pre-mRNA 5' spliced-leader (SL) trans-splicing occurs in some metazoan groups but not in others. Genome-wide characterization of the trans-spliced mRNA subpopulation has not yet been reported for any metazoan. We carried out a high-throughput analysis of the SL trans-spliced mRNA population of the ascidian tunicate Ciona intestinalis by 454 Life Sciences (Roche) pyrosequencing of SL-PCR-amplified random-primed reverse transcripts of tailbud embryo RNA. We obtained approximately 250,000 high-quality reads corresponding to 8790 genes, approximately 58% of the Ciona total gene number. The great depth of this data revealed new aspects of trans-splicing, including the existence of a significant class of "infrequently trans-spliced" genes, accounting for approximately 28% of represented genes, that generate largely non-trans-spliced mRNAs, but also produce trans-spliced mRNAs, in part through alternative promoter use. Thus, the conventional qualitative dichotomy of trans-spliced versus non-trans-spliced genes should be supplanted by a more accurate quantitative view recognizing frequently and infrequently trans-spliced gene categories. Our data include reads representing approximately 80% of Ciona frequently trans-spliced genes. Our analysis also revealed significant use of closely spaced alternative trans-splice acceptor sites which further underscores the mechanistic similarity of cis- and trans-splicing and indicates that the prevalence of +/-3-nt alternative splicing events at tandem acceptor sites, NAGNAG, is driven by spliceosomal mechanisms, and not nonsense-mediated decay, or selection at the protein level. The breadth of gene representation data enabled us to find new correlations between trans-splicing status and gene function, namely the overrepresentation in the frequently trans-spliced gene class of genes associated with plasma/endomembrane system, Ca(2+) homeostasis, and actin cytoskeleton.

  16. Breeding programs for smallholder sheep farming systems: I. Evaluation of alternative designs of breeding schemes.

    PubMed

    Gizaw, S; Rischkowsky, B; Valle-Zárate, A; Haile, A; van Arendonk, J A M; Mwai, A O; Dessie, T

    2014-10-01

    Village- and central nucleus-based schemes were simulated and evaluated for their relative bio-economic efficiencies, using Ethiopia's Menz sheep as example. The schemes were: village-based 2-tier (Scheme-1) and 1-tier (Scheme-2) cooperative village breeding schemes, dispersed village-based nuclei scheme (Scheme-3), conventional 2-tier central nucleus-based scheme (Scheme-4), and schemes linking a central nucleus and village multiplier nuclei with selection in central nucleus (Scheme-5) or in both central and village nuclei (Scheme-6). Among village-based schemes, Scheme-1 gave the highest genetic progress, while Scheme-2 was economically the most efficient with genetic gain in the breeding objective of Birr 5.6 and a profit of Birr 37.2/ewe/year. The central nucleus schemes were more efficient than the village schemes. Scheme-4 was the most efficient with genetic gain in the breeding objective of Birr 13.5 and a profit of Birr 71.2, but is operationally more difficult as it requires a very large central nucleus. The choice between village and central nucleus-based schemes would depend on local conditions (availability of infrastructure, logistics and technical knowhow and support). Linking central nucleus with village-based nuclei (Scheme-6) would be a feasible option to overcome the operational difficulties of the conventional central nucleus scheme. If a village-based breeding program is envisaged as should be the 1st step in most low-input systems, then Scheme-2 is the most efficient. To scale out to an entire Menz breed level, Scheme-3 would be recommended.

  17. Fleet Compliance Results for MY 2010/FY 2011, EPAct Alternative Fuel Transportation Program: State and Alternative Fuel Provider Fleet Compliance Annual Report (Brochure)

    SciTech Connect

    Not Available

    2012-03-01

    This annual report summarizes the compliance results of state and alternative fuel provider fleets covered by the Energy Policy Act of 1992 (EPAct) for model year 2010/fiscal year 2011. The U.S. Department of Energy (DOE) regulates covered state and alternative fuel provider (SFP) fleets under the Energy Policy Act of 1992 (EPAct), as amended. For model year (MY) 2010, the compliance rate for the 2911 covered SFP fleets was 100%. Fleets used either Standard Compliance or Alternative Compliance. The 279 fleets that used Standard Compliance exceeded their aggregate MY 2010 acquisition requirements by 61%. The 12 covered fleets that complied using Alternative Compliance exceeded their aggregate MY 2010 petroleum-use-reduction requirements by 89%. Overall, DOE saw modest decreases from MY 2009 in biodiesel fuel use credits earned and in the number of light-duty vehicles (LDVs) acquired. Compared to years before MY 2009, these rates were far lower. Because covered fleets acquired fewer new vehicles overall in MY 2010, the requirement for alternative fuel vehicles (AFVs), which is proportional to new acquisitions, also dropped.

  18. The maize rough sheath2 gene and leaf development programs in monocot and dicot plants.

    PubMed

    Tsiantis, M; Schneeberger, R; Golz, J F; Freeling, M; Langdale, J A

    1999-04-02

    Leaves of higher plants develop in a sequential manner from the shoot apical meristem. Previously it was determined that perturbed leaf development in maize rough sheath2 (rs2) mutant plants results from ectopic expression of knotted1-like (knox) homeobox genes. Here, the rs2 gene sequence was found to be similar to the Antirrhinum PHANTASTICA (PHAN) gene sequence, which encodes a Myb-like transcription factor. RS2 and PHAN are both required to prevent the accumulation of knox gene products in maize and Antirrhinum leaves, respectively. However, rs2 and phan mutant phenotypes differ, highlighting fundamental differences in monocot and dicot leaf development programs.

  19. Education and the energy crisis: policies and actions for the Department of Energy. [Options and alternatives, DOE Education Programs Div

    SciTech Connect

    1980-01-22

    This report is the result of a study carried out to determine options and alternatives for the Education Programs Division (EPD) of the Department of Energy. In the conduct of this study, numerous individuals from various concerned institutions were interviewed. While the project scope clearly precluded contact with every involved or potentially involved party, a concerted effort was made to obtain a representative sampling of the opinions and views of relevant government, academic and private sector agencies and organizations. A listing of those contacted, excluding the Department of Energy, is provided. In addition to interviews, an extensive range of literature was drawn upon including memoranda, brochures, program statements, school-enrollment data, speeches and the like. It was determined during this study that a wide range of public and private institutions are actively involved in the energy-education field. Oil companies, utilities, public interest groups, schools, agencies at every level of government, and others are formulating and delivering education which is enormously varied. It was concluded, however, that the public is not being reached, partially because current efforts are unfocused and partially because the public has become inured to problems and resistant to many of the traditional means of education. The study found that within this crowded and varied energy education field the Department of Energy is well placed to begin to provide direction and focus to the widespread activity now occurring.

  20. Expression of functional alternative telomerase RNA component gene in mouse brain and in motor neurons cells protects from oxidative stress

    PubMed Central

    Eitan, Erez; Tamar, Admoni; Yossi, Grin; Peleg, Refael; Braiman, Alex; Priel, Esther

    2016-01-01

    Telomerase, a ribonucleoprotein, is highly expressed and active in many tumor cells and types, therefore it is considered to be a target for anti-cancer agents. On the other hand, recent studies demonstrated that activation of telomerase is a potential therapeutic target for age related diseases. Telomerase mainly consists of a catalytic protein subunit with a reverse transcription activity (TERT) and an RNA component (TERC), a long non-coding RNA, which serves as a template for the re-elongation of telomeres by TERT. We previously showed that TERT is highly expressed in distinct neuronal cells of the mouse brain and its expression declined with age. To understand the role of telomerase in non-mitotic, fully differentiated cells such neurons we here examined the expression of the other component, TERC, in mouse brain. Surprisingly, by first using bioinformatics analysis, we identified an alternative TERC gene (alTERC) in the mouse genome. Using further experimental approaches we described the presence of a functional alTERC in the mouse brain and spleen, in cultures of motor neurons- like cells and neuroblastoma tumor cells. The alTERC is similar (87%) to mouse TERC (mTERC) with a deletion of 18 bp in the TERC conserved region 4 (CR4). This alTERC gene is expressed and its product interacts with the endogenous mTERT protein and with an exogenous human TERT protein (hTERT) to form an active enzyme. Overexpression of the alTERC and the mTERC genes, in mouse motor neurons like cells, increased the activity of TERT without affecting its protein level. Under oxidative stress conditions, alTERC significantly increased the survival of motor neurons cells without altering the level of TERT protein or its activity. The results suggest that the expression of the alTERC gene in the mouse brain provides an additional way for regulating telomerase activity under normal and stress conditions and confers protection to neuronal cells from oxidative stress. PMID:27823970