Sample records for vmac meeting transcript

  1. Direct Detection of Stereospecific Soman Hydrolysis by Wild-Type Human Serum Paraoxonase

    DTIC Science & Technology

    2007-01-01

    was used as Tc = (Ao/VmaA)(1 - (C/Co)( Kmc /KwA)(VmaxA/Vmac)) the carrier gas at a linear velocity of 45 crns-1. The oven + (B0/VmaxB)(1 - (C/Co)( Kmc ...KmB)(VmaxB/Vm.c)) temperature was held initially at 80 ’C for 14 min, pro- + (Co/Vmac)(1 - (C/Co)( Kmc / Kmc )(Vm.c/Vmac)) grammed from 80 to 90 ’C at 5...oC’min-1, and held at + (DO/VmaD)(1 - (C/Co)(K.C/KmD)(Vm.D1/V.aC)) 90 ’C for 3 min. Split injections of 1 tiL volume were made ( Kmc /VmaxC) Log(C/Co

  2. The influence of maturity of VMAC5 (Cocos nucifera L. ‘makapuno’) on its physicochemical, proximate composition and fatty acid profile

    NASA Astrophysics Data System (ADS)

    Leorna, M.; Israel, K. A.

    2018-01-01

    “Makapuno” is one of the promising commodities of the Philippines with good nutritional quality. VMAC5 is the most recent “makapuno” variety developed by the Visayas State University, Baybay City, Leyte, Philippines. Maximum utilization of this commodity is dependent on its thorough characterization. This study aimed to determine the influence of nut maturity on its physicochemical, proximate composition and fatty acid profile. Results revealed that VMAC5 nuts were affected by maturity. An 8-month old nuts exhibited heavier weight compared to mature nuts. The total sugar decreased with maturity. TSS and pH were not affected by maturity. Proximate composition were affected by maturity with moisture content of 59.17-86.88%, crude protein of 1.58-2.62%, crude fiber of 2.24-5.43% and crude fat of 3.06-12.14% of which >50% were medium chain fatty acids (MCFA).

  3. Clinical trials update: highlights of the scientific sessions of the American Heart Association year 2000: Val HeFT, COPERNICUS, MERIT, CIBIS-II, BEST, AMIOVIRT, V-MAC, BREATHE, HEAT, MIRACL, FLORIDA, VIVA and the first human cardiac skeletal muscle myoblast transfer for heart failure.

    PubMed

    Thackray, S D; Witte, K K; Khand, A; Dunn, A; Clark, A L; Cleland, J G

    2001-01-01

    This article continues a series of reports summarising recent research developments pertinent to the topic of heart failure. This is a summary of presentations made at scientific sessions of the American Heart Association in November 2000. Clinical studies of particular interest to people caring for patients with heart failure include Val-HeFT, AMIOVIRT and V-MAC. New data from beta-blockers trials are reviewed, highlights from some important developments in post-infarction care, including MIRACL and FLORIDA, discussed and results of some early studies of gene therapy reported.

  4. Development of vehicle magnetic air conditioner (VMAC) technology. Final report

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Gschneidner, Karl A., Jr.; Pecharsky, V.K.; Jiles, David

    2001-08-28

    The objective of Phase I was to explore the feasibility of the development of a new solid state refrigeration technology - magnetic refrigeration - in order to reduce power consumption of a vehicle air conditioner by 30%. The feasibility study was performed at Iowa State University (ISU) together with Astronautics Corporation of America Technology Center (ACATC), Madison, WI, through a subcontract with ISU.

  5. The magnetic early B-type stars I: magnetometry and rotation

    NASA Astrophysics Data System (ADS)

    Shultz, M. E.; Wade, G. A.; Rivinius, Th; Neiner, C.; Alecian, E.; Bohlender, D.; Monin, D.; Sikora, J.; MiMeS Collaboration; BinaMIcS Collaboration

    2018-04-01

    The rotational and magnetic properties of many magnetic hot stars are poorly characterized, therefore the Magnetism in Massive Stars and Binarity and Magnetic Interactions in various classes of Stars collaborations have collected extensive high-dispersion spectropolarimetric data sets of these targets. We present longitudinal magnetic field measurements for 52 early B-type stars (B5-B0), with which we attempt to determine their rotational periods Prot. Supplemented with high-resolution spectroscopy, low-resolution Dominion Astrophysical Observatory circular spectropolarimetry, and archival Hipparcos photometry, we determined Prot for 10 stars, leaving only five stars for which Prot could not be determined. Rotational ephemerides for 14 stars were refined via comparison of new to historical magnetic measurements. The distribution of Prot is very similar to that observed for the cooler Ap/Bp stars. We also measured v sin i and vmac for all stars. Comparison to non-magnetic stars shows that v sin i is much lower for magnetic stars, an expected consequence of magnetic braking. We also find evidence that vmac is lower for magnetic stars. Least-squares deconvolution profiles extracted using single-element masks revealed widespread, systematic discrepancies in between different elements: this effect is apparent only for chemically peculiar stars, suggesting it is a consequence of chemical spots. Sinusoidal fits to H line measurements (which should be minimally affected by chemical spots), yielded evidence of surface magnetic fields more complex than simple dipoles in six stars for which this has not previously been reported; however, in all six cases, the second- and third-order amplitudes are small relative to the first-order (dipolar) amplitudes.

  6. 37 CFR 251.15 - Transcripts of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 37 Patents, Trademarks, and Copyrights 1 2010-07-01 2010-07-01 false Transcripts of closed... PROCEDURE Public Access to Copyright Arbitration Royalty Panel Meetings § 251.15 Transcripts of closed meetings. (a) All meetings closed to the public shall be subject either to a complete transcript or, in the...

  7. 22 CFR 1004.8 - Transcripts, recording of closed meetings.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 22 Foreign Relations 2 2013-04-01 2009-04-01 true Transcripts, recording of closed meetings. 1004.8 Section 1004.8 Foreign Relations INTER-AMERICAN FOUNDATION RULES FOR IMPLEMENTING OPEN MEETINGS WITHIN THE INTER-AMERICAN FOUNDATION § 1004.8 Transcripts, recording of closed meetings. (a) The IAF...

  8. 17 CFR 147.9 - Requests for copies of transcripts, recordings or minutes of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ..., recordings or minutes of closed meetings. (a) Copies of a transcript transcription of an electronic recording... § 147.8(a), shall be furnished to any person at the actual cost of duplication or transcription pursuant...)(9), (d) and (e). (b) Requests for copies of transcripts, transcriptions of electronic recordings or...

  9. 17 CFR 147.9 - Requests for copies of transcripts, recordings or minutes of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., recordings or minutes of closed meetings. (a) Copies of a transcript transcription of an electronic recording... § 147.8(a), shall be furnished to any person at the actual cost of duplication or transcription pursuant...)(9), (d) and (e). (b) Requests for copies of transcripts, transcriptions of electronic recordings or...

  10. 12 CFR 604.435 - Record of closed meetings or closed portion of a meeting.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... this part. Copies of such transcript or minutes, or a transcription of such recording disclosing the... transcription. (d) The Farm Credit Administration shall maintain a complete verbatim copy of the transcript, a...

  11. 12 CFR 604.435 - Record of closed meetings or closed portion of a meeting.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... this part. Copies of such transcript or minutes, or a transcription of such recording disclosing the... transcription. (d) The Farm Credit Administration shall maintain a complete verbatim copy of the transcript, a...

  12. 16 CFR 16.10 - Minutes and transcripts of meetings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Minutes and transcripts of meetings. 16.10 Section 16.10 Commercial Practices FEDERAL TRADE COMMISSION ORGANIZATION, PROCEDURES AND RULES OF PRACTICE ADVISORY COMMITTEE MANAGEMENT § 16.10 Minutes and transcripts of meetings. (a) Detailed minutes of each...

  13. 45 CFR 503.28 - Record of closed meetings, or closed portion of a meeting.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... may be withheld under § 503.24. Copies of the transcript or minutes, or a transcription of the... duplication or transcription. (d) The Commission will maintain a complete verbatim copy of the transcript, a...

  14. 45 CFR 503.28 - Record of closed meetings, or closed portion of a meeting.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... may be withheld under § 503.24. Copies of the transcript or minutes, or a transcription of the... duplication or transcription. (d) The Commission will maintain a complete verbatim copy of the transcript, a...

  15. 22 CFR 1004.8 - Transcripts, recording of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Transcripts, recording of closed meetings. 1004.8 Section 1004.8 Foreign Relations INTER-AMERICAN FOUNDATION RULES FOR IMPLEMENTING OPEN MEETINGS... each meeting, or portion of a meeting, closed to the public, except that in the case of a meeting, or...

  16. 10 CFR 1704.8 - Transcripts, recordings, or minutes of closed meetings.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 10 Energy 4 2014-01-01 2014-01-01 false Transcripts, recordings, or minutes of closed meetings. 1704.8 Section 1704.8 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD RULES IMPLEMENTING THE GOVERNMENT IN THE SUNSHINE ACT § 1704.8 Transcripts, recordings, or minutes of closed meetings. Along with the...

  17. 10 CFR 1704.8 - Transcripts, recordings, or minutes of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 10 Energy 4 2010-01-01 2010-01-01 false Transcripts, recordings, or minutes of closed meetings. 1704.8 Section 1704.8 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD RULES IMPLEMENTING THE GOVERNMENT IN THE SUNSHINE ACT § 1704.8 Transcripts, recordings, or minutes of closed meetings. Along with the...

  18. 10 CFR 1704.8 - Transcripts, recordings, or minutes of closed meetings.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 10 Energy 4 2013-01-01 2013-01-01 false Transcripts, recordings, or minutes of closed meetings. 1704.8 Section 1704.8 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD RULES IMPLEMENTING THE GOVERNMENT IN THE SUNSHINE ACT § 1704.8 Transcripts, recordings, or minutes of closed meetings. Along with the...

  19. 10 CFR 1704.8 - Transcripts, recordings, or minutes of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 10 Energy 4 2011-01-01 2011-01-01 false Transcripts, recordings, or minutes of closed meetings. 1704.8 Section 1704.8 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD RULES IMPLEMENTING THE GOVERNMENT IN THE SUNSHINE ACT § 1704.8 Transcripts, recordings, or minutes of closed meetings. Along with the...

  20. 10 CFR 1704.8 - Transcripts, recordings, or minutes of closed meetings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 10 Energy 4 2012-01-01 2012-01-01 false Transcripts, recordings, or minutes of closed meetings. 1704.8 Section 1704.8 Energy DEFENSE NUCLEAR FACILITIES SAFETY BOARD RULES IMPLEMENTING THE GOVERNMENT IN THE SUNSHINE ACT § 1704.8 Transcripts, recordings, or minutes of closed meetings. Along with the...

  1. 12 CFR 407.6 - Transcripts, recordings and minutes of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Transcripts, recordings and minutes of closed meetings. 407.6 Section 407.6 Banks and Banking EXPORT-IMPORT BANK OF THE UNITED STATES REGULATIONS GOVERNING PUBLIC OBSERVATION OF EX-IM BANK MEETINGS § 407.6 Transcripts, recordings and minutes of closed...

  2. 12 CFR 407.6 - Transcripts, recordings and minutes of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 4 2011-01-01 2011-01-01 false Transcripts, recordings and minutes of closed meetings. 407.6 Section 407.6 Banks and Banking EXPORT-IMPORT BANK OF THE UNITED STATES REGULATIONS... meetings. Eximbank will maintain a complete transcript or electronic recording of the proceedings of every...

  3. 18 CFR 1301.47 - Transcripts of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... meetings. 1301.47 Section 1301.47 Conservation of Power and Water Resources TENNESSEE VALLEY AUTHORITY PROCEDURES Government in the Sunshine Act § 1301.47 Transcripts of closed meetings. (a) For every meeting closed pursuant to § 1301.46, the presiding officer of the meeting shall prepare a statement setting...

  4. 19 CFR 201.41 - Public inspection and copying of records; applicable fees.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... of transcripts, minutes of Commission meetings, or transcriptions of electronic recordings of Commission meetings, which disclose the identity of each speaker, at the actual cost of transcription or...

  5. 19 CFR 201.41 - Public inspection and copying of records; applicable fees.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... of transcripts, minutes of Commission meetings, or transcriptions of electronic recordings of Commission meetings, which disclose the identity of each speaker, at the actual cost of transcription or...

  6. 7 CFR 1600.8 - Transcript, recording or minutes; availability to the public.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., transcription of the recording, or minutes of the discussion of any item on the agenda of a Board meeting..., minutes, or transcriptions of electronic recordings of a Board meeting will disclose the identity of each speaker, and will be furnished to any person at the actual cost of transcription or duplication. ...

  7. 7 CFR 1600.8 - Transcript, recording or minutes; availability to the public.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., transcription of the recording, or minutes of the discussion of any item on the agenda of a Board meeting..., minutes, or transcriptions of electronic recordings of a Board meeting will disclose the identity of each speaker, and will be furnished to any person at the actual cost of transcription or duplication. ...

  8. 29 CFR 1209.08 - Transcripts, recordings or minutes of closed meetings; retention; public availability.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ...) NATIONAL MEDIATION BOARD PUBLIC OBSERVATION OF NATIONAL MEDIATION BOARD MEETINGS § 1209.08 Transcripts... Board meetings shall be directed to the Chief of Staff, National Mediation Board, Washington, DC 20572...

  9. 12 CFR 311.8 - Transcripts and minutes of meetings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Transcripts and minutes of meetings. 311.8 Section 311.8 Banks and Banking FEDERAL DEPOSIT INSURANCE CORPORATION PROCEDURE AND RULES OF PRACTICE RULES GOVERNING PUBLIC OBSERVATION OF MEETINGS OF THE CORPORATION'S BOARD OF DIRECTORS § 311.8...

  10. 28 CFR 16.207 - Public access to nonexempt transcripts and minutes of closed Commission meetings-Documents used...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Public access to nonexempt transcripts and minutes of closed Commission meetings-Documents used at meetings-Record retention. 16.207 Section 16.207 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR...

  11. The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Karen S. Browning; Marie Petrocek; Bonnie Bartel

    2006-06-01

    The 5th Symposium on Post-Transcriptional Regulation of Plant Gene Expression (PTRoPGE) will be held June 8-12, 2005 at the University of Texas at Austin. Exciting new and ongoing discoveries show significant regulation of gene expression occurs after transcription. These post-transcriptional control events in plants range from subtle regulation of transcribed genes and phosphorylation, to the processes of gene regulation through small RNAs. This meeting will focus on the regulatory role of RNA, from transcription, through translation and finally degradation. The cross-disciplinary design of this meeting is necessary to encourage interactions between researchers that have a common interest in post-transcriptional genemore » expression in plants. By bringing together a diverse group of plant molecular biologist and biochemists at all careers stages from across the world, this meeting will bring about more rapid progress in understanding how plant genomes work and how genes are finely regulated by post-transcriptional processes to ultimately regulate cells.« less

  12. 29 CFR 1209.08 - Transcripts, recordings or minutes of closed meetings; retention; public availability.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... provisions of 5 U.S.C. 552b(c), copies of transcripts or minutes, or transcriptions of electronic recordings... transcription. Requests for copies of transcripts or minutes, or transcriptions of electronic recordings of...

  13. Gα proteins Gvm2 and Gvm3 regulate vegetative growth, asexual development, and pathogenicityon apple in Valsa mali.

    PubMed

    Song, Na; Dai, Qingqing; Zhu, Baitao; Wu, Yuxing; Xu, Ming; Voegele, Ralf Thomas; Gao, Xiaoning; Kang, Zhensheng; Huang, Lili

    2017-01-01

    In fungi, heterotrimeric guanine-nucleotide binding proteins (G-proteins) are key elements of signal transduction pathways, which control growth, asexual and sexual development, as well as virulence. In this study, we have identified two genes encoding heterotrimeric G protein alpha subunits, named Gvm2 and Gvm3, from Valsa mali, the causal agent of apple Valsa canker. Characterization of Gvm2 and Gvm3 mutants indicates that Gvm3 may be a crucial regulator of vegetative growth. Deletion of the corresponding gene results in a 20% reduction in growth rate. Besides, Gvm2 and Gvm3 seem to be involved in asexual reproduction, and mutants are hypersensitive to oxidative and cell membrane stresses. Interestingly, both G protein alpha subunits were most probably involved in V. mali virulence. In infection assays using Malus domestica cv. 'Fuji' leaves and twigs, the size of lesions caused by deletion mutants △Gvm2, or △Gvm3 are significantly reduced. Furthermore, many genes encoding hydrolytic enzymes-important virulence factors in V. mali-are expressed at a lower level in these deletion mutants. Our results suggest that Gvm2 and Gvm3 play an important role in virulence probably by regulation of expression of cell wall degrading enzymes. △Gvm2, and △Gvm3 mutants were further analyzed with respect to their impact on the transcript levels of genes in the cAMP/PKA pathway. The expression of the genes encoding adenylate cyclase VmAC, protein kinase A (PKA) regulatory subunit VmPKR, and PKA catalytic subunit VmPKA1 are down-regulated in both mutants. Further analyses indicated that intracellular cAMP level and PKA activity are down-regulated in the △Gvm3 mutant, but are basically unchanged in the △Gvm2 mutant. Overall, our findings indicate that both Gvm2 and Gvm3 play diverse roles in the modulation of vegetative growth, asexual development, and virulence in V. mali.

  14. 28 CFR 16.206 - Transcripts, minutes, and miscellaneous documents concerning Commission meetings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Transcripts, minutes, and miscellaneous documents concerning Commission meetings. 16.206 Section 16.206 Judicial Administration DEPARTMENT OF JUSTICE PRODUCTION OR DISCLOSURE OF MATERIAL OR INFORMATION Public Observation of Parole Commission...

  15. 22 CFR 1004.8 - Transcripts, recording of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... under § 1004.4. Copies of such transcript, or a transcription of such recording disclosing the identity of each speaker, shall be furnished to any person at the actual cost of duplication or transcription...

  16. 29 CFR 102.142 - Transcripts, recordings or minutes of closed meetings; public availability; retention.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ..., or transcriptions of electronic recordings including the identification of speakers, shall to the... cost of transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a...

  17. 29 CFR 102.142 - Transcripts, recordings or minutes of closed meetings; public availability; retention.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ..., or transcriptions of electronic recordings including the identification of speakers, shall to the... cost of transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a...

  18. 22 CFR 1500.9 - Transcripts, recording of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... contain information which may be withheld under § 1500.5. Copies of such transcript, or a transcription of... cost of duplication or transcription. The Foundation shall maintain a complete verbatim copy of the...

  19. 32 CFR 242a.7 - Transcripts, recordings, and minutes of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... transcript, or minutes, or a transcription of such recording disclosing the identity of each speaker, shall be available at the actual cost of duplication or transcription. (3) The determination of the...

  20. 32 CFR 242a.7 - Transcripts, recordings, and minutes of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... transcript, or minutes, or a transcription of such recording disclosing the identity of each speaker, shall be available at the actual cost of duplication or transcription. (3) The determination of the...

  1. 17 CFR 200.408 - Public access to transcripts and minutes of closed Commission meetings; record retention.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... § 200.402 or otherwise. Copies of such transcript, or minutes, or a transcription of such recording..., as set forth in § 200.80e, and, if a transcript is prepared, the actual cost of such transcription...

  2. 22 CFR 1413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a complete copy of the...

  3. 22 CFR 1413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (c) The agency shall maintain a complete verbatim copy of the transcript, a complete copy of the...

  4. 17 CFR 200.408 - Public access to transcripts and minutes of closed Commission meetings; record retention.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... § 200.402 or otherwise. Copies of such transcript, or minutes, or a transcription of such recording..., as set forth in § 200.80e, and, if a transcript is prepared, the actual cost of such transcription...

  5. 22 CFR 1500.9 - Transcripts, recording of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ..., closed to the public. (b) The Foundation, after review by the General Counsel, shall make promptly... 22 Foreign Relations 2 2010-04-01 2010-04-01 true Transcripts, recording of closed meetings. 1500.9 Section 1500.9 Foreign Relations AFRICAN DEVELOPMENT FOUNDATION SUNSHINE REGULATIONS § 1500.9...

  6. 76 FR 10755 - Practices and Procedures, Board Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-02-28

    ... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... transcription. (3) The Board shall maintain a complete verbatim copy of the transcript, a complete copy of the...

  7. 28 CFR 16.207 - Public access to nonexempt transcripts and minutes of closed Commission meetings-Documents used...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .... Copies of nonexempt transcripts, or minutes, or a transcription of such recording disclosing the identity of each speaker, shall be furnished to any person at the actual cost of duplication or transcription...

  8. 40 CFR 1517.7 - Records of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... provisions of § 1517.5. Copies of such transcript, minutes, or transcription of an electronic recording... or transcription. (e) [Reserved] (f) Requests to review or obtain copies of records other than...

  9. 45 CFR 1802.7 - Transcripts, recordings, minutes of meetings.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... transcription of such recording disclosing the identify of each speaker, shall be available at the actual cost of duplication or transcription. (3) The determination of the General Counsel to withhold information...

  10. 45 CFR 1802.7 - Transcripts, recordings, minutes of meetings.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... transcription of such recording disclosing the identify of each speaker, shall be available at the actual cost of duplication or transcription. (3) The determination of the General Counsel to withhold information...

  11. 22 CFR 708.6 - Records of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... such transcript, or minutes, or a transcription of such recording disclosing the identify of each speaker, shall be furnished to any person at the actual cost of duplication or transcription. (e) The...

  12. 78 FR 67201 - Sunshine Act Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-08

    ... Institutional Advancement Committee will meet telephonically on November 22, 2013. The meeting will commence at... of the closed session meeting of the Institutional Advancement Committee. The transcript of any... 1973 Rehabilitation Act. Upon request, meeting notices and materials will be made available in...

  13. 29 CFR 2203.7 - Transcripts, recordings and minutes of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... transcription of the recording disclosing the identity of each speaker, with the deletions noted in the preceding sentence, will be furnished to any person at the actual cost of duplication or transcription...

  14. 29 CFR 2203.7 - Transcripts, recordings and minutes of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... transcription of the recording disclosing the identity of each speaker, with the deletions noted in the preceding sentence, will be furnished to any person at the actual cost of duplication or transcription...

  15. 78 FR 40515 - Sunshine Act Meeting Notice

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-07-05

    ... Corporation's Institutional Advancement Committee will meet telephonically on July 9, 2013. The meeting will... transcript will be made of the closed session meeting of the Institutional Advancement Committee. The... the 1973 Rehabilitation Act. Upon request, meeting notices and materials will be made available in...

  16. 5 CFR 2413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... schedule of fees set forth in § 2411.10 of this subchapter and the actual cost of transcription. (c) The...

  17. 5 CFR 2413.7 - Transcripts, recordings or minutes of closed meeting; public availability; retention.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... pursuant to the provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of... schedule of fees set forth in § 2411.10 of this subchapter and the actual cost of transcription. (c) The...

  18. 75 FR 70617 - Practices and Procedures, Board Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-18

    ... provisions of 5 U.S.C. 552b(c). Copies of transcripts or minutes, or transcriptions of electronic recordings... furnished to any person, subject to the payment of duplication costs or the actual cost of transcription. (3...

  19. 78 FR 20356 - Sunshine Act Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-04

    ... Institutional Advancement Committee will meet telephonically on April 9, 2013. The meeting will commence at 4:00... verbatim written transcript will be made of each closed session meeting of the Institutional Advancement... Rehabilitation Act. Upon request, meeting notices and materials will be made available in alternative formats to...

  20. 77 FR 10003 - Sunshine Act Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-21

    ..., 2011) (Tentative). b. Crow Butte Resources, Inc. (License Renewal for the In Situ Leach Facility... appropriate. If you need a reasonable accommodation to participate in these public meetings, or need this meeting notice or the transcript or other information from the public meetings in another format (e.g...

  1. 77 FR 10575 - Sunshine Act Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-22

    ...) (Tentative) b. Crow Butte Resources, Inc. (License Renewal for the In Situ Leach Facility, Crawford, Nebraska... participate in these public meetings, or need this meeting notice or the transcript or other information from the public meetings in another format (e.g. braille, large print), please notify Bill Dosch, Chief...

  2. 47 CFR 0.607 - Transcript, recording or minutes; availability to the public.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Transcript, recording or minutes; availability to the public. 0.607 Section 0.607 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMISSION ORGANIZATION Meeting Procedures § 0.607 Transcript, recording or minutes; availability to the...

  3. 47 CFR 0.607 - Transcript, recording or minutes; availability to the public.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Transcript, recording or minutes; availability to the public. 0.607 Section 0.607 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL COMMISSION ORGANIZATION Meeting Procedures § 0.607 Transcript, recording or minutes; availability to the...

  4. 77 FR 27254 - Sunshine Act Meeting

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-05-09

    ...-AI77) (Tentative). b. Strata Energy Inc. (Ross In Situ Recovery Uranium Project), Appeal by NRC Staff... participate in these public meetings, or need this meeting notice or the transcript or other information from the public meetings in another format (e.g. braille, large print), please notify Bill Dosch, Chief...

  5. 75 FR 44818 - Advisory Committee on Reactor Safeguards (ACRS): Meeting of the ACRS Subcommittee on Plant...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-29

    ... Renewal Application and the associated Safety Evaluation Report (SER) with open items prepared by the..., (74 FR 58268-58269). Detailed meeting agendas and meeting transcripts are available on the NRC Web...

  6. Towards a Computational Analysis of Status and Leadership Styles on FDA Panels

    NASA Astrophysics Data System (ADS)

    Broniatowski, David A.; Magee, Christopher L.

    Decisions by committees of technical experts are increasingly impacting society. These decision-makers are typically embedded within a web of social relations. Taken as a whole, these relations define an implicit social structure which can influence the decision outcome. Aspects of this structure are founded on interpersonal affinity between parties to the negotiation, on assigned roles, and on the recognition of status characteristics, such as relevant domain expertise. This paper build upon a methodology aimed at extracting an explicit representation of such social structures using meeting transcripts as a data source. Whereas earlier results demonstrated that the method presented here can identify groups of decision-makers with a contextual affinity (i.e., membership in a given medical specialty or voting clique), we now can extract meaningful status hierarchies, and can identify differing facilitation styles among committee chairs. Use of this method is demonstrated on the transcripts of U.S. Food and Drug Administration (FDA) advisory panel meeting transcripts; nevertheless, the approach presented here is extensible to other domains and requires only a meeting transcript as input.

  7. Office Organization and Procedures in the Office--Calendar; Commencement Procedure; Publications; Records; Registration; Reports; Scheduling; Staffing; Testing; Transcripts

    ERIC Educational Resources Information Center

    College and University, 1977

    1977-01-01

    Proceedings of AACRAO's 63rd annual meeting cover: calendar conversion; publications economy; class schedules; fraudulent transcripts; student retention; student ID numbers; veteran student reporting; financial aid reporting; faculty activity analyses; time management; registration; and transcript forms for nontraditional programs. (LBH)

  8. 75 FR 66401 - Advisory Committee on Reactor Safeguards (ACRS); Meeting of the ACRS Subcommittee on U.S...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-10-28

    ... review Chapters 8 and 13 of the Safety Evaluation report (SER) associated with the US-APWR design... October 14, 2009 (74 FR 58268-58269). Detailed meeting agendas and meeting transcripts are available on...

  9. 12 CFR 261b.11 - Transcripts, recordings, and minutes.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Transcripts, recordings, and minutes. 261b.11 Section 261b.11 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM RULES REGARDING PUBLIC OBSERVATION OF MEETINGS § 261b.11 Transcripts, recordings, and...

  10. Meeting report for Odd Pols 2016: Ann Arbor 2.0.

    PubMed

    Roy-Engel, Astrid M

    2017-05-15

    The Tenth International Conference on Transcription by RNA Polymerases I, III, IV and V (the 'Odd Pols') was held June 24-28, 2016 at the University of Michigan, Ann Arbor, USA and organized by David Engelke, Deborah Johnson, Richard Maraia, Lawrence Rothblum, David Schneider, Andrzej Wierzbicki and Astrid Engel. The organizers are grateful for the support from the Rackham Graduate School of the University of Michigan for providing the meeting venue. The environment provided a great background with unexpected encounters with fireflies, free live music and a festive fireworks display. The meeting was composed of eleven oral sessions and a poster session. The keynote speaker, Dave Engelke, opened the meeting with his presentation entitled "A personal history of pol III transcription - how we got here from the 'good old days'." The meeting drew attendees from sixteen countries that shared their research discoveries. Here we present some of the highlights from the meeting using summaries provided by the participants. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. 16 CFR 1013.5 - Recordkeeping requirements.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... the presiding Commissioner setting forth the date, time and place of the meeting and the persons present. (3) The transcript, recording, or minutes of any Commission meeting may include attachments such...

  12. 21 CFR 10.65 - Meetings and correspondence.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 21 Food and Drugs 1 2010-04-01 2010-04-01 false Meetings and correspondence. 10.65 Section 10.65 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES GENERAL... religion. (e) An official transcript, recording, or memorandum summarizing the substance of any meeting...

  13. 12 CFR 791.18 - Public availability of meeting records and other documents.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., minutes or transcription of a recording, disclosing the identity of each speaker, shall be furnished to... shall be furnished at the actual cost of duplication or transcription unless waived by the Secretary of...

  14. 12 CFR 791.18 - Public availability of meeting records and other documents.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., minutes or transcription of a recording, disclosing the identity of each speaker, shall be furnished to... shall be furnished at the actual cost of duplication or transcription unless waived by the Secretary of...

  15. 76 FR 4113 - Independent Scientific Peer Review Panel Meeting on an In Vitro

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-01-24

    ... Vitro Estrogen Receptor Transcriptional Activation Test Method for Endocrine Disruptor Chemical... Vitro Estrogen Receptor Transcriptional Activation Test Method for Endocrine Disruptor Chemical... the information included in the BRD supports ICCVAM's draft test method recommendations. NICEATM...

  16. Using Transcripts To Validate Institutional Mission: The Role of the Community College in the Postsecondary Experience of a Generation. ASHE Annual Meeting Paper.

    ERIC Educational Resources Information Center

    Adelman, Clifford

    Information is presented on the use of transcripts to validate institutional mission, proposing that transcript archives can serve as grounds against which the validity of an institution's claimed mission with respect to its primary beneficiaries can be measured. This is done with a focus on the community college. The National Longitudinal Study…

  17. Transcript of the Joint FAA/Industry Symposium on Level B Airplane simulator aeromodel validation requirements

    DOT National Transportation Integrated Search

    1996-03-13

    "This is the transcript of the Joint FAA/Industry Symposium on Level B Airplane Simulator Aeromodel Validation Requirements held on March 13-14, 1996, at the Washington Dulles Airport Hilton. The purpose of the meeting was to discuss the aeromodeling...

  18. 76 FR 37062 - Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-06-24

    ..., computer assisted real-time transcription (CART), and sign language interpreters will be available at the... Washington, DC, Monday through Wednesday, July 11-13, 2011, at the times and location noted below. DATES: The... Governments; and Terry Moakley, Association of Travel Instruction). 1:30-3 p.m.--Board Meeting (guest speaker...

  19. 12 CFR 261b.13 - Fees.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Fees. 261b.13 Section 261b.13 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM RULES REGARDING PUBLIC OBSERVATION OF MEETINGS § 261b.13 Fees. (a) Copies of transcripts, recordings or transcriptions of recordings...

  20. 77 FR 72356 - Animal Drug User Fee Act; Public Meeting; Request for Comments

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-05

    ..., please contact Jacqueline Farmer at least 7 days in advance. Transcripts: Please be advised that as soon... at the Division of Dockets Management (HFA-305), Food and Drug Administration, 5630 Fishers Lane, rm... Dockets Management (see Transcripts) or electronic comments to http://www.regulations.gov . It is only...

  1. 12 CFR 261b.13 - Fees.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 3 2011-01-01 2011-01-01 false Fees. 261b.13 Section 261b.13 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM RULES REGARDING PUBLIC OBSERVATION OF MEETINGS § 261b.13 Fees. (a) Copies of transcripts, recordings or transcriptions of recordings...

  2. 18 CFR 1301.48 - Public availability of transcripts and other documents.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 18 Conservation of Power and Water Resources 2 2010-04-01 2010-04-01 false Public availability of... VALLEY AUTHORITY PROCEDURES Government in the Sunshine Act § 1301.48 Public availability of transcripts and other documents. (a) Public announcements of meetings pursuant to § 1301.44, written copies of...

  3. Public meeting: Western New York Nuclear Service Center options study. [Problem of West Valley plant

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    None

    This document is a transcript of the meeting, with additional written comments. The main topic is the West Valley Processing Plant and how to dispose of it and its high-level wastes. Objective is to get public input on this topic. (DLC)

  4. 12 CFR 791.17 - Maintenance of meeting records.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Maintenance of meeting records. 791.17 Section 791.17 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING THE OPERATIONS OF... the control of the agency, the Board shall maintain a complete transcript or electronic recording...

  5. 12 CFR 791.17 - Maintenance of meeting records.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 12 Banks and Banking 6 2011-01-01 2011-01-01 false Maintenance of meeting records. 791.17 Section 791.17 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING THE OPERATIONS OF... the control of the agency, the Board shall maintain a complete transcript or electronic recording...

  6. 12 CFR 261b.12 - Procedures for inspection and obtaining copies of transcriptions and minutes.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 12 Banks and Banking 3 2010-01-01 2010-01-01 false Procedures for inspection and obtaining copies of transcriptions and minutes. 261b.12 Section 261b.12 Banks and Banking FEDERAL RESERVE SYSTEM (CONTINUED) BOARD OF GOVERNORS OF THE FEDERAL RESERVE SYSTEM RULES REGARDING PUBLIC OBSERVATION OF MEETINGS...

  7. Transcription and recombination: when RNA meets DNA.

    PubMed

    Aguilera, Andrés; Gaillard, Hélène

    2014-08-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription-replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. Copyright © 2014 Cold Spring Harbor Laboratory Press; all rights reserved.

  8. Transcription and Recombination: When RNA Meets DNA

    PubMed Central

    Aguilera, Andrés; Gaillard, Hélène

    2014-01-01

    A particularly relevant phenomenon in cell physiology and proliferation is the fact that spontaneous mitotic recombination is strongly enhanced by transcription. The most accepted view is that transcription increases the occurrence of double-strand breaks and/or single-stranded DNA gaps that are repaired by recombination. Most breaks would arise as a consequence of the impact that transcription has on replication fork progression, provoking its stalling and/or breakage. Here, we discuss the mechanisms responsible for the cross talk between transcription and recombination, with emphasis on (1) the transcription–replication conflicts as the main source of recombinogenic DNA breaks, and (2) the formation of cotranscriptional R-loops as a major cause of such breaks. The new emerging questions and perspectives are discussed on the basis of the interference between transcription and replication, as well as the way RNA influences genome dynamics. PMID:25085910

  9. International Meeting To Discuss Audio Technology as Applied to Library Services for Blind Individuals (3rd, Toronto, Ontario, Canada, April 20-22, 1995). Volumes 1-3.

    ERIC Educational Resources Information Center

    Library of Congress, Washington, DC. National Library Service for the Blind and Physically Handicapped.

    This three-day conference on the subject of audio technology for the production of materials for the blind, takes the court reporter approach to recording the speeches and discussions of the meeting. The result is a three volume set of complete transcripts, one volume for each day of the meeting, but continuous in form. The highlights of each…

  10. Innovative Delivery Systems to Meet School Staffing Needs. Proceedings of the Annual Meeting of the National Association of State Directors of Teacher Education and Certification (53rd, Williamsburg, VA, June 23-25, 1981).

    ERIC Educational Resources Information Center

    Mackey, Charles C., Jr., Ed.

    Presentations delivered at the 1981 annual meeting of the National Association of State Directors of Teacher Education and Certification are presented in this publication. The papers consist of: (1) an edited transcript of a discussion on "Innovative Delivery Systems" (W. Robert Houston, Dwight Allen, and Fred Wood); (2) "Delivery Systems in a…

  11. Postsecondary Support for Competency-Based High School Transcripts: Lessons from the Competency-Based Transcripts Postsecondary Convening (Washington, DC, May 29-30, 2014)

    ERIC Educational Resources Information Center

    Achieve, Inc., 2015

    2015-01-01

    In December 2013, while attending Achieve's Annual State Leadership Team Meeting in Alexandria, VA, leaders from Connecticut, Maine, New Hampshire, Rhode Island, and Vermont issued a call to action to create a national movement for postsecondary leaders to signal their support for proficiency-based and competency-based high school diplomas and…

  12. Training of Residential Social Care Staff to Meet the Needs of Older People with Intellectual Disabilities Who Develop Age-Related Health Problems: An Exploratory Study

    ERIC Educational Resources Information Center

    Northway, Ruth; Jenkins, Robert; Holland-Hart, Daniella

    2017-01-01

    Background: Despite awareness of the age related health needs of people with intellectual disabilities little is known regarding how residential social care staff are prepared to meet such needs. Methods: Data were gathered via semi-structured interviews from 14 managers of supported living settings. Transcripts were thematically analysed.…

  13. Summary of the 2016 Alcohol and Immunology Research Interest Group (AIRIG) meeting.

    PubMed

    Boule, Lisbeth A; Ju, Cynthia; Agudelo, Marisela; Parira, Tiyash; Cannon, Abigail; Davis, Booker; Eby, Jonathan; Cresci, Gail; Samuelson, Derrick R; Shukla, Pradeep; Alrefai, Waddah A; Sureshchandra, Suhas; Pandey, Subhash C; Schnabl, Bernd; Curtis, Brenda J; Wyatt, Todd A; Choudhry, Mashkoor A; Kovacs, Elizabeth J

    2018-02-01

    On November 18, 2016 the 21st annual Alcohol and Immunology Research Interest Group (AIRIG) meeting was held at the Center for Translational Research and Education at Loyola University Chicago's Health Sciences Campus in Maywood, IL. The 2016 meeting focused broadly on alcohol and inflammation, epigenetics, and the microbiome. The four plenary sessions of the meeting were Alcohol, Inflammation, and Immunity; Alcohol and Epigenetics; Alcohol, Transcriptional Regulation, and Epigenetics; and Alcohol, Intestinal Mucosa, and the Gut Microbiome. Presentations in all sessions of the meeting explored putative underlying causes for chronic diseases and mortality associated with alcohol consumption, shedding light on future work and potential therapeutic targets to alleviate the negative effects of alcohol misuse. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Network of Women in Higher Education in the Pacific (NetWHEP). Report of Meeting of September 28-October 1, 1996.

    ERIC Educational Resources Information Center

    Network of Women in Higher Education in the Pacific, Suva (Fiji).

    This report of a meeting of the Network of Women in Higher Education in the Pacific (NetWHEP) contains transcripts of major addresses, a copy of the program, statistics and summary information relating to the status of women in higher education for nine countries, and general information about the NetWHEP organization. Included are: a transcript…

  15. Makerere University Student Interview Transcript: MedlinePlus

    MedlinePlus

    ... was a picture of people gathering under a tree, (shown) which is basically typical of our African culture. Mostly village meetings are conducted under the trees, under temporary shelter, it is something that somebody ...

  16. 39 CFR 7.6 - Certification and transcripts of closed meetings.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Corporate Communications Department at Postal Service Headquarters, or in another place easily accessible to... of this electronic recording disclosing the identity of each speaker, to any person at the actual...

  17. 39 CFR 7.6 - Certification and transcripts of closed meetings.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Corporate Communications Department at Postal Service Headquarters, or in another place easily accessible to... of this electronic recording disclosing the identity of each speaker, to any person at the actual...

  18. 39 CFR 7.6 - Certification and transcripts of closed meetings.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Corporate Communications Department at Postal Service Headquarters, or in another place easily accessible to... of this electronic recording disclosing the identity of each speaker, to any person at the actual...

  19. 39 CFR 7.6 - Certification and transcripts of closed meetings.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Corporate Communications Department at Postal Service Headquarters, or in another place easily accessible to... of this electronic recording disclosing the identity of each speaker, to any person at the actual...

  20. 39 CFR 7.6 - Certification and transcripts of closed meetings.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Corporate Communications Department at Postal Service Headquarters, or in another place easily accessible to... of this electronic recording disclosing the identity of each speaker, to any person at the actual...

  1. Annual Volume of Proceedings, Addresses, and Research Papers [of the] Association of School Business Officials of the United States and Canada (62nd, Boston, Massachusetts, October 2-6, 1976).

    ERIC Educational Resources Information Center

    Foster, Charles W., Ed.; Esau, Dwight B., Ed.

    This publication presents a comprehensive record of the 62nd Annual Meeting of the Association of School Business Officials, which was held in October 1976 in Boston. Included are transcripts of the meeting's three general sessions, including keynote addresses by Dr. Paul Salmon and Senator Edward Kennedy, as well as reports summarizing the…

  2. Security training symposium: Meeting the challenge: Firearms and explosives recognition and detection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1990-09-01

    These conference proceedings have been prepared in support of the US Nuclear Regulatory Commission's Security Training Symposium on Meeting the Challenge -- Firearms and Explosives Recognition and Detection,'' November 28 through 30, 1989, in Bethesda, Maryland. This document contains the edited transcripts of the guest speakers. It also contains some of the speakers' formal papers that were distributed and some of the slides that were shown at the symposium (Appendix A).

  3. 12 CFR 311.8 - Transcripts and minutes of meetings.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... describe all matters discussed and will provide a full and accurate summary of any actions taken, and the... furnish copies at a cost of 10 cents per page. Whenever the Corporation determines that in the public...

  4. 12 CFR 311.8 - Transcripts and minutes of meetings.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... describe all matters discussed and will provide a full and accurate summary of any actions taken, and the... furnish copies at a cost of 10 cents per page. Whenever the Corporation determines that in the public...

  5. How is research publishing going to progress in the next 20 years?: transcription of session for editors, associate editors, publishers and others with an interest in scientific publishing held at IADR meeting in Seattle on Wednesday, 20 March 2013.

    PubMed

    Eaton, Kenneth A; Rex Holland, G; Giannobile, William V; Hancocks, Stephen; Robinson, Peter G; Lynch, Christopher D

    2014-03-01

    On March 20th 2013, a one-hour session for Editors, Associate Editors, Publishers and others with an interest in scientific publishing was held at the IADR International Session in Seattle. Organised by Kenneth Eaton and Christopher Lynch (Chair and Secretary, respectively, of the British Dental Editors Forum), the meeting sought to bring together leading international experts in dental publishing, as well as authors, reviewers and students engaged in research. The meeting was an overwhelming success, with more than 100 attendees. A panel involving four leading dental editors led a discussion on anticipated developments in publishing dental research with much involvement and contribution from audience members. This was the third such meeting held at the IADR for Editors, Associate Editors, Publishers and others with an interest in scientific publishing. A follow-up session will take place in Cape Town on 25 June 2014 as part of the annual IADR meeting. The transcript of the Seattle meeting is reproduced in this article. Where possible speakers are identified by name. At the first time of mention their role/position is also stated, thereafter only their name appears. We are grateful to Stephen Hancocks Ltd. for their generous sponsorship of this event. For those who were not able to attend the authors hope this article gives a flavour of the discussions and will encourage colleagues to attend future events. Involvement is open to Editors, Associate Editors, Publishers and others with an interest in scientific publishing. It is a very open group and all those with an interest will be welcome to join in. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. 7 CFR 1780.83 - Bond transcript documents.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) Copies of general incumbency certificate; (c) Certified copies of minutes or excerpts from all meetings... statutory requirements incident to calling and holding a favorable bond election, if one is necessary; (e..., with any attached coupons; (h) Attorney's no-litigation certificate; (i) Certified copies of...

  7. A method for studying decision-making by guideline development groups.

    PubMed

    Gardner, Benjamin; Davidson, Rosemary; McAteer, John; Michie, Susan

    2009-08-05

    Multidisciplinary guideline development groups (GDGs) have considerable influence on UK healthcare policy and practice, but previous research suggests that research evidence is a variable influence on GDG recommendations. The Evidence into Recommendations (EiR) study has been set up to document social-psychological influences on GDG decision-making. In this paper we aim to evaluate the relevance of existing qualitative methodologies to the EiR study, and to develop a method best-suited to capturing influences on GDG decision-making. A research team comprised of three postdoctoral research fellows and a multidisciplinary steering group assessed the utility of extant qualitative methodologies for coding verbatim GDG meeting transcripts and semi-structured interviews with GDG members. A unique configuration of techniques was developed to permit data reduction and analysis. Our method incorporates techniques from thematic analysis, grounded theory analysis, content analysis, and framework analysis. Thematic analysis of individual interviews conducted with group members at the start and end of the GDG process defines discrete problem areas to guide data extraction from GDG meeting transcripts. Data excerpts are coded both inductively and deductively, using concepts taken from theories of decision-making, social influence and group processes. These codes inform a framework analysis to describe and explain incidents within GDG meetings. We illustrate the application of the method by discussing some preliminary findings of a study of a National Institute for Health and Clinical Excellence (NICE) acute physical health GDG. This method is currently being applied to study the meetings of three of NICE GDGs. These cover topics in acute physical health, mental health and public health, and comprise a total of 45 full-day meetings. The method offers potential for application to other health care and decision-making groups.

  8. Risk management policy and black-box warnings: a qualitative analysis of US FDA proceedings.

    PubMed

    Cook, Daniel M; Gurugubelli, Rama K; Bero, Lisa A

    2009-01-01

    The US FDA increasingly applies risk management to drug safety policy. Little is known about the process by which the FDA approves labelling changes. Although advisory committees can recommend any of the risk management tools, including the use of 'black-box warnings', it is unknown whether they deliberate on these questions or how they apply the principles of risk minimization or management during their considerations of drug licensing. To examine the process by which risk management is considered by the FDA, including the role of FDA advisory committees. We also aimed to identify and describe drug labelling changes and additions, including the prevalence of black-box warnings. We electronically obtained publicly available information regarding drug approvals, drug revisions and advisory committee meetings over 3 years (2004-6) from the FDA. Data in the form of meeting transcripts and full histories of labelling changes were collected on drugs discussed by advisory committees. We then searched and qualitatively analysed the meeting transcripts to identify themes in the discussion. We also created a database of all prescription drug labelling changes for 3 years and examined which drugs have had the most changes. We describe the risk management consideration process and report the frequency and characteristics of labelling changes. Excerpts from the transcripts are selected to illustrate both typical and atypical features of the discussion. A total of 174 black-box changes were made in the 3-year period of our study, of which 77 were new black-box warnings and 97 were revisions in black-box warnings. Of 77 new black-box warning additions, only 11 drugs were discussed by the advisory committees. Of the 17 most frequently revised drug labels in these 3 years, two were discussed in the advisory committee meetings. Advisory meeting discussions revealed confusion about black-box warnings and emphasized potential consequences of the warnings rather than their content. The safety labelling of drugs on the market is changed often. Panels of advisors consider only a few drugs, rarely discuss the labelling requirements, and display confusion about applying black-box warnings. The creation and application of black-box warnings on prescription medications should receive closer attention from the FDA and its advisors.

  9. 1492: Multiple Perspectives. Transcript.

    ERIC Educational Resources Information Center

    National Council for the Social Studies, Washington, DC.

    This National Council for the Social Studies (NCSS) board of directors substantive issue session initiated the process of developing a position statement for the educational observance of the Quincentenary of Columbus' landing in the Americas. The meeting consisted of proposal statements by panelists and advocated the development of a united…

  10. 40 CFR 154.15 - Docket for the Special Review.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... the Secretary of Agriculture or the Scientific Advisory Panel. (6) A transcript of all public meetings held by the Scientific Advisory Panel or conducted by the Agency for the purpose of gathering... information, each memorandum shall describe fully and accurately all significant positions taken, arguments...

  11. 40 CFR 154.15 - Docket for the Special Review.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... the Secretary of Agriculture or the Scientific Advisory Panel. (6) A transcript of all public meetings held by the Scientific Advisory Panel or conducted by the Agency for the purpose of gathering... information, each memorandum shall describe fully and accurately all significant positions taken, arguments...

  12. 40 CFR 154.15 - Docket for the Special Review.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... the Secretary of Agriculture or the Scientific Advisory Panel. (6) A transcript of all public meetings held by the Scientific Advisory Panel or conducted by the Agency for the purpose of gathering... information, each memorandum shall describe fully and accurately all significant positions taken, arguments...

  13. 40 CFR 154.15 - Docket for the Special Review.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... the Secretary of Agriculture or the Scientific Advisory Panel. (6) A transcript of all public meetings held by the Scientific Advisory Panel or conducted by the Agency for the purpose of gathering... information, each memorandum shall describe fully and accurately all significant positions taken, arguments...

  14. When aging meets microgravity: whole genome promoters and enchancers transcription landscape in zebrafish onboard ISS

    NASA Astrophysics Data System (ADS)

    Arshanovskii, Kirill; Gusev, Oleg; Sychev, Vladimir; Poddubko, Svetlana; Deviatiiarov, Ruslan

    2016-07-01

    In order to gen new insights of gene regulation changes under conditions of real spaceflight, we have conducted whole-genome analysis of dynamic of promotes and enhancers transcriptional changes in zebrafish during prolonged exposure to real spaceflight. In the frame of Russia-Japan joint experiments "Aquatic Habitat"-"Aquarium" we have conducted Cap Analysis of Gene Expression (CAGE) assay of zebrafish in the rage from 7 to 40 days of real spaceflight onboard ISS. The analysis showed that both gene expression patterns and architecture of shapes and types of the promoters are affected by spaceflight environment.

  15. American Hero(es).

    ERIC Educational Resources Information Center

    Valore, Thomas G.

    2002-01-01

    Entering Re-ED (Reeducation of Emotional Disturbed Children) at age 15, Alex, spent three years working and learning together to reach the goals that Alex speaks to in his culminating story. Presents a transcript of a videotaped Petition to Graduate meeting held at the Positive Education Program as an example of the Re-ED philosophy, its…

  16. 45 CFR 1703.404 - Copying and transcription charges.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... LIBRARIES AND INFORMATION SCIENCE GOVERNMENT IN THE SUNSHINE ACT Maintenance of Meeting Records § 1703.404.... Requested information will not be released until the deposit is received. Fees shall be paid by check or money order made payable to the National Commission on Libraries and Information Science. (b) The...

  17. 45 CFR 1703.404 - Copying and transcription charges.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... LIBRARIES AND INFORMATION SCIENCE GOVERNMENT IN THE SUNSHINE ACT Maintenance of Meeting Records § 1703.404.... Requested information will not be released until the deposit is received. Fees shall be paid by check or money order made payable to the National Commission on Libraries and Information Science. (b) The...

  18. 76 FR 28689 - Microbiology Devices; Classification of In Vitro Diagnostic Device for Bacillus Species Detection

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-18

    .... FDA-2011-N-0103] Microbiology Devices; Classification of In Vitro Diagnostic Device for Bacillus... of the Microbiology Devices Advisory Panel (the Panel). In addition, the proposed rule would... in the Federal Register. 1. Transcript of the FDA Microbiology Devices Panel meeting, March 7, 2002...

  19. Defense.gov - Special Report

    Science.gov Websites

    FORUM - U.S. Defense Secretary Robert M. Gates addresses the audience as Canadian Minister of National issues that Defense Secretary Robert M. Gates and Canadian Defense Minister Peter MacKay discussed during a bilateral meeting here today. Story | Transcript U.S., Canadian Defense Chiefs Answer Afghanistan

  20. Changing Teacher Attitudes and Actions To Promote Better Parent-Teacher Communication.

    ERIC Educational Resources Information Center

    Schweiker-Marra, Karyn E.

    2000-01-01

    Using qualitative information (faculty meeting transcripts) and a survey, researchers showed that seven statements pertaining to parent-teacher communication at a large rural middle school were poorly rated. A subsequent survey showed improved teacher attitudes, thanks to a monthly newspaper, parent hotline, web page, and other changes. (Contains…

  1. Educational, Social, Technological and Scientific Trends and the Deaf Consumer.

    ERIC Educational Resources Information Center

    Denton, David M.; And Others

    1987-01-01

    The report of a section meeting of the 1987 Forum on Deafness contains transcripts of the following presentations: "Century 21: Social Trends and Deafness" (Raymond Trybus); "Technology and Science in the Management of Deafness" (Arthur Boothroyd); "Trends in Education" (Eva Baker). Highlights of the discussion following the presentations are…

  2. Upgrading a Social Media Strategy to Increase Twitter Engagement During the Spring Annual Meeting of the American Society of Regional Anesthesia and Pain Medicine.

    PubMed

    Schwenk, Eric S; Jaremko, Kellie M; Gupta, Rajnish K; Udani, Ankeet D; McCartney, Colin J L; Snively, Anne; Mariano, Edward R

    Microblogs known as "tweets" are a rapid, effective method of information dissemination in health care. Although several medical specialties have described their Twitter conference experiences, Twitter-related data in the fields of anesthesiology and pain medicine are sparse. We therefore analyzed the Twitter content of 2 consecutive spring meetings of the American Society of Regional Anesthesia and Pain Medicine using publicly available online transcripts. We also examined the potential contribution of a targeted social media campaign on Twitter engagement during the conferences. The original Twitter meeting content was largely scientific in nature and created by meeting attendees, the majority of whom were nontrainee physicians. Physician trainees, however, represent an important and increasing minority of Twitter contributors. Physicians not in attendance predominantly contributed via retweeting original content, particularly picture-containing tweets, and thus increased reach to nonattendees. A social media campaign prior to meetings may help increase the reach of conference-related Twitter discussion.

  3. Academic Freedom and National Security

    ERIC Educational Resources Information Center

    Academe, 2004

    2004-01-01

    This article contains the transcript of a speech that Robert ONeil delivered on June 12 in Washington, D.C., at the Ninetieth Annual Meeting of the American Association of University Professors. ONeil is professor of law and former president of the University of Virginia, where he directs the Thomas Jefferson Center for Protection of Free…

  4. 30 CFR 250.191 - How does MMS conduct incident investigations?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... following requirements apply to any panel meetings involving persons giving testimony: (a) A person giving testimony may have legal or other representative(s) present to provide advice or counsel while the person is giving testimony. The chairperson may require a verbatim transcript to be made of all oral testimony. The...

  5. 75 FR 56147 - Announcement of Public Meeting Transcript and Comment Period

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-15

    ... written statements to Ms. Angela Bailey, Deputy Associate Director for Recruitment and Diversity, 1900 E... Federal workforce and, if so, why that is the case; (2) to ascertain from those who believe that it is not... Bailey, Deputy Associate Director for Recruitment and Diversity, on or before September 29, 2010, to the...

  6. Scholarly Observations and Meditations: Perspectives on September 11, 2001.

    ERIC Educational Resources Information Center

    Carey, James W.; Drucker, Susan J.; Gozzi, Raymond, Jr.; Gumpert, Gary; Thaler, Paul; Wilder, Carol

    2002-01-01

    Presents a transcription of a panel (at the annual meeting of the New York State Communication Association) consisting of internationally known and respected communication scholars, and New Yorkers, who offered their thoughts and meditations on September 11, 2001. Notes the only appropriate frames of understanding in those few short weeks after…

  7. Active Ingredients for an Embedded Intervention within the Early Childhood Classroom

    ERIC Educational Resources Information Center

    Blackwell, Angela Labrie; Dunn, Winnie

    2016-01-01

    As public education moves toward a tiered model of intervention (Response to Intervention), occupational therapists need to understand how to effectively implement interventions at each tier. The purpose of this article is to report about a process of examining teacher-therapist meeting transcripts from a feasibility study to find the active…

  8. Nonassertive Mothers, Aggressive Teens: Toughlove as a Community Intervention.

    ERIC Educational Resources Information Center

    Klug, Wayne

    A process study was conducted in two phases to measure the effects of whether a mother's participation in a Toughlove program improved her child's behavior. During phase 1, small-group Toughlove meetings were used for observation and then were tape-recorded and transcribed. Transcriptions were coded to identify instances of social support;…

  9. Differential gene transcription across the life cycle in Daphnia magna using a new all genome custom-made microarray.

    PubMed

    Campos, Bruno; Fletcher, Danielle; Piña, Benjamín; Tauler, Romà; Barata, Carlos

    2018-05-18

    Unravelling the link between genes and environment across the life cycle is a challenging goal that requires model organisms with well-characterized life-cycles, ecological interactions in nature, tractability in the laboratory, and available genomic tools. Very few well-studied invertebrate model species meet these requirements, being the waterflea Daphnia magna one of them. Here we report a full genome transcription profiling of D. magna during its life-cycle. The study was performed using a new microarray platform designed from the complete set of gene models representing the whole transcribed genome of D. magna. Up to 93% of the existing 41,317 D. magna gene models showed differential transcription patterns across the developmental stages of D. magna, 59% of which were functionally annotated. Embryos showed the highest number of unique transcribed genes, mainly related to DNA, RNA, and ribosome biogenesis, likely related to cellular proliferation and morphogenesis of the several body organs. Adult females showed an enrichment of transcripts for genes involved in reproductive processes. These female-specific transcripts were essentially absent in males, whose transcriptome was enriched in specific genes of male sexual differentiation genes, like doublesex. Our results define major characteristics of transcriptional programs involved in the life-cycle, differentiate males and females, and show that large scale gene-transcription data collected in whole animals can be used to identify genes involved in specific biological and biochemical processes.

  10. 75 FR 26225 - Frequency Regulation Compensation in the Organized Wholesale Power Markets; Notice of Technical...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-11

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. AD10-11-000] Frequency... Meeting Room at the Federal Energy Regulatory Commission, 888 First Street, NE., Washington, DC 20426. All...-Federal Reporters, Inc. (202-347-3700 or 1-800-336-6646). The transcripts will be available for free on...

  11. University Eligibility: Are Locally Reported Figures Comparable to the Commission's Estimates? Factsheet 06-03

    ERIC Educational Resources Information Center

    California Postsecondary Education Commission, 2006

    2006-01-01

    The Commission periodically releases university eligibility rates for California high school graduates. These figures, which are based on a review of transcripts collected from schools, show the percentage of high school graduates who meet the admission requirements of the University of California (UC) and the California State University (CSU).…

  12. 75 FR 23759 - Frequency Regulation Compensation in the Organized Wholesale Power Markets; Notice of Technical...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-04

    ... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. AD10-11-000] Frequency... Meeting Room at the Federal Energy Regulatory Commission, 888 First Street, NE., Washington, DC 20426. All...-Federal Reporters, Inc. (202-347-3700 or 1-800-336-6646). The transcripts will be available for free on...

  13. 75 FR 36662 - Center for Scientific Review; Notice of Closed Meetings

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-06-28

    ...; Neurogenesis, Stem Cells, and Transcription Factors. Date: July 29, 2010. Time: 12 p.m. to 2 p.m. Agenda: To...: Translational Research in Pediatric and Obstetric Pharmacology. Date: July 21, 2010. Time: 11 a.m. to 2:30 p.m... for Scientific Review Special Emphasis Panel; Review of the Mass Spectrometry Research Center. Date...

  14. Public Access; Public Interest. The Network Project. Notebook Number 11.

    ERIC Educational Resources Information Center

    Columbia Univ., New York, NY. Network Project.

    The transcript of a panel discussion and an essay on public access to and control of society's information resources are presented. It is contended that the electronic Media--including radio, television, and communication satellites--are controlled by a select group of individuals and corporations and that they are not meeting the public interest.…

  15. Individualized Education Program Team Decisions: A Preliminary Study of Conversations, Negotiations, and Power

    ERIC Educational Resources Information Center

    Ruppar, Andrea L.; Gaffney, Janet S.

    2011-01-01

    Given the centrality of the Individualized Education Program (IEP) to services for students with disabilities, the decision-making process during the IEP meeting deserves attention in research and implementation. In this case study, IEP team decision-making is examined as a socially situated practice. Transcripts of an initial evaluation and IEP…

  16. 16 CFR 1013.6 - Public availability of transcripts, recordings and minutes of Commission meetings.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ...) through (10) of § 1013.4 need not be made available to the public. (b) Procedures for making available... Commission for decision. In that event, the Commission decision shall be made within the time limits set... attention of the Chairman, Consumer Product Safety Commission, Washington, D.C. 20207. (ii) The Commission...

  17. Managing a Statewide Virtual Reference Service: How Q and A NJ Works.

    ERIC Educational Resources Information Center

    Bromberg, Peter

    2003-01-01

    Describes the live virtual reference service, Q and A NJ (Question and Answer New Jersey), strategies used to meet the challenges of day-to-day management, scaled growth and quality control. Describes how it began; how long it took; how to manage a large project (constant communication; training and practice; transcript analysis and privacy;…

  18. Expanding Horizons: Pacesetters in Adult Education for Work

    ERIC Educational Resources Information Center

    Chisman, Forrest P.

    2009-01-01

    The publication is based on the "Adult Readiness Roundtable" Project co-sponsored by CAAL and the National Center on Education and the Economy on April 6-7, 2009. It is not a transcript of the Roundtable discussion; instead it reports on a two-day discussion meeting among a group of exemplary adult-education-for-work programs from around the…

  19. Critiquing Teacher Professional Development: Teacher Learning within the Field of Teachers' Work

    ERIC Educational Resources Information Center

    Hardy, Ian

    2010-01-01

    This study is an empirical account of the professional development (PD) practices that constituted part of the work of a group of teachers and school-based administrators working together in a cluster of six schools in southeast Queensland, Australia, during a period of intense educational reform. The data comprise meeting transcripts and…

  20. Minutes 1972. Association of Physical Plant Administrators Annual Meeting. (59th, Cincinnati, Ohio, April 30-May 3, 1972).

    ERIC Educational Resources Information Center

    Association of Physical Plant Administrators of Universities and Colleges, Washington, DC.

    This presentation is comprised of 17 session papers and the transcripts of two group discussions all dealing with various aspects of campus physical plant maintenance. Among the subjects covered are: the post-traditional campus, central environmental control, contract management service, operational and maintenance planning, air handling systems,…

  1. 77 FR 52741 - MDEpiNet 2012 Annual Meeting: The Medical Device Epidemiology Network as a Partnership for...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-30

    ...) proposed partnership structure and governance; (3) MDEpiNet as a framework for medical device postmarket.... 1061, Rockville, MD 20852 or electronic comments to http://www.regulations.gov . It is only necessary... transcript is available, it will be accessible at http://www.regulations.gov . It may be viewed at the...

  2. Faculty Experience with College Students with Autism Spectrum Disorders: A Qualitative Study of Challenges and Solutions

    ERIC Educational Resources Information Center

    Gobbo, Ken; Shmulsky, Solvegi

    2014-01-01

    This article reports the findings of a qualitative inquiry involving two focus groups made up of experienced faculty who met to discuss academic concerns faced by college students with autism spectrum disorders, including Asperger's disorder. Analysis of group meeting transcripts indicated that student concerns fell into categories related to…

  3. Nutrient sensing by the mitochondrial transcription machinery dictates oxidative phosphorylation

    PubMed Central

    Liu, Lijun; Nam, Minwoo; Fan, Wei; Akie, Thomas E.; Hoaglin, David C.; Gao, Guangping; Keaney, John F.; Cooper, Marcus P.

    2014-01-01

    Sirtuin 3 (SIRT3), an important regulator of energy metabolism and lipid oxidation, is induced in fasted liver mitochondria and implicated in metabolic syndrome. In fasted liver, SIRT3-mediated increases in substrate flux depend on oxidative phosphorylation (OXPHOS), but precisely how OXPHOS meets the challenge of increased substrate oxidation in fasted liver remains unclear. Here, we show that liver mitochondria in fasting mice adapt to the demand of increased substrate oxidation by increasing their OXPHOS efficiency. In response to cAMP signaling, SIRT3 deacetylated and activated leucine-rich protein 130 (LRP130; official symbol, LRPPRC), promoting a mitochondrial transcriptional program that enhanced hepatic OXPHOS. Using mass spectrometry, we identified SIRT3-regulated lysine residues in LRP130 that generated a lysine-to-arginine (KR) mutant of LRP130 that mimics deacetylated protein. Compared with wild-type LRP130 protein, expression of the KR mutant increased mitochondrial transcription and OXPHOS in vitro. Indeed, even when SIRT3 activity was abolished, activation of mitochondrial transcription and OXPHOS by the KR mutant remained robust, further highlighting the contribution of LRP130 deacetylation to increased OXPHOS in fasted liver. These data establish a link between nutrient sensing and mitochondrial transcription that regulates OXPHOS in fasted liver and may explain how fasted liver adapts to increased substrate oxidation. PMID:24430182

  4. Condition of America's Schools and Colleges. Hearing Examining Whether the Nation Is Meeting Its Education Goals and To Review Proposals To Reauthorize the Higher Education Act, Focusing on Problems and Reforms in Elementary and Secondary Education, Strengths and Weaknesses of Higher Education, and Access to Student Federal Aid Programs, before the Committee on Labor and Human Resources, United States Senate, One Hundred Second Congress, First Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. Senate Committee on Labor and Human Resources.

    This report provides a transcription of the speeches and written statements presented at a Senate hearing concerning the state of crisis within American education. The hearing examines whether the nation is meeting its education goals and reviews proposals to reauthorize the Higher Education Act. It focuses on problems and reforms in elementary…

  5. Research in Education of the Handicapped. Project Directors' Meeting (3rd, Washington, D.C., July 10-12, 1988). Proceedings.

    ERIC Educational Resources Information Center

    Council for Exceptional Children, Reston, VA.

    This conference brought together directors of research grants and research-based contracts funded by the Division of Innovation and Development of the Office of Special Education and Rehabilitation Services (OSERS). The proceedings contain copies of three speeches given at the conference, along with transcripts of the question-and-answer sessions…

  6. Joint Congressional Hearing on the Changing Information Needs of Rural America: The Role of Libraries and Information Technology.

    ERIC Educational Resources Information Center

    National Commission on Libraries and Information Science, Washington, DC.

    Topics of importance to rural America in three general areas--rural community and individual information needs, available answers to these needs, and policies and strategies to meet these needs--were addressed in a joint congressional hearing held at the Fourth General Assembly of the World Future Society in July 1982. This transcript presents…

  7. Nutrition Frontiers - Summer 2017 | Division of Cancer Prevention

    Cancer.gov

    Volume 8, Issue 3 Dear Colleague, The summer issue of Nutrition Frontiers showcases insulin-like growth factor and vitamin D in prostate cancer risk, bile acid and FXR inactivation and gender dissimilarity, and CerS6, a novel transcriptional target of p53 protein. Meet our spotlight investigator, Dr. Wendy Russell, and her research on the functional role of the gut microbiota.

  8. Report of the Aesthetic Education Center (American Educational Theatre Association Convention, Chicago, Illinois, August, 1971).

    ERIC Educational Resources Information Center

    Rosenblatt, Bernard S., Ed.; Ingham, Susan D., Ed.

    This report is a transcription of the proceedings of the Aesthetic Education Center meeting of 1971, sponsored by AETA and CEMREL, Inc. Following an opening statement, the report summarizes a panel discussion on "What Is Aesthetic Education?" which centered on finding approaches to relating the arts programs in schools more closely and in new ways…

  9. CEM-designer: design of custom expression microarrays in the post-ENCODE Era.

    PubMed

    Arnold, Christian; Externbrink, Fabian; Hackermüller, Jörg; Reiche, Kristin

    2014-11-10

    Microarrays are widely used in gene expression studies, and custom expression microarrays are popular to monitor expression changes of a customer-defined set of genes. However, the complexity of transcriptomes uncovered recently make custom expression microarray design a non-trivial task. Pervasive transcription and alternative processing of transcripts generate a wealth of interweaved transcripts that requires well-considered probe design strategies and is largely neglected in existing approaches. We developed the web server CEM-Designer that facilitates microarray platform independent design of custom expression microarrays for complex transcriptomes. CEM-Designer covers (i) the collection and generation of a set of unique target sequences from different sources and (ii) the selection of a set of sensitive and specific probes that optimally represents the target sequences. Probe design itself is left to third party software to ensure that probes meet provider-specific constraints. CEM-Designer is available at http://designpipeline.bioinf.uni-leipzig.de. Copyright © 2014 Elsevier B.V. All rights reserved.

  10. Meeting Report: The Role of the Mobilome in Cancer

    PubMed Central

    Ardeljan, Daniel; Taylor, Martin S.; Burns, Kathleen H.; Boeke, Jef D.; Espey, Michael Graham; Woodhouse, Elisa C.; Howcroft, T. Kevin

    2016-01-01

    Approximately half of the human genome consists of repetitive sequence attributed to the activities of mobile DNAs, including DNA transposons, RNA transposons, and endogenous retroviruses. Of these, only Long INterspersed Elements (LINE-1 or L1) and sequences copied by LINE-1 remain mobile in our species today. Although cells restrict L1 activity by both transcriptional and post-transcriptional mechanisms, L1 de-repression occurs in developmental and pathologic contexts, including many types of cancers. However, we have limited knowledge of the extent and consequences of L1 expression in premalignancies and cancer. Participants in this NIH strategic workshop considered key questions to enhance our understanding of mechanisms and roles the mobilome may play in cancer biology. PMID:27527733

  11. Meet the terminator: The phosphatase PP2A puts brakes on IRF-3 activation.

    PubMed

    Chattopadhyay, Saurabh; Sen, Ganes C

    2014-04-24

    Cellular interferon response to microbial infection is transient. In a recent paper in Immunity, Long et al. (2014) identify protein phosphatase 2A (PP2A) as a deactivator of phospho-interferon regulatory factor 3, the key transcription factor for interferon synthesis, thus providing one basis for the observed transiency. Copyright © 2014 Elsevier Inc. All rights reserved.

  12. Tweeting the Meeting: Twitter Use at The American Society of Breast Surgeons Annual Meeting 2013-2016.

    PubMed

    Attai, Deanna J; Radford, Diane M; Cowher, Michael S

    2016-10-01

    Twitter social media is being used to disseminate medical meeting information. Meeting attendees and other interested parties have the ability to follow and participate in conversations related to meeting content. We analyzed Twitter activity generated from the 2013-2016 American Society of Breast Surgeons Annual Meetings. The Symplur Signals database was used to determine number of tweets, tweets per user, and impressions for each meeting. The number of unique physicians, patients/caregivers/advocates, and industry participants was determined. Physician tweeters were cross-referenced with membership and attendance rosters. Tweet transcripts were analyzed for content and tweets were categorized as either scientific, social, administrative, industry promotion, or irrelevant. From 2013 to 2016, the number of tweets increased by 600 %, the number of Twitter users increased by 450 %, and the number of physician tweeters increased by 457 %. The number of impressions (tweets × followers) increased from more than 3.5 million to almost 20.5 million, an increase of 469 %. The majority of tweets were informative (70-80 %); social tweets ranged from 13 to 23 %. A small percentage (3-6 %) of tweets were related to administrative matters. There were very few industry or irrelevant tweets. Twitter social media use at the American Society of Breast Surgeons annual meeting showed a substantial increase during the time period evaluated. The use of Twitter during professional meetings is a tremendous opportunity to share information. The authors feel that medical conference organizers should encourage Twitter participation and should be educating attendees on the proper use of Twitter.

  13. Aerobic glycolysis tunes YAP/TAZ transcriptional activity

    PubMed Central

    Enzo, Elena; Santinon, Giulia; Pocaterra, Arianna; Aragona, Mariaceleste; Bresolin, Silvia; Forcato, Mattia; Grifoni, Daniela; Pession, Annalisa; Zanconato, Francesca; Guzzo, Giulia; Bicciato, Silvio; Dupont, Sirio

    2015-01-01

    Increased glucose metabolism and reprogramming toward aerobic glycolysis are a hallmark of cancer cells, meeting their metabolic needs for sustained cell proliferation. Metabolic reprogramming is usually considered as a downstream consequence of tumor development and oncogene activation; growing evidence indicates, however, that metabolism on its turn can support oncogenic signaling to foster tumor malignancy. Here, we explored how glucose metabolism regulates gene transcription and found an unexpected link with YAP/TAZ, key transcription factors regulating organ growth, tumor cell proliferation and aggressiveness. When cells actively incorporate glucose and route it through glycolysis, YAP/TAZ are fully active; when glucose metabolism is blocked, or glycolysis is reduced, YAP/TAZ transcriptional activity is decreased. Accordingly, glycolysis is required to sustain YAP/TAZ pro-tumorigenic functions, and YAP/TAZ are required for the full deployment of glucose growth-promoting activity. Mechanistically we found that phosphofructokinase (PFK1), the enzyme regulating the first committed step of glycolysis, binds the YAP/TAZ transcriptional cofactors TEADs and promotes their functional and biochemical cooperation with YAP/TAZ. Strikingly, this regulation is conserved in Drosophila, where phosphofructokinase is required for tissue overgrowth promoted by Yki, the fly homologue of YAP. Moreover, gene expression regulated by glucose metabolism in breast cancer cells is strongly associated in a large dataset of primary human mammary tumors with YAP/TAZ activation and with the progression toward more advanced and malignant stages. These findings suggest that aerobic glycolysis endows cancer cells with particular metabolic properties and at the same time sustains transcription factors with potent pro-tumorigenic activities such as YAP/TAZ. PMID:25796446

  14. Targeting MUC1-Mediated Tumor-Stromal Metabolic Interaction in Triple-Negative Breast Cancer

    DTIC Science & Technology

    2014-10-01

    to MUC1 interaction with hypoxia-inducible factor alpha (HIF1α), a key regulator of glycolysis . We previously observed that ectopic overexpression of...nuclear localization and transcriptional activation of the cytoplasmic tail of MUC1. Additionally, MUC1 enhanced glutamine uptake that was increased...rate (OCR) and extracellular acidification rate (ECAR), indicative of cells utilizing glycolysis and/or oxidative phosphorylation to meet energy

  15. Responsiveness summary, bomarc missile site proposed plan. Final report, November 1989-May 1992

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Vest, G.

    1992-11-20

    A Public Meeting on the United States Air Force proposed plan for the clean-up of contamination at the BOMARC Missile Site, McGuire Air Force Base, New Jersey was conducted at Fort Dix, Now Jersey on June 20, 1992. A summary of responses to comments provided at the Public Meeting is provided. Responses to written comments are provided. A transcript of the public hearing is provided as Appendix A. A copy of all letters provided to the United States Air Force are provided as Appendix B. The BOMARC Missile Site became contaminated in 1960 as the result of a fire whichmore » partially consumed a nuclear warhead-equipped BOMARC missile.« less

  16. 2004 Environmental Mutagen Society Annual Meeting - Genes, Mutations and Disease: The Environmental Connection

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Samson, Leona D.

    2004-08-23

    The Meeting consisted of 9 Symposia, 4 Keynote Lectures, 3 Platform Sessions and 4 Poster Sessions. In addition there were Breakfast Meetings for Special Interest Groups designed to inform attendees about the latest advances in environmental mutagenesis research. Several of the topics to be covered at this broad meeting will be of interest to the Department of Energy, Office of Science. The relevance of this meeting to the DOE derives from the fact that low dose radiation may represent one of the most significant sources of human mutations that are attributable to the environment. The EMS membership, and those whomore » attended the EMS Annual Meeting were interested in both chemical and radiation induced biological effects, such as cell death, mutation, teratogenesis, carcinogenesis and aging. These topics thate were presented at the 2004 EMS Annual meeting that were of clear interest to DOE include: human variation in cancer susceptibility, unusual mechanisms of mutation, germ and stem cell mutagenesis, recombination and the maintenance of genomic stability, multiple roles for DNA mismatch repair, DNA helicases, mutation, cancer and aging, Genome-wide transcriptional responses to environmental change, Telomeres and genomic stability: when ends don?t meet, systems biology approach to cell phenotypic decision processes, and the surprising biology of short RNAs. Poster and platform sessions addressed topics related to environmental mutagen exposure, DNA repair, mechanisms of mutagenesis, epidemiology, genomic and proteomics and bioinformatics. These sessions were designed to give student, postdocs and more junior scientists a chance to present their work.« less

  17. Speaker diarization system on the 2007 NIST rich transcription meeting recognition evaluation

    NASA Astrophysics Data System (ADS)

    Sun, Hanwu; Nwe, Tin Lay; Koh, Eugene Chin Wei; Bin, Ma; Li, Haizhou

    2007-09-01

    This paper presents a speaker diarization system developed at the Institute for Infocomm Research (I2R) for NIST Rich Transcription 2007 (RT-07) evaluation task. We describe in details our primary approaches for the speaker diarization on the Multiple Distant Microphones (MDM) conditions in conference room scenario. Our proposed system consists of six modules: 1). Least-mean squared (NLMS) adaptive filter for the speaker direction estimate via Time Difference of Arrival (TDOA), 2). An initial speaker clustering via two-stage TDOA histogram distribution quantization approach, 3). Multiple microphone speaker data alignment via GCC-PHAT Time Delay Estimate (TDE) among all the distant microphone channel signals, 4). A speaker clustering algorithm based on GMM modeling approach, 5). Non-speech removal via speech/non-speech verification mechanism and, 6). Silence removal via "Double-Layer Windowing"(DLW) method. We achieves error rate of 31.02% on the 2006 Spring (RT-06s) MDM evaluation task and a competitive overall error rate of 15.32% for the NIST Rich Transcription 2007 (RT-07) MDM evaluation task.

  18. Identifying Stress Transcription Factors Using Gene Expression and TF-Gene Association Data

    PubMed Central

    Wu, Wei-Sheng; Chen, Bor-Sen

    2007-01-01

    Unicellular organisms such as yeasts have evolved to survive environmental stresses by rapidly reorganizing the genomic expression program to meet the challenges of harsh environments. The complex adaptation mechanisms to stress remain to be elucidated. In this study, we developed Stress Transcription Factor Identification Algorithm (STFIA), which integrates gene expression and TF-gene association data to identify the stress transcription factors (TFs) of six kinds of stresses. We identified some general stress TFs that are in response to various stresses, and some specific stress TFs that are in response to one specific stress. The biological significance of our findings is validated by the literature. We found that a small number of TFs may be sufficient to control a wide variety of expression patterns in yeast under different stresses. Two implications can be inferred from this observation. First, the adaptation mechanisms to different stresses may have a bow-tie structure. Second, there may exist extensive regulatory cross-talk among different stress responses. In conclusion, this study proposes a network of the regulators of stress responses and their mechanism of action. PMID:20066130

  19. "Could you sit down please?" A qualitative analysis of employees' experiences of standing in normally-seated workplace meetings.

    PubMed

    Mansfield, Louise; Hall, Jennifer; Smith, Lee; Rasch, Molly; Reeves, Emily; Dewitt, Stephen; Gardner, Benjamin

    2018-01-01

    Office workers spend most of their working day sitting, and prolonged sitting has been associated with increased risk of poor health. Standing in meetings has been proposed as a strategy by which to reduce workplace sitting but little is known about the standing experience. This study documented workers' experiences of standing in normally seated meetings. Twenty-five participants (18+ years), recruited from three UK universities, volunteered to stand in 3 separate, seated meetings that they were already scheduled to attend. They were instructed to stand when and for however long they deemed appropriate, and gave semi-structured interviews after each meeting. Verbatim transcripts were analysed using Framework Analysis. Four themes, central to the experience of standing in meetings, were extracted: physical challenges to standing; implications of standing for meeting engagement; standing as norm violation; and standing as appropriation of power. Participants typically experienced some physical discomfort from prolonged standing, apparently due to choosing to stand for as long as possible, and noted practical difficulties of fully engaging in meetings while standing. Many participants experienced marked psychological discomfort due to concern at being seen to be violating a strong perceived sitting norm. While standing when leading the meeting was felt to confer a sense of power and control, when not leading the meeting participants felt uncomfortable at being misperceived to be challenging the authority of other attendees. These findings reveal important barriers to standing in normally-seated meetings, and suggest strategies for acclimatising to standing during meetings. Physical discomfort might be offset by building standing time slowly and incorporating more sit-stand transitions. Psychological discomfort may be lessened by notifying other attendees about intentions to stand. Organisational buy-in to promotional strategies for standing may be required to dispel perceptions of sitting norms, and to progress a wider workplace health and wellbeing agenda.

  20. Archaea: From Genomics to Physiology and the Origin of Life

    NASA Technical Reports Server (NTRS)

    Vothknecht, Ute C.; Tumbula, Debra L.

    1999-01-01

    This document represents a report on a meeting about Archaea. The meeting had an unusually diversified mix of topics all related to Archaea highlighting their differences and similarities with other kingdoms of life. Thus, a large number of scientists from others areas of biology participated in this conference. One-third of the speakers (11 of 33) represented laboratories whose main interests have not been archaea and who have not previously participated in similar symposia or workshops. Thus, this symposium provided a unique opportunity for archaeal researchers to interact in a wider forum. Because of the broad range of topics covered, the conference also introduced many of the participants to new areas of archaeal research. The discussions of genomics, molecular mechanisms of transcription, metabolic pathways and evolution were at a very high level. Talks and posters provided detailed discussions of the state of the current knowledge in RNA processing, transcriptional initiation, chromatin structure, aminoacyl-tRNA synthetases, autotrophic CO2 fixation, Upid biosynthesis and a wide range of other topics. In addition to providing overviews, major areas of scientific argument were clearly delineated, particularly in the discussions of genomics and evolution. Some of the questions raised included: how representative are individual gene trees of organismal evolution, how prevalent is horizontal evolution, how reliable are functional assignments in genomics? On these topics, the different points of view were well represented. The future of any field depends on the enthusiasm and intellectual engagement of young scientists working in the area. Therefore, the participation of 29 graduate and postdoctoral students (out of about 135 participants) was a highlight of the meeting. This was the consequence of funding contributions by NSF and NASA.

  1. White House Technology Reinvestment Project Briefing And Transcripts

    DTIC Science & Technology

    1993-04-12

    commercial standard accounting NASA, and the Air Force, to develop an entirely new practices meeting Generally Accepted Accounting class of materials for use...diversion, and what we’ll call new very effective public servants. We are product development . This is not going extremely impressed with them. I can... develop new products and new demonstrably our nation’s competitive, markets. This project has generated enormous By supporting innovative interest in the

  2. Annexin V-MACS in infertile couples as method for separation of sperm without DNA fragmentation.

    PubMed

    Troya, Jhon; Zorrilla, Ingrid

    2015-05-01

    To determine the effect of using MACS technology on clinical pregnancy, as a method for separation of damaged sperm in infertile patients. 136 infertile men having normal semen parameters in accordance with WHO 2010 criterion, undergoing ICSI cycle were enrolled during the course of the study. The patients were prospectively randomized and enrolled after oocyte retrieval and were assigned to the ICSI group, PICSI group or MACS group. Embryo development and clinical pregnancy were assessed. In 17 randomized MACS patients, sperm DNA fragmentation was tested in the presumptive apoptotic and no apoptotic spermatozoa fractions. Similar results were obtained between groups for the following parameters: fertilization rates of 78.97% (95% confidence interval [CI]:74.37-83.57), 70.15 %(95% CI:63.98-76.33) and 80.28%(95% CI:73.74-86.81) for ICSI, PICSI and MACS group, respectively; Number of Day-3 embryos was 5.04 (95% CI:4.09-5.98), 5.17(95% CI:4.24-6.10) and 5.59(95% CI:4.31-6.87) for ICSI, PICSI and MACS group, respectively; number of freezing embryos in blastocyst stage was 0.78 (95% CI:0.25- 1.31), 0.70(95% CI:0.27-1.14) and 1 (95% CI:0.37-1.6) for ICSI, PICSI and MACS group, respectively. However, clinical pregnancy rates of 58.1% for MACS group versus 40.4% and 27.3% for PICSI and ICSI group, respectively, were showed statistical difference (P=0.019). DNA fragmentation index for the two sperm MACS fraction showed statistical differences (P=0.000), MACS reduced the D.F.I of the sperm sample. The use of MACS technology improves the clinical pregnancy on infertile couples and can be applied as a method for sperm separation, discriminating sperm with high DNA fragmentation.

  3. Quantitative Detection of Low-Abundance Transcripts at Single-Cell Level in Human Epidermal Keratinocytes by Digital Droplet Reverse Transcription-Polymerase Chain Reaction.

    PubMed

    Auvré, Frédéric; Coutier, Julien; Martin, Michèle T; Fortunel, Nicolas O

    2018-05-08

    Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized. Accordingly, there is presently great demand for methods and technologies enabling molecular investigation at single-cell level. Also, most current methods used to analyze gene expression at RNA level, such as RT-qPCR, do not directly provide quantitative data, but rather comparative ratios between two conditions. A second important need in skin biology is thus to determine the number of RNA molecules in a given cell sample. Here, we describe a workflow that we have set up to meet these specific needs, by means of transcript quantification in cellular micro-samples using flow cytometry sorting and reverse transcription-digital droplet polymerase chain reaction. As a proof-of-principle, the workflow was tested for the detection of transcription factor transcripts expressed at low levels in keratinocyte precursor cells. A linear correlation was found between quantification values and keratinocyte input numbers in a low quantity range from 40 cells to 1 cell. Interpretable signals were repeatedly obtained from single-cell samples corresponding to estimated expression levels as low as 10-20 transcript copies per keratinocyte or less. The present workflow may have broad applications for the detection and quantification of low-abundance nucleic acid species in single cells, opening up perspectives for the study of cell-to-cell genetic and molecular heterogeneity. Interestingly, the process described here does not require internal references such as house-keeping gene expression, as it is initiated with defined cell numbers, precisely sorted by flow cytometry.

  4. Meeting on flows of granular materials in complex geometries

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Passman, S.L.; Fukushima, E.; Evans, R.E.

    1994-11-01

    The International Energy Agency Fossil Fuel Multiphase Flow Sciences Agreement has been in effect since 1986. The traditional mechanism for the effort has been information exchange, effected by the inclusion of scientists in annual Executive committee meetings, by exchange of reports and papers, and by visits of scientists to one another`s institutions. In a sequence of informal meetings and at the 1993 Executive committee meeting, held in Pittsburgh, US in March 1994, it was decided that more intensive interactions could be productive. A candidate for such interactions would be specific projects. Each of these would be initiated through a meetingmore » of scientists in which feasibility of the particular project was decided, followed by relatively intense international co-operation in which the work would be done. This is a report of the first of these meetings. Official or unofficial representatives from Canada, italy, japan, mexico, the United Kingdom, and the US met in Albuquerque, New Mexico, US, to consider the subject Flows of Granular Materials in Complex Geometries. Representatives of several other countries expressed interest but were unable to attend this meeting. Sixteen lectures were given on aspects of this topic. It was decided that a co-operative effort was desirable and possible. The most likely candidate for the area of study would be flows in bins and hoppers. Each of the countries wishing to co-operate will pursue funding for its effort. This report contains extended abstracts of the sixteen presentations and a transcription of the final discussion.« less

  5. Oncologic Drugs Advisory Committee Recommendations and Approval of Cancer Drugs by the US Food and Drug Administration.

    PubMed

    Tibau, Ariadna; Ocana, Alberto; Anguera, Geòrgia; Seruga, Bostjan; Templeton, Arnoud J; Barnadas, Agustí; Amir, Eitan

    2016-06-01

    The US Food and Drug Administration (FDA) advisory committees influence decisions relating to the regulatory approval of drugs in the United States. Outside of the field of oncology, prosponsor voting bias has been observed among members with financial conflicts of interest (FCOIs). To explore factors associated with Oncologic Drugs Advisory Committee (ODAC) recommendations and the influence ODAC members' FCOIs on the drug approval process. Retrospective analysis of 82 ODAC meeting transcripts between January 2000 and December 2014. Analysis was restricted to meetings at which votes were cast relating to oncologic drugs. The influence of methodology of trials supporting approval and frequency and type of self-reported FCOIs of voting members was explored using logistic regression. ODAC recommendation for drug approval and subsequent FDA approval. Eighty-two transcripts of ODAC meetings between January 2000 and December 2014 were available for analysis. During the time period analyzed, ODAC members voted on 68 applications in 79 meetings (the remaining 3 meetings included voting questions regarding postmarketing safety or trial design). There was agreement between ODAC recommendations and final FDA approval; FDA approval was received for all 41 drugs that ODAC recommended approval. Additionally, the FDA approved 7 out of 41 agents that were not recommended for approval by ODAC (κ = 0.83). In 51 of 79 meetings, more than 1 trial was available to support the indication of a particular drug, and favorable ODAC recommendations were more likely when this was the case (odds ratio [OR], 1.82; 95% CI, 1.19-2.78; P = .01). Availability of randomized data did not appear to be important with selected single-arm phase 2 trials leading to recommendations for approval, especially in rare diseases. There has been a significant reduction in FCOIs over time (31 of 77 voting members [40%] in 2000 vs 0 of 20 voting members in 2014 [0%]; P < .001). Recommendations for approval were made in 28 of 47 meetings with members reporting FCOIs while among meetings with no reported FCOIs, recommendations for approval were made in 13 of 35 meetings (OR, 1.19; 95% CI, 0.97-1.46; P = .10). No significant association between ODAC recommendations and FDA approval was observed for members with FCOIs with the sponsor (OR, 1.79; 95% CI, 0.97-1.46; P = .19 and OR, 3.48; 95% CI, 0.84-14.35; P = .09, respectively) compared with members with FCOIs with competitors (OR, 1.06; 95% CI, 0.78-1.44; P = .72 and OR, 0.94; 95% CI, 0.69-1.28; P = .69, respectively). Availability of multiple trials is associated with higher odds of ODAC recommendation and drug approval. Availability of randomized data appears less important. Declaration of FCOIs among ODAC members was frequent during the time period of interest but has decreased significantly over time. There is no apparent association between FCOIs and ODAC recommendations and subsequent FDA approval.

  6. Non-metabolic functions of glycolytic enzymes in tumorigenesis.

    PubMed

    Yu, X; Li, S

    2017-05-11

    Cancer cells reprogram their metabolism to meet the requirement for survival and rapid growth. One hallmark of cancer metabolism is elevated aerobic glycolysis and reduced oxidative phosphorylation. Emerging evidence showed that most glycolytic enzymes are deregulated in cancer cells and play important roles in tumorigenesis. Recent studies revealed that all essential glycolytic enzymes can be translocated into nucleus where they participate in tumor progression independent of their canonical metabolic roles. These noncanonical functions include anti-apoptosis, regulation of epigenetic modifications, modulation of transcription factors and co-factors, extracellular cytokine, protein kinase activity and mTORC1 signaling pathway, suggesting that these multifaceted glycolytic enzymes not only function in canonical metabolism but also directly link metabolism to epigenetic and transcription programs implicated in tumorigenesis. These findings underscore our understanding about how tumor cells adapt to nutrient and fuel availability in the environment and most importantly, provide insights into development of cancer therapy.

  7. Coordinated regulation of photosynthesis in rice increases yield and tolerance to environmental stress

    PubMed Central

    Ambavaram, Madana M. R.; Basu, Supratim; Krishnan, Arjun; Ramegowda, Venkategowda; Batlang, Utlwang; Rahman, Lutfor; Baisakh, Niranjan; Pereira, Andy

    2014-01-01

    Plants capture solar energy and atmospheric carbon dioxide (CO2) through photosynthesis, which is the primary component of crop yield, and needs to be increased considerably to meet the growing global demand for food. Environmental stresses, which are increasing with climate change, adversely affect photosynthetic carbon metabolism (PCM) and limit yield of cereals such as rice (Oryza sativa) that feeds half the world. To study the regulation of photosynthesis, we developed a rice gene regulatory network and identified a transcription factor HYR (HIGHER YIELD RICE) associated with PCM, which on expression in rice enhances photosynthesis under multiple environmental conditions, determining a morpho-physiological programme leading to higher grain yield under normal, drought and high-temperature stress conditions. We show HYR is a master regulator, directly activating photosynthesis genes, cascades of transcription factors and other downstream genes involved in PCM and yield stability under drought and high-temperature environmental stress conditions. PMID:25358745

  8. Plant developmental biologists meet on stairways in Matera.

    PubMed

    Beeckman, Tom; Friml, Jiri

    2012-10-01

    The third EMBO Conference on Plant Molecular Biology, which focused on 'Plant development and environmental interactions', was held in May 2012 in Matera, Italy. Here, we review some of the topics and themes that emerged from the various contributions; namely, steering technologies, transcriptional networks and hormonal regulation, small RNAs, cell and tissue polarity, environmental control and natural variation. We intend to provide the reader who might have missed this remarkable event with a glimpse of the recent progress made in this blossoming research field.

  9. FROM THE HISTORY OF PHYSICS: Stories by Yurii Borisovich Rumer

    NASA Astrophysics Data System (ADS)

    Rumer, Yurii B.

    2001-10-01

    Yurii Borisovich Rumer (Yu B) was an excellent story-teller. Grateful listeners long remembered his stories about life in the first years after the 1917 Great Socialist Revolution in Russia, about the Göttingen School, about Albert Einstein, about Soviet physicists, about the years he spent in prison and in the secret research institution where all researchers and staff were prisoners. Unfortunately, nobody was perceptive enough to record these stories for posterity. Yu B himself would not agree to it as after the many years of his gruesome prison experience he was always cautious and carefully censored his stories himself according to the audience and the political climate of the period. The few reminiscences published in his lifetime also exhibit evidence of such self-censorship. M P Kemoklidze made detailed records but she says she destroyed them after publishing the book Quantum age (1989) for which they were intended. Here we are publishing a transcript of the tape recording made by Anna Livanova in 1962 when Yu B visited her in Moscow (she knew him from her days as a student of the Physics Department of Moscow State University). When Livanova was on a business trip to the Novosibirsk Academy Town she attended a talk given by Yu B to the students of Novosibirsk University at which they asked him to tell of the most important occasion in his life. He said it was his meeting with Einstein. In Moscow Livanova recorded an extended version of that talk. Livanova used the recording for writing the essays ''Academy Town in Siberia'' (Znamya magazine, No. 11, 12, 1962) and ''Physicists about Physicists'' (in the book Roads to the Unknown — Writers Telling about Science in which a section was entitled 'Meeting with Einstein'), and her book 'Physicists about Physicists' (Moscow: 'Molodaya Gvardiya' Publishers, 1968) which also included a section on Rumer's meeting with Einstein. The publications were significantly edited and only a part of the recording transcript was used. It was the unflagging support of L V Al'tshuler and the technical assistance rendered by his grandchildren that made it possible to resurrect the old magnetic tape and make a new transcript. Of course, the stories often repeated by Yu B who referred to them as my 'discs' include some inconsistencies caused by lapses of memory. They present a lively picture of the science community and its life, however, as well as a congenial portrait of the story-teller himself. When we prepared the transcript for publication we practically did not edit it. We believe that the emotional and expressive story presented in exactly the way it was told with inevitable slips and errors better conveys the stirring atmosphere of those distant events than a polished and verified historical treatise. We deciphered the passages on the tapes that were difficult to make out from our personal recollections of Rumer's stories and added our comments to the text. I F Ginzburg, M Yu Mikhailov (Rumer)

  10. Monitoring CML patients responding to treatment with tyrosine kinase inhibitors: review and recommendations for harmonizing current methodology for detecting BCR-ABL transcripts and kinase domain mutations and for expressing results

    PubMed Central

    Hughes, Timothy; Deininger, Michael; Hochhaus, Andreas; Branford, Susan; Radich, Jerald; Kaeda, Jaspal; Baccarani, Michele; Cortes, Jorge; Cross, Nicholas C. P.; Druker, Brian J.; Gabert, Jean; Grimwade, David; Hehlmann, Rüdiger; Kamel-Reid, Suzanne; Lipton, Jeffrey H.; Longtine, Janina; Martinelli, Giovanni; Saglio, Giuseppe; Soverini, Simona; Stock, Wendy; Goldman, John M.

    2006-01-01

    The introduction in 1998 of imatinib mesylate (IM) revolutionized management of patients with chronic myeloid leukemia (CML) and the second generation of tyrosine kinase inhibitors may prove superior to IM. Real-time quantitative polymerase chain reaction (RQ-PCR) provides an accurate measure of the total leukemiacell mass and the degree to which BCR-ABL transcripts are reduced by therapy correlates with progression-free survival. Because a rising level of BCR-ABL is an early indication of loss of response and thus the need to reassess therapeutic strategy, regular molecular monitoring of individual patients is clearly desirable. Here we summarize the results of a consensus meeting that took place at the National Institutes of Health (NIH) in Bethesda in October 2005. We make suggestions for (1) harmonizing the differing methodologies for measuring BCR-ABL transcripts in patients with CML undergoing treatment and using a conversion factor whereby individual laboratories can express BCR-ABL transcript levels on an internationally agreed scale; (2) using serial RQ-PCR results rather than bone marrow cytogenetics or fluorescence in situ hybridization (FISH) for the BCR-ABL gene to monitor individual patients responding to treatment; and (3) detecting and reporting Philadelphia (Ph) chromosome-positive subpopulations bearing BCR-ABL kinase domain mutations. We recognize that our recommendations are provisional and will require revision as new evidence emerges. (Blood. 2006;108:28-37) PMID:16522812

  11. Qualitative Analysis of Resources and Barriers for Borderline Personality Disorder in the U.S.

    PubMed Central

    Lohman, Matthew C.; Whiteman, Karen L.; Yeomans, Frank E.; Cherico, Sheila A.; Christ, Winifred R.

    2016-01-01

    Objective Resources and treatment for individuals with borderline personality disorder (BPD) are limited and often difficult to obtain. Experiences and preferences of individuals seeking care are seldom examined but important elements in determining challenges to obtaining appropriate care. This article aimed to identify key resources for and barriers to obtaining supportive and treatment services for BPD, from the perspective of individuals seeking care. Methods Data came from transcripts of resource requests made to the Borderline Personality Disorder Resource Center from January 2008 to December 2015 (N=6,253). Basic statistics regarding requested BPD service types, demographic information, and national distribution of requests were generated for all eligible transcripts. Qualitative analysis was used to identify themes, challenges, and common experiences reported among a random subset of those seeking services (N=500). Results Primary services or resources requested were outpatient services (51%), informational materials (13%), and daycare programs (9%). Care-seekers identified family services, crisis intervention, and mental health literacy as areas where available resources did not meet current demand and which could be improved and/or expanded. Factors identified as potential barriers to finding and obtaining appropriate treatment for BPD included stigmatization and marginalization within mental healthcare systems, financial concerns, and comorbidity with psychiatric or medical disorders. Conclusions Individuals seeking supportive services and treatment for BPD face numerous barriers to obtaining appropriate care. Expanded services and resources to connect individuals with treatment are needed to meet the current demands and preferences of those seeking care. PMID:27691382

  12. The Role of Retinal Determination Gene Network (RDGN) in Hormone Signaling Transduction and Prostate Tumorigenesis

    DTIC Science & Technology

    2013-10-01

    Wu K, Wang L, Jiao X, Ju X, Li Z, Ertel A, Addya S, McCue P, Lisanti MP, Wang C, Davis RJ, Mardon G, Pestell RG. Androgen therapy resistant...Li Z, Hu J, Chen K, Wu J, Pestell RG. DACH1 inhibited prostate cancer cellular proliferation and Interleukon-6 signaling. AACR 103rd Annual Meeting...March 31 – April 4, 2012, Chicago, IL.  Wang J, Cai S, Chen K, Sun Y, Li S, Pestell RG, Wu K. Regulation of AR transcriptional activity and

  13. First Lady praises California for work in health care debate.

    PubMed

    Clinton, H R

    1993-01-01

    Hillary Rodham Clinton called California's health care delivery system a model for the nation during a live teleconference at the CAHHS Annual Meeting Oct. 13 in San Diego. In her first-ever address before a state hospital association, the first lady told nearly 1,000 people that California "has its own place of honor in the health care debate" and praised the state for being "years ahead of Washington (D.C.) in recognizing what's right about American health care." What follows is the transcript from her address.

  14. Opportunities During Early Life for Cancer Prevention: Highlights From a Series of Virtual Meetings With Experts

    PubMed Central

    Holman, Dawn M.; Buchanan, Natasha D.

    2018-01-01

    Compelling evidence suggests that early life exposures can affect lifetime cancer risk. In 2014, the Centers for Disease Control and Prevention’s (CDC’s) Cancer Prevention Across the Lifespan Workgroup hosted a series of virtual meetings with select experts to discuss the state of the evidence linking factors during the prenatal period and early childhood to subsequent risk of both pediatric and adult cancers. In this article, we present the results from a qualitative analysis of the meeting transcripts and summarize themes that emerged from our discussions with meeting participants. Themes included the state of the evidence linking early life factors to cancer risk, research gaps and challenges, the level of evidence needed to support taking public health action, and the challenges of communicating complex, and sometimes conflicting, scientific findings to the public. Opportunities for collaboration among public health agencies and other stakeholders were identified during these discussions. Potential next steps for the CDC and its partners included advancing and building upon epidemiology and surveillance work, developing and using evidence from multiple sources to inform decision-making, disseminating and communicating research findings in a clear and effective way, and expanding collaborations with grantees and other partners. As the science on early life factors and cancer risk continues to evolve, there are opportunities for collaboration to translate science into actionable public health practice. PMID:27940972

  15. Moving Technology to the Center of Instruction: How One Experienced Teacher Incorporates a Web-based Environment Over Time

    NASA Astrophysics Data System (ADS)

    Williams, Michelle

    2008-08-01

    The paper reports on a 3-year study of an experienced fifth grade teacher learning to integrate a Web-based Inquiry Science Environment (WISE) into his core science instruction. Data from this study included videotapes and transcripts of classroom instruction, and audiotapes and transcripts of professional development meetings and interviews conducted with the teacher as he was implementing the curriculum. The results suggest that the teacher's classroom practices shifted meaningfully over time, thus moving WISE from the peripheral to the center of his science class instruction. There was an increased integrated use of the technology by this teacher during the WISE enactments in years two and three. The teacher also engaged his students in significantly more science dialogues during the WISE online investigations. Further findings suggest that this shift in pedagogy can be attributed to repeated opportunities for the instructor to teach an inquiry-based curriculum, as well as reflecting on his teaching experiences.

  16. Transcriptional and Cell Cycle Alterations Mark Aging of Primary Human Adipose-Derived Stem Cells.

    PubMed

    Shan, Xiaoyin; Roberts, Cleresa; Kim, Eun Ji; Brenner, Ariana; Grant, Gregory; Percec, Ivona

    2017-05-01

    Adult stem cells play a critical role in the maintenance of tissue homeostasis and prevention of aging. While the regenerative potential of stem cells with low cellular turnover, such as adipose-derived stem cells (ASCs), is increasingly recognized, the study of chronological aging in ASCs is technically difficult and remains poorly understood. Here, we use our model of chronological aging in primary human ASCs to examine genome-wide transcriptional networks. We demonstrate first that the transcriptome of aging ASCs is distinctly more stable than that of age-matched fibroblasts, and further, that age-dependent modifications in cell cycle progression and translation initiation specifically characterize aging ASCs in conjunction with increased nascent protein synthesis and a distinctly shortened G1 phase. Our results reveal novel chronological aging mechanisms in ASCs that are inherently different from differentiated cells and that may reflect an organismal attempt to meet the increased demands of tissue and organ homeostasis during aging. Stem Cells 2017;35:1392-1401. © 2017 AlphaMed Press.

  17. Negative autoregulation matches production and demand in synthetic transcriptional networks.

    PubMed

    Franco, Elisa; Giordano, Giulia; Forsberg, Per-Ola; Murray, Richard M

    2014-08-15

    We propose a negative feedback architecture that regulates activity of artificial genes, or "genelets", to meet their output downstream demand, achieving robustness with respect to uncertain open-loop output production rates. In particular, we consider the case where the outputs of two genelets interact to form a single assembled product. We show with analysis and experiments that negative autoregulation matches the production and demand of the outputs: the magnitude of the regulatory signal is proportional to the "error" between the circuit output concentration and its actual demand. This two-device system is experimentally implemented using in vitro transcriptional networks, where reactions are systematically designed by optimizing nucleic acid sequences with publicly available software packages. We build a predictive ordinary differential equation (ODE) model that captures the dynamics of the system and can be used to numerically assess the scalability of this architecture to larger sets of interconnected genes. Finally, with numerical simulations we contrast our negative autoregulation scheme with a cross-activation architecture, which is less scalable and results in slower response times.

  18. Risk and Exploration: Earth, Sea and Stars

    NASA Technical Reports Server (NTRS)

    Dick, Steven J. (Editor); Cowing, Keith L. (Editor)

    2005-01-01

    The NASA History Division is pleased to present the record of a unique meeting on risk and exploration held under the auspices of the NASA Administrator, Sean O Keefe, at the Naval Postgraduate School in Monterey, California, from September 26-29, 2004. The meeting was the brainchild of Keith Cowing and astronaut John Grunsfeld, NASA's chief scientist at the time. Its goals, stated in the letter of invitation published herein, were precipitated by the ongoing dialogue on risk and exploration in the wake of the Columbia Shuttle accident, the Hubble Space Telescope servicing question, and, in a broader sense, by the many NASA programs that inevitably involve a balance between risk and forward-looking exploration. The meeting, extraordinarily broad in scope and participant experience, offers insights on why we explore, how to balance risk and exploration, how different groups defi ne and perceive risk differently, and the importance of exploration to a creative society. At NASA Headquarters, Bob Jacobs, Trish Pengra, and Joanna Adamus of NASA Public Affairs led the meeting's implementation. The Naval Postgraduate School, commanded by Rear Admiral Patrick W. Dunne, provided a congenial venue. The meeting was broadcast on NASA TV, and thanks are due in this regard to Al Feinberg, Tony Stewart, Jim Taylor, and the planners collaborative: Mark Shaddock and Spotlight Productions, Donovan Gates of Donovan Gates Production, and Michael Ditertay and his staff on this 30-person television crew. Thanks to their efforts, a DVD record of the meeting has also been produced. Thanks are also due to the moderators: Miles O Brien of CNN, Chris McKay of NASA Ames, David Halpern of the White House Office of Science and Technology Policy, and John Grunsfeld, NASA Headquarters. In order to maintain the informal flavor of the meetings, these proceedings are based on transcripts that have been lightly edited for grammar and punctuation. Most references to slides shown during the presentations have been deleted.

  19. Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Papoutsakis, Elefterios

    This is the final project report for project "Experimental Systems-Biology Approaches for Clostridia-Based Bioenergy Production" for the funding period of 9/1/12 to 2/28/2015 (three years with a 6-month no-cost extension) OVERVIEW AND PROJECT GOALS The bottleneck of achieving higher rates and titers of toxic metabolites (such as solvents and carboxylic acids that can used as biofuels or biofuel precursors) can be overcome by engineering the stress response system. Thus, understanding and modeling the response of cells to toxic metabolites is a problem of great fundamental and practical significance. In this project, our goal is to dissect at the molecular systemsmore » level and build models (conceptual and quantitative) for the stress response of C. acetobutylicum (Cac) to its two toxic metabolites: butanol (BuOH) and butyrate (BA). Transcriptional (RNAseq and microarray based), proteomic and fluxomic data and their analysis are key requirements for this goal. Transcriptional data from mid-exponential cultures of Cac under 4 different levels of BuOH and BA stress was obtained using both microarrays (Papoutsakis group) and deep sequencing (RNAseq; Meyers and Papoutsakis groups). These two sets of data do not only serve to validate each other, but are also used for identification of stress-induced changes in transcript levels, small regulatory RNAs, & in transcriptional start sites. Quantitative proteomic data (Lee group), collected using the iTRAQ technology, are essential for understanding of protein levels and turnover under stress and the various protein-protein interactions that orchestrate the stress response. Metabolic flux changes (Antoniewicz group) of core pathways, which provide important information on the re-allocation of energy and carbon resources under metabolite stress, were examined using 13C-labelled chemicals. Omics data are integrated at different levels and scales. At the metabolic-pathway level, omics data are integrated into a 2nd generation genome-scale model (GSM) (Maranas group). Omics data are also integrated using bioinformatics (Wu and Huang group), whereby regulatory details of gene and protein expression, protein-protein interactions and metabolic flux regulation are incorporated. The PI (Papoutsakis) facilitated project integration through monthly meeting and reports, conference calls, and collaborative manuscript preparation. The five groups collaborated extensively and made a large number of presentations in national and international meetings. It has also published several papers, with several more in the preparation stage. Several PhD, MS and postdoctoral students were trained as part of this collaborative and interdisciplinary project.« less

  20. Open Source Subtitle Editor Software Study for Section 508 Close Caption Applications

    NASA Technical Reports Server (NTRS)

    Murphy, F. Brandon

    2013-01-01

    This paper will focus on a specific item within the NASA Electronic Information Accessibility Policy - Multimedia Presentation shall have synchronized caption; thus making information accessible to a person with hearing impairment. This synchronized caption will assist a person with hearing or cognitive disability to access the same information as everyone else. This paper focuses on the research and implementation for CC (subtitle option) support to video multimedia. The goal of this research is identify the best available open-source (free) software to achieve synchronized captions requirement and achieve savings, while meeting the security requirement for Government information integrity and assurance. CC and subtitling are processes that display text within a video to provide additional or interpretive information for those whom may need it or those whom chose it. Closed captions typically show the transcription of the audio portion of a program (video) as it occurs (either verbatim or in its edited form), sometimes including non-speech elements (such as sound effects). The transcript can be provided by a third party source or can be extracted word for word from the video. This feature can be made available for videos in two forms: either Soft-Coded or Hard-Coded. Soft-Coded is the more optional version of CC, where you can chose to turn them on if you want, or you can turn them off. Most of the time, when using the Soft-Coded option, the transcript is also provided to the view along-side the video. This option is subject to compromise, whereas the transcript is merely a text file that can be changed by anyone who has access to it. With this option the integrity of the CC is at the mercy of the user. Hard-Coded CC is a more permanent form of CC. A Hard-Coded CC transcript is embedded within a video, without the option of removal.

  1. GABP transcription factor is required for development of chronic myelogenous leukemia via its control of PRKD2.

    PubMed

    Yang, Zhong-Fa; Zhang, Haojian; Ma, Leyuan; Peng, Cong; Chen, Yaoyu; Wang, Junling; Green, Michael R; Li, Shaoguang; Rosmarin, Alan G

    2013-02-05

    Hematopoietic stem cells (HSCs) are the source of all blood lineages, and HSCs must balance quiescence, self-renewal, and differentiation to meet lifelong needs for blood cell development. Transformation of HSCs by the breakpoint cluster region-ABL tyrosine kinase (BCR-ABL) oncogene causes chronic myelogenous leukemia (CML). The E-twenty six (ets) transcription factor GA binding protein (GABP) is a tetrameric transcription factor complex that contains GABPα and GABPβ proteins. Deletion in bone marrow of Gabpa, the gene that encodes the DNA-binding component, caused cell cycle arrest in HSCs and profound loss of hematopoietic progenitor cells. Loss of Gabpα prevented development of CML, although mice continued to generate BCR-ABL-expressing Gabpα-null cells for months that were serially transplantable and contributed to all lineages in secondary recipients. A bioinformatic screen identified the serine-threonine kinase protein kinase D2 (PRKD2) as a potential effector of GABP in HSCs. Prkd2 expression was markedly reduced in Gabpα-null HSCs and progenitor cells. Reduced expression of PRKD2 or pharmacologic inhibition decreased cell cycling, and PRKD2 rescued growth of Gabpα-null BCR-ABL-expressing cells. Thus, GABP is required for HSC cell cycle entry and CML development through its control of PRKD2. This offers a potential therapeutic target in leukemia.

  2. Origin of the Wang-Sheeley-Arge solar wind model

    NASA Astrophysics Data System (ADS)

    Sheeley, Neil R., Jr.

    2017-03-01

    A correlation between solar wind speed at Earth and the amount of magnetic field line expansion in the corona was verified in 1989 using 22 years of solar and interplanetary observations. We trace the evolution of this relationship from its birth 15 years earlier in the Skylab era to its current use as a space weather forecasting technique. This paper is the transcript of an invited talk at the joint session of the Historical Astronomy Division and the Solar Physics Division of the American Astronomical Society during its 224th meeting in Boston, MA, on 3 June 2014.

  3. Comment on mRNA-Sequencing Analysis Reveals Transcriptional Changes in Root of Maize Seedlings Treated with Two Increasing Concentrations of a New Biostimulant.

    PubMed

    da Silva, Ronivaldo Rodrigues

    2018-02-28

    Overpopulation is already a reality, and the need for alternative technologies to meet a continuously increasing food demand has been much discussed around the world. In addition, soil decreasing fertility and desertification are obstacles that we will need to be overcome to increase crop productivity with a much-reduced dependence upon inorganic fertilizers. In this context, protein hydrolysates has emerged as an important strategy to reduce the use of inorganic fertilizers, whose applications as biostimulants for plant growth have shown very promising results.

  4. FlyPrimerBank: An Online Database for Drosophila melanogaster Gene Expression Analysis and Knockdown Evaluation of RNAi Reagents

    PubMed Central

    Hu, Yanhui; Sopko, Richelle; Foos, Marianna; Kelley, Colleen; Flockhart, Ian; Ammeux, Noemie; Wang, Xiaowei; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E.

    2013-01-01

    The evaluation of specific endogenous transcript levels is important for understanding transcriptional regulation. More specifically, it is useful for independent confirmation of results obtained by the use of microarray analysis or RNA-seq and for evaluating RNA interference (RNAi)-mediated gene knockdown. Designing specific and effective primers for high-quality, moderate-throughput evaluation of transcript levels, i.e., quantitative, real-time PCR (qPCR), is nontrivial. To meet community needs, predefined qPCR primer pairs for mammalian genes have been designed and sequences made available, e.g., via PrimerBank. In this work, we adapted and refined the algorithms used for the mammalian PrimerBank to design 45,417 primer pairs for 13,860 Drosophila melanogaster genes, with three or more primer pairs per gene. We experimentally validated primer pairs for ~300 randomly selected genes expressed in early Drosophila embryos, using SYBR Green-based qPCR and sequence analysis of products derived from conventional PCR. All relevant information, including primer sequences, isoform specificity, spatial transcript targeting, and any available validation results and/or user feedback, is available from an online database (www.flyrnai.org/flyprimerbank). At FlyPrimerBank, researchers can retrieve primer information for fly genes either one gene at a time or in batch mode. Importantly, we included the overlap of each predicted amplified sequence with RNAi reagents from several public resources, making it possible for researchers to choose primers suitable for knockdown evaluation of RNAi reagents (i.e., to avoid amplification of the RNAi reagent itself). We demonstrate the utility of this resource for validation of RNAi reagents in vivo. PMID:23893746

  5. Induced PTF1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment.

    PubMed

    Jakubison, Brad L; Schweickert, Patrick G; Moser, Sarah E; Yang, Yi; Gao, Hongyu; Scully, Kathleen; Itkin-Ansari, Pamela; Liu, Yunlong; Konieczny, Stephen F

    2018-05-02

    Pancreatic acinar cells synthesize, package, and secrete digestive enzymes into the duodenum to aid in nutrient absorption and meet metabolic demands. When exposed to cellular stresses and insults, acinar cells undergo a dedifferentiation process termed acinar-ductal metaplasia (ADM). ADM lesions with oncogenic mutations eventually give rise to pancreatic ductal adenocarcinoma (PDAC). In healthy pancreata, the basic helix-loop-helix (bHLH) factors MIST1 and PTF1a coordinate an acinar-specific transcription network that maintains the highly developed differentiation status of the cells, protecting the pancreas from undergoing a transformative process. However, when MIST1 and PTF1a gene expression is silenced, cells are more prone to progress to PDAC. In this study, we tested whether induced MIST1 or PTF1a expression in PDAC cells could (i) re-establish the transcriptional program of differentiated acinar cells and (ii) simultaneously reduce tumor cell properties. As predicted, PTF1a induced gene expression of digestive enzymes and acinar-specific transcription factors, while MIST1 induced gene expression of vesicle trafficking molecules as well as activation of unfolded protein response components, all of which are essential to handle the high protein production load that is characteristic of acinar cells. Importantly, induction of PTF1a in PDAC also influenced cancer-associated properties, leading to a decrease in cell proliferation, cancer stem cell numbers, and repression of key ATP-binding cassette efflux transporters resulting in heightened sensitivity to gemcitabine. Thus, activation of pancreatic bHLH transcription factors rescues the acinar gene program and decreases tumorigenic properties in pancreatic cancer cells, offering unique opportunities to develop novel therapeutic intervention strategies for this deadly disease. © 2018 The Authors. Published by FEBS Press and John Wiley & Sons Ltd.

  6. Training of Residential Social Care Staff to Meet the Needs of Older People with Intellectual Disabilities who Develop Age-Related Health Problems: An Exploratory Study.

    PubMed

    Northway, Ruth; Jenkins, Robert; Holland-Hart, Daniella

    2017-09-01

    Despite awareness of the age related health needs of people with intellectual disabilities little is known regarding how residential social care staff are prepared to meet such needs. Data were gathered via semi-structured interviews from 14 managers of supported living settings. Transcripts were thematically analysed. Staff may work in supported living settings with no prior experience of care work, and previous knowledge/experience of supporting people in relation to their health is not required. Whilst health related training is provided there is a lack of specific training regarding healthy ageing, and training seems to be reactive to changing needs of tenants meaning that proactive monitoring for changes in health status may not occur. Whilst some training is provided for residential social care staff in relation to health and ageing a more proactive approach is required which should include a focus on healthy ageing. © 2016 John Wiley & Sons Ltd.

  7. Delivery style moderates study habits in an online nutrition class.

    PubMed

    Connors, Priscilla

    2013-03-01

    To report how the design of an online class affected student ability to stay on task, find critical resources, and communicate with the instructor via e-mail. Audiorecorded focus group meetings at a United States university featured a structured approach to discussions among undergraduate students enrolled in an Internet nutrition class. Meeting transcripts were read and reread by a trained investigator, who coded concepts until themes coalesced, which were authenticated by college students taking online classes. Three themes emerged that described factors moderating study habits in an Internet nutrition course: keeping up, e-mail fatigue, and wayfinding. A well-designed online course plans for productive study habits by posting a schedule of events and maintaining a predictable pattern, supporting navigation that stimulates exploration and return visits to critical information, and constructing e-mail messages that convey a concise message and maximize "open and read." Copyright © 2013 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

  8. Coordinating Council. Third Meeting: STI Strategic Plans

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The NASA Scientific and Technical Information Program Coordinating Council conducts meetings after which both modified transcripts of presentations and interactive discussions are published. The theme for the November 1990 meeting was 'STI Strategic Plans'. This theme was the focus of recorded discussions by members of the council. The last section of the report presents visuals on strategic goals for the STI Information Division. NASA's vision is to be at the forefront of advancements in aeronautics, space science, and exploration. More specific NASA goals are listed followed by the STI Division mission statement. The Strategic Goals for the STI Division are outlined as follows: Implement effective management strategies, Accomplish rapid deployment of the NASA STI Network, Seek out and develop cooperative partnerships, Establish the STI Program as an integral part of the NASA R&D effort, Enhance the quality of our products and services through a focus on the customer, Build an attitude of quality throughout the enterprise, Expand the existing participant community, Assert a NASA leadership role for STI policy, and Develop a program for information science R&D. The STI division mission statement appears on the document cover as follows 'The mission of the NASA STI Program is to advance aerospace knowledge, contribute to U.S. competitiveness, and become an integral partner in NASA R&D programs to support NASA goals.'

  9. Citizenship as practice: Handling communication problems in encounters between persons with dementia and social workers.

    PubMed

    Jh, Österholm; L-C, Hydén

    2016-11-01

    The overall aim of the study was to investigate if and how persons with dementia were able to take part in negotiations for formal support, as cases of citizenship as practice The transcripts used for analysis were from 11 assessment meetings conducted in Sweden, in which the formal applicant was a person with dementia. The findings suggest that the actual participation of persons with dementia in assessment meetings varies. Communication problems were found in the meetings to different degrees and were dealt with differently and with various consequences. For those persons with dementia contributing at the same levels as the other participants, there was an attempt at mutual understanding. For those making fewer contributions, the other interlocutors took over the initiative and thus affected the practice of citizenship by persons with dementia in a negative way. The practice of citizenship is situation based and varies depending on all participants. When the person with dementia is able to participate in the conversation, social workers can facilitate for them to overcome communication problems by giving them more time and signaling acceptance. If the person with dementia has great problems in participating, the other participants can find different strategies to at least involve her or him in the conversation. © The Author(s) 2014.

  10. The evaluator as technical assistant: A model for systemic reform support

    NASA Astrophysics Data System (ADS)

    Century, Jeanne Rose

    This study explored evaluation of systemic reform. Specifically, it focused on the evaluation of a systemic effort to improve K-8 science, mathematics and technology education. The evaluation was of particular interest because it used both technical assistance and evaluation strategies. Through studying the combination of these roles, this investigation set out to increase understanding of potentially new evaluator roles, distinguish important characteristics of the evaluator/project participant relationship, and identify how these roles and characteristics contribute to effective evaluation of systemic science education reform. This qualitative study used interview, document analysis, and participant observation as methods of data collection. Interviews were conducted with project leaders, project participants, and evaluators and focused on the evaluation strategies and process, the use of the evaluation, and technical assistance. Documents analyzed included transcripts of evaluation team meetings and reports, memoranda and other print materials generated by the project leaders and the evaluators. Data analysis consisted of analytic and interpretive procedures consistent with the qualitative data collected and entailed a combined process of coding transcripts of interviews and meetings, field notes, and other documents; analyzing and organizing findings; writing of reflective and analytic memos; and designing and diagramming conceptual relationships. The data analysis resulted in the development of the Multi-Function Model for Systemic Reform Support. This model organizes systemic reform support into three functions: evaluation, technical assistance, and a third, named here as "systemic perspective." These functions work together to support the project's educational goals as well as a larger goal--building capacity in project participants. This model can now serve as an informed starting point or "blueprint" for strategically supporting systemic reform.

  11. Bridge to shared governance: developing leadership of frontline nurses.

    PubMed

    Dearmon, Valorie A; Riley, Bettina H; Mestas, Lisa G; Buckner, Ellen B

    2015-01-01

    Transforming health care systems to improve quality is the responsibility of nurse executives and frontline nurses alike, yet frontline nurses are often ill-prepared to share leadership and accountability needed for transformation. The aim of this qualitative study was to describe the process used to build leadership capacity of frontline nurses engaged in resolving operational failures interrupting nursing care. The leadership development process served to bridge staff transition to shared governance. This institutional review board-approved qualitative research was designed to identify the effects of mentoring by the chief nursing officer and faculty partners on leadership development of frontline nurses working to find solutions to operational failures. Twelve nurses from 4 medical surgical units participated in a Frontline Innovations' nurse-led interdisciplinary group, which met over 18 months. Transcriptions of audiotaped meetings were analyzed for emerging process and outcome themes. The transcripts revealed a robust leadership development journey of frontline nurses engaged in process improvement. Themes that emerged from the mentoring process included engagement, collaboration, empowerment, confidence, and lifelong learning. The mentoring process provided frontline nurses the leadership foundation necessary to initiate shared governance.

  12. Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis

    PubMed Central

    Makita, Yuko; Ng, Kiaw Kiaw; Veera Singham, G.; Kawashima, Mika; Hirakawa, Hideki; Sato, Shusei

    2017-01-01

    Abstract Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar. PMID:28431015

  13. Inversion-mediated gene fusions involving NAB2-STAT6 in an unusual malignant meningioma.

    PubMed

    Gao, F; Ling, C; Shi, L; Commins, D; Zada, G; Mack, W J; Wang, K

    2013-08-20

    Meningiomas are the most common primary intracranial tumours, with ∼3% meeting current histopathologic criteria for malignancy. In this study, we explored the transcriptome of meningiomas using RNA-Seq. Inversion-mediated fusions between two adjacent genes, NAB2 and STAT6, were detected in one malignant tumour, creating two novel in-frame transcripts that were validated by RT-PCR and Sanger sequencing. Gene fusions of NAB2-STAT6 were recently implicated in the pathogenesis of solitary fibrous tumours; our study suggested that similar fusions may also have a role in a malignant meningioma with unusual histopathologic features.

  14. Tyrosine Kinase Inhibitor Treatment for Newly Diagnosed Chronic Myeloid Leukemia.

    PubMed

    Radich, Jerald P; Mauro, Michael J

    2017-08-01

    Chronic myeloid leukemia (CML) is a myeloproliferative disorder that accounts for approximately 10% of new cases of leukemia. The introduction of tyrosine kinase inhibitors has led to a reduction in mortalities. Thus, the estimated prevalence of CML is increasing. The National Comprehensive Cancer Network and the European Leukemia Net guidelines incorporate frequent molecular monitoring of the fusion BCR-ABL transcript to ensure that patients reach and keep treatment milestones. Most patients with CML are diagnosed in the chronic phase, and approximately 10% to 30% of these patients will at some time in their course meet definition criteria of resistance to imatinib. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. STGT program: Ada coding and architecture lessons learned

    NASA Technical Reports Server (NTRS)

    Usavage, Paul; Nagurney, Don

    1992-01-01

    STGT (Second TDRSS Ground Terminal) is currently halfway through the System Integration Test phase (Level 4 Testing). To date, many software architecture and Ada language issues have been encountered and solved. This paper, which is the transcript of a presentation at the 3 Dec. meeting, attempts to define these lessons plus others learned regarding software project management and risk management issues, training, performance, reuse, and reliability. Observations are included regarding the use of particular Ada coding constructs, software architecture trade-offs during the prototyping, development and testing stages of the project, and dangers inherent in parallel or concurrent systems, software, hardware, and operations engineering.

  16. Talk and community: The place of reporting in a life sciences laboratory

    NASA Astrophysics Data System (ADS)

    Swieringa, Robert Cecil

    This study investigates the routine situated communicative practice within the weekly meetings of a life sciences laboratory. The key, constitutive discourse of "reporting" is examined as an activity in which participants jointly sustain the work community of the laboratory and manage their own work within this community. This study seeks to contribute to studies of small groups by focusing upon the multifunctionality and situated nature of the meeting interactions within this enduring "bona fide" group as participants undertake multiple goals associated with their own progress and with the overlapping contexts of the setting. It also seeks to contribute to investigations of institutional talk and activity by examining "reporting" as interaction with institutional and community consequences for members of the community. This study takes a practice-oriented perspective to investigate the laboratory as a community of practice, focusing upon the "activity" of interaction as the overall unit of analysis. Ethnographic materials (involving observation, interviews, conversations, and activity logs) and discourse analysis techniques (involving audiotaping and transcriptions of meetings) were used to locate and record data within a university entomology laboratory over a two year period. Through triangulation of data, "reporting" is identified as a key discourse activity within the laboratory. As situated communicative practice within the weekly meetings, reporting is found to be compelled discourse through which interactants interactively manage one's ongoing goals and activity while temporally situating that activity within the broader stream of laboratory work. This study provides an example of how engagement in situated discursive activity provides for the coordination of individual lines of progress within the ongoing work of a community.

  17. NeuroAIDS, drug abuse, and inflammation: building collaborative research activities.

    PubMed

    Berman, Joan W; Carson, Monica J; Chang, Linda; Cox, Brian M; Fox, Howard S; Gonzalez, R Gilberto; Hanson, Glen R; Hauser, Kurt F; Ho, Wen-Zhe; Hong, Jau-Shyong; Major, Eugene O; Maragos, William F; Masliah, Eliezer; McArthur, Justin C; Miller, Diane B; Nath, Avindra; O'Callaghan, James P; Persidsky, Yuri; Power, Christopher; Rogers, Thomas J; Royal, Walter

    2006-12-01

    Neurological complications of human immunodeficiency virus (HIV) infection are a public health problem despite the availability of active antiretroviral therapies. The neuropathogenesis of HIV infection revolves around a complex cascade of events that include viral infection and glial immune activation, monocyte-macrophage brain infiltration, and secretion of a host of viral and cellular inflammatory and neurotoxic molecules. Although there is evidence that HIV-infected drug abusers experience more severe neurological disease, the biological basis for this finding is unknown. A scientific workshop organized by the National Institute on Drug Abuse (NIDA) was held on March 23-24, 2006 to address this question. The goal of the meeting was to bring together basic science and clinical researchers who are experts in NeuroAIDS, glial immunity, drugs of abuse, and/or pharmacology in order to find new approaches to understanding interactions between drug abuse and neuroAIDS. The format of the meeting was designed to stimulate open discussion and forge new multidisciplinary research collaborations. This report includes transcripts of active discussions and short presentations from invited participants. The presentations were separated into sections that included: Glial Biology, Inflammation, and HIV; Pharmacology, Neurotoxicology, and Neuroprotection; NeuroAIDS and Virology; and Virus-Drug and Immune-Drug Interactions. Research priorities were identified. Additional information about this meeting is available through links from the NIDA AIDS Research Program website ( http://www.nida.nih.gov/about/organization/arp/arp-websites.htm ).

  18. A Staged Reading of the Play: Reykjavik

    NASA Astrophysics Data System (ADS)

    2017-01-01

    Reykjavik is the capital of Iceland, an island country located about 500 miles northwest of Scotland in the North Atlantic. In 1986 Mikhail Gorbachev, the Chairman of the Politburo of the Soviet Union and General Secretary of the Soviet Communist Party, invited Ronald Reagan, the President of the United States, to meet with him. The play Reykjavik is a dramatic reconstruction of the two-day summit meeting during which the world leaders almost reached agreement on the total abolition of their countries' nuclear weapons. The play uses the actual transcripts of the Reykjavik meeting as well as the memoirs of both Reagan and Gorbachev. Join us for a dramatic staged reading of Reykjavik and find out how close the two superpowers, the Soviet Union and the United States, came to eliminating their nuclear weapons. He playwright is Richard Rhodes, the Pulitzer Prize-winning author of 24 books. He has written his first play, and it spins off of his research into the history of nuclear weapons. The staged reading is performed by the Washington based Tonic Theater Company: http://www.tonictheater.org/[tonictheater.org]. After the performance, the play director and actors as well as experts on nuclear disarmament will be available for a talk-back discussion of the play with the audience. Produced by Brian Schwartz, Brooklyn College and the Graduate Center of the City University of New York and Gregory Mack of the APS Washington office.

  19. The needs of siblings of children with cancer: a nursing perspective.

    PubMed

    O'Shea, Eileen R; Shea, Joyce; Robert, Tracey; Cavanaugh, Cathleen

    2012-01-01

    Findings from research studies on the needs of siblings of children with cancer have highlighted the imperative that these siblings be supported and involved in the plan of care when a diagnosis of cancer is made. However, few studies have included the perspective of the nurse when evaluating sibling needs or identifying interventions used to meet the needs. This qualitative descriptive study used a combination of individual interviews and a focus group to capture perspectives from 13 pediatric oncology nurses employed at a leading Children's Hospital located in the northeast. Transcripts were analyzed for content and theme in relation to the 2 research questions. Needs identified included getting attention, wanting to know, having fears/worries, feeling at fault, wanting to help, and wanting a normal routine, whereas interventions identified included recognizing their needs, getting siblings involved, sharing appropriate information, being a resource, giving support, and bending the rules. Findings support previous studies that document the variety of needs experienced by siblings of children with cancer and offer examples of nursing interventions to meet these needs.

  20. Nucleotides Adjacent to the Ligand-Binding Pocket are Linked to Activity Tuning in the Purine Riboswitch

    PubMed Central

    Stoddard, Colby D.; Widmann, Jeremy; Trausch, Jeremiah J.; Marcano-Velázquez, Joan G.; Knight, Rob; Batey, Robert T.

    2013-01-01

    Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs. PMID:23485418

  1. "Taking your place at the table": an autoethnographic study of chaplains' participation on an interdisciplinary research team.

    PubMed

    Kestenbaum, Allison; James, Jennifer; Morgan, Stefana; Shields, Michele; Hocker, Will; Rabow, Michael; Dunn, Laura B

    2015-05-02

    There are many potential benefits to chaplaincy in transforming into a "research-informed" profession. However little is known or has been documented about the roles of chaplains on research teams and as researchers or about the effects of research engagement on chaplains themselves. This report describes the experience and impact of three chaplains, as well as tensions and challenges that arose, on one particular interdisciplinary team researching a spiritual assessment model in palliative care. Transcripts of our research team meetings, which included the three active chaplain researchers, as well as reflections of all the members of the research team provide the data for this descriptive, qualitative, autoethnographic analysis. This autoethnographic project evolved from the parent study, entitled "Spiritual Assessment Intervention Model (AIM) in Outpatient Palliative Care Patients with Advanced Cancer." This project focused on the use of a well-developed model of spiritual care, the Spiritual Assessment and Intervention Model (Spiritual AIM). Transcripts of nine weekly team meetings for the parent study were reviewed. These parent study team meetings were attended by various disciplines and included open dialogue and intensive questions from non-chaplain team members to chaplains about their practices and Spiritual AIM. Individual notes (from reflexive memoing) and other reflections of team members were also reviewed for this report. The primary methodological framework for this paper, autoethnography, was not only used to describe the work of chaplains as researchers, but also to reflect on the process of researcher identity formation and offer personal insights regarding the challenges accompanying this process. Three major themes emerged from the autoethnographic analytic process: 1) chaplains' unique contributions to the research team; 2) the interplay between the chaplains' active research role and their work identities; and 3) tensions and challenges in being part of an interdisciplinary research team. Describing the contributions and challenges of one interdisciplinary research team that included chaplains may help inform chaplains about the experience of participating in research. As an autoethnographic study, this work is not meant to offer generalizable results about all chaplains' experiences on research teams. Research teams that are interdisciplinary may mirror the richness and efficacy of clinical interdisciplinary teams. Further work is needed to better characterize both the promise and pitfalls of chaplains' participation on research teams.

  2. The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue.

    PubMed

    Swift, Joe; Discher, Dennis E

    2014-07-15

    How cells respond to physical cues in order to meet and withstand the physical demands of their immediate surroundings has been of great interest for many years, with current research efforts focused on mechanisms that transduce signals into gene expression. Pathways that mechano-regulate the entry of transcription factors into the cell nucleus are emerging, and our most recent studies show that the mechanical properties of the nucleus itself are actively controlled in response to the elasticity of the extracellular matrix (ECM) in both mature and developing tissue. In this Commentary, we review the mechano-responsive properties of nuclei as determined by the intermediate filament lamin proteins that line the inside of the nuclear envelope and that also impact upon transcription factor entry and broader epigenetic mechanisms. We summarize the signaling pathways that regulate lamin levels and cell-fate decisions in response to a combination of ECM mechanics and molecular cues. We will also discuss recent work that highlights the importance of nuclear mechanics in niche anchorage and cell motility during development, hematopoietic differentiation and cancer metastasis, as well as emphasizing a role for nuclear mechanics in protecting chromatin from stress-induced damage. © 2014. Published by The Company of Biologists Ltd.

  3. Social media and medical education: Exploring the potential of Twitter as a learning tool.

    PubMed

    Jalali, Alireza; Sherbino, Jonathan; Frank, Jason; Sutherland, Stephanie

    2015-04-01

    This study set out to explore the ways in which social media can facilitate learning in medical education. In particular we were interested in determining whether the use of Twitter during an academic conference can promote learning for participants. The Twitter transcript from the annual International Conference on Residency Education (ICRE) 2013 was qualitatively analysed for evidence of the three overarching cognitive themes: (1) preconceptions, (2) frameworks, and (3) metacognition/refl ection in regard to the National Research Council ’ s (NRC) How People Learn framework . Content analysis of the Twitter transcript revealed evidence of the three cognitive themes as related to how people learn. Twitter appears to be most effective at stimulating individuals ’ preconceptions, thereby engaging them with the new material acquired during a medical education conference. The study of social media data, such as the Twitter data used in this study, is in its infancy. Having established that Twitter does hold signifi cant potential as a learning tool during an academic conference, we are now in a better position to more closely examine the spread, depth, and sustainability of such learning during medical education meetings.

  4. The nuclear lamina is mechano-responsive to ECM elasticity in mature tissue

    PubMed Central

    Swift, Joe; Discher, Dennis E.

    2014-01-01

    ABSTRACT How cells respond to physical cues in order to meet and withstand the physical demands of their immediate surroundings has been of great interest for many years, with current research efforts focused on mechanisms that transduce signals into gene expression. Pathways that mechano-regulate the entry of transcription factors into the cell nucleus are emerging, and our most recent studies show that the mechanical properties of the nucleus itself are actively controlled in response to the elasticity of the extracellular matrix (ECM) in both mature and developing tissue. In this Commentary, we review the mechano-responsive properties of nuclei as determined by the intermediate filament lamin proteins that line the inside of the nuclear envelope and that also impact upon transcription factor entry and broader epigenetic mechanisms. We summarize the signaling pathways that regulate lamin levels and cell-fate decisions in response to a combination of ECM mechanics and molecular cues. We will also discuss recent work that highlights the importance of nuclear mechanics in niche anchorage and cell motility during development, hematopoietic differentiation and cancer metastasis, as well as emphasizing a role for nuclear mechanics in protecting chromatin from stress-induced damage. PMID:24963133

  5. Factors that influence engagement in collaborative practice

    PubMed Central

    Herbert, Carol P.; Bainbridge, Lesley; Bickford, Julia; Baptiste, Susan; Brajtman, Susan; Dryden, Trish; Hall, Pippa; Risdon, Cathy; Solomon, Patricia

    2007-01-01

    OBJECTIVE To generate hypotheses regarding factors that might influence engagement in collaborative practice. DESIGN Qualitative study using in-depth interviews. SETTING Participants interviewed each other in dyads. The pairing was based upon geographical location and proximity to each other. PARTICIPANTS Eight professionals from the disciplines of medicine, nursing, occupational therapy, physical therapy, and massage therapy. METHOD Semistructured interviews, lasting 30 to 45 minutes each, were recorded and transcribed verbatim. The transcripts were read by all research team members using independent content analysis for common words, phrases, statements, or units of text for key themes. At a subsequent face-to-face meeting, the team used an iterative process of comparing and contrasting key themes until consensus was reached. The transcripts were then analyzed further for subthemes using NVivo software. MAIN FINDINGS Initial findings suggest that some common characteristics grounded in family history, school experiences, social interactions, and professional training might influence collaborative practice choices. The narrative form of the interview broke down interpersonal and interprofessional barriers, creating a new level of trust and respect that could improve professional collaboration. CONCLUSION This study suggests that life experiences from childhood into later adulthood can and do influence professional choices. PMID:17872847

  6. Spermatozoa with numerical chromosomal abnormalities are more prone to be retained by Annexin V-MACS columns.

    PubMed

    Esbert, M; Godo, A; Soares, S R; Florensa, M; Amorós, D; Ballesteros, A; Vidal, F

    2017-07-01

    Colloidal super-paramagnetic microbeads conjugated with annexin V are effective for separating apoptotic spermatozoa by MACS as a result of the high affinity of annexin V for externalized PS molecules. The effectiveness of the procedure in reducing the percentage of sperm with fragmented DNA and abnormal morphology has also been reported. However, it is still unknown if it could decrease the percentage of aneuploid spermatozoa. The objective of our prospective study, performed on 16 males with abnormal FISH on spermatozoa, was to assess if MACS columns were useful tools to retain spermatozoa carrying chromosomal abnormalities in semen samples processed after density gradient centrifugation (DGC). The pellet obtained after DGC was subjected to MACS, and sperm FISH analyses were performed both in the eluded fraction and in the fraction retained in the column. The observed frequencies of disomy and nullisomy 13, 18, and 21, X and Y, as well as the diploidy rates in the MACS eluded fraction and the fraction retained in the MACS column were recorded. We observed that the frequencies of aneuploidies in the eluded fraction were lower than in the fraction retained in the MACS column (0.59% vs. 0.75%; p = 0.010). DGC determined a significant reduction in sperm concentration (z-ratio = 2.83; p = 0.005) and a significant increase in sperm progressive motility (z-ratio = -3.5; p < 0.001). MACS also led to a significant reduction in sperm concentration (z-ratio = 3.14; p = 0.002) and a significant increase in progressive motility (z-ratio = -2.59; p = 0.01) when compared with the post-DGC sample. Sperm concentration was similar in the two fractions generated by MACS (z-ratio = 0.63; p = 0.52), while progressive motility was significantly higher in the MACS eluded fraction (z-ratio = 2.42; p = 0.02). According to our results, MACS columns are able to selectively retain spermatozoa carrying chromosomal abnormalities. Furthermore, the performance of DGC and MACS on semen samples leads to an enrichment of progressive motility. © 2017 American Society of Andrology and European Academy of Andrology.

  7. Plant chromatin warms up in Madrid

    PubMed Central

    Jarillo, José A; Gaudin, Valerie; Hennig, Lars; Köhler, Claudia; Piñeiro, Manuel

    2014-01-01

    The 3rd European Workshop on Plant Chromatin (EWPC) was held on August 2013 in Madrid, Spain. A number of different topics on plant chromatin were presented during the meeting, including new factors mediating Polycomb Group protein function in plants, chromatin-mediated reprogramming in plant developmental transitions, the role of histone variants, and newly identified chromatin remodeling factors. The function of interactions between chromatin and transcription factors in the modulation of gene expression, the role of chromatin dynamics in the control of nuclear processes and the influence of environmental factors on chromatin organization were also reported. In this report, we highlight some of the new insights emerging in this growing area of research, presented at the 3rd EWPC. PMID:24504145

  8. Waste isolation safety assessment program. Task 4. Third contractor information meeting

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1980-06-01

    The Contractor Information Meeting (October 14 to 17, 1979) was part of the FY-1979 effort of Task 4 of the Waste Isolation Safety Assessment Program (WISAP): Sorption/Desorption Analysis. The objectives of this task are to: evaluate sorption/desorption measurement methods and develop a standardized measurement procedure; produce a generic data bank of nuclide-geologic interactions using a wide variety of geologic media and groundwaters; perform statistical analysis and synthesis of these data; perform validation studies to compare short-term laboratory studies to long-term in situ behavior; develop a fundamental understanding of sorption/desorption processes; produce x-ray and gamma-emitting isotopes suitable for the study ofmore » actinides at tracer concentrations; disseminate resulting information to the international technical community; and provide input data support for repository safety assessment. Conference participants included those subcontracted to WISAP Task 4, representatives and independent subcontractors to the Office of Nuclear Waste Isolation, representatives from other waste disposal programs, and experts in the area of waste/geologic media interaction. Since the meeting, WISAP has been divided into two programs: Assessment of Effectiveness of Geologic Isolation Systems (AEGIS) (modeling efforts) and Waste/Rock Interactions Technology (WRIT) (experimental work). The WRIT program encompasses the work conducted under Task 4. This report contains the information presented at the Task 4, Third Contractor Information Meeting. Technical Reports from the subcontractors, as well as Pacific Northwest Laboratory (PNL), are provided along with transcripts of the question-and-answer sessions. The agenda and abstracts of the presentations are also included. Appendix A is a list of the participants. Appendix B gives an overview of the WRIT program and details the WRIT work breakdown structure for 1980.« less

  9. The Learning Environment Counts: Longitudinal Qualitative Analysis of Study Strategies Adopted by First-Year Medical Students in a Competency-Based Educational Program.

    PubMed

    Bierer, S Beth; Dannefer, Elaine F

    2016-11-01

    The move toward competency-based education will require medical schools and postgraduate training programs to restructure learning environments to motivate trainees to take personal ownership for learning. This qualitative study explores how medical students select and implement study strategies while enrolled in a unique, nontraditional program that emphasizes reflection on performance and competence rather than relying on high-stakes examinations or grades to motivate students to learn and excel. Fourteen first-year medical students volunteered to participate in three, 45-minute interviews (42 overall) scheduled three months apart during 2013-2014. Two medical educators used structured interview guides to solicit students' previous assessment experiences, preferred learning strategies, and performance monitoring processes. Interviews were digitally recorded and transcribed verbatim. Participants confirmed accuracy of transcripts. Researchers independently read transcripts and met regularly to discuss transcripts and judge when themes achieved saturation. Medical students can adopt an assessment for learning mind-set with faculty guidance and implement appropriate study strategies for mastery-learning demands. Though students developed new strategies at different rates during the year, they all eventually identified study and performance monitoring strategies to meet learning needs. Students who had diverse learning experiences in college embraced mastery-based study strategies sooner than peers after recognizing that the learning environment did not reward performance-based strategies. Medical students can take ownership for their learning and implement specific strategies to regulate behavior when learning environments contain building blocks emphasized in self-determination theory. Findings should generalize to educational programs seeking strategies to design learning environments that promote self-regulated learning.

  10. Large-scale collection of full-length cDNA and transcriptome analysis in Hevea brasiliensis.

    PubMed

    Makita, Yuko; Ng, Kiaw Kiaw; Veera Singham, G; Kawashima, Mika; Hirakawa, Hideki; Sato, Shusei; Othman, Ahmad Sofiman; Matsui, Minami

    2017-04-01

    Natural rubber has unique physical properties that cannot be replaced by products from other latex-producing plants or petrochemically produced synthetic rubbers. Rubber from Hevea brasiliensis is the main commercial source for this natural rubber that has a cis-polyisoprene configuration. For sustainable production of enough rubber to meet demand elucidation of the molecular mechanisms involved in the production of latex is vital. To this end, we firstly constructed rubber full-length cDNA libraries of RRIM 600 cultivar and sequenced around 20,000 clones by the Sanger method and over 15,000 contigs by Illumina sequencer. With these data, we updated around 5,500 gene structures and newly annotated around 9,500 transcription start sites. Second, to elucidate the rubber biosynthetic pathways and their transcriptional regulation, we carried out tissue- and cultivar-specific RNA-Seq analysis. By using our recently published genome sequence, we confirmed the expression patterns of the rubber biosynthetic genes. Our data suggest that the cytoplasmic mevalonate (MVA) pathway is the main route for isoprenoid biosynthesis in latex production. In addition to the well-studied polymerization factors, we suggest that rubber elongation factor 8 (REF8) is a candidate factor in cis-polyisoprene biosynthesis. We have also identified 39 transcription factors that may be key regulators in latex production. Expression profile analysis using two additional cultivars, RRIM 901 and PB 350, via an RNA-Seq approach revealed possible expression differences between a high latex-yielding cultivar and a disease-resistant cultivar. © The Author 2017. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  11. Selective recognition of N4-methylcytosine in DNA by engineered transcription-activator-like effectors.

    PubMed

    Rathi, Preeti; Maurer, Sara; Summerer, Daniel

    2018-06-05

    The epigenetic DNA nucleobases 5-methylcytosine (5mC) and N 4-methylcytosine (4mC) coexist in bacterial genomes and have important functions in host defence and transcription regulation. To better understand the individual biological roles of both methylated nucleobases, analytical strategies for distinguishing unmodified cytosine (C) from 4mC and 5mC are required. Transcription-activator-like effectors (TALEs) are programmable DNA-binding repeat proteins, which can be re-engineered for the direct detection of epigenetic nucleobases in user-defined DNA sequences. We here report the natural, cytosine-binding TALE repeat to not strongly differentiate between 5mC and 4mC. To engineer repeats with selectivity in the context of C, 5mC and 4mC, we developed a homogeneous fluorescence assay and screened a library of size-reduced TALE repeats for binding to all three nucleobases. This provided insights into the requirements of size-reduced TALE repeats for 4mC binding and revealed a single mutant repeat as a selective binder of 4mC. Employment of a TALE with this repeat in affinity enrichment enabled the isolation of a user-defined DNA sequence containing a single 4mC but not C or 5mC from the background of a bacterial genome. Comparative enrichments with TALEs bearing this or the natural C-binding repeat provides an approach for the complete, programmable decoding of all cytosine nucleobases found in bacterial genomes.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'. © 2018 The Author(s).

  12. Tailoring a family-based alcohol intervention for Aboriginal Australians, and the experiences and perceptions of health care providers trained in its delivery

    PubMed Central

    2014-01-01

    Background Aboriginal Australians experience a disproportionately high burden of alcohol-related harm compared to the general Australian population. Alcohol treatment approaches that simultaneously target individuals and families offer considerable potential to reduce these harms if they can be successfully tailored for routine delivery to Aboriginal Australians. The Community Reinforcement Approach (CRA) and Community Reinforcement and Family Training (CRAFT) are two related interventions that are consistent with Aboriginal Australians’ notions of health and wellbeing. This paper aims to describe the process of tailoring CRA and CRAFT for delivery to Aboriginal Australians, explore the perceptions of health care providers participating in the tailoring process, and their experiences of participating in CRA and CRAFT counsellor certification. Methods Data sources included notes recorded from eight working group meetings with 22 health care providers of a drug and alcohol treatment agency and Aboriginal Community Controlled Health Service (November 2009-February 2013), and transcripts of semi-structured interviews with seven health care providers participating in CRA and CRAFT counsellor certification (May 2012). Qualitative content analysis was used to categorise working group meeting notes and interview transcripts were into key themes. Results Modifying technical language, reducing the number of treatment sessions, and including an option for treatment of clients in groups, were key recommendations by health care providers for improving the feasibility and applicability of delivering CRA and CRAFT to Aboriginal Australians. Health care providers perceived counsellor certification to be beneficial for developing their skills and confidence in delivering CRA and CRAFT, but identified time constraints and competing tasks as key challenges. Conclusions The tailoring process resulted in Aboriginal Australian-specific CRA and CRAFT resources. The process also resulted in the training and certification of health care providers in CRA and CRAFT and the establishment of a local training and certification program. PMID:24708838

  13. Tailoring a family-based alcohol intervention for Aboriginal Australians, and the experiences and perceptions of health care providers trained in its delivery.

    PubMed

    Calabria, Bianca; Clifford, Anton; Rose, Miranda; Shakeshaft, Anthony P

    2014-04-07

    Aboriginal Australians experience a disproportionately high burden of alcohol-related harm compared to the general Australian population. Alcohol treatment approaches that simultaneously target individuals and families offer considerable potential to reduce these harms if they can be successfully tailored for routine delivery to Aboriginal Australians. The Community Reinforcement Approach (CRA) and Community Reinforcement and Family Training (CRAFT) are two related interventions that are consistent with Aboriginal Australians' notions of health and wellbeing. This paper aims to describe the process of tailoring CRA and CRAFT for delivery to Aboriginal Australians, explore the perceptions of health care providers participating in the tailoring process, and their experiences of participating in CRA and CRAFT counsellor certification. Data sources included notes recorded from eight working group meetings with 22 health care providers of a drug and alcohol treatment agency and Aboriginal Community Controlled Health Service (November 2009-February 2013), and transcripts of semi-structured interviews with seven health care providers participating in CRA and CRAFT counsellor certification (May 2012). Qualitative content analysis was used to categorise working group meeting notes and interview transcripts were into key themes. Modifying technical language, reducing the number of treatment sessions, and including an option for treatment of clients in groups, were key recommendations by health care providers for improving the feasibility and applicability of delivering CRA and CRAFT to Aboriginal Australians. Health care providers perceived counsellor certification to be beneficial for developing their skills and confidence in delivering CRA and CRAFT, but identified time constraints and competing tasks as key challenges. The tailoring process resulted in Aboriginal Australian-specific CRA and CRAFT resources. The process also resulted in the training and certification of health care providers in CRA and CRAFT and the establishment of a local training and certification program.

  14. Stakeholder Views of Nanosilver Linings: Macroethics Education and Automated Text Analysis Through Participatory Governance Role Play in a Workshop Format.

    PubMed

    Dempsey, Joshua; Stamets, Justin; Eggleson, Kathleen

    2017-06-01

    The Nanosilver Linings role play case offers participants first-person experience with interpersonal interaction in the context of the wicked problems of emerging technology macroethics. In the fictional scenario, diverse societal stakeholders convene at a town hall meeting to consider whether a nanotechnology-enabled food packaging industry should be offered incentives to establish an operation in their economically struggling Midwestern city. This original creative work was built with a combination of elements, selected for their established pedagogical efficacy (e.g. active learning, case-based learning) and as topical dimensions of the realistic scenario (e.g. nanosilver in food packaging, occupational safety and health). The product life cycle is used as a framework for integrated consideration of scientific, societal, and ethical issues. The Nanosilver Linings hypothetical case was delivered through the format of the 3-hour workshop Ethics when Biocomplexity meets Human Complexity, providing an immersive, holistic ethics learning experience for STEM graduate students. Through their participation in the Nanosilver Linings case and Ethics when Biocomplexity meets Human Complexity workshop, four cohorts of science and engineering doctoral students reported the achievement of specific learning objectives pertaining to a range of macroethics concepts and professional practices, including stakeholder perspectives, communication, human values, and ethical frameworks. Automated text analysis of workshop transcripts revealed differences in sentiment and in ethical framework (consequentialism/deontology) preference between societal stakeholder roles. These resources have been recognized as ethics education exemplars by the U.S. National Academy of Engineering .

  15. Health promotores' perceptions of their communities' health needs, knowledge, and resource needs in rural Nicaragua.

    PubMed

    McDermott-Levy, Ruth; Weatherbie, Katherine

    2013-03-01

    This study was conducted to determine rural Nicaraguan health promotores' perceptions of their community's health problems, their self-identified learning needs, and resource needs. Despite the valuable contributions of promotores, there is limited research regarding unpaid volunteer promotores' perceptions of their needs in providing care to remote communities. A qualitative descriptive study of 13 unpaid, volunteer promotores in Waslala, Nicaragua, was conducted. Data were collected during individual interviews with seven promotores and two focus groups with 13 promotores. Data were analyzed by reading verbatim transcripts repeatedly and establishing general themes. Promotores confirmed the findings. Waslalan promotores described a synergy of traditional folk health beliefs and natural practices along with use of modern medications while working to meet the health needs of their communities. Without much formal training, the promotores used public health strategies to influence health behaviors and address health disparities in the communities they serve. Serving their communities and God were their motivation in their work. Recommendations include supporting efforts to meet promotores' needs regarding community health education with messages from community leaders and nurses, finding methods to financially compensate promotores, and including promotores in health program planning and evaluation. © 2012 Wiley Periodicals, Inc.

  16. Emancipatory actions displayed by multi-ethnic women: "Regaining control of my health care".

    PubMed

    Alexander, Ivy M

    2010-11-01

    Despite the recognized importance of patient involvement in primary care interactions, little information describing women's needs and expectations for these interactions is available. This participatory action study was based in Critical Action Theory and designed to describe any emancipatory interests that surfaced when eight ethnically diverse women examined their interactions with primary care nurse practitioners (PCNPs) over the course of five successive focus group meetings. Focus group meeting transcripts, field notes, interaction notations, seating maps, and first impression summaries. Participants wanted to learn how to "stand up" for themselves in primary care interactions. They believed this could be accomplished by developing a positive sense of self-esteem. Ultimately, they identified the right way to "talk back" to clinicians and created a method for regaining control of their own health care and maintaining equality in interactions with primary care clinicians. Nurse practitioners working in the primary setting are especially well situated to support self-management and foster patient participation by women as they live with chronic disease, engage in health promotion activities, and deal with common symptomatic problems for themselves and their families. ©2010 The Author Journal compilation ©2010 American Academy of Nurse Practitioners.

  17. Anti-PIT-1 antibody syndrome; a novel clinical entity leading to hypopituitarism.

    PubMed

    Bando, Hironori; Iguchi, Genzo; Yamamoto, Masaaki; Hidaka-Takeno, Ryoko; Takahashi, Yutaka

    2015-03-01

    Various hypothalamic-pituitary diseases cause hypopituitarism. Inflammation related to autoimmunity also causes hypopituitarism. Hypophysitis is a representative disease caused by autoimmunity. Generally, anterior pituitary hormones are non-specifically impaired in this condition, but specific hormone defects have been reported in some cases. Anti-PIT-1 (pituitary-specific transcription factor 1) antibody syndrome is a novel clinical entity that presents an acquired combined pituitary hormone deficiency characterized by a specific defect in growth hormone, prolactin, and thyroid-stimulating hormone. Circulating anti-PIT-1 antibody along with various autoantibodies are detected with multiple endocrine organopathy, meeting the definition of autoimmune polyglandular syndrome. Mechanistically, cytotoxic T lymphocytes that specifically react with PIT-1 protein play an important role in the development of this syndrome.

  18. Commercialization of Children's Television. Hearings on H.R. 3288, H.R. 3966, and H.R. 4125: Bills To Require the FCC To Reinstate Restrictions on Advertising during Children's Television, To Enforce the Obligation of Broadcasters To Meet the Educational Needs of the Child Audience, and for Other Purposes, before the Subcommittee on Telecommunications and Finance of the Committee on Energy and Commerce, House of Representatives, One Hundredth Congress (September 15, 1987 and March 17, 1988).

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Energy and Commerce.

    This report provides transcripts of two hearings held 6 months apart before a subcommittee of the House of Representatives on three bills which would require the Federal Communications Commission to reinstate restrictions on advertising on children's television programs. The texts of the bills under consideration, H.R. 3288, H.R. 3966, and H.R.…

  19. Transcriptional profiling reveals regulated genes in the hippocampus during memory formation

    NASA Technical Reports Server (NTRS)

    Donahue, Christine P.; Jensen, Roderick V.; Ochiishi, Tomoyo; Eisenstein, Ingrid; Zhao, Mingrui; Shors, Tracey; Kosik, Kenneth S.

    2002-01-01

    Transcriptional profiling (TP) offers a powerful approach to identify genes activated during memory formation and, by inference, the molecular pathways involved. Trace eyeblink conditioning is well suited for the study of regional gene expression because it requires the hippocampus, whereas the highly parallel task, delay conditioning, does not. First, we determined when gene expression was most regulated during trace conditioning. Rats were exposed to 200 trials per day of paired and unpaired stimuli each day for 4 days. Changes in gene expression were most apparent 24 h after exposure to 200 trials. Therefore, we profiled gene expression in the hippocampus 24 h after 200 trials of trace eyeblink conditioning, on multiple arrays using additional animals. Of 1,186 genes on the filter array, seven genes met the statistical criteria and were also validated by real-time polymerase chain reaction. These genes were growth hormone (GH), c-kit receptor tyrosine kinase (c-kit), glutamate receptor, metabotropic 5 (mGluR5), nerve growth factor-beta (NGF-beta), Jun oncogene (c-Jun), transmembrane receptor Unc5H1 (UNC5H1), and transmembrane receptor Unc5H2 (UNC5H2). All these genes, except for GH, were downregulated in response to trace conditioning. GH was upregulated; therefore, we also validated the downregulation of the GH inhibitor, somatostatin (SST), even though it just failed to meet criteria on the arrays. By during situ hybridization, GH was expressed throughout the cell layers of the hippocampus in response to trace conditioning. None of the genes regulated in trace eyeblink conditioning were similarly affected by delay conditioning, a task that does not require the hippocampus. These findings demonstrate that transcriptional profiling can exhibit a repertoire of genes sensitive to the formation of hippocampal-dependent associative memories.

  20. Double promoter expression systems for recombinant protein production by industrial microorganisms.

    PubMed

    Öztürk, Sibel; Ergün, Burcu Gündüz; Çalık, Pınar

    2017-10-01

    Using double promoter expression systems is a promising approach to increase heterologous protein production. In this review, current double promoter expression systems for the production of recombinant proteins (r-proteins) by industrially important bacteria, Bacillus subtilis and Escherichia coli; and yeasts, Saccharomyces cerevisiae and Pichia pastoris, are discussed by assessing their potentials and drawbacks. Double promoter expression systems need to be designed to maintain a higher specific product formation rate within the production domain. While bacterial double promoter systems have been constructed as chimeric tandem promoters, yeast dual promoter systems have been developed as separate expression cassettes. To increase production and productivity, the optimal transcriptional activity should be justified either by simultaneously satisfying the requirements of both promoters, or by consecutively stimulating the changeover from one to another in a biphasic process or via successive-iterations. Thus, considering the dynamics of a fermentation process, double promoters can be classified according to their operational mechanisms, as: i) consecutively operating double promoter systems, and ii) simultaneously operating double promoter systems. Among these metabolic design strategies, extending the expression period with two promoters activated under different conditions, or enhancing the transcriptional activity with two promoters activated under similar conditions within the production domain, can be applied independently from the host. Novel studies with new insights, which aim a rational systematic design and construction of dual promoter expression vectors with tailored transcriptional activity, will empower r-protein production with enhanced production and productivity. Finally, the current state-of-the-art review emphasizes the advantages of double promoter systems along with the necessity for discovering new promoters for the development of more effective and adaptive processes to meet the increasing demand of r-protein industry.

  1. Changes in the level of perforin and its transcript during effector and target cell interactions.

    PubMed

    Kim, K K; Blakely, A; Zhou, Z; Davis, J; Clark, W; Kwon, B S

    1993-05-01

    Perforin is a cytoplasmic granule protein expressed in cytotoxic lymphocytes, and is capable of lysing target cells. This protein is induced as cytotoxic T cells are activated, and the mRNA expression is modulated by various stimulators. These observations suggest possible changes in the level of perforin transcripts and protein when killer lymphocytes meet specific target cells leading to target cell death. To address this question, we examined three murine T-cell clones and primary human NK cells in perforin expression. When the cytotoxic lymphocytes were exposed to sensitive targets, perforin mRNA disappeared within 5 to 30 min and appeared within an hour thereafter. Among the murine T cell clones, L3 and OE4 showed two phases of mRNA decrease while human NK cells and the third murine T cell clone, AB.1, showed only one phase of mRNA loss during a 240 min period. The data indicate that when cytotoxic lymphocytes receive signals from a sensitive target, the cells rapidly degrade previously accumulated perforin mRNA and synthesize new transcripts. Interestingly, heat shock protein 70 mRNA was induced as the perforin mRNA levels recovered, while P55 Il-2 receptor mRNA was downregulated within 5 min after exposure to targets. The perforin protein level also rapidly decreased immediately after the interaction with the target, followed by a recovery, and then another decrease as seen in primary human NK cells, OE4 and L3 cells. However, in the AB.1 clone, no change in perforin content was detectable, despite the loss of perforin mRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

  2. Direct and indirect effects of RNA interference against pyridoxal kinase and pyridoxine 5'-phosphate oxidase genes in Bombyx mori.

    PubMed

    Huang, ShuoHao; Yao, LiLi; Zhang, JianYun; Huang, LongQuan

    2016-08-01

    Vitamin B6 comprises six interconvertible pyridine compounds (vitamers), among which pyridoxal 5'-phosphate is a coenzyme involved in a high diversity of biochemical reactions. Humans and animals obtain B6 vitamers from diet, and synthesize pyridoxal 5'-phosphate by pyridoxal kinase and pyridoxine 5'-phosphate oxidase. Currently, little is known on how pyridoxal 5'-phosphate biosynthesis is regulated, and pyridoxal 5'-phosphate is supplied to meet their requirement in terms of cofactor. Bombyx mori is a large silk-secreting insect, in which protein metabolism is most active, and the vitamin B6 demand is high. In this study, we successfully down-regulated the gene expression of pyridoxal kinase and pyridoxine 5'-phosphate oxidase by body cavity injection of synthesized double-stranded small interfering RNA to 5th instar larvae of Bombyx mori, and analyzed the gene transcription levels of pyridoxal 5'-phosphate dependent enzymes, phosphoserine aminotransferase and glutamic-oxaloacetic transaminase. Results show that the gene expression of pyridoxal kinase and pyridoxine 5'-phosphate oxidase has a greater impact on the gene transcription of enzymes using pyridoxal 5'-phosphate as a cofactor in Bombyx mori. Our study suggests that pyridoxal 5'-phosphate biosynthesis and dynamic balance may be regulated by genetic networks. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. Assembling a Cellular User Manual for the Brain.

    PubMed

    Sloan, Steven A; Barres, Ben A

    2018-03-28

    For many years, efforts to decipher the various cellular components that comprise the CNS were stymied by a lack of technical strategies for isolating and profiling the brain's resident cell types. The advent of transcriptional profiling, combined with powerful new purification schemes, changed this reality and transformed our understanding of the macroglial populations within the brain. Here, we chronicle the historical context and scientific setting for our efforts to transcriptionally profile neurons, astrocytes, and oligodendrocytes, and highlight some of the profound discoveries that were cultivated by these data.Following a lengthy battle with pancreatic cancer, Ben Barres passed away during the writing of this Progression piece. Among Ben's innumerable contributions to the greater scientific community, his addition of publicly available transcriptome databases of CNS cell types will forever remain a relic of his generous spirit and boundless scientific curiosity. Although he had impressively committed a majority of these enormous gene lists to memory, Ben could oftentimes be spotted at meetings buried in his cell phone on the Barres RNAseq database. Perhaps the only thing he enjoyed more than exploring these data himself, was knowing how useful these contributions had been (and will hopefully continue to be) to his scientific peers. Copyright © 2018 the authors 0270-6474/18/383149-05$15.00/0.

  4. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs

    PubMed Central

    Takeda, Jun-ichi; Suzuki, Yutaka; Nakao, Mitsuteru; Barrero, Roberto A.; Koyanagi, Kanako O.; Jin, Lihua; Motono, Chie; Hata, Hiroko; Isogai, Takao; Nagai, Keiichi; Otsuki, Tetsuji; Kuryshev, Vladimir; Shionyu, Masafumi; Yura, Kei; Go, Mitiko; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Wiemann, Stefan; Nomura, Nobuo; Sugano, Sumio; Gojobori, Takashi; Imanishi, Tadashi

    2006-01-01

    We report the first genome-wide identification and characterization of alternative splicing in human gene transcripts based on analysis of the full-length cDNAs. Applying both manual and computational analyses for 56 419 completely sequenced and precisely annotated full-length cDNAs selected for the H-Invitational human transcriptome annotation meetings, we identified 6877 alternative splicing genes with 18 297 different alternative splicing variants. A total of 37 670 exons were involved in these alternative splicing events. The encoded protein sequences were affected in 6005 of the 6877 genes. Notably, alternative splicing affected protein motifs in 3015 genes, subcellular localizations in 2982 genes and transmembrane domains in 1348 genes. We also identified interesting patterns of alternative splicing, in which two distinct genes seemed to be bridged, nested or having overlapping protein coding sequences (CDSs) of different reading frames (multiple CDS). In these cases, completely unrelated proteins are encoded by a single locus. Genome-wide annotations of alternative splicing, relying on full-length cDNAs, should lay firm groundwork for exploring in detail the diversification of protein function, which is mediated by the fast expanding universe of alternative splicing variants. PMID:16914452

  5. Expression of SMARCB1 (INI1) mutations in familial schwannomatosis.

    PubMed

    Smith, Miriam J; Walker, James A; Shen, Yiping; Stemmer-Rachamimov, Anat; Gusella, James F; Plotkin, Scott R

    2012-12-15

    Genetic changes in the SMARCB1 tumor suppressor gene have recently been reported in tumors and blood from families with schwannomatosis. Exon scanning of all nine SMARCB1 exons in genomic DNA from our cohort of families meeting the criteria for 'definite' or 'presumptive' schwannomatosis previously revealed constitutional alterations in 13 of 19 families (68%). Screening of four new familial schwannomatosis probands identified one additional constitutional alteration. We confirmed the presence of mRNA transcripts for two missense alterations, four mutations of conserved splice motifs and two additional mutations, in less conserved sequences, which also affect splicing. Furthermore, we found that transcripts for a rare 3'-untranslated region (c.*82C > T) alteration shared by four unrelated families did not produce splice variants but did show unequal allelic expression, suggesting that the alteration is either causative itself or linked to an unidentified causative mutation. Overexpression studies in cells lacking SMARCB1 suggest that mutant SMARCB1 proteins, like wild-type SMARCB1 protein, retain the ability to suppress cyclin D1 activity. These data, together with the expression of SMARCB1 protein in a proportion of cells from schwannomatosis-related schwannomas, suggest that these tumors develop through a mechanism that is distinct from that of rhabdoid tumors in which SMARCB1 protein is completely absent in tumor cells.

  6. Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma

    PubMed Central

    Gatto, Francesco; Nookaew, Intawat; Nielsen, Jens

    2014-01-01

    Several common oncogenic pathways have been implicated in the emergence of renowned metabolic features in cancer, which in turn are deemed essential for cancer proliferation and survival. However, the extent to which different cancers coordinate their metabolism to meet these requirements is largely unexplored. Here we show that even in the heterogeneity of metabolic regulation a distinct signature encompassed most cancers. On the other hand, clear cell renal cell carcinoma (ccRCC) strongly deviated in terms of metabolic gene expression changes, showing widespread down-regulation. We observed a metabolic shift that associates differential regulation of enzymes in one-carbon metabolism with high tumor stage and poor clinical outcome. A significant yet limited set of metabolic genes that explained the partial divergence of ccRCC metabolism correlated with loss of von Hippel-Lindau tumor suppressor (VHL) and a potential activation of signal transducer and activator of transcription 1. Further network-dependent analyses revealed unique defects in nucleotide, one-carbon, and glycerophospholipid metabolism at the transcript and protein level, which contrasts findings in other tumors. Notably, this behavior is recapitulated by recurrent loss of heterozygosity in multiple metabolic genes adjacent to VHL. This study therefore shows how loss of heterozygosity, hallmarked by VHL deletion in ccRCC, may uniquely shape tumor metabolism. PMID:24550497

  7. Proceedings from the NIMH symposium on "NeuroAIDS in Africa: neurological and neuropsychiatric complications of HIV".

    PubMed

    Buch, Shilpa; Chivero, Ernest T; Hoare, Jackie; Jumare, Jibreel; Nakasujja, Noeline; Mudenda, Victor; Paul, Robert; Kanmogne, Georgette D; Sacktor, Ned; Wood, Charles; Royal, Walter; Joseph, Jeymohan

    2016-10-01

    Despite major advances in HIV-1 treatment, the prevalence of HIV-associated neurocognitive disorders (HAND) remains a problem, particularly as individuals on suppressive treatment continue to live longer. To facilitate discussion on emerging and future directions in HAND research, a meeting was held in Durban, South Africa in March 2015 as part of the Society of Neuroscientists of Africa (SONA) conference. The objective of the meeting was to assess the impact of HIV subtype diversity on HAND and immunological dysfunction. The meeting brought together international leaders in the area of neurological complications of HIV-1 infection with special focus on the African population. Research presentations indicated that HAND was highly prevalent and that inflammatory cytokines and immune-activation played important roles in progression of neurocognitive impairment. Furthermore, children on antiretroviral therapy were also at risk for developing neurocognitive impairment. With respect to the effect of HIV-1 subtype diversity, analyses of HIV-1 clade C infection among South Africans revealed that clade C infection induced cognitive impairment that was independent of the substitution in HIV-1 Trans-Activator of Transcription (Tat; C31S). At the cellular level, a Zambian study showed that clade C infection resulted in reduced brain cell death compared with clade B infection suggesting clade specific variations in mediating brain cell injury. Furthermore, ex vivo Tat protein from clade CRF02_AG, prevalent in West/ Central Africa, exhibited reduced disruption of brain endothelium compared with clade B Tat protein. Discussions shed light on future research directions aimed at understanding biomarkers and disease mechanisms critical for HAND.

  8. Blue Ribbon Commission on America's Nuclear Future: Report to the Secretary of Energy

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    None

    2012-01-01

    Preamble The Blue Ribbon Commission on America’s Nuclear Future (BRC) was formed by the Secretary of Energy at the request of the President to conduct a comprehensive review of policies for managing the back end of the nuclear fuel cycle and recommend a new strategy. It was co-chaired by Rep. Lee H. Hamilton and Gen. Brent Scowcroft. Other Commissioners are Mr. Mark H. Ayers, the Hon. Vicky A. Bailey, Dr. Albert Carnesale, Sen. Pete Domenici, Ms. Susan Eisenhower, Sen. Chuck Hagel, Mr. Jonathan Lash, Dr. Allison M. Macfarlane, Dr. Richard A. Meserve, Dr. Ernest J. Moniz, Dr. Per Peterson, Mr.more » John Rowe, and Rep. Phil Sharp. The Commission and its subcommittees met more than two dozen times between March 2010 and January 2012 to hear testimony from experts and stakeholders, to visit nuclear waste management facilities in the United States and abroad, and to discuss the issues identified in its Charter. Additionally, in September and October 2011, the Commission held five public meetings, in different regions of the country, to hear feedback on its draft report. A wide variety of organizations, interest groups, and individuals provided input to the Commission at these meetings and through the submission of written materials. Copies of all of these submissions, along with records and transcripts of past meetings, are available at the BRC website (www.brc.gov). This report highlights the Commission’s findings and conclusions and presents recommendations for consideration by the Administration and Congress, as well as interested state, tribal and local governments, other stakeholders, and the public.« less

  9. Southern California Drosophila Conference: Irvine, CA - September 11, 2009.

    PubMed

    Rattner, Barbara P

    2009-01-01

    As has become tradition, this year's Southern California Drosophila Conference was hosted by the Developmental Biology Center (http://dbc.bio.uci.edu/) at the University of California, Irvine. On September 11, 2009, speakers from institutions in Los Angeles, Orange, Riverside, and San Diego Counties presented their latest results in an informal and friendly atmosphere and had the opportunity to learn about new resources and facilities, establish collaborations, and network about job openings and training opportunities. The talks presented covered the use of flies to study a variety of topics including the mechanisms of action of human pathogens, human diseases, and aging and lifespan extension. In addition, attendees heard about aspects of Drosophila neuronal development, olfactory behavior, transcriptional regulation, and signal transduction. Some of the highlights of the meeting are summarized in this brief report.

  10. Structural and functional adaptations of the mammalian nuclear envelope to meet the meiotic requirements.

    PubMed

    Link, Jana; Jahn, Daniel; Alsheimer, Manfred

    2015-01-01

    Numerous studies in the past years provided definite evidence that the nuclear envelope is much more than just a simple barrier. It rather constitutes a multifunctional platform combining structural and dynamic features to fulfill many fundamental functions such as chromatin organization, regulation of transcription, signaling, but also structural duties like maintaining general nuclear architecture and shape. One additional and, without doubt, highly impressive aspect is the recently identified key function of selected nuclear envelope components in driving meiotic chromosome dynamics, which in turn is essential for accurate recombination and segregation of the homologous chromosomes. Here, we summarize the recent work identifying new key players in meiotic telomere attachment and movement and discuss the latest advances in our understanding of the actual function of the meiotic nuclear envelope.

  11. [Intelligent videosurveillance and falls detection: Perceptions of professionals and managers].

    PubMed

    Lapierre, Nolwenn; Carpentier, Isabelle; St-Arnaud, Alain; Ducharme, Francine; Meunier, Jean; Jobidon, Mireille; Rousseau, Jacqueline

    2016-02-01

    Gerontechnologies can be used to detect accidental falls. However, existing systems do not entirely meet users' expectations. Our team developed an intelligent video-monitoring systems to fill these gaps. Authors advocate consulting potential users at the early stages of the design of gerontechnologies and integrating their suggestions. This study aims to explore health care workers' opinion regarding the intelligent video monitoring to detect falls by older adults living at home. This qualitative study explored the opinions of 31 participants using focus groups. Transcripts were analyzed using predetermined codes based on the competence model. Participants reported several advantages for using the intelligent video monitoring and provided suggestions for improving its use. The participants' suggestions and comments will help to improve the system and match it to users' needs. © CAOT 2015.

  12. Advanced genetic tools for plant biotechnology

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Liu, WS; Yuan, JS; Stewart, CN

    2013-10-09

    Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis ofmore » large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.« less

  13. Advanced genetic tools for plant biotechnology.

    PubMed

    Liu, Wusheng; Yuan, Joshua S; Stewart, C Neal

    2013-11-01

    Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

  14. Meeting Report: The Role of the Mobilome in Cancer.

    PubMed

    Ardeljan, Daniel; Taylor, Martin S; Burns, Kathleen H; Boeke, Jef D; Espey, Michael Graham; Woodhouse, Elisa C; Howcroft, Thomas Kevin

    2016-08-01

    Approximately half of the human genome consists of repetitive sequence attributed to the activities of mobile DNAs, including DNA transposons, RNA transposons, and endogenous retroviruses. Of these, only long interspersed elements (LINE-1 or L1) and sequences copied by LINE-1 remain mobile in our species today. Although cells restrict L1 activity by both transcriptional and posttranscriptional mechanisms, L1 derepression occurs in developmental and pathologic contexts, including many types of cancers. However, we have limited knowledge of the extent and consequences of L1 expression in premalignancies and cancer. Participants in this NIH strategic workshop considered key questions to enhance our understanding of mechanisms and roles the mobilome may play in cancer biology. Cancer Res; 76(15); 4316-9. ©2016 AACR. ©2016 American Association for Cancer Research.

  15. Working Conditions of the Nursing Workforce Excerpts from a Policy Roundtable at AcademyHealth's 2003 Annual Research Meeting

    PubMed Central

    Hope, Hollis A

    2004-01-01

    The role of nursing in the delivery of health care has emerged as a complex and cross-cutting issue ripe for inquiry and multidisciplinary research. Indeed, problems in the nursing workforce have risen high on the agendas on many influential organizations, including the American Academy of Nursing, the Institute of Medicine, the National Quality Forum, The Robert Wood Johnson Foundation, and others. In an effort to clarify current research issues and advance an agenda for future investigations, Dr. Peter Buerhaus at Vanderbilt University organized a round table focused on the working conditions of the nursing workforce at the AcademyHealth 2003 Annual Research Meeting in Nashville, Tenn. Chaired by the University of California, Los Angeles, School of Public Health's Jack Needleman, the “Working Conditions of the Nursing Workforce” roundtable proved to be a provocative exchange of views among researchers and users of research. Participants shared background about their role in advancing the research, identified gaps in current research, and suggested specific areas for further research. What follows is an edited transcript of the Roundtable that, in addition to Dr. Needleman, included Ellen Kurtzman, National Quality Forum; Barbara Mark, University of North Carolina, Chapel Hill; Lori Melichar, The Robert Wood Johnson Foundation; and Donald Steinwachs, Johns Hopkins University. PMID:15149473

  16. "They want to come to school": Work-based education programs to prevent the social exclusion of vulnerable youth.

    PubMed

    Hutchinson, Nancy L; Versnel, Joan; Poth, Cheryl; Berg, Derek; deLugt, Jenn; Dalton, C J; Chin, Peter; Munby, Hugh

    2011-01-01

    This paper describes and compares exemplary work-based education (WBE) programs in Ontario Canada designed to meet the needs of two groups of vulnerable youth - at-risk youth and youth with severe disabilities. Two focus group interviews were held, one with professionals from exemplary programs designed to meet the needs of at-risk youth and one with professionals from exemplary programs for youth with severe disabilities. Standard qualitative analyses were conducted on each focus group transcript to generate themes which were subsequently grouped into larger patterns. Then cross-case analyses identified consistencies and unique features within the two types of WBE programs. Two major patterns that characterize the WBE programs emerged from the analyses: the first pattern described the programmatic approaches to WBE appropriate for each type of type of student (which included themes such as the need for an alternative learning environment for at-risk youth), and the second pattern highlighted the rationale for each kind of program (which included themes like ensuring equity for youth with severe disabilities). The findings suggest that schools should continue to provide distinct WBE programs for each of these groups of vulnerable youth - at-risk youth and youth with severe disabilities.

  17. Information, communication, and online tool needs of Hispanic family caregivers of individuals with Alzheimer's disease and related dementias.

    PubMed

    Iribarren, Sarah; Stonbraker, Samantha; Suero-Tejeda, Niurka; Granja, Maribel; Luchsinger, José A; Mittelman, Mary; Bakken, Suzanne; Lucero, Robert J

    2018-03-05

    To identify the information and communication needs of Hispanic family caregivers for individuals with Alzheimer's Disease and Related Dementias (ADRD) and the manner in which online tools may meet those needs. We conducted 11 participatory design sessions with 10 English- and 14 Spanish-speaking urban-dwelling Hispanic family caregivers and gathered data using a survey, collage assemblage, and audio and video recordings. Four investigators analyzed transcripts of audio recordings with a coding framework informed by several conceptual models. Participants had an average age of 59.7 years, were mostly female (79.2%), and had cared for a family member with ADRD for an average of 6.5 years. All participants accessed the Internet at least once a week with 75% ≥ daily. Most used the Internet to look up health information. All participants reported caregiver attributes including awareness of the disease symptoms or behaviors. The majority reported information needs/tasks (91.7%), communication needs/tasks (87.5%), and need for online tools (79.2%). Hispanic caregivers of individuals with ADRD reported key information and communication needs/tasks. Only Spanish-speaking participants reported Internet and technology use deficits suggesting the requirement for further technology support. Data show a need for online tools to meet the needs of caregivers.

  18. [Modification of nursing practice through reflection: participatory action research].

    PubMed

    Delgado Hito, P; Sola Prado, A; Mirabete Rodríguez, I; Torrents Ros, R; Blasco Afonso, M; Barrero Pedraza, R; Catalá Gil, N; Mateos Dávila, A; Quinteiro Canedo, M

    2001-01-01

    Technology and complex techniques are inevitably playing an increasing role in intensive care units. They continue to characterize nursing care and in some cases dehumanize it. The general aim of this study was to stimulate reflection on nursing care. The study was based on the participation of the investigators with the goal of producing changes in nursing practice. Qualitative methodology in the form of participatory action research and the Kemmis and McTaggart method were used. Data were collected through systematic observation, seven group meetings and document analysis. Eight nurses took part in the study. The meetings were recorded and transcribed verbatim into a computer. This process and the meaning of the verbatim transcription (codification/categorization process and document synthesis cards) were analyzed. The results of this study enabled exploration of the change in nursing practice and showed that the reflection in action method stimulates changes in practice. The new way of conceiving nursing action has increased nursing care quality and its humanization since it shows greater respect for the patient, provides families with closer contact and greater support, improves coordination of nursing care acts and increases collaboration among professionals.In conclusion, participatory action research is a valid and appropriate method that nurses can use to modify their daily practice.

  19. A combined HST and XMM-Newton campaign for the magnetic O9.7 V star HD 54879. Constraining the weak-wind problem of massive stars

    NASA Astrophysics Data System (ADS)

    Shenar, T.; Oskinova, L. M.; Järvinen, S. P.; Luckas, P.; Hainich, R.; Todt, H.; Hubrig, S.; Sander, A. A. C.; Ilyin, I.; Hamann, W.-R.

    2017-10-01

    Context. HD 54879 (O9.7 V) is one of a dozen O-stars for which an organized atmospheric magnetic field has been detected. Despite their importance, little is known about the winds and evolution of magnetized massive stars. Aims: To gain insights into the interplay between atmospheres, winds, and magnetic fields of massive stars, we acquired UV and X-ray data of HD 54879 using the Hubble Space Telescope and the XMM-Newton satellite. In addition, 35 optical amateur spectra were secured to study the variability of HD 54879. Methods: A multiwavelength (X-ray to optical) spectral analysis is performed using the Potsdam Wolf-Rayet (PoWR) model atmosphere code and the xspec software. Results: The photospheric parameters (T∗ = 30.5 kK, log g = 4.0 [cm s-2], log L = 4.45 [L⊙]) are typical for an O9.7 V star. The microturbulent, macroturbulent, and projected rotational velocities are lower than previously suggested (ξph,vmac,vsini ≤ 4 km s-1). An initial mass of 16 M⊙ and an age of 5 Myr are inferred from evolutionary tracks. We derive a mean X-ray emitting temperature of log TX = 6.7 [K] and an X-ray luminosity of LX = 1 × 1032 erg s-1. Short- and long-scale variability is seen in the Hα line, but only a very long period of P ≈ 5 yr could be estimated. Assessing the circumstellar density of HD 54879 using UV spectra, we can roughly estimate the mass-loss rate HD 54879 would have in the absence of a magnetic field as log ṀB = 0 ≈ -9.0 [M⊙ yr-1]. The magnetic field traps the stellar wind up to the Alfvén radius rA ≳ 12 R∗, implying that its true mass-loss rate is log Ṁ ≲ -10.2 [M⊙ yr-1]. Hence, density enhancements around magnetic stars can be exploited to estimate mass-loss rates of non-magnetic stars of similar spectral types, essential for resolving the weak wind problem. Conclusions: Our study confirms that strongly magnetized stars lose little or no mass, and supplies important constraints on the weak-wind problem of massive main sequence stars. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA Member States and NASA.

  20. Expression of SMARCB1 (INI1) mutations in familial schwannomatosis

    PubMed Central

    Smith, Miriam J.; Walker, James A.; Shen, Yiping; Stemmer-Rachamimov, Anat; Gusella, James F.; Plotkin, Scott R.

    2012-01-01

    Genetic changes in the SMARCB1 tumor suppressor gene have recently been reported in tumors and blood from families with schwannomatosis. Exon scanning of all nine SMARCB1 exons in genomic DNA from our cohort of families meeting the criteria for ‘definite’ or ‘presumptive’ schwannomatosis previously revealed constitutional alterations in 13 of 19 families (68%). Screening of four new familial schwannomatosis probands identified one additional constitutional alteration. We confirmed the presence of mRNA transcripts for two missense alterations, four mutations of conserved splice motifs and two additional mutations, in less conserved sequences, which also affect splicing. Furthermore, we found that transcripts for a rare 3′-untranslated region (c.*82C > T) alteration shared by four unrelated families did not produce splice variants but did show unequal allelic expression, suggesting that the alteration is either causative itself or linked to an unidentified causative mutation. Overexpression studies in cells lacking SMARCB1 suggest that mutant SMARCB1 proteins, like wild-type SMARCB1 protein, retain the ability to suppress cyclin D1 activity. These data, together with the expression of SMARCB1 protein in a proportion of cells from schwannomatosis-related schwannomas, suggest that these tumors develop through a mechanism that is distinct from that of rhabdoid tumors in which SMARCB1 protein is completely absent in tumor cells. PMID:22949514

  1. First-Person Perspectives on Dual Diagnosis Anonymous (DDA): A Qualitative Study.

    PubMed

    Roush, Sean; Monica, Corbett; Carpenter-Song, Elizabeth; Drake, Robert E

    2015-01-01

    People with dually diagnosed substance abuse and mental illnesses often feel alienated at traditional 12-step meetings, yet they need the peer support provided by such groups. Dual Diagnosis Anonymous (DDA) is a peer-support program specifically for people with co-occurring disorders, which addresses many of the factors that members find alienating about traditional 12-step groups. This study aimed to elicit first-person perspectives on DDA. Occupational therapy students conducted 13 focus groups with 106 DDA members in three settings: the community (6 groups, n = 36), correctional facilities (5 groups, n = 53), and the state psychiatric hospital (2 groups, n = 17). Researchers inductively analyzed focus group transcripts to identify prominent themes. The vast majority of participants were between the ages of 18 and 49 (n = 87, 82.1%) and were non-Hispanic/White (n = 82, 77.4%). Most participants had been using substances for more than 10 years and had a diagnosed mental illness for more than 10 years. The most common substance of choice among those in the community and corrections setting was multiple substances, while those in the state hospital identified alcohol most often. Bipolar disorder was the most common mental illness diagnosis among participants in the state hospital, but depression and anxiety were the two most common diagnoses in the community and corrections participants. Four primary themes emerged from the qualitative analysis: (1) feeling accepted by others in the group, (2) understanding the interactive nature of dual disorders, (3) the open discussions in DDA meetings, and (4) a focus on hope and recovery from both illnesses. DDA provides a helpful alternative for individuals who do not feel comfortable at traditional 12-step groups due to their mental illness. Members value the acceptance, understanding, discussion, and hope in DDA meetings.

  2. iSeq: Web-Based RNA-seq Data Analysis and Visualization.

    PubMed

    Zhang, Chao; Fan, Caoqi; Gan, Jingbo; Zhu, Ping; Kong, Lei; Li, Cheng

    2018-01-01

    Transcriptome sequencing (RNA-seq) is becoming a standard experimental methodology for genome-wide characterization and quantification of transcripts at single base-pair resolution. However, downstream analysis of massive amount of sequencing data can be prohibitively technical for wet-lab researchers. A functionally integrated and user-friendly platform is required to meet this demand. Here, we present iSeq, an R-based Web server, for RNA-seq data analysis and visualization. iSeq is a streamlined Web-based R application under the Shiny framework, featuring a simple user interface and multiple data analysis modules. Users without programming and statistical skills can analyze their RNA-seq data and construct publication-level graphs through a standardized yet customizable analytical pipeline. iSeq is accessible via Web browsers on any operating system at http://iseq.cbi.pku.edu.cn .

  3. Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms

    PubMed Central

    Groussman, Ryan D.; Parker, Micaela S.; Armbrust, E. Virginia

    2015-01-01

    Ferroproteins arose early in Earth’s history, prior to the emergence of oxygenic photosynthesis and the subsequent reduction of bioavailable iron. Today, iron availability limits primary productivity in about 30% of the world’s oceans. Diatoms, responsible for nearly half of oceanic primary production, have evolved molecular strategies for coping with variable iron concentrations. Our understanding of the evolutionary breadth of these strategies has been restricted by the limited number of species for which molecular sequence data is available. To uncover the diversity of strategies marine diatoms employ to meet cellular iron demands, we analyzed 367 newly released marine microbial eukaryotic transcriptomes, which include 47 diatom species. We focused on genes encoding proteins previously identified as having a role in iron management: iron uptake (high-affinity ferric reductase, multi-copper oxidase, and Fe(III) permease); iron storage (ferritin); iron-induced protein substitutions (flavodoxin/ferredoxin, and plastocyanin/cytochrome c6) and defense against reactive oxygen species (superoxide dismutases). Homologs encoding the high-affinity iron uptake system components were detected across the four diatom Classes suggesting an ancient origin for this pathway. Ferritin transcripts were also detected in all Classes, revealing a more widespread utilization of ferritin throughout diatoms than previously recognized. Flavodoxin and plastocyanin transcripts indicate possible alternative redox metal strategies. Predicted localization signals for ferredoxin identify multiple examples of gene transfer from the plastid to the nuclear genome. Transcripts encoding four superoxide dismutase metalloforms were detected, including a putative nickel-coordinating isozyme. Taken together, our results suggest that the majority of iron metabolism genes in diatoms appear to be vertically inherited with functional diversity achieved via possible neofunctionalization of paralogs. This refined view of iron use strategies in diatoms elucidates the history of these adaptations, and provides potential molecular markers for determining the iron nutritional status of different diatom species in environmental samples. PMID:26052941

  4. Transcriptome of the inflorescence meristems of the biofuel plant Jatropha curcas treated with cytokinin.

    PubMed

    Pan, Bang-Zhen; Chen, Mao-Sheng; Ni, Jun; Xu, Zeng-Fu

    2014-11-17

    Jatropha curcas, whose seed content is approximately 30-40% oil, is an ideal feedstock for producing biodiesel and bio-jet fuels. However, Jatropha plants have a low number of female flowers, which results in low seed yield that cannot meet the needs of the biofuel industry. Thus, increasing the number of female flowers is critical for the improvement of Jatropha seed yield. Our previous findings showed that cytokinin treatment can increase the flower number and female to male ratio and also induce bisexual flowers in Jatropha. The mechanisms underlying the influence of cytokinin on Jatropha flower development and sex determination, however, have not been clarified. This study examined the transcriptional levels of genes involved in the response to cytokinin in Jatropha inflorescence meristems at different time points after cytokinin treatment by 454 sequencing, which gave rise to a total of 294.6 Mb of transcript sequences. Up-regulated and down-regulated annotated and novel genes were identified, and the expression levels of the genes of interest were confirmed by qRT-PCR. The identified transcripts include those encoding genes involved in the biosynthesis, metabolism, and signaling of cytokinin and other plant hormones, flower development and cell division, which may be related to phenotypic changes of Jatropha in response to cytokinin treatment. Our analysis indicated that Jatropha orthologs of the floral organ identity genes known as ABCE model genes, JcAP1,2, JcPI, JcAG, and JcSEP1,2,3, were all significantly repressed, with an exception of one B-function gene JcAP3 that was shown to be up-regulated by BA treatment, indicating different mechanisms to be involved in the floral organ development of unisexual flowers of Jatropha and bisexual flowers of Arabidopsis. Several cell division-related genes, including JcCycA3;2, JcCycD3;1, JcCycD3;2 and JcTSO1, were up-regulated, which may contribute to the increased flower number after cytokinin treatment. This study presents the first report of global expression patterns of cytokinin-regulated transcripts in Jatropha inflorescence meristems. This report laid the foundation for further mechanistic studies on Jatropha and other non-model plants responding to cytokinin. Moreover, the identification of functional candidate genes will be useful for generating superior varieties of high-yielding transgenic Jatropha.

  5. Selenium requirements based on muscle and kidney selenoprotein enzyme activity and transcript expression in the turkey poult (Meleagris gallopavo).

    PubMed

    Taylor, Rachel M; Sunde, Roger A

    2017-01-01

    The current NRC selenium (Se) requirement for turkeys is 0.2 μg Se/g diet. We previously fed turkey poults a Se-deficient diet (0.005 μg Se/g) supplemented with 10 graded levels of Se (0, 0.025, 0.05, 0.1, 0.2, 0.3, 0.4, 0.5, 0.75, 1.0 μg Se/g as Na2SeO3, 5/treatment) for 4 wk, and found that the minimum dietary Se requirement was 0.3 μg Se/g based on selenoprotein enzyme activity in blood, liver, gizzard and pancreas. Because the turkey is primarily a production animal, we expanded this analysis to kidney, heart, breast and thigh. Se concentrations in Se-deficient poults were 5.0, 9.8, 33, and 15% of levels in poults fed 0.4 μg Se/g in liver, kidney, thigh and breast, respectively. Increasing Se supplementation resulted in hyperbolic response curves for all tissues; breakpoint analysis indicated minimum Se requirements of 0.34-0.36 μg Se/g based on tissue Se levels in liver, kidney and thigh. Similarly, GPX1 activity in muscle tissues and kidney responded hyperbolically to increasing dietary Se, reaching well-defined plateaus with breakpoints at 0.30-0.36 μg Se/g. Minimum Se requirements based on GPX4 activity were 0.30-0.32 μg Se/g for breast and thigh. Selenoprotein transcript expression decreased significantly in Se deficiency for only 2, 3, 5, and 6 mRNA in breast, thigh, heart, and kidney, respectively, out of 24 known avian selenoproteins. Se response curves for regulated selenoprotein transcripts were hyperbolic, and reached well-defined plateaus with breakpoints in a narrow range of 0.08-0.19 μg Se/g. No selenoprotein transcript was altered by supernutritional Se. In summary, these results clearly indicate that the NRC dietary Se requirement should be raised to 0.4 μg Se/g, at least for poults, to meet the nutritional needs of the young turkey. The Se response curve plateaus further show that limits for turkey supplementation with selenite could safely be raised to 0.5 μg Se/g diet.

  6. Understanding diagnostic variability in breast pathology: lessons learned from an expert consensus review panel

    PubMed Central

    Allison, Kimberly H; Reisch, Lisa M; Carney, Patricia A; Weaver, Donald L; Schnitt, Stuart J; O’Malley, Frances P; Geller, Berta M; Elmore, Joann G

    2015-01-01

    Aims To gain a better understanding of the reasons for diagnostic variability, with the aim of reducing the phenomenon. Methods and results In preparation for a study on the interpretation of breast specimens (B-PATH), a panel of three experienced breast pathologists reviewed 336 cases to develop consensus reference diagnoses. After independent assessment, cases coded as diagnostically discordant were discussed at consensus meetings. By the use of qualitative data analysis techniques, transcripts of 16 h of consensus meetings for a subset of 201 cases were analysed. Diagnostic variability could be attributed to three overall root causes: (i) pathologist-related; (ii) diagnostic coding/study methodology-related; and (iii) specimen-related. Most pathologist-related root causes were attributable to professional differences in pathologists’ opinions about whether the diagnostic criteria for a specific diagnosis were met, most frequently in cases of atypia. Diagnostic coding/study methodology-related root causes were primarily miscategorizations of descriptive text diagnoses, which led to the development of a standardized electronic diagnostic form (BPATH-Dx). Specimen-related root causes included artefacts, limited diagnostic material, and poor slide quality. After re-review and discussion, a consensus diagnosis could be assigned in all cases. Conclusions Diagnostic variability is related to multiple factors, but consensus conferences, standardized electronic reporting formats and comments on suboptimal specimen quality can be used to reduce diagnostic variability. PMID:24511905

  7. [Pedagogic focus-group in pediatrics].

    PubMed

    Merlin, E; Chausset, A; Verdan, M; Cambon, B; Sarret, C; Kanold, J; Chazal, J; Labbé, A

    2016-08-01

    To assess a new behavioral teaching technique called "focus group pedagogy" (FGP), which consists in a three-step meeting between sick children's parents and medical students (first with students alone, then with parents and students together, then with students alone). This qualitative research ran two sessions (each totaling four to six parents and six students) in which parents were questioned on four main themes: their knowledge of the medical hierarchy, their ability to identify the people in the hospital, their communication with medical staff, and the overall care delivered to their children. A thematic analysis of the verbatim transcript was performed. In the FGP sessions, medical students voiced opinions on their degree of insertion in the medical and paramedical staff, and reported their presence as ambiguous, between care and learning. Parents voiced their experience of their child's hospital stay but also their wider conception of the parent/patient-physician relationship based on their parent-of-patient/parent-as-patient experiences. The meeting of parents and students highlighted divergent narratives on relationships with caregivers, communication, attitudes, knowledge, and competencies. This approach made it possible to hear and learn the point of view "from the other side," which proved beneficial for students, session leaders, and the care unit organization alike. FGP is a novel and easy way to discover diverse narratives and the technique is feasible and beneficial in pediatric settings. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  8. President Barack Obama addresses the 146th annual meeting of the National Academy of Sciences.

    PubMed

    2009-06-16

    On April 27, 2009, President Barack Obama addressed members of the National Academy of Sciences (NAS) gathered at its 146th annual meeting in Washington, D.C. In his speech, the president shared his plans to give science and technology a central role in the nation's future and an immediate place in America's economic renewal. He outlined steps he is taking to increase research spending, achieve energy independence, and improve science education. Included was what Mr. Obama cited as the largest commitment to scientific research in American history-devoting more than 3% of our gross domestic product to research and development. "Next, we are restoring science to its rightful place," Mr. Obama told a packed NAS auditorium audience. "Under my administration, the days of science taking a backseat to ideology are over." He appealed to scientists' sense of personal responsibility to reach and educate young Americans: "I want to challenge you to use your love and knowledge of science to spark a sense of wonder and excitement in a new generation." President Obama was welcomed to the National Academy of Sciences by President Ralph J. Cicerone and John P. Holdren, Assistant to the President for Science and Technology and Director of the White House Office of Science and Technology Policy. The following is a transcript of that speech.

  9. Traditional/restrictive vs patient-centered intensive care unit visitation: perceptions of patients' family members, physicians, and nurses.

    PubMed

    Riley, Bettina H; White, Joseph; Graham, Shannon; Alexandrov, Anne

    2014-07-01

    Patient-centered intensive care units (ICUs) are advocated by professional organizations for critical care nursing and medicine. The patient-centered ICU paradigm recognizes the patient-family unit as inseparable and supports visitation designed to meet the needs of patients and patients' families. To understand perceptions about patient-centered ICUs among patients' family members, physicians, and nurses from 5 ICUs that had restrictive visitation and to guide development of a patient-centered, open visitation paradigm. Patients' family members, nurses, and physicians from 5 ICUs with a traditional/restrictive visitation policy at a southeastern academic, tertiary care hospital were invited to participate in focus group meetings to understand perceptions about patient-centered care. All qualitative work was taped, transcribed, reviewed, and corrected after each session. Corrected transcripts and observer notes were integrated and coded. Patients' families identified facilitators of patient-centeredness as nurses' and physicians' communication, concern, compassion, closeness, and flexibility. However, competing roles of control over the patient's health care served as barriers to a patient-centered paradigm. Patient-centered care is an expectation among patients, patients' families, and health quality advocates. These exploratory methods increased understanding of the powerful perceptions of family members, physicians, and nurses involved with patient care and provided direction to plan interventions to implement patient-centered, family-supportive ICU services. ©2014 American Association of Critical-Care Nurses.

  10. President Barack Obama addresses the 146th Annual Meeting of the National Academy of Sciences

    PubMed Central

    2009-01-01

    On April 27, 2009, President Barack Obama addressed members of the National Academy of Sciences (NAS) gathered at its 146th annual meeting in Washington, D.C. In his speech, the president shared his plans to give science and technology a central role in the nation's future and an immediate place in America's economic renewal. He outlined steps he is taking to increase research spending, achieve energy independence, and improve science education. Included was what Mr. Obama cited as the largest commitment to scientific research in American history—devoting more than 3% of our gross domestic product to research and development. “Next, we are restoring science to its rightful place,” Mr. Obama told a packed NAS auditorium audience. “Under my administration, the days of science taking a backseat to ideology are over.” He appealed to scientists' sense of personal responsibility to reach and educate young Americans: “I want to challenge you to use your love and knowledge of science to spark a sense of wonder and excitement in a new generation.” President Obama was welcomed to the National Academy of Sciences by President Ralph J. Cicerone and John P. Holdren, Assistant to the President for Science and Technology and Director of the White House Office of Science and Technology Policy. The following is a transcript of that speech.* PMID:19502426

  11. Engaging multilevel stakeholders in an implementation trial of evidence-based quality improvement in VA women's health primary care.

    PubMed

    Hamilton, Alison B; Brunner, Julian; Cain, Cindy; Chuang, Emmeline; Luger, Tana M; Canelo, Ismelda; Rubenstein, Lisa; Yano, Elizabeth M

    2017-09-01

    The Veterans Health Administration (VHA) has undertaken primary care transformation based on patient-centered medical home (PCMH) tenets. VHA PCMH models are designed for the predominantly male Veteran population, and require tailoring to meet women Veterans' needs. We used evidence-based quality improvement (EBQI), a stakeholder-driven implementation strategy, in a cluster randomized controlled trial across 12 sites (eight EBQI, four control) that are members of a Practice-Based Research Network. EBQI involves engaging multilevel, inter-professional leaders and staff as stakeholders in reviewing evidence and setting QI priorities. The goal of this analysis was to examine processes of engaging stakeholders in early implementation of EBQI to tailor VHA's medical home for women. Four inter-professional regional stakeholder planning meetings were conducted; these meetings engaged stakeholders by providing regional data about gender disparities in Veterans' care experiences. Subsequent to each meeting, qualitative interviews were conducted with 87 key stakeholders (leaders and staff). Stakeholders were asked to describe QI efforts and the use of data to change aspects of care, including women's health care. Interview transcripts were summarized and coded using a hybrid deductive/inductive analytic approach. The presentation of regional-level data about gender disparities resulted in heightened awareness and stakeholder buy-in and decision-making related to women's health-focused QI. Interviews revealed that stakeholders were familiar with QI, with regional and facility leaders aware of inter-disciplinary committees and efforts to foster organizational change, including PCMH transformation. These efforts did not typically focus on women's health, though some informal efforts had been undertaken. Barriers to engaging in QI included lack of communication across clinical service lines, fluidity in staffing, and lack of protected time. Inter-professional, multilevel stakeholders need to be engaged in implementation early, with data and discussion that convey the importance and relevance of a new initiative. Stakeholder perspectives on institutional norms (e.g., gender norms) and readiness for population-specific QI are useful drivers of clinical initiatives designed to transform care for clinical subpopulations.

  12. Brain pathology in myotonic dystrophy: when tauopathy meets spliceopathy and RNAopathy

    PubMed Central

    Caillet-Boudin, Marie-Laure; Fernandez-Gomez, Francisco-Jose; Tran, Hélène; Dhaenens, Claire-Marie; Buee, Luc; Sergeant, Nicolas

    2013-01-01

    Myotonic dystrophy (DM) of type 1 and 2 (DM1 and DM2) are inherited autosomal dominant diseases caused by dynamic and unstable expanded microsatellite sequences (CTG and CCTG, respectively) in the non-coding regions of the genes DMPK and ZNF9, respectively. These mutations result in the intranuclear accumulation of mutated transcripts and the mis-splicing of numerous transcripts. This so-called RNA gain of toxic function is the main feature of an emerging group of pathologies known as RNAopathies. Interestingly, in addition to these RNA inclusions, called foci, the presence of neurofibrillary tangles (NFT) in patient brains also distinguishes DM as a tauopathy. Tauopathies are a group of nearly 30 neurodegenerative diseases that are characterized by intraneuronal protein aggregates of the microtubule-associated protein Tau (MAPT) in patient brains. Furthermore, a number of neurodegenerative diseases involve the dysregulation of splicing regulating factors and have been characterized as spliceopathies. Thus, myotonic dystrophies are pathologies resulting from the interplay among RNAopathy, spliceopathy, and tauopathy. This review will describe how these processes contribute to neurodegeneration. We will first focus on the tauopathy associated with DM1, including clinical symptoms, brain histology, and molecular mechanisms. We will also discuss the features of DM1 that are shared by other tauopathies and, consequently, might participate in the development of a tauopathy. Moreover, we will discuss the determinants common to both RNAopathies and spliceopathies that could interfere with tau-related neurodegeneration. PMID:24409116

  13. Smartphone-Imaged HIV-1 Reverse-Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) on a Chip from Whole Blood

    PubMed Central

    Damhorst, Gregory L.; Duarte-Guevara, Carlos; Chen, Weili; Ghonge, Tanmay; Cunningham, Brian T.; Bashir, Rashid

    2015-01-01

    Viral load measurements are an essential tool for the long-term clinical care of hum an immunodeficiency virus (HIV)-positive individuals. The gold standards in viral load instrumentation, however, are still too limited by their size, cost, and sophisticated operation for these measurements to be ubiquitous in remote settings with poor healthcare infrastructure, including parts of the world that are disproportionately affected by HIV infection. The challenge of developing a point-of-care platform capable of making viral load more accessible has been frequently approached but no solution has yet emerged that meets the practical requirements of low cost, portability, and ease-of-use. In this paper, we perform reverse-transcription loop-mediated isothermal amplification (RT-LAMP) on minimally processed HIV-spiked whole blood samples with a microfluidic and silicon microchip platform, and perform fluorescence measurements with a consumer smartphone. Our integrated assay shows amplification from as few as three viruses in a ~ 60 nL RT-LAMP droplet, corresponding to a whole blood concentration of 670 viruses per µL of whole blood. The technology contains greater power in a digital RT-LAMP approach that could be scaled up for the determination of viral load from a finger prick of blood in the clinical care of HIV-positive individuals. We demonstrate that all aspects of this viral load approach, from a drop of blood to imaging the RT-LAMP reaction, are compatible with lab-on-a-chip components and mobile instrumentation. PMID:26705482

  14. The past and presence of gene targeting: from chemicals and DNA via proteins to RNA.

    PubMed

    Geel, T M; Ruiters, M H J; Cool, R H; Halby, L; Voshart, D C; Andrade Ruiz, L; Niezen-Koning, K E; Arimondo, P B; Rots, M G

    2018-06-05

    The ability to target DNA specifically at any given position within the genome allows many intriguing possibilities and has inspired scientists for decades. Early gene-targeting efforts exploited chemicals or DNA oligonucleotides to interfere with the DNA at a given location in order to inactivate a gene or to correct mutations. We here describe an example towards correcting a genetic mutation underlying Pompe's disease using a nucleotide-fused nuclease (TFO-MunI). In addition to the promise of gene correction, scientists soon realized that genes could be inactivated or even re-activated without inducing potentially harmful DNA damage by targeting transcriptional modulators to a particular gene. However, it proved difficult to fuse protein effector domains to the first generation of programmable DNA-binding agents. The engineering of gene-targeting proteins (zinc finger proteins (ZFPs), transcription activator-like effectors (TALEs)) circumvented this problem. The disadvantage of protein-based gene targeting is that a fusion protein needs to be engineered for every locus. The recent introduction of CRISPR/Cas offers a flexible approach to target a (fusion) protein to the locus of interest using cheap designer RNA molecules. Many research groups now exploit this platform and the first human clinical trials have been initiated: CRISPR/Cas has kicked off a new era of gene targeting and is revolutionizing biomedical sciences.This article is part of a discussion meeting issue 'Frontiers in epigenetic chemical biology'. © 2018 The Author(s).

  15. The feasibility of ethnodrama as intervention to highlight late-life potential for nursing students and older adults.

    PubMed

    Eaton, Jacqueline

    2015-01-01

    One barrier to the expansion of geriatric health care providers is the limited desire of nursing students to work with older adults. The purpose of this study is to evaluate the feasibility of using ethnodrama as an intervention to highlight late-life potential. Twelve baccalaureate nursing students were paired with 12 residents of an assisted living facility to complete transformative learning activities focused on the topic of late-life potential culminating in a performance of an ethnodrama developed from these data. Transcripts of initial student meetings, self-reflections, the performance, postperformance discussion, and open-ended survey questions were analyzed using in vivo and pattern coding. Older adult participants recognized and emphasized positive late-life potential, whereas students explored potential throughout the life span and reflected on its meaning in their own lives. Increasing discussion about late-life potential may alter the stigma associated with aging.

  16. The new nuclear west: Uranium milling as community on Colorado's western slope

    NASA Astrophysics Data System (ADS)

    Tidwell, Abraham S. D.

    In mid-2007, Energy Fuels, a Toronto-based uranium mining and milling company, announced their intent to build Piñon Ridge, the first new conventional uranium mill in the United States in 30 years. The prospect of a return to uranium milling has mobilized community support to bring back an industry some see as both familiar and capable of supporting and growing their communities. Using transcripts generated during the Colorado Department of Public Health and Environment's public meetings and hearings during 2010 and 2012, this study examines how proponents of the mill frame the socioeconomic advantages of bringing the industry back. Applying Kinsella's bounded constitutive model of communication, this study shows that the community and the uranium mill are bound in a "sorge-enframing" duality where the care generated by each binds the other to the recalcitrant nature of the uranium industry and preconceived notions of socioeconomic development, respectively.

  17. Oxidative Stress in Placenta: Health and Diseases

    PubMed Central

    Wu, Fan; Tian, Fu-Ju; Lin, Yi

    2015-01-01

    During pregnancy, development of the placenta is interrelated with the oxygen concentration. Embryo development takes place in a low oxygen environment until the beginning of the second trimester when large amounts of oxygen are conveyed to meet the growth requirements. High metabolism and oxidative stress are common in the placenta. Reactive oxidative species sometimes harm placental development, but they are also reported to regulate gene transcription and downstream activities such as trophoblast proliferation, invasion, and angiogenesis. Autophagy and apoptosis are two crucial, interconnected processes in the placenta that are often influenced by oxidative stress. The proper interactions between them play an important role in placental homeostasis. However, an imbalance between the protective and destructive mechanisms of autophagy and apoptosis seems to be linked with pregnancy-related disorders such as miscarriage, preeclampsia, and intrauterine growth restriction. Thus, potential therapies to hold oxidative stress in leash, promote placentation, and avoid unwanted apoptosis are discussed. PMID:26693479

  18. The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes.

    PubMed

    Xie, Yuan; Bergström, Tobias; Jiang, Yiwen; Johansson, Patrik; Marinescu, Voichita Dana; Lindberg, Nanna; Segerman, Anna; Wicher, Grzegorz; Niklasson, Mia; Baskaran, Sathishkumar; Sreedharan, Smitha; Everlien, Isabelle; Kastemar, Marianne; Hermansson, Annika; Elfineh, Lioudmila; Libard, Sylwia; Holland, Eric Charles; Hesselager, Göran; Alafuzoff, Irina; Westermark, Bengt; Nelander, Sven; Forsberg-Nilsson, Karin; Uhrbom, Lene

    2015-10-01

    Glioblastoma (GBM) is the most frequent and malignant form of primary brain tumor. GBM is essentially incurable and its resistance to therapy is attributed to a subpopulation of cells called glioma stem cells (GSCs). To meet the present shortage of relevant GBM cell (GC) lines we developed a library of annotated and validated cell lines derived from surgical samples of GBM patients, maintained under conditions to preserve GSC characteristics. This collection, which we call the Human Glioblastoma Cell Culture (HGCC) resource, consists of a biobank of 48 GC lines and an associated database containing high-resolution molecular data. We demonstrate that the HGCC lines are tumorigenic, harbor genomic lesions characteristic of GBMs, and represent all four transcriptional subtypes. The HGCC panel provides an open resource for in vitro and in vivo modeling of a large part of GBM diversity useful to both basic and translational GBM research.

  19. Identification of GPC2 as an Oncoprotein and Candidate Immunotherapeutic Target in High-Risk Neuroblastoma.

    PubMed

    Bosse, Kristopher R; Raman, Pichai; Zhu, Zhongyu; Lane, Maria; Martinez, Daniel; Heitzeneder, Sabine; Rathi, Komal S; Kendsersky, Nathan M; Randall, Michael; Donovan, Laura; Morrissy, Sorana; Sussman, Robyn T; Zhelev, Doncho V; Feng, Yang; Wang, Yanping; Hwang, Jennifer; Lopez, Gonzalo; Harenza, Jo Lynne; Wei, Jun S; Pawel, Bruce; Bhatti, Tricia; Santi, Mariarita; Ganguly, Arupa; Khan, Javed; Marra, Marco A; Taylor, Michael D; Dimitrov, Dimiter S; Mackall, Crystal L; Maris, John M

    2017-09-11

    We developed an RNA-sequencing-based pipeline to discover differentially expressed cell-surface molecules in neuroblastoma that meet criteria for optimal immunotherapeutic target safety and efficacy. Here, we show that GPC2 is a strong candidate immunotherapeutic target in this childhood cancer. We demonstrate high GPC2 expression in neuroblastoma due to MYCN transcriptional activation and/or somatic gain of the GPC2 locus. We confirm GPC2 to be highly expressed on most neuroblastomas, but not detectable at appreciable levels in normal childhood tissues. In addition, we demonstrate that GPC2 is required for neuroblastoma proliferation. Finally, we develop a GPC2-directed antibody-drug conjugate that is potently cytotoxic to GPC2-expressing neuroblastoma cells. Collectively, these findings validate GPC2 as a non-mutated neuroblastoma oncoprotein and candidate immunotherapeutic target. Copyright © 2017 Elsevier Inc. All rights reserved.

  20. A Team Mental Model Perspective of Pre-Quantitative Risk

    NASA Technical Reports Server (NTRS)

    Cooper, Lynne P.

    2011-01-01

    This study was conducted to better understand how teams conceptualize risk before it can be quantified, and the processes by which a team forms a shared mental model of this pre-quantitative risk. Using an extreme case, this study analyzes seven months of team meeting transcripts, covering the entire lifetime of the team. Through an analysis of team discussions, a rich and varied structural model of risk emerges that goes significantly beyond classical representations of risk as the product of a negative consequence and a probability. In addition to those two fundamental components, the team conceptualization includes the ability to influence outcomes and probabilities, networks of goals, interaction effects, and qualitative judgments about the acceptability of risk, all affected by associated uncertainties. In moving from individual to team mental models, team members employ a number of strategies to gain group recognition of risks and to resolve or accept differences.

  1. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device.

    PubMed

    Ball, David A; Lux, Matthew W; Graef, Russell R; Peterson, Matthew W; Valenti, Jane D; Dileo, John; Peccoud, Jean

    2010-01-01

    The concept of co-design is common in engineering, where it is necessary, for example, to determine the optimal partitioning between hardware and software of the implementation of a system features. Here we propose to adapt co-design methodologies for synthetic biology. As a test case, we have designed an environmental sensing device that detects the presence of three chemicals, and returns an output only if at least two of the three chemicals are present. We show that the logical operations can be implemented in three different design domains: (1) the transcriptional domain using synthetically designed hybrid promoters, (2) the protein domain using bi-molecular fluorescence complementation, and (3) the fluorescence domain using spectral unmixing and relying on electronic processing. We discuss how these heterogeneous design strategies could be formalized to develop co-design algorithms capable of identifying optimal designs meeting user specifications.

  2. Remarking on a blackened eye: Persifor Frazer's blow-by-blow account of a fistfight with his dear friend Edward Drinker Cope.

    PubMed

    Brinkman, Paul D

    2015-01-01

    Edward Drinker Cope, a brilliant and prolific American naturalist, was notoriously combative. His infamous feud with Yale paleontologist Othniel Charles Marsh, which played out publicly on the front pages of the New York Herald, was one of the worst scandals of nineteenth-century American science. Cope did not fight exclusively with his pen, however. In 1888, for example, he traded blows with his close friend Persifor Frazer over a matter of honor at the entrance of Philadelphia's hallowed Philosophical Hall, just as a meeting of the American Philosophical Society was getting under way. A six-page letter, handwritten by Persifor Frazer and housed in the Frazer Family Papers at the University of Pennsylvania, details the circumstances of their quarrel. An annotated transcription of Frazer's letter appears here. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Nozzle Initiative Industry Advisory Committee on Standardization of Carbon-Phenolic Test Methods and Specifications

    NASA Technical Reports Server (NTRS)

    Bull, William B. (Compiler); Pinoli, Pat C. (Compiler); Upton, Cindy G. (Compiler); Day, Tony (Compiler); Hill, Keith (Compiler); Stone, Frank (Compiler); Hall, William B.

    1994-01-01

    This report is a compendium of the presentations of the 12th biannual meeting of the Industry Advisory Committee under the Solid Propulsion Integrity Program. A complete transcript of the welcoming talks is provided. Presentation outlines and overheads are included for the other sessions: SPIP Overview, Past, Current and Future Activity; Test Methods Manual and Video Tape Library; Air Force Developed Computer Aided Cure Program and SPC/TQM Experience; Magneto-Optical mapper (MOM), Joint Army/NASA program to assess composite integrity; Permeability Testing; Moisture Effusion Testing by Karl Fischer Analysis; Statistical Analysis of Acceptance Test Data; NMR Phenolic Resin Advancement; Constituent Testing Highlights on the LDC Optimization Program; Carbon Sulfur Study, Performance Related Testing; Current Rayon Specifications and Future Availability; RSRM/SPC Implementation; SRM Test Methods, Delta/Titan/FBM/RSRM; and Open Forum on Performance Based Acceptance Testing -- Industry Experience.

  4. 'They never talked to me about... ': Perspectives on aged care resident transfer to emergency departments.

    PubMed

    Arendts, Glenn; Popescu, Aurora; Howting, Denise; Quine, Susan; Howard, Kirsten

    2015-06-01

    To explore perspectives of three groups concerning transfers from aged care facilities to emergency departments. We sought to reveal factors influencing transfer decisions; how active each group was in making decisions; and to what extent groups ceded decision-making to others. Semi-structured interviews of 11 residents, 14 relatives and 17 staff with content analysis of interview transcripts. The three groups substantially differed in their involvement with initiating, and attitudes towards, transfer. Residents were least likely to be involved in the decision, yet most likely to support transfer. Staff felt conflicted between their desire to provide optimal treatment for one ill resident, and their obligations to other residents under care. Staff perspectives were largely consistent with published data, but we describe new results for other informant groups. Group expectations and preferences differ substantially. Service delivery to meet all preferences presents a challenge for health service design. © 2013 ACOTA.

  5. The significance of alternative transcripts for Caenorhabditis elegans transcription factor genes, based on expression pattern analysis

    PubMed Central

    2013-01-01

    Background Sequence-specific DNA-binding proteins, with their paramount importance in the regulation of expression of the genetic material, are encoded by approximately 5% of the genes in an animal’s genome. But it is unclear to what extent alternative transcripts from these genes may further increase the complexity of the transcription factor complement. Results Of the 938 potential C. elegans transcription factor genes, 197 were annotated in WormBase as encoding at least two distinct isoforms. Evaluation of prior evidence identified, with different levels of confidence, 50 genes with alternative transcript starts, 23 with alternative transcript ends, 35 with alternative splicing and 34 with alternative transcripts generated by a combination of mechanisms, leaving 55 that were discounted. Expression patterns were determined for transcripts for a sample of 29 transcription factor genes, concentrating on those with alternative transcript starts for which the evidence was strongest. Seamless fosmid recombineering was used to generate reporter gene fusions with minimal modification to assay expression of specific transcripts while maintaining the broad genomic DNA context and alternative transcript production. Alternative transcription factor gene transcripts were typically expressed with identical or substantially overlapping distributions rather than in distinct domains. Conclusions Increasingly sensitive sequencing technologies will reveal rare transcripts but many of these are clearly non-productive. The majority of the transcription factor gene alternative transcripts that are productive may represent tolerable noise rather than encoding functionally distinct isoforms. PMID:23586691

  6. Patients' perceptions of sharing in decisions: a systematic review of interventions to enhance shared decision making in routine clinical practice.

    PubMed

    Légaré, France; Turcotte, Stéphane; Stacey, Dawn; Ratté, Stéphane; Kryworuchko, Jennifer; Graham, Ian D

    2012-01-01

    Shared decision making is the process in which a healthcare choice is made jointly by the health professional and the patient. Little is known about what patients view as effective or ineffective strategies to implement shared decision making in routine clinical practice. This systematic review evaluates the effectiveness of interventions to improve health professionals' adoption of shared decision making in routine clinical practice, as seen by patients. We searched electronic databases (PubMed, the Cochrane Library, EMBASE, CINAHL, and PsycINFO) from their inception to mid-March 2009. We found additional material by reviewing the reference lists of the studies found in the databases; systematic reviews of studies on shared decision making; the proceedings of various editions of the International Shared Decision Making Conference; and the transcripts of the Society for Medical Decision Making's meetings. In our study selection, we included randomized controlled trials, controlled clinical trials, controlled before-and-after studies, and interrupted time series analyses in which patients evaluated interventions to improve health professionals' adoption of shared decision making. The interventions in question consisted of the distribution of printed educational material; educational meetings; audit and feedback; reminders; and patient-mediated initiatives (e.g. patient decision aids). Two reviewers independently screened the studies and extracted data. Statistical analyses considered categorical and continuous process measures. We computed the standardized effect size for each outcome at the 95% confidence interval. The primary outcome of interest was health professionals' adoption of shared decision making as reported by patients in a self-administered questionnaire. Of the 6764 search results, 21 studies reported 35 relevant comparisons. Overall, the quality of the studies ranged from 0% to 83%. Only three of the 21 studies reported a clinically significant effect for the primary outcome that favored the intervention. The first study compared an educational meeting and a patient-mediated intervention with another patient-mediated intervention (median improvement of 74%). The second compared an educational meeting, a patient-mediated intervention, and audit and feedback with an educational meeting on an alternative topic (improvement of 227%). The third compared an educational meeting and a patient-mediated intervention with usual care (p = 0.003). All three studies were limited to the patient-physician dyad. To reduce bias, future studies should improve methods and reporting, and should analyze costs and benefits, including those associated with training of health professionals. Multifaceted interventions that include educating health professionals about sharing decisions with patients and patient-mediated interventions, such as patient decision aids, appear promising for improving health professionals' adoption of shared decision making in routine clinical practice as seen by patients.

  7. The use of in vitro transcription to probe regulatory functions of viral protein domains.

    PubMed

    Loewenstein, Paul M; Song, Chao-Zhong; Green, Maurice

    2007-01-01

    Adenoviruses (Ads), like other DNA tumor viruses, have evolved specific regulatory genes that facilitate virus replication by controlling the transcription of other viral genes as well as that of key cellular genes. In this regard, the E1A transcription unit contains multiple protein domains that can transcriptionally activate or repress cellular genes involved in the regulation of cell proliferation and cell differentiation. Studies using in vitro transcription have provided a basis for a molecular understanding of the interaction of viral regulatory proteins with the transcriptional machinery of the cell and continue to inform our understanding of transcription regulation. This chapter provides examples of the use of in vitro transcription to analyze transcriptional activation and transcriptional repression by purified, recombinant Ad E1A protein domains and single amino acid substitution mutants as well as the use of protein-affinity chromatography to identify host cell transcription factors involved in viral transcriptional regulation. A detailed description is provided of the methodology to prepare nuclear transcription extract, to prepare biologically active protein domains, to prepare affinity depleted transcription extracts, and to analyze transcription by primer extension and by run-off assay using naked DNA templates.

  8. Contributions of in vitro transcription to the understanding of human RNA polymerase III transcription

    PubMed Central

    Dumay-Odelot, Hélène; Durrieu-Gaillard, Stéphanie; El Ayoubi, Leyla; Parrot, Camila; Teichmann, Martin

    2014-01-01

    Human RNA polymerase III transcribes small untranslated RNAs that contribute to the regulation of essential cellular processes, including transcription, RNA processing and translation. Analysis of this transcription system by in vitro transcription techniques has largely contributed to the discovery of its transcription factors and to the understanding of the regulation of human RNA polymerase III transcription. Here we review some of the key steps that led to the identification of transcription factors and to the definition of minimal promoter sequences for human RNA polymerase III transcription. PMID:25764111

  9. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

    PubMed Central

    Joseph, Shai R; Pálfy, Máté; Hilbert, Lennart; Kumar, Mukesh; Karschau, Jens; Zaburdaev, Vasily; Shevchenko, Andrej; Vastenhouw, Nadine L

    2017-01-01

    Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo. DOI: http://dx.doi.org/10.7554/eLife.23326.001 PMID:28425915

  10. Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos.

    PubMed

    Joseph, Shai R; Pálfy, Máté; Hilbert, Lennart; Kumar, Mukesh; Karschau, Jens; Zaburdaev, Vasily; Shevchenko, Andrej; Vastenhouw, Nadine L

    2017-04-20

    Upon fertilization, the genome of animal embryos remains transcriptionally inactive until the maternal-to-zygotic transition. At this time, the embryo takes control of its development and transcription begins. How the onset of zygotic transcription is regulated remains unclear. Here, we show that a dynamic competition for DNA binding between nucleosome-forming histones and transcription factors regulates zebrafish genome activation. Taking a quantitative approach, we found that the concentration of non-DNA-bound core histones sets the time for the onset of transcription. The reduction in nuclear histone concentration that coincides with genome activation does not affect nucleosome density on DNA, but allows transcription factors to compete successfully for DNA binding. In agreement with this, transcription factor binding is sensitive to histone levels and the concentration of transcription factors also affects the time of transcription. Our results demonstrate that the relative levels of histones and transcription factors regulate the onset of transcription in the embryo.

  11. Swinger RNAs with sharp switches between regular transcription and transcription systematically exchanging ribonucleotides: Case studies.

    PubMed

    Seligmann, Hervé

    2015-09-01

    During RNA transcription, DNA nucleotides A,C,G, T are usually matched by ribonucleotides A, C, G and U. However occasionally, this rule does not apply: transcript-DNA homologies are detectable only assuming systematic exchanges between ribonucleotides. Nine symmetric (X ↔ Y, e.g. A ↔ C) and fourteen asymmetric (X ↔ Y ↔ Z, e.g. A ↔ C ↔ G) exchanges exist, called swinger transcriptions. Putatively, polymerases occasionally stabilize in unspecified swinger conformations, possibly similar to transient conformations causing punctual misinsertions. This predicts chimeric transcripts, part regular, part swinger-transformed, reflecting polymerases switching to swinger polymerization conformation(s). Four chimeric Genbank transcripts (three from human mitochondrion and one murine cytosolic) are described here: (a) the 5' and 3' extremities reflect regular polymerization, the intervening sequence exchanges systematically between ribonucleotides (swinger rule G ↔ U, transcript (1), with sharp switches between regular and swinger sequences; (b) the 5' half is 'normal', the 3' half systematically exchanges ribonucleotides (swinger rule C ↔ G, transcript (2), with an intercalated sequence lacking homology; (c) the 3' extremity fits A ↔ G exchanges (10% of transcript length), the 5' half follows regular transcription; the intervening region seems a mix of regular and A ↔ G transcriptions (transcript 3); (d) murine cytosolic transcript 4 switches to A ↔ U + C ↔ G, and is fused with A ↔ U + C ↔ G swinger transformed precursor rRNA. In (c), each concomitant transcript 5' and 3' extremities match opposite genome strands. Transcripts 3 and 4 combine transcript fusions with partial swinger transcriptions. Occasional (usually sharp) switches between regular and swinger transcriptions reveal greater coding potential than detected until now, suggest stable polymerase swinger conformations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Poly A- transcripts expressed in HeLa cells.

    PubMed

    Wu, Qingfa; Kim, Yeong C; Lu, Jian; Xuan, Zhenyu; Chen, Jun; Zheng, Yonglan; Zhou, Tom; Zhang, Michael Q; Wu, Chung-I; Wang, San Ming

    2008-07-30

    Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

  13. Poly A- Transcripts Expressed in HeLa Cells

    PubMed Central

    Lu, Jian; Xuan, Zhenyu; Chen, Jun; Zheng, Yonglan; Zhou, Tom; Zhang, Michael Q.; Wu, Chung-I; Wang, San Ming

    2008-01-01

    Background Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3′ poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. Methodology/Principal Findings We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3′ poly A tail; 3) applying the 454 sequencing technology for massive 3′ EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3′ ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3′ poly A tail. Most of the poly A- 3′ ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3′ ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. Conclusion/Significance Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts. PMID:18665230

  14. Divergent transcription is associated with promoters of transcriptional regulators

    PubMed Central

    2013-01-01

    Background Divergent transcription is a wide-spread phenomenon in mammals. For instance, short bidirectional transcripts are a hallmark of active promoters, while longer transcripts can be detected antisense from active genes in conditions where the RNA degradation machinery is inhibited. Moreover, many described long non-coding RNAs (lncRNAs) are transcribed antisense from coding gene promoters. However, the general significance of divergent lncRNA/mRNA gene pair transcription is still poorly understood. Here, we used strand-specific RNA-seq with high sequencing depth to thoroughly identify antisense transcripts from coding gene promoters in primary mouse tissues. Results We found that a substantial fraction of coding-gene promoters sustain divergent transcription of long non-coding RNA (lncRNA)/mRNA gene pairs. Strikingly, upstream antisense transcription is significantly associated with genes related to transcriptional regulation and development. Their promoters share several characteristics with those of transcriptional developmental genes, including very large CpG islands, high degree of conservation and epigenetic regulation in ES cells. In-depth analysis revealed a unique GC skew profile at these promoter regions, while the associated coding genes were found to have large first exons, two genomic features that might enforce bidirectional transcription. Finally, genes associated with antisense transcription harbor specific H3K79me2 epigenetic marking and RNA polymerase II enrichment profiles linked to an intensified rate of early transcriptional elongation. Conclusions We concluded that promoters of a class of transcription regulators are characterized by a specialized transcriptional control mechanism, which is directly coupled to relaxed bidirectional transcription. PMID:24365181

  15. Widespread anti-sense transcription in apple is correlated with siRNA production and indicates a large potential for transcriptional and/or post-transcriptional control.

    PubMed

    Celton, Jean-Marc; Gaillard, Sylvain; Bruneau, Maryline; Pelletier, Sandra; Aubourg, Sébastien; Martin-Magniette, Marie-Laure; Navarro, Lionel; Laurens, François; Renou, Jean-Pierre

    2014-07-01

    Characterizing the transcriptome of eukaryotic organisms is essential for studying gene regulation and its impact on phenotype. The realization that anti-sense (AS) and noncoding RNA transcription is pervasive in many genomes has emphasized our limited understanding of gene transcription and post-transcriptional regulation. Numerous mechanisms including convergent transcription, anti-correlated expression of sense and AS transcripts, and RNAi remain ill-defined. Here, we have combined microarray analysis and high-throughput sequencing of small RNAs (sRNAs) to unravel the complexity of transcriptional and potential post-transcriptional regulation in eight organs of apple (Malus × domestica). The percentage of AS transcript expression is higher than that identified in annual plants such as rice and Arabidopsis thaliana. Furthermore, we show that a majority of AS transcripts are transcribed beyond 3'UTR regions, and may cover a significant portion of the predicted sense transcripts. Finally we demonstrate at a genome-wide scale that anti-sense transcript expression is correlated with the presence of both short (21-23 nt) and long (> 30 nt) siRNAs, and that the sRNA coverage depth varies with the level of AS transcript expression. Our study provides a new insight on the functional role of anti-sense transcripts at the genome-wide level, and a new basis for the understanding of sRNA biogenesis in plants. © 2014 INRA. New Phytologist © 2014 New Phytologist Trust.

  16. Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs.

    PubMed

    Dhir, Ashish; Dhir, Somdutta; Proudfoot, Nick J; Jopling, Catherine L

    2015-04-01

    MicroRNAs (miRNAs) play a major part in the post-transcriptional regulation of gene expression. Mammalian miRNA biogenesis begins with cotranscriptional cleavage of RNA polymerase II (Pol II) transcripts by the Microprocessor complex. Although most miRNAs are located within introns of protein-coding transcripts, a substantial minority of miRNAs originate from long noncoding (lnc) RNAs, for which transcript processing is largely uncharacterized. We show, by detailed characterization of liver-specific lnc-pri-miR-122 and genome-wide analysis in human cell lines, that most lncRNA transcripts containing miRNAs (lnc-pri-miRNAs) do not use the canonical cleavage-and-polyadenylation pathway but instead use Microprocessor cleavage to terminate transcription. Microprocessor inactivation leads to extensive transcriptional readthrough of lnc-pri-miRNA and transcriptional interference with downstream genes. Consequently we define a new RNase III-mediated, polyadenylation-independent mechanism of Pol II transcription termination in mammalian cells.

  17. 5 CFR 1632.10 - Transcripts, recordings, and minutes.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... maintain a complete transcript or electronic recording or transcription thereof adequate to record fully.... Transcriptions of recordings will disclose the identity of each speaker. (b) The Board will maintain either such a transcript, recording or transcription thereof, or a set of minutes that will fully and clearly...

  18. 5 CFR 1632.10 - Transcripts, recordings, and minutes.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... maintain a complete transcript or electronic recording or transcription thereof adequate to record fully.... Transcriptions of recordings will disclose the identity of each speaker. (b) The Board will maintain either such a transcript, recording or transcription thereof, or a set of minutes that will fully and clearly...

  19. Diversity of transcripts and transcript processing forms in plastids of the dinoflagellate alga Karenia mikimotoi.

    PubMed

    Dorrell, Richard G; Hinksman, George A; Howe, Christopher J

    2016-02-01

    Plastids produce a vast diversity of transcripts. These include mature transcripts containing coding sequences, and their processing precursors, as well as transcripts that lack direct coding functions, such as antisense transcripts. Although plastid transcriptomes have been characterised for many plant species, less is known about the transcripts produced in other plastid lineages. We characterised the transcripts produced in the fucoxanthin-containing plastids of the dinoflagellate alga Karenia mikimotoi. This plastid lineage, acquired through tertiary endosymbiosis, utilises transcript processing pathways that are very different from those found in plants and green algae, including 3' poly(U) tail addition, and extensive substitutional editing of transcript sequences. We have sequenced the plastid transcriptome of K. mikimotoi, and have detected evidence for divergent evolution of fucoxanthin plastid genomes. We have additionally characterised polycistronic and monocistronic transcripts from two plastid loci, psbD-tRNA (Met)-ycf4 and rpl36-rps13-rps11. We find evidence for a range of transcripts produced from each locus that differ in terms of editing state, 5' end cleavage position, and poly(U) tail addition. Finally, we identify antisense transcripts in K. mikimotoi, which appear to undergo different processing events from the corresponding sense transcripts. Overall, our study provides insights into the diversity of transcripts and processing intermediates found in plastid lineages across the eukaryotes.

  20. 12 CFR 261b.11 - Transcripts, recordings, and minutes.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... minutes. (a) The agency will maintain a complete transcript or electronic recording or transcription... § 261b.5 of this part. Transcriptions of recordings will disclose the identity of each speaker. (b) The agency will maintain either such a transcript, recording or transcription thereof, or a set of minutes...

  1. The transcriptional terminator sequences downstream of the covR gene terminate covR/S operon transcription to generate covR monocistronic transcripts in Streptococcus pyogenes.

    PubMed

    Chiang-Ni, Chuan; Tsou, Chih-Cheng; Lin, Yee-Shin; Chuang, Woei-Jer; Lin, Ming-T; Liu, Ching-Chuan; Wu, Jiunn-Jong

    2008-12-31

    CovR/S is an important two component regulatory system, which regulates about 15% of the gene expression in Streptococcus pyogenes. The covR/S locus was identified as an operon generating an RNA transcript around 2.5-kb in size. In this study, we found the covR/S operon produced three RNA transcripts (around 2.5-, 1.0-, and 0.8-kb in size). Using RNA transcriptional terminator sequence prediction and transcriptional terminator analysis, we identified two atypical rho-independent terminator sequences downstream of the covR gene and showed these terminator sequences terminate RNA transcription efficiently. These results indicate that covR/S operon generates covR/S transcript and monocistronic covR transcripts.

  2. HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies.

    PubMed

    Asamitsu, Kaori; Fujinaga, Koh; Okamoto, Takashi

    2018-04-17

    Transcription is a crucial step in the life cycle of the human immunodeficiency virus type 1 (HIV 1) and is primarily involved in the maintenance of viral latency. Both viral and cellular transcription factors, including transcriptional activators, suppressor proteins and epigenetic factors, are involved in HIV transcription from the proviral DNA integrated within the host cell genome. Among them, the virus-encoded transcriptional activator Tat is the master regulator of HIV transcription. Interestingly, unlike other known transcriptional activators, Tat primarily activates transcriptional elongation and initiation by interacting with the cellular positive transcriptional elongation factor b (P-TEFb). In this review, we describe the molecular mechanism underlying how Tat activates viral transcription through interaction with P-TEFb. We propose a novel therapeutic strategy against HIV replication through blocking Tat action.

  3. Intrinsic disorder in transcription factors†

    PubMed Central

    Liu, Jiangang; Perumal, Narayanan B.; Oldfield, Christopher J.; Su, Eric W.; Uversky, Vladimir N.; Dunker, A. Keith

    2008-01-01

    Intrinsic disorder (ID) is highly abundant in eukaryotes, which reflect the greater need for disorder-associated signaling and transcriptional regulation in nucleated cells. Although several well-characterized examples of intrinsically disordered proteins in transcriptional regulation have been reported, no systematic analysis has been reported so far. To test for a general prevalence of intrinsic disorder in transcriptional regulation, we used the Predictor Of Natural Disorder Regions (PONDR) to analyze the abundance of intrinsic disorder in three transcription factor datasets and two control sets. This analysis revealed that from 94.13% to 82.63% of transcription factors posses extended regions of intrinsic disorder, relative to 54.51% and 18.64% of the proteins in two control datasets, which indicates the significant prevalence of intrinsic disorder in transcription factors. This propensity of transcription factors for intrinsic disorder was confirmed by cumulative distribution function analysis and charge-hydropathy plots. The amino acid composition analysis showed that all three transcription factor datasets were substantially depleted in order-promoting residues, and significantly enriched in disorder-promoting residues. Our analysis of the distribution of disorder within the transcription factor datasets revealed that: (a) The AT-hooks and basic regions of transcription factor DNA-binding domains are highly disordered; (b) The degree of disorder in transcription factor activation regions is much higher than that in DNA-binding domains; (c) The degree of disorder is significantly higher in eukaryotic transcription factors than in prokaryotic transcription factors; (d) The level of α-MoRFs (molecular recognition feature) prediction is much higher in transcription factors. Overall, our data reflected the fact that the eukaryotes with well-developed gene transcription machinery require transcription factor flexibility to be more efficient. PMID:16734424

  4. Nucleoside Triphosphate Phosphohydrolase I (NPH I) Functions as a 5′ to 3′ Translocase in Transcription Termination of Vaccinia Early Genes*

    PubMed Central

    Hindman, Ryan; Gollnick, Paul

    2016-01-01

    Vaccinia virus early genes are transcribed immediately upon infection. Nucleoside triphosphate phosphohydrolase I (NPH I) is an essential component of the early gene transcription complex. NPH I hydrolyzes ATP to release transcripts during transcription termination. The ATPase activity of NPH I requires single-stranded (ss) DNA as a cofactor; however, the source of this cofactor within the transcription complex is not known. Based on available structures of transcription complexes it has been hypothesized that the ssDNA cofactor is obtained from the unpaired non-template strand within the transcription bubble. In vitro transcription on templates that lack portions of the non-template strand within the transcription bubble showed that the upstream portion of the transcription bubble is required for efficient NPH I-mediated transcript release. Complementarity between the template and non-template strands in this region is also required for NPH I-mediated transcript release. This observation complicates locating the source of the ssDNA cofactor within the transcription complex because removal of the non-template strand also disrupts transcription bubble reannealing. Prior studies have shown that ssRNA binds to NPH I, but it does not activate ATPase activity. Chimeric transcription templates with RNA in the non-template strand confirm that the source of the ssDNA cofactor for NPH I is the upstream portion of the non-template strand in the transcription bubble. Consistent with this conclusion we also show that isolated NPH I acts as a 5′ to 3′ translocase on single-stranded DNA. PMID:27189950

  5. Development of a clinical pharmacy model within an Australian home nursing service using co-creation and participatory action research: the Visiting Pharmacist (ViP) study

    PubMed Central

    Lee, Cik Yin; Beanland, Christine; Goeman, Dianne P; Petrie, Neil; Petrie, Barbara; Vise, Felicity; Gray, June

    2017-01-01

    Objective To develop a collaborative, person-centred model of clinical pharmacy support for community nurses and their medication management clients. Design Co-creation and participatory action research, based on reflection, data collection, interaction and feedback from participants and other stakeholders. Setting A large, non-profit home nursing service in Melbourne, Australia. Participants Older people referred to the home nursing service for medication management, their carers, community nurses, general practitioners (GPs) and pharmacists, a multidisciplinary stakeholder reference group (including consumer representation) and the project team. Data collection and analysis Feedback and reflections from minutes, notes and transcripts from: project team meetings, clinical pharmacists’ reflective diaries and interviews, meetings with community nurses, reference group meetings and interviews and focus groups with 27 older people, 18 carers, 53 nurses, 15 GPs and seven community pharmacists. Results The model was based on best practice medication management standards and designed to address key medication management issues raised by stakeholders. Pharmacist roles included direct client care and indirect care. Direct care included home visits, medication reconciliation, medication review, medication regimen simplification, preparation of medication lists for clients and nurses, liaison and information sharing with prescribers and pharmacies and patient/carer education. Indirect care included providing medicines information and education for nurses and assisting with review and implementation of organisational medication policies and procedures. The model allowed nurses to refer directly to the pharmacist, enabling timely resolution of medication issues. Direct care was provided to 84 older people over a 15-month implementation period. Ongoing feedback and consultation, in line with participatory action research principles, informed the development and refinement of the model and identification of enablers and challenges. Conclusions A collaborative, person-centred clinical pharmacy model that addressed the needs of clients, carers, nurses and other stakeholders was successfully developed. The model is likely to have applicability to home nursing services nationally and internationally. PMID:29102998

  6. Directing traffic on DNA-How transcription factors relieve or induce transcriptional interference.

    PubMed

    Hao, Nan; Palmer, Adam C; Dodd, Ian B; Shearwin, Keith E

    2017-03-15

    Transcriptional interference (TI) is increasingly recognized as a widespread mechanism of gene control, particularly given the pervasive nature of transcription, both sense and antisense, across all kingdoms of life. Here, we discuss how transcription factor binding kinetics strongly influence the ability of a transcription factor to relieve or induce TI.

  7. An Optogenetic Platform for Real-Time, Single-Cell Interrogation of Stochastic Transcriptional Regulation.

    PubMed

    Rullan, Marc; Benzinger, Dirk; Schmidt, Gregor W; Milias-Argeitis, Andreas; Khammash, Mustafa

    2018-05-17

    Transcription is a highly regulated and inherently stochastic process. The complexity of signal transduction and gene regulation makes it challenging to analyze how the dynamic activity of transcriptional regulators affects stochastic transcription. By combining a fast-acting, photo-regulatable transcription factor with nascent RNA quantification in live cells and an experimental setup for precise spatiotemporal delivery of light inputs, we constructed a platform for the real-time, single-cell interrogation of transcription in Saccharomyces cerevisiae. We show that transcriptional activation and deactivation are fast and memoryless. By analyzing the temporal activity of individual cells, we found that transcription occurs in bursts, whose duration and timing are modulated by transcription factor activity. Using our platform, we regulated transcription via light-driven feedback loops at the single-cell level. Feedback markedly reduced cell-to-cell variability and led to qualitative differences in cellular transcriptional dynamics. Our platform establishes a flexible method for studying transcriptional dynamics in single cells. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  8. Archaeal RNA polymerase and transcription regulation

    PubMed Central

    Jun, Sung-Hoon; Reichlen, Matthew J.; Tajiri, Momoko; Murakami, Katsuhiko S.

    2010-01-01

    To elucidate the mechanism of transcription by cellular RNA polymerases (RNAPs), high resolution X-ray crystal structures together with structure-guided biochemical, biophysical and genetics studies are essential. The recently-solved X-ray crystal structures of archaeal RNA polymerase (RNAP) allow a structural comparison of the transcription machinery among all three domains of life. The archaea were once thought of closely related to bacteria, but they are now considered to be more closely related to the eukaryote at the molecular level than bacteria. According to these structures, the archaeal transcription apparatus, which includes RNAP and general transcription factors, is similar to the eukaryotic transcription machinery. Yet, the transcription regulators, activators and repressors, encoded by archaeal genomes are closely related to bacterial factors. Therefore, archaeal transcription appears to possess an intriguing hybrid of eukaryotic-type transcription apparatus and bacterial-like regulatory mechanisms. Elucidating the transcription mechanism in archaea, which possesses a combination of bacterial and eukaryotic transcription mechanisms that are commonly regarded as separate and mutually exclusive, can provide data that will bring basic transcription mechanisms across all three domains of life. PMID:21250781

  9. Promoting cultural understanding through pediatric clinical dyads: an education research project.

    PubMed

    McDermott-Levy, Ruth; Cantrell, Mary Ann; Reynolds, Kathryn

    2014-11-01

    This project explored the experiences of six undergraduate nursing students, three American nursing students and three nursing students from the Sultan of Oman, who participated in a faculty initiated education research project as part of their pediatric clinical practicum. Students were placed in dyads, with one American-born student and one Omani student in each dyad. Omani students also were paired with American nurse preceptors. A transcript-based content analysis was used to analyze data generated from qualitative focus group student interviews and student journals. The analysis generated three themes that described how myths were dispelled, cultural barriers were broken down and knowledge gained from another cultural perspective. The nurse preceptors were surveyed at the conclusion of the program. The survey findings suggest that preceptors gained a different cultural perspective of nursing care and they were better informed of the Omani students' learning needs. There was, however, an additional investment of preceptor time in meeting the learning needs of international students. Additional faculty time was also required for preparation and time during clinical conferencing to address differences in nursing practice between U.S. and Oman while meeting course learning objectives. Overall, the educational program provided evidence of enhancing American and Omani student cultural competence and Omani student adaptation to the United States. Coupling a domestic student with an international student to form dyads from the beginning of international students' experience could be a significant enhancement to both groups of students' learning experience. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Sustaining the rural workforce: nursing perspectives on worklife challenges.

    PubMed

    Hunsberger, Mabel; Baumann, Andrea; Blythe, Jennifer; Crea, Mary

    2009-01-01

    Concerns have been raised about the sustainability of health care workforces in rural settings. According to the literature, rural nurses' work satisfaction varies with the resources and supports available to respond to specific challenges. Given the probable effects of stressors on retention, it is essential to understand the unique requirements of nurses in rural practice environments. To investigate whether nurses receive the resources and supports necessary to meet the challenges of rural practice. Semi-structured interviews were conducted with 21 managers and 44 staff nurses in 19 selected rural hospitals in Ontario, Canada. The interviews were taped and transcripts interpreted through a thematic analysis. Major worklife themes were identified and analyzed within a healthy work environment model based on the work of Kristensen. Three interrelated dimensions of the model were relevant to workforce sustainability: the balance between demands and the resources of the person, the level of social support, and the degree of influence. The availability of resources and supports affected whether the nurses perceived challenges as stimulating or overwhelming. Deficits interfered with practice and the well-being of the nurses and patients. The nurses felt frustrated and powerless when they lacked resources, support, and influence to manage negative situations. Strategies to achieve workforce sustainability include resources to reduce stress in the workplace, education to meet the needs of new and experienced nurses, and offering of employment preferences to the workforce. Addressing resources, support, and influence of rural nurses is essential to alleviate workplace challenges and sustain the rural nursing workforce.

  11. Designing a leadership development program for surgeons.

    PubMed

    Jaffe, Gregory A; Pradarelli, Jason C; Lemak, Christy Harris; Mulholland, Michael W; Dimick, Justin B

    2016-01-01

    Although numerous leadership development programs (LDPs) exist in health care, no programs have been specifically designed to meet the needs of surgeons. This study aimed to elicit practicing surgeons' motivations and desired goals for leadership training to design an evidence-based LDP in surgery. At a large academic health center, we conducted semistructured interviews with 24 surgical faculty members who voluntarily applied and were selected for participation in a newly created LDP. Transcriptions of the interviews were analyzed using analyst triangulation and thematic coding to extract major themes regarding surgeons' motivations and perceived needs for leadership knowledge and skills. Themes from interview responses were then used to design the program curriculum specifically to meet the leadership needs of surgical faculty. Three major themes emerged regarding surgeons' motivations for seeking leadership training: (1) Recognizing key gaps in their formal preparation for leadership roles; (2) Exhibiting an appetite for personal self-improvement; and (3) Seeking leadership guidance for career advancement. Participants' interviews revealed four specific domains of knowledge and skills that they indicated as desired takeaways from a LDP: (1) leadership and communication; (2) team building; (3) business acumen/finance; and (4) greater understanding of the health care context. Interviews with surgical faculty members identified gaps in prior leadership training and demonstrated concrete motivations and specific goals for participating in a formal leadership program. A LDP that is specifically tailored to address the needs of surgical faculty may benefit surgeons at a personal and institutional level. Copyright © 2016 Elsevier Inc. All rights reserved.

  12. Pichia pastoris: a recombinant microfactory for antibodies and human membrane proteins.

    PubMed

    Gonçalves, A M; Pedro, A Q; Maia, C; Sousa, F; Queiroz, J A; Passarinha, L A

    2013-05-01

    During the last few decades, it has become evident that the compatibility of the yeast biochemical environment with the ability to process and translate the RNA transcript, along with its capacity to modify a translated protein, are relevant requirements for selecting this host cell for protein expression in several pharmaceutical and clinical applications. In particular, Pichia pastoris is used as an industrial host for recombinant protein and metabolite production, showing a powerful capacity to meet required biomolecular target production levels in high-throughput assays for functional genomics and drug screening. In addition, there is a great advantage to using P. pastoris for protein secretion, even at high molecular weights, since the recovery and purification steps are simplified owing to relatively low levels of endogenous proteins in the extracellular medium. Clearly, no single microexpression system can provide all of the desired properties for human protein production. Moreover, chemical and physical bioprocess parameters, including culture medium formulation, temperature, pH, agitation, aeration rates, induction, and feeding strategies, can highly influence product yield and quality. In order to benefit from the currently available wide range of biosynthesis strategies using P. pastoris, this mini review focuses on the developments and technological fermentation achievements, providing both a comparative and an overall integration analysis. The main aim is to highlight the relevance and versatility of the P. pastoris biosystem to the design of more cost-effective microfactories to meet the increasing demands for recombinant membrane proteins and clinical antibodies for several therapeutic applications.

  13. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications

    PubMed Central

    Xu, Liang; Wang, Wei; Chong, Jenny; Shin, Ji Hyun; Xu, Jun; Wang, Dong

    2016-01-01

    Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress towards understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation. PMID:26392149

  14. Pervasive transcription: detecting functional RNAs in bacteria.

    PubMed

    Lybecker, Meghan; Bilusic, Ivana; Raghavan, Rahul

    2014-01-01

    Pervasive, or genome-wide, transcription has been reported in all domains of life. In bacteria, most pervasive transcription occurs antisense to protein-coding transcripts, although recently a new class of pervasive RNAs was identified that originates from within annotated genes. Initially considered to be non-functional transcriptional noise, pervasive transcription is increasingly being recognized as important in regulating gene expression. The function of pervasive transcription is an extensively debated question in the field of transcriptomics and regulatory RNA biology. Here, we highlight the most recent contributions addressing the purpose of pervasive transcription in bacteria and discuss their implications.

  15. Creating metabolic demand as an engineering strategy in Pseudomonas putida - Rhamnolipid synthesis as an example.

    PubMed

    Tiso, Till; Sabelhaus, Petra; Behrens, Beate; Wittgens, Andreas; Rosenau, Frank; Hayen, Heiko; Blank, Lars Mathias

    2016-12-01

    Metabolic engineering of microbial cell factories for the production of heterologous secondary metabolites implicitly relies on the intensification of intracellular flux directed toward the product of choice. Apart from reactions following peripheral pathways, enzymes of the central carbon metabolism are usually targeted for the enhancement of precursor supply. In Pseudomonas putida , a Gram-negative soil bacterium, central carbon metabolism, i.e., the reactions required for the synthesis of all 12 biomass precursors, was shown to be regulated at the metabolic level and not at the transcriptional level. The bacterium's central carbon metabolism appears to be driven by demand to react rapidly to ever-changing environmental conditions. In contrast, peripheral pathways that are only required for growth under certain conditions are regulated transcriptionally. In this work, we show that this regulation regime can be exploited for metabolic engineering. We tested this driven-by-demand metabolic engineering strategy using rhamnolipid production as an example. Rhamnolipid synthesis relies on two pathways, i.e., fatty acid de novo synthesis and the rhamnose pathway, providing the required precursors hydroxyalkanoyloxy-alkanoic acid (HAA) and activated (dTDP-)rhamnose, respectively. In contrast to single-pathway molecules, rhamnolipid synthesis causes demand for two central carbon metabolism intermediates, i.e., acetyl-CoA for HAA and glucose-6-phosphate for rhamnose synthesis. Following the above-outlined strategy of driven by demand, a synthetic promoter library was developed to identify the optimal expression of the two essential genes ( rhlAB ) for rhamnolipid synthesis. The best rhamnolipid-synthesizing strain had a yield of 40% rhamnolipids on sugar [Cmol RL /Cmol Glc ], which is approximately 55% of the theoretical yield. The rate of rhamnolipid synthesis of this strain was also high. Compared to an exponentially growing wild type, the rhamnose pathway increased its flux by 300%, whereas the flux through de novo fatty acid synthesis increased by 50%. We show that the central carbon metabolism of P. putida is capable of meeting the metabolic demand generated by engineering transcription in peripheral pathways, thereby enabling a significant rerouting of carbon flux toward the product of interest, in this case, rhamnolipids of industrial interest.

  16. Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

    PubMed Central

    2009-01-01

    Background The full power of modern genetics has been applied to the study of speciation in only a small handful of genetic model species - all of which speciated allopatrically. Here we report the first large expressed sequence tag (EST) study of a candidate for ecological sympatric speciation, the apple maggot Rhagoletis pomonella, using massively parallel pyrosequencing on the Roche 454-FLX platform. To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies. Results We obtained 239,531 sequences which assembled into 24,373 contigs. A total of 6810 unique protein coding genes were identified among the contigs and long singletons, corresponding to 48% of all known Drosophila melanogaster protein-coding genes. Their distribution across GO classes suggests that we have obtained a representative sample of the transcriptome. Among these sequences are many candidates for potential R. pomonella "speciation genes" (or "barrier genes") such as those controlling chemosensory and life-history timing processes. Furthermore, we identified important marker loci including more than 40,000 single nucleotide polymorphisms (SNPs) and over 100 microsatellites. An initial search for SNPs at which the apple and hawthorn host races differ suggested at least 75 loci warranting further work. We also determined that developmental expression differences remained even after normalization; transcripts expected to show different expression levels between larvae and pupae in D. melanogaster also did so in R. pomonella. Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora. Conclusions These data provide a much needed resource for exploring mechanisms of divergence in this important model for sympatric ecological speciation. Our description of ESTs from a substantial portion of the R. pomonella transcriptome will facilitate future functional studies of candidate genes for olfaction and diapause-related life history timing, and will enable large scale expression studies. Similarly, the identification of new SNP and microsatellite markers will facilitate future population and quantitative genetic studies of divergence between the apple and hawthorn-infesting host races. PMID:20035631

  17. Mitotic Transcriptional Activation: Clearance of Actively Engaged Pol II via Transcriptional Elongation Control in Mitosis.

    PubMed

    Liang, Kaiwei; Woodfin, Ashley R; Slaughter, Brian D; Unruh, Jay R; Box, Andrew C; Rickels, Ryan A; Gao, Xin; Haug, Jeffrey S; Jaspersen, Sue L; Shilatifard, Ali

    2015-11-05

    Although it is established that some general transcription factors are inactivated at mitosis, many details of mitotic transcription inhibition (MTI) and its underlying mechanisms are largely unknown. We have identified mitotic transcriptional activation (MTA) as a key regulatory step to control transcription in mitosis for genes with transcriptionally engaged RNA polymerase II (Pol II) to activate and transcribe until the end of the gene to clear Pol II from mitotic chromatin, followed by global impairment of transcription reinitiation through MTI. Global nascent RNA sequencing and RNA fluorescence in situ hybridization demonstrate the existence of transcriptionally engaged Pol II in early mitosis. Both genetic and chemical inhibition of P-TEFb in mitosis lead to delays in the progression of cell division. Together, our study reveals a mechanism for MTA and MTI whereby transcriptionally engaged Pol II can progress into productive elongation and finish transcription to allow proper cellular division. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Development, Evaluation, and Integration of a Quantitative Reverse-Transcription Polymerase Chain Reaction Diagnostic Test for Ebola Virus on a Molecular Diagnostics Platform

    PubMed Central

    Cnops, Lieselotte; Van den Eede, Peter; Pettitt, James; Heyndrickx, Leo; De Smet, Birgit; Coppens, Sandra; Andries, Ilse; Pattery, Theresa; Van Hove, Luc; Meersseman, Geert; Van Den Herrewegen, Sari; Vergauwe, Nicolas; Thijs, Rein; Jahrling, Peter B.; Nauwelaers, David; Ariën, Kevin K.

    2016-01-01

    Background. The 2013–2016 Ebola epidemic in West Africa resulted in accelerated development of rapid diagnostic tests for emergency outbreak preparedness. We describe the development and evaluation of the Idylla™ prototype Ebola virus test, a fully automated sample-to-result molecular diagnostic test for rapid detection of Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV). Methods. The Idylla™ prototype Ebola virus test can simultaneously detect EBOV and SUDV in 200 µL of whole blood. The sample is directly added to a disposable cartridge containing all reagents for sample preparation, RNA extraction, and amplification by reverse-transcription polymerase chain reaction analysis. The performance was evaluated with a variety of sample types, including synthetic constructs and whole blood samples from healthy volunteers spiked with viral RNA, inactivated virus, and infectious virus. Results. The 95% limits of detection for EBOV and SUDV were 465 plaque-forming units (PFU)/mL (1010 copies/mL) and 324 PFU/mL (8204 copies/mL), respectively. In silico and in vitro analyses demonstrated 100% correct reactivity for EBOV and SUDV and no cross-reactivity with relevant pathogens. The diagnostic sensitivity was 97.4% (for EBOV) and 91.7% (for SUDV), the specificity was 100%, and the diagnostic accuracy was 95.9%. Conclusions. The Idylla™ prototype Ebola virus test is a fast, safe, easy-to-use, and near-patient test that meets the performance criteria to detect EBOV in patients with suspected Ebola. PMID:27247341

  19. Clinical and Biological Insights from the University of California San Francisco Prospective and Longitudinal Cohort.

    PubMed

    Benn, Bryan S; Lehman, Zoe; Kidd, Sharon A; Ho, Melissa; Sun, Sara; Ramstein, Joris; Arger, Nicholas K; Nguyen, Christine P; Su, Robert; Gomez, Antonio; Gelfand, Jeffrey M; Koth, Laura L

    2017-10-01

    Sarcoidosis is a systemic inflammatory disease characterized by non-necrotizing granulomas in involved organs, most commonly the lung. Description of patient characteristics in the Western United States is limited. Furthermore, blood-based measures that relate to clinical sarcoidosis phenotypes are lacking. We present an analysis of a prospective, longitudinal sarcoidosis cohort at a Northern Californian academic medical center. We enrolled 126 sarcoidosis subjects and 64 healthy controls and recorded baseline demographic and clinical characteristics. We used regression models to identify factors independently associated with pulmonary physiology. We tested whether blood transcript levels at study entry could relate to longitudinal changes in pulmonary physiology. White, non-Hispanics composed ~70% of subjects. Hispanics and Blacks had a diagnostic biopsy at an age ~7 years younger than whites. Obstructive, but not restrictive, physiology characterized Scadding Stage IV patients. Subjects reporting use of immunosuppression had worse FEV1%p, FVC%p, and DLCO%p compared to subjects never treated, regardless of Scadding stage. We defined sarcoidosis disease activity by a drop in pulmonary function over 36 months and found that subjects meeting this definition had significant repression of blood gene transcripts related to T cell receptor signaling pathways, referred to as the "TCR factor." Obstructive pulmonary physiology defined Stage IV patients which were mostly white, non-Hispanics. Genes comprising the composite gene expression score, TCR factor, may represent a blood-derived measure of T-cell activity and an indirect measure of active sarcoidosis inflammation. Validation of this measure could translate into individualized treatment for sarcoidosis patients.

  20. Compensatory hyperinsulinemia in high-fat diet-induced obese mice is associated with enhanced insulin translation in islets

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Kanno, Ayumi, E-mail: akanno@med.kobe-u.ac.jp; Asahara, Shun-ichiro, E-mail: asahara@med.kobe-u.ac.jp; Masuda, Katsuhisa, E-mail: katsuhisa.m.0707@gmail.com

    A high-fat diet (HF) is associated with obesity, insulin resistance, and hyperglycemia. Animal studies have shown compensatory mechanisms in pancreatic β-cells after high fat load, such as increased pancreatic β-cell mass, enhanced insulin secretion, and exocytosis. However, the effects of high fat intake on insulin synthesis are obscure. Here, we investigated whether insulin synthesis was altered in correlation with an HF diet, for the purpose of obtaining further understanding of the compensatory mechanisms in pancreatic β-cells. Mice fed an HF diet are obese, insulin resistant, hyperinsulinemic, and glucose intolerant. In islets of mice fed an HF diet, more storage ofmore » insulin was identified. We analyzed insulin translation in mouse islets, as well as in INS-1 cells, using non-radioisotope chemicals. We found that insulin translational levels were significantly increased in islets of mice fed an HF diet to meet systemic demand, without altering its transcriptional levels. Our data showed that not only increased pancreatic β-cell mass and insulin secretion but also elevated insulin translation is the major compensatory mechanism of pancreatic β-cells. - Highlights: • More stored insulin was recognized in islets of mice fed a high-fat diet. • Insulin translation was not enhanced by fatty acids, but by insulin demand. • Insulin transcription was not altered in islets of mice fed a high-fat diet. • Insulin translation was markedly enhanced in islets of mice fed a high-fat diet. • Non-radioisotope chemicals were used to measure insulin translation in mouse islets.« less

  1. Transcriptional coactivators PGC-1α and PGC-lβ control overlapping programs required for perinatal maturation of the heart

    PubMed Central

    Lai, Ling; Leone, Teresa C.; Zechner, Christoph; Schaeffer, Paul J.; Kelly, Sean M.; Flanagan, Daniel P.; Medeiros, Denis M.; Kovacs, Attila; Kelly, Daniel P.

    2008-01-01

    Oxidative tissues such as heart undergo a dramatic perinatal mitochondrial biogenesis to meet the high-energy demands after birth. PPARγ coactivator-1 (PGC-1) α and β have been implicated in the transcriptional control of cellular energy metabolism. Mice with combined deficiency of PGC-1α and PGC-1β (PGC-1αβ−/− mice) were generated to investigate the convergence of their functions in vivo. The phenotype of PGC-1β−/− mice was minimal under nonstressed conditions, including normal heart function, similar to that of PGC-1α−/− mice generated previously. In striking contrast to the singly deficient PGC-1 lines, PGC-1αβ−/− mice died shortly after birth with small hearts, bradycardia, intermittent heart block, and a markedly reduced cardiac output. Cardiac-specific ablation of the PGC-1β gene on a PGC-1α-deficient background phenocopied the generalized PGC-1αβ−/− mice. The hearts of the PGC-1αβ−/− mice exhibited signatures of a maturational defect including reduced growth, a late fetal arrest in mitochondrial biogenesis, and persistence of a fetal pattern of gene expression. Brown adipose tissue (BAT) of PGC-1αβ−/− mice also exhibited a severe abnormality in function and mitochondrial density. We conclude that PGC-1α and PGC-1β share roles that collectively are necessary for the postnatal metabolic and functional maturation of heart and BAT. PMID:18628400

  2. Differentiation of endosperm transfer cells of barley: a comprehensive analysis at the micro-scale.

    PubMed

    Thiel, Johannes; Riewe, David; Rutten, Twan; Melzer, Michael; Friedel, Swetlana; Bollenbeck, Felix; Weschke, Winfriede; Weber, Hans

    2012-08-01

    Barley endosperm cells differentiate into transfer cells (ETCs) opposite the nucellar projection. To comprehensively analyse ETC differentiation, laser microdissection-based transcript and metabolite profiles were obtained from laser microdissected tissues and cell morphology was analysed. Flange-like secondary-wall ingrowths appeared between 5 and 7 days after pollination within the three outermost cell layers. Gene expression analysis indicated that ethylene-signalling pathways initiate ETC morphology. This is accompanied by gene activity related to cell shape control and vesicle transport, with abundant mitochondria and endomembrane structures. Gene expression analyses indicate predominant formation of hemicelluloses, glucuronoxylans and arabinoxylans, and transient formation of callose, together with proline and 4-hydroxyproline biosynthesis. Activation of the methylation cycle is probably required for biosynthesis of phospholipids, pectins and ethylene. Membrane microdomains involving sterols/sphingolipids and remorins are potentially involved in ETC development. The transcriptional activity of assimilate and micronutrient transporters suggests ETCs as the main uptake organs of solutes into the endosperm. Accordingly, the endosperm grows maximally after ETCs are fully developed. Up-regulated gene expression related to amino acid catabolism, C:N balances, carbohydrate oxidation, mitochondrial activity and starch degradation meets high demands for respiratory energy and carbohydrates, required for cell proliferation and wall synthesis. At 10 days after pollination, ETCs undergo further differentiation, potentially initiated by abscisic acid, and metabolism is reprogrammed as shown by activated storage and stress-related processes. Overall, the data provide a comprehensive view of barley ETC differentiation and development, and identify candidate genes and associated pathways. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

  3. Mechanistic and regulatory aspects of intestinal iron absorption

    PubMed Central

    Gulec, Sukru; Anderson, Gregory J.

    2014-01-01

    Iron is an essential trace mineral that plays a number of important physiological roles in humans, including oxygen transport, energy metabolism, and neurotransmitter synthesis. Iron absorption by the proximal small bowel is a critical checkpoint in the maintenance of whole-body iron levels since, unlike most other essential nutrients, no regulated excretory systems exist for iron in humans. Maintaining proper iron levels is critical to avoid the adverse physiological consequences of either low or high tissue iron concentrations, as commonly occurs in iron-deficiency anemia and hereditary hemochromatosis, respectively. Exquisite regulatory mechanisms have thus evolved to modulate how much iron is acquired from the diet. Systemic sensing of iron levels is accomplished by a network of molecules that regulate transcription of the HAMP gene in hepatocytes, thus modulating levels of the serum-borne, iron-regulatory hormone hepcidin. Hepcidin decreases intestinal iron absorption by binding to the iron exporter ferroportin 1 on the basolateral surface of duodenal enterocytes, causing its internalization and degradation. Mucosal regulation of iron transport also occurs during low-iron states, via transcriptional (by hypoxia-inducible factor 2α) and posttranscriptional (by the iron-sensing iron-regulatory protein/iron-responsive element system) mechanisms. Recent studies demonstrated that these regulatory loops function in tandem to control expression or activity of key modulators of iron homeostasis. In health, body iron levels are maintained at appropriate levels; however, in several inherited disorders and in other pathophysiological states, iron sensing is perturbed and intestinal iron absorption is dysregulated. The iron-related phenotypes of these diseases exemplify the necessity of precisely regulating iron absorption to meet body demands. PMID:24994858

  4. The RNA Export Factor, Nxt1, Is Required for Tissue Specific Transcriptional Regulation

    PubMed Central

    Jiang, Jianqiao; White-Cooper, Helen

    2013-01-01

    The highly conserved, Nxf/Nxt (TAP/p15) RNA nuclear export pathway is important for export of most mRNAs from the nucleus, by interacting with mRNAs and promoting their passage through nuclear pores. Nxt1 is essential for viability; using a partial loss of function allele, we reveal a role for this gene in tissue specific transcription. We show that many Drosophila melanogaster testis-specific mRNAs require Nxt1 for their accumulation. The transcripts that require Nxt1 also depend on a testis-specific transcription complex, tMAC. We show that loss of Nxt1 leads to reduced transcription of tMAC targets. A reporter transcript from a tMAC-dependent promoter is under-expressed in Nxt1 mutants, however the same transcript accumulates in mutants if driven by a tMAC-independent promoter. Thus, in Drosophila primary spermatocytes, the transcription factor used to activate expression of a transcript, rather than the RNA sequence itself or the core transcription machinery, determines whether this expression requires Nxt1. We additionally find that transcripts from intron-less genes are more sensitive to loss of Nxt1 function than those from intron-containing genes and propose a mechanism in which transcript processing feeds back to increase activity of a tissue specific transcription complex. PMID:23754955

  5. DNA residence time is a regulatory factor of transcription repression

    PubMed Central

    Clauß, Karen; Popp, Achim P.; Schulze, Lena; Hettich, Johannes; Reisser, Matthias; Escoter Torres, Laura; Uhlenhaut, N. Henriette

    2017-01-01

    Abstract Transcription comprises a highly regulated sequence of intrinsically stochastic processes, resulting in bursts of transcription intermitted by quiescence. In transcription activation or repression, a transcription factor binds dynamically to DNA, with a residence time unique to each factor. Whether the DNA residence time is important in the transcription process is unclear. Here, we designed a series of transcription repressors differing in their DNA residence time by utilizing the modular DNA binding domain of transcription activator-like effectors (TALEs) and varying the number of nucleotide-recognizing repeat domains. We characterized the DNA residence times of our repressors in living cells using single molecule tracking. The residence times depended non-linearly on the number of repeat domains and differed by more than a factor of six. The factors provoked a residence time-dependent decrease in transcript level of the glucocorticoid receptor-activated gene SGK1. Down regulation of transcription was due to a lower burst frequency in the presence of long binding repressors and is in accordance with a model of competitive inhibition of endogenous activator binding. Our single molecule experiments reveal transcription factor DNA residence time as a regulatory factor controlling transcription repression and establish TALE-DNA binding domains as tools for the temporal dissection of transcription regulation. PMID:28977492

  6. Global effects of the CSR-1 RNA interference pathway on the transcriptional landscape.

    PubMed

    Cecere, Germano; Hoersch, Sebastian; O'Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

    2014-04-01

    Argonaute proteins and their small RNA cofactors short interfering RNAs are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) that are antisense to germline transcripts. However, its role in gene expression regulation remains controversial. Here we used genome-wide profiling of nascent RNA transcripts and found that the CSR-1 RNA interference pathway promoted sense-oriented RNA polymerase II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. On the basis of these findings, we propose that the CSR-1 pathway helps maintain the directionality of active transcription, thereby propagating the distinction between transcriptionally active and silent genomic regions.

  7. Chromatin potentiates transcription

    PubMed Central

    Nagai, Shigeki; Davis, Ralph E.; Mattei, Pierre Jean; Eagen, Kyle Patrick; Kornberg, Roger D.

    2017-01-01

    Chromatin isolated from the chromosomal locus of the PHO5 gene of yeast in a transcriptionally repressed state was transcribed with 12 pure proteins (80 polypeptides): RNA polymerase II, six general transcription factors, TFIIS, the Pho4 gene activator protein, and the SAGA, SWI/SNF, and Mediator complexes. Contrary to expectation, a nucleosome occluding the TATA box and transcription start sites did not impede transcription but rather, enhanced it: the level of chromatin transcription was at least sevenfold greater than that of naked DNA, and chromatin gave patterns of transcription start sites closely similar to those occurring in vivo, whereas naked DNA gave many aberrant transcripts. Both histone acetylation and trimethylation of H3K4 (H3K4me3) were important for chromatin transcription. The nucleosome, long known to serve as a general gene repressor, thus also performs an important positive role in transcription. PMID:28137832

  8. Widespread antisense transcription of Populus genome under drought.

    PubMed

    Yuan, Yinan; Chen, Su

    2018-06-06

    Antisense transcription is widespread in many genomes and plays important regulatory roles in gene expression. The objective of our study was to investigate the extent and functional relevance of antisense transcription in forest trees. We employed Populus, a model tree species, to probe the antisense transcriptional response of tree genome under drought, through stranded RNA-seq analysis. We detected nearly 48% of annotated Populus gene loci with antisense transcripts and 44% of them with co-transcription from both DNA strands. Global distribution of reads pattern across annotated gene regions uncovered that antisense transcription was enriched in untranslated regions while sense reads were predominantly mapped in coding exons. We further detected 1185 drought-responsive sense and antisense gene loci and identified a strong positive correlation between the expression of antisense and sense transcripts. Additionally, we assessed the antisense expression in introns and found a strong correlation between intronic expression and exonic expression, confirming antisense transcription of introns contributes to transcriptional activity of Populus genome under drought. Finally, we functionally characterized drought-responsive sense-antisense transcript pairs through gene ontology analysis and discovered that functional groups including transcription factors and histones were concordantly regulated at both sense and antisense transcriptional level. Overall, our study demonstrated the extensive occurrence of antisense transcripts of Populus genes under drought and provided insights into genome structure, regulation pattern and functional significance of drought-responsive antisense genes in forest trees. Datasets generated in this study serve as a foundation for future genetic analysis to improve our understanding of gene regulation by antisense transcription.

  9. 40 CFR 1603.12 - Availability of transcripts, recordings, and minutes, and applicable fees.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... of § 1603.7. Copies of the nonexempt portions of the transcript or minutes, or transcription of such... transcription or duplication. Requests for transcripts, recordings, or minutes shall be made in writing to the...

  10. 40 CFR 1603.12 - Availability of transcripts, recordings, and minutes, and applicable fees.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... of § 1603.7. Copies of the nonexempt portions of the transcript or minutes, or transcription of such... transcription or duplication. Requests for transcripts, recordings, or minutes shall be made in writing to the...

  11. Transcriptional blood signatures distinguish pulmonary tuberculosis, pulmonary sarcoidosis, pneumonias and lung cancers.

    PubMed

    Bloom, Chloe I; Graham, Christine M; Berry, Matthew P R; Rozakeas, Fotini; Redford, Paul S; Wang, Yuanyuan; Xu, Zhaohui; Wilkinson, Katalin A; Wilkinson, Robert J; Kendrick, Yvonne; Devouassoux, Gilles; Ferry, Tristan; Miyara, Makoto; Bouvry, Diane; Valeyre, Dominique; Dominique, Valeyre; Gorochov, Guy; Blankenship, Derek; Saadatian, Mitra; Vanhems, Phillip; Beynon, Huw; Vancheeswaran, Rama; Wickremasinghe, Melissa; Chaussabel, Damien; Banchereau, Jacques; Pascual, Virginia; Ho, Ling-Pei; Lipman, Marc; O'Garra, Anne

    2013-01-01

    New approaches to define factors underlying the immunopathogenesis of pulmonary diseases including sarcoidosis and tuberculosis are needed to develop new treatments and biomarkers. Comparing the blood transcriptional response of tuberculosis to other similar pulmonary diseases will advance knowledge of disease pathways and help distinguish diseases with similar clinical presentations. To determine the factors underlying the immunopathogenesis of the granulomatous diseases, sarcoidosis and tuberculosis, by comparing the blood transcriptional responses in these and other pulmonary diseases. We compared whole blood genome-wide transcriptional profiles in pulmonary sarcoidosis, pulmonary tuberculosis, to community acquired pneumonia and primary lung cancer and healthy controls, before and after treatment, and in purified leucocyte populations. An Interferon-inducible neutrophil-driven blood transcriptional signature was present in both sarcoidosis and tuberculosis, with a higher abundance and expression in tuberculosis. Heterogeneity of the sarcoidosis signature correlated significantly with disease activity. Transcriptional profiles in pneumonia and lung cancer revealed an over-abundance of inflammatory transcripts. After successful treatment the transcriptional activity in tuberculosis and pneumonia patients was significantly reduced. However the glucocorticoid-responsive sarcoidosis patients showed a significant increase in transcriptional activity. 144-blood transcripts were able to distinguish tuberculosis from other lung diseases and controls. Tuberculosis and sarcoidosis revealed similar blood transcriptional profiles, dominated by interferon-inducible transcripts, while pneumonia and lung cancer showed distinct signatures, dominated by inflammatory genes. There were also significant differences between tuberculosis and sarcoidosis in the degree of their transcriptional activity, the heterogeneity of their profiles and their transcriptional response to treatment.

  12. Maize Iranian mosaic virus shows a descending transcript accumulation order in plant and insect hosts.

    PubMed

    Hortamani, Mozhgan; Massah, Amir; Izadpanah, Keramat

    2018-04-01

    Maize Iranian mosaic virus (MIMV) is a distinct member of the genus Nucleorhabdovirus. In this study, expression of all MIMV genes in maize for four weeks after inoculation and in inoculative planthoppers was examined using a quantitative RT-PCR (RT-qPCR) assay. Accumulation of MIMV P, gene 3, M, G and L transcripts relative to N transcripts was measured and normalized to 18S rRNA in maize plants and to the ribosomal protein S13 gene (RPS13) in planthoppers using the comparative C T method. In plants, higher levels of MIMV N transcripts were found relative to other transcripts, while MIMV L transcripts were at the lowest levels. The highest accumulation of MIMV transcripts was found at 14 days postinoculation (dpi). At 21 dpi, we found the lowest transcript levels for all genes, which increased again at 28 dpi, although in lower amounts than at 14 dpi. In Laodelphax striatellus, MIMV M, G and L transcripts accumulated at lower levels than other transcripts. The gene 3 transcript level was high in both plants and planthoppers. Our results showed that transcript accumulation for the MIMV genes was similar in both hosts and followed the pattern of sequential transcriptional attenuation from the 3' to the 5' end of the genome, similar to vertebrate rhabdoviruses. These results indicate that the regulation of virus gene transcription for this plant-infecting rhabdovirus is similar to that of some vertebrate-infecting rhabdoviruses.

  13. Regulation of circadian clock transcriptional output by CLOCK:BMAL1

    PubMed Central

    Trott, Alexandra J.

    2018-01-01

    The mammalian circadian clock relies on the transcription factor CLOCK:BMAL1 to coordinate the rhythmic expression of 15% of the transcriptome and control the daily regulation of biological functions. The recent characterization of CLOCK:BMAL1 cistrome revealed that although CLOCK:BMAL1 binds synchronously to all of its target genes, its transcriptional output is highly heterogeneous. By performing a meta-analysis of several independent genome-wide datasets, we found that the binding of other transcription factors at CLOCK:BMAL1 enhancers likely contribute to the heterogeneity of CLOCK:BMAL1 transcriptional output. While CLOCK:BMAL1 rhythmic DNA binding promotes rhythmic nucleosome removal, it is not sufficient to generate transcriptionally active enhancers as assessed by H3K27ac signal, RNA Polymerase II recruitment, and eRNA expression. Instead, the transcriptional activity of CLOCK:BMAL1 enhancers appears to rely on the activity of ubiquitously expressed transcription factors, and not tissue-specific transcription factors, recruited at nearby binding sites. The contribution of other transcription factors is exemplified by how fasting, which effects several transcription factors but not CLOCK:BMAL1, either decreases or increases the amplitude of many rhythmically expressed CLOCK:BMAL1 target genes. Together, our analysis suggests that CLOCK:BMAL1 promotes a transcriptionally permissive chromatin landscape that primes its target genes for transcription activation rather than directly activating transcription, and provides a new framework to explain how environmental or pathological conditions can reprogram the rhythmic expression of clock-controlled genes. PMID:29300726

  14. Pervasive Transcription of a Herpesvirus Genome Generates Functionally Important RNAs

    PubMed Central

    Canny, Susan P.; Reese, Tiffany A.; Johnson, L. Steven; Zhang, Xin; Kambal, Amal; Duan, Erning; Liu, Catherine Y.; Virgin, Herbert W.

    2014-01-01

    ABSTRACT Pervasive transcription is observed in a wide range of organisms, including humans, mice, and viruses, but the functional significance of the resulting transcripts remains uncertain. Current genetic approaches are often limited by their emphasis on protein-coding open reading frames (ORFs). We previously identified extensive pervasive transcription from the murine gammaherpesvirus 68 (MHV68) genome outside known ORFs and antisense to known genes (termed expressed genomic regions [EGRs]). Similar antisense transcripts have been identified in many other herpesviruses, including Kaposi’s sarcoma-associated herpesvirus and human and murine cytomegalovirus. Despite their prevalence, whether these RNAs have any functional importance in the viral life cycle is unknown, and one interpretation is that these are merely “noise” generated by functionally unimportant transcriptional events. To determine whether pervasive transcription of a herpesvirus genome generates RNA molecules that are functionally important, we used a strand-specific functional approach to target transcripts from thirteen EGRs in MHV68. We found that targeting transcripts from six EGRs reduced viral protein expression, proving that pervasive transcription can generate functionally important RNAs. We characterized transcripts emanating from EGRs 26 and 27 in detail using several methods, including RNA sequencing, and identified several novel polyadenylated transcripts that were enriched in the nuclei of infected cells. These data provide the first evidence of the functional importance of regions of pervasive transcription emanating from MHV68 EGRs. Therefore, studies utilizing mutation of a herpesvirus genome must account for possible effects on RNAs generated by pervasive transcription. PMID:24618256

  15. The chicken skeletal alpha-actin gene promoter region exhibits partial dyad symmetry and a capacity to drive bidirectional transcription.

    PubMed Central

    Grichnik, J M; French, B A; Schwartz, R J

    1988-01-01

    The chicken skeletal alpha-actin gene promoter region (-202 to -12) provides myogenic transcriptional specificity. This promoter contains partial dyad symmetry about an axis at nucleotide -108 and in transfection experiments is capable of directing transcription in a bidirectional manner. At least three different transcription initiation start sites, oriented toward upstream sequences, were mapped 25 to 30 base pairs from TATA-like regions. The opposing transcriptional activity was potentiated upon the deletion of sequences proximal to the alpha-actin transcription start site. Thus, sequences which serve to position RNA polymerase for alpha-actin transcription may allow, in their absence, the selection of alternative and reverse-oriented start sites. Nuclear runoff transcription assays of embryonic muscle indicated that divergent transcription may occur in vivo but with rapid turnover of nuclear transcripts. Divergent transcriptional activity enabled us to define the 3' regulatory boundary of the skeletal alpha-actin promoter which retains a high level of myogenic transcriptional activity. The 3' regulatory border was detected when serial 3' deletions bisected the element (-91 CCAAA TATGG -82) which reduced transcriptional activity by 80%. Previously we showed that disruption of its upstream counterpart (-127 CCAAAGAAGG -136) resulted in about a 90% decrease in activity. These element pairs, which we describe as CCAAT box-associated repeats, are conserved in all sequenced vertebrate sarcomeric actin genes and may act in a cooperative manner to facilitate transcription in myogenic cells. Images PMID:3211124

  16. A structure-based kinetic model of transcription.

    PubMed

    Zuo, Yuhong; Steitz, Thomas A

    2017-01-01

    During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement.

  17. Asymmetry between Activation and Deactivation during a Transcriptional Pulse.

    PubMed

    Dunham, Lee S S; Momiji, Hiroshi; Harper, Claire V; Downton, Polly J; Hey, Kirsty; McNamara, Anne; Featherstone, Karen; Spiller, David G; Rand, David A; Finkenstädt, Bärbel; White, Michael R H; Davis, Julian R E

    2017-12-27

    Transcription in eukaryotic cells occurs in gene-specific bursts or pulses of activity. Recent studies identified a spectrum of transcriptionally active "on-states," interspersed with periods of inactivity, but these "off-states" and the process of transcriptional deactivation are poorly understood. To examine what occurs during deactivation, we investigate the dynamics of switching between variable rates. We measured live single-cell expression of luciferase reporters from human growth hormone or human prolactin promoters in a pituitary cell line. Subsequently, we applied a statistical variable-rate model of transcription, validated by single-molecule FISH, to estimate switching between transcriptional rates. Under the assumption that transcription can switch to any rate at any time, we found that transcriptional activation occurs predominantly as a single switch, whereas deactivation occurs with graded, stepwise decreases in transcription rate. Experimentally altering cAMP signalling with forskolin or chromatin remodelling with histone deacetylase inhibitor modifies the duration of defined transcriptional states. Our findings reveal transcriptional activation and deactivation as mechanistically independent, asymmetrical processes. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  18. When transcription goes on Holliday: Double Holliday junctions block RNA polymerase II transcription in vitro.

    PubMed

    Pipathsouk, Anne; Belotserkovskii, Boris P; Hanawalt, Philip C

    2017-02-01

    Non-canonical DNA structures can obstruct transcription. This transcription blockage could have various biological consequences, including genomic instability and gratuitous transcription-coupled repair. Among potential structures causing transcription blockage are Holliday junctions (HJs), which can be generated as intermediates in homologous recombination or during processing of stalled replication forks. Of particular interest is the double Holliday junction (DHJ), which contains two HJs. Topological considerations impose the constraint that the total number of helical turns in the DNA duplexes between the junctions cannot be altered as long as the flanking DNA duplexes are intact. Thus, the DHJ structure should strongly resist transient unwinding during transcription; consequently, it is predicted to cause significantly stronger blockage than single HJ structures. The patterns of transcription blockage obtained for RNA polymerase II transcription in HeLa cell nuclear extracts were in accordance with this prediction. However, we did not detect transcription blockage with purified T7 phage RNA polymerase; we discuss a possible explanation for this difference. In general, our findings implicate naturally occurring Holliday junctions in transcription arrest. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Pervasive Targeting of Nascent Transcripts by Hfq.

    PubMed

    Kambara, Tracy K; Ramsey, Kathryn M; Dove, Simon L

    2018-05-01

    Hfq is an RNA chaperone and an important post-transcriptional regulator in bacteria. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), we show that Hfq associates with hundreds of different regions of the Pseudomonas aeruginosa chromosome. These associations are abolished when transcription is inhibited, indicating that they reflect Hfq binding to transcripts during their synthesis. Analogous ChIP-seq analyses with the post-transcriptional regulator Crc reveal that it associates with many of the same nascent transcripts as Hfq, an activity we show is Hfq dependent. Our findings indicate that Hfq binds many transcripts co-transcriptionally in P. aeruginosa, often in concert with Crc, and uncover direct regulatory targets of these proteins. They also highlight a general approach for studying the interactions of RNA-binding proteins with nascent transcripts in bacteria. The binding of post-transcriptional regulators to nascent mRNAs may represent a prevalent means of controlling translation in bacteria where transcription and translation are coupled. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

  20. Establishment of an in vitro transcription system for Peste des petits ruminant virus.

    PubMed

    Yunus, Mohammad; Shaila, Melkote S

    2012-12-05

    Peste-des-petits ruminants virus (PPRV) is a non segmented negative strand RNA virus of the genus Morbillivirus within Paramyxoviridae family. Negative strand RNA viruses are known to carry nucleocapsid (N) protein, phospho (P) protein and RNA polymerase (L protein) packaged within the virion which possess all activities required for transcription, post-transcriptional modification of mRNA and replication. In order to understand the mechanism of transcription and replication of the virus, an in vitro transcription reconstitution system is required. In the present work, an in vitro transcription system has been developed with ribonucleoprotein (RNP) complex purified from virus infected cells as well as partially purified recombinant polymerase (L-P) complex from insect cells along with N-RNA (genomic RNA encapsidated by N protein) template isolated from virus infected cells. RNP complex isolated from virus infected cells and recombinant L-P complex purified from insect cells was used to reconstitute transcription on N-RNA template. The requirement for this transcription reconstitution has been defined. Transcription of viral genes in the in vitro system was confirmed by PCR amplification of cDNAs corresponding to individual transcripts using gene specific primers. In order to measure the relative expression level of viral transcripts, real time PCR analysis was carried out. qPCR analysis of the transcription products made in vitro showed a gradient of polarity of transcription from 3' end to 5' end of the genome similar to that exhibited by the virus in infected cells. This report describes for the first time, the development of an in vitro transcription reconstitution system for PPRV with RNP complex purified from infected cells and recombinant L-P complex expressed in insect cells. Both the complexes were able to synthesize all the mRNA species in vitro, exhibiting a gradient of polarity in transcription.

  1. The individual, the government and the global community: sharing responsibility for health post-2015 in Vanuatu, a small island developing state.

    PubMed

    Ibell, Claire; Sheridan, Simon A; Hill, Peter S; Tasserei, John; Maleb, Marie-France; Rory, Jean-Jacques

    2015-10-24

    The end of 2015 will see the creation of the sustainable development goals - the new global framework for development. The process of creating universally relevant goals has involved community consultation throughout the world. Within this process it is vital that Pacific Island countries are included as they face particular development challenges due to their size and geographical location. As small island developing states, many Pacific Island countries struggle to overcome high rates of poverty and poor health outcomes. In order to include Pacific voices in the new health related sustainable development goals, Vanuatu was selected as a representative of the Pacific for this qualitative study. This paper presents the perspectives of communities throughout Vanuatu on their essential health needs and how best to meet them. This paper examines the perspectives of 102 individuals from throughout Vanuatu. Ten focus group discussions and 2 individual interviews were conducted within communities in September 2013. Discussions focused on community perceptions of health, essential health needs, and responsibility in achieving health needs. Discussions were audio recorded and transcribed. The transcripts were then analysed using a theoretical thematic approach in order to identify central themes and subthemes. Individuals in this study demonstrated a comprehensive understanding of health, defining health in a holistic manner. Participants identified clear environmental and societal factors that impact upon health, and emphasized failures within the current health system as important barriers to attaining good health. Participants described the challenges faced in taking responsibility for one's health, and pointed to both the government and the international community as key players in meeting the essential health needs of communities. As a small island developing state, Vanuatu faces accentuated development challenges - particularly as globalisation and climate change progress. The individuals and communities in this study demonstrate a clear understanding of their needs, and show a strong desire for change. They point to both the government and the international community to assist in meeting health needs, and stress that respect for traditional governance and community involvement in decision-making are vital in this process. In order to ensure that the new health goals effectively meet local needs in Vanuatu such factors must be incorporated into policy and implementation decision-making.

  2. Analysis of the regulation of viral transcription.

    PubMed

    Gloss, Bernd; Kalantari, Mina; Bernard, Hans-Ulrich

    2005-01-01

    Despite the small genomes and number of genes of papillomaviruses, regulation of their transcription is very complex and governed by numerous transcription factors, cis-responsive elements, and epigenetic phenomena. This chapter describes the strategies of how one can approach a systematic analysis of these factors, elements, and mechanisms. From the numerous different techniques useful for studying transcription, we describe in detail three selected protocols of approaches that have been relevant in shaping our knowledge of human papillomavirus transcription. These are DNAse I protection ("footprinting") for location of transcription-factor binding sites, electrophoretic mobility shifts ("gelshifts") for analysis of bound transcription factors, and bisulfite sequencing for analysis of DNA methylation as a prerequisite for epigenetic transcriptional regulation.

  3. Mitochondrial run-on transcription assay using biotin labeling.

    PubMed

    Kühn, Kristina

    2015-01-01

    RNA synthesis and different posttranscriptional processes shape the transcriptome of plant mitochondria. It is believed that mitochondrial transcription in plants is not stringently controlled, and that RNA degradation has a major impact on mitochondrial steady-state transcript levels. Nevertheless, the presence of two RNA polymerases with different gene specificities in mitochondria of dicotyledonous species indicates that transcriptional mechanisms may provide a means to control mitochondrial steady-state RNA pools and gene expression. To experimentally assess transcriptional activities in mitochondria, run-on transcription assays have been developed. These assays measure elongation rates for endogenous transcripts in freshly prepared mitochondrial extracts. The mitochondrial run-on transcription protocol described here has been optimized for the model plant Arabidopsis (Arabidopsis thaliana). It uses mitochondria prepared from soil-grown Arabidopsis plants and employs nonradioactive labeling for the subsequent detection of run-on transcripts.

  4. A structure-based kinetic model of transcription

    PubMed Central

    Steitz, Thomas A.

    2017-01-01

    ABSTRACT During transcription, RNA polymerase moves downstream along the DNA template and maintains a transcription bubble. Several recent structural studies of transcription complexes with a complete transcription bubble provide new insights into how RNAP couples the nucleotide addition reaction to its directional movement. PMID:27656764

  5. Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh

    PubMed Central

    Osborne, Cameron S; Chakalova, Lyubomira; Mitchell, Jennifer A; Horton, Alice; Wood, Andrew L; Bolland, Daniel J; Corcoran, Anne E; Fraser, Peter

    2007-01-01

    Transcription in mammalian nuclei is highly compartmentalized in RNA polymerase II-enriched nuclear foci known as transcription factories. Genes in cis and trans can share the same factory, suggesting that genes migrate to preassembled transcription sites. We used fluorescent in situ hybridization to investigate the dynamics of gene association with transcription factories during immediate early (IE) gene induction in mouse B lymphocytes. Here, we show that induction involves rapid gene relocation to transcription factories. Importantly, we find that the Myc proto-oncogene on Chromosome 15 is preferentially recruited to the same transcription factory as the highly transcribed Igh gene located on Chromosome 12. Myc and Igh are the most frequent translocation partners in plasmacytoma and Burkitt lymphoma. Our results show that transcriptional activation of IE genes involves rapid relocation to preassembled transcription factories. Furthermore, the data imply a direct link between the nonrandom interchromosomal organization of transcribed genes at transcription factories and the incidence of specific chromosomal translocations. PMID:17622196

  6. Global effects of the CSR-1 RNA interference pathway on transcriptional landscape

    PubMed Central

    Cecere, Germano; Hoersch, Sebastian; O’Keeffe, Sean; Sachidanandam, Ravi; Grishok, Alla

    2014-01-01

    Argonaute proteins and their small RNA co-factors short interfering RNAs (siRNAs) are known to inhibit gene expression at the transcriptional and post-transcriptional levels. In Caenorhabditis elegans, the Argonaute CSR-1 binds thousands of endogenous siRNAs (endo-siRNAs) antisense to germline transcripts and associates with chromatin in a siRNA-dependent manner. However, its role in gene expression regulation remains controversial. Here, we used a genome-wide profiling of nascent RNA transcripts to demonstrate that the CSR-1 RNAi pathway promotes sense-oriented Pol II transcription. Moreover, a loss of CSR-1 function resulted in global increase in antisense transcription and ectopic transcription of silent chromatin domains, which led to reduced chromatin incorporation of centromere-specific histone H3. Based on these findings, we propose that the CSR-1 pathway has a role in maintaining the directionality of active transcription thereby propagating the distinction between transcriptionally active and silent genomic regions. PMID:24681887

  7. System-wide analysis of the transcriptional network of human myelomonocytic leukemia cells predicts attractor structure and phorbol-ester-induced differentiation and dedifferentiation transitions

    NASA Astrophysics Data System (ADS)

    Sakata, Katsumi; Ohyanagi, Hajime; Sato, Shinji; Nobori, Hiroya; Hayashi, Akiko; Ishii, Hideshi; Daub, Carsten O.; Kawai, Jun; Suzuki, Harukazu; Saito, Toshiyuki

    2015-02-01

    We present a system-wide transcriptional network structure that controls cell types in the context of expression pattern transitions that correspond to cell type transitions. Co-expression based analyses uncovered a system-wide, ladder-like transcription factor cluster structure composed of nearly 1,600 transcription factors in a human transcriptional network. Computer simulations based on a transcriptional regulatory model deduced from the system-wide, ladder-like transcription factor cluster structure reproduced expression pattern transitions when human THP-1 myelomonocytic leukaemia cells cease proliferation and differentiate under phorbol myristate acetate stimulation. The behaviour of MYC, a reprogramming Yamanaka factor that was suggested to be essential for induced pluripotent stem cells during dedifferentiation, could be interpreted based on the transcriptional regulation predicted by the system-wide, ladder-like transcription factor cluster structure. This study introduces a novel system-wide structure to transcriptional networks that provides new insights into network topology.

  8. Nascent-Seq reveals novel features of mouse circadian transcriptional regulation

    PubMed Central

    Menet, Jerome S; Rodriguez, Joseph; Abruzzi, Katharine C; Rosbash, Michael

    2012-01-01

    A substantial fraction of the metazoan transcriptome undergoes circadian oscillations in many cells and tissues. Based on the transcription feedback loops important for circadian timekeeping, it is commonly assumed that this mRNA cycling reflects widespread transcriptional regulation. To address this issue, we directly measured the circadian dynamics of mouse liver transcription using Nascent-Seq (genome-wide sequencing of nascent RNA). Although many genes are rhythmically transcribed, many rhythmic mRNAs manifest poor transcriptional rhythms, indicating a prominent contribution of post-transcriptional regulation to circadian mRNA expression. This analysis of rhythmic transcription also showed that the rhythmic DNA binding profile of the transcription factors CLOCK and BMAL1 does not determine the transcriptional phase of most target genes. This likely reflects gene-specific collaborations of CLK:BMAL1 with other transcription factors. These insights from Nascent-Seq indicate that it should have broad applicability to many other gene expression regulatory issues. DOI: http://dx.doi.org/10.7554/eLife.00011.001 PMID:23150795

  9. Microarray Analyses and Comparisons of Upper or Lower Flanks of Rice Shoot Base Preceding Gravitropic Bending

    PubMed Central

    Zang, Aiping; Chen, Haiying; Dou, Xianying; Jin, Jing; Cai, Weiming

    2013-01-01

    Gravitropism is a complex process involving a series of physiological pathways. Despite ongoing research, gravitropism sensing and response mechanisms are not well understood. To identify the key transcripts and corresponding pathways in gravitropism, a whole-genome microarray approach was used to analyze transcript abundance in the shoot base of rice (Oryza sativa sp. japonica) at 0.5 h and 6 h after gravistimulation by horizontal reorientation. Between upper and lower flanks of the shoot base, 167 transcripts at 0.5 h and 1202 transcripts at 6 h were discovered to be significantly different in abundance by 2-fold. Among these transcripts, 48 were found to be changed both at 0.5 h and 6 h, while 119 transcripts were only changed at 0.5 h and 1154 transcripts were changed at 6 h in association with gravitropism. MapMan and PageMan analyses were used to identify transcripts significantly changed in abundance. The asymmetric regulation of transcripts related to phytohormones, signaling, RNA transcription, metabolism and cell wall-related categories between upper and lower flanks were demonstrated. Potential roles of the identified transcripts in gravitropism are discussed. Our results suggest that the induction of asymmetrical transcription, likely as a consequence of gravitropic reorientation, precedes gravitropic bending in the rice shoot base. PMID:24040303

  10. Inhibition of host cell RNA polymerase III-mediated transcription by poliovirus: Inactivation of specific transcription factors

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Fradkin, L.G.; Yoshinaga, S.K.; Berk, A.J.

    1987-11-01

    The inhibition of transcription by RNA polymerase III in poliovirus-infected cells was studied. Experiments utilizing two different cell lines showed that the initiation step of transcription by RNA polymerase III was impaired by infection of these cells with the virus. The observed inhibition of transcription was not due to shut-off of host cell protein synthesis by poliovirus. Among four distinct components required for accurate transcription in vitro from cloned DNA templates, activities of RNA polymerase III and transcription factor TFIIIA were not significantly affected by virus infection. The activity of transcription factor TFIIIC, the limiting component required for transcription ofmore » RNA polymerase III genes, was severely inhibited in infected cells, whereas that of transcription factor TFIIIB was inhibited to a lesser extent. The sequence-specific DNA-binding of TFIIIC to the adenovirus VA1 gene internal promoted, however, was not altered by infection of cells with the virus. The authors conclude that (i) at least two transcription factors, TFIIIB and TFIIIC, are inhibited by infection of cells with poliovirtus, (ii) inactivation of TFIIIC does not involve destruction of its DNA-binding domain, and (iii) sequence-specific DNA binding by TFIIIC may be necessary but is not sufficient for the formation of productive transcription complexes.« less

  11. Novel kinase fusion transcripts found in endometrial cancer

    PubMed Central

    Tamura, Ryo; Yoshihara, Kosuke; Yamawaki, Kaoru; Suda, Kazuaki; Ishiguro, Tatsuya; Adachi, Sosuke; Okuda, Shujiro; Inoue, Ituro; Verhaak, Roel G. W.; Enomoto, Takayuki

    2015-01-01

    Recent advances in RNA-sequencing technology have enabled the discovery of gene fusion transcripts in the transcriptome of cancer cells. However, it remains difficult to differentiate the therapeutically targetable fusions from passenger events. We have analyzed RNA-sequencing data and DNA copy number data from 25 endometrial cancer cell lines to identify potential therapeutically targetable fusion transcripts, and have identified 124 high-confidence fusion transcripts, of which 69% are associated with gene amplifications. As targetable fusion candidates, we focused on three in-frame kinase fusion transcripts that retain a kinase domain (CPQ-PRKDC, CAPZA2-MET, and VGLL4-PRKG1). We detected only CPQ-PRKDC fusion transcript in three of 122 primary endometrial cancer tissues. Cell proliferation of the fusion-positive cell line was inhibited by knocking down the expression of wild-type PRKDC but not by blocking the CPQ-PRKDC fusion transcript expression. Quantitative real-time RT-PCR demonstrated that the expression of the CPQ-PRKDC fusion transcript was significantly lower than that of wild-type PRKDC, corresponding to a low transcript allele fraction of this fusion, based on RNA-sequencing read counts. In endometrial cancers, the CPQ-PRKDC fusion transcript may be a passenger aberration related to gene amplification. Our findings suggest that transcript allele fraction is a useful predictor to find bona-fide therapeutic-targetable fusion transcripts. PMID:26689674

  12. Novel kinase fusion transcripts found in endometrial cancer.

    PubMed

    Tamura, Ryo; Yoshihara, Kosuke; Yamawaki, Kaoru; Suda, Kazuaki; Ishiguro, Tatsuya; Adachi, Sosuke; Okuda, Shujiro; Inoue, Ituro; Verhaak, Roel G W; Enomoto, Takayuki

    2015-12-22

    Recent advances in RNA-sequencing technology have enabled the discovery of gene fusion transcripts in the transcriptome of cancer cells. However, it remains difficult to differentiate the therapeutically targetable fusions from passenger events. We have analyzed RNA-sequencing data and DNA copy number data from 25 endometrial cancer cell lines to identify potential therapeutically targetable fusion transcripts, and have identified 124 high-confidence fusion transcripts, of which 69% are associated with gene amplifications. As targetable fusion candidates, we focused on three in-frame kinase fusion transcripts that retain a kinase domain (CPQ-PRKDC, CAPZA2-MET, and VGLL4-PRKG1). We detected only CPQ-PRKDC fusion transcript in three of 122 primary endometrial cancer tissues. Cell proliferation of the fusion-positive cell line was inhibited by knocking down the expression of wild-type PRKDC but not by blocking the CPQ-PRKDC fusion transcript expression. Quantitative real-time RT-PCR demonstrated that the expression of the CPQ-PRKDC fusion transcript was significantly lower than that of wild-type PRKDC, corresponding to a low transcript allele fraction of this fusion, based on RNA-sequencing read counts. In endometrial cancers, the CPQ-PRKDC fusion transcript may be a passenger aberration related to gene amplification. Our findings suggest that transcript allele fraction is a useful predictor to find bona-fide therapeutic-targetable fusion transcripts.

  13. Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I

    PubMed Central

    Kadota, Shinichi; Nagata, Kyosuke

    2014-01-01

    Chromatin structure and its alteration play critical roles in the regulation of transcription. However, the transcriptional silencing mechanism with regard to the chromatin structure at an unstimulated state of the interferon (IFN)-stimulated gene (ISG) remains unclear. Here we investigated the role of template activating factor-I (TAF-I, also known as SET) in ISG transcription. Knockdown (KD) of TAF-I increased ISG transcript and simultaneously reduced the histone H1 level on the ISG promoters during the early stages of transcription after IFN stimulation from the unstimulated state. The transcription factor levels on the ISG promoters were increased in TAF-I KD cells only during the early stages of transcription. Furthermore, histone H1 KD also increased ISG transcript. TAF-I and histone H1 double KD did not show the additive effect in ISG transcription, suggesting that TAF-I and histone H1 may act on the same regulatory pathway to control ISG transcription. In addition, TAF-I KD and histone H1 KD affected the chromatin structure near the ISG promoters. On the basis of these findings, we propose that TAF-I and its target histone H1 are key regulators of the chromatin structure at the ISG promoter to maintain the silent state of ISG transcription. PMID:24878923

  14. Transcriptional Blood Signatures Distinguish Pulmonary Tuberculosis, Pulmonary Sarcoidosis, Pneumonias and Lung Cancers

    PubMed Central

    Bloom, Chloe I.; Graham, Christine M.; Berry, Matthew P. R.; Rozakeas, Fotini; Redford, Paul S.; Wang, Yuanyuan; Xu, Zhaohui; Wilkinson, Katalin A.; Wilkinson, Robert J.; Kendrick, Yvonne; Devouassoux, Gilles; Ferry, Tristan; Miyara, Makoto; Bouvry, Diane; Dominique, Valeyre; Gorochov, Guy; Blankenship, Derek; Saadatian, Mitra; Vanhems, Phillip; Beynon, Huw; Vancheeswaran, Rama; Wickremasinghe, Melissa; Chaussabel, Damien; Banchereau, Jacques; Pascual, Virginia; Ho, Ling-pei; Lipman, Marc; O’Garra, Anne

    2013-01-01

    Rationale New approaches to define factors underlying the immunopathogenesis of pulmonary diseases including sarcoidosis and tuberculosis are needed to develop new treatments and biomarkers. Comparing the blood transcriptional response of tuberculosis to other similar pulmonary diseases will advance knowledge of disease pathways and help distinguish diseases with similar clinical presentations. Objectives To determine the factors underlying the immunopathogenesis of the granulomatous diseases, sarcoidosis and tuberculosis, by comparing the blood transcriptional responses in these and other pulmonary diseases. Methods We compared whole blood genome-wide transcriptional profiles in pulmonary sarcoidosis, pulmonary tuberculosis, to community acquired pneumonia and primary lung cancer and healthy controls, before and after treatment, and in purified leucocyte populations. Measurements and Main Results An Interferon-inducible neutrophil-driven blood transcriptional signature was present in both sarcoidosis and tuberculosis, with a higher abundance and expression in tuberculosis. Heterogeneity of the sarcoidosis signature correlated significantly with disease activity. Transcriptional profiles in pneumonia and lung cancer revealed an over-abundance of inflammatory transcripts. After successful treatment the transcriptional activity in tuberculosis and pneumonia patients was significantly reduced. However the glucocorticoid-responsive sarcoidosis patients showed a significant increase in transcriptional activity. 144-blood transcripts were able to distinguish tuberculosis from other lung diseases and controls. Conclusions Tuberculosis and sarcoidosis revealed similar blood transcriptional profiles, dominated by interferon-inducible transcripts, while pneumonia and lung cancer showed distinct signatures, dominated by inflammatory genes. There were also significant differences between tuberculosis and sarcoidosis in the degree of their transcriptional activity, the heterogeneity of their profiles and their transcriptional response to treatment. PMID:23940611

  15. 5' diversity of human hepatic PXR (NR1I2) transcripts and identification of the major transcription initiation site.

    PubMed

    Kurose, Kouichi; Koyano, Satoru; Ikeda, Shinobu; Tohkin, Masahiro; Hasegawa, Ryuichi; Sawada, Jun-Ichi

    2005-05-01

    The human pregnane X receptor (PXR) is a crucial regulator of the genes encoding several major cytochrome P450 enzymes and transporters, such as CYP3A4 and MDR1, but its own transcriptional regulation remains unclear. To elucidate the transcriptional mechanisms of human PXR gene, we first endeavored to identify the transcription initiation site of human PXR using 5'-RACE. Five types of 5'-variable transcripts (a, b, c, d, and e) with common exon 2 sequence were found, and comparison of these sequences with the genomic sequence suggested that their 5' diversity is derived from initiation by alternative promoters and alternative splicing. None of the exons found in our study contain any new in-frame coding regions. Newly identified introns IVS-a and IVS-b were found to have CT-AC splice sites that do not follow the GT-AG rule of conventional donor and acceptor splice sites. Of the five types of 5' variable transcripts identified, RT-PCR showed that type-a was the major transcript type. Four transcription initiation sites (A-D) for type-a transcript were identified by 5'-RACE using GeneRacer RACE Ready cDNA (human liver) constructed by the oligo-capping method. Putative TATA boxes were located approximately 30 bp upstream from the transcriptional start sites of the major transcript (C) and the longest minor transcript (A) expressed in the human liver. These results indicate that the initiation of transcription of human PXR is more complex than previously reported.

  16. De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing

    PubMed Central

    2011-01-01

    Background Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas. Results From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis. Conclusion The large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of jatropha to increase oil content, and to modify oil composition. PMID:21492485

  17. De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.

    PubMed

    Natarajan, Purushothaman; Parani, Madasamy

    2011-04-15

    Jatropha curcas L. is an important non-edible oilseed crop with promising future in biodiesel production. However, factors like oil yield, oil composition, toxic compounds in oil cake, pests and diseases limit its commercial potential. Well established genetic engineering methods using cloned genes could be used to address these limitations. Earlier, 10,983 unigenes from Sanger sequencing of ESTs, and 3,484 unique assembled transcripts from 454 pyrosequencing of uncloned cDNAs were reported. In order to expedite the process of gene discovery, we have undertaken 454 pyrosequencing of normalized cDNAs prepared from roots, mature leaves, flowers, developing seeds, and embryos of J. curcas. From 383,918 raw reads, we obtained 381,957 quality-filtered and trimmed reads that are suitable for the assembly of transcript sequences. De novo contig assembly of these reads generated 17,457 assembled transcripts (contigs) and 54,002 singletons. Average length of the assembled transcripts was 916 bp. About 30% of the transcripts were longer than 1000 bases, and the size of the longest transcript was 7,173 bases. BLASTX analysis revealed that 2,589 of these transcripts are full-length. The assembled transcripts were validated by RT-PCR analysis of 28 transcripts. The results showed that the transcripts were correctly assembled and represent actively expressed genes. KEGG pathway mapping showed that 2,320 transcripts are related to major biochemical pathways including the oil biosynthesis pathway. Overall, the current study reports 14,327 new assembled transcripts which included 2589 full-length transcripts and 27 transcripts that are directly involved in oil biosynthesis. The large number of transcripts reported in the current study together with existing ESTs and transcript sequences will serve as an invaluable genetic resource for crop improvement in jatropha. Sequence information of those genes that are involved in oil biosynthesis could be used for metabolic engineering of jatropha to increase oil content, and to modify oil composition.

  18. 46 CFR 502.165 - Official transcript.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... incremental cost of transcription above the regular copy transcription cost borne by the Commission, in... full cost of transcription being borne by the Commission. (B) In the event a request for daily copy is... of transcription over and above that borne by the Commission, i.e., the incremental cost between that...

  19. 46 CFR 502.165 - Official transcript.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... incremental cost of transcription above the regular copy transcription cost borne by the Commission, in... full cost of transcription being borne by the Commission. (B) In the event a request for daily copy is... of transcription over and above that borne by the Commission, i.e., the incremental cost between that...

  20. The Intertwined Roles of Transcription and Repair Proteins

    PubMed Central

    Fong, Yick W.; Cattoglio, Claudia; Tjian, Robert

    2014-01-01

    Transcription is apparently risky business. Its intrinsic mutagenic potential must be kept in check by networks of DNA repair factors that monitor the transcription process to repair DNA lesions that could otherwise compromise transcriptional fidelity and genome integrity. Intriguingly, recent studies point to an even more direct function of DNA repair complexes as co-activators of transcription and the unexpected role of “scheduled” DNA damage/repair at gene promoters. Paradoxically, spontaneous DNA double-strand breaks also induce ectopic transcription that is essential for repair. Thus, transcription, DNA damage and repair may be more physically and functionally intertwined than previously appreciated. PMID:24207023

  1. Investigating transcription reinitiation through in vitro approaches

    PubMed Central

    Dieci, Giorgio; Fermi, Beatrice; Bosio, Maria Cristina

    2014-01-01

    By influencing the number of RNA molecules repeatedly synthesized from the same gene, the control of transcription reinitiation has the potential to shape the transcriptome. Transcription reinitiation mechanisms have been mainly addressed in vitro, through approaches based on both crude and reconstituted systems. These studies support the notion that transcription reinitiation and its regulation rely on dedicated networks of molecular interactions within transcription machineries. At the same time, comparison with in vivo transcription rates suggests that additional mechanisms, factors and conditions must exist in the nucleus, whose biochemical elucidation is a fascinating challenge for future in vitro transcription studies. PMID:25764113

  2. Alternative polyadenylation of the gene transcripts encoding a rat DNA polymerase beta.

    PubMed

    Konopiński, R; Nowak, R; Siedlecki, J A

    1996-10-17

    Rat cells produce two different transcripts of DNA polymerase beta (beta-Pol). The low-molecular-weight transcript (1.4 kb) was already sequenced. We report here the cloning and sequencing of the full-length cDNA, corresponding to the high-molecular-weight (HMW) transcript (4.0 kb) of beta-Pol. Sequence data strongly suggest that both transcripts are produced from a single gene by alternative polyadenylation. The HMW transcript contains the entire 1.4 kb transcript sequence and additional 2.2 kb on the 3' end. The 3' UTR of the HMW transcript contains some regulatory sequences which are not present in the 1.4-kb transcript. The A + U-rich fragment and (GU)21 sequence are believed to influence the stability of the mRNA. The functional significance of the A-rich region locally destabilizing double-stranded secondary structure remains unknown.

  3. Transcriptional bursting is intrinsically caused by interplay between RNA polymerases on DNA

    NASA Astrophysics Data System (ADS)

    Fujita, Keisuke; Iwaki, Mitsuhiro; Yanagida, Toshio

    2016-12-01

    Cell-to-cell variability plays a critical role in cellular responses and decision-making in a population, and transcriptional bursting has been broadly studied by experimental and theoretical approaches as the potential source of cell-to-cell variability. Although molecular mechanisms of transcriptional bursting have been proposed, there is little consensus. An unsolved key question is whether transcriptional bursting is intertwined with many transcriptional regulatory factors or is an intrinsic characteristic of RNA polymerase on DNA. Here we design an in vitro single-molecule measurement system to analyse the kinetics of transcriptional bursting. The results indicate that transcriptional bursting is caused by interplay between RNA polymerases on DNA. The kinetics of in vitro transcriptional bursting is quantitatively consistent with the gene-nonspecific kinetics previously observed in noisy gene expression in vivo. Our kinetic analysis based on a cellular automaton model confirms that arrest and rescue by trailing RNA polymerase intrinsically causes transcriptional bursting.

  4. Fatty Acid–Regulated Transcription Factors in the Liver

    PubMed Central

    Jump, Donald B.; Tripathy, Sasmita; Depner, Christopher M.

    2014-01-01

    Fatty acid regulation of hepatic gene transcription was first reported in the early 1990s. Several transcription factors have been identified as targets of fatty acid regulation. This regulation is achieved by direct fatty acid binding to the transcription factor or by indirect mechanisms where fatty acids regulate signaling pathways controlling the expression of transcription factors or the phosphorylation, ubiquitination, or proteolytic cleavage of the transcription factor. Although dietary fatty acids are well-established regulators of hepatic transcription factors, emerging evidence indicates that endogenously generated fatty acids are equally important in controlling transcription factors in the context of glucose and lipid homeostasis. Our first goal in this review is to provide an up-to-date examination of the molecular and metabolic bases of fatty acid regulation of key transcription factors controlling hepatic metabolism. Our second goal is to link these mechanisms to nonalcoholic fatty liver disease (NAFLD), a growing health concern in the obese population. PMID:23528177

  5. A Synthetic Biology Framework for Programming Eukaryotic Transcription Functions

    PubMed Central

    Khalil, Ahmad S.; Lu, Timothy K.; Bashor, Caleb J.; Ramirez, Cherie L.; Pyenson, Nora C.; Joung, J. Keith; Collins, James J.

    2013-01-01

    SUMMARY Eukaryotic transcription factors (TFs) perform complex and combinatorial functions within transcriptional networks. Here, we present a synthetic framework for systematically constructing eukaryotic transcription functions using artificial zinc fingers, modular DNA-binding domains found within many eukaryotic TFs. Utilizing this platform, we construct a library of orthogonal synthetic transcription factors (sTFs) and use these to wire synthetic transcriptional circuits in yeast. We engineer complex functions, such as tunable output strength and transcriptional cooperativity, by rationally adjusting a decomposed set of key component properties, e.g., DNA specificity, affinity, promoter design, protein-protein interactions. We show that subtle perturbations to these properties can transform an individual sTF between distinct roles (activator, cooperative factor, inhibitory factor) within a transcriptional complex, thus drastically altering the signal processing behavior of multi-input systems. This platform provides new genetic components for synthetic biology and enables bottom-up approaches to understanding the design principles of eukaryotic transcriptional complexes and networks. PMID:22863014

  6. Quality Issues of Court Reporters and Transcriptionists for Qualitative Research

    PubMed Central

    Hennink, Monique; Weber, Mary Beth

    2015-01-01

    Transcription is central to qualitative research, yet few researchers identify the quality of different transcription methods. We described the quality of verbatim transcripts from traditional transcriptionists and court reporters by reviewing 16 transcripts from 8 focus group discussions using four criteria: transcription errors, cost and time of transcription, and effect on study participants. Transcriptionists made fewer errors, captured colloquial dialogue, and errors were largely influenced by the quality of the recording. Court reporters made more errors, particularly in the omission of topical content and contextual detail and were less able to produce a verbatim transcript; however the potential immediacy of the transcript was advantageous. In terms of cost, shorter group discussions favored a transcriptionist and longer groups a court reporter. Study participants reported no effect by either method of recording. Understanding the benefits and limitations of each method of transcription can help researchers select an appropriate method for each study. PMID:23512435

  7. Microprocessor mediates transcriptional termination in long noncoding microRNA genes

    PubMed Central

    Dhir, Ashish; Dhir, Somdutta; Proudfoot, Nick J.; Jopling, Catherine L.

    2015-01-01

    MicroRNA (miRNA) play a major role in the post-transcriptional regulation of gene expression. Mammalian miRNA biogenesis begins with co-transcriptional cleavage of RNA polymerase II (Pol II) transcripts by the Microprocessor complex. While most miRNA are located within introns of protein coding genes, a substantial minority of miRNA originate from long non coding (lnc) RNA where transcript processing is largely uncharacterized. We show, by detailed characterization of liver-specific lnc-pri-miR-122 and genome-wide analysis in human cell lines, that most lnc-pri-miRNA do not use the canonical cleavage and polyadenylation (CPA) pathway, but instead use Microprocessor cleavage to terminate transcription. This Microprocessor inactivation leads to extensive transcriptional readthrough of lnc-pri-miRNA and transcriptional interference with downstream genes. Consequently we define a novel RNase III-mediated, polyadenylation-independent mechanism of Pol II transcription termination in mammalian cells. PMID:25730776

  8. Transcription through enhancers suppresses their activity in Drosophila

    PubMed Central

    2013-01-01

    Background Enhancer elements determine the level of target gene transcription in a tissue-specific manner, providing for individual patterns of gene expression in different cells. Knowledge of the mechanisms controlling enhancer action is crucial for understanding global regulation of transcription. In particular, enhancers are often localized within transcribed regions of the genome. A number of experiments suggest that transcription can have both positive and negative effects on regulatory elements. In this study, we performed direct tests for the effect of transcription on enhancer activity. Results Using a transgenic reporter system, we investigated the relationship between the presence of pass-through transcription and the activity of Drosophila enhancers controlling the expression of the white and yellow genes. The results show that transcription from different promoters affects the activity of enhancers, counteracting their ability to activate the target genes. As expected, the presence of a transcriptional terminator between the inhibiting promoter and the affected enhancer strongly reduces the suppression. Moreover, transcription leads to dislodging of the Zeste protein that is responsible for the enhancer-dependent regulation of the white gene, suggesting a 'transcription interference’ mechanism for this regulation. Conclusions Our findings suggest a role for pass-through transcription in negative regulation of enhancer activity. PMID:24279291

  9. Imaging Transcriptional Regulation of Eukaryotic mRNA Genes: Advances and Outlook.

    PubMed

    Yao, Jie

    2017-01-06

    Regulation of eukaryotic transcription in vivo occurs at distinct stages. Previous research has identified many active or repressive transcription factors (TFs) and core transcription components and studied their functions in vitro and in vivo. Nonetheless, how individual TFs act in concert to regulate mRNA gene expression in a single cell remains poorly understood. Direct observation of TF assembly and disassembly and various biochemical reactions during transcription of a single-copy gene in vivo is the ideal approach to study this problem. Research in this area requires developing novel techniques for single-cell transcription imaging and integrating imaging studies into understanding the molecular biology of transcription. In the past decade, advanced cell imaging has enabled unprecedented capabilities to visualize individual TF molecules, to track single transcription sites, and to detect individual mRNA in fixed and living cells. These studies have raised several novel insights on transcriptional regulation such as the "hit-and-run" model and transcription bursting that could not be obtained by in vitro biochemistry analysis. At this point, the key question is how to achieve deeper understandings or discover novel mechanisms of eukaryotic transcriptional regulation by imaging transcription in single cells. Meanwhile, further technical advancements are likely required for visualizing distinct kinetic steps of transcription on a single-copy gene in vivo. This review article summarizes recent progress in the field and describes the challenges and opportunities ahead. Copyright © 2016 Elsevier Ltd. All rights reserved.

  10. Identification and Classification of New Transcripts in Dorper and Small-Tailed Han Sheep Skeletal Muscle Transcriptomes.

    PubMed

    Chao, Tianle; Wang, Guizhi; Wang, Jianmin; Liu, Zhaohua; Ji, Zhibin; Hou, Lei; Zhang, Chunlan

    2016-01-01

    High-throughput mRNA sequencing enables the discovery of new transcripts and additional parts of incompletely annotated transcripts. Compared with the human and cow genomes, the reference annotation level of the sheep genome is still low. An investigation of new transcripts in sheep skeletal muscle will improve our understanding of muscle development. Therefore, applying high-throughput sequencing, two cDNA libraries from the biceps brachii of small-tailed Han sheep and Dorper sheep were constructed, and whole-transcriptome analysis was performed to determine the unknown transcript catalogue of this tissue. In this study, 40,129 transcripts were finally mapped to the sheep genome. Among them, 3,467 transcripts were determined to be unannotated in the current reference sheep genome and were defined as new transcripts. Based on protein-coding capacity prediction and comparative analysis of sequence similarity, 246 transcripts were classified as portions of unannotated genes or incompletely annotated genes. Another 1,520 transcripts were predicted with high confidence to be long non-coding RNAs. Our analysis also revealed 334 new transcripts that displayed specific expression in ruminants and uncovered a number of new transcripts without intergenus homology but with specific expression in sheep skeletal muscle. The results confirmed a complex transcript pattern of coding and non-coding RNA in sheep skeletal muscle. This study provided important information concerning the sheep genome and transcriptome annotation, which could provide a basis for further study.

  11. Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes.

    PubMed

    Osato, Naoki

    2018-01-19

    Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes. Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone, independent of transcriptional target genes. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5-60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes. Human putative transcriptional target genes showed significant functional enrichments. Functional enrichments were related to the cellular functions. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.

  12. Oxytocin, a main breastfeeding hormone, prevents hypertension acquired in utero: A therapeutics preview.

    PubMed

    Vargas-Martínez, Froylán; Schanler, Richard J; Abrams, Steven A; Hawthorne, Keli M; Landers, Susan; Guzman-Bárcenas, José; Muñoz, Onofre; Henriksen, Tore; Petersson, Maria; Uvnäs-Moberg, Kerstin; Jiménez-Estrada, Ismael

    2017-01-01

    Hypertension is a major risk factor for ischemic heart disease and stroke, leading causes of morbidity and death worldwide. Intrauterine growth restriction (IUGR), caused by an excess of glucocorticoid exposure to the fetus, produces an imbalance in oxidative stress altering many biochemical and epigenetic gene transcription processes exposing the fetus and neonate to the 'thrifty' phenotype and pervasive polymorphisms appearance damaging health, cognitive, and behavioral processes in later life. OT is a major regulator of oxidative stress radicals that plays a major role in neonatal maturation of the central nervous system and many peripheral tissues expressing oxytocin/oxytocin-receptor (OT/OTR) system in the early postnatal period. OT and OTR are damaged by IUGR and early stress. This review highlights the fact that hypertension is likely to be a legacy of preterm birth due to IUGR and failure to meet nutritional needs in early infancy when fed formula instead of breastfeeding or human milk. Copyright © 2016. Published by Elsevier B.V.

  13. CACTI: free, open-source software for the sequential coding of behavioral interactions.

    PubMed

    Glynn, Lisa H; Hallgren, Kevin A; Houck, Jon M; Moyers, Theresa B

    2012-01-01

    The sequential analysis of client and clinician speech in psychotherapy sessions can help to identify and characterize potential mechanisms of treatment and behavior change. Previous studies required coding systems that were time-consuming, expensive, and error-prone. Existing software can be expensive and inflexible, and furthermore, no single package allows for pre-parsing, sequential coding, and assignment of global ratings. We developed a free, open-source, and adaptable program to meet these needs: The CASAA Application for Coding Treatment Interactions (CACTI). Without transcripts, CACTI facilitates the real-time sequential coding of behavioral interactions using WAV-format audio files. Most elements of the interface are user-modifiable through a simple XML file, and can be further adapted using Java through the terms of the GNU Public License. Coding with this software yields interrater reliabilities comparable to previous methods, but at greatly reduced time and expense. CACTI is a flexible research tool that can simplify psychotherapy process research, and has the potential to contribute to the improvement of treatment content and delivery.

  14. The BRG1 chromatin remodeling enzyme links cancer cell metabolism and proliferation

    PubMed Central

    Wu, Qiong; Madany, Pasil; Dobson, Jason R.; Schnabl, Jake M.; Sharma, Soni; Smith, Tara C.; van Wijnen, Andre J.; Stein, Janet L.; Lian, Jane B.; Stein, Gary S.; Muthuswami, Rohini; Imbalzano, Anthony N.; Nickerson, Jeffrey A.

    2016-01-01

    Cancer cells reprogram cellular metabolism to meet the demands of growth. Identification of the regulatory machinery that regulates cancer-specific metabolic changes may open new avenues for anti-cancer therapeutics. The epigenetic regulator BRG1 is a catalytic ATPase for some mammalian SWI/SNF chromatin remodeling enzymes. BRG1 is a well-characterized tumor suppressor in some human cancers, but is frequently overexpressed without mutation in other cancers, including breast cancer. Here we demonstrate that BRG1 upregulates de novo lipogenesis and that this is crucial for cancer cell proliferation. Knockdown of BRG1 attenuates lipid synthesis by impairing the transcription of enzymes catalyzing fatty acid and lipid synthesis. Remarkably, exogenous addition of palmitate, the key intermediate in fatty acid synthesis, rescued the cancer cell proliferation defect caused by BRG1 knockdown. Our work suggests that targeting BRG1 to reduce lipid metabolism and, thereby, to reduce proliferation, has promise for epigenetic therapy in triple negative breast cancer. PMID:27223259

  15. Abortion training at multiple sites: an unexpected curriculum for teaching systems-based practice.

    PubMed

    Herbitter, Cara; Kumar, Vanita; Karasz, Alison; Gold, Marji

    2010-04-01

    In 1999, the Accreditation Council for Graduate Medical Education endorsed systems-based practice as one of six general competencies. The objective is to explore the paradigm of teaching residents systems-based practice during a women's health rotation that included abortion training in multiple settings. During a routine women's health rotation, residents from two urban family medicine residency programs received early abortion training at a high-volume abortion clinic and their continuity clinic. Thirty-min semistructured interviews were conducted with all 26 residents who rotated between July 2005 and August 2006. Transcripts were analyzed using thematic codes. Through exposure to different healthcare delivery systems, residents learned about systems-based practice, including understanding the failure of the larger system to meet patients' reproductive healthcare needs, differences between two systems, and potential systems barriers they might face as providers. Abortion training in multiple settings may serve as a paradigm for teaching systems-based practice during other rotations that include training in multiple sites.

  16. Proposed methods for testing and selecting the ERCC external RNA controls

    PubMed Central

    2005-01-01

    The External RNA Control Consortium (ERCC) is an ad-hoc group with approximately 70 members from private, public, and academic organizations. The group is developing a set of external RNA control transcripts that can be used to assess technical performance in gene expression assays. The ERCC is now initiating the Testing Phase of the project, during which candidate external RNA controls will be evaluated in both microarray and QRT-PCR gene expression platforms. This document describes the proposed experiments and informatics process that will be followed to test and qualify individual controls. The ERCC is distributing this description of the proposed testing process in an effort to gain consensus and to encourage feedback from the scientific community. On October 4–5, 2005, the ERCC met to further review the document, clarify ambiguities, and plan next steps. A summary of this meeting and changes to the test plan are provided as an appendix to this manuscript. PMID:16266432

  17. The Aryl Hydrocarbon Receptor Meets Immunology: Friend or Foe? A Little of Both

    PubMed Central

    Julliard, Walker; Fechner, John H.; Mezrich, Joshua D.

    2014-01-01

    The aryl hydrocarbon receptor (AHR) has long been studied by toxicologists as a ligand-activated transcription factor that is activated by dioxin and other environmental pollutants such as polycyclic aromatic hydrocarbons (PAHs). The hallmark of AHR activation is the upregulation of the cytochrome P450 enzymes that metabolize many of these toxic compounds. However, recent findings demonstrate that both exogenous and endogenous AHR ligands can alter innate and adaptive immune responses including effects on T-cell differentiation. Kynurenine, a tryptophan breakdown product, is one such endogenous ligand of the AHR. Expression of indoleamine 2,3-dioxygenase by dendritic cells causes accumulation of kynurenine and results in subsequent tolerogenic effects including increased regulatory T-cell activity. At the same time, PAHs found in pollution enhance Th17 differentiation in the lungs of exposed mice via the AHR. In this perspective, we will discuss the importance of the AHR in the immune system and the role this might play in normal physiology and response to disease. PMID:25324842

  18. Recent Advances in Understanding and Managing Autism Spectrum Disorders

    PubMed Central

    Germain, Blair; Eppinger, Melissa A.; Mostofsky, Stewart H.; DiCicco-Bloom, Emanuel; Maria, Bernard L.

    2017-01-01

    Autism spectrum disorder in children is a group of neurodevelopmental disorders characterized by difficulties with social communication and behavior. Growing scientific evidence in addition to clinical practice has led the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) to categorize several disorders into the broader category of autism spectrum disorder. As more is learned about how autism spectrum disorder manifests, progress has been made toward better clinical management including earlier diagnosis, care, and when specific interventions are required. The 2014 Neurobiology of Disease in Children symposium, held in conjunction with the 43rd annual meeting of the Child Neurology Society, aimed to (1) describe the clinical concerns involving diagnosis and treatment, (2) review the current status of understanding in the pathogenesis of autism spectrum disorder, (3) discuss clinical management and therapies for autism spectrum disorder, and (4) define future directions of research. The article summarizes the presentations and includes an edited transcript of question-and-answer sessions. PMID:26336201

  19. Sharing for Health: A Study of Chinese Adolescents' Experiences and Perspectives on Using Social Network Sites to Share Health Information.

    PubMed

    Zhang, Ni; Teti, Michele; Stanfield, Kellie; Campo, Shelly

    2017-07-01

    This exploratory qualitative study examines Chinese adolescents' health information sharing habits on social network sites. Ten focus group meetings with 76 adolescents, ages 12 to 17 years, were conducted at community-based organizations in Chicago's Chinatown. The research team transcribed the recording and analyzed the transcripts using ATLAS.ti. Chinese adolescents are using different social network sites for various topics of health information including food, physical activity, and so on. Adolescents would share useful and/or interesting health information. Many adolescents raised credibility concerns regarding health information and suggested evaluating the information based on self-experience or intuition, word-of-mouth, or information online. The findings shed lights on future intervention using social network sites to promote health among Chinese adolescents in the United States. Future interventions should provide adolescents with interesting and culturally sensitive health information and educate them to critically evaluate health information on social network sites.

  20. Johnston Atoll Chemical Agent Disposal System (JACADS) Final Second Supplemental Environmental Impact Statement (SSEIS)

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Not Available

    1990-06-01

    This Final Second Supplemental Environmental Impact Statement (SSEIS) to the Johnston Atoll Chemical Agent Disposal System (JACADS) Environmental Impact Statement (EIS) assesses the effects of receiving, storing, and ultimately destructing the United States stockpile of lethal unitary chemical munitions currently stored in the Federal Republic of Germany (FRG) (European stockpile) at the Army's JACADS facility located on Johnston Atoll in the Pacific Ocean. This Final SSEIS addresses the effects of the following proposed European stockpile activities: the transport of the European stockpile from the territorial limit to Johnston Island, the unloading of munitions from transportation ships, the on-island munitions transportmore » and handling, on-island munitions storage, the disposal of munitions in the JACADS facility, the disposal of incineration wastes, and alternatives to the proposed action. This document also updates information in the 1983 EIS and the 1988 SEIS, as appropriate. This volume contains reproduced letters from various agencies, reproduced written comments received from the public, and a transcript from the public meeting.« less

  1. Molecular Mechanisms Underlying Cardiac Adaptation to Exercise

    PubMed Central

    Vega, Rick B.; Konhilas, John P.; Kelly, Daniel P.; Leinwand, Leslie A.

    2017-01-01

    Exercise elicits coordinated multi-organ responses including skeletal muscle, vasculature, heart and lung. In the short term, the output of the heart increases to meet the demand of strenuous exercise. Long term exercise instigates remodeling of the heart including growth and adaptive molecular and cellular re-programming. Signaling pathways such as the insulin-like growth factor 1/PI3K/Akt pathway mediate many of these responses. Exercise-induced, or physiologic, cardiac growth contrasts with growth elicited by pathological stimuli such as hypertension. Comparing the molecular and cellular underpinnings of physiologic and pathologic cardiac growth has unveiled phenotype-specific signaling pathways and transcriptional regulatory programs. Studies suggest that exercise pathways likely antagonize pathological pathways, and exercise training is often recommended for patients with chronic stable heart failure or following myocardial infarction. Herein, we summarize the current understanding of the structural and functional cardiac responses to exercise as well as signaling pathways and downstream effector molecules responsible for these adaptations. PMID:28467921

  2. Sing Your Lungs Out: a qualitative study of a community singing group for people with chronic obstructive pulmonary disease (COPD)

    PubMed Central

    McNaughton, Amanda; Aldington, Sarah; Williams, Gayle; Levack, William M M

    2016-01-01

    Objective To explore the ways in which participation in a community singing group contributed to the health and well-being of patients with chronic obstructive pulmonary disease (COPD). Design Qualitative description, based on transcripts from individual interviews and a focus group meeting with people with COPD participating in the singing group, regarding their experience. Setting Urban community, Wellington, New Zealand. Participants 23 people (13 women and 10 men), 51–91 years with COPD (21) or interstitial lung disease (2). Results The weekly singing group was a well-attended activity, with self-reported benefits to health and well-being. 4 key themes were identified: being in the ‘right space’, connection, purpose and growth, and participation in a meaningful physical activity. Conclusions This study helps us to better understand how participation in a community singing group can benefit the health and well-being of patients with COPD. Trial registration number ACTRN12615000736549; Results. PMID:27650768

  3. The rational choice model in family decision making at the end of life.

    PubMed

    Karasz, Alison; Sacajiu, Galit; Kogan, Misha; Watkins, Liza

    2010-01-01

    Most end-of-life decisions are made by family members. Current ethical guidelines for family decision making are based on a hierarchical model that emphasizes the patient's wishes over his or her best interests. Evidence suggests that the model poorly reflects the strategies and priorities of many families. Researchers observed and recorded 26 decision-making meetings between hospital staff and family members. Semi-structured follow-up interviews were conducted. Transcriptions were analyzed using qualitative techniques. For both staff and families, consideration of a patient's best interests generally took priority over the patient's wishes. Staff generally introduced discussion of the patient's wishes for rhetorical purposes, such as persuasion. Competing moral frameworks, which de-emphasized the salience of patients' autonomy and "right to choose," played a role in family decision making. The priority given to the patients' wishes in the hierarchical model does not reflect the priorities of staff and families in making decisions about end-of-life care.

  4. In silico methods for co-transcriptional RNA secondary structure prediction and for investigating alternative RNA structure expression.

    PubMed

    Meyer, Irmtraud M

    2017-05-01

    RNA transcripts are the primary products of active genes in any living organism, including many viruses. Their cellular destiny not only depends on primary sequence signals, but can also be determined by RNA structure. Recent experimental evidence shows that many transcripts can be assigned more than a single functional RNA structure throughout their cellular life and that structure formation happens co-transcriptionally, i.e. as the transcript is synthesised in the cell. Moreover, functional RNA structures are not limited to non-coding transcripts, but can also feature in coding transcripts. The picture that now emerges is that RNA structures constitute an additional layer of information that can be encoded in any RNA transcript (and on top of other layers of information such as protein-context) in order to exert a wide range of functional roles. Moreover, different encoded RNA structures can be expressed at different stages of a transcript's life in order to alter the transcript's behaviour depending on its actual cellular context. Similar to the concept of alternative splicing for protein-coding genes, where a single transcript can yield different proteins depending on cellular context, it is thus appropriate to propose the notion of alternative RNA structure expression for any given transcript. This review introduces several computational strategies that my group developed to detect different aspects of RNA structure expression in vivo. Two aspects are of particular interest to us: (1) RNA secondary structure features that emerge during co-transcriptional folding and (2) functional RNA structure features that are expressed at different times of a transcript's life and potentially mutually exclusive. Copyright © 2017. Published by Elsevier Inc.

  5. ABA signaling is necessary but not sufficient for RD29B transcriptional memory during successive dehydration stresses in Arabidopsis thaliana.

    PubMed

    Virlouvet, Laetitia; Ding, Yong; Fujii, Hiroaki; Avramova, Zoya; Fromm, Michael

    2014-07-01

    Plants subjected to a prior dehydration stress were seen to have altered transcriptional responses during a subsequent dehydration stress for up to 5 days after the initial stress. The abscisic acid (ABA) inducible RD29B gene of Arabidopsis thaliana was strongly induced after the first stress and displayed transcriptional memory with transcript levels nine-fold higher during the second dehydration stress. These increased transcript levels were due to an increased rate of transcription and are associated with an altered chromatin template during the recovery interval between the dehydration stresses. Here we use a combination of promoter deletion/substitutions, mutants in the trans-acting transcription factors and their upstream protein kinases, and treatments with exogenous ABA or dehydration stress to advance our understanding of the features required for transcriptional memory of RD29B. ABA Response Elements (ABREs) are sufficient to confer transcriptional memory on a minimal promoter, although there is a context effect from flanking sequences. Different mutations in Snf1 Related Protein Kinase 2 (SnRK2) genes positively and negatively affected the response, suggesting that this effect is important for transcriptional memory. Although exogenous ABA treatments could prime transcriptional memory, a second ABA treatment was not sufficient to activate transcriptional memory. Therefore, we concluded that transcriptional memory requires ABA and an ABA-independent factor that is induced or activated by a subsequent dehydration stress and directly or indirectly results in a more active RD29B chromatin template. These results advance our knowledge of the cis- and trans-acting factors that are required for transcriptional memory of RD29B. © 2014 The Authors The Plant Journal © 2014 John Wiley & Sons Ltd.

  6. Silencing of IFN-stimulated gene transcription is regulated by histone H1 and its chaperone TAF-I.

    PubMed

    Kadota, Shinichi; Nagata, Kyosuke

    2014-07-01

    Chromatin structure and its alteration play critical roles in the regulation of transcription. However, the transcriptional silencing mechanism with regard to the chromatin structure at an unstimulated state of the interferon (IFN)-stimulated gene (ISG) remains unclear. Here we investigated the role of template activating factor-I (TAF-I, also known as SET) in ISG transcription. Knockdown (KD) of TAF-I increased ISG transcript and simultaneously reduced the histone H1 level on the ISG promoters during the early stages of transcription after IFN stimulation from the unstimulated state. The transcription factor levels on the ISG promoters were increased in TAF-I KD cells only during the early stages of transcription. Furthermore, histone H1 KD also increased ISG transcript. TAF-I and histone H1 double KD did not show the additive effect in ISG transcription, suggesting that TAF-I and histone H1 may act on the same regulatory pathway to control ISG transcription. In addition, TAF-I KD and histone H1 KD affected the chromatin structure near the ISG promoters. On the basis of these findings, we propose that TAF-I and its target histone H1 are key regulators of the chromatin structure at the ISG promoter to maintain the silent state of ISG transcription. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  7. iTAK: A program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators and protein kinases

    USDA-ARS?s Scientific Manuscript database

    Transcription factors (TFs) are proteins that regulate the expression of target genes by binding to specific elements in their regulatory regions. Transcriptional regulators (TRs) also regulate the expression of target genes; however, they operate indirectly via interaction with the basal transcript...

  8. 5 CFR 1632.11 - Procedures for inspection and obtaining copies of transcriptions and minutes.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... copies of transcriptions and minutes. 1632.11 Section 1632.11 Administrative Personnel FEDERAL RETIREMENT... inspection and obtaining copies of transcriptions and minutes. (a) Any person may inspect or copy a transcript, a recording or transcription, or minutes described in § 1632.10(c) of this part. (b) Requests for...

  9. 5 CFR 1632.11 - Procedures for inspection and obtaining copies of transcriptions and minutes.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... copies of transcriptions and minutes. 1632.11 Section 1632.11 Administrative Personnel FEDERAL RETIREMENT... inspection and obtaining copies of transcriptions and minutes. (a) Any person may inspect or copy a transcript, a recording or transcription, or minutes described in § 1632.10(c) of this part. (b) Requests for...

  10. Relationships between Translation and Transcription Processes during fMRI Connectivity Scanning and Coded Translation and Transcription in Writing Products after Scanning in Children with and without Transcription Disabilities

    PubMed Central

    Wallis, Peter; Richards, Todd; Boord, Peter; Abbott, Robert; Berninger, Virginia

    2018-01-01

    Students with transcription disabilities (dysgraphia/impaired handwriting, n = 13 or dyslexia/impaired word spelling, n = 16) or without transcription disabilities (controls) completed transcription and translation (idea generating, planning, and creating) writing tasks during fMRI connectivity scanning and compositions after scanning, which were coded for transcription and translation variables. Compositions in both groups showed diversity in genre beyond usual narrative-expository distinction; groups differed in coded transcription but not translation variables. For the control group specific transcription or translation tasks during scanning correlated with corresponding coded transcription or translation skills in composition, but connectivity during scanning was not correlated with coded handwriting during composing in dysgraphia group and connectivity during translating was not correlated with any coded variable during composing in dyslexia group. Results are discussed in reference to the trend in neuroscience to use connectivity from relevant seed points while performing tasks and trends in education to recognize the generativity (creativity) of composing at both the genre and syntax levels. PMID:29600113

  11. The Mediator Complex: At the Nexus of RNA Polymerase II Transcription.

    PubMed

    Jeronimo, Célia; Robert, François

    2017-10-01

    Mediator is an essential, large, multisubunit, transcriptional co-activator highly conserved across eukaryotes. Mediator interacts with gene-specific transcription factors at enhancers as well as with the RNA polymerase II (RNAPII) transcription machinery bound at promoters. It also interacts with several other factors involved in various aspects of transcription, chromatin regulation, and mRNA processing. Hence, Mediator is at the nexus of RNAPII transcription, regulating its many steps and connecting transcription with co-transcriptional events. To achieve this flexible role, Mediator, which is divided into several functional modules, reorganizes its conformation and composition while making transient contacts with other components. Here, we review the mechanisms of action of Mediator and propose a unifying model for its function. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. The MluI cell cycle box (MCB) motifs, but not damage-responsive elements (DREs), are responsible for the transcriptional induction of the rhp51+ gene in response to DNA replication stress.

    PubMed

    Sartagul, Wugangerile; Zhou, Xin; Yamada, Yuki; Ma, Ning; Tanaka, Katsunori; Furuyashiki, Tomoyuki; Ma, Yan

    2014-01-01

    DNA replication stress induces the transcriptional activation of rhp51+, a fission yeast recA homolog required for repair of DNA double strand breaks. However, the mechanism by which DNA replication stress activates rhp51+ transcription is not understood. The promoter region of rhp51+ contains two damage-responsive elements (DREs) and two MluI cell cycle box (MCB) motifs. Using luciferase reporter assays, we examined the role of these elements in rhp51+ transcription. The full-length rhp51+ promoter and a promoter fragment containing MCB motifs only, but not a fragment containing DREs, mediated transcriptional activation upon DNA replication stress. Removal of the MCB motifs from the rhp51+ promoter abolished the induction of rhp51+ transcription by DNA replication stress. Consistent with a role for MCB motifs in rhp51+ transcription activation, deletion of the MBF (MCB-binding factor) co-repressors Nrm1 and Yox1 precluded rhp51+ transcriptional induction in response to DNA replication stress. Using cells deficient in checkpoint signaling molecules, we found that the Rad3-Cds1/Chk1 pathway partially mediated rhp51+ transcription in response to DNA replication stress, suggesting the involvement of unidentified checkpoint signaling pathways. Because MBF is critical for G1/S transcription, we examined how the cell cycle affected rhp51+ transcription. The transcription of rhp51+ and cdc18+, an MBF-dependent G1/S gene, peaked simultaneously in synchronized cdc25-22 cells. Furthermore, DNA replication stress maintained transcription of rhp51+ similarly to cdc18+. Collectively, these results suggest that MBF and its regulators mediate rhp51+ transcription in response to DNA replication stress, and underlie rhp51+ transcription at the G1/S transition.

  13. Method to determine transcriptional regulation pathways in organisms

    DOEpatents

    Gardner, Timothy S.; Collins, James J.; Hayete, Boris; Faith, Jeremiah

    2012-11-06

    The invention relates to computer-implemented methods and systems for identifying regulatory relationships between expressed regulating polypeptides and targets of the regulatory activities of such regulating polypeptides. More specifically, the invention provides a new method for identifying regulatory dependencies between biochemical species in a cell. In particular embodiments, provided are computer-implemented methods for identifying a regulatory interaction between a transcription factor and a gene target of the transcription factor, or between a transcription factor and a set of gene targets of the transcription factor. Further provided are genome-scale methods for predicting regulatory interactions between a set of transcription factors and a corresponding set of transcriptional target substrates thereof.

  14. Analyses of advanced rice anther transcriptomes reveal global tapetum secretory functions and potential proteins for lipid exine formation.

    PubMed

    Huang, Ming-Der; Wei, Fu-Jin; Wu, Cheng-Cheih; Hsing, Yue-Ie Caroline; Huang, Anthony H C

    2009-02-01

    The anthers in flowers perform important functions in sexual reproduction. Several recent studies used microarrays to study anther transcriptomes to explore genes controlling anther development. To analyze the secretion and other functions of the tapetum, we produced transcriptomes of anthers of rice (Oryza sativa subsp. japonica) at six progressive developmental stages and pollen with sequencing-by-synthesis technology. The transcriptomes included at least 18,000 unique transcripts, about 25% of which had antisense transcripts. In silico anther-minus-pollen subtraction produced transcripts largely unique to the tapetum; these transcripts include all the reported tapetum-specific transcripts of orthologs in other species. The differential developmental profiles of the transcripts and their antisense transcripts signify extensive regulation of gene expression in the anther, especially the tapetum, during development. The transcriptomes were used to dissect two major cell/biochemical functions of the tapetum. First, we categorized and charted the developmental profiles of all transcripts encoding secretory proteins present in the cellular exterior; these transcripts represent about 12% and 30% of the those transcripts having more than 100 and 1,000 transcripts per million, respectively. Second, we successfully selected from hundreds of transcripts several transcripts encoding potential proteins for lipid exine synthesis during early anther development. These proteins include cytochrome P450, acyltransferases, and lipid transfer proteins in our hypothesized mechanism of exine synthesis in and export from the tapetum. Putative functioning of these proteins in exine formation is consistent with proteins and metabolites detected in the anther locule fluid obtained by micropipetting.

  15. Sequential changes in chromatin structure during transcriptional activation in the beta globin LCR and its target gene.

    PubMed

    Kim, Kihoon; Kim, AeRi

    2010-09-01

    Chromatin structure is modulated during transcriptional activation. The changes include the association of transcriptional activators, formation of hypersensitive sites and covalent modifications of histones. To understand the order of the various changes accompanying transcriptional activation, we analyzed the mouse beta globin gene, which is transcriptionally inducible in erythroid MEL cells over a time course of HMBA treatment. Transcription of the globin genes requires the locus control region (LCR) consisting of several hypersensitive sites (HSs). Erythroid specific transcriptional activators such as NF-E2, GATA-1, TAL1 and EKLF were associated with the LCR in the uninduced state before transcriptional activation. The HSs of the LCR were formed in this state as revealed by high sensitivity to DNase I and MNase attack. However the binding of transcriptional activators and the depletion of histones were observed in the promoter of the beta globin gene only after transcriptional activation. In addition, various covalent histone modifications were sequentially detected in lysine residues of histone H3 during the activation. Acetylation of K9, K36 and K27 was notable in both LCR HSs and gene after induction but before transcriptional initiation. Inactive histone marks such as K9me2, K36me2 and K27me2 were removed coincident with transcriptional initiation in the gene region. Taken together, these results indicate that LCR has a substantially active structure in the uninduced state while transcriptional activation serially adds active marks, including histone modifications, and removes inactive marks in the target gene of the LCR. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

  16. The Smad3 linker region contains a transcriptional activation domain

    PubMed Central

    2004-01-01

    Transforming growth factor-β (TGF-β)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-β/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-β transcriptional activation responses, although it can be phosphorylated by the TGF-β receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-β. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control. PMID:15588252

  17. The Smad3 linker region contains a transcriptional activation domain.

    PubMed

    Wang, Guannan; Long, Jianyin; Matsuura, Isao; He, Dongming; Liu, Fang

    2005-02-15

    Transforming growth factor-beta (TGF-beta)/Smads regulate a wide variety of biological responses through transcriptional regulation of target genes. Smad3 plays a key role in TGF-beta/Smad-mediated transcriptional responses. Here, we show that the proline-rich linker region of Smad3 contains a transcriptional activation domain. When the linker region is fused to a heterologous DNA-binding domain, it activates transcription. We show that the linker region physically interacts with p300. The adenovirus E1a protein, which binds to p300, inhibits the transcriptional activity of the linker region, and overexpression of p300 can rescue the linker-mediated transcriptional activation. In contrast, an adenovirus E1a mutant, which cannot bind to p300, does not inhibit the linker-mediated transcription. The native Smad3 protein lacking the linker region is unable to mediate TGF-beta transcriptional activation responses, although it can be phosphorylated by the TGF-beta receptor at the C-terminal tail and has a significantly increased ability to form a heteromeric complex with Smad4. We show further that the linker region and the C-terminal domain of Smad3 synergize for transcriptional activation in the presence of TGF-beta. Thus our findings uncover an important function of the Smad3 linker region in Smad-mediated transcriptional control.

  18. Technical Advance: Transcription factor, promoter, and enhancer utilization in human myeloid cells.

    PubMed

    Joshi, Anagha; Pooley, Christopher; Freeman, Tom C; Lennartsson, Andreas; Babina, Magda; Schmidl, Christian; Geijtenbeek, Teunis; Michoel, Tom; Severin, Jessica; Itoh, Masayoshi; Lassmann, Timo; Kawaji, Hideya; Hayashizaki, Yoshihide; Carninci, Piero; Forrest, Alistair R R; Rehli, Michael; Hume, David A

    2015-05-01

    The generation of myeloid cells from their progenitors is regulated at the level of transcription by combinatorial control of key transcription factors influencing cell-fate choice. To unravel the global dynamics of this process at the transcript level, we generated transcription profiles for 91 human cell types of myeloid origin by use of CAGE profiling. The CAGE sequencing of these samples has allowed us to investigate diverse aspects of transcription control during myelopoiesis, such as identification of novel transcription factors, miRNAs, and noncoding RNAs specific to the myeloid lineage. We further reconstructed a transcription regulatory network by clustering coexpressed transcripts and associating them with enriched cis-regulatory motifs. With the use of the bidirectional expression as a proxy for enhancers, we predicted over 2000 novel enhancers, including an enhancer 38 kb downstream of IRF8 and an intronic enhancer in the KIT gene locus. Finally, we highlighted relevance of these data to dissect transcription dynamics during progressive maturation of granulocyte precursors. A multifaceted analysis of the myeloid transcriptome is made available (www.myeloidome.roslin.ed.ac.uk). This high-quality dataset provides a powerful resource to study transcriptional regulation during myelopoiesis and to infer the likely functions of unannotated genes in human innate immunity. © The Author(s).

  19. Mechanisms of specificity in neuronal activity-regulated gene transcription

    PubMed Central

    Lyons, Michelle R.; West, Anne E.

    2011-01-01

    The brain is a highly adaptable organ that is capable of converting sensory information into changes in neuronal function. This plasticity allows behavior to be accommodated to the environment, providing an important evolutionary advantage. Neurons convert environmental stimuli into long-lasting changes in their physiology in part through the synaptic activity-regulated transcription of new gene products. Since the neurotransmitter-dependent regulation of Fos transcription was first discovered nearly 25 years ago, a wealth of studies have enriched our understanding of the molecular pathways that mediate activity-regulated changes in gene transcription. These findings show that a broad range of signaling pathways and transcriptional regulators can be engaged by neuronal activity to sculpt complex programs of stimulus-regulated gene transcription. However, the shear scope of the transcriptional pathways engaged by neuronal activity raises the question of how specificity in the nature of the transcriptional response is achieved in order to encode physiologically relevant responses to divergent stimuli. Here we summarize the general paradigms by which neuronal activity regulates transcription while focusing on the molecular mechanisms that confer differential stimulus-, cell-type-, and developmental-specificity upon activity-regulated programs of neuronal gene transcription. In addition, we preview some of the new technologies that will advance our future understanding of the mechanisms and consequences of activity-regulated gene transcription in the brain. PMID:21620929

  20. E6-associated transcription patterns in human papilloma virus 16-positive cervical tissues.

    PubMed

    Lin, Kezhi; Lu, Xulian; Chen, Jun; Zou, Ruanmin; Zhang, Lifang; Xue, Xiangyang

    2015-01-01

    The change in transcription pattern induced by post-transcriptional RNA splicing is an important mechanism in the regulation of the early gene expression of human papilloma virus (HPV). The present study was conducted to establish a method to specifically amplify HPV-16 E6-associated transcripts. The E6-related transcripts from 63 HPV-16-positive cervical tumor tissue samples were amplified, consisting of eight cases of low-risk intraepithelial lesions, 38 cases of high-risk intraepithelial lesions and 17 cases of cervical cancer (CxCa). The appropriate amplified segments were recovered following agarose gel electrophoresis, and subjected to further sequencing and sequence alignment analysis. Six groups of E6 transcription patterns were identified from HPV-16-positive cervical tumor tissue, including five newly-discovered transcripts. Different HPV-16 E6-associated transcription patterns were detected during the development of CxCa. Over the course of the progression of the low-grade squamous intraepithelial lesions to CxCa, the specific HPV-16 E6-associated transcription patterns and the dominant transcripts were all different. As indicated by this study, the transcription pattern of the E6 early gene of HPV-16 was closely associated with the stages of cervical carcinogenesis, and may also be involved in the development of CxCa.

  1. A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

    PubMed Central

    Hsiung, Chris C.-S.; Bartman, Caroline R.; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J.; Keller, Cheryl A.; Face, Carolyne; Jahn, Kristen S.; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C.; Raj, Arjun; Blobel, Gerd A.

    2016-01-01

    During mitosis, RNA polymerase II (Pol II) and many transcription factors dissociate from chromatin, and transcription ceases globally. Transcription is known to restart in bulk by telophase, but whether de novo transcription at the mitosis–G1 transition is in any way distinct from later in interphase remains unknown. We tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. Unexpectedly, during the earliest rounds of transcription at the mitosis–G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. Enhancer–promoter chromatin contacts are depleted during mitosis and restored rapidly upon G1 entry but do not spike. Of the chromatin-associated features examined, histone H3 Lys27 acetylation levels at individual loci in mitosis best predict the mitosis–G1 transcriptional spike. Single-molecule RNA imaging supports that the mitosis–G1 transcriptional spike can constitute the maximum transcriptional activity per DNA copy throughout the cell division cycle. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. Our results raise the possibility that passage through the mitosis–G1 transition might predispose cells to diverge in gene expression states. PMID:27340175

  2. Acetyl Coenzyme A Stimulates RNA Polymerase II Transcription and Promoter Binding by Transcription Factor IID in the Absence of Histones

    PubMed Central

    Galasinski, Shelly K.; Lively, Tricia N.; Grebe de Barron, Alexandra; Goodrich, James A.

    2000-01-01

    Protein acetylation has emerged as a means of controlling levels of mRNA synthesis in eukaryotic cells. Here we report that acetyl coenzyme A (acetyl-CoA) stimulates RNA polymerase II transcription in vitro in the absence of histones. The effect of acetyl-CoA on basal and activated transcription was studied in a human RNA polymerase II transcription system reconstituted from recombinant and highly purified transcription factors. Both basal and activated transcription were stimulated by the addition of acetyl-CoA to transcription reaction mixtures. By varying the concentrations of general transcription factors in the reaction mixtures, we found that acetyl-CoA decreased the concentration of TFIID required to observe transcription. Electrophoretic mobility shift assays and DNase I footprinting revealed that acetyl-CoA increased the affinity of the general transcription factor TFIID for promoter DNA in a TBP-associated factor (TAF)-dependent manner. Interestingly, acetyl-CoA also caused a conformational change in the TFIID-TFIIA-promoter complex as assessed by DNase I footprinting. These results show that acetyl-CoA alters the DNA binding activity of TFIID and indicate that this biologically important cofactor functions at multiple levels to control gene expression. PMID:10688640

  3. Acetyl coenzyme A stimulates RNA polymerase II transcription and promoter binding by transcription factor IID in the absence of histones.

    PubMed

    Galasinski, S K; Lively, T N; Grebe De Barron, A; Goodrich, J A

    2000-03-01

    Protein acetylation has emerged as a means of controlling levels of mRNA synthesis in eukaryotic cells. Here we report that acetyl coenzyme A (acetyl-CoA) stimulates RNA polymerase II transcription in vitro in the absence of histones. The effect of acetyl-CoA on basal and activated transcription was studied in a human RNA polymerase II transcription system reconstituted from recombinant and highly purified transcription factors. Both basal and activated transcription were stimulated by the addition of acetyl-CoA to transcription reaction mixtures. By varying the concentrations of general transcription factors in the reaction mixtures, we found that acetyl-CoA decreased the concentration of TFIID required to observe transcription. Electrophoretic mobility shift assays and DNase I footprinting revealed that acetyl-CoA increased the affinity of the general transcription factor TFIID for promoter DNA in a TBP-associated factor (TAF)-dependent manner. Interestingly, acetyl-CoA also caused a conformational change in the TFIID-TFIIA-promoter complex as assessed by DNase I footprinting. These results show that acetyl-CoA alters the DNA binding activity of TFIID and indicate that this biologically important cofactor functions at multiple levels to control gene expression.

  4. The WRKY transcription factor family in Brachypodium distachyon.

    PubMed

    Tripathi, Prateek; Rabara, Roel C; Langum, Tanner J; Boken, Ashley K; Rushton, Deena L; Boomsma, Darius D; Rinerson, Charles I; Rabara, Jennifer; Reese, R Neil; Chen, Xianfeng; Rohila, Jai S; Rushton, Paul J

    2012-06-22

    A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors.

  5. The WRKY transcription factor family in Brachypodium distachyon

    PubMed Central

    2012-01-01

    Background A complete assembled genome sequence of wheat is not yet available. Therefore, model plant systems for wheat are very valuable. Brachypodium distachyon (Brachypodium) is such a system. The WRKY family of transcription factors is one of the most important families of plant transcriptional regulators with members regulating important agronomic traits. Studies of WRKY transcription factors in Brachypodium and wheat therefore promise to lead to new strategies for wheat improvement. Results We have identified and manually curated the WRKY transcription factor family from Brachypodium using a pipeline designed to identify all potential WRKY genes. 86 WRKY transcription factors were found, a total higher than all other current databases. We therefore propose that our numbering system (BdWRKY1-BdWRKY86) becomes the standard nomenclature. In the JGI v1.0 assembly of Brachypodium with the MIPS/JGI v1.0 annotation, nine of the transcription factors have no gene model and eleven gene models are probably incorrectly predicted. In total, twenty WRKY transcription factors (23.3%) do not appear to have accurate gene models. To facilitate use of our data, we have produced The Database of Brachypodium distachyon WRKY Transcription Factors. Each WRKY transcription factor has a gene page that includes predicted protein domains from MEME analyses. These conserved protein domains reflect possible input and output domains in signaling. The database also contains a BLAST search function where a large dataset of WRKY transcription factors, published genes, and an extensive set of wheat ESTs can be searched. We also produced a phylogram containing the WRKY transcription factor families from Brachypodium, rice, Arabidopsis, soybean, and Physcomitrella patens, together with published WRKY transcription factors from wheat. This phylogenetic tree provides evidence for orthologues, co-orthologues, and paralogues of Brachypodium WRKY transcription factors. Conclusions The description of the WRKY transcription factor family in Brachypodium that we report here provides a framework for functional genomics studies in an important model system. Our database is a resource for both Brachypodium and wheat studies and ultimately projects aimed at improving wheat through manipulation of WRKY transcription factors. PMID:22726208

  6. "Hit-and-Run" transcription: de novo transcription initiated by a transient bZIP1 "hit" persists after the "run".

    PubMed

    Doidy, Joan; Li, Ying; Neymotin, Benjamin; Edwards, Molly B; Varala, Kranthi; Gresham, David; Coruzzi, Gloria M

    2016-02-03

    Dynamic transcriptional regulation is critical for an organism's response to environmental signals and yet remains elusive to capture. Such transcriptional regulation is mediated by master transcription factors (TF) that control large gene regulatory networks. Recently, we described a dynamic mode of TF regulation named "hit-and-run". This model proposes that master TF can interact transiently with a set of targets, but the transcription of these transient targets continues after the TF dissociation from the target promoter. However, experimental evidence validating active transcription of the transient TF-targets is still lacking. Here, we show that active transcription continues after transient TF-target interactions by tracking de novo synthesis of RNAs made in response to TF nuclear import. To do this, we introduced an affinity-labeled 4-thiouracil (4tU) nucleobase to specifically isolate newly synthesized transcripts following conditional TF nuclear import. Thus, we extended the TARGET system (Transient Assay Reporting Genome-wide Effects of Transcription factors) to include 4tU-labeling and named this new technology TARGET-tU. Our proof-of-principle example is the master TF Basic Leucine Zipper 1 (bZIP1), a central integrator of metabolic signaling in plants. Using TARGET-tU, we captured newly synthesized mRNAs made in response to bZIP1 nuclear import at a time when bZIP1 is no longer detectably bound to its target. Thus, the analysis of de novo transcripomics demonstrates that bZIP1 may act as a catalyst TF to initiate a transcriptional complex ("hit"), after which active transcription by RNA polymerase continues without the TF being bound to the gene promoter ("run"). Our findings provide experimental proof for active transcription of transient TF-targets supporting a "hit-and-run" mode of action. This dynamic regulatory model allows a master TF to catalytically propagate rapid and broad transcriptional responses to changes in environment. Thus, the functional read-out of de novo transcripts produced by transient TF-target interactions allowed us to capture new models for genome-wide transcriptional control.

  7. Ras-Induced Changes in H3K27me3 Occur after Those in Transcriptional Activity

    PubMed Central

    Hosogane, Masaki; Funayama, Ryo; Nishida, Yuichiro; Nagashima, Takeshi; Nakayama, Keiko

    2013-01-01

    Oncogenic signaling pathways regulate gene expression in part through epigenetic modification of chromatin including DNA methylation and histone modification. Trimethylation of histone H3 at lysine-27 (H3K27), which correlates with transcriptional repression, is regulated by an oncogenic form of the small GTPase Ras. Although accumulation of trimethylated H3K27 (H3K27me3) has been implicated in transcriptional regulation, it remains unclear whether Ras-induced changes in H3K27me3 are a trigger for or a consequence of changes in transcriptional activity. We have now examined the relation between H3K27 trimethylation and transcriptional regulation by Ras. Genome-wide analysis of H3K27me3 distribution and transcription at various times after expression of oncogenic Ras in mouse NIH 3T3 cells identified 115 genes for which H3K27me3 level at the gene body and transcription were both regulated by Ras. Similarly, 196 genes showed Ras-induced changes in transcription and H3K27me3 level in the region around the transcription start site. The Ras-induced changes in transcription occurred before those in H3K27me3 at the genome-wide level, a finding that was validated by analysis of individual genes. Depletion of H3K27me3 either before or after activation of Ras signaling did not affect the transcriptional regulation of these genes. Furthermore, given that H3K27me3 enrichment was dependent on Ras signaling, neither it nor transcriptional repression was maintained after inactivation of such signaling. Unexpectedly, we detected unannotated transcripts derived from intergenic regions at which the H3K27me3 level is regulated by Ras, with the changes in transcript abundance again preceding those in H3K27me3. Our results thus indicate that changes in H3K27me3 level in the gene body or in the region around the transcription start site are not a trigger for, but rather a consequence of, changes in transcriptional activity. PMID:24009517

  8. 12 CFR 261b.12 - Procedures for inspection and obtaining copies of transcriptions and minutes.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... of transcriptions and minutes. 261b.12 Section 261b.12 Banks and Banking FEDERAL RESERVE SYSTEM... § 261b.12 Procedures for inspection and obtaining copies of transcriptions and minutes. (a) Any person may inspect or copy a transcript, a recording or transcription of a recording, or minutes described in...

  9. USE OF TRANSCRIPTIONAL COUPLING AND KEGG PATHWAY ANALYSIS OF GLOBAL GENE EXPRESSION TO REVEAL TRANSCRIPTIONAL CHANGES BETWEEN STATIONARY- AND LOG-PHASE SALMONELLA TYPHIMURIUM LT2

    EPA Science Inventory

    DNA microarray analysis is plagued by a lack of data reproducibility and by limits to the detectability of transcripts by hybridization. To mitigate these limitations, we employed transcriptional coupling within the S. typhimurium genome. This genome has 2664 transcriptionally co...

  10. HALO--a Java framework for precise transcript half-life determination.

    PubMed

    Friedel, Caroline C; Kaufmann, Stefanie; Dölken, Lars; Zimmer, Ralf

    2010-05-01

    Recent improvements in experimental technologies now allow measurements of de novo transcription and/or RNA decay at whole transcriptome level and determination of precise transcript half-lives. Such transcript half-lives provide important insights into the regulation of biological processes and the relative contributions of RNA decay and de novo transcription to differential gene expression. In this article, we present HALO (Half-life Organizer), the first software for the precise determination of transcript half-lives from measurements of RNA de novo transcription or decay determined with microarrays or RNA-seq. In addition, methods for quality control, filtering and normalization are supplied. HALO provides a graphical user interface, command-line tools and a well-documented Java application programming interface (API). Thus, it can be used both by biologists to determine transcript half-lives fast and reliably with the provided user interfaces as well as software developers integrating transcript half-life analysis into other gene expression profiling pipelines. Source code, executables and documentation are available at http://www.bio.ifi.lmu.de/software/halo.

  11. Modelling reveals kinetic advantages of co-transcriptional splicing.

    PubMed

    Aitken, Stuart; Alexander, Ross D; Beggs, Jean D

    2011-10-01

    Messenger RNA splicing is an essential and complex process for the removal of intron sequences. Whereas the composition of the splicing machinery is mostly known, the kinetics of splicing, the catalytic activity of splicing factors and the interdependency of transcription, splicing and mRNA 3' end formation are less well understood. We propose a stochastic model of splicing kinetics that explains data obtained from high-resolution kinetic analyses of transcription, splicing and 3' end formation during induction of an intron-containing reporter gene in budding yeast. Modelling reveals co-transcriptional splicing to be the most probable and most efficient splicing pathway for the reporter transcripts, due in part to a positive feedback mechanism for co-transcriptional second step splicing. Model comparison is used to assess the alternative representations of reactions. Modelling also indicates the functional coupling of transcription and splicing, because both the rate of initiation of transcription and the probability that step one of splicing occurs co-transcriptionally are reduced, when the second step of splicing is abolished in a mutant reporter.

  12. Interdependence between transcription and mRNP processing and export, and its impact on genetic stability.

    PubMed

    Luna, Rosa; Jimeno, Sonia; Marín, Mercedes; Huertas, Pablo; García-Rubio, María; Aguilera, Andrés

    2005-06-10

    The conserved eukaryotic THO-TREX complex acts at the interface between transcription and mRNA export and affects transcription-associated recombination. To investigate the interdependence of nuclear mRNA processes and their impact on genomic integrity, we analyzed transcript accumulation and recombination of 40 selected mutants covering representative steps of the biogenesis and export of the messenger ribonucleoprotein particle (mRNP). None of the mutants analyzed shared the strong transcript-accumulation defect and hyperrecombination of THO mutants. Nevertheless, mutants in 3' end cleavage/polyadenylation, nuclear exosome, and mRNA export showed a weak but significant effect on recombination and transcript accumulation. Mutants of the nuclear exosome (rrp6) and 3' end processing factors (rna14 and rna15) showed inefficient transcription elongation and genetic interactions with THO. The results suggest a tight interdependence among mRNP biogenesis steps and transcription and an unexpected effect of the nuclear exosome and the cleavage/polyadenylation factors on transcription elongation and genetic integrity.

  13. CDK regulation of transcription by RNAP II: Not over 'til it's over?

    PubMed

    Fisher, Robert P

    2017-03-15

    Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the "torpedo" exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle.

  14. CDK regulation of transcription by RNAP II: Not over ‘til it's over?

    PubMed Central

    Fisher, Robert P.

    2017-01-01

    ABSTRACT Transcription by RNA polymerase (RNAP) II is regulated at multiple steps by phosphorylation, catalyzed mainly by members of the cyclin-dependent kinase (CDK) family. The CDKs involved in transcription have overlapping substrate specificities, but play largely non-redundant roles in coordinating gene expression. Novel functions and targets of CDKs have recently emerged at the end of the transcription cycle, when the primary transcript is cleaved, and in most cases polyadenylated, and transcription is terminated by the action of the “torpedo” exonuclease Xrn2, which is a CDK substrate. Collectively, various functions have been ascribed to CDKs or CDK-mediated phosphorylation: recruiting cleavage and polyadenylation factors, preventing premature termination within gene bodies while promoting efficient termination of full-length transcripts, and preventing extensive readthrough transcription into intergenic regions or neighboring genes. The assignment of precise functions to specific CDKs is still in progress, but recent advances suggest ways in which the CDK network and RNAP II machinery might cooperate to ensure timely exit from the transcription cycle. PMID:28005463

  15. Alternative splicing of the tyrosinase gene transcript in normal human melanocytes and lymphocytes.

    PubMed

    Fryer, J P; Oetting, W S; Brott, M J; King, R A

    2001-11-01

    We have identified and isolated ectopically expressed tyrosinase transcripts in normal human melanocytes and lymphocytes and in a human melanoma (MNT-1) cell line to establish a baseline for the expression pattern of this gene in normal tissue. Tyrosinase mRNA from human lymphoblastoid cell lines was reverse transcribed and amplified using specific "nested" primers. This amplification yielded eight identifiable transcripts; five that resulted from alternative splicing patterns arising from the utilization of normal and alternative splice sequences. Identical splicing patterns were found in transcripts from human primary melanocytes in culture and a melanoma cell line, indicating that lymphoblastoid cell lines provide an accurate reflection of transcript processing in melanocytes. Similar splicing patterns have also been found with murine melanocyte tyrosinase transcripts. Our results demonstrate that alternative splicing of human tyrosinase gene transcript produces a number of predictable and identifiable transcripts, and that human lymphoblastoid cell lines provide a source of ectopically expressed transcripts that can be used to study the biology of tyrosinase gene expression in humans.

  16. Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma

    PubMed Central

    Gilmore, Sarah A.; Voorhies, Mark; Gebhart, Dana; Sil, Anita

    2015-01-01

    Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. PMID:26177267

  17. Bombyx mori Transcription Factors: Genome-Wide Identification, Expression Profiles and Response to Pathogens by Microarray Analysis

    PubMed Central

    Huang, Lulin; Cheng, Tingcai; Xu, Pingzhen; Fang, Ting; Xia, Qingyou

    2012-01-01

    Transcription factors are present in all living organisms, and play vital roles in a wide range of biological processes. Studies of transcription factors will help reveal the complex regulation mechanism of organisms. So far, hundreds of domains have been identified that show transcription factor activity. Here, 281 reported transcription factor domains were used as seeds to search the transcription factors in genomes of Bombyx mori L. (Lepidoptera: Bombycidae) and four other model insects. Overall, 666 transcription factors including 36 basal factors and 630 other factors were identified in B. mori genome, which accounted for 4.56% of its genome. The silkworm transcription factors' expression profiles were investigated in relation to multiple tissues, developmental stages, sexual dimorphism, and responses to oral infection by pathogens and direct bacterial injection. These all provided rich clues for revealing the transcriptional regulation mechanism of silkworm organ differentiation, growth and development, sexual dimorphism, and response to pathogen infection. PMID:22943524

  18. Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma.

    PubMed

    Gilmore, Sarah A; Voorhies, Mark; Gebhart, Dana; Sil, Anita

    2015-07-01

    Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5' leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature.

  19. A new paradigm for transcription factor TFIIB functionality

    PubMed Central

    Gelev, Vladimir; Zabolotny, Janice M.; Lange, Martin; Hiromura, Makoto; Yoo, Sang Wook; Orlando, Joseph S.; Kushnir, Anna; Horikoshi, Nobuo; Paquet, Eric; Bachvarov, Dimcho; Schaffer, Priscilla A.; Usheva, Anny

    2014-01-01

    Experimental and bioinformatic studies of transcription initiation by RNA polymerase II (RNAP2) have revealed a mechanism of RNAP2 transcription initiation less uniform across gene promoters than initially thought. However, the general transcription factor TFIIB is presumed to be universally required for RNAP2 transcription initiation. Based on bioinformatic analysis of data and effects of TFIIB knockdown in primary and transformed cell lines on cellular functionality and global gene expression, we report that TFIIB is dispensable for transcription of many human promoters, but is essential for herpes simplex virus-1 (HSV-1) gene transcription and replication. We report a novel cell cycle TFIIB regulation and localization of the acetylated TFIIB variant on the transcriptionally silent mitotic chromatids. Taken together, these results establish a new paradigm for TFIIB functionality in human gene expression, which when downregulated has potent anti-viral effects. PMID:24441171

  20. Repression of Meiotic Genes by Antisense Transcription and by Fkh2 Transcription Factor in Schizosaccharomyces pombe

    PubMed Central

    Chen, Huei-Mei; Rosebrock, Adam P.; Khan, Sohail R.; Futcher, Bruce; Leatherwood, Janet K.

    2012-01-01

    In S. pombe, about 5% of genes are meiosis-specific and accumulate little or no mRNA during vegetative growth. Here we use Affymetrix tiling arrays to characterize transcripts in vegetative and meiotic cells. In vegetative cells, many meiotic genes, especially those induced in mid-meiosis, have abundant antisense transcripts. Disruption of the antisense transcription of three of these mid-meiotic genes allowed vegetative sense transcription. These results suggest that antisense transcription represses sense transcription of meiotic genes in vegetative cells. Although the mechanism(s) of antisense mediated transcription repression need to be further explored, our data indicates that RNAi machinery is not required for repression. Previously, we and others used non-strand specific methods to study splicing regulation of meiotic genes and concluded that 28 mid-meiotic genes are spliced only in meiosis. We now demonstrate that the “unspliced” signal in vegetative cells comes from the antisense RNA, not from unspliced sense RNA, and we argue against the idea that splicing regulates these mid-meiotic genes. Most of these mid-meiotic genes are induced in mid-meiosis by the forkhead transcription factor Mei4. Interestingly, deletion of a different forkhead transcription factor, Fkh2, allows low levels of sense expression of some mid-meiotic genes in vegetative cells. We propose that vegetative expression of mid-meiotic genes is repressed at least two independent ways: antisense transcription and Fkh2 repression. PMID:22238674

  1. Caracteristiques de trois systemes informatiques de transcription phonetique et graphemique (Characteristics of Three Computer-Based Systems of Phonetic and Graphemic Transcription).

    ERIC Educational Resources Information Center

    Marty, Fernand

    Three computer-based systems for phonetic/graphemic transcription of language are described, compared, and contrasted. The text is entirely in French, with examples given from the French language. The three approaches to transcription are: (1) text entered in standard typography and exiting in phonetic transcription with markers for rhythmic…

  2. TAFII-independent activation mediated by human TBP in the presence of the positive cofactor PC4.

    PubMed Central

    Wu, S Y; Kershnar, E; Chiang, C M

    1998-01-01

    TFIID is a multiprotein complex comprised of the TATA-binding protein (TBP) and an array of TBP-associated factors (TAFIIs). Whereas TBP is sufficient for basal transcription in conjunction with other general transcription factors and RNA polymerase II, TAFIIs are additionally required for activator-dependent transcription in mammalian cell-free transcription systems. However, recent in vivo studies carried out in yeast suggest that TAFIIs are not globally required for activator function. The discrepancy between in vivo yeast studies and in vitro mammalian cell-free systems remains to be resolved. In this study, we describe a mammalian cell-free transcription system reconstituted with only recombinant proteins and epitope-tagged multiprotein complexes. Transcriptional activation can be recapitulated in this highly purified in vitro transcription system in the absence of TAFIIs. This TBP-mediated activation is not induced by human mediator, another transcriptional coactivator complex potentially implicated in activator response. In contrast, general transcription factors TFIIH and TFIIA play a significant role in TBP-mediated activation, which can be detected in vitro with Gal4 fusion proteins containing various transcriptional activation domains. Our data, therefore, suggest that TFIIH and TFIIA can mediate activator function in the absence of TAFIIs. PMID:9687514

  3. mRNA Cap Methyltransferase, RNMT-RAM, Promotes RNA Pol II-Dependent Transcription.

    PubMed

    Varshney, Dhaval; Lombardi, Olivia; Schweikert, Gabriele; Dunn, Sianadh; Suska, Olga; Cowling, Victoria H

    2018-05-01

    mRNA cap addition occurs early during RNA Pol II-dependent transcription, facilitating pre-mRNA processing and translation. We report that the mammalian mRNA cap methyltransferase, RNMT-RAM, promotes RNA Pol II transcription independent of mRNA capping and translation. In cells, sublethal suppression of RNMT-RAM reduces RNA Pol II occupancy, net mRNA synthesis, and pre-mRNA levels. Conversely, expression of RNMT-RAM increases transcription independent of cap methyltransferase activity. In isolated nuclei, recombinant RNMT-RAM stimulates transcriptional output; this requires the RAM RNA binding domain. RNMT-RAM interacts with nascent transcripts along their entire length and with transcription-associated factors including the RNA Pol II subunits SPT4, SPT6, and PAFc. Suppression of RNMT-RAM inhibits transcriptional markers including histone H2BK120 ubiquitination, H3K4 and H3K36 methylation, RNA Pol II CTD S5 and S2 phosphorylation, and PAFc recruitment. These findings suggest that multiple interactions among RNMT-RAM, RNA Pol II factors, and RNA along the transcription unit stimulate transcription. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

  4. Polymerase III transcription factor B activity is reduced in extracts of growth-restricted cells.

    PubMed Central

    Tower, J; Sollner-Webb, B

    1988-01-01

    Extracts of cells that are down-regulated for transcription by RNA polymerase I and RNA polymerase III exhibit a reduced in vitro transcriptional capacity. We have recently demonstrated that the down-regulation of polymerase I transcription in extracts of cycloheximide-treated and stationary-phase cells results from a lack of an activated subform of RNA polymerase I which is essential for rDNA transcription. To examine whether polymerase III transcriptional down-regulation occurs by a similar mechanism, the polymerase III transcription factors were isolated and added singly and in pairs to control cell extracts and to extracts of cells that had reduced polymerase III transcriptional activity due to cycloheximide treatment or growth into stationary phase. These down-regulations result from a specific reduction in TFIIIB; TFIIIC and polymerase III activities remain relatively constant. Thus, although transcription by both polymerase III and polymerase I is substantially decreased in extracts of growth-arrested cells, this regulation is brought about by reduction of different kinds of activities: a component of the polymerase III stable transcription complex in the former case and the activated subform of RNA polymerase I in the latter. Images PMID:3352599

  5. Differentiation Driven Changes in the Dynamic Organization of Basal Transcription Initiation

    PubMed Central

    Giglia-Mari, Giuseppina; Mourgues, Sophie; Nonnekens, Julie; Andrieux, Lise O.; de Wit, Jan; Miquel, Catherine; Wijgers, Nils; Maas, Alex; Fousteri, Maria; Hoeijmakers, Jan H. J.; Vermeulen, Wim

    2009-01-01

    Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes, such as transcription initiation, are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion. This dynamic nature allows quick adaptation of transcription to changing conditions. However, it is unknown to what extent this dynamic transcription organization holds for postmitotic cells embedded in mammalian tissue. To allow analysis of transcription initiation dynamics directly into living mammalian tissues, we created a knock-in mouse model expressing fluorescently tagged TFIIH. Surprisingly and in contrast to what has been observed in cultured and proliferating cells, postmitotic murine cells embedded in their tissue exhibit a strong and long-lasting transcription-dependent immobilization of TFIIH. This immobilization is both differentiation driven and development dependent. Furthermore, although very statically bound, TFIIH can be remobilized to respond to new transcriptional needs. This divergent spatiotemporal transcriptional organization in different cells of the soma revisits the generally accepted highly dynamic concept of the kinetic framework of transcription and shows how basic processes, such as transcription, can be organized in a fundamentally different fashion in intact organisms as previously deduced from in vitro studies. PMID:19841728

  6. Therapeutic potential of Mediator complex subunits in metabolic diseases.

    PubMed

    Ranjan, Amol; Ansari, Suraiya A

    2018-01-01

    The multisubunit Mediator is an evolutionary conserved transcriptional coregulatory complex in eukaryotes. It is needed for the transcriptional regulation of gene expression in general as well as in a gene specific manner. Mediator complex subunits interact with different transcription factors as well as components of RNA Pol II transcription initiation complex and in doing so act as a bridge between gene specific transcription factors and general Pol II transcription machinery. Specific interaction of various Mediator subunits with nuclear receptors (NRs) and other transcription factors involved in metabolism has been reported in different studies. Evidences indicate that ligand-activated NRs recruit Mediator complex for RNA Pol II-dependent gene transcription. These NRs have been explored as therapeutic targets in different metabolic diseases; however, they show side-effects as targets due to their overlapping involvement in different signaling pathways. Here we discuss the interaction of various Mediator subunits with transcription factors involved in metabolism and whether specific interaction of these transcription factors with Mediator subunits could be potentially utilized as therapeutic strategy in a variety of metabolic diseases. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  7. The Mission Transcript Collection: U.S. Human Spaceflight Missions from Mercury Redstone 3 to Apollo 17

    NASA Technical Reports Server (NTRS)

    2000-01-01

    Aboard every U.S. piloted spacecraft, from Mercury through Apollo, NASA installed tape recorders that captured nearly every word spoken by the astronauts during their history-making flights into space. For the first time ever, NASA has digitally scanned all of the transcripts made from both the onboard tapes and those tape recordings made on the ground from the air-to-ground transmissions and placed them on this two CD-ROM set. Gathered in this special collection are 80 transcripts totaling nearly 45,000 pages of text that cover every US human spaceflight from the first human Mercury mission through the last lunar landing flight of Apollo 17. Users of this CD will note that the quantity and type of transcripts made for each mission vary. For example, the Mercury flights each had one transcript whereas the Gemini missions produced several. Starting with the Gemini flights, NASA produced a Public Affairs Office (PAO) commentary version, as well as at least one "technical" air-to-ground transcript version, per mission. Most of the Apollo missions produced four transcripts per flight. These included the onboard voice data recorder transcripts made from the Data Storage Equipment (DSE) on the Command Module (CM), and the Data Storage Electronics Assembly (DSEA) onboard the Lunar Module (LM), in addition to the PAO commentary and air-to-ground technical transcripts. The CD set includes an index listing each transcript file by name. Some of the transcripts include a detailed explanation of their contents and how they were made. Also included in this collection is a listing of all the original air-to-ground audiotapes housed in NASA's archives from which many of these transcripts were made. We hope you find this collection of transcripts interesting and useful.

  8. New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

    PubMed

    Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

    2014-01-01

    The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37) in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1). Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

  9. New Insights into Transcription Fidelity: Thermal Stability of Non-Canonical Structures in Template DNA Regulates Transcriptional Arrest, Pause, and Slippage

    PubMed Central

    Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

    2014-01-01

    The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (−ΔGo 37) in the presence of 20 wt% PEG was more than 8.2 kcal mol−1. Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs. PMID:24594642

  10. An extensive requirement for transcription factor IID-specific TAF-1 in Caenorhabditis elegans embryonic transcription.

    PubMed

    Walker, Amy K; Shi, Yang; Blackwell, T Keith

    2004-04-09

    The general transcription factor TFIID sets the mRNA start site and consists of TATA-binding protein and associated factors (TAF(II)s), some of which are also present in SPT-ADA-GCN5 (SAGA)-related complexes. In yeast, results of multiple studies indicate that TFIID-specific TAF(II)s are not required for the transcription of most genes, implying that intact TFIID may have a surprisingly specialized role in transcription. Relatively little is known about how TAF(II)s contribute to metazoan transcription in vivo, especially at developmental and tissue-specific genes. Previously, we investigated functions of four shared TFIID/SAGA TAF(II)s in Caenorhabditis elegans. Whereas TAF-4 was required for essentially all embryonic transcription, TAF-5, TAF-9, and TAF-10 were dispensable at multiple developmental and other metazoan-specific promoters. Here we show evidence that in C. elegans embryos transcription of most genes requires TFIID-specific TAF-1. TAF-1 is not as universally required as TAF-4, but it is essential for a greater proportion of transcription than TAF-5, -9, or -10 and is important for transcription of many developmental and other metazoan-specific genes. TAF-2, which binds core promoters with TAF-1, appears to be required for a similarly substantial proportion of transcription. C. elegans TAF-1 overlaps functionally with the coactivator p300/CBP (CBP-1), and at some genes it is required along with the TBP-like protein TLF(TRF2). We conclude that during C. elegans embryogenesis TAF-1 and TFIID have broad roles in transcription and development and that TFIID and TLF may act together at certain promoters. Our findings imply that in metazoans TFIID may be of widespread importance for transcription and for expression of tissue-specific genes.

  11. The glucose sensor Snf1 and the transcription factors Msn2 and Msn4 regulate transcription of the vacuolar iron importer gene CCC1 and iron resistance in yeast.

    PubMed

    Li, Liangtao; Kaplan, Jerry; Ward, Diane M

    2017-09-15

    The budding yeast Saccharomyces cerevisiae stores iron in the vacuole, which is a major resistance mechanism against iron toxicity. One key protein involved in vacuolar iron storage is the iron importer Ccc1, which facilitates iron entry into the vacuole. Transcription of the CCC1 gene is largely regulated by the binding of iron-sulfur clusters to the activator domain of the transcriptional activator Yap5. Additional evidence, however, suggests that Yap5-independent transcriptional activation of CCC1 also contributes to iron resistance. Here, we demonstrate that components of the signaling pathway involving the low-glucose sensor Snf1 regulate CCC1 transcription and iron resistance. We found that SNF1 deletion acts synergistically with YAP5 deletion to regulate CCC1 transcription and iron resistance. A kinase-dead mutation of Snf1 lowered iron resistance as did deletion of SNF4 , which encodes a partner protein of Snf1. Deletion of all three alternative partners of Snf1 encoded by SIT1 , SIT2 , and GAL83 decreased both CCC1 transcription and iron resistance. The Snf1 complex is known to activate the general stress transcription factors Msn2 and Msn4. We show that Msn2 and Msn4 contribute to Snf1-mediated CCC1 transcription. Of note, SNF1 deletion in combination with MSN2 and MSN4 deletion resulted in additive effects on CCC1 transcription, suggesting that other activators contribute to the regulation of CCC1 transcription. In conclusion, we show that yeast have developed multiple transcriptional mechanisms to regulate Ccc1 expression and to protect against high cytosolic iron toxicity. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  12. Gene expression alterations at baseline and following moderate exercise in patients with Chronic Fatigue Syndrome, and Fibromyalgia Syndrome

    PubMed Central

    Light, A.R.; Bateman, L.; Jo, D.; Hughen, R. W.; VanHaitsma, T.A.; White, A.T.; Light, K.C.

    2011-01-01

    Objectives To determine mRNA expression differences in genes involved in signaling and modulating sensory fatigue, and muscle pain in patients with Chronic Fatigue Syndrome (CFS) and Fibromyalgia Syndrome (FM) at baseline, and following moderate exercise. Design Forty eight Patients with CFS-only, or CFS with comorbid FM, 18 Patients with FM that did not meet criteria for CFS, and 49 healthy Controls underwent moderate exercise (25 minutes at 70% maximum age predicted heart-rate). Visual-analogue measures of fatigue and pain were taken before, during, and after exercise. Blood samples were taken before, and 0.5, 8, 24, and 48 hours after exercise. Leukocytes were immediately isolated from blood, number coded for blind processing and analyses, and flash frozen. Using real-time, quantitative PCR, the amount of mRNA for 13 genes (relative to control genes) involved in sensory, adrenergic, and immune functions was compared between groups at baseline, and following exercise. Changes in amounts of mRNA were correlated with behavioral measures, and functional clinical assessments. Results No gene expression changes occurred following exercise in Controls. In 71% of CFS patients, moderate exercise increased most sensory and adrenergic receptor’s and one cytokine gene’s transcription for 48 hours. These post-exercise increases correlated with behavioral measures of fatigue and pain. In contrast, for the other 29% of CFS patients, adrenergic α-2A receptor’s transcription was decreased at all time points after exercise; other genes were not altered. History of orthostatic intolerance was significantly more common in the α-2A decrease subgroup. FM only patients showed no post-exercise alterations in gene expression, but their pre-exercise baseline mRNA for two sensory ion channels and one cytokine were significantly higher than Controls. Conclusions At least two subgroups of CFS patients can be identified by gene expression changes following exercise. The larger subgroup showed increases in mRNA for sensory and adrenergic receptors and a cytokine. The smaller subgroup contained most of the CFS patients with orthostatic intolerance, showed no post-exercise increases in any gene, and was defined by decreases in mRNA for α-2A. FM only patients can be identified by baseline increases in 3 genes. Post-exercise increases for 4 genes meet published criteria as an objective biomarker for CFS, and could be useful in guiding treatment selection for different subgroups. PMID:21615807

  13. The exosome component Rrp6 is required for RNA polymerase II termination at specific targets of the Nrd1-Nab3 pathway.

    PubMed

    Fox, Melanie J; Gao, Hongyu; Smith-Kinnaman, Whitney R; Liu, Yunlong; Mosley, Amber L

    2015-01-01

    The exosome and its nuclear specific subunit Rrp6 form a 3'-5' exonuclease complex that regulates diverse aspects of RNA biology including 3' end processing and degradation of a variety of noncoding RNAs (ncRNAs) and unstable transcripts. Known targets of the nuclear exosome include short (<1000 bp) RNAPII transcripts such as small noncoding RNAs (snRNAs), cryptic unstable transcripts (CUTs), and some stable unannotated transcripts (SUTs) that are terminated by an Nrd1, Nab3, and Sen1 (NNS) dependent mechanism. NNS-dependent termination is coupled to RNA 3' end processing and/or degradation by the Rrp6/exosome in yeast. Recent work suggests Nrd1 is necessary for transcriptome surveillance, regulating promoter directionality and suppressing antisense transcription independently of, or prior to, Rrp6 activity. It remains unclear whether Rrp6 is directly involved in termination; however, Rrp6 has been implicated in the 3' end processing and degradation of ncRNA transcripts including CUTs. To determine the role of Rrp6 in NNS termination globally, we performed RNA sequencing (RNA-Seq) on total RNA and perform ChIP-exo analysis of RNA Polymerase II (RNAPII) localization. Deletion of RRP6 promotes hyper-elongation of multiple NNS-dependent transcripts resulting from both improperly processed 3' RNA ends and faulty transcript termination at specific target genes. The defects in RNAPII termination cause transcriptome-wide changes in mRNA expression through transcription interference and/or antisense repression, similar to previously reported effects of depleting Nrd1 from the nucleus. Elongated transcripts were identified within all classes of known NNS targets with the largest changes in transcription termination occurring at CUTs. Interestingly, the extended transcripts that we have detected in our studies show remarkable similarity to Nrd1-unterminated transcripts at many locations, suggesting that Rrp6 acts with the NNS complex globally to promote transcription termination in addition to 3' end RNA processing and/or degradation at specific targets.

  14. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb.

    PubMed

    Kuzmina, Alona; Krasnopolsky, Simona; Taube, Ran

    2017-05-27

    Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb.

  15. Super elongation complex promotes early HIV transcription and its function is modulated by P-TEFb

    PubMed Central

    Kuzmina, Alona; Krasnopolsky, Simona; Taube, Ran

    2017-01-01

    ABSTRACT Early work on the control of transcription of the human immunodeficiency virus (HIV) laid the foundation for our current knowledge of how RNA Polymerase II is released from promoter-proximal pausing sites and transcription elongation is enhanced. The viral Tat activator recruits Positive Transcription Elongation Factor b (P-TEFb) and Super Elongation Complex (SEC) that jointly drive transcription elongation. While substantial progress in understanding the role of SEC in HIV gene transcription elongation has been obtained, defining of the mechanisms that govern SEC functions is still limited, and the role of SEC in controlling HIV transcription in the absence of Tat is less clear. Here we revisit the contribution of SEC in early steps of HIV gene transcription. In the absence of Tat, the AF4/FMR2 Family member 4 (AFF4) of SEC efficiently activates HIV transcription, while gene activation by its homolog AFF1 is substantially lower. Differential recruitment to the HIV promoter and association with Human Polymerase-Associated Factor complex (PAFc) play key role in this functional distinction between AFF4 and AFF1. Moreover, while depletion of cyclin T1 expression has subtle effects on HIV gene transcription in the absence of Tat, knockout (KO) of AFF1, AFF4, or both proteins slightly repress this early step of viral transcription. Upon Tat expression, HIV transcription reaches optimal levels despite KO of AFF1 or AFF4 expression. However, double AFF1/AFF4 KO completely diminishes Tat trans-activation. Significantly, our results show that P-TEFb phosphorylates AFF4 and modulates SEC assembly, AFF1/4 dimerization and recruitment to the viral promoter. We conclude that SEC promotes both early steps of HIV transcription in the absence of Tat, as well as elongation of transcription, when Tat is expressed. Significantly, SEC functions are modulated by P-TEFb. PMID:28340332

  16. The Werner Syndrome Protein Is Involved in RNA Polymerase II Transcription

    PubMed Central

    Balajee, Adayabalam S.; Machwe, Amrita; May, Alfred; Gray, Matthew D.; Oshima, Junko; Martin, George M.; Nehlin, Jan O.; Brosh, Robert; Orren, David K.; Bohr, Vilhelm A.

    1999-01-01

    Werner syndrome (WS) is a human progeroid syndrome characterized by the early onset of a large number of clinical features associated with the normal aging process. The complex molecular and cellular phenotypes of WS involve characteristic features of genomic instability and accelerated replicative senescence. The gene involved (WRN) was recently cloned, and its gene product (WRNp) was biochemically characterized as a helicase. Helicases play important roles in a variety of DNA transactions, including DNA replication, transcription, repair, and recombination. We have assessed the role of the WRN gene in transcription by analyzing the efficiency of basal transcription in WS lymphoblastoid cell lines that carry homozygous WRN mutations. Transcription was measured in permeabilized cells by [3H]UTP incorporation and in vitro by using a plasmid template containing the RNA polymerase II (RNA pol II)–dependent adenovirus major late promoter. With both of these approaches, we find that the transcription efficiency in different WS cell lines is reduced to 40–60% of the transcription in cells from normal individuals. This defect can be complemented by the addition of normal cell extracts to the chromatin of WS cells. Addition of purified wild-type WRNp but not mutated WRNp to the in vitro transcription assay markedly stimulates RNA pol II–dependent transcription carried out by nuclear extracts. A nonhelicase domain (a direct repeat of 27 amino acids) also appears to have a role in transcription enhancement, as revealed by a yeast hybrid–protein reporter assay. This is further supported by the lack of stimulation of transcription when mutant WRNp lacking this domain was added to the in vitro assay. We have thus used several approaches to show a role for WRNp in RNA pol II transcription, possibly as a transcriptional activator. A deficit in either global or regional transcription in WS cells may be a primary molecular defect responsible for the WS clinical phenotype. PMID:10436020

  17. Transcriptional Control in Marine Copiotrophic and Oligotrophic Bacteria with Streamlined Genomes.

    PubMed

    Cottrell, Matthew T; Kirchman, David L

    2016-10-01

    Bacteria often respond to environmental stimuli using transcriptional control, but this may not be the case for marine bacteria such as "Candidatus Pelagibacter ubique," a cultivated representative of the SAR11 clade, the most abundant organism in the ocean. This bacterium has a small, streamlined genome and an unusually low number of transcriptional regulators, suggesting that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. Transcriptome sequencing during batch culture growth revealed that only 0.1% of protein-encoding genes appear to be under transcriptional control in Pelagibacter and in another oligotroph (SAR92) whereas >10% of genes were under transcriptional control in the copiotrophs Polaribacter sp. strain MED152 and Ruegeria pomeroyi When growth levels changed, transcript levels remained steady in Pelagibacter and SAR92 but shifted in MED152 and R. pomeroyi Transcript abundances per cell, determined using an internal RNA sequencing standard, were low (<1 transcript per cell) for all but a few of the most highly transcribed genes in all four taxa, and there was no correlation between transcript abundances per cell and shifts in the levels of transcription. These results suggest that low transcriptional control contributes to the success of Pelagibacter and possibly other oligotrophic microbes that dominate microbial communities in the oceans. Diverse heterotrophic bacteria drive biogeochemical cycling in the ocean. The most abundant types of marine bacteria are oligotrophs with small, streamlined genomes. The metabolic controls that regulate the response of oligotrophic bacteria to environmental conditions remain unclear. Our results reveal that transcriptional control is lower in marine oligotrophic bacteria than in marine copiotrophic bacteria. Although responses of bacteria to environmental conditions are commonly regulated at the level of transcription, metabolism in the most abundant bacteria in the ocean appears to be regulated by other mechanisms. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  18. Genome wide interactions of wild-type and activator bypass forms of σ54.

    PubMed

    Schaefer, Jorrit; Engl, Christoph; Zhang, Nan; Lawton, Edward; Buck, Martin

    2015-09-03

    Enhancer-dependent transcription involving the promoter specificity factor σ(54) is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ(54)-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since activators can be bypassed in vitro, bypass transcription in vivo could be a source of emergent gene expression along evolutionary pathways yielding new control networks and transcription patterns. At a single test promoter in vivo bypass transcription was not observed. We now use genome-wide transcription profiling, genome-wide mutagenesis and gene over-expression strategies in Escherichia coli, to (i) scope the range of bypass transcription in vivo and (ii) identify genes which might alter bypass transcription in vivo. We find little evidence for pervasive bypass transcription in vivo with only a small subset of σ(54) promoters functioning without activators. Results also suggest no one gene limits bypass transcription in vivo, arguing bypass transcription is strongly kept in check. Promoter sequences subject to repression by σ(54) were evident, indicating loss of rpoN (encoding σ(54)) rather than creating rpoN bypass alleles would be one evolutionary route for new gene expression patterns. Finally, cold-shock promoters showed unusual σ(54)-dependence in vivo not readily correlated with conventional σ(54) binding-sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  19. Genome wide interactions of wild-type and activator bypass forms of σ54

    PubMed Central

    Schaefer, Jorrit; Engl, Christoph; Zhang, Nan; Lawton, Edward; Buck, Martin

    2015-01-01

    Enhancer-dependent transcription involving the promoter specificity factor σ54 is widely distributed amongst bacteria and commonly associated with cell envelope function. For transcription initiation, σ54-RNA polymerase yields open promoter complexes through its remodelling by cognate AAA+ ATPase activators. Since activators can be bypassed in vitro, bypass transcription in vivo could be a source of emergent gene expression along evolutionary pathways yielding new control networks and transcription patterns. At a single test promoter in vivo bypass transcription was not observed. We now use genome-wide transcription profiling, genome-wide mutagenesis and gene over-expression strategies in Escherichia coli, to (i) scope the range of bypass transcription in vivo and (ii) identify genes which might alter bypass transcription in vivo. We find little evidence for pervasive bypass transcription in vivo with only a small subset of σ54 promoters functioning without activators. Results also suggest no one gene limits bypass transcription in vivo, arguing bypass transcription is strongly kept in check. Promoter sequences subject to repression by σ54 were evident, indicating loss of rpoN (encoding σ54) rather than creating rpoN bypass alleles would be one evolutionary route for new gene expression patterns. Finally, cold-shock promoters showed unusual σ54-dependence in vivo not readily correlated with conventional σ54 binding-sites. PMID:26082500

  20. Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites.

    PubMed

    Wang, Guohua; Wang, Fang; Huang, Qian; Li, Yu; Liu, Yunlong; Wang, Yadong

    2015-01-01

    Transcription factors are proteins that bind to DNA sequences to regulate gene transcription. The transcription factor binding sites are short DNA sequences (5-20 bp long) specifically bound by one or more transcription factors. The identification of transcription factor binding sites and prediction of their function continue to be challenging problems in computational biology. In this study, by integrating the DNase I hypersensitive sites with known position weight matrices in the TRANSFAC database, the transcription factor binding sites in gene regulatory region are identified. Based on the global gene expression patterns in cervical cancer HeLaS3 cell and HelaS3-ifnα4h cell (interferon treatment on HeLaS3 cell for 4 hours), we present a model-based computational approach to predict a set of transcription factors that potentially cause such differential gene expression. Significantly, 6 out 10 predicted functional factors, including IRF, IRF-2, IRF-9, IRF-1 and IRF-3, ICSBP, belong to interferon regulatory factor family and upregulate the gene expression levels responding to the interferon treatment. Another factor, ISGF-3, is also a transcriptional activator induced by interferon alpha. Using the different transcription factor binding sites selected criteria, the prediction result of our model is consistent. Our model demonstrated the potential to computationally identify the functional transcription factors in gene regulation.

  1. A hyperactive transcriptional state marks genome reactivation at the mitosis-G1 transition.

    PubMed

    Hsiung, Chris C-S; Bartman, Caroline R; Huang, Peng; Ginart, Paul; Stonestrom, Aaron J; Keller, Cheryl A; Face, Carolyne; Jahn, Kristen S; Evans, Perry; Sankaranarayanan, Laavanya; Giardine, Belinda; Hardison, Ross C; Raj, Arjun; Blobel, Gerd A

    2016-06-15

    During mitosis, RNA polymerase II (Pol II) and many transcription factors dissociate from chromatin, and transcription ceases globally. Transcription is known to restart in bulk by telophase, but whether de novo transcription at the mitosis-G1 transition is in any way distinct from later in interphase remains unknown. We tracked Pol II occupancy genome-wide in mammalian cells progressing from mitosis through late G1. Unexpectedly, during the earliest rounds of transcription at the mitosis-G1 transition, ∼50% of active genes and distal enhancers exhibit a spike in transcription, exceeding levels observed later in G1 phase. Enhancer-promoter chromatin contacts are depleted during mitosis and restored rapidly upon G1 entry but do not spike. Of the chromatin-associated features examined, histone H3 Lys27 acetylation levels at individual loci in mitosis best predict the mitosis-G1 transcriptional spike. Single-molecule RNA imaging supports that the mitosis-G1 transcriptional spike can constitute the maximum transcriptional activity per DNA copy throughout the cell division cycle. The transcriptional spike occurs heterogeneously and propagates to cell-to-cell differences in mature mRNA expression. Our results raise the possibility that passage through the mitosis-G1 transition might predispose cells to diverge in gene expression states. © 2016 Hsiung et al.; Published by Cold Spring Harbor Laboratory Press.

  2. Impact of the INBRE summer student mentored research program on undergraduate students in Arkansas.

    PubMed

    McSweeney, Jean C; Hudson, Teresa J; Prince, Latrina; Beneš, Helen; Tackett, Alan J; Miller Robinson, Caroline; Koeppe, Roger; Cornett, Lawrence E

    2018-03-01

    The Institutional Development Award (IDeA) program, housed within the National Institute for General Medical Sciences, administers the Networks of Biomedical Research Excellence (INBRE) as a strategic mission to broaden the geographic distribution of National Institutes of Health (NIH) funding within the United States. Undergraduate summer student mentored research programs (SSMRP) are a common feature of INBRE programs and are designed to increase undergraduate student interest in research careers in the biomedical sciences. Little information is available about student perspectives on how these programs impact their choices relative to education and careers. Therefore, we conducted qualitative interviews with 20 participants from the Arkansas INBRE SSMRP in the years 2002-2012. Each telephone interview lasted 30-45 min. An interview guide with a broad "grand tour" question was used to elicit student perspectives on SSMRP participation. Interviews were digitally recorded, then transcribed verbatim, and the transcript checked for accuracy. Content analysis and constant comparison were used to identify nine themes that were grouped into three temporal categories: before, during, and after the SSMRP experience. Students viewed the experience as positive and felt it impacted their career choices. They emphasized the value of mentoring in the program, and some reported maintaining a relationship with the mentor after the summer experience ended. Students also valued learning new laboratory and presentation skills and felt their research experience was enhanced by meeting students and scientists with a wide range of career interests. These data suggest that the Arkansas INBRE and the NIH IDeA program are successfully meeting the goal of increasing interest in research among undergraduates.

  3. Delivery of Clinical Preventive Services in Family Medicine Offices

    PubMed Central

    Crabtree, Benjamin F.; Miller, William L.; Tallia, Alfred F.; Cohen, Deborah J.; DiCicco-Bloom, Barbara; McIlvain, Helen E.; Aita, Virginia A.; Scott, John G.; Gregory, Patrice B.; Stange, Kurt C.; McDaniel, Reuben R.

    2005-01-01

    BACKGROUND This study aimed to elucidate how clinical preventive services are delivered in family practices and how this information might inform improvement efforts. METHODS We used a comparative case study design to observe clinical preventive service delivery in 18 purposefully selected Midwestern family medicine offices from 1997 to 1999. Medical records, observation of outpatient encounters, and patient exit cards were used to calculate practice-level rates of delivery of clinical preventive services. Field notes from direct observation of clinical encounters and prolonged observation of the practice and transcripts from in-depth interviews of practice staff and physicians were systematically examined to identify approaches to delivering clinical preventive services recommended by the US Preventive Services Task Force. RESULTS Practices developed individualized approaches for delivering clinical preventive services, with no one approach being successful across practices. Clinicians acknowledged a 3-fold mission of providing acute care, managing chronic problems, and prevention, but only some made prevention a priority. The clinical encounter was a central focus for preventive service delivery in all practices. Preventive services delivery rates often appeared to be influenced by competing demands within the clinical encounter (including between different preventive services), having a physician champion who prioritized prevention, and economic concerns. CONCLUSIONS Practice quality improvement efforts that assume there is an optimal approach for delivering clinical preventive services fail to account for practices’ propensity to optimize care processes to meet local contexts. Interventions to enhance clinical preventive service delivery should be tailored to meet the local needs of practices and their patient populations. PMID:16189059

  4. Realising their potential? Exploring interprofessional perceptions and potential of the advanced practitioner role: a qualitative analysis

    PubMed Central

    Powell, Tom; Watkins, Dianne; Kelly, Daniel

    2015-01-01

    Objectives To explore perceptions of the current practice and future potential of advanced practitioners (APs) from the perspectives of different professional groups in Wales UK. Design A qualitative study consisting of nine focus group interviews. Methods Initially verbatim transcriptions of each focus group interviews were analysed thematically before themes were merged to represent perceptions for the whole data set. Participants Data were gathered from a total of 67 stakeholders—including APs from a variety of professional groups (eg, nursing, physiotherapy, paramedics) as well as managers, workforce developers, educators and medical staff who have a role developing and supporting APs in practice. Results The results are presented in four themes: (1) demand, policy context and future priorities, (2) role clarity and standardisation, (3) agreement and understanding of the role and (4) interprofessional working. The context within which current and future AP roles were considered was influenced by inexorable demands for healthcare and the requirements to meet health policy priorities. Developing AP roles were hampered currently by a lack of shared understanding and ‘joined-up’ working between different groups such as medical practitioners, managers, commissioners and educators. Conclusions For the AP role to flourish more ‘joined-up’ thinking, support and development opportunities are required between APs, managers, senior clinicians, commissioners and educators. Working together to plan and deliver education, innovation and service delivery is of prime importance to meeting ever increasing complex health needs. This will ensure that future APs are adequately prepared and supported to reach their full potential and help deliver necessary innovations in current models of care delivery. PMID:26656024

  5. A qualitative analysis of the nutritional requirements of palliative care patients.

    PubMed

    Muir, C I; Linklater, G T

    2011-10-01

    The National Health Servive (NHS) Quality Improvement Scotland developed nutritional Clinical Standards to address the problem of malnutrition in hospitals. NHS palliative care units are obliged to incorporate these standards into nutritional aspects of care. The nutritional needs of this patient population are under-researched. The present study aimed to explore patients' views of nutrition, to begin to understand their concerns and to determine whether such standards meet the needs of patients in the palliative care setting. A qualitative study was conducted in 2009 in an NHS Palliative Care Unit. Six inpatients were involved in one-to-one interviews, which were audiotaped and transcribed verbatim. The transcripts were subject to qualitative data analysis in accordance with a previous framework. A recurring theme that emerged was that of change and uncertainty. Four main areas subject to change were: disease state, symptoms, oral dietary intake and weight. Each change could exert control over, or be controlled by, the patient. When patients were eventually unable to exert control, they accepted the change, either willingly or enforced, thereby unintentionally setting their own targets. The present study enables a deeper understanding of the concerns that palliative care patients have regarding their oral dietary intake and weight. Their 'malnutrition' not only refers to physical malnutrition alone, but also incorporates psychological and social 'malnutrition'. When applying standards or protocols regarding nutritional care, these wider issues must be taken into account to meet patients' nutritional needs. © 2011 The Authors. Journal of Human Nutrition and Dietetics © 2011 The British Dietetic Association Ltd.

  6. Designing a Leadership Development Program for Surgeons

    PubMed Central

    Jaffe, Gregory A.; Pradarelli, Jason C.; Lemak, Christy Harris; Mulholland, Michael W.; Dimick, Justin B.

    2015-01-01

    Background Although numerous leadership development programs exist in healthcare, no programs have been specifically designed to meet the needs of surgeons. This study aimed to elicit practicing surgeons’ motivations and desired goals for leadership training in order to design an evidence-based Leadership Development Program (LDP) in surgery. Materials and Methods At a large academic health center, we conducted semi-structured interviews with 24 surgical faculty members who voluntarily applied and were selected for participation in a newly created LDP. Transcriptions of the interviews were analyzed using analyst triangulation and thematic coding in order to extract major themes regarding surgeons’ motivations and perceived needs for leadership knowledge and skills. Themes from interview responses were then used to design the program curriculum specifically to meet the leadership needs of surgical faculty. Results Three major themes emerged regarding surgeons’ motivations for seeking leadership training: 1) Recognizing key gaps in their formal preparation for leadership roles; 2) Exhibiting an appetite for personal self-improvement; and 3) Seeking leadership guidance for career advancement. Participants’ interviews revealed four specific domains of knowledge and skills that they indicated as desired takeaways from a leadership development program: 1) leadership and communication; 2) team building; 3) business acumen/finance; and 4) greater understanding of the healthcare context. Conclusions Interviews with surgical faculty members identified gaps in prior leadership training and demonstrated concrete motivations and specific goals for participating in a formal leadership program. A Leadership Development Program that is specifically tailored to address the needs of surgical faculty may benefit surgeons at a personal and institutional level. PMID:26323368

  7. Development, Evaluation, and Integration of a Quantitative Reverse-Transcription Polymerase Chain Reaction Diagnostic Test for Ebola Virus on a Molecular Diagnostics Platform.

    PubMed

    Cnops, Lieselotte; Van den Eede, Peter; Pettitt, James; Heyndrickx, Leo; De Smet, Birgit; Coppens, Sandra; Andries, Ilse; Pattery, Theresa; Van Hove, Luc; Meersseman, Geert; Van Den Herrewegen, Sari; Vergauwe, Nicolas; Thijs, Rein; Jahrling, Peter B; Nauwelaers, David; Ariën, Kevin K

    2016-10-15

     The 2013-2016 Ebola epidemic in West Africa resulted in accelerated development of rapid diagnostic tests for emergency outbreak preparedness. We describe the development and evaluation of the Idylla™ prototype Ebola virus test, a fully automated sample-to-result molecular diagnostic test for rapid detection of Zaire ebolavirus (EBOV) and Sudan ebolavirus (SUDV).  The Idylla™ prototype Ebola virus test can simultaneously detect EBOV and SUDV in 200 µL of whole blood. The sample is directly added to a disposable cartridge containing all reagents for sample preparation, RNA extraction, and amplification by reverse-transcription polymerase chain reaction analysis. The performance was evaluated with a variety of sample types, including synthetic constructs and whole blood samples from healthy volunteers spiked with viral RNA, inactivated virus, and infectious virus.  The 95% limits of detection for EBOV and SUDV were 465 plaque-forming units (PFU)/mL (1010 copies/mL) and 324 PFU/mL (8204 copies/mL), respectively. In silico and in vitro analyses demonstrated 100% correct reactivity for EBOV and SUDV and no cross-reactivity with relevant pathogens. The diagnostic sensitivity was 97.4% (for EBOV) and 91.7% (for SUDV), the specificity was 100%, and the diagnostic accuracy was 95.9%.  The Idylla™ prototype Ebola virus test is a fast, safe, easy-to-use, and near-patient test that meets the performance criteria to detect EBOV in patients with suspected Ebola. © The Author 2016. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail journals.permissions@oup.com.

  8. Carbohydrate availability and exercise training adaptation: too much of a good thing?

    PubMed

    Bartlett, Jonathan D; Hawley, John A; Morton, James P

    2015-01-01

    Traditional nutritional approaches to endurance training have typically promoted high carbohydrate (CHO) availability before, during and after training sessions to ensure adequate muscle substrate to meet the demands of high daily training intensities and volumes. However, during the past decade, data from our laboratories and others have demonstrated that deliberately training in conditions of reduced CHO availability can promote training-induced adaptations of human skeletal muscle (i.e. increased maximal mitochondrial enzyme activities and/or mitochondrial content, increased rates of lipid oxidation and, in some instances, improved exercise capacity). Such data have led to the concept of 'training low, but competing high' whereby selected training sessions are completed in conditions of reduced CHO availability (so as to promote training adaptation), but CHO reserves are restored immediately prior to an important competition. The augmented training response observed with training-low strategies is likely regulated by enhanced activation of key cell signalling kinases (e.g. AMPK, p38MAPK), transcription factors (e.g. p53, PPARδ) and transcriptional co-activators (e.g. PGC-1α), such that a co-ordinated up-regulation of both the nuclear and mitochondrial genomes occurs. Although the optimal practical strategies to train low are not currently known, consuming additional caffeine, protein, and practising CHO mouth-rinsing before and/or during training may help to rescue the reduced training intensities that typically occur when 'training low', in addition to preventing protein breakdown and maintaining optimal immune function. Finally, athletes should practise 'train-low' workouts in conjunction with sessions undertaken with normal or high CHO availability so that their capacity to oxidise CHO is not blunted on race day.

  9. Neutrophil-Related Gene Expression And Low-Density Granulocytes Associated with Disease Activity and Response to Treatment in ANCA-Associated Vasculitis

    PubMed Central

    Grayson, Peter C.; Carmona-Rivera, Carmelo; Xu, Lijing; Lim, Noha; Gao, Zhong; Asare, Adam L.; Specks, Ulrich; Stone, John H.; Seo, Philip; Spiera, Robert F.; Langford, Carol A.; Hoffman, Gary S.; Kallenberg, Cees G.M.; St Clair, E. William; Tchao, Nadia K.; Ytterberg, Steven R.; Phippard, Deborah J.; Merkel, Peter A.; Kaplan, Mariana J.; Monach, Paul A.

    2015-01-01

    Objectives To discover biomarkers involved in the pathophysiology of ANCA-associated vasculitis (AAV) and determine if low-density granulocytes (LDGs) contribute to gene expression signatures in AAV. Methods The source of clinical data and linked biospecimens was a randomized controlled treatment trial in AAV. RNA-sequencing of whole blood from patients with AAV was performed during active disease at the baseline visit (BL) and during remission 6 months later (6M). Gene expression was compared between patients who met versus did not meet the primary trial outcome of clinical remission at 6M (responders vs. nonresponders). Measurement of neutrophil-related gene expression was confirmed in PBMCs to validate findings in whole blood. A negative selection strategy isolated LDGs from PBMC fractions. Results Differential expression between responders (n=77) and nonresponders (n=35) was detected in 2,346 transcripts at BL visit (p<0.05). Unsupervised hierarchical clustering demonstrated a cluster of granulocyte-related genes, including myeloperoxidase (MPO) and proteinase 3 (PR3). A granulocyte multi-gene composite score was significantly higher in nonresponders than responders (p<0.01) and during active disease compared to remission (p<0.01). This signature strongly overlapped an LDG signature identified previously in lupus (FDRGSEA<0.01). Transcription of PR3 measured in PBMCs was associated with active disease and treatment response (p<0.01). LDGs isolated from patients with AAV spontaneously formed neutrophil extracellular traps containing PR3 and MPO. Conclusions In AAV an increased expression of a granulocyte gene signature is associated with disease activity and decreased response to treatment. The source of this signature is likely LDGs, a potentially pathogenic cell type in AAV. PMID:25891759

  10. Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial.

    PubMed

    Aung, Kyaw L; Fischer, Sandra E; Denroche, Robert E; Jang, Gun-Ho; Dodd, Anna; Creighton, Sean; Southwood, Bernadette; Liang, Sheng-Ben; Chadwick, Dianne; Zhang, Amy; O'Kane, Grainne M; Albaba, Hamzeh; Moura, Shari; Grant, Robert C; Miller, Jessica K; Mbabaali, Faridah; Pasternack, Danielle; Lungu, Ilinca M; Bartlett, John M S; Ghai, Sangeet; Lemire, Mathieu; Holter, Spring; Connor, Ashton A; Moffitt, Richard A; Yeh, Jen Jen; Timms, Lee; Krzyzanowski, Paul M; Dhani, Neesha; Hedley, David; Notta, Faiyaz; Wilson, Julie M; Moore, Malcolm J; Gallinger, Steven; Knox, Jennifer J

    2018-03-15

    Purpose: To perform real-time whole genome sequencing (WGS) and RNA sequencing (RNASeq) of advanced pancreatic ductal adenocarcinoma (PDAC) to identify predictive mutational and transcriptional features for better treatment selection. Experimental Design: Patients with advanced PDAC were prospectively recruited prior to first-line combination chemotherapy. Fresh tumor tissue was acquired by image-guided percutaneous core biopsy for WGS and RNASeq. Laser capture microdissection was performed for all cases. Primary endpoint was feasibility to report WGS results prior to first disease assessment CT scan at 8 weeks. The main secondary endpoint was discovery of patient subsets with predictive mutational and transcriptional signatures. Results: Sixty-three patients underwent a tumor biopsy between December 2015 and June 2017. WGS and RNASeq were successful in 62 (98%) and 60 (95%), respectively. Genomic results were reported at a median of 35 days (range, 19-52 days) from biopsy, meeting the primary feasibility endpoint. Objective responses to first-line chemotherapy were significantly better in patients with the classical PDAC RNA subtype compared with those with the basal-like subtype ( P = 0.004). The best progression-free survival was observed in those with classical subtype treated with m-FOLFIRINOX. GATA6 expression in tumor measured by RNA in situ hybridization was found to be a robust surrogate biomarker for differentiating classical and basal-like PDAC subtypes. Potentially actionable genetic alterations were found in 30% of patients. Conclusions: Prospective genomic profiling of advanced PDAC is feasible, and our early data indicate that chemotherapy response differs among patients with different genomic/transcriptomic subtypes. Clin Cancer Res; 24(6); 1344-54. ©2017 AACR . ©2017 American Association for Cancer Research.

  11. WRKY transcription factors.

    PubMed

    Rushton, Paul J; Somssich, Imre E; Ringler, Patricia; Shen, Qingxi J

    2010-05-01

    WRKY transcription factors are one of the largest families of transcriptional regulators in plants and form integral parts of signalling webs that modulate many plant processes. Here, we review recent significant progress in WRKY transcription factor research. New findings illustrate that WRKY proteins often act as repressors as well as activators, and that members of the family play roles in both the repression and de-repression of important plant processes. Furthermore, it is becoming clear that a single WRKY transcription factor might be involved in regulating several seemingly disparate processes. Mechanisms of signalling and transcriptional regulation are being dissected, uncovering WRKY protein functions via interactions with a diverse array of protein partners, including MAP kinases, MAP kinase kinases, 14-3-3 proteins, calmodulin, histone deacetylases, resistance proteins and other WRKY transcription factors. WRKY genes exhibit extensive autoregulation and cross-regulation that facilitates transcriptional reprogramming in a dynamic web with built-in redundancy. 2010 Elsevier Ltd. All rights reserved.

  12. A Transcription and Translation Protocol for Sensitive Cross-Cultural Team Research.

    PubMed

    Clark, Lauren; Birkhead, Ana Sanchez; Fernandez, Cecilia; Egger, Marlene J

    2017-10-01

    Assurance of transcript accuracy and quality in interview-based qualitative research is foundational for data accuracy and study validity. Based on our experience in a cross-cultural ethnographic study of women's pelvic organ prolapse, we provide practical guidance to set up step-by-step interview transcription and translation protocols for team-based research on sensitive topics. Beginning with team decisions about level of detail in transcription, completeness, and accuracy, we operationalize the process of securing vendors to deliver the required quality of transcription and translation. We also share rubrics for assessing transcript quality and the team protocol for managing transcripts (assuring consistency of format, insertion of metadata, anonymization, and file labeling conventions) and procuring an acceptable initial translation of Spanish-language interviews. Accurate, complete, and systematically constructed transcripts in both source and target languages respond to the call for more transparency and reproducibility of scientific methods.

  13. Integrating hidden Markov model and PRAAT: a toolbox for robust automatic speech transcription

    NASA Astrophysics Data System (ADS)

    Kabir, A.; Barker, J.; Giurgiu, M.

    2010-09-01

    An automatic time-aligned phone transcription toolbox of English speech corpora has been developed. Especially the toolbox would be very useful to generate robust automatic transcription and able to produce phone level transcription using speaker independent models as well as speaker dependent models without manual intervention. The system is based on standard Hidden Markov Models (HMM) approach and it was successfully experimented over a large audiovisual speech corpus namely GRID corpus. One of the most powerful features of the toolbox is the increased flexibility in speech processing where the speech community would be able to import the automatic transcription generated by HMM Toolkit (HTK) into a popular transcription software, PRAAT, and vice-versa. The toolbox has been evaluated through statistical analysis on GRID data which shows that automatic transcription deviates by an average of 20 ms with respect to manual transcription.

  14. Traveling Rocky Roads: The Consequences of Transcription-Blocking DNA Lesions on RNA Polymerase II.

    PubMed

    Steurer, Barbara; Marteijn, Jurgen A

    2017-10-27

    The faithful transcription of eukaryotic genes by RNA polymerase II (RNAP2) is crucial for proper cell function and tissue homeostasis. However, transcription-blocking DNA lesions of both endogenous and environmental origin continuously challenge the progression of elongating RNAP2. The stalling of RNAP2 on a transcription-blocking lesion triggers a series of highly regulated events, including RNAP2 processing to make the lesion accessible for DNA repair, R-loop-mediated DNA damage signaling, and the initiation of transcription-coupled DNA repair. The correct execution and coordination of these processes is vital for resuming transcription following the successful repair of transcription-blocking lesions. Here, we outline recent insights into the molecular consequences of RNAP2 stalling on transcription-blocking DNA lesions and how these lesions are resolved to restore mRNA synthesis. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  15. Bacterial Transcription as a Target for Antibacterial Drug Development

    PubMed Central

    Ma, Cong; Yang, Xiao

    2016-01-01

    SUMMARY Transcription, the first step of gene expression, is carried out by the enzyme RNA polymerase (RNAP) and is regulated through interaction with a series of protein transcription factors. RNAP and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. Despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. The determination of the three-dimensional structures of RNAP and transcription complexes at high resolution over the last 15 years has led to renewed interest in targeting this essential process for antibiotic development by utilizing rational structure-based approaches. In this review, we describe the inhibition of the bacterial transcription process with respect to structural studies of RNAP, highlight recent progress toward the discovery of novel transcription inhibitors, and suggest additional potential antibacterial targets for rational drug design. PMID:26764017

  16. Chromatin looping and eRNA transcription precede the transcriptional activation of gene in the β-globin locus

    PubMed Central

    Kim, Yea Woon; Lee, Sungkung; Yun, Jangmi; Kim, AeRi

    2015-01-01

    Enhancers are closely positioned with actively transcribed target genes by chromatin looping. Non-coding RNAs are often transcribed on active enhancers, referred to as eRNAs (enhancer RNAs). To explore the kinetics of enhancer–promoter looping and eRNA transcription during transcriptional activation, we induced the β-globin locus by chemical treatment and analysed cross-linking frequency between the β-globin gene and locus control region (LCR) and the amount of eRNAs transcribed on the LCR in a time course manner. The cross-linking frequency was increased after chemical induction but before the transcriptional activation of gene in the β-globin locus. Transcription of eRNAs was increased in concomitant with the increase in cross-linking frequency. These results show that chromatin looping and eRNA transcription precedes the transcriptional activation of gene. Concomitant occurrence of the two events suggests functional relationship between them. PMID:25588787

  17. Human Promoters Are Intrinsically Directional

    PubMed Central

    Duttke, Sascha H.C.; Lacadie, Scott A.; Ibrahim, Mahmoud M.; Glass, Christopher K.; Corcoran, David L.; Benner, Christopher; Heinz, Sven; Kadonaga, James T.; Ohler, Uwe

    2015-01-01

    Divergent transcription, in which reverse-oriented transcripts occur upstream of eukaryotic promoters in regions devoid of annotated genes, has been suggested to be a general property of active promoters. Here we show that the human basal RNA polymerase II transcriptional machinery and core promoter are inherently unidirectional, and that reverse-oriented transcripts originate from their own cognate reverse-directed core promoters. In vitro transcription analysis and mapping of nascent transcripts in cells revealed that sequences at reverse start sites are similar to those of their forward counterparts. The use of DNase I accessibility to define proximal promoter borders revealed that up to half of promoters are unidirectional and that unidirectional promoters are depleted at their upstream edges of reverse core promoter sequences and their associated chromatin features. Divergent transcription is thus not an inherent property of the transcription process, but rather the consequence of the presence of both forward- and reverse-directed core promoters. PMID:25639469

  18. Dynamical behavior of psb gene transcripts in greening wheat seedlings. I. Time course of accumulation of the pshA through psbN gene transcripts during light-induced greening.

    PubMed

    Kawaguchi, H; Fukuda, I; Shiina, T; Toyoshima, Y

    1992-11-01

    The time course of the accumulation of the transcripts from 13 psb genes encoding a major part of the proteins composing photosystem II during light-induced greening of dark-grown wheat seedlings was examined focusing on early stages of plastid development (0.5 h through 72 h). The 13 genes can be divided into three groups. (1) The psbA gene is transcribed as a single transcript of 1.3 kb in the dark-grown seedlings, but its level increases 5- to 7-fold in response to light due to selective increase in RNA stability as well as in transcription activity. (2) The psbE-F-L-J operon, psbM and psbN genes are transcribed as a single transcript of 1.1 kb, two transcripts of 0.5 and 0.7 kb and a single transcript of 0.3 kb, respectively, in the dark-grown seedlings. The levels of accumulation of every transcript remain unchanged or rather decrease during plastid development under illumination. (3) The psbK-I-D-C gene cluster and psbB-H operon exhibit fairly complicated northern hybridization patterns during the greening process. When a psbC or psbD gene probe was used for northern hybridization, five transcripts differing in length were detected in the etioplasts from 5-day old dark-grown seedlings. After 2 h illumination, two new transcripts of different length appeared. Light induction of new transcripts was also observed in the psbB-H operon.

  19. Multiple circadian transcriptional elements cooperatively regulate cell-autonomous transcriptional oscillation of Period3, a mammalian clock gene.

    PubMed

    Matsumura, Ritsuko; Akashi, Makoto

    2017-09-29

    Cell-autonomous oscillation in clock gene expression drives circadian rhythms. The development of comprehensive analytical techniques, such as bioinformatics and ChIP-sequencing, has enabled the genome-wide identification of potential circadian transcriptional elements that regulate the transcriptional oscillation of clock genes. However, detailed analyses using traditional biochemical and molecular-biological approaches, such as binding and reporter assays, are still necessary to determine whether these potential circadian transcriptional elements are actually functional and how significantly they contribute to driving transcriptional oscillation. Here, we focused on the molecular mechanism of transcriptional oscillations in the mammalian clock gene Period3 ( Per3 ). The PER3 protein is essential for robust peripheral clocks and is a key component in circadian output processes. We found three E box-like elements located upstream of human Per3 transcription start sites that additively contributed to cell-autonomous transcriptional oscillation. However, we also found that Per3 is still expressed in a circadian manner when all three E box-like elements are functionally impaired. We noted that Per3 transcription was activated by the synergistic actions of two D box-like elements and the three E box-like elements, leading to a drastic increase in circadian amplitude. Interestingly, circadian expression of Per3 was completely disrupted only when all five transcriptional elements were functionally impaired. These results indicate that three E box-like and two D box-like elements cooperatively and redundantly regulate cell-autonomous transcriptional oscillation of Per3 . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  20. Repression of TFIIH Transcriptional Activity and TFIIH-Associated cdk7 Kinase Activity at Mitosis

    PubMed Central

    Long, John J.; Leresche, Anne; Kriwacki, Richard W.; Gottesfeld, Joel M.

    1998-01-01

    Nuclear transcription is repressed when eukaryotic cells enter mitosis. Mitotic repression of transcription of various cellular and viral gene promoters by RNA polymerase II can be reproduced in vitro either with extracts prepared from cells arrested at mitosis with the microtubule polymerization inhibitor nocodazole or with nuclear extracts prepared from asynchronous cells and the mitotic protein kinase cdc2/cyclin B. Purified cdc2/cyclin B kinase is also sufficient to inhibit transcription in reconstituted transcription reactions with biochemically purified and recombinant basal transcription factors and RNA polymerase II. The cyclin-dependent kinase inhibitor p21Waf1/Cip1/Sdi1 can reverse the effect of cdc2/cyclin B kinase, indicating that repression of transcription is due to protein phosphorylation. Transcription rescue and inhibition experiments with each of the basal factors and the polymerase suggest that multiple components of the transcription machinery are inactivated by cdc2/cyclin B kinase. For an activated promoter, targets of repression are TFIID and TFIIH, while for a basal promoter, TFIIH is the major target for mitotic inactivation of transcription. Protein labeling experiments indicate that the p62 and p36 subunits of TFIIH are in vitro substrates for mitotic phosphorylation. Using the carboxy-terminal domain of the large subunit of RNA polymerase II as a test substrate for phosphorylation, the TFIIH-associated kinase, cdk7/cyclin H, is inhibited concomitant with inhibition of transcription activity. Our results suggest that there exist multiple phosphorylation targets for the global shutdown of transcription at mitosis. PMID:9488463

  1. Chronic nicotine treatment leads to induction of tyrosine hydroxylase in locus ceruleus neurons: the role of transcriptional activation.

    PubMed

    Sun, Baoyong; Chen, Xiqun; Xu, Lu; Sterling, Carol; Tank, A William

    2004-10-01

    Chronic nicotine treatment (two daily subcutaneous injections administered approximately 12 h apart for 14 days) is associated with long-term inductions of tyrosine hydroxylase (TH) protein and TH mRNA in locus ceruleus (LC) neurons. These increases persist for at least 3 days after the final nicotine injection in LC cell bodies and for at least 7 to 10 days in LC nerve terminal regions. We tested whether this long-term response is due to sustained stimulation of TH gene transcription rate. A semiquantitative reverse transcription-polymerase chain reaction assay was developed to assess changes in the levels of TH RNA primary transcripts; these changes are an indirect measurement of changes in TH gene transcription rate. TH RNA primary transcript levels increase rapidly in the LC after a single nicotine administration and return to basal levels by 24 h. A similar rapid and transient induction of LC TH RNA primary transcripts occurs after chronic nicotine administration. In contrast, TH RNA primary transcript levels remain elevated for a sustained period of time (at least 1 day) in the adrenal medulla after chronic nicotine administration. Similar rapid, but transient changes in LC TH RNA primary transcript levels are observed after repeated immobilization stress. These results suggest that TH gene transcription rate in the LC is stimulated rapidly after each nicotine injection; however, in contrast to the adrenal medulla, there is no sustained transcriptional response elicited by chronic nicotine treatment or repeated immobilization stress in the LC, suggesting that post-transcriptional mechanisms may also play a role in these long-term responses.

  2. The relationship between gene transcription and combinations of histone modifications

    NASA Astrophysics Data System (ADS)

    Cui, Xiangjun; Li, Hong; Luo, Liaofu

    2012-09-01

    Histone modification is an important subject of epigenetics which plays an intrinsic role in transcriptional regulation. It is known that multiple histone modifications act in a combinatorial fashion. In this study, we demonstrated that the pathways within constructed Bayesian networks can give an indication for the combinations among 12 histone modifications which have been studied in the TSS+1kb region in S. cerevisiae. After Bayesian networks for the genes with high transcript levels (H-network) and low transcript levels (L-network) were constructed, the combinations of modifications within the two networks were analyzed from the view of transcript level. The results showed that different combinations played dissimilar roles in the regulation of gene transcription when there exist differences for gene expression at transcription level.

  3. Transcription Regulation in Archaea

    PubMed Central

    Gehring, Alexandra M.; Walker, Julie E.

    2016-01-01

    The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. Accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. Archaea are reliant on a single RNA polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcription mimic strategies also employed for eukaryotic and bacterial species. Novel mechanisms of transcription regulation have become apparent by increasingly sophisticated in vivo and in vitro investigations of archaeal species. This review emphasizes recent progress in understanding archaeal transcription regulatory mechanisms and highlights insights gained from studies of the influence of archaeal chromatin on transcription. PMID:27137495

  4. Trichomonas vaginalis ribosomal RNA: identification and characterisation of the transcription promoter and terminator sequences.

    PubMed

    Franco, Bernardo; Hernández, Roberto; López-Villaseñor, Imelda

    2012-09-01

    Trichomonas vaginalis is a parasitic protozoan of both medical and biological relevance. Transcriptional studies in this organism have focused mainly on type II pol promoters, whereas the elements necessary for transcription by polI or polIII have not been investigated. Here, with the aid of a transient transcription system, we characterised the rDNA intergenic region, defining both the promoter and the terminator sequences required for transcription. We defined the promoter as a compact region of approximately 180 bp. We also identified a potential upstream control element (UCE) that was located 80 bp upstream of the transcription start point (TSP). A transcription termination element was identified within a 34 bp region that was located immediately downstream of the 28S coding sequence. The function of this element depends upon polarity and the presence of both a stretch of uridine residues (U's) and a hairpin structure in the transcript. Our observations provide a strong basis for the study of DNA recognition by the polI transcriptional machinery in this early divergent organism. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. A BEN-domain-containing protein associates with heterochromatin and represses transcription.

    PubMed

    Sathyan, Kizhakke M; Shen, Zhen; Tripathi, Vidisha; Prasanth, Kannanganattu V; Prasanth, Supriya G

    2011-09-15

    In eukaryotes, higher order chromatin structure governs crucial cellular processes including DNA replication, transcription and post-transcriptional gene regulation. Specific chromatin-interacting proteins play vital roles in the maintenance of chromatin structure. We have identified BEND3, a quadruple BEN domain-containing protein that is highly conserved amongst vertebrates. BEND3 colocalizes with HP1 and H3 trimethylated at K9 at heterochromatic regions in mammalian cells. Using an in vivo gene locus, we have been able to demonstrate that BEND3 associates with the locus only when it is heterochromatic and dissociates upon activation of transcription. Furthermore, tethering BEND3 inhibits transcription from the locus, indicating that BEND3 is involved in transcriptional repression through its interaction with histone deacetylases and Sall4, a transcription repressor. We further demonstrate that BEND3 is SUMOylated and that such modifications are essential for its role in transcriptional repression. Finally, overexpression of BEND3 causes premature chromatin condensation and extensive heterochromatinization, resulting in cell cycle arrest. Taken together, our data demonstrate the role of a novel heterochromatin-associated protein in transcriptional repression.

  6. A BEN-domain-containing protein associates with heterochromatin and represses transcription

    PubMed Central

    Sathyan, Kizhakke M.; Shen, Zhen; Tripathi, Vidisha; Prasanth, Kannanganattu V.; Prasanth, Supriya G.

    2011-01-01

    In eukaryotes, higher order chromatin structure governs crucial cellular processes including DNA replication, transcription and post-transcriptional gene regulation. Specific chromatin-interacting proteins play vital roles in the maintenance of chromatin structure. We have identified BEND3, a quadruple BEN domain-containing protein that is highly conserved amongst vertebrates. BEND3 colocalizes with HP1 and H3 trimethylated at K9 at heterochromatic regions in mammalian cells. Using an in vivo gene locus, we have been able to demonstrate that BEND3 associates with the locus only when it is heterochromatic and dissociates upon activation of transcription. Furthermore, tethering BEND3 inhibits transcription from the locus, indicating that BEND3 is involved in transcriptional repression through its interaction with histone deacetylases and Sall4, a transcription repressor. We further demonstrate that BEND3 is SUMOylated and that such modifications are essential for its role in transcriptional repression. Finally, overexpression of BEND3 causes premature chromatin condensation and extensive heterochromatinization, resulting in cell cycle arrest. Taken together, our data demonstrate the role of a novel heterochromatin-associated protein in transcriptional repression. PMID:21914818

  7. The histone chaperone TAF-I/SET/INHAT is required for transcription in vitro of chromatin templates.

    PubMed

    Gamble, Matthew J; Erdjument-Bromage, Hediye; Tempst, Paul; Freedman, Leonard P; Fisher, Robert P

    2005-01-01

    To uncover factors required for transcription by RNA polymerase II on chromatin, we fractionated a mammalian cell nuclear extract. We identified the histone chaperone TAF-I (also known as INHAT [inhibitor of histone acetyltransferase]), which was previously proposed to repress transcription, as a potent activator of chromatin transcription responsive to the vitamin D3 receptor or to Gal4-VP16. TAF-I associates with chromatin in vitro and can substitute for the related protein NAP-1 in assembling chromatin onto cloned DNA templates in cooperation with the remodeling enzyme ATP-dependent chromatin assembly factor (ACF). The chromatin assembly and transcriptional activation functions are distinct, however, and can be dissociated temporally. Efficient transcription of chromatin assembled with TAF-I still requires the presence of TAF-I during the polymerization reaction. Conversely, TAF-I cannot stimulate transcript elongation when added after the other factors necessary for assembly of a preinitiation complex on naked DNA. Thus, TAF-I is required to facilitate transcription at a step after chromatin assembly but before transcript elongation.

  8. Coupled Evolution of Transcription and mRNA Degradation

    PubMed Central

    Dori-Bachash, Mally; Shema, Efrat; Tirosh, Itay

    2011-01-01

    mRNA levels are determined by the balance between transcription and mRNA degradation, and while transcription has been extensively studied, very little is known regarding the regulation of mRNA degradation and its coordination with transcription. Here we examine the evolution of mRNA degradation rates between two closely related yeast species. Surprisingly, we find that around half of the evolutionary changes in mRNA degradation were coupled to transcriptional changes that exert opposite effects on mRNA levels. Analysis of mRNA degradation rates in an interspecific hybrid further suggests that opposite evolutionary changes in transcription and in mRNA degradation are mechanistically coupled and were generated by the same individual mutations. Coupled changes are associated with divergence of two complexes that were previously implicated both in transcription and in mRNA degradation (Rpb4/7 and Ccr4-Not), as well as with sequence divergence of transcription factor binding motifs. These results suggest that an opposite coupling between the regulation of transcription and that of mRNA degradation has shaped the evolution of gene regulation in yeast. PMID:21811398

  9. 49 CFR 804.10 - Availability and retention of transcripts, recordings, and minutes, and applicable fees.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... transcript or minutes, or transcription of such recordings disclosing the identity of each speaker, shall be furnished to any person at the actual cost of transcription or duplication. the NTSB shall maintain a...

  10. 7 CFR 1409.8 - Public inspection and copying of records; applicable fees.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ..., electronic recording, transcription of the recording, or minutes of the discussion of any item on the agenda...., Washington, DC 20250. (c) The transcripts, minutes, or transcriptions of electronic recordings of a Board... of transcription or duplication. ...

  11. 49 CFR 804.10 - Availability and retention of transcripts, recordings, and minutes, and applicable fees.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... transcript or minutes, or transcription of such recordings disclosing the identity of each speaker, shall be furnished to any person at the actual cost of transcription or duplication. the NTSB shall maintain a...

  12. 7 CFR 1409.8 - Public inspection and copying of records; applicable fees.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ..., electronic recording, transcription of the recording, or minutes of the discussion of any item on the agenda...., Washington, DC 20250. (c) The transcripts, minutes, or transcriptions of electronic recordings of a Board... of transcription or duplication. ...

  13. Switch Transcripts in Immunoglobulin Class Switching

    NASA Astrophysics Data System (ADS)

    Lorenz, Matthias; Jung, Steffen; Radbruch, Andreas

    1995-03-01

    B cells can exchange gene segments for the constant region of the immunoglobulin heavy chain, altering the class and effector function of the antibodies that they produce. Class switching is directed to distinct classes by cytokines, which induce transcription of the targeted DNA sequences. These transcripts are processed, resulting in spliced "switch" transcripts. Switch recombination can be directed to immunoglobulin G1 (IgG1) by the heterologous human metallothionein II_A promoter in mutant mice. Induction of the structurally conserved, spliced switch transcripts is sufficient to target switch recombination to IgG1, whereas transcription alone is not.

  14. An evolutionarily conserved RNase-based mechanism for repression of transcriptional positive autoregulation

    PubMed Central

    Wurtmann, Elisabeth J.; Ratushny, Alexander V.; Pan, Min; Beer, Karlyn D.; Aitchison, John D.; Baliga, Nitin S.

    2014-01-01

    Summary It is known that environmental context influences the degree of regulation at the transcriptional and post-transcriptional levels. However, the principles governing the differential usage and interplay of regulation at these two levels are not clear. Here, we show that the integration of transcriptional and post-transcriptional regulatory mechanisms in a characteristic network motif drives efficient environment-dependent state transitions. Through phenotypic screening, systems analysis, and rigorous experimental validation, we discovered an RNase (VNG2099C) in Halobacterium salinarum that is transcriptionally co-regulated with genes of the aerobic physiologic state but acts on transcripts of the anaerobic state. Through modeling and experimentation we show that this arrangement generates an efficient state-transition switch, within which RNase-repression of a transcriptional positive autoregulation (RPAR) loop is critical for shutting down ATP-consuming active potassium uptake to reserve energy required for salinity adaptation under aerobic, high potassium, or dark conditions. Subsequently, we discovered that many Escherichia coli operons with energy-associated functions are also putatively controlled by RPAR indicating that this network motif may have evolved independently in phylogenetically distant organisms. Thus, our data suggest that interplay of transcriptional and post-transcriptional regulation in the RPAR motifis a generalized principle for efficient environment-dependent state transitions across prokaryotes. PMID:24612392

  15. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks.

    PubMed

    Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra

    2016-05-10

    RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.

  16. [Transcriptome analysis of Dunaliella viridis].

    PubMed

    Zhu, Shuai-qi; Gong, Yi-fu; Hang, Yu-qing; Liu, Hao; Wang, He-yu

    2015-08-01

    In order to understand the gene information, function, haloduric pathway (glycerolipid metabolism) and related key genes for Dunaliella viridis, we used Illumina HiSeqTM 2000 high-throughput sequencing technology to sequence its transcriptome. Trinity soft was used to assemble the data to form transcripts. Based on the Clusters of Orthologous Groups (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG ) databases, we carried out functional annotation and classification, pathway annotation, and the opening reading fragment (ORF) sequence prediction of transcripts. The key genes in the glycerolipid metabolism were analyzed. The results suggested that 81,593 transcripts were found, and 77,117 ORF sequences were predicted, accounting for 94.50% of all transcripts. COG classification results showed that 16,569 transcripts were assigned to 24 categories. GO classification annotated 76,436 transcripts. The number of transcripts for biologcial processes was 30,678, accounting for 40.14% of all transcripts. KEGG pathway analysis showed that 26,428 transcripts were annotated to 317 pathways, and 131 pathways were related to metabolism, accounting for 41.32% of all annotated pathways. Only one transcript was annotated as coding the key enzyme dihydroxyacetone kinase involved in the glycerolipid pathway. This enzyme could be related to glycerol biosynthesis under salt stress. This study further improved the gene information and laid the foundation of metabolic pathway research for Dunaliella viridis.

  17. Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks

    NASA Astrophysics Data System (ADS)

    Nishtala, Sneha; Neelamraju, Yaseswini; Janga, Sarath Chandra

    2016-05-01

    RNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.

  18. Purification and characterization of FBI-1, a cellular factor that binds to the human immunodeficiency virus type 1 inducer of short transcripts.

    PubMed

    Pessler, F; Pendergrast, P S; Hernandez, N

    1997-07-01

    The human immunodeficiency virus (HIV-1) promoter directs the synthesis of two classes of RNA molecules, short transcripts and full-length transcripts. The synthesis of short transcripts depends on a bipartite DNA element, the inducer of short transcripts (IST), located in large part downstream of the HIV-1 start site of transcription. IST does not require any viral product for function and is thought to direct the assembly of transcription complexes that are incapable of efficient elongation. Nothing is known, however, about the biochemical mechanisms that mediate IST function. Here, we report the identification and purification of a factor that binds specifically to the IST. This factor, FBI-1, recognizes a large bipartite binding site that coincides with the bipartite IST element. It is constituted at least in part by an 86-kDa polypeptide that can be specifically cross-linked to IST. FBI-1 also binds to promoter and attenuation regions of a number of cellular and viral transcription units that are regulated by a transcription elongation block. This observation, together with the observation that the binding of FBI-1 to IST mutants correlates with the ability of these mutants to direct IST function, suggests that FBI-1 may be involved in the establishment of abortive transcription complexes.

  19. Different types of pausing modes during transcription initiation.

    PubMed

    Lerner, Eitan; Ingargiola, Antonino; Lee, Jookyung J; Borukhov, Sergei; Michalet, Xavier; Weiss, Shimon

    2017-08-08

    In many cases, initiation is rate limiting to transcription. This due in part to the multiple cycles of abortive transcription that delay promoter escape and the transition from initiation to elongation. Pausing of transcription in initiation can further delay promoter escape. The previously hypothesized pausing in initiation was confirmed by two recent studies from Duchi et al. 1 and from Lerner, Chung et al. 2 In both studies, pausing is attributed to a lack of forward translocation of the nascent transcript during initiation. However, the two works report on different pausing mechanisms. Duchi et al. report on pausing that occurs during initiation predominantly on-pathway of transcript synthesis. Lerner, Chung et al. report on pausing during initiation as a result of RNAP backtracking, which is off-pathway to transcript synthesis. Here, we discuss these studies, together with additional experimental results from single-molecule FRET focusing on a specific distance within the transcription bubble. We show that the results of these studies are complementary to each other and are consistent with a model involving two types of pauses in initiation: a short-lived pause that occurs in the translocation of a 6-mer nascent transcript and a long-lived pause that occurs as a result of 1-2 nucleotide backtracking of a 7-mer transcript.

  20. Profilin Is Required for Optimal Actin-Dependent Transcription of Respiratory Syncytial Virus Genome RNA

    PubMed Central

    Burke, Emily; Mahoney, Nicole M.; Almo, Steven C.; Barik, Sailen

    2000-01-01

    Transcription of human respiratory syncytial virus (RSV) genome RNA exhibited an obligatory need for the host cytoskeletal protein actin. Optimal transcription, however, required the participation of another cellular protein that was characterized as profilin by a number of criteria. The amino acid sequence of the protein, purified on the basis of its transcription-optimizing activity in vitro, exactly matched that of profilin. RSV transcription was inhibited 60 to 80% by antiprofilin antibody or poly-l-proline, molecules that specifically bind profilin. Native profilin, purified from extracts of lung epithelial cells by affinity binding to a poly-l-proline matrix, stimulated the actin-saturated RSV transcription by 2.5- to 3-fold. Recombinant profilin, expressed in bacteria, stimulated viral transcription as effectively as the native protein and was also inhibited by poly-l-proline. Profilin alone, in the absence of actin, did not activate viral transcription. It is estimated that at optimal levels of transcription, every molecule of viral genomic RNA associates with approximately the following number of protein molecules: 30 molecules of L, 120 molecules of phosphoprotein P, and 60 molecules each of actin and profilin. Together, these results demonstrated for the first time a cardinal role for profilin, an actin-modulatory protein, in the transcription of a paramyxovirus RNA genome. PMID:10623728

  1. RHON1 mediates a Rho-like activity for transcription termination in plastids of Arabidopsis thaliana.

    PubMed

    Chi, Wei; He, Baoye; Manavski, Nikolay; Mao, Juan; Ji, Daili; Lu, Congming; Rochaix, Jean David; Meurer, Jörg; Zhang, Lixin

    2014-12-01

    Although transcription termination is essential to generate functional RNAs, its underlying molecular mechanisms are still poorly understood in plastids of vascular plants. Here, we show that the RNA binding protein RHON1 participates in transcriptional termination of rbcL (encoding large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase) in Arabidopsis thaliana. Inactivation of RHON1 leads to enhanced rbcL read-through transcription and to aberrant accD (encoding β-subunit of the acetyl-CoA carboxylase) transcriptional initiation, which may result from inefficient transcription termination of rbcL. RHON1 can bind to the mRNA as well as to single-stranded DNA of rbcL, displays an RNA-dependent ATPase activity, and terminates transcription of rbcL in vitro. These results suggest that RHON1 terminates rbcL transcription using an ATP-driven mechanism similar to that of Rho of Escherichia coli. This RHON1-dependent transcription termination occurs in Arabidopsis but not in rice (Oryza sativa) and appears to reflect a fundamental difference between plastomes of dicotyledonous and monocotyledonous plants. Our results point to the importance and significance of plastid transcription termination and provide insights into its machinery in an evolutionary context. © 2014 American Society of Plant Biologists. All rights reserved.

  2. Transcriptional organization of the DNA region controlling expression of the K99 gene cluster.

    PubMed

    Roosendaal, B; Damoiseaux, J; Jordi, W; de Graaf, F K

    1989-01-01

    The transcriptional organization of the K99 gene cluster was investigated in two ways. First, the DNA region, containing the transcriptional signals was analyzed using a transcription vector system with Escherichia coli galactokinase (GalK) as assayable marker and second, an in vitro transcription system was employed. A detailed analysis of the transcription signals revealed that a strong promoter PA and a moderate promoter PB are located upstream of fanA and fanB, respectively. No promoter activity was detected in the intercistronic region between fanB and fanC. Factor-dependent terminators of transcription were detected and are probably located in the intercistronic region between fanA and fanB (T1), and between fanB and fanC (T2). A third terminator (T3) was observed between fanC and fanD and has an efficiency of 90%. Analysis of the regulatory region in an in vitro transcription system confirmed the location of the respective transcription signals. A model for the transcriptional organization of the K99 cluster is presented. Indications were obtained that the trans-acting regulatory polypeptides FanA and FanB both function as anti-terminators. A model for the regulation of expression of the K99 gene cluster is postulated.

  3. Antisense transcriptional interference mediates condition-specific gene repression in budding yeast.

    PubMed

    Nevers, Alicia; Doyen, Antonia; Malabat, Christophe; Néron, Bertrand; Kergrohen, Thomas; Jacquier, Alain; Badis, Gwenael

    2018-05-18

    Pervasive transcription generates many unstable non-coding transcripts in budding yeast. The transcription of such noncoding RNAs, in particular antisense RNAs (asRNAs), has been shown in a few examples to repress the expression of the associated mRNAs. Yet, such mechanism is not known to commonly contribute to the regulation of a given class of genes. Using a mutant context that stabilized pervasive transcripts, we observed that the least expressed mRNAs during the exponential phase were associated with high levels of asRNAs. These asRNAs also overlapped their corresponding gene promoters with a much higher frequency than average. Interrupting antisense transcription of a subset of genes corresponding to quiescence-enriched mRNAs restored their expression. The underlying mechanism acts in cis and involves several chromatin modifiers. Our results convey that transcription interference represses up to 30% of the 590 least expressed genes, which includes 163 genes with quiescence-enriched mRNAs. We also found that pervasive transcripts constitute a higher fraction of the transcriptome in quiescence relative to the exponential phase, consistent with gene expression itself playing an important role to suppress pervasive transcription. Accordingly, the HIS1 asRNA, normally only present in quiescence, is expressed in exponential phase upon HIS1 mRNA transcription interruption.

  4. Permissive Sense and Antisense Transcription from the 5′ and 3′ Long Terminal Repeats of Human T-Cell Leukemia Virus Type 1

    PubMed Central

    Polakowski, Nicholas; Hoang, Kimson

    2016-01-01

    ABSTRACT Human T-cell leukemia virus type 1 (HTLV-1) is a retrovirus, and, as such, its genome becomes chromosomally integrated following infection. The resulting provirus contains identical 5′ and 3′ peripheral long terminal repeats (LTRs) containing bidirectional promoters. Antisense transcription from the 3′ LTR regulates expression of a single gene, hbz, while sense transcription from the 5′ LTR controls expression of all other viral genes, including tax. Both the HBZ and Tax proteins are implicated in the development of adult T-cell leukemia (ATL), a T-cell malignancy caused by HTLV-1 infection. However, these proteins appear to harbor opposing molecular functions, indicating that they may act independently and at different time points prior to leukemogenesis. Here, we used bidirectional reporter constructs to test whether transcriptional interference serves as a mechanism that inhibits simultaneous expression of Tax and HBZ. We found that sense transcription did not interfere with antisense transcription from the 3′ LTR and vice versa, even with strong transcription emanating from the opposing direction. Therefore, bidirectional transcription across the provirus might not restrict hbz or tax expression. Single-cell analyses revealed that antisense transcription predominates in the absence of Tax, which transactivates viral sense transcription. Interestingly, a population of Tax-expressing cells exhibited antisense but not activated sense transcription. Consistent with the ability of Tax to induce cell cycle arrest, this population was arrested in G0/G1 phase. These results imply that cell cycle arrest inhibits Tax-mediated activation of sense transcription without affecting antisense transcription, which may be important for long-term viral latency. IMPORTANCE The chromosomally integrated form of the retrovirus human T-cell leukemia virus type 1 (HTLV-1) contains identical DNA sequences, known as long terminal repeats (LTRs), at its 5′ and 3′ ends. The LTRs modulate transcription in both forward (sense) and reverse (antisense) directions. We found that sense transcription from the 5′ LTR does not interfere with antisense transcription from the 3′ LTR, allowing viral genes encoded on opposite DNA strands to be simultaneously transcribed. Two such genes are tax and hbz, and while they are thought to function at different times during the course of infection to promote leukemogenesis of infected T cells, our results indicate that they can be simultaneously transcribed. We also found that the ability of Tax to induce cell cycle arrest inhibits its fundamental function of activating viral sense transcription but does not affect antisense transcription. This regulatory mechanism may be important for long-term HTLV-1 infection. PMID:26792732

  5. Identification of Poly(ADP-Ribose) Polymerase as a Transcriptional Coactivator of the Human T-Cell Leukemia Virus Type 1 Tax Protein

    PubMed Central

    Anderson, Mark G.; Scoggin, Kirsten E. S.; Simbulan-Rosenthal, Cynthia M.; Steadman, Jennifer A.

    2000-01-01

    Human T-cell leukemia virus type 1 (HTLV-1) encodes a transcriptional activator, Tax, whose activity is believed to contribute significantly to cellular transformation. Tax stimulates transcription from the proviral promoter as well as from promoters for a variety of cellular genes. The mechanism through which Tax communicates to the general transcription factors and RNA polymerase II has not been completely determined. We investigated whether Tax could function directly through the general transcription factors and RNA polymerase II or if other intermediary factors or coactivators were required. Our results show that a system consisting of purified recombinant TFIIA, TFIIB, TFIIE, TFIIF, CREB, and Tax, along with highly purified RNA polymerase II, affinity-purified epitope-tagged TFIID, and semipurified TFIIH, supports basal transcription of the HTLV-1 promoter but is not responsive to Tax. Two additional activities were required for Tax to stimulate transcription. We demonstrate that one of these activities is poly(ADP-ribose) polymerase (PARP), a molecule that has been previously identified to be the transcriptional coactivator PC1. PARP functions as a coactivator in our assays at molar concentrations approximately equal to those of the DNA and equal to or less than those of the transcription factors in the assay. We further demonstrate that PARP stimulates Tax-activated transcription in vivo, demonstrating that this biochemical approach has functionally identified a novel target for the retroviral transcriptional activator Tax. PMID:10666246

  6. c-Jun binds the N terminus of human TAF(II)250 to derepress RNA polymerase II transcription in vitro.

    PubMed

    Lively, T N; Ferguson, H A; Galasinski, S K; Seto, A G; Goodrich, J A

    2001-07-06

    c-Jun is an oncoprotein that activates transcription of many genes involved in cell growth and proliferation. We studied the mechanism of transcriptional activation by human c-Jun in a human RNA polymerase II transcription system composed of highly purified recombinant and native transcription factors. Transcriptional activation by c-Jun depends on the TATA-binding protein (TBP)-associated factor (TAF) subunits of transcription factor IID (TFIID). Protein-protein interaction assays revealed that c-Jun binds with high specificity to the largest subunit of human TFIID, TAF(II)250. The region of TAF(II)250 bound by c-Jun lies in the N-terminal 163 amino acids. This same region of TAF(II)250 binds to TBP and represses its interaction with TATA boxes, thereby decreasing DNA binding by TFIID. We hypothesized that c-Jun is capable of derepressing the effect of the TAF(II)250 N terminus on TFIID-driven transcription. In support of this hypothesis, we found that c-Jun increased levels of TFIID-driven transcription in vitro when added at high concentrations to a DNA template lacking activator protein 1 (AP-1) sites. Moreover, c-Jun blocked the repression of TBP DNA binding caused by the N terminus of TAF(II)250. In addition to revealing a mechanism by which c-Jun activates transcription, our studies provide the first evidence that an activator can bind directly to the N terminus of TAF(II)250 to derepress RNA polymerase II transcription in vitro.

  7. Splicing and transcription touch base: co-transcriptional spliceosome assembly and function

    PubMed Central

    Herzel, Lydia; Ottoz, Diana S. M.; Alpert, Tara; Neugebauer, Karla M.

    2018-01-01

    Several macromolecular machines collaborate to produce eukaryotic messenger RNA. RNA polymerase II (Pol II) translocates along genes that are up to millions of base pairs in length and generates a flexible RNA copy of the DNA template. This nascent RNA harbours introns that are removed by the spliceosome, which is a megadalton ribonucleoprotein complex that positions the distant ends of the intron into its catalytic centre. Emerging evidence that the catalytic spliceosome is physically close to Pol II in vivo implies that transcription and splicing occur on similar timescales and that the transcription and splicing machineries may be spatially constrained. In this Review, we discuss aspects of spliceosome assembly, transcription elongation and other co-transcriptional events that allow the temporal coordination of co-transcriptional splicing. PMID:28792005

  8. Sense transcription through the S region is essential for immunoglobulin class switch recombination

    PubMed Central

    Haddad, Dania; Oruc, Zéliha; Puget, Nadine; Laviolette-Malirat, Nathalie; Philippe, Magali; Carrion, Claire; Le Bert, Marc; Khamlichi, Ahmed Amine

    2011-01-01

    Class switch recombination (CSR) occurs between highly repetitive sequences called switch (S) regions and is initiated by activation-induced cytidine deaminase (AID). CSR is preceded by a bidirectional transcription of S regions but the relative importance of sense and antisense transcription for CSR in vivo is unknown. We generated three mouse lines in which we attempted a premature termination of transcriptional elongation by inserting bidirectional transcription terminators upstream of Sμ, upstream of Sγ3 or downstream of Sγ3 sequences. The data show, at least for Sγ3, that sense transcriptional elongation across S region is absolutely required for CSR whereas its antisense counterpart is largely dispensable, strongly suggesting that sense transcription is sufficient for AID targeting to both DNA strands. PMID:21378751

  9. Pervasive, Genome-Wide Transcription in the Organelle Genomes of Diverse Plastid-Bearing Protists.

    PubMed

    Sanitá Lima, Matheus; Smith, David Roy

    2017-11-06

    Organelle genomes are among the most sequenced kinds of chromosome. This is largely because they are small and widely used in molecular studies, but also because next-generation sequencing technologies made sequencing easier, faster, and cheaper. However, studies of organelle RNA have not kept pace with those of DNA, despite huge amounts of freely available eukaryotic RNA-sequencing (RNA-seq) data. Little is known about organelle transcription in nonmodel species, and most of the available eukaryotic RNA-seq data have not been mined for organelle transcripts. Here, we use publicly available RNA-seq experiments to investigate organelle transcription in 30 diverse plastid-bearing protists with varying organelle genomic architectures. Mapping RNA-seq data to organelle genomes revealed pervasive, genome-wide transcription, regardless of the taxonomic grouping, gene organization, or noncoding content. For every species analyzed, transcripts covered ≥85% of the mitochondrial and/or plastid genomes (all of which were ≤105 kb), indicating that most of the organelle DNA-coding and noncoding-is transcriptionally active. These results follow earlier studies of model species showing that organellar transcription is coupled and ubiquitous across the genome, requiring significant downstream processing of polycistronic transcripts. Our findings suggest that noncoding organelle DNA can be transcriptionally active, raising questions about the underlying function of these transcripts and underscoring the utility of publicly available RNA-seq data for recovering complete genome sequences. If pervasive transcription is also found in bigger organelle genomes (>105 kb) and across a broader range of eukaryotes, this could indicate that noncoding organelle RNAs are regulating fundamental processes within eukaryotic cells. Copyright © 2017 Sanitá Lima and Smith.

  10. Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

    PubMed Central

    Vilborg, Anna; Sabath, Niv; Wiesel, Yuval; Nathans, Jenny; Levy-Adam, Flonia; Yario, Therese A.; Steitz, Joan A.; Shalgi, Reut

    2017-01-01

    Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a genome-wide mapping of transcriptional readthrough, using nuclear RNA-Seq, comparing heat shock, osmotic stress, and oxidative stress in NIH 3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough, both in levels and length, under all stress conditions, with significant, yet not complete, overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Analysis of public datasets detected increases in polymerase II occupancy in DoG regions after heat shock, supporting our findings. Interestingly, DoGs tend to be produced in the vicinity of neighboring genes, leading to a marked increase in their antisense-generating potential. Finally, we examine genomic features of readthrough transcription and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state. PMID:28928151

  11. Sex-biased gene expression and sequence conservation in Atlantic and Pacific salmon lice (Lepeophtheirus salmonis).

    PubMed

    Poley, Jordan D; Sutherland, Ben J G; Jones, Simon R M; Koop, Ben F; Fast, Mark D

    2016-07-04

    Salmon lice, Lepeophtheirus salmonis (Copepoda: Caligidae), are highly important ectoparasites of farmed and wild salmonids, and cause multi-million dollar losses to the salmon aquaculture industry annually. Salmon lice display extensive sexual dimorphism in ontogeny, morphology, physiology, behavior, and more. Therefore, the identification of transcripts with differential expression between males and females (sex-biased transcripts) may help elucidate the relationship between sexual selection and sexually dimorphic characteristics. Sex-biased transcripts were identified from transcriptome analyses of three L. salmonis populations, including both Atlantic and Pacific subspecies. A total of 35-43 % of all quality-filtered transcripts were sex-biased in L. salmonis, with male-biased transcripts exhibiting higher fold change than female-biased transcripts. For Gene Ontology and functional analyses, a consensus-based approach was used to identify concordantly differentially expressed sex-biased transcripts across the three populations. A total of 127 male-specific transcripts (i.e. those without detectable expression in any female) were identified, and were enriched with reproductive functions (e.g. seminal fluid and male accessory gland proteins). Other sex-biased transcripts involved in morphogenesis, feeding, energy generation, and sensory and immune system development and function were also identified. Interestingly, as observed in model systems, male-biased L. salmonis transcripts were more frequently without annotation compared to female-biased or unbiased transcripts, suggesting higher rates of sequence divergence in male-biased transcripts. Transcriptome differences between male and female L. salmonis described here provide key insights into the molecular mechanisms controlling sexual dimorphism in L. salmonis. This analysis offers targets for parasite control and provides a foundation for further analyses exploring critical topics such as the interaction between sex and drug resistance, sex-specific factors in host-parasite relationships, and reproductive roles within L. salmonis.

  12. Long-read sequencing of nascent RNA reveals coupling among RNA processing events.

    PubMed

    Herzel, Lydia; Straube, Korinna; Neugebauer, Karla M

    2018-06-14

    Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates. Here, we overcome this obstacle through long-read RNA sequencing of nascent, multi-intron transcripts in the fission yeast Schizosaccharomyces pombe Most multi-intron transcripts were fully spliced, consistent with rapid cotranscriptional splicing. However, an unexpectedly high proportion of transcripts were either fully spliced or fully unspliced, suggesting that splicing of any given intron is dependent on the splicing status of other introns in the transcript. Supporting this, mild inhibition of splicing by a temperature-sensitive mutation in prp2 , the homolog of vertebrate U2AF65, increased the frequency of fully unspliced transcripts. Importantly, fully unspliced transcripts displayed transcriptional read-through at the polyA site and were degraded cotranscriptionally by the nuclear exosome. Finally, we show that cellular mRNA levels were reduced in genes with a high number of unspliced nascent transcripts during caffeine treatment, showing regulatory significance of cotranscriptional splicing. Therefore, overall splicing of individual nascent transcripts, 3' end formation, and mRNA half-life depend on the splicing status of neighboring introns, suggesting crosstalk among spliceosomes and the polyA cleavage machinery during transcription elongation. © 2018 Herzel et al.; Published by Cold Spring Harbor Laboratory Press.

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

    PubMed

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

    2017-08-04

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

  14. A novel mode for transcription inhibition mediated by PNA-induced R-loops with a model in vitro system.

    PubMed

    D'Souza, Alicia D; Belotserkovskii, Boris P; Hanawalt, Philip C

    2018-02-01

    The selective inhibition of transcription of a chosen gene by an artificial agent has numerous applications. Usually, these agents are designed to bind a specific nucleotide sequence in the promoter or within the transcribed region of the chosen gene. However, since optimal binding sites might not exist within the gene, it is of interest to explore the possibility of transcription inhibition when the agent is designed to bind at other locations. One of these possibilities arises when an additional transcription initiation site (e.g. secondary promoter) is present upstream from the primary promoter of the target gene. In this case, transcription inhibition might be achieved by inducing the formation of an RNA-DNA hybrid (R-loop) upon transcription from the secondary promoter. The R-loop could extend into the region of the primary promoter, to interfere with promoter recognition by RNA polymerase and thereby inhibit transcription. As a sequence-specific R-loop-inducing agent, a peptide nucleic acid (PNA) could be designed to facilitate R-loop formation by sequestering the non-template DNA strand. To investigate this mode for transcription inhibition, we have employed a model system in which a PNA binding site is localized between the T3 and T7 phage RNA polymerase promoters, which respectively assume the roles of primary and secondary promoters. In accord with our model, we have demonstrated that with PNA-bound DNA substrates, transcription from the T7 promoter reduces transcription from the T3 promoter by 30-fold, while in the absence of PNA binding there is no significant effect of T7 transcription upon T3 transcription. Copyright © 2018 Elsevier B.V. All rights reserved.

  15. Relationships Between RNA Polymerase II Activity and Spt Elongation Factors to Spt- Phenotype and Growth in Saccharomyces cerevisiae

    PubMed Central

    Cui, Ping; Jin, Huiyan; Vutukuru, Manjula Ramya; Kaplan, Craig D.

    2016-01-01

    The interplay between adjacent transcription units can result in transcription-dependent alterations in chromatin structure or recruitment of factors that determine transcription outcomes, including the generation of intragenic or other cryptic transcripts derived from cryptic promoters. Mutations in a number of genes in Saccharomyces cerevisiae confer both cryptic intragenic transcription and the Suppressor of Ty (Spt-) phenotype for the lys2-128∂ allele of the LYS2 gene. Mutants that suppress lys2-128∂ allow transcription from a normally inactive Ty1 ∂ promoter, conferring a LYS+ phenotype. The arrangement of transcription units at lys2-128∂ is reminiscent of genes containing cryptic promoters within their open reading frames. We set out to examine the relationship between RNA Polymerase II (Pol II) activity, functions of Spt elongation factors, and cryptic transcription because of the previous observation that increased-activity Pol II alleles confer an Spt- phenotype. We identify both cooperating and antagonistic genetic interactions between Pol II alleles and alleles of elongation factors SPT4, SPT5, and SPT6. We find that cryptic transcription at FLO8 and STE11 is distinct from that at lys2-128∂, though all show sensitivity to reduction in Pol II activity, especially the expression of lys2-128∂ found in Spt- mutants. We determine that the lys2-128∂ Spt- phenotypes for spt6-1004 and increased activity rpo21/rpb1 alleles each require transcription from the LYS2 promoter. Furthermore, we identify the Ty1 transcription start site (TSS) within the ∂ element as the position of Spt- transcription in tested Spt- mutants. PMID:27261007

  16. Convergent transcription in the butyrolactone regulon in Streptomyces coelicolor confers a bistable genetic switch for antibiotic biosynthesis.

    PubMed

    Chatterjee, Anushree; Drews, Laurie; Mehra, Sarika; Takano, Eriko; Kaznessis, Yiannis N; Hu, Wei-Shou

    2011-01-01

    cis-encoded antisense RNAs (cis asRNA) have been reported to participate in gene expression regulation in both eukaryotic and prokaryotic organisms. Its presence in Streptomyces coelicolor has also been reported recently; however, its role has yet to be fully investigated. Using mathematical modeling we explore the role of cis asRNA produced as a result of convergent transcription in scbA-scbR genetic switch. scbA and scbR gene pair, encoding repressor-amplifier proteins respectively, mediates the synthesis of a signaling molecule, the γ-butyrolactone SCB1 and controls the onset of antibiotic production. Our model considers that transcriptional interference caused by convergent transcription of two opposing RNA polymerases results in fatal collision and transcriptional termination, which suppresses transcription efficiency. Additionally, convergent transcription causes sense and antisense interactions between complementary sequences from opposing strands, rendering the full length transcript inaccessible for translation. We evaluated the role of transcriptional interference and the antisense effect conferred by convergent transcription on the behavior of scbA-scbR system. Stability analysis showed that while transcriptional interference affects the system, it is asRNA that confers scbA-scbR system the characteristics of a bistable switch in response to the signaling molecule SCB1. With its critical role of regulating the onset of antibiotic synthesis the bistable behavior offers this two gene system the needed robustness to be a genetic switch. The convergent two gene system with potential of transcriptional interference is a frequent feature in various genomes. The possibility of asRNA regulation in other such gene-pairs is yet to be examined.

  17. Stereochemical analysis of the functional significance of the conserved inverted CCAAT and TATA elements in the rat bone sialoprotein gene promoter.

    PubMed

    Su, Ming; Lee, Daniel; Ganss, Bernhard; Sodek, Jaro

    2006-04-14

    Basal transcription of the bone sialoprotein gene is mediated by highly conserved inverted CCAAT (ICE; ATTGG) and TATA elements (TTTATA) separated by precisely 21 nucleotides. Here we studied the importance of the relative position and orientation of the CCAAT and TATA elements in the proximal promoter by measuring the transcriptional activity of a series of mutated reporter constructs in transient transfection assays. Whereas inverting the TTTATA (wild type) to a TATAAA (consensus TATA) sequence increased transcription slightly, transcription was reduced when the flanking dinucleotides were also inverted. In contrast, reversing the ATTGG (wild type; ICE) to a CCAAT (RICE) sequence caused a marked reduction in transcription, whereas both transcription and NF-Y binding were progressively increased with the simultaneous inversion of flanking nucleotides (f-RICE-f). Reducing the distance between the ICE and TATA elements produced cyclical changes in transcriptional activity that correlated with progressive alterations in the relative positions of the CCAAT and TATA elements on the face of the DNA helix. Minimal transcription was observed after 5 nucleotides were deleted (equivalent to approximately one half turn of the helix), whereas transcription was fully restored after deleting 10 nucleotides (approximately one full turn of the DNA helix), transcriptional activity being progressively lost with deletions beyond 10 nucleotides. In comparison, when deletions were made with the ICE in the reversed (f-RICE-f) orientation transcriptional activity was progressively lost with no recovery. These results show that, although transcription can still occur when the CCAAT box is reversed and/or displaced relative to the TATA box, the activity is dependent upon the flexibility of the intervening DNA helix needed to align the NF-Y complex on the CCAAT box with preinitiation complex proteins that bind to the TATA box. Thus, the precise location and orientation of the CCAAT element is necessary for optimizing basal transcription of the bone sialoprotein gene.

  18. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lee, Brady D.; Thompson, David N.; Apel, William A.

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of modulating transcription or transcription or transcriptional control using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  19. 40 CFR 1610.4 - Deposition Transcripts.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Deposition Transcripts. 1610.4 Section... INVESTIGATIONS § 1610.4 Deposition Transcripts. (a) Transcripts of depositions of witnesses compelled by subpoena... by the person conducting the deposition. (b) Such a witness, after completing the compelled testimony...

  20. 40 CFR 1610.4 - Deposition Transcripts.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Deposition Transcripts. 1610.4 Section... INVESTIGATIONS § 1610.4 Deposition Transcripts. (a) Transcripts of depositions of witnesses compelled by subpoena... by the person conducting the deposition. (b) Such a witness, after completing the compelled testimony...

  1. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods

    DOEpatents

    Lee, Brady Deneys; Thompson, David N; Apel, William A.; Thompson, Vicki Slavchev; Reed, David W; Lacey, Jeffrey A

    2014-05-06

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of modulating transcription or transcription or transcriptional control using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  2. Transcriptional control in Alicyclobacillus acidocaldarius and associated genes, proteins, and methods

    DOEpatents

    Lee, Brady D.; Thompson, David N.; Apel, William A.; Thompson, Vicki S.; Reed, David W.; Lacey, Jeffrey A.

    2015-11-17

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of modulating transcription or transcription or transcriptional control using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  3. Transcriptional control in alicyclobacillus acidocaldarius and associated genes, proteins, and methods

    DOEpatents

    Lee, Brady D; Thompson, David N; Apel, William A; Thompson, Vicki S; Reed, David W; Lacey, Jeffrey A

    2016-11-22

    Isolated and/or purified polypeptides and nucleic acid sequences encoding polypeptides from Alicyclobacillus acidocaldarius are provided. Further provided are methods of modulating transcription or transcription or transcriptional control using isolated and/or purified polypeptides and nucleic acid sequences from Alicyclobacillus acidocaldarius.

  4. Backtracking dynamics of RNA polymerase: pausing and error correction.

    PubMed

    Sahoo, Mamata; Klumpp, Stefan

    2013-09-18

    Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

  5. Backtracking dynamics of RNA polymerase: pausing and error correction

    NASA Astrophysics Data System (ADS)

    Sahoo, Mamata; Klumpp, Stefan

    2013-09-01

    Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

  6. Chromatin-Specific Regulation of Mammalian rDNA Transcription by Clustered TTF-I Binding Sites

    PubMed Central

    Diermeier, Sarah D.; Németh, Attila; Rehli, Michael; Grummt, Ingrid; Längst, Gernot

    2013-01-01

    Enhancers and promoters often contain multiple binding sites for the same transcription factor, suggesting that homotypic clustering of binding sites may serve a role in transcription regulation. Here we show that clustering of binding sites for the transcription termination factor TTF-I downstream of the pre-rRNA coding region specifies transcription termination, increases the efficiency of transcription initiation and affects the three-dimensional structure of rRNA genes. On chromatin templates, but not on free rDNA, clustered binding sites promote cooperative binding of TTF-I, loading TTF-I to the downstream terminators before it binds to the rDNA promoter. Interaction of TTF-I with target sites upstream and downstream of the rDNA transcription unit connects these distal DNA elements by forming a chromatin loop between the rDNA promoter and the terminators. The results imply that clustered binding sites increase the binding affinity of transcription factors in chromatin, thus influencing the timing and strength of DNA-dependent processes. PMID:24068958

  7. Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex

    PubMed Central

    Liu, Zhijie; Merkurjev, Daria; Yang, Feng; Li, Wenbo; Oh, Soohwan; Friedman, Meyer J.; Song, Xiaoyuan; Zhang, Feng; Ma, Qi; Ohgi, Kenneth; Krones, Anna; Rosenfeld, Michael G.

    2014-01-01

    Summary Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2 MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. PMID:25303530

  8. TIF-IC, a factor involved in both transcription initiation and elongation of RNA polymerase I.

    PubMed

    Schnapp, G; Schnapp, A; Rosenbauer, H; Grummt, I

    1994-09-01

    We have characterized a transcription factor from Ehrlich ascites cells that is required for ribosomal gene transcription by RNA polymerase I (Pol I). This factor, termed TIF-IC, has a native molecular mass of 65 kDa, associates with Pol I, and is required both for the assembly of Sarkosyl-resistant initiation complexes and for the formation of the first internucleotide bonds. In addition to its function in transcription initiation, TIF-IC also plays a role in elongation of nascent RNA chains. At suboptimal levels of TIF-IC, transcripts with heterogeneous 3' ends are formed which are chased into full-length transcripts by the addition of more TIF-IC. Moreover, on a tailed template, which allows initiation in the absence of auxiliary factors, TIF-IC was found to stimulate the overall rate of transcription elongation and suppress pausing of Pol I. Thus TIF-IC appears to serve a function similar to the Pol II-specific factor TFIIF which is required for Pol II transcription initiation and elongation.

  9. Designed Transcriptional Regulation in Mammalian Cells Based on TALE- and CRISPR/dCas9.

    PubMed

    Lebar, Tina; Jerala, Roman

    2018-01-01

    Transcriptional regulation lies at the center of many cellular processes and is the result of cellular response to different external and internal signals. Control of transcription of selected genes enables an unprecedented access to shape the cellular response. While orthogonal transcription factors from bacteria, yeast, plants, or other cells have been used to introduce new cellular logic into mammalian cells, the discovery of designable modular DNA binding domains, such as Transcription Activator-Like Effectors (TALEs) and the CRISPR system, enable targeting of almost any selected DNA sequence. Fusion or conditional association of DNA targeting domain with transcriptional effector domains enables controlled regulation of almost any endogenous or ectopic gene. Moreover, the designed regulators can be linked into genetic circuits to implement complex responses, such as different types of Boolean functions and switches. In this chapter, we describe the protocols for achieving efficient transcriptional regulation with TALE- and CRISPR-based designed transcription factors in mammalian cells.

  10. Real-time observation of the initiation of RNA polymerase II transcription.

    PubMed

    Fazal, Furqan M; Meng, Cong A; Murakami, Kenji; Kornberg, Roger D; Block, Steven M

    2015-09-10

    Biochemical and structural studies have shown that the initiation of RNA polymerase II transcription proceeds in the following stages: assembly of the polymerase with general transcription factors and promoter DNA in a 'closed' preinitiation complex (PIC); unwinding of about 15 base pairs of the promoter DNA to form an 'open' complex; scanning downstream to a transcription start site; synthesis of a short transcript, thought to be about 10 nucleotides long; and promoter escape. Here we have assembled a 32-protein, 1.5-megadalton PIC derived from Saccharomyces cerevisiae, and observe subsequent initiation processes in real time with optical tweezers. Contrary to expectation, scanning driven by the transcription factor IIH involved the rapid opening of an extended transcription bubble, averaging 85 base pairs, accompanied by the synthesis of a transcript up to the entire length of the extended bubble, followed by promoter escape. PICs that failed to achieve promoter escape nevertheless formed open complexes and extended bubbles, which collapsed back to closed or open complexes, resulting in repeated futile scanning.

  11. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers

    PubMed Central

    Latgé, Guillaume; Poulet, Christophe; Bours, Vincent; Jerusalem, Guy

    2018-01-01

    Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers. PMID:29301303

  12. Natural Antisense Transcripts: Molecular Mechanisms and Implications in Breast Cancers.

    PubMed

    Latgé, Guillaume; Poulet, Christophe; Bours, Vincent; Josse, Claire; Jerusalem, Guy

    2018-01-02

    Natural antisense transcripts are RNA sequences that can be transcribed from both DNA strands at the same locus but in the opposite direction from the gene transcript. Because strand-specific high-throughput sequencing of the antisense transcriptome has only been available for less than a decade, many natural antisense transcripts were first described as long non-coding RNAs. Although the precise biological roles of natural antisense transcripts are not known yet, an increasing number of studies report their implication in gene expression regulation. Their expression levels are altered in many physiological and pathological conditions, including breast cancers. Among the potential clinical utilities of the natural antisense transcripts, the non-coding|coding transcript pairs are of high interest for treatment. Indeed, these pairs can be targeted by antisense oligonucleotides to specifically tune the expression of the coding-gene. Here, we describe the current knowledge about natural antisense transcripts, their varying molecular mechanisms as gene expression regulators, and their potential as prognostic or predictive biomarkers in breast cancers.

  13. Illegitimate transcription: transcription of any gene in any cell type.

    PubMed Central

    Chelly, J; Concordet, J P; Kaplan, J C; Kahn, A

    1989-01-01

    Using in vitro amplification of cDNA by the polymerase chain reaction, we have detected spliced transcripts of various tissue-specific genes (genes for anti-Müllerian hormone, beta-globin, aldolase A, and factor VIIIc) in human nonspecific cells, such as fibroblasts, hepatoma cells, and lymphoblasts. In rats, erythroid- and liver-type pyruvate kinase transcripts were also detected in brain, lung, and muscle. The abundance of these "illegitimate" transcripts is very low; yet, their existence and the possibility of amplifying them by the cDNA polymerase chain reaction provide a powerful tool to analyze pathological transcripts of any tissue-specific gene by using any accessible cell. Images PMID:2495532

  14. Transcriptome analysis by strand-specific sequencing of complementary DNA

    PubMed Central

    Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

    2009-01-01

    High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online. PMID:19620212

  15. Transcriptome analysis by strand-specific sequencing of complementary DNA.

    PubMed

    Parkhomchuk, Dmitri; Borodina, Tatiana; Amstislavskiy, Vyacheslav; Banaru, Maria; Hallen, Linda; Krobitsch, Sylvia; Lehrach, Hans; Soldatov, Alexey

    2009-10-01

    High-throughput complementary DNA sequencing (RNA-Seq) is a powerful tool for whole-transcriptome analysis, supplying information about a transcript's expression level and structure. However, it is difficult to determine the polarity of transcripts, and therefore identify which strand is transcribed. Here, we present a simple cDNA sequencing protocol that preserves information about a transcript's direction. Using Saccharomyces cerevisiae and mouse brain transcriptomes as models, we demonstrate that knowing the transcript's orientation allows more accurate determination of the structure and expression of genes. It also helps to identify new genes and enables studying promoter-associated and antisense transcription. The transcriptional landscapes we obtained are available online.

  16. A critical role for topoisomerase IIb and DNA double strand breaks in transcription

    PubMed Central

    Calderwood, Stuart K.

    2016-01-01

    ABSTRACT Recent studies have indicated a novel role for topoisomerase IIb in transcription. Transcription of heat shock genes, serum-induced immediate early genes and nuclear receptor-activated genes, each required DNA double strands generated by topoisomerase IIb. Such strand breaks seemed both necessary and sufficient for transcriptional activation. In addition, such transcription was associated with initiation of the DNA damage response pathways, including the activation of the enzymes: ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase and poly (ADP ribose) polymerase 1. DNA damage response signaling was involved both in transcription and in repair of DNA breaks generated by topoisomerase IIb. PMID:27100743

  17. A critical role for topoisomerase IIb and DNA double strand breaks in transcription.

    PubMed

    Calderwood, Stuart K

    2016-05-26

    Recent studies have indicated a novel role for topoisomerase IIb in transcription. Transcription of heat shock genes, serum-induced immediate early genes and nuclear receptor-activated genes, each required DNA double strands generated by topoisomerase IIb. Such strand breaks seemed both necessary and sufficient for transcriptional activation. In addition, such transcription was associated with initiation of the DNA damage response pathways, including the activation of the enzymes: ataxia-telangiectasia mutated (ATM), DNA-dependent protein kinase and poly (ADP ribose) polymerase 1. DNA damage response signaling was involved both in transcription and in repair of DNA breaks generated by topoisomerase IIb.

  18. Transcriptional Regulation in Saccharomyces cerevisiae: Transcription Factor Regulation and Function, Mechanisms of Initiation, and Roles of Activators and Coactivators

    PubMed Central

    Hahn, Steven; Young, Elton T.

    2011-01-01

    Here we review recent advances in understanding the regulation of mRNA synthesis in Saccharomyces cerevisiae. Many fundamental gene regulatory mechanisms have been conserved in all eukaryotes, and budding yeast has been at the forefront in the discovery and dissection of these conserved mechanisms. Topics covered include upstream activation sequence and promoter structure, transcription factor classification, and examples of regulated transcription factor activity. We also examine advances in understanding the RNA polymerase II transcription machinery, conserved coactivator complexes, transcription activation domains, and the cooperation of these factors in gene regulatory mechanisms. PMID:22084422

  19. Co-localization of polar replication fork barriers and rRNA transcription terminators in mouse rDNA.

    PubMed

    López-estraño, C; Schvartzman, J B; Krimer, D B; Hernández, P

    1998-03-27

    We investigated the replication of the region where transcription terminates in mouse rDNA. It contains a replication fork barrier (RFB) that behaves in a polar manner, arresting only replication forks moving in the direction opposite to transcription. This RFB consists of several closely spaced fork arrest sites that co-localize with the transcription terminator elements, known as Sal boxes. Sal boxes are the target for mTTF-I (murine transcription termination factor I). These results suggest that both termination of rRNA transcription and replication fork arrest may share cis-acting as well as trans-acting factors. Copyright 1998 Academic Press Limited.

  20. The DNA Replication Checkpoint Directly Regulates MBF-Dependent G1/S Transcription▿

    PubMed Central

    Dutta, Chaitali; Patel, Prasanta K.; Rosebrock, Adam; Oliva, Anna; Leatherwood, Janet; Rhind, Nicholas

    2008-01-01

    The DNA replication checkpoint transcriptionally upregulates genes that allow cells to adapt to and survive replication stress. Our results show that, in the fission yeast Schizosaccharomyces pombe, the replication checkpoint regulates the entire G1/S transcriptional program by directly regulating MBF, the G1/S transcription factor. Instead of initiating a checkpoint-specific transcriptional program, the replication checkpoint targets MBF to maintain the normal G1/S transcriptional program during replication stress. We propose a mechanism for this regulation, based on in vitro phosphorylation of the Cdc10 subunit of MBF by the Cds1 replication-checkpoint kinase. Replacement of two potential phosphorylation sites with phosphomimetic amino acids suffices to promote the checkpoint transcriptional program, suggesting that Cds1 phosphorylation directly regulates MBF-dependent transcription. The conservation of MBF between fission and budding yeast, and recent results implicating MBF as a target of the budding yeast replication checkpoint, suggests that checkpoint regulation of the MBF transcription factor is a conserved strategy for coping with replication stress. Furthermore, the structural and regulatory similarity between MBF and E2F, the metazoan G1/S transcription factor, suggests that this checkpoint mechanism may be broadly conserved among eukaryotes. PMID:18662996

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