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BNAT

Basic Neuroscience Advanced Training


Angeles Ribera
BNAT Director

BNAT stands for Basic Neuroscience Advanced Training. We work closely with the UCD Neuroscience Program, providing support for 4 postdocs and advanced predocs. We offer training in all aspects of advanced basic neuroscience research, including electrophysiological and molecular biological techniques, and especially fluorescence imaging. The 15 BNAT faculty are drawn from five departments at the C.U. Medical School. Our trainees have exceptional research opportunities, for example, with sophisticated instruments in the Light and Electron Microscopy Facilities, and with advanced capabilities of the new Transgenic Vector Facility. In addition, the BNAT program sponsors:

  • An Imaging Course, Fluorophores and Microscopes
  • A biennial Teaching Workshop, Becoming a Teacher
  • A Journal Club/Seminar Series

Introduction.

The BNAT Program supports four trainees who are conducting research in the laboratories of BNAT Faculty members. Appointments begin July 1 and last for one year. They are renewable.

Eligibility

BNAT is an acronym for Basic Neuroscience Advanced Training. Our trainees are drawn from advanced graduate students and postdoctoral trainees working in BNAT labs.
Applicants must meet NIH guidelines for eligibility. This includes U.S. citizenship or green card holder, and fewer than three years of support from this or other NIH training grants (including National Research Service Award (NRSA).

Advanced usually means that an applicant has completed her/his comprehensive exam, although in some situations, such as MSTP students, applications may be accepted before the comprehensive exam is completed.

Selection Criteria

The most important criteria are your scientific qualifications, and the quality of your research proposal. In addition, the following may be considered:

  • Mix of trainees. We seek to have both pre- and post-doctoral trainees in the program.
  • Junior BNAT faculty. We seek to nurture and promote the research and training programs of junior faculty.
  • New research area. When established faculty change research directions or otherwise undertake new research projects, if pilot data appear promising, we favor applicants working on such projects.
  • History of support. We try to maintain a reasonably even distribution of trainees between trainers.
  • Emergency support. If a BNAT trainer temporarily loses a grant, and if that grant provides support for a trainee who meets the qualifications for joining the BNAT program, then we try to accommodate the trainee.

The BNAT Training Committee selects awardees. The committee comprises Angie Ribera, Tom Finger, Nathan Schoppa, Sukumar Vijayaraghavan, and Bill Betz (ex officio).

Application Process

The application deadline is May 1 of every year. Awards are announced June 1. Appointments begin July 1. Application Packages should be submitted electronically to the BNAT Director (bill.betz@ucdenver.edu). The Application Package should be prepared single-spaced, 12-point type, with one inch margins. Page limits for specific sections are indicated below.

Application Package

  • Applicant’s CV. Pre-doctoral applicants are to supply a copy of their Graduate School Transcript. Submitted by applicant.
  • Research project (Five pages or fewer, excluding References). The reference list should contain the full title of article/chapter. Submitted by applicant.
  • Career goals and description of the impact of the training on applicant’s career development (one page or less). Submitted by applicant.
  • Supporting letter from applicant's BNAT mentor. The letter should provide information about the current positions of previous BNAT trainees and the total number of trainees (BNAT and other) currently in the laboratory. The Mentor should indicate sources of funding for research during the proposed training period of the applicant. The Mentor should comment on the extent to which the applicant contributed to the development of the proposed research project. Submitted by faculty mentor.
  • Two supporting letters from qualified individuals. A post-doctoral applicant should obtain a reference letter from his/her thesis mentor. The most effective reference letters address the applicant’s qualifications for the proposed research project and assess the candidate's potential for a successful independent research career. Referees should rank the applicant with respect to intellectual capacity and research potential in comparison to previous trainees at a comparable career stage. Submitted by letter authors.

Kurt Beam
Professor

Physiology & Biophysics

Bill Betz
Professor and Chairman


Physiology & Biophysics

John H. Caldwell
Professor

Cell & Developmental Biology

Mark Dell'Acqua
Associate Professor

Pharmacology

Gidon Felsen
Assistant Professor

Physiology & Biophysics

Thomas E. Finger
Professor


Cell & Developmental Biology

Achim Klug
Assistant Professor


Physiology & Biophysics

Rock Levinson
Professor

Physiology & Biophysics

Cathy Proenza
Assistant Professor

Physiology & Biophysics

Diego Restrepo
Professor


Cell & Developmental Biology

Angeles Ribera
BNAT Director
Professor


Physiology & Biophysics

Bill Sather
Associate Professor


Pharmacology

Nathan Schoppa
Associate Professor


Physiology & Biophysics

Nick Seeds
Professor

Biochemistry & Molecular Genetics

Celia Sladek
Professor


Physiology & Biophysics

Dan Tollin
Assistant Professor

Physiology & Biophysics

Sukumar Vijayaraghavan
Professor

Physiology & Biophysics

Nancy Zahniser
Professor

Pharmacology

David Gire
Postdoctoral Fellow

Phone: 303-724-4525
E-mail: David.Gire@ucdenver.edu
Office Location: Research One North (RC1-North), Room 7403-G
Department: Physiology and Biophysics

 

Eric Larson
Predoctoral

Phone: 303-724-3008
E-mail: Eric.Larson@ucdenver.edu
Office Location: Research One North (RC1-North), Room 7404-G
Department: Physiology and Biophysics

Eric Larson is focused on a multi-protein signaling complex that regulates PKA phosphorylation of HCN4 ion channels in the mouse sinoatrial node.

 

No Photo

 

Clint Perry
Postdoctoral Fellow

Phone: 303-724-4527
E-mail: Clint.Perry@ucdenver.edu
Office Location: Research One North (RC1-North), Room 7404-A
Department: Physiology and Biophysics

Clint Perry is studying metacognition using a novel behavioral paradigm in rats. To what extent can rats assess their level of confidence in a senory dicision? Future studies will examine the neural mechanisms of metacognition by recording brain activity in animals performing the behavioral task.

 

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Kevin Woolfrey
Postdoctoral Fellow

Phone: 303-724-3612
E-mail: Kevin.Woolfrey@ucdenver.edu
Office Location: Research One North (RC1-North), Room 6402A
Department: Pharmacology

 


Fluorophores and Microscopes

The faculty of the Basic Neuroscience Advanced Training (BNAT) program offer a course called “Fluorophores and Microscopes.” The course features classroom sessions (lectures, student and faculty presentations) and didactic and independent laboratory work (utilizing the four advanced microscopes in the Light Microscopy Facility). This course is designed to provide both a theoretical background and practical experience for students in fluorescence microscopy and the use of exogenous and genetically engineered fluorophores.

Who: BNAT trainees and other PhD students, postdoctoral fellows, and faculty. Enrollment limited to 12.

When: Tue & Thu, 1.5 hrs each meeting; Spring semester, 2006. 29 sessions total. Time of day TBA.

Where: Neuroscience /Physiology & Biophysics conference room, RC1 north, 7th floor

Text: There is no required text. Copies of relevant textbooks will be made available as appropriate. Handouts, online materials, and original papers will also be provided.

Evaluation of students (by faculty) is according to performance on individual laboratory projects and classroom and laboratory participation. There are no written examinations. Evaluation of faculty (by students) is according to clarity of presentations, appropriateness of content, availability for and helpfulness of consultation.

Faculty: BNAT trainers: Drs. Beam, Betz, Ribera, Caldwell, Dell’Acqua,Finger, Levinson, Restrepo, Sather; BNAT trainee Dr. Joe Johnson, non-BNAT faculty: Dr. Nicholas Barry, Assistant Professor, Dept. of Medicine; Dr. Amy Palmer, Assistant Professor, Chemisty & Biochemistry (Boulder campus) Teaching Assistants: BNAT trainee Dan Sdrulla; Former BNAT trainee Dr. Ernie Salcedo; Light Microscopy Facility Manager Fadul; Other trainees Dr. Sophie Breusegem, Michael Gaffield, Marc Yonkers.

Content: The course is divided into seven parts. Part 1 is an overview of the entire course. It is largely didactic and relatively highly structured. Part 2 gives hands-on experience with advanced microscopes in the Light Microscopy Facility (LMF) or Electron Microscopy Facility (EMF). Part 3 is back in the classroom for discussion of special techniques. Part 4 involves faculty research seminars (presenters chosen by students). The focus is on advanced techniques (faculty lectures and student presentations). Parts 5-7 involve advanced topics and student lab projects that focus on technology, not biology, although students may use preparations of their choosing.

Administration. Anisha Phillips-Thomas, UCD at Fitzsimons, RC1 North Tower Room P18-7130. Phone: 303-724-4500. email: Anisha.phillips-thomas@ucdenver.edu

Schedule: FLUOROPHORES AND MICROSCOPES

PART I: Course overview. The first session, students will tour the LMF, which is directly adjacent to the classroom. The next 4 sessions will be an overview of the course, and provide the basic tools for understanding the sessions that follow.

Jan 24

Betz/Fadul

Introduction, tour of LMF (microscope demos by senior trainees)

Jan 26

Beam/Betz

Optics (diffraction limit, resolution, illumination, image formation, filter sets), Microscopes (conventional, laser scanning confocal, digital deconvolution, two photon, TIRF, STED-4pi)

Feb 2

Levinson/Johnson

Fluorescence (chemistry of fluorophores, excited state, emission and excitation spectra, photobleaching, other fluorescence phenomena)

Feb 7

Levinson/Palmer

Fluorophores (exogenous dyes, immunofluorescence, genetically encoded fluorescent proteins)

Feb 9

Restrepo/Barry

Image acquisition (CCD cameras, laser scanners), Image processing (enhancement, feature extraction)


PART II: Laboratory hands-on experience. Students will divide into 4 groups and rotate each week for 4 weeks to the 4 microscopes in the LMF. The objectives are to become familiar with using each instrument, and to understand in detail the principles by which they operate. A teaching assistant or faculty member will assist at each microscope. See http://lightmicroscopy.ucdenver.edu/ for a detailed description of the microscopes.

Feb 14

Lab

The 4 microscopes are:

  • Zeiss 510 NLO (two photon) Meta; HP Fluorimeter
  • Olympus TIRF
  • Deltavision Digital Deconvolution
  • Olympus spinning disk

Feb 16

Lab

Feb 21

Lab

Feb 23

Lab


PART III: Techniques. In these classroom sessions, the major techniques by which fluorophores are created and used will be discussed and (in some cases) demonstrated.

Feb 28

Caldwell/Sather

FRAP, FLIP, exogenous fluorophores

Mar 2

Sather/Beam/Dell’Acqua

FRET

Mar 7

Barry/Beam

FCS, FLIM (demo and discussion at 9th Avenue Campus (Moshe Levi’s lab – 4th floor, BRB)

Mar 9

Dell’Acqua/Ribera

Fluorescent proteins, tour of transgenic core facility

Mar 14

TBA

Other (e.g., 2nd harmonic generation, calcium imaging, quantum dots)


PART IV: Faculty research presentations. Faculty will present research seminars that illustrate the use of these optical techniques. Faculty will be selected by the students.

Mar 16

TBA

 

Mar 28

TBA

 

Mar 30

TBA

 

Apr 4

TBA

 


PART V: Student presentations. Each day for 4 sessions, 3 students will present an advanced topic, a journal article, or a proposal for his/her independent laboratory project. Each will rehearse with a faculty member, who will be present during the presentation.

Apr 6

Student presentations

 

Apr 11

Student presentations

 

Apr 13

Student presentations

 

Apr 18

Student presentations

 


PART VI: Student lab projects. Students will work on projects, either independently or in teams, using equipment in the LMF (or electron microscopy facility). Projects can be independently proposed, or chosen from a list. NOTE: Work does not have to be confined to class schedule, since the LMF is open 24/7, and students will be qualified users of the instruments.

Apr 20

Lab projects

Potential Projects (students may also design independent projects)

  • Point-spread function: Measure the PSF of two microscopes in the LMF
  • Bleedthrough: Given fixed material that is dually stained, measure the amount of emission ‘bleedthrough.’ Compare results with that obtained by using the Zeiss Meta.
  • FRET: Measure FRET of cameleon transfected into tissue culture cells.
  • FCS: Measure the diffusion coefficient of GFP in tissue culture cells (9th Ave campus), or fluorescent beads in media of different viscosities.
  • TIRF: Compare the Brownian movements of fluorescent beads of different sizes. Measure the airy Airy disk of diffraction-limited beads.
  • Confocality: Measure the effects on xy axis and z axis resolution by adding or removing the nipkow Nipkow disk in the Olympus spinning disk microscope.
  • Image processing: Given an image stack, examine methods of feature extraction (e.g., nodes of Ranvier, secretory granules).
  • Photobleach: Compare the effects of various anti-fade’ agents (e.g., Profade, Vectashield,Prolong on bleaching of fluorophores
  • Meta (Zeiss) versus fluorimeter: Measure emission spectra with both instruments and compare results
  • 2-photon imaging: image GFP transfected motor neurons in zebrafish embryos

Apr 25

Lab projects

Apr 27

Lab projects

May 2

Lab projects


PART VII: Student presentations. Students will present and discuss results from their laboratory projects (4 presentations per session)

May 4

Student presentations

Students will analyze results from their laboratory projects, rehearse with appropriate BNAT faculty, and then present their work in class.

May 9

Student presentations

May 11

Student presentations