STUDY BOOK PhD Programme for Non-Medical Students

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STUDY BOOK

PhD Programme

for Non-Medical Students

Medical Faculty of the

University Medical Centre

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PhD Programme for non-medical students at the Medical Faculty

This study guide gives an overview of the curriculum of the PhD Programme for

non-medical students offered by the Medical Faculty of the University Hamburg.

1. Degree

.After completion of the three-year programme the students receive a PhD degree or

as equivalent the German Dr. rer. biol. hum.

2. PhD Coursework Requirements

Coursework of the PhD programme includes three different types of courses:



Academic key skills seminars



Interdisciplinary courses



Research method courses

Completion of the coursework is a prerequisite for receiving a PhD degree at the end

of the programme. In total, the PhD students are required to obtain 30 Credit Points

for their coursework during the three years (see specifics below).

The programme is divided into a

compulsory

and an

optional

part.

2.1. Compulsory Coursework

PhD students have to complete the following courses:

Key Skills Seminars



Advanced Writing Skills for Science and Research,



Presentation Skills for Science and Research



Good Scientific Practice



Funding instruments



Project management

Interdisciplinary courses



Seminar: Statistics



Seminar: Publication process



Colloquium of doctoral candidates



Conference participation

2.2. Optional Coursework

As optional part of the course programme PhD students can choose from a variety of

classes either offered by the Faculty and UKE institutes (e.g. journal clubs, core

facility workshops) or by institutions like the Career Center of the University of

Hamburg (e.g. different key skill seminars).

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2.3. Credit Points

For each of the seminars or workshops credit points will be assigned (see also figure

below).In each of the three different programme parts (academic key skills seminars,

interdisciplinary seminars and research method courses) a certain number of credit

points have to be obtained:



at least 7 CP in the academic key skill course part



at least 9 CP in the interdisciplinary course part



at least 2 CP in the research methods course part

For the remaining 12 Credit Points the PhD students can choose freely between the

different courses.

For more information about the Study Book please contact

); Tel: 040 7410-53041

); Tel: 040 7410-51834

Further information available at the website of the PhD Programme

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ACADEMIC KEY SKILLS SEMINARS

Study Programme Advanced Writing Skills for Science and Research

Module type Academic key skill seminar Responsible Lecturer External lecturer

Study Objective General goal of this course is the professionalization of written English skills specifically for publication of scientific research.

Length 2 days from 9 am to 5 pm

Literature -

Classification compulsory subject

Participants max. 12

Prerequisites good English skills are of advantage but are not a requirement

Points 1 credit point

Semester at the beginning of the PhD Programme

Course description The seminar is divided in two parts. The basic knowledge and vocabulary needed for independent writing of a successful cover letter to a publication, a short biography and descriptions of methods and or data will be developed on day one. The results of this work will be expanded on for a publication abstract and feedback with some proofreading skills which will be practiced and discussed during day two.

Specific areas of emphasis in the course include the non-personal scientific style, scientific vocabulary, language and cultural difference, language interference, academic writing styles, proposal organization and syntax skills.

Resource materials and strategies for verifying the specificity and correctness of specialty vocabulary for scientific papers and publications will be made available to the participants and discussed. These materials can be used by the participants to continue improvement of writing skills after the seminar.

A proposal in the scientist’s special area of research should be written for the course. The style and tone of an advantageous biographical statement accompanying a paper submitted to a professor will also be dealt with.

Contact Deanery

KEY

S

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Study Programme Presentation Skills for Science and Research

Study Objective General goal of this course is the professionalization of presentations in English specifically for scientific research.

Literature -

Prerequisites good English skills are of advantage but are not a requirement

Points 2 credit points

Course description The seminar is divided in three parts. The basic knowledge and vocabulary needed for independent, scientific presentation in English will be developed on day one.

The results of this work will be expanded on, practiced and discussed during day two.

Then the participants have time to prepare their own presentation about their area of research for a presentation with peer and lecturer feedback on day three.

The seminar is very hands-on, which means the scientists will be expected to practice new skills in the seminar and will be given specific feedback and tips on strategies to improve their texts.

Each presentation skill includes a hand out which will be discussed and used as a jumping off point for an exercise in the specific skill needed while, for the most part, using vocabulary from the scientist’s medical specialty. This specificity of the vocabulary is made possible by making internet resources available so that the scientists can review their vocabulary and phrases in the online literature before putting them to on slides.

Most of the exercises in the seminar will be in groups of two or three, although some of the exercises include the entire group. This facilitates the use of peer feedback in addition to the lecturer’s feedback.

Contact Deanery

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Study Programme Good Scientific Practice

Module type Academic key skill seminar Responsible Lecturer External Lecturer

Study Objective This seminar is a fundamental introduction to the principles for safeguarding good scientific practice as proposed by the Deutsche Forschungsgesellschaft (DFG) and the University of Hamburg.

Literature Guidelines for good scientific practice by the German Research Foundation (DFG) and the University of Hamburg.

Prerequisites -

Semester preferably at the beginning of the PhD Programme

Course description Guidelines for good scientific practice will be presented to the PhD candidates at the beginning of their PhD Programme. The guidelines are based on the general guidelines by the German Research Foundation (DFG) and the University of Hamburg.

Topics covered are for example:

- scientific misconduct

- data management

- intellectual property

- responsibilities of PhD students and supervisors

- ethical regulations Contact Deanery

KEY

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Study Programme Funding instruments

Module type Academic key skill seminar Responsible Lecturer External and internal lecturers

Study Objective The workshop will communicate fundraising knowledge from the strategic initial considerations to the funding application.

Length 1-2 days

Literature to be determined

Participants to be determined

Prerequisites to be determined

Semester flexible

Course description This seminar addresses tips and strategies on how to get funding for research projects. Emphasis should be given on both practical and conceptual aspects that are important to the proposal-writing of young researchers. The Deanery plans to involve PIs from UKE and funding agencies like DFG or BMBF in the seminar.

Contact Deanery

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Study Programme Project management

Study Objective Students are introduced to major principles of efficient project management and offered various tools for planning, controlling and managing projects.

Length 2 days

Semester flexible Course description to be determined

Contact Deanery

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KILLS

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Study Programme Workshops offered by other graduate schools/ graduate programme or external providers

Module type Academic key skill seminar Responsible Lecturer N.N

Study Objective

Length N.N

Literature N.N.

Classification optional subject

Points dependent on length of the class

Semester flexible

Course description Following graduate schools and programmes cooperate with the PhD Programme:

- Integrated graduate programme of SFB 841 - Integrated graduate programme of SFB 936 - Graduate programme GRK 1459

- Graduate school SDI - Graduate school neurodapt - Graduate programme CINACS

- Graduate programme Molecular Biology

Workshops from following external providers can be visited: - Career Center from the University Hamburg

- Others if approved by the Faculty

Information about the classes will be either announced at the websites of the programmes and external provider or can be received from the programme managers. Interested PhD-students should contact latter ones directly for free capacity in the classes

Contact        

KEY

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INTERDISCIPLINARY COURSES

Study Programme Statistics seminar

Module type Interdisciplinary courses

Responsible Lecturer Department of Medical Biometry and Epidemiology Study Objective

Length 3 days

Literature -

Participants unlimited Prerequisites -

Points 1-2 credit points

Semester flexible Course description wird von Wegscheider geliefert

Contact Deanery

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Study Programme Publication process

Module type Interdisciplinary courses Responsible Lecturer N.N.

Study Objective Young scientists receive an overview over the different aspects of the publication process.

Length 1 day

Literature -

Semester at the end of the PhD Programme

Course description Experienced PIs, editors and reviewers will share their insights on how to choose the right journal, how journal editors think, how the review process works, and how to maximize the likelihood that your manuscript will be published.

Contact Deanery

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Study Programme Colloquium of doctoral candidates

Module type Interdisciplinary courses Responsible Lecturer -

Study Objective Students should give their first presentation and get the opportunity to interact with each other.

Length

Literature -

Course description Student groups will be formed based on the topic of the conducted research projects and each student will present the research outlines of his or her PhD thesis.

Contact Deanery

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Study Programme Conference participation

Study Objective dependent on the topic of the conference

Length at least 1 day

Literature -

Points 1 credit point for participation

+ 1 credit points for poster presentation at the conference (optional) + 2 credit points for talk at the conference (with or without poster presentation) (optional)

Semester flexible

Course description dependent on the topic of the conference. Students can visit all types of scientific conferences. Contact -

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Study Programme Department Seminars / Institute Seminars

Module type Interdisciplinary courses Responsible Lecturer N.N.

Study Objective dependent on the topic of the seminar

Length students have to visit at least 10 seminars to receive 1 credit point Literature -

Points 1 Credit Point for 10 seminars

Semester flexible

Course description dependent on the topic of the seminar: students can visit all seminars of the institutes at the UKE. Information about these seminars is available at the department homepages.

Contact please contact your department for further information

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Study Programme Organization + Attendance “UKE Research Day of Young Scientists”

Study Objective The event should give students the opportunity to organize a mini-symposium and to present their research outcome to a broader scientific community.

Length 1 day

Literature -

Semester at the end of the PhD programme

Course description Using the Moodle system third-year students can connect with each other to organize a mini-symposium where they present the findings of their research projects and may invite external speakers. The event will be supported by the Deanery.

Contact Deanery

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Study Programme Journal Clubs

Responsible Lecturer N.N.

Study Objective dependent on the topic of the Journal Club

Length Students have to visit 10 Journal Clubs to get 1 Credit Point Literature -

Participants - Prerequisites -

Points 1 credit point for participating at least at 10 meetings of the journal club

Semester flexible

Course description -

Contact please contact your department for further information

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Study Programme All-day advanced training

Responsible Lecturer Internal or external provider of the seminar Study Objective dependent on the topic of the seminar

Length at least 1 day

Literature dependent on the topic of the seminar

Participants - Prerequisites -

Semester flexible

Course description dependent on the topic of the seminar Contact -

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RESEARCH METHOD COURSES

Study Programme Histological analysis of mouse tissue- from antigen retrieval to stereological evaluation

Module type Research method course

Responsible Lecturer Dr. Melanie Neumann

Study Objective Introduction in immunohistochemistry using paraffin embedded histological specimen

Length 2,5 days

Literature script

Participants max. 5

Prerequisites none

Semester flexible

Course description Histological analysis is the method of choice, if you want to localize a protein within a given tissue or even within a single cell. Moreover, with the help of a stereological device it is possible to quantify cell populations within a tissue compartment and to determine deregulations of proteins in transgenic or knockout mouse models as well as changes after injury and disease.

This class will give you an overview about how to prepare a tissue for histological analysis. You will learn to process histological specimens including paraffin-embedding, cutting with a microtome, and H&E staining. Also you will do a classical immunohistochemical staining, where you will get to know different methods of antigen retrieval to improve the immunoreactivity of formalin-fixed tissue. Last but not least, you will learn to document your results using light-microscopy and to quantify a cell population within the tissue with the help of a stereological system.

Contact 58492

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Study Programme AAV vector production and iPS cell techniques

Responsible Lecturer Dr. Sandra Laufer, Dr. Aya Shibamiya, Dr. Ingke Braren, Dr. Michaela Miehe

Study Objective Theoretical and practical introduction into AAV vectors and induced pluripotent stem cells (iPS cells)

Length 3,5 days

Literature script

Participants max. 3

Prerequisites scientific project in the field of vector production or stem / iPS cells; cell culture experience

Semester flexible

Course description This class is a theoretical and practical introduction into AAV vectors and induced pluripotent stem cells (iPS cells). Topics covered include the transfection of HEK293 cells with plasmids for AAV vector production and the harvest of viral supernatant and subsequent transduction of target cells. Furthermore, students will be instructed into passaging and in vitro differentiation of iPS cells.

Contact Dr. Sandra Laufer (),

Dr. Aya Shi Dr. Ingke Braren ( Dr. Michaela Miehe ()

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Study Programme Advanced imaging methods

Responsible Lecturer Dr. Antonio Virgilio Faila, Dr. Bernd Zobiak Study Objective Introduction into advanced imaging methods

Length 2 days

Literature script

Participants max. 3

Prerequisites none

Semester flexible

Course description This workshop will introduce students in the basic technicques and applications of bright field /epifluorescence and confocal laser scanning microscopy. Recent imaging technologies will be presented (TIRFM, Spinning Disk, Multiphotone, Superresolution). During the class, students will prepare 2D/3D pictures. Furthermore, they will prepare probes for multi-dimensional time-lapse microscopy and will perform a 5D analysis of the results.

Contact Dr. Antonio Virgilio Failla (

51984 ); Tel: 040 7410-51984

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Study Programme Applied Bioinformatics

Responsible Lecturer Malik Alawi

Study Objective Bioinformatics techniques for laboratory use

Length 2 days

Literature script

Participants 10-14 Prerequisites none

Semester flexible

Course description The workshop focuses on bioinformatics techniques for laboratory use. Hands-on exercises include retrieving information from public databases, primer design, searching sequence databases with BLAST. Furthermore the workshop introduces possibilities for multiple sequence alignments like: ClustalW and MAFFT. The class also covers resources for information about protein families like TIGRFAM, SMART and HMMER.

Contact ); Tel: 040 48051-288

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Study Programme Introduction to Flow-Cytometry with concrete

applications

Responsible Lecturer Prof. Fehse, other PIs of the institute Regine Thiele, Melanie Lachmann

Study Objective Theoretical and practical introduction in flow cytometry

Length 1,5 days

Literature script

Participants max. 6, splitted for practical part (max. 3) Prerequisites none

Points 1,5 Credit Points

Semester flexible

Course description This course will give an introduction in flow cytometry methods. The theoretical part of the class will cover the technique behind the method (scatter, fluorescence, compensation etc). It will also give an in-depth overview of different sample preparations like Ag-Ab-reactions and dyes. In the practical part of the class, students will perform different cell stainings and later analyze the cells at the FACS CantoII. Students will be specially introduced in the use of the FACSDiVA software. They can also bring their own cells for the experiments. As optional part, the class further covers the cell-sorter FACS Aria.

Contact Regine Thiele (

Melanie Lachmann ( 52306

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Study Programme Production, purification and conjugation of antibodies

Responsible Lecturer Prof. Friedrich Nolte

Study Objective Learn to produce, purify, and conjugate antibodies for laboratory use

Length 2 days

Literature script

Participants 2-4 Prerequisites none

Semester flexible

Course description Polyclonal (pAbs), monoclonal (mAbs) and recombinant single domain antibodies (sdAbs) are important experimental tools. For production of antibodies, the starting material (synthetic peptide, cDNA, V-regions) and protocols (immunization of animals, hybridoma technique, phage display technique) depend on the aimed antibody type.

This course will give a theoretical introduction in the production process. In the practical part you will learn how to purify antibodies from immune sera (pAb)s, hybridoma supernatants (mAbs, fusionproteins from sdAbs) and E.coli-lysates (sdAbs).

The class will further demonstrate how to conjugate purified antibodies to fluorochrome and biotin.

Contact Dr. Friedrich Koch-Nolt); Tel: 040

7410-53612

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Study Programme _{Minimal residual disease - Methods to detect and}

characterize rare cells in the blood of tumour patients

Responsible Lecturer _{Dr. Sabine Riethdorf, Oliver Mauermann}

Study Objective _{Theoretical and practical introduction into different methods} to enrich, detect and characterize circulating tumour cells

Length _{2 days}

Literature _Script

Classification Optional subject

Participants _{2 or 4}

Prerequisites _{Scientific project in oncology}

Points _{2 credit points}

Semester _flexible

Course description This course will give a theoretical introduction in the molecular basics of the metastatic process as well as a practical and theoretical excursion in the different techniques that are available to detect and characterize circulating tumour cells.

The practical part of the course is variable and will be adapted to the student’s needs, which will be discussed in a short meeting 2-3 weeks before the start of the course. It may contain a demonstration of the FDA-approved CellSearch System, sample preparation with different enrichment methods (such as Ficoll-density gradient, magnetic bead enrichment, erythrocyte lysis protocols), the detection of rare tumour cells by immunocytochemistry or immunofluorescence, or an introduction in the molecular analysis of a single cell by PCR-techniques after micromanipulation.

Contact

52628;

Oliver Maue), Tel.:

040-7410-57417

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Study Programme Lab courses for learning special techniques

Responsible Lecturer N.N

Study Objective dependent on the subject

Length to be determined

Semester flexible

Course description Other lab courses than the ones offered by the core facilities can be credited to the curriculum. Claims for recognition of the coursework should be submitted to the Deanery. After passing the initial check, the Promotionsausschuss will recognize the coursework based on the necessary workload.

Contact respective provider

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Study Programme Method seminars

Semester flexible

Course description A seminar covering a specific method can be credited to the curriculum. Seminars that cover a regularly applied method in the lab of the requesting student and are taught by a member of the group are usually exempted from recognition. Claims for recognition of the coursework should be submitted to the Deanery. After passing the initial check, the

Promotionsausschuss will recognize the coursework based

on the necessary workload.

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Study Programme Equipment tutorial

Semester flexible

Course description Equipment tutorials can be credited to the curriculum, if the tutorial refers to a highly technologically advanced technique and last several days. Exempted from recognition are usually tutorials which refer to a regularly used technique in the lab of the requesting student. Claims for recognition of the coursework should be submitted to the Deanery. After passing the initial check, the Promotionsausschuss will recognize the coursework based on the necessary workload.

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Study Programme Workshops offered by other graduate schools/ graduate

programmes

Responsible Lecturer N.N Study Objective

Length N.N

Literature N.N.

Points dependent on length of the class

Semester flexible

Course description Following graduate schools and programmes cooperate with the PhD Programme:

- Integrated graduate programme of SFB 841 - Integrated programme of SFB 936

- Graduate programme GRK 1459 - Graduate school SDI

- Graduate school neurodapt - Graduate programme CINACS

- Graduate programme Molecular Biology

Information about the classes will be either announced at the websites of the programmes or can be received from the programme managers. Interested PhD-students should contact latter ones directly for free capacity in the classes

Contact Websites of the graduate programmes:

      

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