STUDY BOOK PhD Programme for Non-Medical Students

Transcription

1 STUDY BOOK PhD Programme for Non-Medical Students Medical Faculty of the University Medical Centre Hamburg-Eppendorf

2 PhD Programme for non-medical students at the Medical Faculty This study guide gives an overview of the curriculum of the PhD Programme for nonmedical 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 for their coursework during the three years (see specifics below). The programme is divided into a compulsory and an optional part 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). 2

3 2.3. Credit 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 the PhD students can choose freely between the different courses. For more information about the Study Book please contact Dr. Anne Wulf ([email protected]); Tel: Antke Wolter ([email protected]); Tel: Further information available at the website of the PhD Programme 3

4 KEY SKILLS ACADEMIC KEY SKILLS SEMINARS Advanced Writing Skills for Science and Research Academic key skill seminar External lecturer General goal of this course is the professionalization of written English skills specifically for publication of scientific research. 2 days from 9 am to 5 pm - compulsory subject Participants max. 12 good English skills are of advantage but are not a requirement 1 credit point at the beginning of the PhD Programme 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. Deanery 4

5 KEY SKILLS Presentation Skills for Science and Research Academic key skill seminar External lecturer General goal of this course is the professionalization of presentations in English specifically for scientific research. 3 days from 9 am to 5 pm - compulsory subject Participants max. 12 good English skills are of advantage but are not a requirement 2 credit points at the beginning of the PhD Programme 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. Deanery 5

6 KEY SKILLS Good Scientific Practice Academic key skill seminar External Lecturer 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. 2 days from 9 am to 5 pm Guidelines for good scientific practice by the German Research Foundation (DFG) and the University of Hamburg. compulsory subject Participants max credit point preferably at the beginning of the PhD Programme 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 Deanery 6

7 KEY SKILLS Participants Funding instruments Academic key skill seminar External and internal lecturers The workshop will communicate fundraising knowledge from the strategic initial considerations to the funding application. 1-2 days compulsory subject 1 credit point 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. Deanery 7

8 KEY SKILLS Participants Project management Academic key skill seminar External lecturer Students are introduced to major principles of efficient project management and offered various tools for planning, controlling and managing projects. 2 days compulsory subject 1 credit point Deanery 8

9 KEY SKILLS Workshops offered by other graduate schools/ graduate programme or external providers Academic key skill seminar N.N Participants N.N N.N. dependent on length of the class Following graduate schools and programmes cooperate with the PhD Programme: - Integrated graduate programme of SFB Integrated graduate programme of SFB Graduate programme GRK 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 Integrated graduate programme of SFB 841 Integrated graduate programme of SFB 936 Graduate programme GRK 1459 Graduate school Hamburg school for structure and dynamics in infection SDI Graduate school neurodapt! Graduate programme CINACS Career Center from the University Hamburg Graduate Programme Molecular Biology 9

10 INTERDISCIPLINARY COURSES INTERDISCIPLINARY COURSES Statistics seminar Interdisciplinary courses Department of Medical Biometry and Epidemiology 3 days - Participants compulsory subject unlimited credit points wird von Wegscheider geliefert Deanery 10

11 INTERDISCINIPLARY COURSES Publication process Interdisciplinary courses N.N. Young scientists receive an overview over the different aspects of the publication process. 1 day - Participants compulsory subject unlimited - 1 credit point at the end of the PhD Programme 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. Deanery 11

12 INTERDISCIPLINARY COURSES - Colloquium of doctoral candidates Interdisciplinary courses Students should give their first presentation and get the opportunity to interact with each other. - Participants compulsory subject unlimited - 1 credit point at the beginning of the PhD Programme 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. Deanery 12

13 INTERDISCIPLINARY COURSES Conference participation Interdisciplinary courses - dependent on the topic of the conference at least 1 day - Participants compulsory subject unlimited - 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) dependent on the topic of the conference. Students can visit all types of scientific conferences. - 13

14 INTERDISCIPLINARY COURSES Department Seminars / Institute Seminars Interdisciplinary courses N.N. dependent on the topic of the seminar students have to visit at least 10 seminars to receive 1 credit point - Participants unlimited - 1 Credit Point for 10 seminars 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. please contact your department for further information 14

15 INTERDISCIPLINARY COURSES - Organization + Attendance UKE Research Day of Young Scientists Interdisciplinary courses The event should give students the opportunity to organize a minisymposium and to present their research outcome to a broader scientific community. 1 day - Participants unlimited - 3 credit points at the end of the PhD programme 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. Deanery 15

16 INTERDISCIPLINARY COURSES Journal Clubs Interdisciplinary courses N.N. dependent on the topic of the Journal Club Students have to visit 10 Journal Clubs to get 1 Credit Point - Participants credit point for participating at least at 10 meetings of the journal club - please contact your department for further information 16

17 INTERDISCIPLINARY COURSES All-day advanced training Interdisciplinary courses Internal or external provider of the seminar dependent on the topic of the seminar at least 1 day dependent on the topic of the seminar Participants credit point dependent on the topic of the seminar - 17

18 RESEARCH METHOD COURSES RESEARCH METHOD COURSES Histological analysis of mouse tissue- from antigen retrieval to stereological evaluation Research method course Dr. Melanie Neumann Introduction in immunohistochemistry using paraffin embedded histological specimen 2,5 days script Participants max. 5 none 2 credit points 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 lightmicroscopy and to quantify a cell population within the tissue with the help of a stereological system. Dr. Melanie Neumann ([email protected]); Tel:

19 RESEARCH METHOD COURSES AAV vector production and ips cell techniques Research method course Dr. Sandra Laufer, Dr. Aya Shibamiya, Dr. Ingke Braren, Dr. Michaela Miehe Theoretical and practical introduction into AAV vectors and induced pluripotent stem cells (ips cells) 3,5 days script Participants max. 3 scientific project in the field of vector production or stem / ips cells; cell culture experience 2 credit points 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. Dr. Sandra Laufer ([email protected]), Dr. Aya Shibamiya ([email protected]), Dr. Ingke Braren ([email protected]), Dr. Michaela Miehe ([email protected])

20 RESEARCH METHOD COURSES Advanced imaging methods Research method course Dr. Antonio Virgilio Faila, Dr. Bernd Zobiak Introduction into advanced imaging methods 2 days script Participants max. 3 none 2 credit points 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. Dr. Antonio Virgilio Failla ([email protected]), Tel: Dr. Bernd Zobiak ([email protected]); Tel:

21 RESEARCH METHOD COURSES Applied Bioinformatics Research method course Malik Alawi Bioinformatics techniques for laboratory use 2 days script Participants none 2 credit points 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. Malik Alawi ([email protected]); Tel:

22 RESEARCH METHOD COURSES Introduction to Flow-Cytometry with concrete applications Research method course Prof. Fehse, other PIs of the institute Regine Thiele, Melanie Lachmann Theoretical and practical introduction in flow cytometry 1,5 days script Participants max. 6, splitted for practical part (max. 3) none 1,5 Credit 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. Regine Thiele Tel.: Melanie Lachmann Tel:

23 RESEARCH METHOD COURSES Production, purification and conjugation of antibodies Research method course Prof. Friedrich Nolte Learn to produce, purify, and conjugate antibodies for laboratory use 2 days script Participants 2-4 none 2 credit points 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.colilysates (sdabs). The class will further demonstrate how to conjugate purified antibodies to fluorochrome and biotin. Dr. Friedrich Koch-Nolte ([email protected]); Tel:

24 RESEARCH METHOD COURSES Minimal residual disease - Methods to detect and characterize rare cells in the blood of tumour patients Research method course Dr. Sabine Riethdorf, Oliver Mauermann Theoretical and practical introduction into different methods to enrich, detect and characterize circulating tumour cells 2 days Script Optional subject Participants 2 or 4 Scientific project in oncology 2 credit points 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. Dr. Sabine Riethdorf ([email protected]); Tel.: ; Oliver Mauermann ([email protected]), Tel.:

25 RESEARCH METHOD COURSES Participants Lab courses for learning special techniques Research method course N.N dependent on the subject 1-2 credit points 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. respective provider 25

26 RESEARCH METHOD COURSES Participants Method seminars Research method course N.N dependent on the subject 1-2 credit points 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. respective provider 26

27 RESEARCH METHOD COURSES Participants Equipment tutorial Research method course N.N dependent on the subject 1-2 credit points 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. respective provider 27

28 RESEARCH METHOD COURSES Participants Workshops offered by other graduate schools/ graduate programmes Research method course N.N N.N N.N. dependent on length of the class Following graduate schools and programmes cooperate with the PhD Programme: - Integrated graduate programme of SFB Integrated programme of SFB Graduate programme GRK 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 Websites of the graduate programmes: Integrated graduate programme of SFB 841 Integrated graduate programme of SFB 936 Graduate programme GRK 1459 Graduate school Hamburg school for structure and dynamics in infection SDI Graduate school neurodapt! Graduate programme CINACS Graduate programme Molecular Biology 28