Program XVth Course
Biomedical Research Techniques
October 31-November 4, 2016
Final vs 161024
PhD students (and others) often experience that not all expertise for biomedical techniques or assays they need to perform for their research project is readily available in their department. The organization of the Postgraduate school offers the wonderful opportunity to exchange this expertise. Therefore, the course ‘Biomedical Research Techniques’ is organized to create an overview of techniques routinely used in the various departments. This course is issued the 15th time after the big success of the previous ones.This course is also part of the Research MSc Infection & Immunity.
Site visits: planned on Wednesdaymorningafternoon and Thursday morning.Please register during the course. There are limited places available (max. 10/group).
The program is organized according to a logical order in 5 steps: DNA, RNA, Proteome, Cell, Tissue and Organ.
This implies the following program in 5 days:
Day 1: primers and probes, sequencing, SNP-analysis, methylation
Day 2: RNA, RNA expression arrays, RT PCR, siRNA, data mining
Day 3: proteomes, mass spectrometry; (afternoon) site visit core facilities labs genomics;
Day 4: (morning) site visits proteomics labs; (afternoon) Flow cytometry, ELISA & Cytotoxicity
Day 5: (morning) microscopy: quantitative confocal microscopy, image analysis, FRET, FRAP & computer modeling; (afternoon) Applied Molecular Imaging: MRI, CT, Nuclear, Optical in vivo
ECTS: when you are fully present, the course is rewarded with 1,5 ECTS.
Organized by Frank van Vliet. Thanks to all moderators for their support & advices to the program!
For details and registration: or contact Frank van Vliet: tel. +31(0)10 70 380 53; GSM +31(0)6 5474 6408;
First Day, Monday 31/10: primers and probes, sequencing, SNP-analysis, methylation
Moderator: Wilfred van IJcken, core facility Biomics
Room: Ae 4.06Time / Speaker / Title/ room
09.45 – 10.00 / Coffee & registration
10.00 – 10.15 / Wilfred van IJcken, core facility Biomics / Introduction and overview of techniques
10.15 – 10.45 / Wilfred van IJcken, core facility Biomics / General introduction of NGS techniques
10.45 – 11.30 / Jules Meijerink, Dept. of Paediatrics / PCR and RT PCR, (RQ-)PCR
11.30 – 11.45 / Coffee break
11.45 – 12.15 /
Susan Pas, Viroscience
/ Primer probes12.15 – 12.45 /
Joyce van Meurs, Dept. of Internal Medicine
/ SNP-analysis12.45 – 14.15 /
Lunchin Ee 3rd floor opposite to coffee bar
14.15 – 15.00 / Peter Verrijzer, Dept. of Biochemistry / Chromatin remodeling in development and disease15.00 – 15.15 / Coffee break
15.15 – 15.45 / Wilfred van IJcken, core facility Biomics / High throughput sequencing
15.45 – 16.15 / Erwin Brosens, Dept. of Clinical Genetics / Molecular cytogenetics: karyotyping, FISH, SNP arrays, Exon sequening
16.15 – 16.30 / Wilfred van IJcken / Evaluation and discussion
Second Day, Tuesday 1/11: RNA, RNA expression arrays, RT PCR, siRNA, datamining
Moderator: John Martens, Dept. of Medical Oncology
Room: Ae 4.06Time / Speaker / Title
No lunch; coffee at entrance
13.30 – 13.45 /
John Martens,Dept. of Medical Oncology
/ Introduction to the afternoon; overview of techniques13.45 – 14.15 / John Martens, Dept. of Medical Oncology / Introduction to next generation RNA- sequencing
14.15 – 14.30 / Coffee break
14.30 – 15.00 / John Martens, Dept. of Medical Oncology / Bioinformatic analysis of transcriptomes generated through RNA-seq
15.00 – 15.30 / Emma de Pater, Dept. of Hematology / A basic introduction in the CRISPR-Cas9 genome editing technology
15.30 – 15.45 / Coffee break
15.45 - 16.15 / Erik Wiemer, Dept.of Medical Oncology / MiRNA profiling and miRNA function
16.15 – 16.45 / Pim French,
Dept. of Neurology / OMICS techniques on degraded tissue samples
16.45 – 17.00 / John Martens / Evaluation and discussion
Third Day, Wednesday 2/11,morning:site visits to the core facilities genomics
NB all groups A, B, C & D have the same program!
Rooms: Site visit labsEe 6.87 Ee 6.91
Time / Speaker / Title
09.30– 10.15 / GROUP A: Genomics, Ee 6.87 (Christel Kockx)
GROUP B: Genomics, Ee 6.91 (Wilfred van IJcken)
Third Day, Wednesday 2/11, morning & afternoon: proteomes, mass spectrometry
Room: Ae 4.06
Time / Speaker / Title
Moderator: Jeroen Demmers, ProteomicsCenter
10.30 – 11.00 / Jeroen Demmers, ProteomicsCenter, Dept. of Biochemistry / Principles - Overview of available techniques for proteomics: basics, protein identification and quantitation and ana-lysis of post-translational modifications
11.00 – 11.30 / Karel Bezstarosti, ProteomicsCenter, Dept. of Biochemistry / Practical issues - Sample preparation, peptide and protein prefractionation techniques
11.30 – 11.45 / Coffee break
11.45 – 12.15 / Lennart van der Wal, Proteomics Center / Analysis of the dynamic ubiquitinome upon proteasome inhibition
12.15 – 12.30 / Jeroen Demmers, ProteomicsCenter / Evaluation and discussion
12.30 – 13.30 / Lunchin Ae 4.06
Moderator: Theo Luider, Dept. of Neurology & Clinical and Cancer Proteomics
13.30 – 14.00 / Peter Burgers, Dept. of Neurology / Mass spectrometry: how can it be used for medical research?
14.00 – 14.30 / Lennart Dekker, Dept. of Neurology / HPLC as front-end to mass spectrometry in proteomics
14.30 – 14.45 / Coffee break
14.45 – 15.15 / Diana Nijholt, Dept. of Neurology / Quantitative analysis of peptides and proteins by mass spectrometry
15.15 – 15.30 / Theo Luider, Dept. of Neurology / Evaluation and discussion
Third Day, Wednesday 2/11,afternoon:site visits to the core facilities genomics
NB all groups A, B, C & D have the same program!
Rooms: Site visit labs Ee 6.87 & Ee 6.91
Time / Speaker / Title
15.45 - 16.30 / GROUP C: Genomics, Ee 6.87 (Christel Kockx)
GROUP D: Genomics, Ee 6.91 (Wilfred van IJcken)
Fourth Day, Thursday 3/11, morning: Site visits to themass spectrometry facilities; all groups have the same program
Room: Ae-4.06& site visit labs
11.00 – 11.45 / GROUP A: ProteomicsCenter, Ee 6.26 (Jeroen Demmers/ Dick Dekkers)
GROUP B: ProteomicsCenter, Ee 6.26 (Karel Bezstarosti)
GROUP C: Neurology Department & Clinical and Cancer Proteomics, Ee 6.77 (Peter Burgers)
GROUP D: Neurology Department & Clinical and Cancer Proteomics, Ee 19.81 (Nick van Huizen)
11.45 – 12.30 / GROUP A: Neurology Department & Clinical and Cancer Proteomics, Ee 6.77 (Peter Burgers)
GROUP B: Neurology Department & Clinical and Cancer Proteomics, Ee 19.81 (Nick van Huizen)
GROUP C: Proteomics Center, Ee 6.26 (Jeroen Demmers/ Dick Dekkers)
GROUP D: ProteomicsCenter, Ee 6.26 (Karel Bezstarosti)
Fourth Day, Thursday 3/11, afternoon: Flow cytometry, ELISA & Cytotoxicity
Moderator: Reno Debets, Dept. Medical OncologyRoom: Ae 4.06
Time / Speaker / Title
12.30 – 13.30 / Lunchin Ae 4.06
13.30 – 14.00 / Reno Debets, Dept. of Medical Oncology / General introduction and overview of techniques
14.00 – 14.30 / Jaco Kraan, Dept. of Medical Oncology / Flow cytometry
14.30 – 15.00 / André Kunert, Dept. of Medical Oncology / ELISA
15.00 – 15.15 / Coffee break
15.15 – 15.45 / Wim Dik,Dept. of Immunology / Multiplex technologies
15.45 – 16.15 / Cor Berrevoets,
Dept. of Medical Oncology / Cytotoxicity
16.15 – 16.45 / Reno Debets, Dept. Medical Oncology / Evaluation and discussion; when to use which technique for cell analysis
Fifth Day, Friday 4/11, morning: Microscopy, Quantitative confocal microscopy, 4 Pi microscope, FRET, FRAP & computer modeling
Moderator: Gert van Cappellen, Dept. of Reproduction & Development, OIC
Room: Ae 4.06Time / Speaker / Title
09.30 – 10.00 / Gert van Cappellen, Dept. of Pathology/OIC / Introduction of the Erasmus Optical Imaging Centre (OIC)
10.00 – 10.30 / Gert-Jan Kremers, Dept. of Pathology/OIC / Introduction to fluorescent microscopy, machines and dyes
10.30 – 10.45 / Coffee break
10.45 – 11.15 / Adriaan Houtsmuller, Dept. of Pathology/OIC / Live cell imaging, the F-techniques (FRAP, FRET etc.)
11.15 – 11.45 / Johan Slotman, Dept. of Pathology/OIC / Super resolution microscopy (SIM, PALM, STORM etc
11.45 – 12.15 / Ihor Smal, Dept. of Medical Informatics & Radiology / Image analysis
12.15 – 13.00 / Lunchin Ae 4.06
Fifth Day, Friday 4/11,afternoon: Applied Molecular Imaging: Ultrasound, MRI, CT, Nuclear, Optical in vivo
Moderator: Joost Haeck, Dept. of Nuclear medicine
Room: Ae-406
Time /
Speaker
/ Title13.00 – 13.15 / Joost Haeck, Dept. of Nuclear medicine / Introduction and overview of techniques
13.15 – 13.45 / Ann Seynhave, Dept. of Surgical Oncology / Intravital Imaging: real time examination in vivo
13.45 – 14.15 / Klazina Kooiman, Dept. of Biomedical Engineering / Ultrasound molecular imaging: oncology & cardiology applications
14.15 – 14.30 / Coffee break
14.30 – 15.00 / Marcel van Straten, Dept. of Radiology / CT
15.00 – 15.30 / Joost Haeck, Dept. of Nuclear medicine / MRI
15.30 – 15.45 / Coffee break
15.45 – 16.15 / Jan de Swart, Dept. of Nuclear medicine / Nuclear Imaging
16.15 – 16.30 / Joost Haeck, Dept. of Nuclear medicine / Evaluation and discussion
16.30 - … / Drinks for all participants and speakers of the BRT course
Attendance fees
The subscription fee of non-commercial participants for the Course is €650. This is also the fee when the participants pay the fee from his/her ‘personal budget’.
All participants from MolMedand Res. master I&I get a discount of 100 % and pay €0.
PhD studentshave 50% discount and pay €325.
For other Research master students we calculate €100/ECTS so €150.
Research master students who pay it themselves have 75% discount and pay €162,50.
If these financial requirements pose a problem but you wish to attend the Course, please contact Frank van Vliet, managing director of the Erasmus Postgraduate School Mol Med, at: .
Invoice
Fees can be paid upon an INVOICE. Shortly after your registration you will receive the INVOICE per mail. Payment per bank can be done together with the number on your INVOICE.
Late participants can also pay in cash upon signing in for the Course.
Cancellations
The fees are for all the days of the Course. There is no discount for partaking only in part of the Course. Our cancellation policy is that cancellation is possible up to one week before the start of the Course. Later cancellation will not be accepted, but you are allowed to send a substitute.
Commercial participants & sponsors
Companies are invited to inquire for participation and sponsoring.
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