a During this week the students get acquainted with the following equipment: RNA analyzer (Agilent 2100 Bioanalyzer, Agilent Technologies), spotter (MicroGrid II, Biorobotics), scanner (ScanArray Lite, GSI Lumonics, Packard Bioscience), and a real-time PCR instrument (LightCycler, Roche Diagnostics).
A specialized training year in post-genomics for highly skilled technicians
Article first published online: 3 NOV 2006
Copyright © 2003 International Union of Biochemistry and Molecular Biology, Inc.
Biochemistry and Molecular Biology Education
Volume 31, Issue 6, pages 437–439, November 2003
How to Cite
Loncle, D. and Rossier, J. (2003), A specialized training year in post-genomics for highly skilled technicians. Biochem. Mol. Biol. Educ., 31: 437–439. doi: 10.1002/bmb.2003.494031060301
- Issue published online: 3 NOV 2006
- Article first published online: 3 NOV 2006
- Manuscript Received: 17 OCT 2003
With the recent availability of the complete DNA sequence of various genomes, a new biological discipline, functional genomics, has emerged in the last few years. This new discipline generates a high demand for skilled persons at various levels of competencies. In this article, we describe our new curriculum for training skilled technicians in this new discipline. The goal of our teaching program in functional genomics is, within a 1-year period, to train technical engineers in new techniques and the operation of recently developed instrumentation (e.g. mass spectrometry, DNA sequencers, and DNA arrays). At the end of the training period, the trainees should be able to analyze the raw data generated and be comfortable with the daily use of several basic tools in bioinformatics. The teaching pedagogy emphasizes a critical approach of the new technology leading the students to autonomy.
This program has been in existence for 2 years of existence and has started its third year in the Fall of 2003. Therefore, it time to make an appraisal. Each year, 12 students, of a mean age of 20.5 years, were enrolled for a 10-month program. They were already trained in basic biochemical analysis and held the diploma of senior technician (Brevet de Technicien Supérieur, B.T.S., a national diploma in the French education system, equivalent to the diploma given in U. S. community colleges) or a Bachelor's degree in technology from a university. All the students enrolled had at least 2 years of higher education experience after graduating from high school.
The school, Ecole Nationale de Chimie, Physique et Biologie (ENCPB),11 or National School of Chemistry, Physics and Biology, is located on the left bank of Paris, in close vicinity to prestigious graduate schools and universities. The school is large and enrolls 2000 students, half of whom are in the programs that award the national B.T.S. diploma in applied science. The 250 teachers at the school devote their time solely to teaching, while remaining in close contact with the professional sector (including industry, laboratories, and hospitals). ENCPB is at the forefront of the technical educational system in France and more details on the school can be obtained at www.encpb.org.
Since the inception of the program, most of the students who were enrolled in the ENCPB were coming from our school. They were, indeed, known by us for their good past performance in their school curriculum and their motivation. We are now ready to accept more students from other schools, including foreign students.
Functional genomics, with its ancillary disciplines, bioinformatics, transcriptomics, and proteomics, is evolving rapidly and could not be taught easily in traditional schools and colleges. Indeed, teaching practical functional genomics requires access to expensive instruments such as DNA sequencers, DNA spotters and readers, matrix-assisted laser desorption ionization (MALDI) and electrospray ionization quadrupole time-of-flight (ESI-Q TOF) mass spectrometers. The price tags of these instruments go far beyond the usual budget of a strictly teaching institution. It was, therefore, imperative to cooperate with a well-established center for functional genomics in the vicinity of the school. The center that was found was a nearby graduate school, the Ecole Supérieure de Physique et de Chimie Industrielles (ESPCI). This school is closely associated with the Centre National de la Recherche Scientifique and is proud to have counted Pierre Curie as one of its former professors. Indeed, it was at this school that Pierre and Marie Curie isolated radium, and several of the teachers at the school were Nobel Laureates in physics or chemistry. More details on this graduate school can be obtained at www.espci.fr.
The implementation of this new discipline in functional genomics has relied on the close collaboration of the two authors of this article. Daniel Loncle is Professor and head of the senior technician biotechnology curriculum at ENCPB. Jean Rossier is Professor and head of a research biological laboratory at ESPCI. His laboratory is very much involved in transcriptomics and proteomics. Details on the laboratory of Professor Jean Rossier can be obtained at www.bio.espci.fr.
At the end of the year 2000, both of us realized that the rapid development of functional genomics was hampered by the lack of trained technicians. The present shortage of senior technicians trained in functional genomics is exemplified by the outcome of the first class graduates. Ten of the 12 students enrolled found jobs related to their curriculum within weeks of graduating from the school. The remaining two students did not look for jobs but enrolled in a university Master's degree. The same outcome was seen for the second class, at this time of writing (November, 2003).
In order to get exposure to as much of the new technologies as possible, students spend more than half of the school year as trainees in research laboratories that specialize in functional genomics. These laboratories are divided between academic laboratories and preclinical research centers from the pharmaceutical industries and biotechnology companies. To prepare for this internship period, students receive basic educational training, with lessons, tutorials, and laboratory practical exercises at the ENCPB school, during the first 13 weeks of the school year. The next 2 weeks are spent in the Center for Functional Genomics at ESPCI where students learn how to use DNA sequencers, DNA spotters, DNA chip readers, and MALDI and ESI-Q-TOF mass spectrometers. At the end of this period (September to January), students are required to perform several tests before enrolling as internship trainees for the next 18 weeks in selected academic or industrial laboratories. At the end of the internship period, they write a 30–50-page essay describing the work performed in the research laboratory. The final examination takes the form of a public, 20-min defense presentation, using a PowerPoint (Microsoft Corp., Redmond, WA) presentation, followed by questions from a formal jury, in the presence of the tutor from the host laboratory.
During the first 13 weeks at the school, the lessons are devoted to basic chemistry and physics in conjunction with the instrumentation used in functional genomics technology. In view of automated DNA sequencing and microarrays, students receive basic training in the physic and chemistry of electrophoretic separation and fluorescence detection. In view of the use of mass spectrometry, they received basic training in the physics of mass determination, ionization, vacuum, distribution of natural isotopes, ion detection, etc. They also receive an important additional training in molecular biology, protein chemistry, and cellular biology. Students also receive a good amount of practical bioinformatics with the use of Basic Local Alignment Search Tool (BLAST) and other commonly used bioinformatics tools. For French-speaking students, it was important to improve their command of English, particularly the reading of technical papers, by a specialized series of lessons on technical English language.
As seen in the schedule of a typical week (Table I), the students spend a day and a half per week doing practical laboratory work. The fair student-to-professor ratio (12 students for one professor) allows the organization of very interactive laboratory exercises, on the themes of quantitative PCR and protein two-dimensional gel electrophoresis. Some of the exercise themes include preparation of molecular biology kits. For example, the composition of a commercial kit for a miniprep is analyzed, and a similar kit is prepared using raw materials and tested. Another laboratory exercise is to prepare, purify, and assay an expensive restriction enzyme isolated from a bacteria. A detailed program of a typical week (weeks 1–13) is given in Table I. The program of the 2 weeks spent at ESPCI is shown in Tables II and III.
The ENCPB school is well known in the Paris area, and industrial and academic laboratories are keen to receive interns from the school. During their internship, the students are sponsored by a single tutor from the host laboratory, and the independent project will be in the area of functional genomics. The student will be visited at least twice by a professor from the school. During these 1–2-hour visits, the professor evaluates the student's progress, reviews the student's laboratory notebook, and determines whether the project is following the objectives of the program. The professor may also communicate to the student or the tutor guidance and criticism that could not be spontaneously expressed by either. The professor also receives very important benefits from these visits, including a better grasp of the current needs of the industry, the discovery of new technology, and how to adapt the program accordingly. There is also the opportunity to meet leaders in the field of functional genomics, who can come to the school to lecture or offer jobs to the students.
Because most of the techniques of functional genomics were not in use a few years ago, the organization of such technical education scheme was badly needed. The academic and industrial laboratories, therefore, have been very interested in internships and have offered more internships than are needed. This interest created the opportunity for students to choose between several internship projects or locations.
The ingredient for success of this new program is to be found in the students' keen interest in a specialization in an area where they feel that their daily job life will be interesting. The success of the program was also made possible by the interest of academic and industrial laboratories in hiring skilled technical workers.
|Morning||Molecular biology or genetics; formal lecture followed by student exercises|
|Morning||Statistic or physics of instrumentation or analytical chemistry|
|Afternoon||English; introduction to economy and law; legislation and safety on the work place; quality control; patents|
|Afternoon||Personal work; reading of technical papers; analysis with a tutor|
|All day||Laboratory work: molecular and cell biology; molecular genetics|
|The laboratory work is designed to be a small research project over several weeks|
|Morning||Bioinformatics: lessons and hands-on exercises|
|End of Thursdays laboratory work|
|Afternoon||Seminar by an industrial scientist|
|Visit of a laboratory in Paris and suburbs (e.g. pharmaceutical industry, biotech start up, instrumentation company)|
|Morning||Seminars by scientists: “Introduction to microarrays technologies”; “Bioinformatic tools in microarrays analysis”|
|Afternoon||Laboratory work: RNA extraction from biological samples|
|Morning||Laboratory work: mRNA purification and quantification; post-spotting processing of the slides|
|Afternoon||Seminars by scientists: “Array design” followed by spotting demonstration; “Data mining”|
|Laboratory work: cDNA labeling|
|Morning||Seminars by scientists: “Tumors characterization and classification using microarrays”|
|Afternoon||Laboratory work: cDNA purification and hybridization, reverse transcription|
|All day||Laboratory work: washing, scanning, image analysis, data mining|
|All day||Laboratory work: real-time PCR|
|Morning||Seminars by scientists: “Introduction to proteomics”|
|Laboratory work: in-gel protein digestion|
|Afternoon||Seminars by scientists: “Introduction to mass spectrometry”|
|Laboratory work: Peptide extraction and desalting|
|Morning||Seminars by scientists: “Fundamental principles of MALDI and TOF”|
|Afternoon||Laboratory work: spotting and MALDI-TOF analysis|
|Morning||Seminars by scientists: “Principles of searches in data bank with peptide mass finger print”; “Limitations of peptide mass finger print”; “Principles of electrospray”|
|Laboratory work: Searches in data bank|
|Afternoon||Laboratory work: Electrospray analysis, peptide fragmentation, and interpretation|
|Morning||Seminars by scientists: “Principles of searches in data bank with mass fragmentation spectra”|
|Laboratory work: Searches in data bank with mass fragmentation spectra|
|Afternoon||Seminars by scientists: “2D gel and image analysis”; “Application in a proteomic analysis”|
|Morning||Seminars by scientists: “Alternative methods: LC-MSMS, LC-2D, ICAT…”; “Protein identification by LC-MSMS”|
|Afternoon||Seminars by scientists:“Proteomic analysis automation”|
The authors thank Gerard Colpin, Director, ENCPB, for his enthusiasm in supporting ab conceptio this new program; the professors of ENCPB for their participation and support of this new initiative and particularly Fabienne Tabarié, Véronique Lesueur, and Brunehild Sallen; Jean Pierre Le Caer for setting up the proteomic laboratory exercises, and Dr. Marie Claude Potier for setting up the DNA chips technology course; all instructors from ESPCI, Dr. Luce Dauphinot, Nathalie Gibelin, Imman Haddad, Valérie Labas, Delphine Pflieger, Dr. Joelle Vinh, and Jean Figarella, Inspecteur Général de l'Education Nationale, for his continuous support and highly valuable advice for obtaining governmental support for this new initiative.
The abbreviations used are: ENCPB, Ecole Nationale de Chimie, Physique et Biologie; ESPCI, Ecole Supérieure de Physique et de Chimie Industrielles.