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ITTO-GMU/ER-04/20001022A Training Report No. 4A
ITTO Project PO 16/96 Rev.4(F)
EX SITU CONSERVATION OF SHOREA LEPROSULA AND
LOPHOPETALUM MULTlNERVIUM AND THEIR USE FOR
FUTURE BREEDING AND BIOTECHNOLOGY
SHORT COURSE ON
INTRODUCTION TO MOLECULAR GENETICS AND
BIOTECHNOLOGY OF FOREST TREES
YOGYAKARTA, 5-9 SEPTEMBER 2000
PART I
FACULTY OF FORESTRY
GADJAH MADA UNIVERSITY
YOGYAKARTA
2000
Foreword
This report is a result of the third training course organized by the Project as
scheduled in the workplan. It consists of 2 parts: Part I contains the Management and
Evaluation, and Part 11 contains Handouts. The course was primarily designed for
personnel engaged in implementing the project activities, especially those assist in
laboratory works.
As part of the transfer of technology activities, a consultant on molecular genetics
from Oregon State University, Prof. Steven H. Strauss, Ph.D was invited to lead the
course.
As reported by the Course Leader, the class was highly successful in introducing
basic concepts and methods of molecular genetics and biotechnology to the
participants.
Attended by 15 participants, the course was funded by ITTO in cooperation with
Peru m Perhutani.
Yogyakarta, September 2000
Prof. Oemi Hani'in Suseno
Chairperson
Table of Contents
Part I. Management and Evaluation
1. Introduction ........................................................................................ 1
2. The rationale............. ......................................................................... 1
3. Venue and Dates ............... ......... .......... ........... ....... .................. ......... 2
4. Objectives..................................................... ..................................... 2
5. Organization...................................................................................... 3
6. Opening Session ............................................... ................................. 3
7. Participants and Resource Persons.................................................... 3
8. Programs ...... ....... ......... ...... ............................ ....... ....... ...... ........ ....... 3
9. Closing Session.. ........... ........... ....... ....... ..... ...................... ................ 4
10. Evaluation of the Training .................................................................. 5
Appendices:
I. The Opening remarks
11. List of Participants
Ill. List of Resource Persons
IV. Programs
V. The Closing remarks
VI. Evaluation
Short Course on Introduction to
Molecular Genetics and Biotechnology of Forest Trees
Introduction
Ex situ conservation refers to the conservation of components of biological diversity
outside their native habitats. Ex situ conservation is achieved by preservation of samples of
plant genetic resources in gene collections and gene banks.
ITTO project PO 16/96 Rev. 4(F) on ex situ conservation of two selected species and their
use for future breeding and biotechnology initiates fundamental research activities that will:
1) avert a decline in the genetic variability within Shorea /eprosu/a and Lophopeta/um
multinervium, and 2) use these genetic collections for more efficient breeding and
biotechnology programs in the future.
One of the specific objectives of the project is to create effective programs of education
and technology transfer that may be used to train appropriate personnel in methods for ex
situ conservation of tropical forest tree.
To support the breeding programs in the future, fundamental genetic information of the two
species is needed so that genetic improvement can be made. One way of obtaining the
genetic information is through biomolecular analysis.
The Short Course on Introduction to Molecular Genetic and Biotechnology of Forest Trees
was aimed at introducing the basic concepts of molecular genetics and their applications to
the staff and management involved with forest regeneration and research.
The Rationale
The Tropical Rain Forest of Indonesia is widely acknowledged as one of the most species I
rich and complex terrestrial ecosystems in the world. It is also known as a Center of
biological diversity and a Center of endemism and, therefore, Indonesia is also
1
acknowledged as containing mega diversity. The global interests in this ecosystem are in
part stimulated by the recognition that the Tropical Rain Forest is a treasure house of
potentially useful species, whether as a gene pool of domesticated species, as a source of
timber or minor forest products, or biologically active compounds.
Recognizing the limitations of existing management capability and personnel available to
implement the ITTO project PO 16/96 Rev.4(F), the project personnel with technical
assistance from Oregon University, organized a Short Course on Introduction to Molecular
Genetics and Biotechnology of Forest Trees.
During the Short Course, the trainees were introduced to the basic concepts of molecular
genetics and biotechnology of forest trees.
Venue and Dates
The Short Course was held primarily at the Forest Biotechnology and Tree Improvement
Research and Development Center, and the laboratory demonstrations were conducted
both at the same institute and at the Faculty of Forestry, Gadjah Mada University, from 5 to
9 September 2000.
Objectives
At the end of the course, the participants would:
1. Have gained a better understanding on the basic concept of molecular genetics
2. Have gained a better understanding on the basic methods and application of
biotechnology of forest trees
3. Understand the concepts of genetic engineering and genetic markers.
Organization
The course was organized by the ITTO project PO 16/96 Rev. 4(F) based at the Faculty of
Forestry, Gadjah Mada University, with a guest lecturer from the College of Forestry,
Oregon State University, USA.
2
Opening Session
The Short Course on Introduction to Molecular Genetics and Biotechnology of Forest Trees
was officially opened on Tuesday, 5 September 2000. Opening remarks were made by
Prof. Oemi Hani'in Suseno, Chairperson of the ITTO project, followed by comments from
Prof. Steven H. Strauss, PhD, the course leader. The speeches are attached as Appendix
I.
Participants and Resource Persons
A total of 15 participants attended the course, consisting of 5 participants from Perum
Perhutani, 2 persons from PT. INHUTANII, 4 participants from FBTIRDC, and 4 persons
from the the Faculty of Forestry, Gadjah Mada University. The Course was led by Prof.
Steven H. Strauss, PhD., with Dr. M. Na'iem and Dr. Anto Rimbawanto as co-lecturers.
The list of participants is attached as Appendix 11 and the names of the resource persons is
attached as Appendix Ill.
Program
The course program consisted of lectures and laboratory demonstrations (see Appendix
IV)
The subject matter of the class included:
+ The nature of cells and development
+ The different genomes in plant cells and their inheritance
+ DNA structure and expression via RNA and protein
+ How genes are cloned to enable their detailed study and manipulation
+ Methods for study of gene expression and genetic diversity at DNA and protein level
+ Laboratory demonstrations of the allozyme (protein) technique for studying genetic
diversity
+ Laboratory demonstration of the RAPD (DNA) method for studying genetic diversity
+ The polymerase chain reaction (PCR) and its diverse uses in biotechnology and
genetic marker studies
+ Southern blots and their use for studying diversity and transgenic organisms
• Methods for isolation unknown genes that affect traits of economic importance
3
• Methods of gene transfer and plant regeneration
• The molecular mechanisms of gene transfer by Agrobacterium
• Current progress in agricultural biotechnology
• Research nearing commercial uses in forestry biotechnology
• Political and scientific concerns about transgenic plants in agriculture and forestry
In addition to lectures and laboratory demonstrations, students participated directly in the
class by two exercises:
• Two small group projects where subsets of students attempted to solve a problem and
then communicated the results to the entire class and answered questions. The two
problems were:
o Propose a research project for genetic engineering of flowering in teak,
including consideration of possible ecological effects
o Propose research for a genetic marker study to help guide conservation of a
poorly known, endangered tropical tree species
• Students submitted three written questions where they sought clarification of material
covered in the class, or more detailed discussion. The questions were discussed in
front of the class so all could hear the answers and ask questions. This allowed
students of diverse backgrounds to seek help with the class material. Questions
ranged from advanced inquiries (e.g., about tissue culture regeneration methods, gene
expression control, methylation, transposons) to basic questions (e.g., about the
meaning of "cloning" and basic steps employed to study the safety of genetically
modified foods).
Closing Session
The course was closed on 9 September 2000. The course leader made a concluding
remarks, after which certificates were awarded to the participants. The official closing
remarks was made by Or. M. Na'iem representing the Chairperson. The speeches during
the closing session are attached as Appendix V.
4
Evaluation of the Training
To acquire feedback from the participants, an evaluation questionnaire was distributed at
the end of the course. Such an evaluation is important for measuring the success of this
activity, and for designing future programs. The results of the evaluation are given in
Appendix VI.
5
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Appendix I
Opening remarks by the Chairperson of ITTO project
Prof. Steven H. Strauss, Ph.D Professor of Forest Science and Program Leader of Genetic Engineering Research Cooperative, College of Forestry, Oregon State University, USA
Prof. Soekotjo, Or. M. Na'iem and Dr. Anto Rimbawanto, co-resource persons of the short course
Or. Rudjiman, Head of the Forest Science Department, Faculty of Forestry, GMU, who will also join the short course as participant,
Dear participants,
Good morning to everybody, and welcome to the Short Course on Introduction to Molecular Genetics and Biotechnology of Forest Trees.
This is the third course conducted by our project, but it is the first one on this subject area. The course will be led by Prof. Steven Strauss and it is attended by 14 participants from the forest companies, Rand 0 office and the university. Prof. Steven Strauss is a well known expert in biotechnology whom we invited as our consultant. I would like to extend may warm welcome to Prof. Strauss, and appreciate him very much for coming over a long way from home, despite of his hectic schedule. We hope that his presence will stimulate and inspire his colleagues here to develop more research on forest biotechnology.
Or. Na'iem and Dr. Anto Rimbawanto will become the partners of Prof. Strauss while he is here.
I understand that molecular biology is a new subject to most of the Indonesian scientists, therefore this course is directed towards just an introductory one, to attract more people to work on this area.
It is my hope that the participants will not only gain the knowledge, but also have a chance to know better about ITTO project being undertaken.
Finally, may I extend our gratitude to ITTO and Perum Perhutani for the financial support provided for this course.
Good luck and have a nice time.
Prof. Oemi Hani'in Suseno
Remarks during opening ceremony from Dr. Strauss
Dear students and colleagues. Thank you for the chance to share my expertise with you during
this course. I know little about Indonesia and the kinds of forestry problems you have, thus I
know that I can learn as much from you as you can from me.
I will attempt to speak slowly, as I know many of you will be struggling to understand English.
However, I must confess that I am not known for slow speed of speech in the USA. Quite the
opposite I am afraid! I will try my best, but ask that you are courageous enough to put up your
hand and ask for clarification about any word or point during my lectures. I want this class to be
useful to you and your questions help to ensure this. I have also provided detailed written
notes, soon to be copied and distributed to you after our computer compatibility problems are
worked out.
I look forward to many exciting exchanges during the next few days!
.Participants
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Ir. Sri Wahyuni S, MP
Surakarta, 27 April t 964
Master's degree
Perum Perhutani
JI. Wonosari, Batokan, Tromol Pos 6 Cepu
(0296) 42 t 233
(0296) 422 439
Ir. Wakhid Nurdin, M.Sc
Trenggalek, 29 Februari 1968
Master's degree
Perum Perhutani
Gd. Manggala Wanabakti Blok VII, Lt. t t JI. Gatot Subroto, Senayan, Jakarta
(02l) 572 t 282
(02 t)
Drs. Anton Sudiharto
Bandung, 7 April 1967
Bachelor's degree
Perum Perhutani
JI. Wonosari, Batokan, Tromol Pos 6 Cepu
(0296) 42 t 233
(0296) 422 439
Appendix 11
Name Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Imam Suhudi, A.Md Kendal, to Mei t 975
0111
Perum Perhutani
JI. Wonosari, Batokan, Tromol Pos 6 Cepu (0296) 42 t 233
(0296) 422 439
Dedi, BScF
Sumedang, t 3 Juli t 967
0111
Perum Perhutani
JI. Wonosari, Batokan, Tromol Pos 6 Cepu
(0296) 42 t 233
(0296) 42 t 233
(0296) 422 439 [email protected]
Shinta Arianasofa, SP
Nunukan, to Maret 1973
Bachelor's degree
PT. INHUTANI I Gd. Manggala Wanabakti Blok VII, Lt. 12 JI. Gatot Subroto, Senayan Jakarta
(021) 573 1724
(021) 573 4335
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile E-mail
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile E-mail
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Ir. Putri C. Budilistyani
Bogor, 22 April 1965
Bachelor's degree
JKLT PT. INHUTANII
Gd. Manggala Wanabakti Blok VII, Lt. 1 2 JI. Gatot Subroto, Senayan Jakarta (021) 573 t 724
(021) 573 4335
putti@jklt or id
Dr. Rudjiman
Bantul, 16 Juni 1944
Ph. 0
Fakultas Kehutanan UGM
Jurusan Budi Daya Hutan Fakultas Kehutanan UGM Bulaksumur, Yogyakarta 55281
(0274) 901 400
(0274) 902 220 [email protected] ac id
Ir. Handojo Hadi Nurjanto, M.Sc
Ponorogo, 21 April 1966
Master's degree
Fakultas Kehutanan UGM
Jurusan Budi Daya Hutan Fakultas Kehutanan UGM Bulaksumur, Yogyakarta 55281
(0274) 901 400
(0274) 902 220 fofgmu@ugmgtw lIgm.ac.id
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
M. Gunawan Wibisono, S.Hut
Surakarta, 9 April 1970
Bachelor's degree
Fakultas Kehutanan UGM
)urusan Budi Daya Hutan Fakultas Kehutanan UGM Bulaksumur, Yogyakarta 55281
(0274) 901 400
(0274) 902 220
Yeni W.N. Ratnaningrum, S.Hut
Yogyakarta, 9 )anllari 1974
Bachelor's degree
Fakultas Kehutanan UGM
)urusan Budi Daya Hutan Fakultas Kehutanan UGM Bulaksumur, Yogyakarta 55281
(0274) 901 400
(0274) 902 220
Y eni_ wn [email protected]
Istiana Prihatini, S.Si
Teluk Betung, 4 April 1974
Bachelor's degree
P3BPTH
)1. Palagan Tentara Pelajar Km. 15 PUlwobinangun, Pakem, Sleman
(0274) 895 954
(0274) 895 954
Isti. [email protected]
Name Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile E-mail
Noor Khomsah Kartikawati, S.Hut, MP
Klaten, 25 Nopember t 972
Master's degree
P3BPTH
JI. Palagan Tentara Pelajar Km. t 5 Purwobinangun, Pakem, Sleman
(0274) 895 954
(0274) 895 954
Ir. M. Charomaini
Y ogyakarta, t 0 Oktober t 95 t
Bachelor's degree
P3BPTH
JI. Palagan Tentara Pelajar Km. t 5 Purwobinangun, Pakem, Sleman
(0274) 895 954
(0274) 895 954
Ir. Rina Laksmi Hendrati
Yogyakarta, 22 Januari t 964
Bachelor's degree
P3BPTH
JI. Palagan Tentara Pelajar Km. t 5 Purwobinangun, Pakem, Sleman
(0274) 895 954
(0274) 895 954
Rien _ [email protected]
Resource persons
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address Telephone
Facsimile
Name
Place, date of birth
Education
Institution
Address
Telephone
Facsimile E-mail
Prof. Steven H. Strauss, Ph.D
28 Nopember t 955
Ph.D
Oregon State University
Department of Forest Science Oregon State University, FSL 020 Corvallis, Oregon, USA 9733 t -5705
(0541) 737-6583
(054 t) 737 t 393
. Prof. Dr. Oemi Hani'in Suseno
Surakarta, t Januari t 93 t Ph.D
Fakultas Kehutanan UGM
Bulaksumur, Yogyakarta 5528 t
(0274) 5450639
(0274) 545 639
Prof. Dr. Soekotjo
Ngawi, t Januari t 934
Ph.D Fakultas Kehutanan UGM
Bulaksumur, Yogyakarta 5528 t
(0274) 5450639
(0274) 545 639
Appendix III
Nama
T empat, tgl Lahir
Pendidikan
Asal Instansi
Alamat Instansi
Telp.
Fax. E-mail
Nama
T empat, tgl Lahir
Pendidikan
Asallnstansi
Alamat Instansi
Telp.
Fax. E-mail
Dr. Ir. Mohammad Na'iem, M.Agr
Cepu, 16 April 1954
S 3
Puslitbang Bioteknologi dan Pemuliaan Tanaman Hutan
JI. Palagan Tentara Pelajar Km. 15 Purwobinangun, Pakem, Sleman Yogyakarta 55582
(0274) 895 954, 896080
(0274) 895 954
Dr. Ir. Anto Rimbawanto
S 3
Puslitbang Bioteknologi dan Pemuliaan Tanaman Hutan
JI. Palagan Tentara Pelajar Km. 15 Purwobinangun, Pakem, Sleman Yogyakarta 55582
(0274) 895 954, 896080
(0274) 895 954
Appendix IV
Short Course on Introduction to Molecular Genetics and Biotechnology of Forest Trees
Yogyakarta, 5 -9 September PROGRAMS
MONDAY, SEPTEMBER 4, 2000
Prof. S.H. Ph.D
Appendix V
Remarks during closing ceremony from Dr. Strauss
Dear students and co-instructors. I have enjoyed the last few days, and feel that you students
have learned a great deal despite some real struggles with language and the very complex
concepts presented by molecular genetics. Your written questions and solutions to our
exercises show me that most of you have mastered the key ideas we hoped to impart. I
understand you valued the lab exercises conducted by Or. Na'iem and Rimbawanto greatly.
Maybe someday we will have a lab exercise in teak transformation!
I also hope that you better understand why I think that genetic engineering can be used to
benefit, and used safely, when compared to conventional agriculture or forestry. I also
encourage you to consider carefully the agendas and level of knowledge of those who provide
information about the GMO controversy around the world. I can insure you that a number of
NGOs feel so strongly that they have distorted science greatly to further their own personal
philosophies, finances, and world visions. I think they have greatly damaged the prospects for a
more secure food supply, economic development, and protection of the environment for the
millions of less privileged in the developed and developing worlds as a consequence of their
campaigns. The explosion of knowledge about genomes enable an extraordinary number of
new ways to produce more food, better food, and fight disease but little of it will materialize with
the excessively stringent regulatory regimes, and hysteria among the public, that the NGOs
appear to be succeeding in imposing on all of us.
But, this is my opinion. You must judge for yourselves.
My main hope is that this class has provided you with a strong foundation from which you can
continue to learn, and thus to make sound judgments, about biotechnology as it develops and
begins to affect you and your families for years to come.
The prospects are thrilling, and the needs are urgent.
Closing remarks by Dr. Mohammad Na'iem Representing the Chairperson of ITTO Project
Dear Prof. Steve Strauss, the Course Leader Or. Anto Rimbawanto, my co-resource person And dear participants
First of all may I extend Prof. Oemi and Prof. Soekotjo's apology for not being able to share with you the last moment of this course, due to some other commitment.
They left soon after the opening of this course for Central Kalimantan to see the result of the plantation established by this ITTO project. Therefore, I am here now to represent the chairperson of ITTO Project PO 16/96 Rev.4(F) to close the course.
I am pleased to say that most of the participants have shown their full participation throughout the course. We understand that many of the participants have difficulties in understanding the topics discussed due to two reasons. The first reason is that the subject is quite new to some of them, and secondly, language barrier made it more difficult to understand it.
We owe to Or. Anto Rimbawanto for his willingness to volunteer as an interpreter to the class in addition to being a resource person, and we are very grateful for that.
For Prof. Steve Strauss may we once again extend our gratitude for being so patient and yet full of enthusiasm in leading the course.
To the participants may I extend our congratulation to their successful participation in the course and bid them farewell, and be success in their future work.
To the head and staff of FTIROC please accept our gratitude for their excellent cooperation.
On behalf of the chairperson, may I now declare the course closed.
M. Na'iem
APPENDIX VI
Summary of the Participants Evaluation *)
Part I. Participants' background
1. The highest academic degree attained by the participants are: a. Master's degree (82) 2 b. Bachelor's degree (81) 8 c. Diploma III 1
2. Out of 11 participants, three persons are working in molecular biology laboratory
Part 11. The Course Program
1. The importance of the topics The participants gave an average rating of 4.78 (on a scale of 5 as very important) on the subject matter given during the course. All of the subjects were considered important. Following are the individual ratings given by the participants.
1.1 Introduction to molecular genetics 4.81 1.2 Biochemical genetic markers - methods and application 4.72 1.3 DNA markers - methods and application 4.90 1.4 Genetic engineering and regeneration methods 4.63 1.5 Laboratory demonstration: Allozymes technique 4.81 1.6 Laboratory demonstration: DNA technique 4.81
2. The usefulness of the topics
<)
The usefulness of the topics to support their present or future work was rated 4.63 in average on a scale of 5 as very useful. The topics given during the training were useful for them. The individual ratings of the topics are as follows:
2.1 Introduction to molecular genetics 4.63 2.2 Biochemical genetic markers - methods and application 4.63 2.3 DNA markers - methods and application 4.63 2.4 Genetic engineering and regeneration methods 4.63 2.5 Laboratory demonstration: Allozymes technique 4.63 2.6 Laboratory demonstration: DNA technique 4.63
Participants evaluation to the course was obtained through questionnaire. Only 11 out of 15 participants returned the questionnaire.
3. The knowledge gained from this course The additional knowledge gained during the course was rated 4.51 in average on a scale of 5 as very much. The following ratings were given on every topic.
3.1 Introduction to molecular genetics 3.2 Biochemical genetic markers - methods and application 3.3 DNA markers - methods and application 3.4 Genetic engineering and regeneration methods 3.5 Laboratory demonstration: Allozymes technique 3.6 Laboratory demonstration: DNA technique
4. Time adequacy
4.36 4.27 4.54 4.54 4.63 4.72
Most of the participants considered the time allocation for lectures and discussions was not sufficient. This can be seen from the average rate of time adequacy 2.78 on a scale of 5 as very sufficient. The individual ratings of each subject matter is as follows:
4.1 Introduction to molecular genetics 3.27 4.2 Biochemical genetic markers - methods and application 2.72 4.3 DNA markers - methods and application 2.72 4.4 Genetic engineering and regeneration methods 2.36 4.5 Laboratory demonstration: Allozymes technique 2.81 4.6 Laboratory demonstration: DNA technique 2.81
5. The clarify of instruction The average rate given by the participants on the instruction clarity was 4.05 on a scale of 5 being very clear. From the individual score given to every topics it is obvious that this clarity problem is related to the language barrier. The individual ratings of each lecture is as follows:
5.1 Introduction to molecular genetics Prof. Steven H. Strauss, Ph.D
5.2 Biochemical genetic markers - methods and application Or. Moh. Na'iem
5.3 DNA markers - methods and application Dr. Anto Rimbawanto
5.4 Genetic engineering and regeneration methods Prof. Steven H. Strauss, Ph.D
5.5 Laboratory demonstration: Allozymes technique Sapto Indrioko, S.Hut, MP
5.6 Laboratory demonstration: DNA technique Or. Anto Rimbawanto
3.54
3.90
4.27
3.81
4.45
4.36
Part Ill. Comments and suggestions from the participants
The participants were also invited to give their comments and suggestions to improve the organization of the course in the future. 1. Due to the complexity of the subject matters discussed, the participants desired additional
time for lectures and discussion. This is because most of the participants had little prior exposure to biotechnology, and unfamiliarity with many new English scientific terms.
2. Some of them who had basic knowledge on biotechnology expected to have more advance course in the future.
3. Lecture notes in English need to be distributed in advance of the lectures. Unfortunately, due to incompatibility of software which need a special effort to solve, the notes could not be printed on time, although they had been prepared in advance.
Part IV. Conclusion
The short course was very effective in introducing the basic concepts and methods of molecular genetics and biotechnology to the participants. The presence of a voluntary interpreter who is also an expert in DNA (Dr. Anto Rimbawanto) gave an additional value, because communication gap could be overcome.