Nir Carmi October 2008
Part I: CURRICULUM VITAE
I. Personal
1962 Born in Tel Aviv, Israel.
1978-1981 High school, Sedeh-Boker.
1981-1985 Military service as an air-defense officer.
Marital status: Divorced+ two children
II.UniversityEducation and Additional Training
1985-1988 B.Sc. in Biology at Bar-IlanUniversity.
1988-1990 M.Sc.in Botany at Tel-AvivUniversity.
Title of thesis: Mechanism of herbicide resistance induced by mutagenesis of the fern Pteris vitatta. Supervised by: Dr. A. Zilberstein.
1991-1996 Ph.D.in Genetics at the HebrewUniversity, Faculty of Agriculture.
Title of thesis: 1) Promoter analysis of a tomato fruit-specific gene and 2) expression of the bacterial rolB gene in transgenic plants under the control of this promoter in order to obtain parthenocarpic fruits. Supervised by: Dr. Y. Salts.
1996-1998 Postdoctoral position at the Department of Molecular Developmental and Cellular Biology, YaleUniversity. Research subject: in vitro selection of self-cleaving DNA and rational design of a DNA enzyme. Supervised by: Dr. R. Breaker.
1998 Postdoctoral position at the Department of Cell Biology, Howard Hughes Medical Institute, School of Medicine, YaleUniversity. Research subject: RNA processing. Supervised by: Dr. S. Wolin.
1999- 2000 Postdoctoral position at the Department of Vegetable Crops, A.R.O. Research subject: Molecular biology of sugar metabolism of fruits. Supervised by: Dr. A. Schaffer.
III. Position Held and Academic Status
2001-to present Research scientist at the Plant Sciences Institute, Department of
FruitTree Sciences, A.R.O., VolcaniCenter.
IV. Training / Teaching Experience (including supervision of students and foreign scholars)
2003 Lecturer at the HebrewUniversity, Faculty of Agriculture.Embryo and fruitdevelopment.
M.Sc. students:
Laura Backerman,2002-2004. Title of thesis: Genetic manipulation for seedlessness in Citrus.
Adva Merom,2003-2005. Title of thesis: Dwarfing Citrus via genetic manipulation.
Post-doctoral trainees:
Talia Saraf-Levy, 2004-2006. “Recombination of asymmetric lox site by heterotetramer Cre recombinase.”
Noa Matrasso, 2005-2006. “Moleculardirected evolution of Cre recombinase.”
Irina Sobolev, 2007- to present. “Site-specific integration of DNA fragments into the plant genome.”
V. Membership in Scientific and Agricultural Committees
2003- to present.Citrus Board- Citrus varieties committee.
2009- Scientific Advisory Committee. The 2nd International Citrus Biotechnology Symposium,30th November to 2ndDecember, Catania, Italy.
VI. Editorial Responsibilities
2007 / Reviewer of manuscripts for Plant Breeding.VII. Participation in International Meetings, Seminars, Courses, Tours and Similar Functions
1992 UNESCO international meeting and training in plant molecular
biology, Godollo, Hungary.
1994 4th International Congress of Plant Molecular Biology. Amsterdam, Netherlands. Poster was presented.
1998 Invited to DIMACS workshop on nucleic acid selection. Princeton University, New Jersey, USA. Poster was presented.
2003 7th International Congress of Plant Molecular Biology,Barcelona, Spain.
2004 InvitedtoInternational Biotech Summit at University of California, Berkeley, USA.
2006 Invitedto Frontiers in Structural Biology.Keystone, Colorado, USA.
2007 Invitedlecture in the UK. Invited by MTK Ltd and Chingford Ltd. to speak
about promoting citrus varieties.This lecture was published as an article
entitled “Israel builds up its status” FPJ March: 34-36.
VIII. Invitations from Professional Societies in Israel
2003 Committeeorganizer for the Annual Israeli Citrus Meeting.
2003, 2006, 2009 Invited lecture delivered to the Annual Israeli Citrus Meeting.
IX.Membership in Professional Societies
International Society for Plant Molecular Biology, ISPMB
X. Contributions to the Scientific Community
2006 Participation in an agricultural educational TV program.
2004, 2005 Participation in the “MASHOV” agricultural exhibition.
Our citrus exhibit was awarded the prize for “Best presentation”.
2009 Participation in radio program and an article in newspaper “Ha’ aretz”.
XI. Research Grants
(A) International Competitive Grants
2003-2007 BARD grant. Ttle: Creating an ally from an adversary: genetic manipulation of Citrus tristeza virus.
Co-PI, for 4 years. Budget: Total $50,000/year
(B)Local Research Grants
2001-2005 Citrus Board Grant. Title: Breeding of new seedless citrus varieties. PI,Budget: Total:$90,000/year.
2006-2010 Citrus Board Grant. Title: Breeding of new seedless citrus varieties. PI,Budget: Total:$200,000/year.
2004 The Agricultural Research Organization, Director Grant. Development of a site-specific recombination system based on asymmetric sites.
Co-PI for 1 year, Budget: Total $35,000/year.
2007-2010 Chief Scientist of the Ministry of Agriculture grant. Targeted transgene integration into native sites in the plant genome, toward engineering environmentally friendly and stable transgenic traits in crop plants.
Co-PI for 3 years, Budget: $38,000/year.
(C)Commercial Research Grants
2005-2006 Privatecompany grant, Recogene LTD.Moleculardirected evolution
of Cre recombinase for therapeutic purposes.
PI for 2 years,Budget:$160,000/year.
XII. Awards and Scholarships
1986 Wolf Foundation Scholarship for Undergraduate Students,Bar-IlanUniversity.
1994 I.C.A. Foundation Scholarship for Graduate Students, A.R.O.
Part II: LIST OF PUBLICATIONS
All publications have been classified into four major categories.
The letter following each number indicates the appropriate category.
a Publications produced exclusively within the candidate’s research group (including graduate and post-graduate students, technicians, associated scientists, etc.)b Joint publications with other research group(s) in which the candidate played the major role.
c Joint publications with other research groups for which the candidate’s contributionwas comparable in weight to that (those) of the other research group(s).
d Joint publications with other research groups for which the candidate’s group played a secondary role.
Articles in Reviewed Journals
1.aCarmi, N., Shultz, L.A. Breaker, R.R., (1996).
In vitro selection of self-cleaving DNA.
Chemistry & Biology 3: 1039-1046.
2.cBarg, R., Pilowsky, M., Shabtai, S., Carmi, N., Szechtman, A.D., Dedicova, B., Salts, Y., (1997).
The TYLCV tolerant line MP-1 is characterized by superior transformation competence.
Journal of Experimental Botany 48: 1919-1923.
3.aCarmi, N., Balkhi R.S. Breaker R.R. (1998).
Cleaving DNA with DNA.
Proceedings of the National Academy of Sciences USA 95: 2233-2237.
Publications since last promotion:
4.aCarmi, N., Breaker, R.R. (2001).
Characterization of a DNA-cleaving deoxyribozyme.
Bioorganic Medicinal Chemistry 9:2589-2600.
5.cMiron, D., Petreikov M, Carmi, N., Shen, S., Levin, I., Granot, D., Zamski, E., Schaffer, A.A. (2002).
Sucrose uptake, invertase localization and gene expression in developing fruit of L. esculentum and the sucrose-accumulating L. hirsutum.
Physiologia Plantarium 114: 1-12.
6.a Carmi, N., Zhang, G., Petreikov, M., Gao, Z., Eyal, Y., Granot, D., Schaffer, A.A. (2003).
Cloning and functional expression of alkaline -galactosidase from melon fruit: Similarity to plant SIP proteins uncovers a novel family of plant glycosyl hydrolases.
Plant Journal33: 97-106.
7.a Carmi, N., Dedicova, B., Shabtai, S., & Barg, R. (2003).
Induction of parthenocarpy in tomato via specific expression of the rolB gene in the ovary.
Planta 217: 726-35.
8.aSaraf-Levy, T., Santoro, S.W., Volpin, H., Kushnirsky, T., Eyal,Y., Schultz, P.G., Gidoni, D., Carmi, N. (2006).
Site-specific recombination of asymmetric sites mediated by a heterotetrameric Cre recombinase complex.
Bioorganic Medicinal Chemistry14:3081-9.
9.aVardi, A., Levin,I., Carmi, N. (2008).
Induction of seedlesness in Citrus: From classical to emerging biotechnological approaches.
Journal of the American Society for Horticultural Science 133: 117-126.
10.a Spiegel-Roy, P., Vardi, A., Elhanati, A. Yaniv, Y., Fanberstein, L., Carmi, N. (2007).
'Ayelet' and 'Galya' - New seedless lemon cultivars.
Hortscience. 42:1723–1724.
11.a Gidoni, D., Carmi, N. (2007).
Mutagenesis for seedlessness in Citrus.
Israeli Journal of Plant Sciences. 55: 133-135.
12.b Gidoni, D., Srivastava, V., Carmi, N. (2008).
Site-specific excisional recombination strategies for elimination of undesirable transgenes from crop plants.
In Vitro Cell. & Dev. Biol – Plant.44: 457-467.
Five selected Publications
Publications in Acta Horticulturae
- c Szechtman, A.D., Salts, Y., Carmi, N., Shabtai, S., Pilowsky, M. & Barg, R. (1997). Seedless fruit setting in response to NAM treatment of transgenic tomato expressing the iaaH gene specifically in the ovary.
Acta Horticulturae 447: 597-598.
- a Carmi, N., Salts, Y., Dedicova, B., Shabtai, S., Pilowsky, M., & Barg, R. (1997).
Transgenic parthenocarpy due to specific over-sensitization of the ovary to auxin.
Acta Horticulturae 447: 579-582.
- c Barg, R., Shabtai, S., Carmi, N., Pilowsky, M., Salts, Y. (2001). Transgenic parthenocarpy in determinate and indeterminate tomato cultivars.
Acta Horticulturae 560:207-210.
Articles in ReviewedJournals in Hebrew
- c Salts, Y., Carmi, N., Szechtman, A.D., Shabtai, S., Pilowsky, M., & Barg, R. (1997).
Innovation in genetic engineering.
Ha'sadeh 77: 16.
- a Carmi, N., Vardi, A., Spiegel-Roy, P.,Eyal, Y., Yaniv, Y., Elhanati, A., Fanberstein, L., Neumann H. & Friedman-Sahni, A. (2004).
Developing new grapefruits and pummelos.
Alon Ha'noteah 58: 380-381.
- a Carmi, N. (2006).
Developing new seedless lemon varieties.
Alon Ha'noteah60: 46.
Allowed Patents and Registered Cultivars
Patents since last promotion:
- Carmi, N., Zhang, G., Petreikov, M., Gao, Z., Eyal, Y., Granot, D., Schaffer, A.A. (2003). Polynucleotide sequences encoding alkaline-a-galactosidases and methods of using same.Application #: 20050208520.
- Gidoni, D., Schultz, P.G., Santoro, S.W., Eyal,Y., Carmi,N. (2004).Compositions and methods for asymmetric recombination.International Application No.: PCT/IL2005/000230.
- Matarasso, N., Hanania, U., Gidoni, D., &Carmi, N. (2006). A conservedregionof HIV andusethereof. International Application No.: PCT/IL2008/000968
Citrus Varieties
1.Carmi, N., Vardi, A., Spiegel-Roy, P.,Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Odem’ (2003) - Hybrid of ‘Ora’ and ‘Shani’: Easy peeling late mandarin, red color, seedless, medium size.
2.Carmi, N., Vardi, A., Spiegel-Roy, P.,Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Dana’ (2003) - Hybrid of ‘Ora’ and ‘Murkot’: Easy peeling late mandarin, orange color, seedless, big size.
3.Carmi, N., Vardi, A., Spiegel-Roy, P.,Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Ayelet’ (2003) - Seedless ‘Villafranka’ lemon.
4.Carmi, N., Vardi, A., Spiegel-Roy, P.,Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Galya’ (2003) - Seedless ‘Eureka’ lemon.
5.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Flamingo’(2006) - Hybrid of ‘Chandler’pummelo x ‘Shamouti’clementine: Pummelo, red pulp, seedless.
6.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Aliza’(2006)- Hybrid of ‘Ora’ and ‘Chandler’pummelo: Sweet grapefruit, seedless.
7.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A.,‘Einat’ (2006) - Hybrid of acid-less pummelo and ‘Hudson’: Triploid pink grapefruit, seedless
8.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Orit’(2008) - Hybrid of ‘Edit’ and ‘Nova’: easy peeling early mandarin, red color, seedless, , medium size.
9.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Meravit’(2008) - Hybrid of ‘Wilking’ and ‘Michal’: easy peeling mid season mandarin, red color, seedless, , medium size.
10.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Rishonit’ (2008)- Triploid ‘Rishon’: Triploid easy peeling early mandarin, medium size.
11.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Hanna’(2008) -Hybrid of ‘Tahiti’ Pummelo and’Chandler’ Pummelo: Sweet Pummelo, seedless.
12.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Yael’(2008) - Hybrid of ‘Ora’ and ‘Shani’: easy peeling late mandarin, red color, seedless, medium size.
13.Carmi, N., Vardi, A., Eyal, Y., Yaniv, Y., Fanberstein, L., Elhanati, A., Neumann H., Friedman-Sahni, A., ‘Vardit’(2008) – Seedless ‘vered’: easy peeling mandarin, orange color, seedless, big size.
14.Carmi, N., Vardi, A., Yaniv, Y., Fanberstein, L., Elhanati, A., Friedman-Sahni, A., ‘Yifat’ (2008)- - Hybrid of ‘Yafit’ and ‘Tample’: easy peeling late mandarin, red color, seedless, big size.
15.Carmi, N., Vardi, A., Yaniv, Y., Fanberstein, L., Elhanati, A., Friedman-Sahni, A., Kanonich Joshua., ‘Danit’ (2009) - Hybrid of ‘Ora’ and ‘Murkot’: Easy peeling late mandarin, orange color, seedless, medium size.
16.Carmi, N., Vardi, A., Yaniv, Y., Fanberstein, L., Elhanati, A., Friedman-Sahni, A., Kanonich Joshua., ‘Ronit’ (2009) - Hybrid of ‘Ora’ and ‘Shani’: Easy peeling late mandarin, orange color, seedless, medium size.
17.Carmi, N., Yaniv, Y., Fanberstein, L., Friedman-Sahni, A., Kanonich Joshua., ‘Hinanit’ (2009) – Seedless ‘Daisy’: Easy peeling late mandarin, orange color, seedless, medium size.
18.Carmi, N., Yaniv, Y., Fanberstein, L., Friedman-Sahni, A., Kanonich Joshua., ‘Meital’ (2009) – Seedless ‘GP377’: Easy peeling early mandarin, orange color, seedless, medium size.
19.Carmi, N., Yaniv, Y., Elhanati, A., Fanberstein, L., Friedman-Sahni, A., Kanonich Joshua., ‘Bambi’ (2009) – Seedless ‘Kumquat’.
Abstracts
- Carmi, N., Barg, R., & Salts, Y. (1994). Expression of a tomato young fruit specific proline-rich coding gene. In: 4th International Congress of Plant Molecular Biology. Amsterdam, Netherlands.
- Carmi, N., Balkhi R.S., & Breaker, R.R. (1998). Cleaving DNA with DNA. DIMACS Workshop on Nucleic Acid Selection. PrincetonUniversity. New Jersey, USA.
- Carmi, N., Burger, Y., Zhang, G., Katzir, N., Petreikov, M., Yeselson, Y., Shen, S., Granot, D., & Schaffer, A.A. (2000) Sucrose accumulation in melon (Cucumis melo L.)fruit: Role of expression of sucrose transporter (sut) and invertase genes. 6th International Congress of Plant Molecular Biology. Quebec, Canada
- Dai, N., Cohen, S., Carmi, N., Zhang, G., Portnoy, V., Katzir, N., Schaffer, A. A. (2006). Cloning and expression analysis of the raffinose sugar metabolism pathway in melon fruit: Development of a CPM- (Complete Pathway Macroarray). ISPMB meeting, Weizmann Institute, Israel. Israel Journal of Plant Sciences.
5. Gidoni, D.,Ben-Daniel, B-H., Mett, A., Feiler, J., Sobolev, I., Carmi N., &
Nir, U. (2007).Excision of a selectable marker gene mediated by trans
activated FLP recombinase in tobacco cells.
In Vitro Cell. & Dev. Biol. 43: S26, P-1005 (Abstracts of the World Congress
of the Society for In Vitro Biology, 9-13 June, 2007, Indianapolis, IN, USA).
LIST OF MAJOR ACHIEVEMENTS
1. General contribution to agricultural science
Parthenocarpy
During my studies of the molecular control of parthenocarpy I carried out promoter analyses that led to an understanding of promoter expression at early stage of fruit set. As part of this research I contributed in developing a transgenic tomato capable of setting fruit without pollination and producing parthenocarpic tomato fruit. Transgenic plants are able to set fruits under extreme climatic conditions that affect pollen viability and prevent pollination and fruit set. In addition, parthenocarpy is of considerable importance for the canning industry, which spends large sums to remove seeds from tomato paste.
I am presently continuing this area of research and development, in collaboration with Drs Gidoni, Barg and Salts, we are in the process of developing a site-specific recombination system for the propagation of transgenic parthenocarpic strains.
Tomato cultivar with a superior transformation competence
In addition, during the course of my work, I discovered a tomato cultivar with a superior transformation competence, the MP-1 cultivar (Journal of Experimental Botany 48: 1919-1923). Today, plants of this selected cultivar are the standard cultivar used for practically all transformation research at the Volcani Center, due to its excellent regeneration capabilities and the cultivar has starred in numerous publications reporting the effects of genes in transgenic tomatoes.
Carbohydrate metabolism
When I returned from my postdoctoral work at Yale, I spent one year working in Arthur Schaffer’s laboratory at the Volcani Center in the area of plant carbohydrate metabolism and its molecular control. During that period, I discovered and cloned a novel alkaline -galactosidase from the Cucurbitaceae family which contributed significantly to our understanding of the initial steps of metabolism during sink import in this novel stachyose and raffinose translocating family. The enzyme is the first committed step in sink import metabolism and its identification also led to the functional characterization of the previously undefined SIP family of proteins. The enzyme cleaves the galactose residues of stachyose and raffinose under neutral pH and is presently being developed for applications in the food and pharmaceutical industries.
In addition, I cloned the first sucrose transporter and invertase genes from melon plants. A functional analysis of these genes was conducted for sweet and non-sweet genotypes of melon and variation in developmental expression of these genes was revealed. These genes, which were found to play a key role in sugar accumulation in melon fruits, are currently being used in a breeding program conducted in collaboration with the cucurbit group of Neve Ya’ar.
Moleculardirected evolution of Cre recombinase
We obtained a scientific breakthrough in our development of a new recombinase system platform by using molecular directed evolution of Cre recombinase to develop anHIV1 provirusexcision process to be used for therapeutic purposes. We already applied for two PCT patents in connection with this work. Recogene LTD, has taken this project for developing and commercializing.
2. Achievements in applied research specifying major contribution to agriculture in Israel and abroad
Citrus Breeding
For the last seven years, I have led the Volcani Citrus Breeding program, which is aimed at developing new seedless Citrus varieties. The program is supported by the Citrus board and the chief scientist of the ministry of agriculture who both have increased their funding in light of our successful results and has also benefited royalties from South Africa and California. The decision to emphasize seedless cultivars was taken in light of European market demands. Our advantage versus our competitors is mainly the producing of late season easy peeling mandarin cultivars. The staff working in the breeding program includes three technicians. The breeding program at the 10 hectare field in Volcani combines breeding and selection strategies together with inducing mutations.
To date, nineteen commercially important selected cultivars for local and foreign markets have been registered. These include selections of lemons, mandarins, grapefruit, pomeloes and kumquat. Among the mandarins we have selected an easy peeling mandarin cultivar name ‘Yael’ that has the potential to replace the ‘Or’ cultivar as worldwide leading cultivar. We have also developed the sweet grapefruit cultivar ‘Aliza’, ranked with a very high in flavor test. The latter may become a dominant cultivar in the grapefruit market. Additionally, we have also selected high lycopen pomelo cultivar named ‘Flamingo’ which has recently become commercially available.
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