Dr. David Lior

Research Interests:

My research interests are focused in genetics and evolution of complex traits in fish and yeast. I study the genetic basis of resistance to viral infection by Cyprinids herpes virus-3 using various strains and crossbred lines of common carp and Koi fish. The goal is to identify genes that control disease resistant and use them to produce genetically resistant strains allowing sustainable production of food and ornamental carps. In addition, I study the inheritance and genetic basis of color traits in the Japanese ornamental carp (koi), some of which show a complex mode of inheritance. I also use the carp, a natural tetraploid species, to study evolution of complex traits after whole-genome duplication. 
Another arm of my research uses the model yeast, Saccharomyces cerevisiae, to uncover genic and allelic contributions to complex phenotypes as well as to understand the contribution of interactions between alleles and genes to phenotypic variation. I study the genetic basis of growth at high temperature, a trait that assists clinical yeast strains to infect human and animal hosts, as a model complex trait. I also use “evolution in the lab” methods to study how new regulation of genes evolves and contributes to formation of new phenotypes. This research helps to understand the contribution of regulatory variation to evolution of complex traits and enables characterization of the cellular mechanisms that support the dynamic process of evolution of new phenotypes and forms.

Research Projects:

  • Development of genomic tools and resources for genetic research in common carp
  • Development of carp strains genetically resistant to viral infection of CyHV-3
  • Genetics of color patterns in the Japanese ornamental carp (koi)
  • Genetic variation and biodiversity of fish species and populations
  • Evolutionary aspects of genome duplication and its contribution to functional complexity
  • The genetic basis of growth at high temperature in yeast
  • Genetic and epigenetic mechanisms in evolution of new regulatory networks in yeast

koi
See also: Lior David

 

See also: Lior David

Curriculum Vitae

Born in 1966, Israel.
Received his Ph.D. in 2002 from the Hebrew University of Jerusalem.
Lecturer since 2006.

 

See also: Lior David

Lab members

rachelshapira
See also: Lior David

Rachel Shapira, Ph.D
Lab manager

My ph.D. studies focused on characterized and dissecting the genetic bases of complex quantitative traits, using different aspects of research like association studies, linkage analysis, sequential elimination of different effects on the trait and etc. In my studies I generated 120 hybrids collection of 16 divergent strains, backcrosses, F1 and F2 populations and etc. High temperature growth of sacchromyces cerevisiae- budding yeast is a quantitative, heterotic trait  which I used as a trait model. In my work I identified seven different genes inside a mild effect locus contribute the trait and another five different genes with an over-dominant mode of inheritance affecting heterosis (hybrid vigor), which has a great importance in food production fields.

Publications:
-Shapira R, Levy T, Shaked S, Fridman E, David L. Extesive heterosis in growth of yeast hybrids is explained by a combination of genetic models. Heredity. 2014; 113(4):316-26.
-Talmor-Cohen A, Tomashov-Mater R, Eliyahu E, Shapira R, Shalgi R. Are Src kinases involved in cell cycle resumption in rat egg? Reproduction, 2004, 127(4): 455-63.

ronitadmor
See also: Lior David

Roni Tadmor
PhD student

My work is focused on the genetics of complex traits in the common carp (Cyprinus carpio), a fish of high economic value and fascinating genetics. The common carp has a tetraploid genome, due to recent (12 MYA) genome duplication. The first part of my research aims to construct a genetic map that will capture the complex nature of carp genime and describe the relations between the paralogic areas that evolved after duplication. In another part of my work, I am working on the genetic basis of several complex traits, especially for resistance to CyHV-3 virus that causes mortality in aquaculture production of common carp. The research I am involved in combines practicable implementations such as breeding CvHV-3 resistant of common carp, as well as evolutionary aspects of the nature of duplicated genomes and the impact of duplicated genes on speciation.

tomerborovski
See also: Lior David

Tomer Borovski
M.Sc. student

In my master project I am characterized the genetic variation and the population structure of Amnon Galilee (Sarotherodongalilaeus) in the Kinneret, Israel. We estimate the genetic diversity of the population, and compare it among others to population in Africa and try to understand its implications on the stability of the population. We are trying to develop different ways to preserve the genetic diversity, as increasing the efficiency of the annual populating to the Sea of Galilee and the establishment of a data base for identifying genetic Kinneret fish and freshwater species in Israel.

tallevy
See also: Lior David

Tal Levy
M.Sc. student

Our laboratory has been studying epigenetic evolutionary in which we expose yeast cells (Sacchromyces cerevisiae-budding yeast) to environmental conditions they did not encountered before. Cells that succeed with the adaptation process inherit the adaptation phenotype to their progeny. We examine and want to understand that changes (genetic and/or epigenetic) accompanying this adaptation process in the cells. In my master's project I examine the hypothesis that there are some epigenetic factors that influence and contribute to the process of adaptation to new environmental conditions and characterize them.

efratasulin
See also: Lior David

Efrat Asulin
M.Sc. strudent

In my research I am dealing with enhancement of resistant of common carp strains to KHV (Koi Herpes Virus) virus, by genetic tools. KHV is a deadly virus to these species and cause enormous damage to the aquaculture industry. The main method I am using in my project is the development of SNP markers on the genes that are linkage to the survival phenotype. Simultaneously I am working for better understanding of the resistance mechanism and the differences between susceptible and survival fishes in spreading the virus. All these will enable better genetic selection for resistant fishes in low cost and high effectiveness

 

See also: Lior David

List of Publications

Selected publications

Books

1. David L. (2009) Inheritance of colors and evolution of koi and carp. VDM Verlag Dr. Muller, Germany, 99 pp.

Book Chapters

1. David L., Clauder-Munster S. and Steinmetz L. M. (2011) A high-resolution map of transcription in the yeast genome. In: Yeast Systems Biology, Springer Press, USA. Eds. Castrillo JI. and Oliver SG. Methods Mol Biol. 2011;759:3-28. https://dx.doi.org/10.1007/978-1-61779-173-4

2. Braun E. and David L. (2011) Cellular plasticity and dynamic processes underlie adaptation of genome rewired cells to an unforeseen regulatory challenge. In: Transformations of Lamarckism; From Subtle Fluids to Molecular Biology. Vienna Series in Theoretical Biology MIT Press, Cambridge, MA, USA. Series Eds. Gissis S.B. and Jablonka E. PP.181-192.  https://doi.org/10.7551/mitpress/9780262015141.001.0001

Papers

2017

1. Yasur-Landau D, Jaffe C.L, Doron-Faigenboim A, David L and Baneth G. (2017) Induction of allopurinol resistance in Leishmania infantum isolated from dogs. PLoS Neglected Tropical Diseases, 11(9), p.e0005910. https://doi.org/10.1371/journal.pntd.0005910

2. Tadmor-Levi, R., Asoulin, E., Hulata, G. and David, L., 2017. Studying the Genetics of Resistance to CyHV-3 Disease Using Introgression from Feral to Cultured Common Carp Strains. Frontiers in Genetics, 8,24. https://doi.org/10.3389/fgene.2017.00024

3. Petit, J., David, L., Dirks, R. and Wiegertjes, G.F., 2017. Genomic and transcriptomic approaches to study immunology in cyprinids: What is next?. Developmental & Comparative Immunologyhttps://doi.org/10.1016/j.dci.2017.02.022

2016

4. Shapira R, David L. (2016) Genes with a Combination of Over-Dominant and Epistatic Effects Underlie Heterosis in Growth of Saccharomyces cerevisiae at High Temperature. Frontiers in Genetics, 7, 72. https://doi.org/10.3389/fgene.2016.00072

5. Wiegertjes GF, Lorenzen N, Secombes CJ, Collet B, Fischer U, Tafalla C, Parra D, Scapigliati G, Boudinot P, Evensen ØAdamsA, ToffanA, Buchmann K, VeselyT, David LMuleroV, SmithP, Aspehaug V, Engell-Sørensen K, SoberJ, WallisT, RødT, Flores M, MarchJ, Stratmann A, Christofilogiannis P, TobarJ, Henriksen NH, Sigholt T, de las Heras A. (2016) TargetFish - Targeted disease prophylaxis in European fish farming. Bulletin of the European Association of Fish Pathologists. 36:52-56.

6. Yasur-Landau D, Jaffe CL, David L, Baneth G. (2016) Allopurinol Resistance in Leishmania infantum from Dogs with Disease Relapse. PLoS neglected tropical diseases. 10(1):e0004341. https://doi.org/10.1371/journal.pntd.0004341

2014

7. Khedkar GD, Lutzky S, Rathod S, Kalyankar A, David L. (2014) A dual role of dams in fragmentation and support of fish diversity across the Godavari River basin in India. Ecohydrology. 7:1560-1573. DOI: 10.1002/eco.1470.

8. Shapira R, Levy T, Shaked S, Fridman E, David L. (2014) Extensive heterosis in growth of yeast hybrids is explained by a combination of genetic models. Heredity. 113:316-326. DOI: 10.1038/hdy.2014.33

9. Moore L.S., Wei W., Stolovicki E., Benbenishty T., Wilkening S., Steinmetz L.M., Braun E., David L. (2014) Induced Mutations in Yeast Cell Populations Adapting to an Unforeseen Challenge. PLOS ONE 9, e111133. https://doi.org/10.1371/journal.pone.0111133

10. Khedkar G.D., Jamdade R., Naik S., David L., Haymer D. (2014) DNA barcodes for the fishes of the Narmada, the third longest river of India. PLOS ONE 9, e101460. DOI: 10.1371/journal.pone.0101460

11. Granevitze Z., David L., Twito T., Weigend S., Feldman M., Hillel J. (2014) Phylogenetic resolution power of microsatellites and various SNP types assessed in ten divergent chicken populations. Animal Genetics 45(1):87-95. DOI: 10.1111/age.12088

2013

12. David L., Ben-Harosh Y., Stolovicki E., Moore L.S., Nguyen M., Tamse R., Dean J., Mancera E., Steinmetz L.M., Braun E. (2013) Multiple genomic changes associated with reorganization of gene regulation and adaptation in yeast. Molecular Biology and Evolution 30(7):1514–1526. https://doi.org/10.1093/molbev/mst071

13. Ohad D.G., Avrahami A., Waner T., and David L.(2013) The occurrence and suspected mode of inheritance of congenital subaortic stenosis and tricuspid valve dysplasia in Dogue de Bordeaux dogs.  The Veterinary Journal 197:351-357. DOI: 10.1016/j.tvjl.2013.01.012

14. Bar I., Kaddar E., Velan A. and David L.PI (2013). Melanocortin receptor 1 and black pigmentation in the Japanese ornamental carp (Cyprinus carpio Var. Koi). Frontiers in Genetics 4,DOI: 10.3389/fgene.2013.00006

2011

15. Kongchum, P., Sandel E., Lutzky S., Hallerman, EM, Hulata, G, David, L; Palti, Y (2011) Association between IL-10a single nucleotide polymorphisms and resistance to cyprinid herpesvirus-3 infection in common carp (Cyprinus carpio). Aquaculture 315(3-4):417-421. https://doi.org/10.1016/j.aquaculture.2011.02.035

16. Kongchum, P. ,  Hallerman, EM., Hulata, G., David, L.; Palti, Y. (2011) Molecular cloning, characterization and expression analysis of TLR9MyD88 and TRAF6 genes in common carp (Cyprinus carpio). Fish Shellfish Immunol. 30(1): 361-371. DOI: 10.1016/j.fsi.2010.11.012

2010

17. David L., Stolovicki E., Haziz E. and Braun E. (2010) Inherited adaptation of genome-rewired cells in response to a challenging environment, HFSP Journal 4:131-141. DOI: 10.2976/1.3353782

18. Kongchum P., Palti Y., Hallerman E.M., Hulata G., David L. (2010) SNP discovery and development of genetic markers for mapping innate immune response genes in common carp (Cyprinus carpio).Fish Shellfish Immunol. 29(2): 356-361. DOI: 10.1016/j.fsi.2010.04.013  

19. Kongchum P., Rexroad III C. E., Hallerman E. M., David L., Palti Y. (2009) Single nucleotide polymorphism identification, genetic mapping and tissue expression of the rainbow trout TLR9gene. Anim. Genet. 40(6):1001-1001. DOI: 10.1111/j.1365-2052.2009.01924.x

2009 and Before

20. Sinha H*., David L.*, Pascon RC., Clauder MS., Krishnakumar S., Nguyen M., Shi G., Jed Dean, Oefner PJ., McCusker JH., Steinmetz LM. (2008) Sequential elimination of major-effect contributors identifies additional quantitative trait loci conditioning high- temperature growth in yeast.  Genetics, 180(3):1661-70. * Co-first authors, equal contributions. DOI: 10.1534/genetics.108.092932

21. Wei W., McCusker JH., Hyman RW., Jones T., Ning Y., Cao Z., Gu Z., Bruno D., Miranda M., Nguyen M., Wilhelmy J., Komp C., Tamse R., Wang X., Jia P., Luedi P., Oefner PJ., David L., Dietrich FS., Li Y., Davis RW., and Steinmetz LM. (2007) Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789. Proc. Natl. Acad. Sci. USA., 104(31): 12825-30. DOI: 10.1073/pnas.0701291104

22. Granevitze Z., Blum S., Cheng H., Vignal A., Morisson M., Ben-Ari G., David L., Feldman MW., Weigend S., Hillel J. (2007) Female-Specific DNA Sequences in the chicken genome. J. Hered.,98(3): 238-42. DOI: 10.1093/jhered/esm010

23. David L., Rosenberg NA., Lavi U., Feldman MW. and Hillel J. (2007) Genetic diversity and population structure inferred from the partially duplicated genome of domesticated carp, Cyprinus carpio L.  Genet. Sel. Evol. 39:319-340. DOI: 10.1051/gse:2007006

24. Ben-Ari G., Zenvirth D., Sherman A., David L., Klutstein M., Lavi U., Hillel J. and Simchen G. (2005) Four linked QTLs control sporulation efficiency in budding yeast. PLoS Genetics.2(11):e195. DOI: 10.1371/journal.pgen.0020195

25. Yue GH, David L, Orban L. (2006) Mutation rate and pattern of microsatellites in common carp (Cyprinus carpio L.). Genetica. 129 (3): 329-331 DOI: 10.1007/s10709-006-0003-8

26. Gagneur J., David L., Steinmetz LM.(2006) Capturing cellular machines by systematic screens of protein complexes. Trends Microbiol. 14(8):336-9. DOI: 10.1016/j.tim.2006.06.002

27. David L., Huber W., Granovskaia M., Toedling J., Palm CJ., Bofkin L., Jones T., Davis RW. and Steinmetz LM. (2006) A high-resolution map of transcription in the yeast genome. Proc. Natl. Acad. Sci. USA. 103(14):5320-5. DOI: 10.1073/pnas.0601091103

28. Iwashita S. Ueno S., Nakashima K., Song SY., Ohshima K., Tanaka K., Endo H., Kimura J., Kurohmaru M., Fukuta K., David L. and Osada N. (2006)  A tandem gene duplication followed by recruitment of a retrotransposon created the paralogous bucentaur gene (bcntp97) in the ancestral ruminant. Mol. Biol. Evol. 23(4):798-806.  DOI: 10.1093/molbev/msj088

29. Hillel J., Gefel D., Kalman R., Ben-Ari G., David L., Orion O., Feldman MW., Bar-On H., Blum S., Raz I., Schaap T., Shpirer I., Lavi U., Shafrir E. and Ziv E. (2005) Evidence for a major gene affecting the transition from normoglycaemia to hyperglycaemia in Psammomys obesusHeredity,95(2):158-65. DOI: 10.1038/sj.hdy.6800701

30. Ben-Ari G., David L., Blum S., Twito T., Vignal A., Weigend S., Feldman M. W., Lavi U. and Hillel J. (2004) Single Nucleotide Polymorphism (SNPs) in chicken: resources and possible applications. In: Second report on chicken genes and chromosomes 2005. Cytogenet. Genome Res., 109(4):415-79. DOI: 10.1159/000084205

31. Gu Z., David L., Petrov D., Jones T., Davis RW. and Steinmetz LM. (2005) Elevated evolutionary rates in the laboratory strain of Saccharomyces cerevisiaeP. Natl. Acad. Sci. USA,102(4):1092-7. DOI: 10.1073/pnas.0409159102

32. Hon-Nami K., Ueno S., Endo H., Nishimura H., Igarashi T., David L. and Iwashita S. (2004) A novel Giraffidae-specific interspersed repeat with a microsatellite, originally found in an intron of a ruminant paralogous p97bcnt gene. Gene, 13:340(2):283-90. DOI:10.1016/j.gene.2004.07.016

33. Prokisch H., Scharfe C., Camp DG., Xiao W. David L., Andreoli C., Monroe ME., Moore R J., Gritsenko MA., Kozany C., Hixson KK., Mottaz HM., Zischka H. Ueffing M., Herman ZS., Davis RW., Meitinger T., Oefner PJ., Smith RD. and Steinmetz LM. (2004) Integrative Analysis of the Mitochondrial Proteome in Yeast. PLoS Biology, 2(6):795-804. DOI:10.1371/journal.pbio.0020160

34. McKinnon JS., Mori S., Blackman B., David L., Kingsley D., Jamieson L., Chou J. and Schluter D. (2004) Evidence for ecology’s role in speciation. Nature, 429(6989):294-8. DOI: 10.1038/nature02556

35. David L., Rothbard S., Rubinstein I., Katzman H., Hulata G., Hillel J.,  Lavi U. (2004) Aspects of red and black color inheritance in the Japanese ornamental (Koi) carp (Cyprinus carpio L.). Aquaculture, 233(1-4):129-147. https://doi.org/10.1016/j.aquaculture.2003.10.033

36. David L., Blum S., Feldman MW., Lavi U., Hillel J. (2003) Recent duplication of the common carp (Cyprinus carpio L.) genome as revealed by analyses of microsatellite loci. Mol. Biol. Evol., 20(9): 1425-1434. DOI: 10.1093/molbev/msg173

37. Hillel J., Groenen MAM., Tixier-Boichard M., Korol AB., David L., Kirzhner VM., Burke T., Barre-Dirie A., Crooijmans RPMA., Elo K., Feldman MW, Freidlin PJ., Mäki-Tanila A., Oortwijn M., Thomson P., Vignal A., Wimmers K. and Weigend S. (2003) Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet. Sel. Evol., 35(5):533-557.DOI:10.1051/gse:2003038

38. David, L., Jinggui, F., Palanisamy, R., Hillel, J. and Lavi, U. (2001) Polymorphism in ornamental and common carp strains (Cyprinus carpio L.) as revealed by AFLP analysis and a new set of microsatellite markers. Mol. Gen. Genomics, 266: 353-362. DOI: 10.1007/s004380100569

39. Rothbard, S., Shelton, W.L., Rubinshtein, I., Hinits Y. and David, L. (2000) Induction of all-female triploids in Grass carp (Ctenophringodon idella) by integration of hormonal sex inversion and ploidy manipulations. Israeli J. Aquacult. - Bamidgeh, 52(4):133-150.

40. Rothbard, S., Rubinshtein, I. and David, L. (1999) Coloration in crosses between two variants of goldfish, Carassius auratus. Israeli J. Aquacult. - Bamidgeh, 51(3):133-140.

41. Rothbard, S., Rubinshtein, I., David, L. and Shelton, W.L. (1999). Ploidy manipulations aimed to produce androgenetic Japanese ornamental (Koi) carp, Cyprinus carpio L. Israel J. Aquacult. - Bamidgeh, 51(1): 26-39.

 

See also: Lior David

Photo Gallery

See also: Lior David