Welcome to the home webpage for the research lab of Dr. L. Kevin Lewis
B.S. Chemistry, Ohio University Ph.D. Molecular and Cellular Biology, University of Arizona
Below: Description of Research Projects, Recent Journal Publications, Photographs of Graduate Research Students, Titles of Graduate Student Theses.
Description of Research Projects:
The chromosomes within animal and plant cells are continually engaged in a cycle of DNA damage and repair. One common type of damage involves breakage of one or both strands of the DNA double helix. This type of DNA damage is particularly prevalent after exposure of cells to agents such as X-rays or radon gas and is also induced by many chemicals used in cancer chemotherapy.
Restoration of the broken DNA double helix requires the coordinated activities of a large number of cellular proteins. The laboratory is applying modern techniques of molecular biology and biochemistry to identify and characterize genes involved in repair of strand breaks and other types of DNA damage in the model organism Saccharomyces cerevisiae (budding yeast). Several genes identified in this work have been found to affect other aspects of DNA metabolism, including cell cycle checkpoint responses and telomere stability. Furthermore, a subset of genes encode proteins homologous to human proteins previously implicated in a number of human diseases including cancer. Understanding these processes and the multiple pathways involved in DNA strand break repair are major goals of current research in the lab.
A second major effort in the lab involves the study of cellular aging. Most human cells stop producing telomerase, a DNA polymerase enzyme, early in development. Both in vivo and when grown in culture, telomerase-deficient cells undergo progressive shortening at the ends of their chromosomes, at regions called telomeres. A new system developed in the lab allows modulated expression of telomerase inside cells. This expression system has been used to perform critical tests of current models for cell aging. In addition, the impacts on the rate of cellular aging of mutations in DNA repair, replication and recombination genes, as well as cellular exposure to chemicals that modify DNA, are being investigated.
The lab also has multiple ongoing collaborative projects investigating the interactions between nucleic acids and nanomaterials that have potential for use in gene delivery and drug delivery into cells.
Recent Publications:
1. Shubha R. L. Malla†, Archana Gujjari†, Carlos E. Corona‡, Gary W. Beall and L. Kevin Lewis*. 2023. Spectrophotometric and nucleic acid-binding properties of halloysite clay nanotubes and kaolinite. Heliyon 9:e13009.
2. Cory L. Holland, Monica F. Weis†, Corbin J. England†, Armand M. Berry†, Paige Hall‡ and L. Kevin Lewis*. 2023. Deficiency in homologous recombination is associated with changes in cell cycling and morphology in Saccharomyces cerevisiae. Experimental Cell Research 430:113701.
3. O’Taveon R. Fitzgerald†, Nestor D. Rodriguez† and L. Kevin Lewis*. 2022. High efficiency plasmid DNA transformation in yeast. Invited paper: Methods in Molecular Biology. 2513:15-22.
4. Cory L. Holland, Brian A. Sanderson†, James K. Titus†, Monica F. Weis†, Angelica M. Riojas†, Eric Malczewskyj†, Brian M. Wasko and L. Kevin Lewis*. 2021. Role of DNA repair and replication factors in the suppression of telomere instability in Saccharomyces cerevisiae yku70 mutants. Genes, Genomes & Genetics 11: jkab359.
5. Corbin J. England†, Tanner C. Gray‡, Shubha R. L. Malla†, Samantha A. Oliveira‡, Benjamin R. Martin, Gary W. Beall and L. Kevin Lewis*. 2020. pH-dependent sedimentation of DNA in the presence of divalent, but not monovalent, metal ions. Analytical Biochemistry 616:114099.
6. Neda Z. Ghanem†, Shubha R. L. Malla†, Naoko Araki† and L. Kevin Lewis*. 2019. Quantitative assessment of changes in cell growth, size and morphology during telomere-initiated cellular senescence in Saccharomyces cerevisiae. Experimental Cell Research 381:18-28.
7. Jennifer A. Ream‡, L. Kevin Lewis and Karen A. Lewis. 2018. Horizontal agarose gel mobility shift assay for protein-RNA complexes. Methods in Molecular Biology, 1855:363-370. Published online 11-14-18.
8. Archana Gujjari†, Blanca V. Rodriguez†, Jorge Pescador‡, Corina Maeder, Gary W. Beall and L. Kevin Lewis*. 2017. Factors affecting the association of single- and double-stranded RNAs with montomorillonite nanoclays. International Journal of Biological Macromolecules, 109:551-559. Epub Dec 22, 2017.
9. Whitney N. Wood‡, Kyle D. Smith‡, Jennifer A. Ream‡, and L. Kevin Lewis*. 2016. Enhancing yields of low and single copy number plasmid DNAs from Escherichia coli cells. Journal of Microbiological Methods. 133:46-51. Published online on 12-23-16. DOI: 10.1016/j.mimet.2016.12.016
10. Jennifer A. Ream‡, L. Kevin Lewis and Karen A. Lewis. 2016. Rapid agarose gel electrophoretic mobility shift assay for quantitating protein:RNA interactions. Analytical Biochemistry 511:36-41.
11. Blanca V. Rodriguez†, Jorge Pescador‡, Nicole Pollok‡, Gary W. Beall, Corina Maeder and L. Kevin Lewis*. 2015. Impact of size, secondary structure and counterions on the binding of small RNAs to layered double hydroxide nanoparticles. Biointerphases 10(4):041007.
12. Blanca V. Rodriguez†, Eric T. Malczewskyj†, Joshua M. Cabiya‡, L. Kevin Lewis and Corina Maeder. 2015. Identification of an RNase-resistant population of RNAs in Saccharomyces cerevisiae extracts: separation from chromosomal DNA by selective precipitation. Analytical Biochemistry 492:69-75. (Epub 2015 Sep 28)
13. Brian A. Sanderson†, Naoko Araki†, Jennifer L. Lilley‡, Gilberto Guerrero‡ and L. Kevin Lewis*. 2014. Modification of gel architecture and TBE/TAE buffer composition to minimize heating during agarose gel electrophoresis. Analytical Biochemistry 454:44-52.
14. Jennifer Summers McKinney†, Sunaina Sethi†, Jennifer DeMars Tripp†, Thuy N. Nguyen†, Brian A. Sanderson†, James W. Westmoreland, Michael A. Resnick and L. Kevin Lewis*. 2013. A multistep genomic screen identifies new genes required for repair of DNA double-strand breaks in Saccharomyces cerevisiae. BMC Genomics 14:251-266.
15. Jennifer DeMars Tripp†, Jennifer L. Lilley‡, Whitney N. Wood‡ and L. Kevin Lewis*. 2013. Enhancement of plasmid DNA transformation efficiencies in early stationary phase yeast cell cultures. Yeast 30:191-200.
16. Brian A. Sanderson‡, Drew S. Sowersby‡, Sergio Crosby, Marcus Goss, L. Kevin Lewis and Gary W. Beall. 2013. Charge density and particle size effects on oligonucleotide and plasmid DNA binding to nanosized hydrotalcite. Biointerphases 8:8-18.
17. Sandra C. Becerra†, Hiranthi T. Thambugala†, Alison Russell Erickson†, Christopher K. Lee† and L. Kevin Lewis*. 2012. Reversibility of replicative senescence in Saccharomyces cerevisiae: effect of homologous recombination and cell cycle checkpoints. DNA Repair 11:35-45.
18. Christopher K. Lee†, Naoko Araki†, Drew S. Sowersby† and L. Kevin Lewis*. 2011. Factors affecting chemical-based purification of DNA from Saccharomyces cerevisiae. Yeast [Online] doi: 10.1002/yea.1918 (accessed Nov 15, 2011).
19. L. Kevin Lewis*, Michael H. Robson†, Yelena Vecherkina, Chang Ji and Gary W. Beall. 2010. Interference with spectrophotometric analysis of nucleic acids and proteins by leaching of chemicals from plastic tubes. Biotechniques 48:297-302.
Recent students:
Diego Valdez-Oranday and Yogesh Nepal
O’taveon Fitzgerald and Shubha Malla
Corbin England and Nestor Rodriguez
Archana Gujjari, Shubha Malla, Angelica Riojas and Monica Weis
Top: Jennifer Lilley and James Titus
Bottom: Blanca Rodriguez and Neda Ghanem
Brian Sanderson and Eric Malczewskyj
Jennifer DeMars-Tripp and Naoko Araki
Thuy Nguyen and Drew Sowersby
Mike Robson, Sunaina Sethi and Chris Lee
Jennifer Summers-McKinney and Rachel Roberts
Sandra Becerra and Cory Holland
Hiranthi Thambugala, Brian Wasko and Allison Russell
Jared Cassiano and Shanna Calero
Graduate student thesis titles:
2021: Shubha Malla – “New approaches for separation of DNAs with different structures by selective sedimentation using nanoparticles and metals”
2021: Diego Valdez-Oranday – “Development of new assays for the simultaneous measurement of DNA double-strand break repair by alternative pathways”
2020: O’taveon Fitzgerald – “Impact of DNA end structure and cellular growth phase on DNA repair by nonhomologous end-joining (NHEJ) in Saccharomyces cerevisiae”
2018: Corbin England – “Role of spontaneous DNA damage and single-stranded DNA in generation of enlarged G2 phase cells in rad52 mutants of Saccharomyces cerevisiae”
2018: Nestor Rodriguez – “Differential requirements for nonhomologous end- joining (NHEJ) pathway genes in DNA repair”
2017: Monica Weis – “DNA double-strand break repair deficiency is associated with changes in cell cycling and cell morphology in Saccharomyces cerevisiae”
2016: Shubha Malla – “Quantitative assessment of changes in cellular morphology and cell division number during telomere-initiated senescence in the yeast Saccharomyces cerevisiae”
2016: Angelica Riojas – “Roles of genes affecting telomere lengths, chromatin remodeling, and cell cycle checkpoints in maintenance of chromosome stability in yeast yku70 mutants”
2015: Blanca Rodriguez – “Investigation of the binding affinity of RNA molecules for hydrotalcite and montmorillonite as potential RNA interference-based therapy delivery systems”
2015: Neda Ghanem – “Telomere-initiated cellular aging in Saccharomyces cerevisiae: impact of nutrient availability and factors affecting genetic exchange”
2015: James Titus – “Stabilization of the ends of chromosomes in yeast yku70 mutants: role of telomerase complex subunits and telomere-associated proteins”
2015: Jennifer Lilley – “Analysis of NHEJ DNA repair efficiency and accuracy in new mutants of Saccharomyces cerevisiae”
2013: Brian Sanderson – “Investigation of the functions of new genes involved in repair of DNA double-strand breaks in Saccharomyces cerevisiae”
2012: Thuy Nguyen – “Investigation of DNA stability in Saccharomyces cerevisiae mutants defective in the repair of broken chromosomes”
2012: Eric Malczewskyj – “Analysis of genes that affect telomere stability in yku70 mutants and new approaches for separation of yeast nucleic acids”
2012: Drew Sowersby – “Exploring gene overexpression as a strategy to increase alcohol resistance in the yeast Saccharomyces cerevisiae”
2011: Jennifer DeMars – “Use Of A Novel Genomics Approach To Identify New DNA Repair Genes And Development Of Improved Repair Assays”
2011: Naoko Araki – “Improved methods for analysis of telomere-initiated cellular senscence and telomere shortening in Saccharomyces cerevisiae”
2010: Sunaina Sethi – “Characterization of new genes required for DNA double-strand break repair in Saccharomyces cerevisiae”
2009: Christopher Lee – “Development of new techniques for telomere length analysis in aging yeast cells and in senescent cells rescued by reactivation of telomerase”
2009: Michael Robson – “Sorption studies of oligonucleotide DNA on montmorillonite clay: development of an improved assay protocol”
2008: Rachel Roberts – “Development of new assays to identify Saccharomyces cerevisiae genes required for efficient repair of a single site-specific DNA double-strand break”
2008: Cory Holland – “Role of telomerase in regulation of chromosome stability in cells lacking the Ku70/Ku80 heterodimer”
2008: Jennifer Summers – “Application of a novel endonuclease sensitivity assay to identify new genes that affect DNA repair and chromosome stability”
2007: Sandra Becerra – “Mechanism of establishment and bypass of in vitro cell aging”
2006: Alison Russell – “Role of reactive oxygen species and altered biochemical pathways in cellular aging”
2006: Brian Wasko – “Interactions between double-strand break repair proteins and the telomerase DNA replication complex”
2005: Hiranthi Thambugala – “Use of a new regulatable telomerase expression system to monitor in vitro cell aging and the effects of DNA damage on replicative senescence”
2004: Jared Cassiano – “DNA damage resistance determined by interplay between telomerase and DNA repair complexes”
2003: Natashya Waring – “Isolation and characterization of DNA polymerase epsilon mutants affecting DNA replication, repair and cell cycle checkpoints in Saccharomyces cerevisiae”
2003: Shanna Calero – “Repair of DNA double-strand breaks in chromosomes: impact of telomerase”