Shehre-Banoo Malik

Postdoctoral Fellow, 12/2007-present, Laboratory of Dr. Jane M. Carlton, New York University Department of Medical Parasitology. [CONTACT]

Postdoctoral Research Scholar, 8-12/2007. Laboratory of John M. Logsdon, Roy J. Carver Center for Comparative Genomics, Department of Biological Sciences, University of Iowa.

Ph.D., 2007, Biology, University of Iowa, laboratory of Dr. J.M. Logsdon. Thesis: The early evolution of meiotic genes. ProQuest Digital Dissertations database Publication # AAT 3273491. 8/2000 - 8/2003 at Population Biology, Ecology and Evolution Program, Dept of Biology, Emory University, Atlanta GA & 8/2003 - 7/2007 at the University of Iowa.

Protistology Workshop, 2005. Marine Biological Laboratory, Woods Hole MA.

Workshop on Molecular Evolution and Extended Topics Session, 2001. Marine Biological Laboratory, Woods Hole MA.

M.Sc., 2000, Biology [abstract], University of Ottawa, laboratory of Dr. Guy Drouin. Thesis: The evolution of land plants inferred using regions D-F of the largest subunit of RNA polymerase II, ProQuest Digital Dissertations database Publication # AAT MQ48169.

B.Sc., 1995, Honors, Biology, University College of Cape Breton. Thesis: Cloning and characterization of the DNA polymerase epsilon gene from Trichomonas vaginalis. Advised by Dr. W. Ford Doolittle, Dalhousie University.

Current Research:Evolution of meiotic and housekeeping genes in trichomonads and comparative genomics, in the Carlton laboratory.

2000-2007 Research:

1. How are the eukaryotes related to one another? The tree of life is the framework to explore the evolution of features such as meiosis which are novel to eukaryotes. Protists represent the greatest diversity of eukaryotic organisms and thus hold the key to elucidating the prokaryote-to-eukaryote transition,yet their biology and history is the least understood. Molecular data collected from key protist lineages is useful to help establish which extant eukaryotic lineages can provide us with the most clues about the evolution and ancestry of eukaryotes. I used degenerate PCR to isolate the largest subunit of RNA polymerase II (RPB1) from early-branching eukaryotes, particularly Excavates, and am studying their evolutionary relationships (in collaboration with Jing Yuan, Joel Dacks, Kate McKiernan, Glenn Morse, Nevin Sebastian and Cindy Brochu). This project is part of the "Eu-Tree" initiative for assembling the tree of eukaryotic life.

2. Meiosis is a eukaryotic innovation to which DNA repair is central. What is the role of multigene families in the evolution of meiosis? Meiosis the component of sexual reproduction in the life cycles of eukaryotic cells where ploidy is halved by a reduction division. Homologous chromosomes replicate, recombine and synapse during the initial stages of meiosis. The meiotic recombination machinery is studied in depth in animals, fungi and plants. The details of this process in protists require illumination at the molecular level, though. I conducted detailed bioinformatic surveys to identify the conserved core of 34 meiotic genes in the genomes of protists and other eukaryotes from public databases (as in Ramesh, Malik & Logsdon, 2005 and Malik, Ramesh et al , 2007). We have identified meiotic genes in protists that were putatively ancient asexuals. Check out the Logsdon Lab Bioinformatics Toolkit! The goal is to ascertain the diversity of eukaryotic organisms from which these sequences are available and the degree of sequence conservation across this group of organisms, thus establishing a "meiosis detection kit". Together with John Logsdon, Art Pightling and Marilee Ramesh, all of these protein sequences were aligned and we identified conserved regions of the alignments and designed degenerate PCR primers to target the conserved regions of the genes in other organisms. With Art, I am also exploring the evolution of MutS and MutL homologs across the tree of life. I isolated MutS genes by degenerate PCR from diverse early-branching protists to help elucidate the evolutionary relationships of the eukaryotic multigene family of mutS homologs.

3. Genes can hop across species boundaries and remain functional! We have identified some independent lateral gene transfers (LGT) of IMPDH between bacteria and protists, studied in collaboration with the laboratories of Dr. Boris Striepen, Dr. Rick Tarleton (University of Georgia, Center for Tropical and Emerging Global Disease) and others. This has implications for the evolution of purine salvage pathways in eukaryotic microorganisms.

Affiliations:

Secretary of the International Society of Evolutionary Protistology, 2006-2008. Member since 2005.
Member of the International Society of Protistologists, 2008. 
Member of the New York Academy of Sciences, 2008.
Treasurer of the University of Ottawa Biology Graduate Students' Association, 1995-1996.
University College of Cape Breton Recycling Council, 1991 - 1993.
City of Sydney Human Rights Affirmative Action Committee, 1989 - 1990.

Publications:

Malik S.-B., Pightling A.W., Stefaniak L.M., Schurko A.M., Logsdon J.M. Jr. (2008) An expanded inventory of conserved meiotic genes provides evidence for sex
in Trichomonas vaginalis. Public Library of Science - One, 3(8): e2879. doi:10.1371/journal.pone.0002879. [article] [supplemental material] [comments]

Malik S.-B., Ramesh M.A., Hulstrand A.M. and J.M. Logsdon Jr (2007). Protist homologs of meiotic Spo11 genes and topoisomerase VI reveal an evolutionary history of gene duplication and lineage-specific loss. Molecular Biology and Evolution, 24:12:2827-2841.[article] [supplemental material]

Carlton J.M., Hirt R.P., Silva J.C., Delcher A.L., Schatz M., Zhao Q., Wortman J.R., Bidwell S.L., Alsmark U.C.M., Besteiro S., Sicheritz-Ponten T., Noel C.J., Dacks J.B., Foster P.G., Simillion C., van der Peer Y., Miranda-Saavedra D., Barton G.J., Westrop G.D., Muller S., Dessi D., Fiori P.L., Ren Q., Paulsen I., Zhang H., Bastida-Corcuera F.D., Simoes-Barbosa A., Brown M.T., Hayes R.D., Mukherjee M., Okumura C.Y., Schneider R., Smith A.J., Vanacova S., Villalvazo M., Haas B.J., Pertea M., Feldblyum T., Utterback T.R., Shu C.-L., Osoegawa K., de Jong P.J., Hrdl I., Horvathova L., Zubacova Z., Dolezal P., Malik S.-B., Logsdon J.M. Jr., Henze K., Gupta A., Wang C.C., Dunne R.L., Upcroft J.A., Upcroft P., White O., Salzberg S.L., Tang P., Chiu C.-H., Lee Y.-S., Embley T.M., Coombs G.H., Mottram J.C., Tachezy J., Fraser-Liggett C.M. and P.J. Johnson (2007) Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis. Science, 315:5807:207-212. [article] [supporting online material]

Nicholson A.C.*, Malik S.-B.*, Logsdon J.M. Jr. and E.G. van Meir (2005) Functional evolution of ADAMTS genes: Evidence from analyses of phylogeny and gene organization. BMC Evolutionary Biology, 5:11. [PDF, additional files 1 and 2] *equal contributions.

Ramesh M.A.*, Malik S.-B.* and J.M. Logsdon Jr. (2005) A phylogenomic inventory of meiotic genes: Evidence for sex in Giardia and an early eukaryotic origin of meiosis. Current Biology, 15:2:185-191. *equal contributions. [PDF and supplemental material] Related articles in: Current Biology, The Scientist, NPR, ScienceNews, Roanoke College E-News.

Striepen B., White M.W., Li C., Guerini M.N., Malik S.-B., Logsdon J.M. Jr., Liu C. and M.S. Abrahamsen (2002) Genetic complementation in Apicomplexan parasites. Proceedings of the National Academy of Sciences U.S.A., 99: 6304 - 6309. [abstract] [PDF]

Edgell D.R., Malik S.-B. and W.F. Doolittle (1998) Evidence of independent gene duplications during the evolution of archaeal and eukaryotic family B DNA polymerases. Molecular Biology and Evolution, 15: 1207 - 1217. [abstract] [PDF]

Manuscripts in preparation:

Malik S.-B., Logsdon J.M. Jr. Meiosis-specific MutS homologs MSH4 and MSH5 are broadly distributed in protists: Implications for crossover interference.

Malik S.-B., Pightling A.W., Logsdon J.M. Jr. Origin and evolution of meiotic genes by duplication.

collaboration with Yuan J., Dacks, J.B., Brochu C.D., Morse G.J., McKiernan K.R., Sebastian N. and J.M. Logsdon Jr. Phylogeny of eukaryotes inferred from the RNA polymerase II largest subunit RPB1.

collaboration with Kanchagar C., Lim H.-C., Hedstrom L., Subramanya S., Mensa-Wilmot K., Tarleton R.L., Logsdon J.M. Jr. and B. Striepen. Two phylogenetically divergent IMP dehydrogenases in the life cycle of Trypanosoma brucei.

Malik S.-B., Pightling A.W. Gene duplication and lateral gene transfer during the evolutionary history of eukaryotic MutS and MutL homologs.

Awards & Honors:

2008: New York University School of Medicine Sackler-Fisher Postdoctoral Travel Grant for Protist 2008 meeting
2007: Society for Molecular Biology and Evolution Graduate Student Travel Award.
2006: International Society of Evolutionary Protistology Founder's Fund Student Scholarship.
2006: University of Iowa Scholarly Presentation Awards for the ISEP XVI meeting from International Programs, Women in Science and Engineering, the Graduate Student Senate, Student Government and Department of Biological Sciences.
2006: Avis Cone Summer Fellowship, University of Iowa.
2006: First place, Outstanding Graduate Student Mentor, Biological & Health Sciences, University of Iowa. [picture]
2005: Graduate College Summer Fellowship, University of Iowa.
2005: University of Iowa Biological Sciences travel award for ISEP XV meeting.
2004: Avis Cone Summer Fellowship, University of Iowa.
9/2000 - 8/2003: Graduate Fellowship and tuition waiver, Graduate Division of Biological and Biomedical Sciences, Emory University.
2001 ­ 2003: Travel awards from Emory University to present posters at scientific meetings: SMBE 2001, ISEP XIV 2002 & GSC 2003.
2003: Genetics Society of Canada student travel prize for annual meeting.
2002: Burroughs-Wellcome Fund student travel prize for ISEP XIV Meeting.
2001: Scholarships for Workshop on Molecular Evolution from M.B.L. & Emory University.
1993: Silver Medalist (BSc), Highest academic standing, University College of Cape Breton.
1990 ­ 1993: Dean's List Na Gaisgich University College of Cape Breton.
1992: University College of Cape Breton Scholarship.
1990: University College of Cape Breton Bruce and Dorothy Rosetti Entrance Scholarship.
1990: J. Victor Fraser Memorial Scholarship.
1990: John J. Gillis Memorial Scholarship for proficiency in English.
1990: Dalhousie University Entrance Scholarship and Canada Scholarship (declined).
1989: Dr. William Mould Medal, Sydney Academy.

Other research:

Plant mitochondrial gene organization and transfer. Research Assistant (9/1999 - 8/2000). Laboratory of Dr. Linda Bonen, Biology Dept., University of Ottawa.
Dystrophin enhancer transfection and expression in fibroblasts and mouse genotyping. Research Assistant (5/1999 - 8/1999). Laboratory of Dr. Ronald G. Worton, Ottawa Hospital Research Institute.

Teaching Experience:

Introduction to Bioinformatics (Fall 2004). 002:170, Department of Biological Sciences, University of Iowa, with Dr. J. Fassler and Dr. D. Bhattacharya. Grading and lab demonstrations.
Investigative Evolution Lab (Fall 2001). Bio471, Biology Department, Emory College, with Dr. C. Beck and Dr. J. Logsdon. Reagent preparation, lab setup and cleanup, lab demonstration, advising students, writing instructions for handouts.
Genetics Lab (Winter 1999). Bio2123, Biology Dept., University of Ottawa, with Dr. Peter Heinermann. Lab demonstration, grading & advising students. Student evaluation rating mean of 3.81/5, 59 students.
Introduction to Cell Biology Lab (Fall 1996, 1997, 1998). Bio1110, Biology Dept., University of Ottawa, with Dr. Peter Heinermann. Lab demonstration, grading & advising students.
Genetics (Winter 1998). Bio2123, Biology Dept., University of Ottawa, with Dr. Linda Bonen and Dr. Robert Charlebois. Tutorials, grading and advising students.
Physiological Concepts Lab (Winter 1996). Bio1111, Biology Dept., University of Ottawa, with Dr. Peter Heinermann. Lab demonstration, grading & advising students.
Introduction to Plant Science Lab (Fall 1995). Bio2122, Biology Dept., University of Ottawa, with Dr. Peter Heinermann. Lab demonstration, grading & advising students.
Introductory Chemistry Lab (Fall 1992 - Spring 1993). Chem120, University College of Cape Breton, with J. Richardson. Lab demonstration and grading.

Graduate Coursework Summary:

University of Iowa: Molecular Phylogenetics, and Topics courses in Ecology and Evolution of Sex, Cell Cycle Control, Writing in the Natural Sciences, and microRNAs
Emory University: Evolution, Molecular Evolution, Biostatistics, Ecology, Quantitative Methods in Population Biology, Graduate seminar; Advanced topics courses in Viral Pathogenesis, Major Transitions in Evolution and Coevolution
University of Georgia: Biology of Protists
University of Ottawa: Introductory bioinformatics and molecular evolution, Recent advances in biology, Graduate seminar

Skills:

Cell culture: Culturing trichomonads, E.coli, Hartmanella, Tetrahymena, Naegleria and fibroblasts.

Molecular biology: nuclear and mitochondrial RNA and DNA extraction, degenerate PCR amplification, RT-PCR, cloning, library screening, sequencing, Northern and Southern blot hybridizations, luciferase assays. Lab responsibilities have included purchasing lab supplies and management of biological, chemical and radioactive waste.

Informatics: Mac, Windows and Unix operating systems; webmaster and system administrator, UNIX and lab MacOsX systems, 9/2001 to the present.
General software: MSOffice, Corel Wordperfect, Adobe Photoshop, Adobe Pagemill, Adobe Acrobat, Canvas, Appleworks, BBEdit, EditPad.
Bioinformatic software: Sequencher, BLAST, ClustalW, ClustalX, Codons, Li93, GDE, BioEdit, MacClade, PHYLIP, PAUP*, Tree-Puzzle, MrBayes, Treetool, Treeview.

Presentations:

Malik S.-B., Pightling A.W., Conrad M., Ostrer L., Logsdon J.M. Jr., Carlton J.M. 7/2008. Sex and meiosis in trichomonads. Platform talk, Protist 2008 - XVII Meeting of the International Society for Evolutionary Protistology, Dalhousie University, Halifax, Canada.
Malik S.-B., Yuan J., Brochu, C.D., Dorrell R., Morse G.J., McKiernan K.R., Sebastian N., Dacks J.B., J.M. Logsdon Jr. 7/2008. Phylogeny of eukaryotes inferred from the RNA polymerase II largest subunit. Poster, Protist 2008 - XVII Meeting of the International Society for Evolutionary Protistology, Dalhousie University, Halifax, Canada.
Malik S.-B., Pightling A.W., Ramesh M.A., Hulstrand A.M., Stefaniak L.M. and J.M. Logsdon Jr. 1/2008. The early evolution of meiosis. Contributed talk. Annual New York Microbial Evolution Meeting, New York NY.
Malik S.-B., Pightling A.W., Ramesh M.A., Stefaniak L.M., Hulstrand A.M., and J.M. Logsdon Jr. 6/2007. Early evolution of meiosis-specific genes by gene duplications in protists. Contributed talk, Annual Meeting of the Society for Molecular Biology and Evolution, Dalhousie University, Halifax, Canada.
Malik S.-B., Pightling A.W., Ramesh M.A., Hulstrand A.M., Stefaniak L.M., Yuan J., Olszewski J.M., and J.M. Logsdon Jr. 6/2007. The early evolution of meiotic recombination machinery. Invited seminar. University of Georgia Center for Tropical and Emerging Global Disease, Athens GA.
Malik S.-B., Pightling A.W., Ramesh M.A., Hulstrand A.M., Stefaniak L.M., Yuan J., Olszewski J.M., and J.M. Logsdon Jr. 6/2007. Pervasive gene duplication in the origin of meiosis revealed by Trichomonas. Invited seminar. New York University School of Medicine Department of Medical and Molecular Parasitology, New York NY.
Malik S.-B., Yuan J., Morse G.J., McKiernan K.R., Sebastian N., Brochu, C.D., Dacks J.B. and J.M. Logsdon Jr. 2007. Phylogeny of eukaryotes inferred from the RNA polymerase II largest subunit. Talk, Annual group meeting, Assembling the Tree of Life - Reconstructing Eukaryotic Phylogeny through Multigene Analyses of Microbial Eukaryotes, Iowa City IA.
Malik S.-B., Yuan J., Morse G.J., Sebastian N. and J.M. Logsdon Jr. 11/2006. Phylogeny of eukaryotes inferred from the RNA polymerase II largest subunit. Poster, First Annual Biological Sciences Graduate Program Retreat, Dubuque IA.
Malik S.-B., Pightling A.W., Stefaniak L.M., Ramesh M.A., Hulstrand A.M., Yuan J., Olszewski J.M., Schurko A.M., and J.M. Logsdon Jr. 11/2006. Origin of meiotic genes by duplications early in the evolution of eukaryotes. Poster, First Annual Biological Sciences Graduate Program Retreat, Dubuque IA.
Malik S.-B., Pightling A.W., Ramesh M.A., Hulstrand A.M., Sahni N., Stefaniak L.M., Yuan J., Olszewski J., Schurko A.M. and J.M. Logsdon Jr. 8/2006. Early evolution of meiosis-specific genes by gene duplications. Platform talk, XVI Meeting of the International Society for Evolutionary Protistology, University of Wroclaw, Wroclow, Poland.
Malik S.-B., Pightling A.W., Hulstrand A.M., Sahni N., Yuan J., Ramesh M.A., Stefaniak L.M., Schurko A.M., Ramesh M.A. and J.M. Logsdon Jr. 3/2006. Investigating the evolution of meiosis by studies of gene duplication that include the protists. Talk, James F. Jakobsen Conference, University of Iowa. [abstract]
Malik S.-B., Ramesh M.A., Pightling A.W., Stefaniak L.M., Logsdon J.M. Jr. 4/2005. Phylogenomic analyses reveal an early origin of meiosis in protists. Talk, James F. Jakobsen Graduate Student Senate Forum, University of Iowa. Third prize winner. [abstract]
Malik S.-B., Ramesh M.A., Pightling A.W., Stefaniak L.M. and J.M. Logsdon Jr. 4/2005. Phylogenomic analyses reveal an early origin of meiosis in protists. Talk, Roy J. Carver Center for Comparative Genomics Seminar Series, University of Iowa.
Malik S.-B., Ramesh M.A., Pightling A.W., Stefaniak L.M., Logsdon J.M. Jr. 2/2005. Phylogenomic analyses reveal the early origin of meiosis in protists. Platform talk, XV Meeting of the International Society for Evolutionary Protistology, University of Melbourne, Melbourne, Australia.
Malik S.-B., Ramesh M.A., Stefaniak L.M., Schurko A.M., Pightling A.W. and J.M. Logsdon Jr. 3/2004. The evolution of eukaryotes and meiosis. Poster, Jakobsen Graduate Student Senate Forum, University of Iowa. [abstract]
Malik S.-B. & J.M. Logsdon Jr. 6/2003. The evolution of eukaryotes and molecular origins of meiosis. Poster, 46th Annual Conference of the Genetics Society of Canada, King's College, Halifax, Canada [abstract]
Malik S.-B., Ramesh M.A., and J.M. Logsdon Jr. 2/2003. The evolution of eukaryotes and early steps in the evolution of meiosis. Talk, Population Biology, Ecology and Evolution Seminar, Emory University, Atlanta, GA.
Malik S.-B., Striepen B., Logsdon J.M. Jr. 6/2002. Lateral transfer of inosine-monophosphate dehydrogenase genes from bacteria to eukaryotes. Poster, XIV Meeting of the International Society for Evolutionary Protistology 6/02 University of British Columbia, Vancouver, Canada, and Bionorth2002 11/02 Ottawa, Canada. [abstract]
Ramesh M.A., Malik S.-B. & J.M. Logsdon Jr. 7/2001. Elucidating the origins of meiosis: Strategies to isolate meiotic genes from diverse protozoa. Poster, Society for Molecular Biology & Evolution Annual Meeting, Athens GA.
Malik S.-B. and G. Drouin. 1998. Evolutionary relationships of RPB1 in land plants. Biology Departmental Seminar, University of Ottawa, Ottawa Canada.
Malik S.-B. & G. Drouin. 7/1996. Evolution of RPB1 in Animals, Plants and Fungi. Poster, Canadian Institute for Advanced Research Program in Evolutionary Biology Student Meeting, Dalhousie University, Halifax, Canada.
Malik S.-B., Edgell D.R., Doolittle W.F. 1995. Isolating the DNA polymerase epsilon gene from Trichomonas vaginalis. Talk, 9th Annual Cameron Conference of Biology Honors Students. Dalhousie University, Halifax, Canada.
 

Personnel trained:

7/2008: Lily Ostrer, High school student Volunteer, NYU. Prevalence and polymorphism of Trichomonas tenax.
4 - 6/2008: Melissa Conrad, NYU PhD rotation student. Prevalence and polymorphism of Trichomonas vaginalis.
Spring 2007: Kate McKiernan, University of Iowa senior undergraduate. Degenrate PCR and cloning of protist RPB1 genes.
11/2005 - 2/2006: Alissa Hulstrand, Rotation PhD student, University of Iowa. Bioinformatic analyses and cloning of protist Spo11 homologs.
11/2005 - 2/2006: Nidhi Sahni, Rotation PhD Student, University of Iowa. Degenerate PCR, cloning and sequencing of protist RecA homologs for inference of the tree of eukaryotes.
Summer 2005: Justine Olszewski, high school student. Sequencing Hartmanella MSH2 and BLAST analyses of Trichomonas meiotic genes.
Spring 2005: Jing Yuan, Rotation PhD Student, University of Iowa. PCR of Hartmanella MSH2.
Sept. 2003 - August 2004: Lauren Stefaniak, Research Assistant, general lab maintenance, cloning, sequencing and database mining of meiotic genes.
Fall 2003: Courtney Smith, University of Iowa Biology freshman work-study lab assistant.
Summer 2003: Betsy Chaitkin, Emory University Biology junior. Database mining and phylogenetic analyses of protist RecA homologs, and research poster preparation.
Spring 2003: Joel Boggan, Emory University Biology Honors student. Cloning, database mining and phylogenetic analyses of eukaryotic RNA polymerase II subunits RPB1 and RPB2.
Fall 1997 - Spring 1998: Marc Carrier, University of Ottawa Biology Honors student. Cloning and substitution rate analyses of actin genes and processed pseudogenes in the Solanaceae.
Summer 1997: Carla Densmore, University of Ottawa NSERC summer research assistant. Cloning and sequencing of plant RPB1 genes.

Links, Pictures (Lab, ISEP XIV), Canadian news, newspapers, airfares

Last modified 19th August 2008. copyright SBM