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Howard M. Laten, Ph.D.

[Teaching] [Research] [Recent Publications and Meeting Abstracts] [Bioinformatics Links] [Sequence Links]

[Loyola University Chicago Home Page] [Biology Dept.] [Bioinformatics B.S. Program]

Biographic and Contact Information

Position	Professor of Biology Director, Bioinformatics B.S. Program Adjunct Professor of Chemistry
Address	Loyola University Chicago 6525 N. Sheridan Road Office: Quinlan Life Science Center 325 Chicago, IL 60626 Lab: Quinlan Life Science Center 336
email	hlaten@luc.edu
office phone lab phone fax	1-773-508-3640 1-773-508-3641 1-773-508-3646
Education	Ph.D. Biochemistry, 1978, University of Wisconsin-Madison B.S. Biology, 1971, Baldwin-Wallace College

Teaching

Genetics (BIOL 282)

Fall 2005 Description Schedule
Textbook: iGenetics: A Mendelian Approach

Bioinformatics (BIOL 388)

Fall 2005 Description Schedule
Textbooks: Bioinformatics and Molecular Evolution

An Introduction to Bioinformatics Algorithms (recommended but not required)

Human Molecular Genetics (BIOL 482)

Spring 2005 Description
Textbook: Human Molecular Genetics3

Dr. Laten was the 2002 co-recipient of the Edwin T. and ViviJeanne F. Sujack Award For Teaching Excellence in the College of Arts and Sciences.

Research

My investigations are focused on the characterization and evolution of a unique family of plant retroelements that resemble mammalian retroviruses. Retroelements are a class of DNA and RNA genetic entities that utilize the enzyme reverse transcriptase to sponsor the replication of their small genomes. The best known retroelement is the human immunodeficiency virus, the causative agent of AIDS. Non-infectious retrotransposons constitute a second major class of retroelements and are found in virtually every eukaryote. While their genomes are similar to those of the retroviruses, they lack genes necessary for intercellular transfer. The proliferation of both classes of retroelements involves the integration of reverse transcribed DNA copies into the hosts' chromosomes. These copies become permanent residents (endogenous) and record present, past, and even ancient encounters with retroelements. Once considered by many to be pesky genetic parasites, these endogenous elements were dubbed "selfish DNA" because they can proliferate with-in chromosomes. However, they may actually be key players in the modification of host genomes during critical periods of large-scale evolutionary change. The retroelement we discovered, SIRE-1, was first encountered in the soybean genome as a family of a thousand structurally conserved members with the standard complement of retroelement genes. But unlike other plant retroelements known at the time, SIRE-1 also codes for a protein unique to retroviruses -- an envelope-like protein. In retroviruses, the envelope protein confers infectivity. We have now confirmed the presence of SIRE-1 relatives in several other plant species, and expect it was once and may still be a highly successful retrovirus transmitted to plants by aphids or some other invertebrate vector.Our attention is focused on three primary questions: 1) Is SIRE-1 an active plant retrovirus - do host cells make SIRE-1 mRNAs, proteins, virions? 2) Can invertebrate vectors be found? And 3) Can molecular systematic approaches reveal the precise evolutionary relationships among retroviruses and retrotransposons?

In a second project, we are using bioinformatics tools to recover and assemble full-length consensus repetitive DNA elements from short unannotated DNA sequences that have been deposited in GenBank. This exercise provides a detailed preview of the repetitive DNA content of organisms whose genomes are not substantially sequenced and enables fractured elements to be fully characterized.

Recent Publications and Meeting Abstracts

Yano, S.T., B. Panbehi, A. Das & H.M. Laten. 2005. Diaspora, a novel Gypsy/Ty3 retrotransposon-like family in the soybean genome related to plant endogenous retroviruses does not encode an envelope-like protein. BMC Evolutionary Biology 5, 30. Full Text

Grande, T., H.M. Laten & J.A. Lopez. 2004. Phylogenetic relationships of extant esocid species (Teleostei: Salmoniformes) based on morphological and molecular characters. Copiea 2004 (4), 743-757. Full text

Laten, H.M., E.R. Havecker, L.M. Farmer & D.F. Voytas. 2003. SIRE1, an endogenous retrovirus family from Glycine max, is highly homogeneous and evolutionarily young. Mol. Biol. Evol. 20, 1222-1230 Full Text Abstract Supplementary Data

Laten, H.M., E.R. Havecker, L.M. Farmer, E. Lin & D.F. Voytas. 2002. Endogenous retroviruses as transgenic vectors - the ubiquitous SIRE1 family. Ninth Biennial Conference of the Cellular and Molecular Biology of the Soybean. Abstract

Laten, H.M., E.R. Havecker, L.M. Farmer & D.F. Voytas. 2002. Plant endogenous retroviruses -- Poised for transformation. International Conference on Legume Genetics and Genomics. Abstract

Peterson-Burch, B.D., D.A. Wright, H.M. Laten &. D.F Voytas. 2000. Retroviruses in Plants? Trends Genet. 16, 151-152. Full text

Laten, H.M. 1999. Phylogenetic evidence for Ty1-copia-like endogenous retroviruses in plant genomes. Genetica 107, 87-93. Full text

Laten, H.M., A. Majumdar, & E.A. Gaucher. 1998. SIRE1, a Copia/Ty1-like Retroelement from Soybean, Encodes a Retroviral Envelope-like Protein. Proc. Natl. Acad. Sci. USA 95, 6897-6902. Full text Abstract

Bi, Y.-A. & H.M. Laten. 1996. Sequence Analysis of a cDNA containing the gag and prot regions of the Soybean Retrovirus-like Element, SIRE1, Plant Mol. Biol.30, 1315-1319. Abstract

Patents

Plant Retroviral Polynucleotides and Methods for use thereof

Current Personnel and Recent Graduates

	Present affiliation
Eftychia Gouvas, M.S.
Christi Lindorfer B.S.
Meg Garland, B.S.
Edward Badal, B.S.
Deany Villasenor, B.S.
Lukasz Gierut, B.S. 2005
Sho Yano, B.S. 2003	University of Chicago Department of Molecular Genetics and Cell Biology
Heather Mears, B.S. 2003 Research Associate	Northwestern University
Erich Gerhardt, B.S. 2003	Nova Southeastern College of Osteopathic Medicine
Jessica Smith, B.S. 2002 Research Assistant	Northwestern University
Lisa Farmer, B.S. 2002	University of Wisconsin-Madison Department of Genetics
Amina Habib	Cornell University Health Adminstration program
Leah Anderson, B.S. 2002, Research Associate	Case-Western Reserve University Evolutionary Biology Program
Queenie Chan, M.S. 2002	University of Illinois at Chicago School of Pharmacy
Dawn Wilson, B.S. 2001	The University of Chicago Genetics program

Sequence Links

SIRE1-1a	SIRE1-3	SIRE1-8	SIRE1-13	SIRE1 PCR (Gm776)
SIRE1-1b	SIRE1-4	SIRE1-9	SIRE1-14	Endovir1-1
SIRE1-2	SIRE1-7	SIRE1-10	SIRE1 cDNA1	diaspora1

Bioinformatics Links

NCBI	SIGNAL SCAN	GRAIL	FGENES	GENEID
BIOLOGY WORKBENCH	GENSCAN	HMMgene	MZEF