James Lake

email:  lake[at]mbi.ucla.edu
phone:  (310) 825-2546
office:  232 MBI
lab:  232
homepage:  http://www.lifesci.ucla.edu/mcdbio/html/lake.htm

Education

B.A., , University of Colorado 1963
Ph.D., , University of Wisconsin 1967

Research Interests

Our lab is interested in Genomics, Bioinformatics, and Molecular Evolution. We want to understand the evolution of genomes, including the origin of eukaryotes and the origin of life, and want to relate their evolution to the molecular, cell and developmental events that have occurred. Five specific interests are described below. Origin of the Multicellular Animals For years scientists have wanted to know how the multicellular animals originated, but the morphological properties they had to work with were not particularly informative. With molecular sequences available, this has changed and we are obtaining sequences and starting to understand their evolution. We would particularly like to understand the separation of the deuterostomes (vertebrates, echinoderms, etc.) from the protostome (fruit flies, nematodes, etc.) groups and to relate it to the evolution of their genomes and developmental plans. (Nature, 1997). Prokaryotic Ancestors of Eukaryotes A fundamental challenge in biology is to discover the origins of the eukaryotic cell. We are searching for the immediate prokaryotic relatives of the eukaryotes. The strongest evidence to date is that eocyte prokaryotes (sulfur metabolizing, hyperthermophilic bacteria) are the immediate relatives of eukaryotes comes from the sequencing of elongation factor Tu genes in our lab (Science, 1992). Other recent evidence on the origin of eukaryotes from our lab have been the identification and characterization of an eukaryotic type I topoisomerase in a hyperthermophile, Methanopyrus, and the X-ray determination of a histone complex in Methanopyrus which has the structure of one-half of an eukaryotic nucleosome. Genomic analyses Analyses of complete genomes are providing unprecidented insights into the evolution of eukaryotes and prokaryotes. For example in a recent analyses of complete genomes (Rivera, et al., 1998; Jain, et al., 1999), we showed that both prokaryotes and eukaryotes contain two types of genes, and both types have different inheritances. One class of genes, informational genes (genes primarily involved in translation, transcription, replication, etc.), is a deeply diverging lineage which has been transferred in a tree-like pattern. In contrast, operational genes (genes primarily involved in housekeeping), have been inherited by horizontal transfer. These findings are rapidly changing our perceptions, of the evolution of life, and we are vigorously pursuing genome-level analyses Computational Genomics Our lab is also interested in the computational aspects of genomics. In addition to developing methods for studies of genome evolution, we are also developing tools for the identificaiton of genes within genomes. A particularily difficult problem is the determination of the locations of introns and exons within the human genome. Using novel, mathematically optimal algorithms, we are discovering new methods for analysis of the human genome and are deeply involved in the analysis of syntenic regions common to the human and mouse genomes. Molecular Sequence Analysis The computational analysis of gene evolution is still in it?s infancy and yet forms the technical basis for the field of molecular evolution. Our lab is currently working on three different aspects of sequence analysis: phylogeny reconstruction, sequence alignment, and the stochastic nature of sequence analysis. These areas are becoming increasingly important as we try to use sequences to probe deeper and deeper into the past.

Selected Publications

Professors

Professor Emeriti
in residence

Lecturers and
Academic
Coordinators

Adjunct