Professor of Biological Sciences
Department
of Biological Sciences,
Director,
Center for Science Education, University of South Carolina
Ph.D., 1973,
ely@sc.edu
or 803-777-2768
Bacterial Genome Evolution
We are studying the genomes of the caulobacters and the bacteriophage that attack them to understand the roles of genome rearrangements, mutations, and horizontal gene transfer in genome evolution. Caulobacters have an interesting life cycle as shown above. We have shown that extensive genome rearrangements have occurred among the Caulobacter species studied to date. However, similar rearrangements have not occurred among the phages that infect these bacteria. This project involves the isolation of bacteria and bacteriophage from the wild, characterization of the isolates, genome sequencing, and bioinformatics. We are also interested in comparing the genomes of isolates from aquatic environments to those isolated from soil to determine if there are differences in the composition of the genome that are characteristic of the habitat where they live.
West African Genetic Diversity:
We no longer accept requests for DNA testing. Inexpensive DNA tests are available from the National Geographic Society at https://genographic.nationalgeographic.com/genographic/lan/en/genealogy.html
Application and Information for Graduate Studies
Friedman, R. and B. Ely. 2012. Codon usage methods
for horizontal gene transfer detection generate an abundance of false positive
and false negative results. Current Microbiology 65:639-642. doi:10.1007/s00284-012-0205-5
Bacteria acquire new DNA in
a process known as horizontal gene transfer (HGT). To investigate the
evolutionary impact of this transfer of DNA, various methods have been
developed to detect past HGT events. For example, codon usage-based methods
detect the presence of transferred genes by identifying atypical patterns of
codon usage. However, some inherited genes exhibit atypical codon usage and
some transferred genes have codon usage patterns similar to those of the
inherited genes. In this study, we used a comparative phylogenetic approach
with Methylobacterium and Caulobacter species to demonstrate that
even well-designed codon usage methods fail to detect many HGT events and
generate a high rate of false positives (60–75 %) and false negatives
(23–61 %). Therefore, we recommend caution when employing codon usage
methods to identify transferred genes and suggest that the rapidly increasing
availability of bacterial genome sequences makes the phylogenetic approach the
method of choice.
Guerrero-Ferreira, R. C., P. H. Viollier, B. Ely, J. S. Poindexter, M. Georgieva,
G. J. Jensen, and E. R. Wright. 2011. A novel mechanism for bacteriophage
adsorption to the motile bacterium Caulobacter
crescentus. Proceedings of the National Academy of Sciences USA 108:9963-9968. doi:10.1073/pnas.1012388108.
2D and 3D cryo-electron
microscopy, together with adsorption kinetics assays of ϕCb13 and ϕCbK phage-infected Caulobacter crescentus, provides
insight into the mechanisms of infection. ϕCb13 and ϕCbK actively interact with the flagellum and
subsequently attach to receptors on the cell pole. We present evidence that the
first interaction of the phage with the bacterial flagellum takes place through
a filament on the phage head. This contact with the flagellum facilitates
concentration of phage particles around the receptor (i.e., the pilus portals)
on the bacterial cell surface, thereby increasing the likelihood of infection.
Phage head filaments have not been well characterized and their function is
described here. Phage head filaments may systematically underlie the initial
interactions of phages with their hosts in other systems and possibly represent
a widespread mechanism of efficient phage propagation.
Lightfield, J., N. R.
Fram, and B. Ely. 2011. Across
bacterial phyla distantly-related genomes with similar genomic GC content have
similar patterns of amino acid usage. PLoS ONE 6(3):
e17677.
The GC content of bacterial
genomes ranges from 16% to 75% and wide ranges of genomic GC content are
observed within many bacterial phyla, including both Gram negative and Gram
positive phyla. Thus, divergent genomic GC content has evolved repeatedly in
widely separated bacterial taxa. Since genomic GC content influences codon
usage, we examined codon usage patterns and predicted protein amino acid
content as a function of genomic GC content within eight different phyla or
classes of bacteria. We found that similar patterns of codon usage and protein
amino acid content have evolved independently in all eight groups of bacteria.
For example, in each group, use of amino acids encoded by GC-rich codons
increased by approximately 1% for each 10% increase in genomic GC content,
while the use of amino acids encoded by AT-rich codons decreased by a similar
amount. This consistency within every phylum and class studied led us to
conclude that GC content appears to be the primary determinant of the codon and
amino acid usage patterns observed in bacterial genomes. These results also indicate
that selection for translational efficiency of highly expressed genes is
constrained by the genomic parameters associated with the GC content of the
host genome.
Wilson, J. L., B.
Ely and B. A. Jackson. 2010. Evaluating African-derived mtDNA haplotype
diversity via independent sample collections. Canadian Journal of Forensic
Sciences 43:65-74.
Since
the sample sizes for forensic cases, as well as studies of African ethnic
groups, are usually low, and independent samples are rare, it has been difficult
to determine whether small samples contain an accurate representation of a
sampled population. In this study, two independent samples of the Bamileke had
similar values with regard to standard and molecular diversity indices and
selective neutrality. The two Fulbe samples were also similar, but they
differed with respect to selective neutrality values. In both ethnic groups,
shared haplotypes were present at low frequencies. However, the Fulbe had fewer
exclusive matches with outside ethnic groups compared to the Bamileke.
Nevertheless, in both ethnic groups, within-group matches were more common than
matches to any other Cameroonian ethnic group. Only a small percentage of the
observed mtDNA haplotypes have the potential for being ethnic and/or region specific.
To assess this potential, sample sizes will have to be orders of magnitude
larger in order to observe significant numbers of those relatively rare
haplotypes. However, as database size is increased, haplotype sharing will
correspondingly increase; and many haplotypes that are common in a single
ethnic group will also be found in multiple ethnic groups.
Liu, J. and
B. Ely. 2010. Evolution of an
A
nucleotide sequence analysis of a fragment of a Morone MHC class Ia
gene detected high levels of polymorphism in striped bass Morone saxatilis,
white perch Morone americana and yellow bass Morone
mississippiensis. Extremely low levels of MHC diversity, however, were
detected in white bass Morone chrysops, suggesting the possibility of
a severe population bottleneck for this species.
Cunningham, J. E., A. J. Montero, E. Garrett-Mayer, H. J. Berkel, and B. Ely. 2010. Racial differences in the incidence of breast cancer subtypes defined by combined histologic grade and hormone receptor status. Cancer Causes and Control 21:399-409.
Breast
cancer encompasses several distinct clinical entities of very different
characteristics and behaviors, a fact which likely contributes to the higher
breast cancer mortality in African-Americans (AA) despite the higher incidence
in European-Americans (EA). We are interested in how incidence variability in
cancer subtypes defined by combined estrogen receptor (ER) and grade
contributes to racial mortality disparities. As an initial step, we compared
age-specific and age-adjusted incidence rates for each ER/Grade subtype in
South Carolina (SC—a southern state) with Ohio (a northern mid-western state),
using state registry data for 1996–2004. Each ER/Grade subtype had a distinct
incidence pattern and rate, with three striking racial/geographic differences.
First, the racial incidence disparity in ER negative (ER−) cancers was
mostly within the ER−/G3 subtype, of which AAs had ~65% higher incidence
than did EAs; ER−/G2 was much less common, but of significantly higher
incidence in AAs. Second, the racial disparity in ER positive (ER+) cancers was
in the ER+/lower-grade cancers, with a marked EA excess in both states. Third,
AA incidence of the ER+/lower-grade subtypes was ~26% higher in Ohio than in
SC. The other subtypes (ER−/G1 and ER+/G3) varied minimally by race and
state, and the latter showed a strong association with age. Age adjustment
halved the racial difference in mean age at diagnosis to about 2 years
younger in AAs, compared to 4 years younger in case comparisons. Use of
age-adjusted and age-specific rates of breast cancer subtypes may improve
understanding of racial incidence and mortality disparities over time and
geography. This approach also may aid in estimating the race-specific incidence
rates of triple-negative breast cancer.
Liu, J. and B. Ely. 2009. Sibship reconstruction demonstrates the extremely low effective population size of striped bass Morone saxatilis in the Santee-Cooper system, South Carolina, USA. Molecular Ecology 18:4112-4120.
For
organisms with great fecundity and high mortality in early life stages, such as
shellfish or fishes, the need to match reproductive activity with environmental
conditions conducive to spawning, fertilization, larval development and
recruitment may result in extreme variance in reproductive success among
individuals. The main objective of this study was to investigate evidence of
large variance in the reproductive success of the striped bass Morone
saxatilis in the Santee–Cooper system, South Carolina, USA. Seven
microsatellite loci were analysed in 603 recruits representing three yearly
cohorts from 1992 to 1994, and a group analysis was performed to identify full-sib
families. Large variance in reproductive success was detected, with a few
large, full-sib families contributing disproportionately to each of the
cohorts. The severity of sweepstakes reproductive success varied among cohorts
depending on environmentally imposed mortality. Estimations of the effective
number of breeders in these long-lived fish ranged from 24 in 1992 to 44 in
1994. Furthermore, the estimated genetic effective population size (Ne = 93)
is approximately four orders of magnitude lower than estimates of adult census
size (N = 362 000). Furthermore, the presence
of large full-sib families indicates that striped bass engage in pair mating in
the wild. Heterogeneity in genetic composition was also observed among cohorts,
suggesting that genetically different adults contribute to different cohorts
and that chance rather than fitness variation determines reproductive success.
Liu, J. and B. Ely. 2009. Complex evolution of a highly-conserved microsatellite locus in several fish species. Journal of Fish Biology 75:442-447.
The
evolutionary dynamics of a highly conserved microsatellite locus (Dla 11)
were studied in several fish species. The data indicated that multiple types of
compound microsatellites arose through point mutations that were sometimes
followed by expansion of the derived motif. Furthermore, extensive length
variation was detected among species in the regions immediately flanking the
repeat region.
Ely,
B., J. L. Wilson, F. Jackson, and B. A. Jackson. 2006. African-American
mitochondrial DNAs often match mtDNAs found in multiple African ethnic groups. BMC Biology 4:34. Published correction Can
a database of mtDNA HvsI sequences properly assign Africans to their country of
origin?
Alvarado
Bremer, J.R., J. Mejuto, J. Gómez-Márquez, F. Boán, P. Carpintero, J.M.
Rodríguez, J. Viñas, T.W. Greig, and B. Ely. 2005. Hierarchical analyses of
genetic variation of samples from breeding and feeding grounds confirm the
genetic partitioning of northwest Atlantic and
Ely, B., J. Viñas, J. R. Alvarado Bremer, D. Black, L. Lucas, K. Covello, A. Labrie, and E. Thelen. 2005. Consequences of the historical demography on the global population structure of two highly migratory cosmopolitan marine fishes: the yellowfin tuna (Thunnus albacares) and the skipjack tuna (Katsuwonus pelamis). BMC Evolutionary Biology 5:19.
Jackson, B. A., J. L. Wilson,
S. Kirbah, S. S. Sidney, J. Rosenberger, L. Bassie, J. A. D. Alie, D. C.
McLean, W. T. Garvey, and B. Ely. 2005. Genetic diversity among four ethnic
groups in Sierra Leone. American Journal of Physical
Anthropology 128:156-163.
Alvarado Bremer, J. R., J.
Viñas, J. Mejuto, B. Ely, and C. Pla. 2005. Comparative phylogeography of
Atlantic bluefin tuna and swordfish: The combined effects of vicariance,
secondary contact, introgression, and population expansion on the regional
phylogenies of two highly migratory pelagic fishes. Molecular Phylogenetics and Evolution
26:169-187.
Bulak,
J. S., C. S. Thomason, K. Han, and B. Ely. 2004. Distinctiveness
and management of striped bass populations in the coastal rivers of South
Carolina. North American Journal of Fisheries Management 24:1322-1329.
Osborne, R. L., L. O. Taylor, K. Han, B. Ely, and J. H. Dawson. 2004. A. ornata dehaloperoxidase: enhanced activity for the catalytic active globin using MCPBA. Biochemical and Biophysical Research Communications, 324 (4): 1194-1198.
Ely, B., D. S. Stoner, J. R. Alvarado Bremer, J. M. Dean, P.
Addis, A. Cau, E. J. Thelen, W. J. Jones, D. E. Black, L. Smith, K. Scott, I.
Naseri and J. M. Quattro. 2002. Analyses of nuclear ldhA gene and mtDNA control region
sequences of Atlantic northern bluefin tuna populations. Marine Biotechnology 4:583-588.
Han, K. and B. Ely. 2002. Use of AFLP analyses to assess genetic variation in Morone
and Thunnus species. Marine Biotechnology 4:155-162.
William C. Nierman and 36 others.2001. Complete genome sequence of Caulobacter crescentus. Proceedings of the National Academy of Sciences 98:4136-4141
Han,
K., S. A. Woodin, D. E. Lincoln, K. T. Fielman, and B. Ely. 2001
Amphitrite ornata, a marine worm, contains two
dehaloperoxidase genes. Marine Biotechnology 3: 287-292.
Han, K., Li, L., Leclerc, G. M., Hays,A. M., and B. Ely. 2000. Isolation and Characterization of Microsatellite Loci for striped bass (Morone saxatilis).Molecular Biotechnology 2:405-408.
Diaz, M., D. Wethey, J. Bulak, and B. Ely. 2000. Effect of harvest and effective population size on genetic diversity in a striped bass population. Transactions of the American Fisheries Society 129:1250-1255.
Ely, B., T. W. Ely, W. B. Crymes, Jr., and S. A. Minnich. 2000. A family of six flagellin genes contributes to the Caulobacter crescentus flagellar filament. Journal of Bacteriology 182:5001-5004.