Useful
Information 
Locations
Resources
Course
Material
- Short Loan Collection
Please
remember that the Short Loan Collection is located on
Level 1 of the Kate Edger Information Commons
Lecture Readings
Course readings may only be used for the
University's educational purposes. You may print a copy for your own
use, but you may not make a further copy for any other purpose. You may
not copy or distribute any part of the reading to any other person.
Failure to comply with these terms may expose you to legal action for
copyright infringement and/or disciplinary action by the University.
In order to gain access to the electronic readings you will need to
enter in your NetID and Password after clicking on the reading links
below.
Please note that some readings are not available electronically, but
are available in the printed journals collection on Level M in the
General Library, and can be photocopied from there. Other readings
are not available from the library at all, if you require these readings
please contact the lecturer who prescribed them.
Lectures by Associate Professor Brian Murray
1.
Genome organization: chromosome number and genome size
- Gregory, T. R. (2001).
Coincidence,
coevolution or causation? DNA content, cell size and the C-value
enigma. Biological
Reviews, 76, 65-101.(Scroll down to see viewing
options for the
required article)
- Leitch, I. J., Soltis, D. E., Soltis, P. S., & Bennett, M. D. (2005). Evolution of DNA amounts across land
plants (Embryophyta). Annals
of Botany, 95, 207-217.
- Gupta, P.K. & Rees, H. (1975). Tolerance of Lolium hybrids to
quantitative variation in nuclear DNA. Nature 257,
587-588.
2.
Genome organization: sequence composition and organization
- Schmidt, T. & Heslop-Harrison, J.S. (1998). Genomes,
genes and junk: the large-scale organization of plant chromosomes.
Trends in Plant Science, 3, 195-199.
- The Arabidopsis Genome Initiative (2000). Analysis
of the genome sequences of the flowering plant Arabidopsis
thaliana. Nature, 408, 796-813.
- Deloukas, P. et al. (2001). The
DNA sequence and comparative analysis of human chromosome 20.
Nature, 414, 865-871.
- Saccone, S., Pavlicek, A., Federico, C., Paces, J. & Bernardi, G.
(2001). Genes,
isochores and bands in human chromosomes 21 and 22. Chromosome Research,
9, 533-539.
- International
Human Genome Sequencing Consortium (2001). Initial sequencing and
analysis of the human genome. Nature, 409, 860-920.
3.
Structure of the chromosome: chromatin, heterochromatin and telomeres
- Cohen, P. (1995). Creators of the forty-seventh chromosome.
New Scientist, 148, 34-37.
- Cubizolles, F. & Gasser, S.M. (2001). The
nucleosome: from
wallflower to Queen of the Ball. Genome Biology, 2, reports4023.1-4023.4.
- Redi, C.A., Garagna, S., Zacharias, H., Zuccotti, M. & Capanna, E.
(2001). The other
chromatin. Chromosoma 110: 136-147.
- Blackburn, E.H. (1994). Telomeres: No end in
sight. Cell, 77,
621-623.
- Louis, E.J. (2002). Are Drosophila telomeres an exception or the
rule? Genome Biology, 3, reviews 0007.1-0007.6
- Riha, K., Fajkus, J., Siroky, J., & Vyskot, B. (1998) Developmental
control of telomere lengths and telomerase activity in plants.
The Plant Cell, 10, 1691-1698.
4.
Chromosome structure: centromeres and NORs
- Henikoff, S., Ahmad,
K. & Malik, H. S.
(2001). The
centromere paradox: stable inheritance with rapidly evolving DNA.
Science, 293, 1098-1102
- Amor,
, J. A., Kalitsis, P., Sumer, H. & Choo, K.
H. A. (2004). Building
the centromere: from foundation proteins to 3D organization. Trends
in Cell Biology, 14, 359-368.
5.
Chromosome banding and gene distribution
- Sumner, A.T. (1990) Chromosome
Banding, London, Unwin Hyman.
- Gill, K.S., Gill, B.S. & Endo, T.R. (1993) A chromosome
region-specific mapping strategy reveals gene-rich telomeric ends in
wheat. Chromosoma 102: 374-381.
6.
Nuclear organization: position and expression
- Anamthawat-Jónsson, K. & Heslop-Harrison, J.S. (1990). Centromeres,
telomeres and chromatin in the interphase nucleus of cereals.
Caryologia, 43, 205-213.
- Leitch, A.R. (2000). Higher levels of organization in the
interphase nucleus of cycling and differentiated cells. Microbiology and Molecular Biology Reviews,
64, 138-152.
- Bridger, J.M. & Bickmore, W. (1998) Putting the genome on the
map. Trends in Genetics, 14, 403-409.
- Callimassia, M.A., Murray, B.G., Hammett, K.R.W., Bennett, M.D.
(1994). Parental genome separation and asynchronous centromere
division in interspecific F1 hybrids in Lathyrus. Chromosome
Research, 2, 383-397.
- Schwarzacher, T., Heslop-Harrison, J.S., Anamthawat-Jónsson, K.,
Finch, R.A. & Bennett, M.D. (1992). Parental genome separation in
reconstructions of somatic and premeiotic metaphases of Hordeum
vulgare x H. bulbosum. Journal of Cell Science, 101, 13-24.
- Heslop-Harrison, J.S. (1990) Gene expression and parental
dominance in hybrid plants. Development (Supplement) 21-28.
7.
Nuclear organization: imprinting, inactivation and elimination
- Day, S. (1993) Why genes have a gender. New Scientist,
138,
34-38.
- Ferguson-Smith, A.C., Surani, M.A. (2001) Imprinting and the
epigenetic asymmetry between parental genomes. Science,
293,
1086-1089.
- Migeon, B.R. (1994) X-chromosome inactivation: molecular
mechanisms and genetic consequences. Trends in Genetics,
10,
230-235.
- Puertas, M.J., Jiménez, M.M., Romera, F., Vega, J.M. & Díez, M.
(1990) Maternal imprinting effect on B chromosome transmission in
rye. Heredity, 64, 197-204.
- Tobler, H., Etter, A. & Müller, F. (1992) Chromatin diminution in
nematode development. Trends in Genetics, 8, 427-432.
- Laurie, D.A. & Bennett, M.D. (1988) Chromosome behaviour in wheat x
maize, wheat x sorghum and barley x maize crosses. In Brandham,
P.E. (ed.) Kew Chromosome Conference
III: 167-177.
- Finch, R.A. (1983) Tissue specific elimination of alternative
whole parental genomes in one barley hybrid. Chromosoma,
88,
386-393.
8.
Meiosis: homologue recognition and synapsis
- Loidl, J. (1990) The initiation of meiotic chromosome pairing: the
cytological view. Genome, 33, 759-778.
- Hawley, R.S. & Arbel, T. (1993) Yeast genetics and the fall of the
classical view of meiosis. Cell, 72, 301-303.
- Schwarzacher, T. (1997) Three stages of meiotic homologous
chromosome pairing in wheat: cognition, alignment and synapsis.
Sexual Plant Reproduction, 10, 324-331.
- Franklin, A.E. & Cande, W.Z. (1999) Nuclear organization and
chromosome segregation. The Plant cell, 11, 523-534.
9. Meiosis:
chiasmata and recombination
- Rees, H. (1961) Genotypic control of chromosome form and behaviour.
Botanical Review, 27, 288-318.
- Gill, K.S., Gill, B.S. & Endo, T.R. (1993) A chromosome
region-specific mapping strategy reveals gene-rich telomeric ends in
wheat. Chromosoma, 102, 374-381.
- Schmidt, R. et al. (1995) Physical map and organization of
Arabidopsis thaliana chromosome 4. Science, 270, 480-483.
- Craig, J.M. & Bickmore, W.A. (1994) The distribution of CpG islands
in mammalian chromosomes. Nature Genetics, 7, 376-380.
- Wallace, H., Wallace, B. & Badawy, G.M.I. (1997)
Lampbrush
chromosomes and chiasmata of sex-reversed crested newts. Chromosoma,
106, 526-533.
- Liharska, T. et al. (1996) Tomato chromosome 6: effect of alien
chromosome segments on recombinant frequencies. Genome, 39,
485-491.
10.
Chromosome evolution: Polyploidy 1
- Leitch, I.J. & Bennett, M.D. (1997) Polyploidy in
angiosperms. Trends in Plant Science, 2, 470-476.
- Ozkan, H. et al. (2003) Nonadditive changes in genome size during
allopolyploidization in the wheat (Aegilops-Triticum) group.
Journal of Heredity, 94, 260-264.
- Shaked, H. et al. (2001) Sequence elimination and cytosine
methylation are rapid and reproducible responses of the genome to
wide hybridization and allopolyploidy in wheat. The Plant Cell,
13, 1749-1759.
- Otto, S.P. (2003) In
polyploids, one plus one does not equal two. Trends in Ecology and Evolution,
18, 431-433.
11.
Chromosome evolution: Polyploidy
2
- Moore, G. (2002) Meiosis in allopolyploids – the importance of
‘Teflon’ chromosomes. Trends in Genetics, 18, 456-463.
- Normann, G.A. & Quarín, C.L. (1987) Permanent odd polyploidy in a
grass (Andropogon ternatus). Genome, 29, 340-344.
- Stöck, M. et al. (2002) A bisexually reproducing all-triploid
vertebrate. Nature Genetics, 30, 325-328.
12.
Techniques for studying chromosome evolution
- Brown, J.R. (1996) Preparing for the flood: Evolutionary biology
in the age of genomics. Trends in Ecology and Evolution,
11,
510-513.
- Moore, G., Devos, K.M., Wang, Z., Gale, M.D. (1995) Cereal
genome evolution: grasses, line
up and form a circle. Current Biology, 5, 737-739.
- Bennett, S.T., Kenton, A.Y. & Bennett, M.D. (1992) Genomic in situ
hybridization reveals the allopolyploid nature of Milium montianum (Gramineae).
Chromosoma, 101, 420-424.
- Ran, Y., Hammett, K.R.W. & Murray, B.G. (2001) Phylogenetic
analysis and karyotype evolution in the genus Clivia
(Amaryllidaceae). Annals of Botany, 87, 823-830.
Lectures by Professor Paul Rainey - The Power of Bacterial
Genetics
Lecture 1: Mutation I: Conditional Lethal Mutations
- Horowitz, N. H. & Leupold, U. R. S. (1951). Some
recent studies bearing on the one gene-one enzyme hypothesis.
Cold Spring Harbor Symposia on Quantitative Biology 16,
65-74.
- Austin, S. J., Tittawella, I. P. B., Hayward, R. S. & Scaife,
J. G. (1971). Amber
mutations of Escherichia coli RNA polymerase. Nature, 232,
133-136.
Lecture 2: Mutation II: The Nature of Mutation
- Crick, F. H. C., Barnett, L., Brenner, S. & Watts-Tobin R. J.
(1961). General
nature of the genetic code for proteins. Nature, 192,
1227-1232.
- Shapiro, J. A. (1969). Mutations
caused by the insertion of genetic material into the galactose
operon of Escherichia coli. Journal of Molecular
Biology, 40, 93-105.
Lecture 3: Mutation III: Nonsense Mutations
- Benzer, S. & Champe S. P. (1962). A
change from nonsense to sense in the genetic code. Proceedings
of the National Academy of Sciences, 48, 1114-1121.
- Brenner, S. & Stretton, A. O. W. (1965). Phase
shifting of Amber and Ochre mutants. Journal of Molecular
Biology, 13, 944-946.
- Brenner, S., Stretton, A. O. W. & Kaplan, S. (1965). Genetic
code: the nonsense triplets for chain termination and their
suppression. Nature, 206, 994-998.
Lecture 4: Mutation IV: Origin of Mutants
- Luria , S. E. & Delbruck, M. (1943). Mutations of bacteria
from virus sensitivity to virus resistance. Genetics, 28,
491-511.
- Cairns, J., Overbaugh, J. & Miller, S. (1988). The
origin of mutants. Nature, 335, 142-145.
- Andersson, D. I., Slechta, E. S. & Roth, J. R. (1998).
Evidence that gene amplification underlies adaptive mutability of
the bacterial lac operon. Science, 282, 1133-35
Lecture 5: Mutation V: Mutators
- Nghiem, Y., Cabrera, M., Cupples, C. G. & Miller, J. H.
(1988). The
mutY gene: A mutator locus in Escherichia coli that generates G.C to
T.A transversions. Proceedings of the National Academy of
Sciences USA, 85, 2709-2713.
- Glickman, B. W. & Radman, M. (1980). Escherichia coli mutator
mutants deficient in methylation-instructed DNA mismatch correction.
Proceedings of the National Academy of Sciences USA, 77,
1063-1067.
- Kenyon, C. J. & Walker, G. C. (1980). DNA-damaging agents
stimulate gene expression at specific loci in Escherichia coli.
Proceedings of the National Academy of Sciences USA, 77, 2819-2823.
Lecture 6: Suppression I
Lecture 7: Suppression II
- Spiers, A. J., Kahn, S. G., Bohannon, J., Travisano, M. &
Rainey, P. B. (2002). Adaptive divergence in experimental
populations of Pseudomonas fluorescens. I. Genetic and phenotypic
bases of wrinkly spreader fitness. Genetics, 161, 33-46
- Rainey, B. P., Travisano, M. (1998). Adaptive radiation in a
heterogeneous environment. Nature, 394, 69-72.
Lecture 8: Regulation I
- Pardee, A. B., Jacob, F. & Monod, J. (1959). The genetic
control and cytoplasmic expression of "inducibility" in
the synthesis of b-galactosidase by E. coli. Journal of Molecular
Biology, 1, 165-178.
- Jacob, F., Perrin, D., Sanchez, C. & Monod, J. (1960). The
operon: A group of genes whose expression is coordinated by an
operator. Comptes Rendus des Deances de l'Acadamie des Sciences, 250,
1727-1729.
- Englesberg, E., Sheppard, D., Squires, C. & Meronk Jr, F.
(1969). An analysis of revertants of a deletion mutant in the C gene
of the L-arabinose gene complex in Escherichia coli B/r: Isolation
of initiator constitutive mutants (Ic). Journal of Molecular
Biology,
43, 281-298.
- Judson, H. F. (1979) The Eighth Day of Creation, pp 400-435.
Jonathon Cape. (for a very well told account of the evolution of
ideas)
Lecture 9: Regulation II
- Eisen, H., Brachet, P., Pereira da Silva, L. & Jacob, F.
(1970). Regulation of repressor expression in
lambda. Proceedings of
the National Academy of Sciences USA 66, 855-862.
- Irani, M. H. & Orosz, L. (1983). A control element within a
structural gene: the gal operon of Escherichia coli. Cell 32,
783-788.
- Dunn, T. M., Hahn, S., Ogden, S. & Schleif, R. F. (1984). An
operator at -280 base pairs that is required for repression of
araBAD operon promoter: addition of DNA helical tuyrns between the
operator and promoter cyclically hinders repression. Proceedings of
the National Academy of Sciences USA 81, 5017-5020.
- Johnston, H. M. & Roth, J. R. (1981). Genetic analysis of the
histidine operon control region of Salmonella typhimurium. Journal
of Molecular Biology, 145, 713-734.
- Johnston, H. M. & Roth, J. R. (1981). DNA sequence changes of
mutations altering attenuation control of the histidine operon of
Salmonella typhimurium. Journal of Molecular Biology, 145, 735-756.
Lecture 10: Protein Targeting
- Emr, S. D., Schwartz, M. & Silhavy, T. J. (1978). Mutations
altering the cellular localization of the phage l receptor, an
Escherichia coli outer membrane protein. Proceedings of the National
Academy of Sciences USA, 75, 5802-5806.
- Emr, S. D., Hedgpeth, J., Clement, J.-M., Silhavy, T. J. &
Hofnung, M. (1980). Sequence analysis of mutations that prevent
export of l receptor, an Escherichia coli outer membrane protein.
Nature, 285, 82-85.
- Emr, S. D. & Silhavy, T. J. (1983). Importance of secondary
structure in the signal sequence for protein secretion. Proceedings
of the National Academy of Sciences USA, 80, 4599-4603.
- Manoil, C. & Beckwith, J. (1986). A genetic approach to
analyzing membrane protein topology. Science, 233, 1403-1408.
- Oliver, D. B. & Beckwith, J. (1981) E. coli mutant
pleiotropically defective in the export of secreted proteins. Cell,
25, 765-772.
- Shuman, H. A. & Silhavy, T. J. (2003). The art and design of
genetic screens: Escherichia coli. Nature Reviews Genetics, 4,
419-431.
Lecture 11: Regulation at the Membrane
- Hall, M. N. & Silhavy, T. J. (1981). Genetic analysis of the
ompB locus in Escherichia coli K-12. Journal of Molecular Biology,
151, 1-15.
- Ronson, C. W., Nixon, B. T. & Ausubel, F. M. (1987). Conserved
domains in bacterial regulatory proteins that respond to
environmental stimuli. Cell, 49, 579-581.
- Miller, V. L., Taylor, R. K. & Mekalanos, J. J. (1987).
Cholera toxin transcriptional activator ToxR is a transmembrane DNA
binding protein. Cell, 48, 271-279.
- Ames, P. & Parkinson, J. S. (1988). Transmembrane signaling by
bacterial chemoreceptors: E. coli transducers with locked signal
output. Cell, 55, 817-826.
- Oosawa, K. & Simon, M. (1986). Analysis of mutations in the
transmembrane region of the aspartate chemoreceptor in Escherichia
coli. Proceedings of the National Academy of Sciences USA, 83,
6930-6934.
Lectures by Associate Professor Don Love
Lecture 5
- Dunning, A. M., Durocher, F., Healey, C. S.,
Teare, M. D., McBride, S. E., Carlomagno, F., et al. (2000). The
extent of linkage disequilibrium in four populations with distinct
demographic histories. American Journal of Human Genetics, 67, pp.1544-1554.
- Patil, N., Berno, A. J., Hinds, D. A., Barrett,
W. A., Doshi, J. M., Hacker, C. R., et al. (2001). Blocks of limited haplotype
diversity revealed by high-resolution scanning of human chromosome
21. Science, 294, pp 1719-1723.
- Lai, C. S. L., Fisher, S. E., Hurst, J.
A., Vargha-Khadem, F. & Monaco, A. P. (2001). A
forkhead-domain gene is mutated in
a severe speech and language disorder. Nature, 413, pp 519- 523.
Lecture 10
- Brown, C. J., Lafreniere, R. G., Powers, V. E.,
Sebastio, G., Ballabio, A., Pettigrew, A. L., et al. (1991). Localization of the X inactivation
centre on the human X chromosome in Xq13. Nature, 349, pp 83-85.
- Brown, C. J., Ballabio, A., Rupert, J. L.,
Lafreniere, R. G., Grompe, M., Tonlorenzi, R., et al, (1991). A gene from the region of the human X
inactivation centre is expressed exclusively from the inactive X
chromosome. Nature, 349, pp 38-45.
- Duthie, S. M., Nesterova, T. B., Formstone, E.
J., Keohane, A. M., Turner, B. M., Zakian, S. M., et al. (1999). Xist
RNA
exhibits a banded localization on the inactive X chromosome and is
excluded from autosomal material in cis. Human Molecular Genetics, 8, pp 195-204
- Hitchins, M.P. & Moore, G.E. (2002) Genomic
imprinting in fetal growth and development. Expert Reviews in
Molecular Medicine 4 (11): 1-19.
- Migeon, B. R. (2001). X-chromosome
inactivation: counting, choice and initiation. Nature Reviews Genetics, 2, pp 59-67.
- Reik, W. & Walter, J. (2001). Genomic imprinting:
parental influence on the genome. Nature Reviews Genetics, 2, pp 21-32.
- Persec, I. & Bartolomei, M. S. (2002). Do X chromosomes set
boundaries?. Science, 295, pp 287-288.
- Chao, W., Huynh, K. D., Spencer, R. J., Davidow,
L. S. & Lee, J. T. (2002). CTCF, a candidate trans-acting
factor for X-inactivation choice. Science, 295, pp 344-347.
Lecture 12
- Maughan, N. J., Lewis, F. J. & Smith, V. (2001). An introduction to arrays.
Journal of Pathology, 195, pp 3-6.
- King, H. C., & Sinha, A. A. (2001). Gene expression profile analysis
by DNA microarrays. J.A.M.A., 286, pp 2280-2288.
- Ross, D. T. (2000). Systematic variation in gene
expression patterns in human cancer cell lines. Nature Genetics,
24, pp 227- 235.
|