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Series B. 329,595-611. RUSSELL, N. J. (1992). Physiology and molecular biology of psychrophilic microorganisms. In: Molecular Biology and Biotechnology of Extremophiles. Herbert, R. A. & Sharp, R. J. (Eds. ) 203-224. Blackie. London. RUSSELL, N. J. and HAMAMOTO, T. (1998). Psychrophiles. In: Extremophile. ti. Microbial Life in Extreme Environments. Horikoshi. K. and Grant W. D. (Eds. ) 25-45. Wiley-Liss. Inc. RUSSELL, N. J. and NICHOLS, D. S. (1999). Polyunsaturated fatty acids in marine bacteria -a dogma rewritten. Microbiology. 45,767-779. SACKIN, M. J. (1987). Computer programs for classification and identification. . 1Ic'ihods in Microbiology. 19,459-494. SAKALA, R. M., HAYASHIDANI, H., KATO, Y., HIRATA, T.. MAKINO, Y FUKUSHIMA, A., YAMADA, T., KANEUCHI. C. and OGAWA, M. (2002). Change in the composition of the microflora on vacuum-packaged beef during chiller storage. International Journal of Food Microbiology. 74.1-2,87-99. SAMBROOK, J., FRITSCH, E. F. and MANIATIS, T. (1989). Molecular Cloning. A Laboratory Manual. 2nd edition. Cold Spring Harbour Press, U. S. A. SANGER, F., NICKLEN, S. and COULSON, A. R. (1977). DNA sequencing with chain- terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74,12,5463-5467. SASS, A. M., SASS, H., COOLEN, M. J., CYPIONKA, H., OVERMANN, J. (2001) Microbial communities in the chemocline of a hypersaline deep-sea basin (Urania basin, Mediterranean Sea). Applied and Environmental Microbiology. 67,12. 5395-5402. SCHÄFER, H., BERNARD, L., COURTIES, C., LEBARON, P., SERVAIS. P.. PUKALL, R., STACKEBRANDT, E., TROUSSELLIER, M.. GUINDULAIN. T., VIVES-REGO, J. and MUYZER, G. (2001). Microbial community dynamics in Mediterranean nutrient-enriched seawater mesocosms: changes in the genetic diversity of bacterial populations. FEATS Microbiology Ecology. 34.243-253. SCHOUTEN, S., RUPSTRA, W. I. C., KOK, M.. HOPMANS. E. C., SUMMONS, R. F., VOLKMAN, J. K. and SINNINGHE DAMSTE. J. S. (2001). Molecular organic 226
tracers of biogeochemical processes in a saline meromictic lake (Ace Lake). Geochimica et Cosmochimica Acta. 65,10,1629-1640. SCOTT, G. K., HEW, C. L. and DAVIES, P. L. (1985). Antifreeze protein genes are tandemly linked and clustered in the genome of the winter flounder. Proceedings of the National Academy of Science. USA. 82,2613-2617. SCOTT, G. K., DAVIES, P. L., SHEARS, M. A. and FLETCHER. G. L. (1987). Structural variation in the alanine-rich antifreeze proteins of the Pleuronectidae. European Journal of Biochemistry. 168,629-633. SCOTT, G. K., HAYES, P. H., FLETCHER, G. L. and DAVIES, P. L. (1988). Wolffish antifreeze protein genes are primarily organised as tandem repeats that each contain two genes in inverted orientation. Molecular Cell Biology. 8,3670-3675. SHERIDAN, P. and BRENCHLEY, J. E. (2000). Characterization of a salt tolerant family 42 U-galactosidase from a psychrophilic Antarctic Planococcus isolate. Applied and Environmental Microbiology. 66,2438-2444. SHIVAJI, S., RAO, N. S., SAISREE, L., SHETH, V., REDDY, G. S. and BHARGAVA, P. M. (1989). Isolation and identification of Pseudomonas spp. From Schirmacher Oasis, Antarctica. Applied and Environmental Microbiology. 55,3,767-770. SICHERT, F. and YANG, D. S. C. (1995). Ice-binding structure and mechanism of an antifreeze protein from winter flounder. Nature. 375,427-431. SINGLETON, P. & SAINSBURY, D. 1997. Dictionary of Microbiology and Molecular Biology, second edition. John Wiley Sons., Chichester. SKIRVIN, R. M., KOHLER, E., STEINER, H., AYERS, D., LAUGHNAN, A., NORTON, M. A. and WARMUND, M. (2000). The use of genetically engineered bacteria to control frost on strawberries and potatoes. Whatever happened to all of that research Scientia Horticulturae. 84,179-189. SMAGLIK, P. (1998). How do antifreeze proteins work The Scientist. 12.18,4. SNEATH, P. H. A. and SOKAL, R. R. (1973). Numerical Taxonomy: The Principles and Practice of Numerical Classification. W. H. Freeman. San Francisco. SOMERVILLE, C. C., NIGHT, I. T., STRAUBE, W. L. and COLWELL. R. R. (1989). Simple, rapid method fro direct isolation of nucleic acids from aquatic environments. Applied and Environmental Microbiology. 55.548-554. 227
Page 1 and 2:
COLD ADAPTATION STRATEGIES AND DIVE
Page 3 and 4:
, 71 "If you march your Winter Jour
Page 5 and 6:
1.6.3. Molecular typing techniques
Page 7 and 8:
3.2.1.2.3. DOC and chlorophyll a ..
Page 9 and 10:
5.3.2.5. The Sphingomonas group, is
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LIST OF FIGURES Figure I. I. Diagra
Page 13 and 14:
Figure 3.17a Mean bacterial abundan
Page 15 and 16:
LIST OF TABLES Table 1.1. Types of
Page 17 and 18:
List of Abbreviations AFP AFGP AFLP
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ACKNOWLEDGEMENTS This study was fun
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Chapter 1: INTRODUCTION 1.1 - Tempe
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1999 ; Hand & Burton, 1981) or iden
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Cold adaptation is dependant on the
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not at 25°C is a function of the a
Page 29 and 30:
The most prolific literature on col
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process known as thermal hysteresis
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dominant, role in the ice-growth in
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explanation for this diversity is t
Page 37 and 38:
1.5.3.5 - Membrane bound solute tra
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een well established (Russell & Nic
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& Bowman, 2001; Labrenz & Hirsch, 2
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The reaction mix contains both deox
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gene mixtures and hence can be used
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displaying a high number of common
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AACGTCGAAA AACCTCGAAA (Organism A)
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particular set of environmental par
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Lake Maximum Depth (m) Approximate
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Larsemann Hills __ rp3rtrnent of th
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Sampling trips took two days during
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Sigma, Sigma-Aldrich Company Ltd.,
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oxidized and the sample then conver
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sample. An appropriate volume was l
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min to ensure complete extension of
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Figure 2.3 - Lane delineation image
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Figure 2.6b - Molecular weights are
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RNA 41F (5'-GCT CAG ATT GAA CGC TGG
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I min. The spin column was removed
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compiled using Seqman and any erron
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ecorded and related to the level of
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information regarding the cold adap
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50ppt to 186ppt. Thirteen were sali
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M N N 't M M \p \p 00 kf) M kf) bA
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as would normally be expected, as b
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1444 6ý L CC vý O Q O O NO u 'c z
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5 - 250 3 245 240 G (, -3 235 a 0-
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3.2.2.2.5 - Dissolved organic carbo
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d 14 12 10 14 12 7 10 8 6 4 2 0 00/
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SRP ('g L- 05 10 15 20 2 3 Depth4 5
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3.2.2.3 - Biological characteristic
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a 0 Bacterial Abundance (x 106 ml-1
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3.3 - Discussion 3.3.1 - Summer sam
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to high surface water temperatures
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chemocline (Rankin et al., 1999). M
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a 250 200 150 100 50 70 60 50 40 ý
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The temperature (Fig 3.2a) through
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et al., 1999). No melt out was obse
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increase in ammonium is probably du
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10 7 9 6 8 E ö 7 5 Co u c m c 40 w
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main pigments were chlorophylls a a
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Inorganic nitrogen (NO2, NO3 and NH
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744 -- 7 644 6 19 ü SE 400-- 4 2s
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salinity decreased from July to Sep
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a Bacterial abundance (x 106 1.1) 0
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8 ö a N Ö oý L _> Q O O 4 0 rn O
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undoubtedly true of Club Lake. The
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suggested that input of bacteria an
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Pendant Lake is an unstratified, sa
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non-AFP active peptides from inhibi
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. ter rý :. 'ý Figure 4.2 -Fryka
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-ý- ---- ,. r. __-_-. ___. r. ýý
Page 141 and 142:
4.2 - Results 4.2.1 - Sampling and
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SPLAT score. It has been shown that
Page 145 and 146:
3'E t ý _d M! .PJ r rn 15 3.5 4 3
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4.3 - Discussion Of the 866 bacteri
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arisen in very few species due to c
Page 151 and 152:
Chapter 5: BACTERIAL MOLECULAR TYPI
Page 153 and 154:
Fig 5.1 - Photographs of ARDRA gel
Page 155 and 156:
Coefficient: Dice Algorithm: lPGMAA
Page 157 and 158:
The closest published relative for
Page 159 and 160:
identification was made based on 15
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Isolate number Closest phylogenetic
Page 163 and 164:
e included due to its small sequenc
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5.3.2 - Identification of the AFP a
Page 167 and 168:
explains the fluctuation in related
Page 169 and 170:
contamination was lower as the PCR
Page 171 and 172:
seen to a certain extent in the ARD
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American Type Culture Collection (A
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Phylogenetic cluster alignment of t
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et al., 1994) and the Antarctic SIM
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Chapter 6: BACTERIAL COMMUNITY ANAL
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6.2.1 - Detection of AFP active iso
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using the same PCR protocol as orig
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Figure 6.1 - Denaturing gradient ge
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6.2.2 - Temporal and spatial variat
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Figure 6.4c - Gel I image showing b
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Coefficient: Dice Algorithm: UPGMA
Page 193 and 194:
etween Om and 2m was obviously the
Page 195 and 196: All PCR-based rRNA molecular techni
Page 197 and 198: 6.3.2.3 - Cellular lysis and DNA pu
Page 199 and 200: hybrids should be equal. However, S
Page 201 and 202: contain contaminants. If the profil
Page 203 and 204: (Section 6.3.2.4.3 ) could not be r
Page 205 and 206: most dominant species in the commun
Page 207 and 208: study was characterised as M protea
Page 209 and 210: 11 species) showed AFP activity. Th
Page 211 and 212: that AFP activity could have evolve
Page 213 and 214: 7.2 - Future Work The 19 AFP active
Page 215 and 216: REFERENCES ABYZOV, S. S. (1993). Mi
Page 217 and 218: BELL, E. M. and LAYBOURN-PARRY, J.
Page 219 and 220: Symposium on Environmental Biogeoch
Page 221 and 222: Research. 5,477-493. CLESCERI, L. S
Page 223 and 224: DRICKAMER, K. (1999). C-type lectin
Page 225 and 226: antifreeze proteins from Atlantic s
Page 227 and 228: FRANZMANN, P. D. and DOBSON, S. J.
Page 229 and 230: GRIFFITH, M., ALA, P., YANG. D. S.
Page 231 and 232: IVANOVA, E. P., KIPRIANOVA, E. A.,
Page 233 and 234: Antarctic Ecosystems. G. A. Llano (
Page 235 and 236: Howard-Williams and I. Hawes). Balk
Page 237 and 238: W. (1998). Rep-PCR-mediated genomic
Page 239 and 240: putida strains from Antarctica. Mic
Page 241 and 242: NICHOLS, D., BOWMAN, J., SANDERSON,
Page 243 and 244: PEARCE, D. A. and BUTLER, H. G. (20
Page 245: (1999). Palaeohydrological modellin
Page 249 and 250: R. G. Landes Company, Austin, Texas
Page 251 and 252: partial 16S rDNA sequencing. Applie
Page 253 and 254: YABUUCHI, E., WANG, L., ARAKAWA, M.
Page 255 and 256: APPENDICES Al. Media Tryptic Soya A
Page 257 and 258: "D C 'O I. .. r .. r 6 rr E , 4mo .
Page 259 and 260: . + + + I I I I I I + I + + I I I I
Page 261 and 262: Ö ON N M 1 O - N 'zt "o l'" 00 C N
Page 263 and 264: 1 T 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Page 265 and 266: 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
Page 267 and 268: 1 1 1 1 I 1 + I I 1 I 1 1 I 1 1 1 I
Page 269 and 270: 1 1 1 1 1 1 1 I I 1 I 1 I 1 1 I T I
Page 271 and 272: Cl M 'tt tn '. p t- 00 O\ N M O - (
Page 273 and 274: d' O - (N M 'nt V) \O N. 00 O> N M
Page 275 and 276: 1 1 T 1 1 1 T 1 1 1 1 1 1 1 1 1 1 1
Page 277 and 278: + + i i i i i i " i " . + + + + " +
Page 279 and 280: e O --ý N M t Vn 1,0 [-- 00 O> N M
Page 281 and 282: FT ce + I I r. to \, O t- 00 O\ N M
Page 283 and 284: kn 110 r- 00 Oý N M O - N M Itt vn
Page 285 and 286: , It N M "t N M Iýt N M M M M Oý
Page 287 and 288: gj a - - - - - - - - - - - - - - -
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