Wednesday, November 26, 2008

Late-Nov papers

Some interested papers.

Flowering-time genes modulate meristem determinacy and growth form in Arabidopsis thaliana, Siegbert Melzer, Frederic Lens, Jerôme Gennen, Steffen Vanneste, Antje Rohde and Tom Beeckman, Nature Genetics 40(12):1489 - 1492 (December 2008).
Siegbert Melzer and colleagues report that in Arabidopsis the absence of MADS box proteins SOC1 and FUL leads to phenotypes of perennial woody plants, with indeterminate meristems, secondary growth with wood formation, and recurrent growth cycles.

Metagenomic analysis indicates that stressors induce production of herpes-like viruses in the coral Porites compressa, Rebecca L. Vega Thurber, Katie L. Barott, Dana Hall, Hong Liu, Beltran Rodriguez-Mueller, Christelle Desnues, Robert A. Edwards, Matthew Haynes, Florent E. Angly, Linda Wegley, and Forest L. Rohwer, PNAS 105(47):18413-18418 (November 25, 2008).

Plant Biology: Gibberellins close the lid, Nature 456(7221):455, Peter Hedden.
Gibberellins regulate many aspects of plant growth and development. Crystal structures of their receptors provide a view in unprecedented detail of how these hormones operate at the molecular level.

Gibberellin-induced DELLA recognition by the gibberellin receptor GID1, Nature 456(7221):459, Kohji Murase, Yoshinori Hirano, Tai-ping Sun and Toshio Hakoshima.

Structural basis for gibberellin recognition by its receptor GID1, Nature 456(7221):520, Asako Shimada, Miyako Ueguchi-Tanaka, Toru Nakatsu, Masatoshi Nakajima, Youichi Naoe, Hiroko Ohmiya, Hiroaki Kato & Makoto Matsuoka.

A Genetic Framework for the Control of Cell Division and Differentiation in the Root Meristem, R. D. Ioio et al., Science 322(5906):380 - 1384 (28 November 2008).
The number of stem cells in plant roots is controlled by an auxin-cytokine feedback loop in which a particular gene integrates signals from both hormones.

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Sunday, November 23, 2008

Homologous Recombination

wiki Def of HR: Homologous recombination is a type of genetic recombination, a process of physical rearrangement occurring between two strands of DNA. Homologous recombination involves the alignment of similar sequences, formation of a Holliday junction, and breaking and repair, known as resolution, of the DNA to produce an exchange of material between the strands. The process of homologous recombination naturally occurs in organisms and is also utilized as a molecular biology technique for introducing genetic changes into an organism.

Cloning by HR

Homologous Recombination from a Molecular Perspective



Positive-negative selection is used to enrich for ES cells containing a targeted disruption of a gene.

Transgene silencing
Site-specific gene insertion
Single copy

Homologous recombination: a basis for targeted genome optimization in crop species such as maize, Kathleen D'Halluin, Chantal Vanderstraeten, Ellen Stals, Marc Cornelissen and Rene Ruiter, Plant Biotechnology Journal 6(1):93-102 (12 Nov 2007).

Enhancing gene targeting with designed zinc finger nucleases, Bibikova, M., Beumer, K., Trautman, J.K. and Carroll, D., Science 300:764 (2003).

Lloyd, A., Plaisier, C.L., Carroll, D. and Drews, G.N. (2005) Targeted mutagenesis using zinc-finger nucleases in Arabidopsis. Proc. Natl. Acad. Sci. USA, 102, 2232–2237.

Nahon, E. and Raveh, D. (1998) Targeting a truncated Ho-endonuclease of yeast to novel DNA sites with foreign zinc fingers. Nucleic Acids Res. 26, 1233–1239.

Urnov, F., Miller, J., Lee, Y.-L., Beausejour, C., Rock, J., Augustus, S., Jamieson, A., Porteus, M., Gregory, P. and Holmes, M. (2005) Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature, 435, 646–651.

Wright, D., Townsend, J., Winfrey, R., Irwin, P., Rajagopal, J., Lonosky, P., Hall, B., Jondle, M. and Voytas, D. (2005) High-frequency homologous recombination in plants mediated by zinc-finger nucleases. Plant J. 44, 693–705.

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Friday, November 21, 2008

Dams level

We can view current dams level


Dams level in Oct., 2008



Dams level on April 16, 2009


This web site also list current information (Last Updated: 20th November 2008 9:38am). Well, there was thunderstorm last night, so this is not the most updated one.

Water Storage Status Table:
Item (20th November 2008 9:38am) Wivenhoe Somerset North Pine SEQWater Totals
Full Supply Level (m) AHD 67.00 99.00 39.63 -
Storage Volume @FSL (ML) 1,165,240 379,850 214,960 1,760,050
Lake Level (m) AHD 55.06 98.38 31.98 -
Volume Stored (ML) 321,555 354,466 88,839 764,860
Percentage in Storage 27.60% 93.32% 41.33% 43.46%
Change since yesterday +1.248% +1.466% +1.820% +1.365%
Rainfall at dam site 24 hours to 9am (mm) 75 23 12 45 average











Item (24th November 2008 9:06am) Wivenhoe Somerset North Pine SEQWater Totals
Full Supply Level (m) AHD 67.00 99.00 39.63 -
Storage Volume @FSL (ML) 1,165,240 379,850 214,960 1,760,050
Lake Level (m) AHD 55.88 98.10 32.34 -
Volume Stored (ML) 362,698 343,444 93,141 799,283
Percentage in Storage 31.13% 90.42% 43.33% 45.41%
Change since Friday +1.360% -0.205% +0.507% +0.918%
Rainfall at dam site 72 hours to 9am (mm) 0 0 0 0 average











Item (17th April 2009 8:57am) Wivenhoe Somerset North Pine SEQWater Totals
Full Supply Level (m) AHD 67.00 99.00 39.63 -
Storage Volume @FSL (ML) 1,165,240 379,850 214,960 1,760,050
Lake Level (m) AHD 59.18 98.20 36.57 -
Volume Stored (ML) 536,724 347,340 155,198 1,039,262
Percentage in Storage 46.06% 91.44% 72.20% 59.05%
Change since Friday +2.102% -5.709% +0.321% +0.199%
Rainfall at dam site 24 hours to 9am (mm) 0 0 0 0 average


Read more!

Mid-Nov 2008 papers

Here are some interesting papers.

Modified genes spread to local maize: Findings reignite debate over genetically modified crops, Rex Dalton, Nature 456:149 (12 November 2008).
Transgenes from genetically modified (GM) maize (corn) crops have been found in traditional 'landrace' maize in the Mexican heartland, a study says. The work largely confirms a similar, controversial result published in Nature in 20011 and may reignite the debate in Mexico over GM crops.

PLANT GENOMICS: A Bunch of Trouble, David Grimm, Science 322(5904):1046 - 1047 (14 November 2008).
The banana is endangered and largely ignored by funding agencies, researchers, and breeders. But things might finally be going its way.

RENEWABLE ENERGY: Minnesota Ecologist Pushes Prairie Biofuels, Eli Kintisch, Science 322(5904):1044 - 1045 (14 November 2008).
David Tilman wants to mix it up by growing native grasses for energy. Many agronomists disagree.

Read more!

Direct PCR

I know that I shouldn't do any advertisement in here, but I just think this is a useful technique when I saw its ad on Nature.

Direct PCR – makes DNA purification irrelevant (Finnzymes)


Direct PCR eliminates the need for DNA extraction or sample preparation prior to PCR.

Would you like to amplify your target DNA fragment from the source material without prior DNA purification? Finnzymes’ robust PCR enzymes allow direct PCR from various starting materials saving time and costs and increasing sample throughput.

Finnzymes' Phusion and Phire DNA Polymerases, due to their unique structure, are highly robust and tolerant of many PCR inhibitors. This resilience provides efficient amplification from many difficult samples. Note that PCR from an unpurified starting material often requires more optimization than standard PCR reactions from purified DNA and may not always be suitable for all applications. So, please read these protocols carefully when planning your direct PCR experiments and contact us or your distributor with questions. We wish you the best of luck with this novel approach to PCR.
Bird feather Muscle tissues

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Monday, November 17, 2008

Precipitation

Here is the rainfall information from Climate statistics for Australian locations

LONG POCKET CSIRO LAB is close to Brisbane. Here is its monthly rainfall with millimetres (mm) as units.






StatisticJanFebMarAprMayJunJulAugSepOctNovDecAnnual
Nov. 1968 - Dec. 2008
Mean132.2141.0100.387.592.449.746.137.532.381.2122.1121.71043.9
Lowest12.221.23.84.63.30.00.20.00.45.03.225.2574.0
5th percentile22.429.315.17.28.01.73.92.52.017.929.353.9644.8
10th percentile26.448.627.810.613.09.86.15.12.522.436.957.4718.0
Median102.695.979.050.753.035.031.426.923.279.1113.497.21020.2
90th percentile250.4312.1190.6195.4188.4105.8103.895.873.8138.8238.5217.91444.2
95th percentile331.1347.0229.4242.2266.8139.4145.898.879.0143.0298.9236.81730.6
Highest710.9438.5420.2470.7649.4257.0299.5135.1111.0374.8366.0403.61866.0
Yearly
200124.0184.8163.834.635.510.331.410.617.871.7 157.4 
200226.772.9113.333.528.963.90.298.423.243.965.4113.7684.0
200312.2195.681.8108.550.849.319.621.113.379.115.494.4741.1
2004350.4112.4102.035.420.211.08.2 28.681.0233.0215.8 
200580.429.413.844.264.299.417.420.220.4 124.859.6 
2006163.675.284.452.413.447.434.050.254.813.657.275.6721.8
200772.055.424.64.644.6104.24.0102.236.486.288.694.2717.0
2008180.0149.646.87.253.0120.096.217.555.268.1320.777.31191.6
200961.2125.445.3


Read more!

Mid-November papers

Here are some interest papers.

Enrichment of tomato fruit with health-promoting anthocyanins by expression of select transcription factors, Eugenio Butelli, Lucilla Titta, Marco Giorgio, Hans-Peter Mock, Andrea Matros, Silke Peterek, Elio G W M Schijlen, Robert D Hall, Arnaud G Bovy, Jie Luo & Cathie Martin, Nature Biotechnology 26, 1301 - 1308 (2008).

Glutamic acid residues in the C-terminal extension of small heat shock protein 25 are critical for structural and functional integrity, Amie M. Morris, Teresa M. Treweek, J. A. Aquilina, John A. Carver and Mark J. Walker, FEBS Journal 275(23):5885 - 5898 (2008).

Modified genes spread to local maize: Findings reignite debate over genetically modified crops, Rex Dalton, Nature 456:149 (12 November 2008).
Transgenes from genetically modified (GM) maize (corn) crops have been found in traditional 'landrace' maize in the Mexican heartland, a study says. The work largely confirms a similar, controversial result published in Nature in 20011 and may reignite the debate in Mexico over GM crops.

PLANT GENOMICS: A Bunch of Trouble, David Grimm, Science 322(5904):1046 - 1047 (14 November 2008).
The banana is endangered and largely ignored by funding agencies, researchers, and breeders. But things might finally be going its way.

RENEWABLE ENERGY: Minnesota Ecologist Pushes Prairie Biofuels, Eli Kintisch, Science 322(5904):1044 - 1045 (14 November 2008).
David Tilman wants to mix it up by growing native grasses for energy. Many agronomists disagree.

Read more!

Thunderstorm

I felt bad when I saw the weather prediction from Nov 16 - 22 in last Saturday night.

It said that it will rain whole week. Sigh! We were thinking to do our laundry on Sunday. What should we do if it rained? It looked OK yesterday morning, so we went to do our laundry and put our clothes outside to dry them in the sun. We took the clothes in around 4:00pm when it became cloudy and dark.

It started thunder, lightening, and raining around 4:30 pm. We were hungry and decided to make lunch-dinner and prepared for today's lunch. The thunder and lightening got stronger and sounded like angry roaming. It was a big thunderstorm.

Our electrical power went off around 5 pm. Hmmm, our rice was half cooked, water and vegetables in pot were warm only, not to mention the noodle. Our landlord brought 2 candles to us in case the power did not come back. We waited and waited, but the power did not come back.

Around 8 pm, our landlord came to ask us if we wanted to use their camping stove to cook our dinner. It was still raining, but we were starving, so we took our pot, water and vegetables, noodle, and sauces and cook with landlord's camping stove. Then we ate our first candle dinner in Australia last night.

We could do nothing without power at night, so we just went to sleep after dinner. Finally, the power came back this morning around 5 am.

It is raining whole day. Sigh! So humid and so wet in here.

Read more!

Wednesday, November 12, 2008

Reef-building Corals

I read the first paper and found it is quite interest. Here are some interesting papers about corals.

Host pigments: potential facilitators of photosynthesis in coral symbioses, SOPHIE G. DOVE, CARLI LOVELL , MAOZ FINE, JEFFRY DECKENBACK, OVE HOEGH-GULDBERG, ROBERTO IGLESIAS-PRIETO & KENNETH R.N. ANTHONY, Plant, Cell & Environment 31(11):1523 - 1533 (2008).

Gene Expression of a Green Fluorescent Protein Homolog as a Host-Specific Biomarker of Heat Stress Within a Reef-Building Coral, C. Smith-Keune and S. Dove, Marine Biotechnology 10(2):166 (2008).

Bleaching, energetics and coral mortality risk: effects of temperature, light and sediment regime, KRN Anthony, SR Connolly & O Hoegh-Guldberg, Limnology and Oceanography 52(2): 716-726 (2007).

Coral mortality following extreme low tides and high solar radiation, KRN Anthony, A Kerswell, Marine Biology 151: 1623-1631 (2007).

The impact of coral bleaching on the pigment profile of the symbiotic alga, Symbiodinium, ALEXANDER A. VENN, MICHAEL A. WILSON, HENRY G. TRAPIDO-ROSENTHAL, BRENDAN J. KEELY & ANGELA E. DOUGLAS, Plant, Cell & Environment 29(12):2133 - 2142 (2006).

Response of holosymbiont pigments from the scleractinian coral Montipora monasteriata to short-term heat stress, Sophie Dove, Juan Carlos Ortiz, Susana Enríquez, Maoz Fine, Paul Fisher, Roberto Iglesias-Prieto, Dan Thornhill, and Ove Hoegh-Guldberg
Limnol. Oceanogr., 51(2):1149–1158 (2006).

Environmental limits to growth: physiological niche boundaries of corals along turbidity-light gradients, KRN Anthony & SR Connolly, Oecologia 141: 373-384 (2004).

Coral Reefs in a Century of Rapid Environmental Change, Ove Hoegh-Guldberg, Symbiosis 37(1-3):1-31 (2004).

Scleractinian corals with photoprotective host pigments are hypersensitive to thermal bleaching, Sophie Dove, Marine Ecology Progress Series 272:99-116 (2004).

Experience shapes the susceptibility of a reef coral to bleaching, B. Brown, R. Dunne, M. Goodson, A. Douglas, Coral Reefs 21(2):119-126 (July, 2002).

Kinetics of photoacclimation in corals, KRN Anthony & O Hoegh-Guldberg, Oecologia 134: 23-31 (2003).

Comparative analysis of energy allocation to tissue and skeletal growth in corals, Kenneth R. N. Anthony, Sean R. Connolly, and Bette L. Willis, Limnol. Oceanogr., 47(5), 2002, 1417–1429 (2002).

Major colour patterns of reef-building corals are due to a family of GFP-like proteins, S.G. Dove, O. Hoegh-Guldberg, and S. Ranganathan, Coral Reefs 19(3):197-204 (January, 2001).

Shifting roles of heterotrophy and autotrophy in coral energy budgets at varying turbidity, KRN Anthony & KE Fabricius, J. Exp. Mar. Biol. Ecol. 252: 221-253 (2000).

Biochemistry, mutagenesis, and oligomerization of DsRed, a red fluorescent protein from coral, Geoffrey S. Baird, David A. Zacharias, and Roger Y. Tsien, PNAS 97(22):11984-11989 (October 24, 2000).

Climate change, coral bleaching and the future of the world's coral reefs, Ove Hoegh-Guldberg, CSIRO Marine Freshwater Research 50:839-866 (1999).

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Monday, November 10, 2008

Car-9-5-8

I guess nobody will understand this title except us.

There is only 2 buses near the place we rent. 415 is to Toowong and Brisbane city and 414 is to UQ. The schedule for 414 is hourly from 7:20 am to 5:30 pm during weekdays and no service in weekend. 415 has a little bit more service than 414, and there is 8 buses on Saturday and 4 on Sunday.

Well, we tend to stay home in weekend due to this inconvenient bus schedule. We have thought about to buy car because we don't want to be trapped at home all the time. We decided to count the number of small white Japanese car on our way to shopping center or coming back and pick the number 10 as our consideration.

Here is the number:
Last Saturday from home to shopping center: 9
Last Saturday from shopping center to home: 5
Today from UQ to home: 8

We did not count to 10 yet. Does this mean that we should not buy a car?

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