Heron Island

We went to Heron Island, Heron Reef, and Wistari Reef during Feb 21-27, 2009. It is a wonderful trip.

We drove about 7 hours on Feb 21 from Brisbane to Gladstone under few hours heavy rain. We stayed in backpacker at night. We took 2 hrs Voyage's ship from Gladstone to Heron island at 11 am on Feb 22, then we stayed in Heron Island Research Station. My husband's lab came here to collect some animals, majority are mantis shrimp. His boss asked me if I wanted to come. Here I am. It is a lovely coral reef island. Very small and surrounding by white sand and huge coral reef. There are many birds live on this island and this makes the island stink. There is one kind of bird makes baby crying and howling noise at night. That's kind of annoying. If you don't know that's from that bird, you will think that's ghost whisper. It rained everyday while we were there, sometime the rain was so big that we were almost unable to work under it. But I think the rain did wash away some sting smell. It was quite windy and kind of pain when wind blew sands onto our skin.

We snorkeled everyday, broke coral reef to catch the shrimps every afternoon at low tide. We walked around the beach of island every night to look for turtle laying eggs and hatching. We saw just hatched green turtle trying to crawl into the ocean, we saw big and young adult green turtles digging big and deep nest holes for hours, we saw one laying eggs, and we saw them covering the nest up for more than 1 hour. We went to check the coverred nest during day time and it is hard to tell where it is. It is very exciting to see this. We also tried to rescue some baby turtle from bird's mouth or took some miss-orientation baby turtles back to ocean. This is an amazing experience to hold them on our hands.

We saw many marine animals, such as
(1) many climbing, digging hole, laying eggs and covering eggs adult Green Turtle or just hatching baby green turtles
(from wiki),

(2) many different gobies (family Gobiidae) and some have shrimps with them
(from wiki),

(3) many giant clam
(from wiki), .....,

(4) many different colorful damselfish (family Pomacentridae)
(from wiki), .....,

(5) two stingray
(from wiki),

(6) 1 shovelnose,
(from FishBase)

(7) 1 pufferfish (Diodontidae)
(from wiki),

(8) 1 lionfish
(from wiki),

(9) at least one Labroides dimidiatus (cleaning fish)
(from FishBase)
many unknown or name forgotten big and small fishes, ...

I did not dive, so I did not see clown fish.

If I can come again with my husband's lab, I will come. I love this trip.

Feb 21: driving 7 hours from Brisbane to Gladstone, heavy rain, staying in backpacker
Feb 22: taking 2 hours Voyage's ship to Heron island, a little bit bumpy, hire snorkeling stuffs for me, breaking rock several hours to get animals in the afternoon
Feb 23: driving boat to Wistari Reef to collect animals in the afternoon (ps. stop boat at ~50 m distance to the reef, then snorkeling to the edge and climbing onto it, very pretty). Heavy rain.
Feb 24: driving boat to north of Heron reef in the afternoon, other people went diving and I stayed on the boat. Rain.
Feb 25: snorkeling in the morning and afternoon, we couldn't go out because the shipping ship blocked the harbor, we collected animals on the reef around island. Rain.
Feb 26: snorkeling in the morning and afternoon, we couldn't go out because it was too windy and nobody was allowed to go out with boat, we collected animals on the reef around island. Rain.
Feb 27: Organize and pack all animals and personal stuffs. Clean up the place we lived and all the tanks, take Voyage's ship back to Gladstone, drive back and put animals into tanks. Sunny.

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Baking Soda

I got an email from friend. It said that we can use baking soda, i.e. sodium bicarbonate, to remove pesticide residue from fruit and vegetable and chlorine residue from tape water.

This method is suggested by Dr. Chen Yaokuan from Chaoyang University of Technology, Taiwan.

Add 1 tablespoon baking soda + suitable amount of water
-> soak fruits and vegetables in it 2-3 minutes

Why baking soda can dechlorinate and remove pesticide? The chemical formula of sodium bicarbonate is NaHCO3. Na+ are positively charged. It will react with negatively charged chlorine into sodium chloride. This is how it can remove chlorine from tap water.

NaHCO3 is weak base and most of the pesticides are acidic, then adding NaHCO3 in water can accelerate the removal of pesticides attached on fruits and vegetables.

They also suggest adding baking soda before boiling vegetables can prevent the loss of chlorophyll and maintain greener color.

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Bi- and Di-

We walked around in the campus after lunch. I saw a bicycle parking rack with "Bicycles" sign. Hmmm, bicycles = bi + cycles, i.e. a thing with 2 cycles.

Then I am wondering why is bi-cycles, why not di-cycles? When will people use bi- or di- to describe "two", "twice"?
==================
Definition of bicycle from dictionary.com
1868, coined from bi- "two" + Gk. kyklos "circle, wheel" (see cycle), on the pattern of tricycle; both the word and the vehicle superseding earlier velocipede. Probably not from Fr., though often said to be. The confusion apparently is because Pierre Lallement, employee of a Fr. carriage works, improved Macmillan's 1839 pedal velocipede in 1865 and took the invention to America. See also penny-farthing.

I list 3 definitions from dictionary.com about bi-
(1) bi- 
a combining form meaning "twice", "two", used in the formation of compound words: bifacial; bifarious.

(2) bi- or bin-
pref.
1.
a. Two: biform.
b. Both: binaural.
c. Both sides, parts, or directions: biconcave.
d. Occurring at intervals of two: bicentennial.
e. Usage Problem Occurring twice during: biweekly.
f. Containing twice the proportion of a specified chemical element or group necessary for stability: bicarbonate.
g. Containing two chemical atoms, radicals, or groups: biphenyl.
2.
a. Occurring at intervals of two: bicentennial.
b. Usage Problem Occurring twice during: biweekly.
c. Containing twice the proportion of a specified chemical element or group necessary for stability: bicarbonate.
d. Containing two chemical atoms, radicals, or groups: biphenyl.
3.
a. Containing twice the proportion of a specified chemical element or group necessary for stability: bicarbonate.
b. Containing two chemical atoms, radicals, or groups: biphenyl.

(3) Bi-
Bi-\ [L. bis twice, which in composition drops the -s, akin to E. two. See Bis-, Two, and cf. Di-, Dis-.]
1. In most branches of science bi- in composition denotes two, twice, or doubly; as, bidentate, two-toothed; biternate, doubly ternate, etc.
2. (Chem.) In the composition of chemical names bi- denotes two atoms, parts, or equivalents of that constituent to the name of which it is prefixed, to one of the other component, or that such constituent is present in double the ordinary proportion; as, bichromate, bisulphide. Be- and di- are often used interchangeably.

I list 3 definitions from dictionary.com about di-
(1) di- 
a prefix occurring in loanwords from Greek, where it meant “two,” “twice,” “double” (diphthong); on this model, freely used in the formation of compound words (dicotyledon; dipolar) and in chemical terms (diatomic; disulfide).

(2) di-
pref.
Two; twice; double: dichromatic.
Containing two atoms, radicals, or groups: dichloride.

(3) Di-
Di-\ [Gr. di`s- twice; akin to two, L. bis twice. See Two, and cf. Bi-, Dia-. The L. pref. dis- sometimes assumes the form di-. See Dis-.] A prefix, signifying twofold, double, twice; (Chem.) denoting two atoms, radicals, groups, or equivalents, as the case may be. See Bi-, 2.

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ARC Coral Reef Studies

We just watched the Australian story on ABC1. It talked about what professor Hoegh-Guldberg and ARC Centre of Excellence Coral Reef Studies are doing. They use scientific results to establish the relationship between coral bleach and climate change and urge people to change their life style to save the earth and themselves. I encourage people to watch it.

The heat of the moment: Australian Story ABC1, 8:00pm: 9 Febuary 2009
Professor Ove Hoegh-Guldberg is waking up the world to the impact of climate change on the Great Barrier Reef. This summer has seen unprecedented high ocean temperatures across the region; a strong indicator of another coral bleaching event. If we don't act to drastically lower carbon emissions, Ove believes that the world's largest coral reef system will die within 50 years.

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sick?

I have severe headache and cold sweat, and suffer from vomiting and diarrhea since yesterday afternoon.

First, it was irregular headache starting after 11 am. Then the headache became very painful after 3 pm combined with strong vomiting feeling. I tried very hard to tolerate these painful feeling because I have several experiments need to finish. I went for diarrhea and started cold sweat badly after 4:30 pm. My whole body was shaking when I prepared gel loading sample and loaded my gels and could barely stand after 5 pm. I almost couldn't hold stuffs when I scanned my gels around 6 pm.

I was too sick to start bacteria culture and ligation for today's experiments. I left lab and walked to my husband's lab around 6:15 pm. I asked my husband to drive car to school to pick me up because I had no energy to walk to its parking location.

I took pain killer to stop the continuous painful headache after we got home, but it didn't work. I rested on our sofa to comfort my body, but it did not help. Suddenly the vomiting feeling became unbearable and I run to the kitchen sink to vomit. Most vomit stuffs got into sink, but some of them came out onto floor, cabinet, kitchen towel, and dish holder before I reached the sink. It was really disgusting, but my husband helped to clean it up. I think that I emptied my stomach because the sink was half full and I have worried it the sink would be stuck. Luckily, the sink was fine.

After this, the vomiting feeling was eased very much. I went to brush my teeth and took one more pain killer because I thought the previous might be in the sink now. My headache was still unbearable. I would scream if I still had energy.

My husband made dinner, but I have no appetite to eat anything because anything got into my stomach made me vomiting.

I tried to sleep, but the headache kept me awake until this morning sometimes. I still feel sick now, but it is better than last night.

==============
This is an email I sent to my labmate:

I have suffered severe headache, cold sweat, and vomiting and diarrhea since yesterday afternoon. I am not sure if I am sick or something else. I would like to stay home today because I still feel weak and bad even I am better than yesterday.

I barely finished the following works yesterday afternoon
(1) transformation for PCR# 187 (RACodNos), 188 (RACodNosV2) into pGEM-T EZ,
(2) gel running for the colony PCR of PUKR-RACodNos, and
(3) gel running for the digestion result of pDNA 175-5 (TuIntron in pGEM-T EZ), 176-1 (AcIntron in pGEM-T EZ), and 186-8 (ZF sites).

There were some good colonies in colony PCR. I felt too sick to write down information on the gel image, start the new culture and ligation yesterday.

If you are sick and unable to go to school today, you could stay home because I already asked Lilian's help to take yesterday's transformation plates out today for us.

If you are OK and want to start bacteria culture for PUKR-RACodNos and cloning for pDNA 175-5, 176-1 and 186-8, the information on that gel images are
(2) PUKR-RACodNos: in the order of colony #1-22 and followed with PUKR's Ubi in the last column.
(3) pDNA 175-5, 176-1 and 186-8: no cut and Roche clean up of 175-5, no cut and Roche clean up of 176-1, no cut, double digestion, and gel extraction with QIAEX of 186-8. Each loading is 2 uL of sample except the gel extraction with QIAEX is 4 uL. The last 2 columns are lambda DNA which indicates 50 and 100 ng.
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Bushfire and Flood

It looks like that the beginning of 2009 is not peaceful for Australia. Flood in northern Queensland and severe bushfire in Victoria. May God bless Australia.

Information from wiki:
Bushfire: A bushfire is a fire that occurs in the bush (collective term for scrub, woodland or grassland of Australia, New Zealand, New Caledonia). In south east Australia, bushfires tend to be most common and most severe during summer and autumn, in drought years, and particularly severe in El Niño years. Subsequently south east Australia is considered one of the most fire prone areas of the world. In the north of Australia, bushfires usually occur during winter (the dry season), and fire severity tends to be more associated with seasonal weather patterns. In the southwest, similarly, bushfires occur in the summer dry season and severity is usually related to seasonal growth. Fire frequency in the north is difficult to assess, as the vast majority of fires are caused by human activity, however lightning strikes are as common a cause as human ignited fires and arson.

The February 2009 Victorian bushfires are a series of at least 31 bushfires across the Australian state of Victoria, resulting in at least 135 deaths and caused major property damage, destroying at least 750 homes, mostly in Kinglake and surrounding areas and up to 330,000 ha of property. The fires are the deadliest natural disaster in Australia's recorded history. They occurred during an exceptional heat wave, and began on Saturday 7 February, a day when several localities across the state, including the state capital of Melbourne, recorded their highest temperatures since records began over 150 years previously. The numerous fires are largely the result of recent lightning strikes, although some are suspected to have been deliberately lit by arsonists — Australian Prime Minister Kevin Rudd described them as "mass murder."

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32 oC Lab

The lab I work was hot and humid when I walked in there after lunch break.

There was no cool AC wind blowing. I took one thermometer out of its waterbath to measure the room temperature because it was a little bit unbearable, especially when I need to wear lab coat. Two thermometers told me that the room temperature near me is 32 oC. Can you image to wear jacket under 32 oC environment? You might suggest me to take off my labcoat to cool down myself, but I would rather sweat than let all kinds of chemicals get onto my own clothes.

Many labmates left much earlier due to this heat.
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Feb 2009 papers

Here are some interest papers.

Synthetic biology: The yin and yang of nature, Jeff Gore & Alexander van Oudenaarden, Nature 457:271-272 (15 January 2009).
Oscillations in gene expression regulate various cellular processes and so must be robust and tunable. Interactions between both negative and positive feedback loops seem to ensure these features.

Plant development: Genes turn on for a new leaf, Mary Muers, Nature Reviews Genetics 10, 74-75 (February 2009). A Research Highlights for following paper:
A Conserved Molecular Framework for Compound Leaf Development, Thomas Blein, Amada Pulido, Aurélie Vialette-Guiraud, Krisztina Nikovics, Halima Morin, Angela Hay, Ida Elisabeth Johansen, Miltos Tsiantis, Patrick Laufs, Science 322(5909):1835 - 1839 (19 December 2008).

Small silencing RNAs: an expanding universe, Megha Ghildiyal & Phillip D. Zamore, Nature Reviews Genetics 10:94-108 (February 2009).

The NAC-domain transcription factor GOBLET specifies leaflet boundaries in compound tomato leaves, Yael Berger, Smadar Harpaz-Saad, Arnon Brand, Hadas Melnik, Neti Sirding, John Paul Alvarez, Michael Zinder, Alon Samach, Yuval Eshed, and Naomi Ori, Development 136:823-832.

Alterations in the Endogenous Ascorbic Acid Content Affect Flowering Time in Arabidopsis
Simeon O. Kotchoni, Katherine E. Larrimore, Madhumati Mukherjee, Chase F. Kempinski, and Carina Barth, Plant Physiol. 149:803-815.

The Arabidopsis Abscisic Acid Catabolic Gene CYP707A2 Plays a Key Role in Nitrate Control of Seed Dormancy, Theodoros Matakiadis, Alessandro Alboresi, Yusuke Jikumaru, Kiyoshi Tatematsu, Olivier Pichon, Jean-Pierre Renou, Yuji Kamiya, Eiji Nambara,
and Hoai-Nam Truong, Plant Physiol. 149:949-960.

Histone H2B Deubiquitination Is Required for Transcriptional Activation of FLOWERING LOCUS C and for Proper Control of Flowering in Arabidopsis, Robert Jeffrey Schmitz, Yosuke Tamada, Mark Robert Doyle, Xiaoyu Zhang, and Richard Mark Amasino, Plant Physiol. 149:1196-1204.

Merck joins the biotech game, Victor Bethencourt, Nature Biotechnology 27:104.

GM poplars to grow next door, Hayley Birch, Nature Biotechnology 27:107.

Land use stirs biofuels ruckus, Susan Kim, Nature Biotechnology 27:109.

Proprietary science, open science and the role of patent disclosure: the case of zinc-finger proteins, Subhashini Chandrasekharan, Sapna Kumar, Cory M Valley & Arti Rai, Nature Biotechnology 27:140 - 144.
A closer look at the large patent estate now covering both the engineering and use of zinc-finger proteins.

Prediction of high-responding peptides for targeted protein assays by mass spectrometry, Vincent A Fusaro, D R Mani, Jill P Mesirov & Steven A Carr, Nature Biotechnology 27:190 - 198.
Development of sensitive mass spectrometry–based assays for complex biofluids depends on the ability to identify signature peptides that produce the strongest signals. Fusaro et al. use protein physicochemical properties to predict high-responding peptides in data obtained from complex samples such as plasma.

Splice-site pairing is an intrinsically high fidelity process, Kristi L. Fox-Walsh and Klemens J. Hertel, PNAS 2009 106:1766-1771.




RICHARD RICHARDS PROFILE: Making Every Drop Count in the Buildup to a Blue Revolution, Science 323(5917):1004 - 1005 (20 February 2009).
Richard Richards, a geneticist at CSIRO Plant Industry, is breeding wheat varieties that can tough out prolonged droughts--and keep people fed.

ATMOSPHERIC SCIENCE: A Matter of Humidity, A. E. Dessler and S. C. Sherwood, Science 323(5917):1020 (20 February 2009).
How strong a part does water vapor play in global warming?

CELL BIOLOGY: Stress Response and Aging, L. R. Saunders and E. Verdin, Science 323(5917):1021 (20 February 2009).
Transcriptional regulators that respond to stress also influence life span.

A Genetic Defect Caused by a Triplet Repeat Expansion in Arabidopsis thaliana, Sridevi Sureshkumar, Marco Todesco, Korbinian Schneeberger, Ramya Harilal, Sureshkumar Balasubramanian, Detlef Weigel, Science 323(5917):1060-1063 (20 February 2009).
A strain of Arabidopsis provides a plant model for the harmful effects of repeat nucleotide expansions in populations.

Molecular processes underlying the floral transition in the soybean shoot apical meristem, Chui E. Wong, Mohan B. Singh, Prem L. Bhalla, The Plant Journal 57(5):832 - 845.

MERISTEM-DEFECTIVE, an RS domain protein, is required for the correct meristem patterning and function in Arabidopsis, Stuart A. Casson, Jennifer F. Topping, Keith Lindsey, The Plant Journal 57(5):857-869.

Resetting and regulation of FLOWERING LOCUS C expression during Arabidopsis reproductive development, Jean Choi, Youbong Hyun, Min-Jeong Kang, Hye In Yun, Jae-Young Yun, Clare Lister, Caroline Dean, Richard M. Amasino, Bosl Noh, Yoo-Sun Noh, Yeonhee Choi, The Plant Journal 57(5):918 - 931.

How plant defence gets hairy, Development 136:e606.

Jasmonic acid control of GLABRA3 links inducible defense and trichome patterning in Arabidopsis, Yuki Yoshida, Ryosuke Sano, Takuji Wada, Junji Takabayashi, and Kiyotaka Okada, Development 136:1039-1048.

Epigenetic inheritance during the cell cycle, Aline V. Probst, Elaine Dunleavy & Geneviéve Almouzni, Nature Reviews Molecular Cell Biology 10(3):192.
Epigenetic inheritance concerns the mechanisms that ensure the transmission of epigenetic marks from mother to daughter cell. Chromatin modifications and nuclear organization are candidate epigenetic marks — whether they fulfil the criterion of heritability and what mechanisms ensure their propagation is an area of intensive research.

Single proteins might have dual but related functions in intracellular and extracellular microenvironments, Derek C. Radisky, Melody Stallings-Mann, Yohei Hirai & Mina J. Bissell, Nature Reviews Molecular Cell Biology 10(3):228.
Maintenance of organ homeostasis and control of appropriate responses to environmental alterations requires the coordination of cellular functions and tissue organization. This coordination could be achieved by proteins that can have distinct but linked functions on both sides of the plasma membrane.

Differential chromatin marking of introns and expressed exons by H3K36me3, Paulina Kolasinska-Zwierz, Thomas Down, Isabel Latorre, Tao Liu, X Shirley Liu and Julie Ahringer, Nature Genetics 41(3):376 - 381.
Julie Ahringer and colleagues show that, in C. elegans, exons are preferentially marked with H3K36me3 relative to introns, and that the difference in H3K36me3 marking between exons and introns is evolutionarily conserved in human and mouse.

Reverse ChIP, Nicole Rusk, Nature Methods 6(3):187.
The combination of a DNA probe and mass spectrometric analysis allows the unbiased identification of chromatin-associated proteins.

Mimicking a pore, Amy Donner, Nature Methods 6(3):188 - 189.
A functionalized polycarbonate nanosorter mimics fundamental properties of the nuclear pore complex.

Quantitative interaction proteomics using mass spectrometry, Alexander Wepf, Timo Glatter, Alexander Schmidt, Ruedi Aebersold & Matthias Gstaiger, Nature Methods 6(3):203 - 205.
Absolute quantitative information about the stoichiometry of protein complex components can be obtained with a modified affinity purification–mass spectrometry method, as demonstrated for the human protein phosphatase 2A network.

Small RNAs: biology's brave new world, Nathan Blow, Nature Methods 6(3):231 - 235.
Small RNA discovery and profiling efforts are dramatically reshaping fundamental concepts of how genes are regulated and are leading to new tools for studying gene function.

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TV shows

Here are some TV shows.

NCIS: Tuesday 8:30 pm - 9:30 pm on channel 10

Lie to Me: Tuesday 9:30 pm - 10:30 pm on channel 10

Criminal Minds: Wednesday 8:30 pm - 9:30 pm on channel 7
House: Wednesday 9:00 pm - 10:00 pm on channel 10
Cold Case: Wednesday 10:30 pm - 11:30 pm channel 9

Inspector Rex: Thursday 7:30 pm - 8:30 pm on channel SBS
CSI: NY: Thursday 9:30 - 10:30 pm on channel 9
Life on Mars: Thursday 9:30 - 10:30 pm on channel 10

Mythbusters: Saturday 7:30 pm - 8:30 pm on channel SBS

Border Security - Australia's Front Line: Sunday 7:30 - 8:00 pm on channel 7
Air Crash Investigation: Sunday 11:20 pm - 12:30 am on channel 7

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