Hyperaccumulation Plant

Phytoremediation describes the treatment of environmental problems (bioremediation) through the use of plants which mitigate the environmental problem without the need to excavate the contaminant material and dispose of it elsewhere.

Hyperaccumulators table – 1 : Al, Ag, As, Be, Cr, Cu, Mn, Hg, Mo, Naphtalene, Pb, Pd, Pt, Se, Zn
Hyperaccumulators table – 2 : Nickel
Hyperaccumulators table – 3 : Radionuclides (Cd, Cs, Co, Pu, Ra, Sr, U), Hydrocarbures, Organic Solvents.

Hypotheses, mechanisms and trade-offs of tolerance and adaptation to serpentine soils: from species to ecosystem level, E. Kazakou, P. G. Dimitrakopoulos, A. J. M. Baker, R. D. Reeves, and A. Y. Troumbis, Biological Reviews 83(4):495 - 508 (Sep 2008).

Using Arabidopsis to explore zinc tolerance and hyperaccumulation, Roosens NH, Willems G, Saumitou-Laprade P., Trends Plant Sci. 13(5):208-15 (2008 May).

Merging methods in molecular and ecological genetics to study the adaptation of plants to anthropogenic metal-polluted sites: implications for phytoremediation, Pauwels M, Willems G, Roosens N, Frérot H, Saumitou-Laprade P., Mol Ecol. 17(1):108-19 (2008 Jan).

Investigating heavy-metal hyperaccumulation using Thlaspi caerulescens as a model system, Milner MJ, Kochian LV., Ann Bot (Lond). 102(1):3-13 (2008 Jul).

Investigation of heavy metal hyperaccumulation at the cellular level: development and characterization of Thlaspi caerulescens suspension cell lines, Klein MA, Sekimoto H, Milner MJ, Kochian LV., Plant Physiol. 147(4):2006-16 (2008 Aug).

Novel nickel resistance genes from the rhizosphere metagenome of plants adapted to acid mine drainage, Mirete S, de Figueras CG, González-Pastor JE., Appl Environ Microbiol. 73(19):6001-11 (2007 Oct).

Improved understanding of hyperaccumulation yields commercial phytoextraction and phytomining technologies, Chaney RL, Angle JS, Broadhurst CL, Peters CA, Tappero RV, Sparks DL, J Environ Qual. 36(5):1429-43 (2007 Sep-Oct).

Perspectives of bacterial ACC deaminase in phytoremediation, Arshad M, Saleem M, Hussain S., Trends Biotechnol. 25(8):356-62 (2007 Aug).

A quantitative trait loci analysis of zinc hyperaccumulation in Arabidopsis halleri, Filatov V, Dowdle J, Smirnoff N, Ford-Lloyd B, Newbury HJ, Macnair MR., New Phytol. 174(3):580-90 (2007).

Expression and functional analysis of metal transporter genes in two contrasting ecotypes of the hyperaccumulator Thlaspi caerulescens, Plaza S, Tearall KL, Zhao FJ, Buchner P, McGrath SP, Hawkesford MJ., J Exp Bot. 58(7):1717-28 (2007).

Comparison of gene expression in segregating families identifies genes and genomic regions involved in a novel adaptation, zinc hyperaccumulation, Filatov V, Dowdle J, Smirnoff N, Ford-Lloyd B, Newbury HJ, Macnair MR., Mol Ecol. 15(10):3045-59 (2006 Sep).

Gene polymorphisms for elucidating the genetic structure of the heavy-metal hyperaccumulating trait in Thlaspi caerulescens and their cross-genera amplification in Brassicaceae, Basic N, Besnard G., J Plant Res. 119(5):479-87 (2006 Sep).

Zinc-dependent global transcriptional control, transcriptional deregulation, and higher gene copy number for genes in metal homeostasis of the hyperaccumulator Arabidopsis halleri, Talke IN, Hanikenne M, Krämer U., Plant Physiol. 142(1):148-67 (2006 Sep).

The heavy metal hyperaccumulator Thlaspi caerulescens expresses many species-specific genes, as identified by comparative expressed sequence tag analysis, Rigola D, Fiers M, Vurro E, Aarts MG., New Phytol. 170(4):753-65 (2006).

A comparison of the Thlaspi caerulescens and Thlaspi arvense shoot transcriptomes, Hammond JP, Bowen HC, White PJ, Mills V, Pyke KA, Baker AJ, Whiting SN, May ST, Broadley MR., New Phytol. 170(2):239-60 (2006).

Comparative transcriptomics -- model species lead the way, van de Mortel JE, Aarts MG., New Phytol. 170(2):199-201 (2006).

Construction of a genetic linkage map of Thlaspi caerulescens and quantitative trait loci analysis of zinc accumulation, Assunção AG, Pieper B, Vromans J, Lindhout P, Aarts MG, Schat H., New Phytol. 170(1):21-32 (2006).

High expression in leaves of the zinc hyperaccumulator Arabidopsis halleri of AhMHX, a homolog of an Arabidopsis thaliana vacuolar metal/proton exchanger, Elbaz B, Shoshani-Knaani N, David-Assael O, Mizrachy-Dagri T, Mizrahi K, Saul H, Brook E, Berezin I, Shaul O., Plant Cell Environ. 29(6):1179-90 (2006 June).

The heavy metal hyperaccumulator Thlaspi caerulescens expresses many species-specific genes, as identified by comparative expressed sequence tag analysis, Rigola D, Fiers M, Vurro E, Aarts MG, New Phytol. 170(4):753-65 (2006).

QTL analysis of cadmium and zinc accumulation in the heavy metal hyperaccumulator Thlaspi caerulescens, Deniau AX, Pieper B, Ten Bookum WM, Lindhout P, Aarts MG, Schat H., Theor Appl Genet. 113(5):907-20 (Sep 2006).

Phytoremediation: novel approaches to cleaning up polluted soils, Krämer U., Curr Opin Biotechnol. 16(2):133-41 (2005 April).

Using hyperaccumulator plants to phytoextract soil Ni and Cd, Chaney RL, Angle JS, McIntosh MS, Reeves RD, Li YM, Brewer EP, Chen KY, Roseberg RJ, Perner H, Synkowski EC, Broadhurst CL, Wang S, Baker AJ, Z Naturforsch 60(3-4):190-8 (2005 Mar-Apr).

Identification of Thlaspi caerulescens genes that may be involved in heavy metal hyperaccumulation and tolerance. Characterization of a novel heavy metal transporting ATPase, Papoyan A, Kochian LV., Plant Physiol. 136(3):3814-23 (2004 Nov).

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Late April 2009 papers

Some interest papers.

Ion channels versus ion pumps: the principal difference, in principle, David C. Gadsby, Nature Reviews Molecular Cell Biology 10:344-352 (May 2009).
Ions move across cell membranes through either ion channels or ion pumps. Recently, atomic-resolution structures and high-resolution functional measurements of examples from both channels and pumps have begun to suggest that these molecules need not be as different as was once thought.

Gene body DNA methylation in plants: a means to an end or an end to a means? Felipe Karam Teixeira and Vincent Colot, The EMBO Journal 28:997 - 998.

Floral stem cell termination involves the direct regulation of AGAMOUS by PERIANTHIA, Pradeep Das, Toshiro Ito, Frank Wellmer, Teva Vernoux, Annick Dedieu, Jan Traas, and Elliot M. Meyerowitz, Development 136:1605-1611.

Dual roles of the bZIP transcription factor PERIANTHIA in the control of floral architecture and homeotic gene expression, Annette T. Maier, Sandra Stehling-Sun, Heike Wollmann, Monika Demar, Ray L. Hong, Silke Haubeiss, Detlef Weigel, and Jan U. Lohmann, Development 136:1613-1620

CAMTA Proteins: A Direct Link between Calcium Signals and Cold Acclimation? Nancy A. Eckardt, Plant Cell 21:697.

Roles for Arabidopsis CAMTA Transcription Factors in Cold-Regulated Gene Expression and Freezing Tolerance, Colleen J. Doherty, Heather A. Van Buskirk, Susan J. Myers, and Michael F. Thomashow, Plant Cell 21:972-984.
The CBF cold response pathway plays a key role in cold acclimation. The authors show that the CBF2 promoter has both positive and negative DNA regulatory elements and establish roles for CAMTA proteins in regulating CBF2 transcription and freezing tolerance. The results suggest a possible mechanism for integrating low-temperature calcium signaling with cold-regulated gene expression.

Systems biology unlimited, Nature Genetics 41(5):505.
Sequencing technologies have unleashed more than enough quantitative data to test systems models of genome function, and sequence data are now driving a new systems biology. The new RNA entities uncovered may require new concepts of how genomes regulate their own expression.

Tiny RNAs associated with transcription start sites in animals, Ryan J Taft, Evgeny A Glazov, et al., Nature Genetics 41(5):572 - 578.
John Mattick and Yoshihide Hayashizaki and colleagues report the identifcation of tiny RNAs approximately 18 nucleotides in length that map near transcription start sites in human, chicken and Drosophila genomes. They call them transcription initiation RNAs (tiRNAs) and show that they associate with highly expressed transcripts and sites of RNA polymerase II binding.

Climate crunch: Sucking it up, Nicola Jones, Nature 458, 1094-1097 (2009)
It's simple to mop carbon dioxide out of the air, but it could cost a lot of money. In the second of three features on the carbon challenge, Nicola Jones talks with the scientists pursuing this strategy.

Chemistry: Fuel from thin air, Nature 458, 1080 (30 April 2009).
Angew. Chem. Int. Edn 48, 3322–3325 (2009)
Carbon dioxide can be sucked out of the air and turned into a useful fuel using a metal-free catalyst.

Exchange of Genetic Material Between Cells in Plant Tissue Grafts, S. Stegemann and R. Bock, Science 324(5927):649 - 651.
Plant genes can transfer between cells and across graft junctions, possibly explaining horizontal gene transfer.

A Yeast Hybrid Provides Insight into the Evolution of Gene Expression Regulation, I. Tirosh et al., Science 324(5927):659 - 662.
Gene expression between species of yeast may diverge, but recombination rewires their offspring into vigorous hybrids.


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2009 H1N1 Swine Flu

Current (May 28, 2009) information on Tracking the progress of H1N1 swine flu


(Note: Below is old news and information)
Not a good news. There are many unconfirmed cases in Australia now.


View H1N1 Swine Flu in a larger map (ps. You can adjust google map as you desire)
Purple marker is confirmed or probable
Pink marker is suspect
Yellow marker is negative
Fatal cases have no dot
Video on improved map and H1N1 swine flu current and future evolution (http://www.wpxi.com/video/19313969/index.html)

WHO Swine influenza: WHO has raised the pandemic flu alert (by the swine Influenza A H1N1) from level 4 to level 5 on April 29, 2009
More information on WHO phases of pandemic alert



2009 swine flue outbreak (wiki)

2009 swine flu outbreak timeline (wiki)

Below is the letter that UQ sent to her employee (Thu 30/04/2009 8:28 PM). I am just wondering what anti-bacterial hand gel can do to virus. Any kind of hand wash soap should do the job.

Swine Influenza outbreak: Advice from University of Queensland

To all staff,

Over the last few days there has been extensive media coverage on a new
influenza virus, "swine Influenza A H1N1".

I thought it opportune to update you on the issue and advise on a few
prudent measures we have taken.

The World Health Organization (WHO) has raised the pandemic flu alert
level from 3 to 5 this week. The WHO definition of this Level 5 is:
characterised by human-to-human spread of the virus into at least two
countries in one WHO region. While most countries will not be affected
at this stage, the declaration of Phase 5 is a strong signal that a
pandemic is imminent and that the time to finalize the organization,
communication, and implementation of the planned mitigation measures is
short.

http://www.who.int/csr/disease/avian_influenza/phase/en/index.html

Action taken by the University includes:

- Regular liaison with the State
and Federal Health Departments (UQ is represented by the Director,
University Health Service);

- Reviewing the extant Crisis Management Plan;

- Ordering protective masks and anti-bacterial hand gel as a precaution;

- Confirming that the Federal Government has large supplies of anti-viral
drugs should the need arise;

- Confirming that no cases have been reported
in Australia;

- Confirming the University Health Service processes and
reporting;

- Contacting the small number of staff and students in Mexico and
advising them to return to Australia and providing advice to a number
of students and staff in other locations;

- Approving an extension of
the free preventative flu inoculation program for staff to reduce the
risk of other flu infections. I strongly encourage you to make use of
this program funded by the University for your benefit. Book online at:

http://www.uq.edu.au/healthservice/staff-vacc.html

Further information on the OHS management of Pandemic Influenza at UQ
is at:

http://www.uq.edu.au/hupp/index.html?page=104001&pid=25015

Travel

Staff who are planning overseas travel, or who are already overseas
need to be alert to the risks associated with the destinations. If
planning to travel you are advised to monitor the Australian
Government's "Smarttraveller" website for important Information at

http://www.smarttraveller.gov.au/index.html

Looking after yourself

At this time, we can all help reduce the spread of any respiratory virus
by following sensible hygiene routines as below. These steps will help
to protect you and your family from possible infection.

- If you have recently returned from travel to Mexico, the US, Canada
or New Zealand (or have any concerns following other recent travel) we
recommend you stay at home if you develop flu-like symptoms and consult
your medical practitioner or seek advice from the University Health
Service. If they recommend remaining at home and resting, please do so.

- Wash your hands frequently - either with soap and water or an alcohol
based gel.

- Use tissues when coughing and sneezing. Dispose of tissues
in a waste receptacle.

- Cover your cough with your arm or elbow rather
than your hand.

Further information can be found at the World Health Organisation
at:

http://www.who.int/csr/disease/swineflu/en/index.html

The Australian Government at:

http://www.healthemergency.gov.au/internet/healthemergency/publishing.nsf/Content/health-swine_influenza-index.htm

The Queensland Government at:

http://www.health.qld.gov.au/swineflu/.

If there are any significant developments I will provide further advice.

Maurie McNarn AO
Executive Director Operations

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Easy Cheese cake

This is from 芝士蛋糕簡單做法 on youtube

Basically, it is 200 mL condensed milk + 200 mL cream + 2 TBSP lemon juice
-> hand mix, solidify, then freeze


We tried to do it. We thought about to do condensed milk by ourself because the one that supermarket sales is 375 mL, but not 200 mL.

200 mL H2O + 200 mL milk powder + 120 g sugar
-> microwave 1+1+1+1+1 minutes to dissolve them
-> lowest heat on stove because there is too much water in it
-> I think we still have 350 mL not so condensed milk (ps. it tasted good)
-> + 200 mL Cream + 3 TBSP lemon juice
-> mix well and put into freezer
It did not solidify because we did not really get condensed milk, but we still put it into freezer because it still tasted good. We should try to do the real condensed milk next time.


Condensed milk (45% sugar) = 1 cup milk powder + 3/4 cup sugar + 1/2 cup water
(ps. 1 cup = 250 mL)
(ps. 200 mL condensed milk = 1/2 cup milk powder + 90 g sugar + 60 g water)
100 g H2O (100 mL) + 100 g Milk powder (200 mL) + 90 g sugar (~90 mL)
-> microwave 1 minute, mix, then 30 sec, and mix to dissolve them
-> + 200 mL Cream + 4 TBSP lemon juice
-> mix well and put into freezer
It looks good and solidify better than exp 1. Well, it is still not like the one on youtube, but it tastes good even it is a little bit too sweet.


80 g H2O (80 mL) + 80 g Milk powder (160 mL) + 60 g sugar (~60 mL)
-> microwave 1 minute, mix, then 30 sec, and mix to dissolve them
-> + 200 mL Cream + 4 TBSP lemon juice
-> mix well and put into freezer

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Strange Labmate

There is one labmate with strange behavior in our lab.

Our lab is a big group with many people, so we use booking note to reserve the time slot for the usage of many equipments including thermal shakers, big centrifuges, PCR machines, laminar hoods, and gene shoot gun.

There is one person who always ignore other people's reservation and put his name on the same time slot and use it without asking the person who already reserves that time slot. It happened to me twice on PCR machines and twice on thermal shakers. It was not a happy thing to see the PCR machine became unavailable when I took the ready-to-go PCR samples to the machine on time. It is not fun when I had my bacteria culture ready to put into shaker and found the shaker has been occupied by other person. I know it happens not just on me but also other people. Sigh! I don't understand why that person keeps doing this.
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Mid April 2009 papers

Some interest papers.

New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology, Robert Henry, Keith Edwards, Plant Biotechnology Journal 7(4):311-311.

Discovering genetic polymorphisms in next-generation sequencing data, Michael Imelfort, Chris Duran, Jacqueline Batley, David Edwards, Plant Biotechnology Journal 7(4):312-317.

Single nucleotide polymorphism discovery in barley using autoSNPdb, Chris Duran, Nikki Appleby, Megan Vardy, Michael Imelfort, David Edwards, Jacqueline Batley, Plant Biotechnology Journal 7(4):326-333.

A unique virulence factor for proliferation and dwarfism in plants identified from a phytopathogenic bacterium, Ayaka Hoshi, Kenro Oshima, Shigeyuki Kakizawa, Yoshiko Ishii, Johji Ozeki, Masayoshi Hashimoto, Ken Komatsu, Satoshi Kagiwada, Yasuyuki Yamaji, and Shigetou Namba, PNAS 106(15):6416-6421 (April 14, 2009).

Obesity: Be cool, lose weight, Stephen R. Farmer, Nature 458:839-840 (16 April 2009).
To lose weight, would you rather diet, exercise or subject yourself to cool temperatures? The last choice is not such an odd one, as adult humans have brown fat tissue that burns calories in response to cold.

Biochemistry: Anchors away, Maria Paola Costi and Stefania Ferrari, Nature 458:840-841 (16 April 2009).
Nature often adopts several approaches to crack the same problem. The finding that the mechanism of a crucial enzyme in certain disease-causing bacteria differs from that in mammals offers scope for drug discovery.

Genetics of gene expression: Putting radiation response on the map, Louisa Flintoft, Nature Reviews Genetics 10:278 (May 2009).

Plant development: Paternal control regulates division, Elizabeth Neame, Nature Reviews Genetics 10:280-281 (May 2009).

Epigenetics: A silent inheritance, Francesca Cesari, Nature Reviews Genetics 10:283 (May 2009).

Linking DNA methylation and histone modification: patterns and paradigms, Howard Cedar & Yehudit Bergman, Nature Reviews Genetics 10:295-304 (May 2009).
DNA methylation and histone modification are important for regulating gene expression and chromatin structure. New evidence suggests there are multiple levels of crosstalk between these marks. Understanding this crosstalk will be important for elucidating the role of epigenetics in development and disease.

Survival of the flexible: hormonal growth control and adaptation in plant development, Hanno Wolters & Gerd Jürgens, Nature Reviews Genetics 10:305-317 (May 2009).
Plant growth is controlled by both intrinsic and environmental signals and is mediated by hormonal signalling. Hormones are important for maintaining and regulating stem cell compartments in postembryonic plants, and current research is revealing many interactions between different hormone pathways.

Validating, augmenting and refining genome-wide association signals, John P. A. Ioannidis, Gilles Thomas & Mark J. Daly, Nature Reviews Genetics 10:318-329 (May 2009).
Genome-wide association studies have identified many promising links between genetic variants and human traits. However, the steps from the initial identification of associated markers to the reliable validation of the causal variant are long and tortuous, as the authors describe.

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Happy Earth Day

Today is Earth Day. Google also made a special logo.

I think government should set Earth Day as a holiday and encourage people to stay home or do something without energy consumption. Sleeping whole day, walking or hiking around neighbor, or just chatting to each other would reduce energy consumption a lot.

Information on wiki about Earth Day:
Earth Day, celebrated April 22, is a day designed to inspire awareness and appreciation for the Earth's environment. It is held annually during both spring in the northern hemisphere and autumn in the southern hemisphere. It was founded by U.S. Senator Gaylord Nelson as an environmental teach-in in 1970 and is celebrated in many countries every year.
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Sick again

I am sick again. I am not sure why I get sick so often after I came to Australia. What's wrong with my immune system? I think I got sick almost every month.

I started to feel sharp headache and body ache and sore throat. The pain is so sharp that I almost couldn't control myself not to scream. I have to eat pain killer to reduce it and wake up every morning due to the pain. I started to have fever since Friday and sneeze since yesterday. God, I feel so bad now, headache, body ache, fever, sore throat, and running nose.
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Bunya Mountains National Park

We went hiking on April 10 in the Bunya Mountains National Park at Queensland during Easter holiday. It was raining. There were many people and no space for camping even we tried to reserve it 1 month ago.

We took the trails to see waterfall. We took Eastern Rainforest Circuits to see rock pools, Festoon Falls, Tim Shea Falls, Big Falls Lookout, and Barker Creek Lookout. The amount of water for these 3 Falls were less or about the amount of bathroom shower. We missed the Great Falls at MD/VA border in USA. Gee! We are so disappointed.

There are many Hoop and Bunya pines in this national park. Bunya pine is elephant-feet like. There is information about Bunya cone drop zone by Bunya Mt. NP website: Avoid lingering under bunya pines between December and March. That is when the soccer-ball sized cones weighing up to 10kg fall from the tops of towering trees.

Below are Bunya pine and Bunya cone in wiki:


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Australian snubfin dolphin

They are so cute. People always love those cute and lovely animals, so do I.

Rare dolphin spits to catch its prey, scientists find - Australian snubfin dolphin fires jets of water from its mouth to round up fish, WWF discovers
by Toni O'Loughlin in Sydney, guardian.co.uk, Tuesday 14 April 2009 15.16 BST

Information from wiki about Snubfin Dolphin
The Australian Snubfin Dolphin (Orcaella heinsohni) is a recently recognised species of dolphin, scientifically described in 2005.
It is closely related to the Irrawaddy dolphin (O. brevirostris), and closely resembles it. Until very recently they were thought to be Irrawaddy dolphins. However, the Australian snubfin is tri-coloured, while the Irrawaddy dolphin only has two colours on its skin. Also the skull and the fins show minor differences between the two species.

The images of Snubfin Dolphin

A RARE Snubfin dolphin peeks over the waves off Northern Australia, showing his distinctive rounded snout. By SARA NELSON Published: 06 Mar 2008


Common name: Irrawaddy Dolphin; Snubfin Dolphin
Scientific name: Orcaella brevirostris
Distribution: South and Southeast Asia, Australia
CITES listing: Appendix I (12/01/05)
Photo: © Department of Fishery of Thailand


The Irrawaddy Dolphin, the closest relative of Townsville's Snubfin Dolphin,
leaps from the water chasing dinner.
Image source: http://www.wwf.org.ph/about.php?pg=wwd&sub1=00004


Adult Australian snubfin dolphin off Townsville. Photo: Guido Parra

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Cover of the Plant Cell

I know that this might sound silly, but I just want to see how it will look like if I put the covers of the Plant Cell, the number 1 journal in plant science, together. Here are the covers from vol 10 to current issue. Very pretty.

All the images are link to the image URL in the Plant Cell.


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