Here is one strategy for combating global warming!

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TheScientist

Magazine of the Life Sciences

http://www.the-scientist.com/news/display/57745/

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By Carrie Arnold

Relief for parched plants

Heat and drought are wreaking havoc on the world's crops, but scientists are engineering plants that may be able to survive such harsh conditions   [Published 14th October 2010 02:47 PM GMT]

Blazing heat and drought across Russia have withered much of the country's wheat crop, triggering a dramatic rise in food prices worldwide. But what if plants could survive long periods without water?
Groups of scientists around the world are working on engineering crops that can do just that. And with temperatures and drought frequency expected to continue to climb, and an increasing demand on dwindling fresh water supplies, the need for drought-resistant plants is more pressing than ever.
"The number one limiting factor on [crop] yield in the world is available water," said Mark Lawson, an agricultural scientist at Monsanto, in St. Louis, Mo. And in many countries around the world, "drought is essentially an annual occurrence."
But scientists are looking for ways to tweak plant physiology to enable crops to feed the world using significantly less water. Many research groups have focused on improving root systems, which function like miniature straws to slurp water. Healthier, more abundant roots mean a plant can take up water from the soil more efficiently. Other scientists have begun to identify the subtle genetic differences between domesticated crops and their more drought-resistant wild relatives in search of water-saving tricks.
Plant biologist Sean Cutler of the University of California, Riverside, for example, has focused on the plant hormone abscisic acid (ABA). When a plant's roots sense a shortage of water in the surrounding soil, they synthesize ABA, which tells the plant to close microscopic pores on their leaves through which moisture can escape. Although closing these microscopic pores, known as stomata, prevents water loss, it also blocks the entry of carbon dioxide, a critical component of photosynthesis. Without sufficient CO2, plants can't photosynthesize and crop yield drops.
By studying how ABA triggers stomata closing, Cutler hopes to harness the plant's ability to conserve water without negatively affecting photosynthesis. His goal is to create a molecule that selectively activates certain ABA pathways under drought conditions to maximize water conservation, as well as photosynthesis. Crop plants don't respond well to a lack of water, he said. "What we want to do is tinker with the physiology a bit so that we can get better yields when conditions aren't ideal."
Paleobotanist Robin Allaby, at the University of Warwick in the UK, thinks that looking at the wild ancestors of current crops may be one of the keys to creating more drought-resistant plants. Domesticated barley (Hordeum vulgare) produces six smaller grains on each stalk, compared to two slightly larger grains on the wild variety. The greater number of grains and their higher protein content give them tremendous advantage as a food source, but previous research has shown that six-grain barley plants need more water than two-grain domestic barley.
In Qasr Ibrim, an archaeological site in southern Egypt, Allaby found evidence that the domestic barley grown there reverted to the wild-type two grain, and he suspects the barley may have evolved rapidly in response to drought conditions. "When plants need to change," he said, "they can change very, very quickly. They're very evolvable." This swift evolutionary response to drought may give scientists genetic clues about how crops can better survive water stress.
One such drought-resistant technique comes in the form of an enzyme known as proton pyrophosphatase in Arabidopsis. Proton pyrophosphatases reside in plant organelle membranes and maintain the proper electrical charge in the organelle by moving protons across the membrane. In Arabidopsis, this enzyme helps the plant survive stress from drought and salty soil by sequestering toxic sodium ions accumulated from the water the plants drink and storing them in the vacuole, a plant cell's storage tank, where they cannot harm the cell.
Furthermore, Roberto Gaxiola of Arizona State University recently found that the enzyme also enlarges the root system, which aids in water absorption under drought conditions. Gaxiola suspects the enzyme may increase the plant's sensitivity to growth hormones known as auxins, leading to greater root growth. "[Arabidopsis] can get water more efficiently because they have an enhanced root system." These plants still can experience drought, he added -- they just experience it later.
Genetically modified corn that carries a single bacterial gene has also shown increased drought resistance. The agricultural giant Monsanto has focused on a type of transgenic corn carrying the cold shock protein B (CSPB) gene from Bacillus subtilis, a common soil bacterium. Plants under stress often have misfolded RNA and proteins. Lawson and his colleagues believe that the CSPB gene may mitigate some of that misfolding and help the plant cell run more efficiently, just as it does in Bacillus. This improves RNA translation and photosynthesis capability, which ultimately increases yield.
The impact of the CSPB transgenic corn, or any other drought-resistant crop, is hard to calculate, Lawson said. Still, "being able to mitigate the effects that drought has on crops would be an extremely important characteristic to get into farmers' hands."
Although their approaches may differ, these scientists believe that more than one pathway exists towards the final goal of improving drought tolerance in crops. Even seemingly small improvements may have large affects.
"If it's a severe drought, like what they have in Russia right now, and we could boost yields by 20 percent in [those] bad years," Cutler said, "that would be huge."
The reader could also vie related stories:

1. Where's the super food?  [September 2009]
2. Video: How roots grow  [9th September 2010]
3. Mendel upended?  [February 2008]

Read more: Relief for parched plants - The Scientist - Magazine of the Life Sciences http://www.the-scientist.com/news/display/57745/#ixzz12QS4uU9e

Feral Communities of Transgenic Canola in the USA

NatureNews published online; opinion posted on 2010-09-04. Can be accessed at http://www.nature.com/news/2010/100806/full/news.2010.393.html .

The Sagers report1 on the establishment of feral communities of two GM herbicide resistant canola varieties (Monsanto's Roundup Ready glyphosate tolerant canola and Bayer Crop Science's Liberty herbicide gluphosinate resistant canola) in the USA is a confirmation of earlier reports from Japan2, Australia and China. Feral communities of cropped plants originating from agrosystems are so common a phenomenon that it does not evoke attention. This is especially so because agrotechnique-pampered domesticated plant species unlike invasive weeds fail to establish communities in highly competitive natural ecosystems.

GM canola has mimicked an invasive weed in its establishment as feral communities and creation of double herbicide resistant hybrids apparently through cross pollination. This is a matter of serious concern. The report also indicates that transgenes do indeed cross genomic barriers albeit intervarietal barriers in the presnt case.

Doubts are rightly raised about the adequacy of GM regulatory procedures that evade provisions for monitoring the flow of transgenes or their parts to non-target genomes. A major flaw in GM biosafety monitoring mechanism is that assessments, if properly carried out, would take several years in most cases. Unfortunately, protocols for the emigration of transgenic plants via the contrivances of wind, flash floods, insects, birds and terrestrial animals are neither adequate nor transparent. GM biosafety mechanisms should include both the flight of transgenics to non-target ecosystems and the flow of transgenes to non-target genomes in a manner to be cost effective and universally reproducible on quick time basis.

Most regulatory mechanisms avoid the monitoring of subsoil residues of GM crops and their effects on rhizosphere biota and genomes of soil microorganism and on extracellular DNA. These aspects should be made essential components of GM biosafety assessment practice. Experimental formats for real time flow of transgenes are suggested here.

Subsoil metagenomic analysis is quick and common place for a moderately equipped laboratory 3, 4, 5 Transfer of large DNA by horizontal transfers across genomic barriers is well known. It would be easy for GM biosafety assessors to monitor relocation of transgenes or their parts to non-target DNA of the metagenome. Simple PCR runs of metagenomic DNA will reveal the presence or absence of the transgene under consideration. Presence of transgene DNA would ensure that transgene migration has indeed occurred.

Extracellular DNA (eDNA) is known to persist in soil environment for long 6, 7, 8. In all likelihood dead roots, mycorrhyzae, leaf litters, left over stubbs etc. will add to soil eDNA pools including the transgene or its part. Persisting eDNA containing the transgene or their parts may be recoursed to HGT to laterally move to other genomes at a later time. Tracing the presence of transgenes or parts thereof on eDNA would caution biosafety assessors about later possibilities of transgene flights from GM crop plants.

These new areas of researches should be publicly funded projects and must not be left to the will and wisdom of GM crop developers and lobbyists.

References

1. Natasha Gilbert 2010 GM crop escapes into the American wild: Transgenic canola found growing freely in North Dakota, Nature News, Published online 6 August 2010, Nature, doi:10.1038/news.2010.393.

2. Japan for Sustainability 2009 Japanese Consumer's Union Finds GM Canola Growing in Chiba Prefectur; International Society for Agricultural Meteorology December 23, 2009 09:47: http://www.agrometeorology.org/news/whats-new/japanese-consumers-union-finds-gm-canola-growing-in-chiba-prefectur; accessed on 4 September 2010.

3. Abulencia, C. B., Wyborski, D. L., Garcia, J. A., Podar, M., Chen, W., Chang, S. H. et al. (2006). Environmental whole-genome amplification to access microbial populations in contaminated sediments. Applied and Environmental Microbiology 725, 3291-3301.

4. Pushpender K. Sharma, Neena Capalash and Jagdeep Kaur 2007 An improved method for single step purification of metagenomic DNA; Molecular Biotechnology Volume 36, Number 1, 61-63.

5. Mei-Fong Pang, Noorlidah Abdullah, Choon-Weng Lee and Ching-Ching Ng 2008 Isolation of High Molecular Weight DNA from Forest Topsoil for Metagenomic Analysis; Asia Pacific Journal of Molecular Biology and Biotechnology, Vol. 16 (2): 35-41.

6. Nielsen KM, Johnsen PJ, Bensasson D, Daffonchio D. 2007 Release and persistence of extracellular DNA in the environment; Environ Biosafety Res., 6:37-53.

7. Mitsuhiro Itaya and Shinya Kaneko 2010 Integration of stable extracellular DNA released from Escherichia coli into the Bacillus subtilis genome vector by culture mix method; Nucleic Acids Research 2010 38(8):2551-2557

8. Paul JH, Jeffrey WH, DeFlaun MF: Production of extracellular nucleic acids by genetically altered bacteria in aquatic-environment microcosms. Appl Environ Microbiol 1987, 55:1865-1869.

S.K.T. Nasar Ph. D. (IIT, Kharagpur)

Professor

Department of Biotechnology

Bengal College of Engineering and Technology

(Affiliated to West Bengal University of Technology)

Durgapur, West Bengal

Former Director of Research

Bidhan Chandra Krishi Viswavidyalaya

(i.e. Bidhan Chandra Agricultural University)

&

Honorary Vice-President

Maromi Human Resource Development Society (NGO)

Kolkata, West Bengal

skt.nasar@gmail.com

Genomic DNA Extraction is Play

Genomic DNA Extraction is Play


S.K.T. Nasar* & S. Farzaan D. Nasar**

Abstract

Application of molecular biology and biotechnology in agriculture has not spread across board because experimental protocols and related infrastructure are much too costly. Low-funded research laboratories and teaching institutions thus lack access to the tools of New Biology. One way to reverse the trend is by reducing costs of experiments without any compromise with quality. This presentation is a first step to that end.
Here we show an inexpensive protocol for the extraction of genomic DNA from living organisms that can be play for kids as well as professional molecular biologists.

The Background Story

We are grand father-grand son duo emotionally intertwined like the two complementary strands of a DNA duplex. Unlike the weak H bonds in the biomolecule, our attachment is due to divine bonds strengthened by a friendship extraordinaire.

Farzaan**, an eight-year old grandson of the 65-year old senior author* is a regular viewer of ‘Backyard Science’ television shows. Some months ago he taunted his grand father, a university teacher of plant molecular cytogenetics to train him perform molecular biology experiments in their home in Kolkata, India.

The kid had jeered at his friend-grandpa: “You bore me incessantly with your books and bla-bla about ‘jeans’ (genes), ‘Diana’ (DNA), ‘Rana’ (RNA). C’mon, shut up and play with me now*.

Grandpa couldn’t figure out the course of action; he didn’t want to distance himself with either Farzaan or DNA. Could DNA be a kid’s play, the Professor wondered! The oldie knew to perform experiments only in well-equipped labs! He was neither trained nor did he ever train his students for molecular experiments outside standard laboratories.

It was a virtually impossible challenge for the professional molecular cytogeneticist* until he stumbled upon ‘The MacGyver Project: Genomic DNA Extraction and Gel Electrophoresis Experiments Using Everyday Materials’1 through a Google search of Do-It-Yourself (DIY) sites. “Oh, no that cannot be true”, was an instant professional’s reaction.

He hesitantly tried the procedure and, it did happen. Wow, it could be play! He then, successfully extracted genomic DNA from a leaf of betel (Piper betle L.) known as paan chewed by many Indians including himself. Once successful with the protocol of Yas Shirazu et alia (2009)1, the present authors began playing the DNA game. Both were happy with the novel eduplay.

They found the MacGyver1 extraction procedure to be the most handy and amenable to home-kitchen experiments among several inexpensive protocols available online.

A bulb of onion (Allium cepa L.) is a preferred material for demonstration of genomic DNA extraction in most protocols. The duo thought of doing something different. They used onion flower-bunch known as inflorescence instead and obtained a substantial yield of DNA.

Protocol

The experimental details are essentially and fundamentally similar to many other procedures already out there. However, items available at home and indigenous materials available in the local Indian market were used.

Procedure

All items i.e. material, brass mortar-pestle, Aquaguard®-filtered drinking water, Vim® liquid dish washing soap, isopropanol or ethanol, homoeopathic vials etc, were pre-chilled in the icebox of a refrigerator.

Onion inflorescences attached to long stalks were purchased from a local vegetable vendor. The spathe (leafy wrap around the inflorescence) was removed. Flowers were, then, scraped from the tip of the stalk and put in a brass pestle for grinding.

One teaspoonful of water and a pinch of Tata® iodised table salt were added to flowers. The flower tissue was crushed by grinding and pulverised to make a viscous solution.

Two drops of Vim® detergent were added. The mixture was stirred gently with plastic ice-cream spoon for a few minutes.

The mixture was carefully poured in to a homoeopathic vial. Isopropanol, the rubbing alcohol, was slowly poured in the vial with an injection syringe to avoid disturbing the tissue suspension. Bubbles started rising almost immediately and in about ten minutes the DNA-cloud was seen between the mucky stratum of tissue-salt-soap mixture below and the clear alcohol layer above. DNA did not float as expected.

Absolute ethyl alcohol was added in place of isopropyl alcohol in our repeat experiments taking due care that all other steps remained unaltered.

A fascinating result was obtained (Fig. 1). Three vials represent the stages of precipitation and floatation of DNA.

Fig. 1 Stages of precipitation and floatation of Genomic DNA of Onion Flower

Epilogue

The duo embarked upon a series of genomic DNA extraction experiments with whatever uncooked live eatables they could lay hands on. The two generations, separated by 55 years, enjoyed every bit of what they did. It was another matter that each experiment left the home kitchen messier and the ladies angrier. It was play!

Good times didn’t last for long. Farzaan** shifted to Morrisville, USA. SKTN* took up teaching assignment at Bengal College of Engineering and Technology at Durgapur, West Bengal, India.

The two friends’ physical separation by continents, however, has not dampened but, in fact, boosted their eagerness. Both are now among the growing crowd of scientists committed to wiping out the psychological fear of Molecular Biology from the minds of all interested persons in homes, students in schools, young freshers in colleges and enterprising researchers in small-time developing laboratories anywhere in the world.

P. S.

The senior author* has since standardized the protocol and has shown (to-be-published work) that genomic DNA as obtained shows exact banding ( Fig. 2) when electrophoresed alongside DNA obtained by standard ‘professional’ protocols and is of equal PCR quality.

Fig.2 Genomic DNA from goat liver and from plant sp. after electrophoresis

He is aware of the ethical debates about DIY Molecular Biology by anyone interested anywhere. He, however, firmly believes that the outreach of Molecular Biology to outside of costly laboratories, as is the case with agricultural technology and information technology, shall attract billions of minds to understanding and application of New Biology to the well being of global citizens at low costs. He is including the inexpensive procedure in course curriculum and research project work of his current Biotechnology students.

Reference

1. Yas Shirazu, Donna Lee, and Esther Abd-Elmessih (2009) The MacGyver Project: Genomic DNA Extraction and Gel Electrophoresis Experiments Using Everyday Materials. Accessed at http://www.scq.ubc.ca/the-macgyver-project-genomic-dna-extraction-and-gel-electrophoresis-experiments-using-everyday-materials/

*Correspondence: Professor, Department of Biotechnology, College of Engineering & Technology, Durgapur-713212, West Bengal, India.

Residence: 26 C Kalupara Lane, Dhakuria, Kolkata-700 031, West Bengal, India//skt.nasar@gmail.com

**Present address: Cedarfork Primary School, Morrisville, NC, USA// farzaan.nasar@gmail.com

Citation: Nasar & Nasar 2010 (29 Jan 2010) Blogger: Issues in Future Agriculture