Plant Genetics, NGS and Bioinformatics
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Accuracy of RNA-Seq and its dependence on sequencing depth

Accuracy of RNA-Seq and its dependence on sequencing depth | Plant Genetics, NGS and Bioinformatics | Scoop.it
Background

The cost of DNA sequencing has undergone a dramatical reduction in the past decade. As a result, sequencing technologies have been increasingly applied to genomic research. RNA-Seq is becoming a common technique for surveying gene expression based on DNA sequencing. As it is not clear how increased sequencing capacity has affected measurement accuracy of mRNA, we sought to investigate that relationship.

Result

We empirically evaluate the accuracy of repeated gene expression measurements using RNA-Seq. We identify library preparation steps prior to DNA sequencing as the main source of error in this process. Studying three datasets, we show that the accuracy indeed improves with the sequencing depth. However, the rate of improvement as a function of sequence reads is generally slower than predicted by the binomial distribution. We therefore used the beta-binomial distribution to model the overdispersion. The overdispersion parameters we introduced depend explicitly on the number of reads so that the resulting statistical uncertainty is consistent with the empirical data that measurement accuracy increases with the sequencing depth. The overdispersion parameters were determined by maximizing the likelihood. We shown that our modified beta-binomial model had lower false discovery rate than the binomial or the pure beta-binomial models.

Conclusion

We proposed a novel form of overdispersion guaranteeing that the accuracy improves with sequencing depth. We demonstrated that the new form provides a better fit to the data.

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Plant Genetics, NGS and Bioinformatics
Papers and topics in plant genetics, NGS and bioinformatics
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Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes

Getting the Hologenome Concept Right: an Eco-Evolutionary Framework for Hosts and Their Microbiomes | Plant Genetics, NGS and Bioinformatics | Scoop.it
Given the complexity of host-microbiota symbioses, scientists and philosophers are asking questions at new biological levels of hierarchical organization—what is a holobiont and hologenome? When should this vocabulary be applied? Are these concepts a null hypothesis for host-microbe systems or limited to a certain spectrum of symbiotic interactions such as host-microbial coevolution? Critical discourse is necessary in this nascent area, but productive discourse requires that skeptics and proponents use the same lexicon. For instance, critiquing the hologenome concept is not synonymous with critiquing coevolution, and arguing that an entity is not a primary unit of selection dismisses the fact that the hologenome concept has always embraced multilevel selection. Holobionts and hologenomes are incontrovertible, multipartite entities that result from ecological, evolutionary, and genetic processes at various levels. They are not restricted to one special process but constitute a wider vocabulary and framework for host biology in light of the microbiome.

Via Francis Martin, Loïc Lepiniec
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Nature Biotech: A pigeonpea gene confers resistance to Asian soybean rust in soybean (2016)

Nature Biotech: A pigeonpea gene confers resistance to Asian soybean rust in soybean (2016) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.


Via The Sainsbury Lab, Kamoun Lab @ TSL
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The Sainsbury Lab's curator insight, April 26, 4:45 AM
Asian soybean rust (ASR), caused by the fungus Phakopsora pachyrhizi, is one of the most economically important crop diseases, but is only treatable with fungicides, which are becoming less effective owing to the emergence of fungicide resistance. There are no commercial soybean cultivars with durable resistance to P. pachyrhizi, and although soybean resistance loci have been mapped, no resistance genes have been cloned. We report the cloning of a P. pachyrhizi resistance gene CcRpp1 (Cajanus cajan Resistance against Phakopsora pachyrhizi 1) from pigeonpea (Cajanus cajan) and show that CcRpp1 confers full resistance to P. pachyrhizi in soybean. Our findings show that legume species related to soybean such as pigeonpea, cowpea, common bean and others could provide a valuable and diverse pool of resistance traits for crop improvement.
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PITCh: An Alternative Use of TALENs and CRISPR/Cas9

PITCh: An Alternative Use of TALENs and CRISPR/Cas9 | Plant Genetics, NGS and Bioinformatics | Scoop.it
A new gene insertion method called Precise Integration into Target Chromosome (PITCh) uses existent gene editing technologies more effectively thanks to MMEJ.
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Microbiomes: Curating communities from plants : Nature : Nature Publishing Group

Microbiomes: Curating communities from plants : Nature : Nature Publishing Group | Plant Genetics, NGS and Bioinformatics | Scoop.it

Large-scale cultivation and genome sequencing of the bacteria that inhabit the leaves and roots of Arabidopsis plants have paved the way for probing how microbial communities assemble and function. 


Via Niklaus Grunwald, Guogen Yang
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Biologists create more precise molecular scissors for genome editing

Biologists create more precise molecular scissors for genome editing | Plant Genetics, NGS and Bioinformatics | Scoop.it
Engineered Cas9 enzyme makes fewer mistakes.

Via Loïc Lepiniec
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DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins

DNA-free genome editing in plants with preassembled CRISPR-Cas9 ribonucleoproteins | Plant Genetics, NGS and Bioinformatics | Scoop.it
Editing plant genomes without introducing foreign DNA into cells may alleviate regulatory concerns related to genetically modified plants. We transfected preassembled complexes of purified Cas9 protein and guide RNA into plant protoplasts of Arabidopsis thaliana, tobacco, lettuce and rice and achieved targeted mutagenesis in regenerated plants at frequencies of up to 46%. The targeted sites contained germline-transmissible small insertions or deletions that are indistinguishable from naturally occurring genetic variation.

Via Biswapriya Biswavas Misra, Loïc Lepiniec
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Biswapriya Biswavas Misra's curator insight, November 5, 2015 9:45 PM

Editing plant genomes without introducing foreign DNA into cells may alleviate regulatory concerns related to genetically modified plants. We transfected preassembled complexes of purified Cas9 protein and guide RNA into plant protoplasts of Arabidopsis thaliana, tobacco, lettuce and rice and achieved targeted mutagenesis in regenerated plants at frequencies of up to 46%. The targeted sites contained germline-transmissible small insertions or deletions that are indistinguishable from naturally occurring genetic variation.

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Next biotech plants: new traits, crops, developers and technologies for addressing global challenges - Ricroch & Henard (2015) - GMCC

Most of the genetically modified (GM) plants currently commercialized encompass a handful of crop species (soybean, corn, cotton and canola) with agronomic characters (traits) directed against some biotic stresses (pest resistance, herbicide tolerance or both) and created by multinational companies.

 

The same crops with agronomic traits already on the market today will continue to be commercialized, but there will be also a wider range of species with combined traits. The timeframe anticipated for market release of the next biotech plants will not only depend on science progress... but also primarily on how demanding regulatory requirements are in countries where marketing approvals are pending.

 

Regulatory constraints, including environmental and health impact assessments, have increased significantly in the past decades, delaying approvals and increasing their costs. This has sometimes discouraged public research entities and small and medium size plant breeding companies from using biotechnology and given preference to other technologies, not as stringently regulated.

 

Nevertheless R&D programs are flourishing in developing countries, boosted by the necessity to meet the global challenges that are food security of a booming world population while mitigating climate change impacts. Biotechnology is an instrument at the service of these imperatives and a wide variety of plants are currently tested for their high yield despite biotic and abiotic stresses...

 

Food security is not only a question of quantity but also of quality of agricultural and food products, to be available and accessible for the ones who need it the most. Many biotech plants (especially staple food) are therefore being developed with nutritional traits, such as biofortification in vitamins and metals.

 

The main international seed companies continue to be the largest investors in plant biotechnology R&D, and often collaborate in the developing world with public institutions, private entities and philanthropic organizations. These partnerships are particularly present in Africa. 

 

In developed countries, plant biotechnology is also used for non-food purposes, such as the pharmaceutical, biofuel, starch, paper and textile industries...

 

Various plant breeding technologies are now used in the entire spectrum of plant biotechnology... Next generation precision gene editing tools are developed in basic research. They include: clustered regularly interspaced short palindromic repeats (CRISPR), oligonucleotide- directed mutagenesis (ODM), transcription activator-like effects nucleases (TALENs) and zinc-finger nuclease (ZFN).

 

http://purl.umn.edu/211484


Via Alexander J. Stein
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Mass spectrometry imaging for plant biology: a review

Mass spectrometry imaging for plant biology: a review | Plant Genetics, NGS and Bioinformatics | Scoop.it
Mass spectrometry imaging (MSI) is a developing technique to measure the spatio-temporal distribution of many biomolecules in tissues. Over the preceding decade, MSI has been adopted by plant biologists and applied in a broad range of areas, including primary metabolism, natural products, plant defense, plant responses to abiotic and biotic stress, plant lipids and the developing field of spatial metabolomics. This review covers recent advances in plant-based MSI, general aspects of instrumentation, analytical approaches, sample preparation and the current trends in respective plant research.

Via Jean-Michel Ané, Guogen Yang
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Eric Vincill's curator insight, October 18, 2015 4:09 PM

The detection of biomolecules in plant tissues  by mass spec. LOVE IT!! I can't tell you how excited I am to see protocols being established that increase the spatiotemporal resolution of the movement of small molecules in the plant.  

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An interdisciplinary shift in demand for talent within the biotech industry : Nature Biotechnology : Nature Publishing Group

An interdisciplinary shift in demand for talent within the biotech industry : Nature Biotechnology : Nature Publishing Group | Plant Genetics, NGS and Bioinformatics | Scoop.it
A shift away from hiring narrowly focused specialists to individuals with interdisciplinary academic training highlights the latest life sciences workforce trends.
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Frontiers: Primer and platform effects on 16S rRNA tag sequencing

Frontiers: Primer and platform effects on 16S rRNA tag sequencing | Plant Genetics, NGS and Bioinformatics | Scoop.it

Sequencing of 16S rRNA gene tags is a popular method for profiling and comparing microbial communities. The protocols and methods used, however, vary considerably with regard to amplification primers, sequencing primers, sequencing technologies; as well as quality filtering and clustering. How results are affected by these choices, and whether data produced with different protocols can be meaningfully compared, is often unknown. Here we compare results obtained using three different amplification primer sets (targeting V4, V6–V8, and V7–V8) and two sequencing technologies (454 pyrosequencing and Illumina MiSeq) using DNA from a mock community containing a known number of species as well as complex environmental samples whose PCR-independent profiles were estimated using shotgun sequencing. We find that paired-end MiSeq reads produce higher quality data and enabled the use of more aggressive quality control parameters over 454, resulting in a higher retention rate of high quality reads for downstream data analysis. While primer choice considerably influences quantitative abundance estimations, sequencing platform has relatively minor effects when matched primers are used. Beta diversity metrics are surprisingly robust to both primer and sequencing platform biases.


Via Stéphane Hacquard
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Chinese Scientists Created Transgenic Crops that Resist Heat While Increase Yields -

Chinese Scientists Created Transgenic Crops that Resist Heat While Increase Yields - | Plant Genetics, NGS and Bioinformatics | Scoop.it
An essay published on Nature Biotechnology on August 17 reveals an exciting achievement of Chinese scientists: they have successfully cultivated transgenic crops with an ERECTA gene (henceforth ER) that can resist heat while increase production.

Researchers from Institute of Plant Physiology & Ecology, SIBS, CAS, together contribute to this essay entitled “Overexpression of Receptor-like Kinase ERECTA Improves Thermotolerance in Rice and Tomato”.

Via Christophe Jacquet, Loïc Lepiniec
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Are GMOs and organic foods compatible? - Sci over Coffee (2015)

[Video] We chat with Professor Ian Godwin from The University of Queensland about genetically modified food crops. Ian believes that GMO foods and organic agriculture are perfectly compatible. He explains that scientists are creating GMO plants to achieve a more sustainable agriculture. The idea is to create plants resistant to pests and diseases... 

 

He points out that our beloved “organic” potato is actually sprayed with copper to control disease and the use of copper fungicides in organic farming may be resulting in increased levels of copper in the soil and the food we eat. So maybe it’s time we embrace GMOs for more sustainable agriculture and healthier food?

 

If you are after more information about this topic, below are a few good articles to get you started... 

 

https://www.youtube.com/watch?v=ZDNOBIqP0Wk

 


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The Arabidopsis Transcription Factor NAC016 Promotes Drought Stress Responses by Repressing AREB1 Transcription through a Trifurcate Feed-Forward Regulatory Loop Involving NAP

The Arabidopsis Transcription Factor NAC016 Promotes Drought Stress Responses by Repressing AREB1 Transcription through a Trifurcate Feed-Forward Regulatory Loop Involving NAP | Plant Genetics, NGS and Bioinformatics | Scoop.it

Drought and other abiotic stresses negatively affect plant growth and development and thus reduce productivity. The plant-specific NAM/ATAF1/2/CUC2 (NAC) transcription factors have important roles in abiotic stress-responsive signaling. Here, we show that Arabidopsis thaliana NAC016 is involved in drought stress responses; nac016 mutants have high drought tolerance, and NAC016-overexpressing (NAC016-OX) plants have low drought tolerance. Using genome-wide gene expression microarray analysis and MEME motif searches, we identified the NAC016-specific binding motif (NAC16BM), GATTGGAT[AT]CA, in the promoters of genes downregulated in nac016-1 mutants. The NAC16BM sequence does not contain the core NAC binding motif CACG (or its reverse complement CGTG). NAC016 directly binds to the NAC16BM in the promoter of ABSCISIC ACID-RESPONSIVE ELEMENT BINDING PROTEIN1 (AREB1), which encodes a central transcription factor in the stress-responsive abscisic acid signaling pathway and represses AREB1 transcription. We found that knockout mutants of the NAC016 target gene NAC-LIKE, ACTIVATED BY AP3/PI (NAP) also exhibited strong drought tolerance; moreover, NAP binds to the AREB1 promoter and suppresses AREB1transcription. Taking these results together, we propose that a trifurcate feed-forward pathway involving NAC016, NAP, and AREB1 functions in the drought stress response, in addition to affecting leaf senescence in Arabidopsis.

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Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016)

Nature Biotech: Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture (2016) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.


Via The Sainsbury Lab, Kamoun Lab @ TSL
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The Sainsbury Lab's curator insight, April 26, 4:14 AM
Wild relatives of domesticated crop species harbor multiple, diverse, disease resistance (R) genes that could be used to engineer sustainable disease control. However, breeding R genes into crop lines often requires long breeding timelines of 5–15 years to break linkage between R genes and deleterious alleles (linkage drag). Further, when R genes are bred one at a time into crop lines, the protection that they confer is often overcome within a few seasons by pathogen evolution1. If several cloned R genes were available, it would be possible to pyramid R genes2 in a crop, which might provide more durable resistance1. We describe a three-step method (MutRenSeq)-that combines chemical mutagenesis with exome capture and sequencing for rapid R gene cloning. We applied MutRenSeq to clone stem rust resistance genes Sr22 and Sr45 from hexaploid bread wheat. MutRenSeq can be applied to other commercially relevant crops and their relatives, including, for example, pea, bean, barley, oat, rye, rice and maize.
Neelam Redekar's curator insight, April 29, 8:19 AM
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Scientists remove HIV-1 from genome of human immune cells

Scientists remove HIV-1 from genome of human immune cells | Plant Genetics, NGS and Bioinformatics | Scoop.it
Scientists edited HIV-1 DNA out of the genome of human immune cells, preventing virus replication and reinfection of the cleared cells.

Via Chad Smithson
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How to build a better PhD

How to build a better PhD | Plant Genetics, NGS and Bioinformatics | Scoop.it
There are too many PhD students for too few academic jobs — but with imagination, the problem could be solved.

Via burkesquires
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The Gene Editing Tsunami | PLOS Synthetic Biology Community

The Gene Editing Tsunami | PLOS Synthetic Biology Community | Plant Genetics, NGS and Bioinformatics | Scoop.it
The Gene Editing Tsunami

Via Loïc Lepiniec
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Swedish Board of Agriculture: a CRISPR-Cas9 mutant is not a GMO - Umeå Univ (2015)

Swedish Board of Agriculture: a CRISPR-Cas9 mutant is not a GMO - Umeå Univ (2015) | Plant Genetics, NGS and Bioinformatics | Scoop.it

The Swedish Board of Agriculture has... confirmed the interpretation that some plants in which the genome has been edited using the CRISPR-Cas9 technology do not fall under the European GMO definition. This is important for the wide use of such plants to contribute to solving some of the escalating challenges of mankind.

CRISPR-Cas9 is a technique... allowing scientists to make small edits in the genetic material of an organism, edits that can also occur naturally. Instead of hoping that such edits occur by natural recombination, they can now be deliberately introduced in a targeted and precise manner. CRISPR-Cas9 can thus be used in many ways in plant science and breeding.

 

Plants that fall within the scope of EU GMO legislation are subject to a very strict regulatory regime (in reality making it impossible to grow them in the field in most EU countries). Plants that fall outside the scope can be grown without restriction. Since “inside or outside of the GMO definition” will decide whether or not plant scientists will be able to use the technique for practical applications, plant scientists and breeders have been waiting for the authorities’ decision concerning CRISPR-Cas9... 

 

Countries such as Argentina have announced that similarly edited plants fall outside their GMO legislation, but no decision has been taken yet inside the EU. A complicating factor is that the technique can be used in several different ways with the consequence that some of the resulting plants may fall outside while others may fall inside the GMO legislation. Now, for the first time, concrete examples have been evaluated by a competent authority, and the Swedish Board of Agriculture announced... that some Arabidopsis plants that have been modified using CRISPR-Cas9 fall within the scope of the legislation while others do not... 

 

“What we now have done pinpoints the problem; using CRISPR-Cas9 we can create a plant that in ALL aspects is identical to one that is not considered to be a GMO. Common sense and scientific logic says that it is impossible to have two identical plants where growth of one is, in reality, forbidden while the other can be grown with no restrictions; how would a court be able to decide if the cultivation was a crime or not? But regulatory logic is not necessarily the same as scientific logic, and it is therefore important that the Swedish Board of Agriculture has interpreted the definition in this way”...  

 

This interpretation opens up the possibility that this technique can be used to address some of the biggest challenges for mankind, expressed in the sustainable development goals recently suggested by the United Nations... “We hope that this clear and logical interpretation will also be applied to other similar cases.

 

The EU commission announced some time ago that it would present its interpretation of the legislation, but has not yet been able to come to an agreement. All ‘GMO issues’ divide the EU and this has led to paralysis for more than a decade. We think that the opinion by the Swedish Board of Agriculture will get a lot of international attention”...  

 

http://www.umu.se/english/about-umu/news-events/news/newsdetailpage/green-light-in-the-tunnel-opinion-of-the-swedish-board-of-agriculture--a-crispr-cas9-mutant-but-not-a-gmo.cid259265

 


Via Alexander J. Stein
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Promoting microbiology education through the iGEM synthetic biology competition

Promoting microbiology education through the iGEM synthetic biology competition | Plant Genetics, NGS and Bioinformatics | Scoop.it

"Promoting microbiology education through the iGEM synthetic biology competition." I'm a huge fan of iGEM and this article summarizes all that it has achieved (so far). It's not just promoting microbiology, it's promoting enthusiasm in science more broadly and a really effective way to show undergraduates (and even high school students) what research is like.
http://femsle.oxfordjournals.org/conte…/…/16/fnv129.abstract


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Teenagers and mutant tomatoes

Teenagers and mutant tomatoes | Plant Genetics, NGS and Bioinformatics | Scoop.it

Wake Forest biology professors Gloria Muday and Carole Gibson and their students use mutant tomatoes grown in the campus garden to teach fundamental biology concepts to local high school students. "Teaching with Tomatoes" is funded by the American Society of Plant Biology Education Foundation and has evolved over the years.


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CRISPR tweak may help gene-edited crops bypass biosafety regulation

CRISPR tweak may help gene-edited crops bypass biosafety regulation | Plant Genetics, NGS and Bioinformatics | Scoop.it

A twist on a revolutionary gene-editing technique may make it possible to modify plant genomes while sidestepping national biosafety regulations, South Korean researchers say.


Plant scientists have been quick to experiment with the popular CRISPR/Cas9 technique, which uses an enzyme called Cas9, guided by two RNA strands, to precisely cut segments of DNA in a genome. By disabling specific genes in wheat and rice, for example, researchers hope to make disease-resistant strains of the crops.


But the process can introduce bits of foreign DNA into plant genomes. And some jurisdictions, such as the European Union, could decide to classify such plants as genetically modified organisms (GMOs)1 — making their acceptance by regulatory bodies contentious, says geneticist Jin-Soo Kim of Seoul National University.


Kim and his team tweaked the technique so that it can delete specific plant genes without introducing foreign DNA, creating plants that he and his colleagues think “might be exempt from current GMO regulations”2.


“In terms of science, our approach is just another improvement in the field of genome editing. However, in terms of regulations and public acceptance, our method could be path-breaking,” says Kim.


Conventionally, researchers get CRISPR/Cas9 working in a plant cell by first shuttling in the gene that codes for the Cas9 enzyme. The gene is introduced on a plasmid — a circular packet of DNA — which is usually carried into a plant by the bacterial pest Agrobacterium tumefaciens. As a result, Agrobacterium DNA can end up in the plant’s genome. Even if the pest is not used, fragments of the Cas9 gene may themselves be incorporated into the plant's genome.


To get around this problem, Kim and his colleagues avoid gene-shuttling altogether. They report a recipe to assemble the Cas9 enzyme together with its guide RNA sequences (which the enzyme requires to find its target) outside the plant, and use solvents to get the resulting protein complex into the plant. The technique works efficiently to knock out selected genes in tobacco plants, rice, lettuce and thale cress, they say, reporting their results in Nature Biotechnology2.


“I think this is a milestone work for plant science,’ says bioethicist Tetsuya Ishii at Hokkaido University in Sapporo, Japan, who has extensively studied the framework of regulation surrounding genetic engineering in plants.


Kim wants to use the technique to edit the banana; the crop's most popular cultivar, the Cavendish variety, is struggling to combat a devastating soil fungus and may go extinct. Gene editing could, for example, be used to knock out the receptor that the fungus uses to invade cells, without any need, in Kim’s view, to classify the resulting banana as a GMO. “We will save the banana so that our children and grandchildren can still enjoy the fruit,” he says.


Via Dr. Stefan Gruenwald
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9 Facts About Biodiesel That Will Rev You Up - YouTube

Biodiesel works as a clean-burning, renewable alternative to petroleum diesel, offering a viable opportunity to diversify the U.S. transportation fuel supply...
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How will we fill 9 billion bowls by 2050? | #9billionbowls | Thomson Reuters

How will we fill 9 billion bowls by 2050? | #9billionbowls | Thomson Reuters | Plant Genetics, NGS and Bioinformatics | Scoop.it
Filling 9 Billion Bowls from Thomson Reuters tells the story of a diverse group of scientists, students, analysts and inventors who are using Big Data and leading edge technologies to face the challenge of feeding 9 billion people in 2050, and revolutionise the way we produce and deliver food.
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All In the Touch Curriculum (ages 10 - 13) Free to download - colorful activities

All In the Touch Curriculum (ages 10 - 13) Free to download - colorful activities | Plant Genetics, NGS and Bioinformatics | Scoop.it

Another terrific set of activities from Peggy Lemaux and Barbara Alonso. Free to download. In lesson 2 - make a tasty plant cell using goodies for the different compartments. I love the idea for how to represent the energetic mitochondria!


Via Mary Williams
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What genetic engineering and organic farming have in common - TED (2015)

What genetic engineering and organic farming have in common - TED (2015) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Genetic engineering and organic farming are often set up in opposition to one another.... Well, in the household of Pam Ronald and Raoul Adamchak, they live together up close and personally, as the genetic scientist and organic farmer are married. Recently, the couple discussed the complexity of modern agriculture, what they see as common misconceptions of genetically engineered crops – and the implications these have on those who need food the most...

The problem with genetic engineering is the communication. “Most consumers accept most science. But there are a few cases where established science is rejected by a segment of the population. Consider for example: vaccination, evolution, global climate change and plant genetics,” says Ronald. “Why do certain aspects of science seize the public’s imagination like this? ... What’s surprising to plant breeders and geneticists is that 50 years ago we were doing much more dramatic things with plants, things like mutagenesis and hybridization, and they never really caught the public’s imagination”... For his part, Raoul Adamchak attributes much... to fear. ”So much of the information about genetically engineered crops is misinformation, and it seems like information that’s intended to produce fear in people”...

Much of the communication around genetic engineering is driven by marketing, not science. “If you look at genetic engineering in isolation, the evidence doesn’t support the claims of some marketers that the food is unhealthy or harmful to agriculture,” says Adamchak. For him, issues such as pesticide use or soil erosion are far more important topics of discussion, yet they haven’t caught the public attention... For her part, Ronald is skeptical about the motives of companies like Chipotle, which have used anti-genetically engineered food language...

 

“In terms of human health and sustainable agriculture, it does not make sense to reject farmers that grow genetically engineered crops... Every major scientific organization has concluded genetically engineered foods are safe to eat. Some of these crops have massively reduced the use of chemical insecticides, benefitting consumers and the environment.” That’s not all. “Chipotle says it’s switching away from ‘GMOs’ because it says there is a problem with herbicide use. That may be true, but Chipotle is not banning crops grown with herbicides. Instead, it’s switching to another genetically modified sunflower that was developed using a different genetic technique, and it’s using a different kind of herbicide, which is more toxic than the type used on genetically engineered crops that has also led to the evolution of herbicide-resistant weeds.”

 

Ronald doesn’t hide her frustration at the misinformation promoted by many groups. “Companies say things like, ‘GMO cultivation hurts the environment,’ but they don’t specify what exactly they mean by this. Every crop is different. There’s clear evidence for the positive environmental benefits of many crops that were developed using genetic engineering, such as decreased soil erosion, decreased insecticide use or increased crop yield”...

All genetically engineered crops are not created equal. “It’s very difficult to talk about GMOs as an entity, because there are very distinctly different genetically engineered crops,” says Adamchak. “The genetically engineered virus-resistant papaya grown in Hawaii has nothing to do with herbicides, has nothing to do with mono-cropping, and has nothing to do with Bt eggplant grown in India. You can’t look at all of the products and say they all have the same sorts of effects, because they’re actually very distinct and have their own benefits and maybe their own issues as well.”

 

So how should consumers think about genetically engineered foods? Adamchak suggests using two lenses: “First, think about how they fit into sustainable agriculture: Do they reduce pesticide use? Do they reduce soil erosion? Do they reduce nitrates leaching into the soil? Do they increase yields? If so, then that’s an improvement to our agricultural system... Next, recognize that technology needs to integrate with other strategies to control pests or reduce soil erosion. Genetic engineering is not a silver-bullet solution; it should be part of an overall strategy to achieve sustainable agriculture.”

As a culture, we’ve become far removed from the reality of farming. “Many of us buy new cell phones in order to have access to the hardware or software,” says Ronald. “Yet we don’t understand that farmers want the latest technology too … and in their case, that means they want the newest, best seeds that can contribute to the health and productivity of their farm.” Farmers plant crops each year, and they’d like to ensure the best yields possible and fight disease using the fewest chemicals, whatever the size of farm they’re maintaining... “You can’t have a productive farm if you don’t take care of it, and you don’t do very well if you don’t have good seed.” Too often, she says, consumers seem to feel that farmers need to make a choice between seeds and good agricultural practices, and that’s a false comparison.

Genetic engineering isn’t just about Monsanto and big business. “The other day someone was earnestly telling me that genetically engineered crops are only grown by farmers in the United States, when in fact there are millions of small farmers with one or two acres growing Bt cotton in India and China and hundreds of farmers growing Bt eggplant in Bangladesh,” says Ronald. “There’s kind of a strange idea that modern plant genetics is only for ‘industrial agriculture,’ even though it’s not clear what people really mean by that.”

 

And what of the legend of the sterile seed produced by Monsanto... Unfamiliarity with seed, says Ronald. ”People think that genetic engineering causes seed sterility... That’s confusing the process of hybridization, used since the 1920s, with genetic engineering,” she says. “The reality is that most farmers in the developed world, including organic farmers, buy hybrid seed from large seed companies. Monsanto, for instance, dominates the vegetable seed market, so organic farmers are buying much of their seed from Monsanto. So you don’t get rid of Monsanto by getting rid of genetic engineering, which is a common idea I hear over and over again”...

Ronald... we should think of food innovations as we view medical breakthroughs. “Synthetic insulin was invented in the 1970s, and is an entirely genetically engineered medicine,” she says. Not to mention, we take for granted products like vitamin D-enriched milk, iron-fortified bread and iodized salt. ”Many people in the developed world add vitamins to their diet, their food. Consumers in the less developed world... often cannot afford to buy them or do not have access to a diverse diet. If farmers in less developed countries could grow vitamin-fortified crops, such as Golden Rice, their children will be healthier.”

It’s time to rethink the backlash against GE foods. “There were riots in Brazil, with protesters attacking plants that were being grown there; it’s almost gotten to the point of civil unrest,” says Ronald. “India has not planted Bt eggplant yet, even though their own scientific agency has stated it’s safe and it’s very clear it would massively reduce insecticide use. But there are some very prominent fear-mongering voices there that really have influenced consumers – and politicians.” Adamchak concurs... “I think the government in India is very much put off by anti-genetic-engineering protests, so they’ve been very shy about allowing products to come to market”...

Farmers need to take a more public stance. “In the developed world, maybe 1 percent of citizens are farmers, and so, often, the public does not connect with farm workers,” says Ronald. “They don’t see the insecticides that are sprayed or the harm to human health and the environment resulting from some of these sprays. The people who suffer are farmers and farmworkers, especially in the less developed world, where there is little access to protective gear.”

 

Adamchak agrees... “many people in the world are very focused on building more sustainable agriculture and feeding people as the population increases... This is what agriculturalists do: try to grow more food as effectively as possible. And I think that’s why farmers have been open to these tools, because they help solve problems. I don’t know how far the world needs to be pushed in terms of crop loss due to climate change or having billions of more mouths to feed before the public starts to see the value in this new technology.”

 

http://ideas.ted.com/what-genetic-engineering-and-organic-farming-have-in-common/

 


Via Alexander J. Stein
Ali Taheri's insight:

http://www.ted.com/talks/pamela_ronald_the_case_for_engineering_our_food?language=en

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