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Rescooped by hunter chen from Publications from The Sainsbury Laboratory
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BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015)

BMC Research Notes: Broad application of a simple and affordable protocol for isolating plant RNA (2015) | Biotech | Scoop.it
Standard molecular biological methods involve the analysis of gene expression in living organisms under diverse environmental and developmental conditions. One of the most direct approaches to quantify gene expression is the isolation of RNA. Most techniques used to quantify gene expression require the isolation of RNA, usually from a large number of samples. While most published protocols, including those for commercial reagents, are either labour intensive, use hazardous chemicals and/or are costly, a previously published protocol for RNA isolation in Arabidopsis thaliana yields high amounts of good quality RNA in a simple, safe and inexpensive manner.

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Rescooped by hunter chen from Publications from The Sainsbury Laboratory
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Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015)

Bioinformatics: bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby (2015) | Biotech | Scoop.it

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Rescooped by hunter chen from Trends in MPMI
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U.S.D.A. Approves Modified Potato. Next Up: French Fry Fans.

U.S.D.A. Approves Modified Potato. Next Up: French Fry Fans. | Biotech | Scoop.it
A potato genetically engineered to reduce the amounts of a potentially harmful ingredient in French fries and potato chips has been approved for commercial planting, the Department of Agriculture announced on Friday.

The potato’s DNA has been altered so that less of a chemical called acrylamide, which is suspected of causing cancer in people, is produced when the potato is fried.

The new potato also resists bruising, a characteristic long sought by potato growers and processors for financial reasons. Potatoes bruised during harvesting, shipping or storage can lose value or become unusable.

The biotech tubers were developed by the J. R. Simplot Company, a privately held company based in Boise, Idaho, which was the initial supplier of frozen French fries to McDonald’s in the 1960s and is still a major supplier. The company’s founder, Mr. Simplot, who died in 2008, became a billionaire.
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Times Topic: Genetically Modified Food

The potato is one of a new wave of genetically modified crops that aim to provide benefits to consumers, not just to farmers as the widely grown biotech crops like herbicide-tolerant soybeans and corn do. The nonbruising aspect of the potato is similar to that of genetically engineered nonbrowning apples, developed by Okanagan Specialty Fruits, which are awaiting regulatory approval.

Via Christophe Jacquet, CP
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Rescooped by hunter chen from Effectors and Plant Immunity
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Infographic: 9 plant diseases that threaten your favorite foods–and how GM can help | Genetic Literacy Project

Infographic: 9 plant diseases that threaten your favorite foods–and how GM can help | Genetic Literacy Project | Biotech | Scoop.it

"Nature is relentless, challenging farmers with weeds, insects and diseases. Advances in genetic modification offer some unique tools that can help increase food production despite these challenges."


Via Mary Williams, Nicolas Denancé
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Rescooped by hunter chen from Bioinformatics, Comparative Genomics and Molecular Evolution
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PLOS Computational Biology: Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison

PLOS Computational Biology: Structure-Based Function Prediction of Uncharacterized Protein Using Binding Sites Comparison | Biotech | Scoop.it
PLOS Computational Biology is an open-access

Via Arjen ten Have
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Scooped by hunter chen
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Cell - Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

Cell - Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity | Biotech | Scoop.it
HighlightsCas9 nickase can facilitate targeted DNA double-strand break using two guide RNAsDouble nicking of DNA reduces off-target mutagenesis by 50- to 1,000-foldMultiplex nicking stimulates homology directed repair, microdeletion, and insertionDouble nicking provides efficient modification of mouse zygotesSummary

Targeted genome editing technologies have enabled a broad range of research and medical applications. The Cas9 nuclease from the microbial CRISPR-Cas system is targeted to specific genomic loci by a 20 nt guide sequence, which can tolerate certain mismatches to the DNA target and thereby promote undesired off-target mutagenesis. Here, we describe an approach that combines a Cas9 nickase mutant with paired guide RNAs to introduce targeted double-strand breaks. Because individual nicks in the genome are repaired with high fidelity, simultaneous nicking via appropriately offset guide RNAs is required for double-stranded breaks and extends the number of specifically recognized bases for target cleavage. We demonstrate that using paired nicking can reduce off-target activity by 50- to 1,500-fold in cell lines and to facilitate gene knockout in mouse zygotes without sacrificing on-target cleavage efficiency. This versatile strategy enables a wide variety of genome editing applications that require high specificity.

 10.1016/j.cell.2013.08.021
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Rescooped by hunter chen from Effectors and Plant Immunity
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Front. Plant Sci.: Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems (2015)

Front. Plant Sci.: Decision tools for bacterial blight resistance gene deployment in rice-based agricultural ecosystems (2015) | Biotech | Scoop.it

Attempting to achieve long-lasting and stable resistance using uniformly deployed rice varieties is not a sustainable approach. The real situation appears to be much more complex and dynamic, one in which pathogens quickly adapt to resistant varieties. To prevent disease epidemics, deployment should be customized and this decision will require interdisciplinary actions. This perspective article aims to highlight the current progress on disease resistance deployment to control bacterial blight in rice. Although the model system rice−Xanthomonas oryzae pv. oryzae has distinctive features that underpin the need for a case-by-case analysis, strategies to integrate those elements into a unique decision tool could be easily extended to other crops.

 

Gerbert Sylvestre Dossa, Adam H. Sparks, Casiana Vera Cruz and Ricardo Oliva


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Rescooped by hunter chen from Plant immunity and legume symbiosis
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From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development

From phenotypes to causal sequences: using genome wide association studies to dissect the sequence basis for variation of plant development | Biotech | Scoop.it
Highlights



Genome Wide Association Studies (GWASs) have been conducted in 22 plant species.


GWASs have uncovered novel mechanisms and genes underlying variation of growth and development.


GWASs frequently identify different sets of genes than those identified by mutant screening.


Phenotypic data for GWAS can be used to comprehend correlations and mechanistic links between traits.


Experimental design, conduct and analysis are keys for successful GWASs.

Tremendous natural variation of growth and development exists within species. Uncovering the molecular mechanisms that tune growth and development promises to shed light on a broad set of biological issues including genotype to phenotype relations, regulatory mechanisms of biological processes and evolutionary questions. Recent progress in sequencing and data processing capabilities has enabled Genome Wide Association Studies (GWASs) to identify DNA sequence polymorphisms that underlie the variation of biological traits. In the last years, GWASs have proven powerful in revealing the complex genetic bases of many phenotypes in various plant species. Here we highlight successful recent GWASs that uncovered mechanistic and sequence bases of trait variation related to plant growth and development and discuss important considerations for conducting successful GWASs.

Via Christophe Jacquet
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Rescooped by hunter chen from Bioinformatics, Comparative Genomics and Molecular Evolution
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Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries

Next generation sequencing shakes up genotype/phenotype correlation, disease discoveries | Biotech | Scoop.it

With the ability to use next generation sequencing technology, researchers have a broadened understanding of the association of genetic changes and disease causation to a much greater resolution, driving new discoveries, said clinical geneticists...


Via Arjen ten Have
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Arjen ten Have's curator insight, August 15, 2014 8:31 AM
An important IMO is that of how we will share all that information. How will dr watson in Nigeria know of it? Breast cancer for instance we know now, thanks to NGS, can often be divided in subtypes that all should be treated differently. Many MD proof databases will need to be developed.
Rescooped by hunter chen from Bioinformatics, Comparative Genomics and Molecular Evolution
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Finding functions for DUF proteins

Finding functions for DUF proteins | Biotech | Scoop.it
A group of scientists is working to characterise some of the millions of proteins designated ‘Domain of Unknown Function’. Penny Coggill explains the project and reveals some early findings.

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Arjen ten Have's curator insight, December 5, 2013 11:47 AM

Nice initiative beyond structural genomics.

Rescooped by hunter chen from Bioinformatics-1
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PLOS Computational Biology: BioStar: An Online Question & Answer Resource for the Bioinformatics Community

PLOS Computational Biology: BioStar: An Online Question & Answer Resource for the Bioinformatics Community | Biotech | Scoop.it
PLOS Computational Biology is an open-access

Via Jon Teets
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