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Tunable Promoters in Synthetic and Systems Biology

Tunable Promoters in Synthetic and Systems Biology | Plant Genetics, NGS and Bioinformatics | Scoop.it

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Tore Dehli, Christian Solem and Peter Ruhdal Jensen

"Synthetic and systems biologists need standardized, modular and orthogonal tools yielding predictable functions in vivo. In systems biology such tools are needed to quantitatively analyze the behavior of biological systems while the efficient engineering of artificial gene networks is central in synthetic biology. A number of tools exist to manipulate the steps in between gene sequence and functional protein in living cells, but out of these the most straight-forward approach is to alter the gene expression level by manipulating the promoter sequence. Some of the promoter tuning tools available for accomplishing such altered gene expression levels are discussed here along with examples of their use, and ideas for new tools are described. The road ahead looks very promising for synthetic and systems biologists as tools to achieve just about anything in terms of tuning and timing multiple gene expression levels using libraries of synthetic promoters now exist."
http://bit.ly/RXfkre


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Plant Genetics, NGS and Bioinformatics
Papers and topics in plant genetics, NGS and bioinformatics
Curated by Ali Taheri
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The Secret to Making Sweeter-Smelling Roses

The Secret to Making Sweeter-Smelling Roses | Plant Genetics, NGS and Bioinformatics | Scoop.it
Geneticists have found the gene that gives roses their scent, and that discovery may help breeders produce sweeter-smelling roses.

Via Mary Williams
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Mary Williams's curator insight, July 12, 7:46 AM

A summary of a paper out in 3 July Science

Biosynthesis of monoterpene scent compounds in roses

http://www.sciencemag.org/content/349/6243/81

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CRISPR-Cas genome surveillance: From basic biology to transformative technology

Dr. Doudna, who specializes in the study of RNA, will present a brief history of the bacterial RNA-guided CRISPR biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism. Using CRISPR-Cas "clustered regularly interspaced short palindromic repeats" technology provides the foundation for remarkable developments in modifying, regulating, or marking genomic loci in a wide variety of cells and organisms. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way to fundamental discoveries in biology with applications in all branches of biotechnology, and strategies for human therapeutics. Dr. Doudna will discuss recent findings regarding the molecular mechanism of Cas9 and its use for targeted cell-based therapies.

About the annual Margaret Pittman Lecture:
This annual lecture honors Dr. Margaret Pittman, NIH’s first female lab chief, who made significant contributions to microbiology and vaccine development, particularly in the areas of pertussis and tetanus, during her long career at the National Institute of Allergy and Infectious Diseases. 


For more information go to http://wals.od.nih.gov

Author: Jennifer Doudna, Ph.D., Li Ka Shing Chancellor's Chair in Biomedical Sciences and Professor, Department of Molecular and Cell Biology and Department of Chemistry at the University of California, Berkeley; Investigator, Howard Hughes Medical Institute 


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Broad Institute, Google Genomics combine bioinformatics and computing expertise

Broad Institute, Google Genomics combine bioinformatics and computing expertise | Plant Genetics, NGS and Bioinformatics | Scoop.it

Broad Institute of MIT and Harvard is teaming up with Google Genomics to explore how to break down major technical barriers that increasingly hinder biomedical research by addressing the need for computing infrastructure to store and process enormous datasets, and by creating tools to analyze such data and unravel long-standing mysteries about human health.

As a first step, Broad Institute’s Genome Analysis Toolkit, or GATK, will be offered as a service on the Google Cloud Platform, as part of Google Genomics. The goal is to enable any genomic researcher to upload, store, and analyze data in a cloud-based environment that combines the Broad Institute’s best-in-class genomic analysis tools with the scale and computing power of Google.

GATK is a software package developed at the Broad Institute to analyze high-throughput genomic sequencing data. GATK offers a wide variety of analysis tools, with a primary focus on genetic variant discovery and genotyping as well as a strong emphasis on data quality assurance. Its robust architecture, powerful processing engine, and high-performance computing features make it capable of taking on projects of any size.

GATK is already available for download at no cost to academic and non-profit users. In addition, business users can license GATK from the Broad. To date, more than 20,000 users have processed genomic data using GATK.

The Google Genomics service will provide researchers with a powerful, additional way to use GATK. Researchers will be able to upload genetic data and run GATK-powered analyses on Google Cloud Platform, and may use GATK to analyze genetic data already available for research via Google Genomics. GATK as a service will make best-practice genomic analysis readily available to researchers who don’t have access to the dedicated compute infrastructure and engineering teams required for analyzing genomic data at scale. An initial alpha release of the GATK service will be made available to a limited set of users.

“Large-scale genomic information is accelerating scientific progress in cancer, diabetes, psychiatric disorders, and many other diseases,” said Eric Lander, President and Director of Broad Institute. “Storing, analyzing, and managing these data is becoming a critical challenge for biomedical researchers. We are excited to work with Google’s talented and experienced engineers to develop ways to empower researchers around the world by making it easier to access and use genomic information.”


Via Dr. Stefan Gruenwald
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A Gene-Edited Potato | MIT Technology Review

A Gene-Edited Potato | MIT Technology Review | Plant Genetics, NGS and Bioinformatics | Scoop.it
Plant scientists can swiftly modify crops in ways that would take years with conventional breeding.

Dan Voytas is a plant geneticist at the University of Minnesota. But two days a week he stops studying the fundamentals of DNA engineering and heads to a nearby company called Cellectis Plant Sciences, where he applies them.

His newest creation, described in a plant journal this month, is a Ranger Russet potato that doesn’t accumulate sweet sugars at typical cold storage temperatures. That will let it last longer, and when it’s fried it won’t produce as much acrylamide, a suspected carcinogen.

What’s different about the potato is that it was bred with the help of gene editing, a new kind of technique for altering DNA that plant scientists say is going to be revolutionary for its simplicity and power. The technology could also be a way to engineer plants that avoid the stigma, and the regulations, normally associated with genetically modified organisms (GMOs).

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Sweet potato naturally 'genetically modified'

Sweet potato naturally 'genetically modified' | Plant Genetics, NGS and Bioinformatics | Scoop.it
Sweet potatoes from all over the world naturally contain genes from the bacterium Agrobacterium, researchers report. Sweet potato is one of the most important food crops for human consumption in the world. Because of the presence of this "foreign" DNA, sweet potato can be seen as a "natural GMO," the researchers say.
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Sequencing consolidates molecular markers with plant breeding practice

Sequencing consolidates molecular markers with plant breeding practice | Plant Genetics, NGS and Bioinformatics | Scoop.it
Key message

Plenty of molecular markers have been developed by contemporary sequencing technologies, whereas few of them are successfully applied in breeding, thus we present a review on how sequencing can facilitate marker-assisted selection in plant breeding.

Abstract

The growing global population and shrinking arable land area require efficient plant breeding. Novel strategies assisted by certain markers have proven effective for genetic gains. Fortunately, cutting-edge sequencing technologies bring us a deluge of genomes and genetic variations, enlightening the potential of marker development. However, a large gap still exists between the potential of molecular markers and actual plant breeding practices. In this review, we discuss marker-assisted breeding from a historical perspective, describe the road from crop sequencing to breeding, and highlight how sequencing facilitates the application of markers in breeding practice.

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Regulatory uncertainty over genome editing - Nature Plants

Regulatory uncertainty over genome editing - Nature Plants | Plant Genetics, NGS and Bioinformatics | Scoop.it

Jones 2015

Genome editing opens up opportunities for the precise and rapid alteration of crops to boost yields, protect against pests and diseases and enhance nutrient content. The extent to which applied plant research and crop breeding benefit will depend on how the EU decides to regulate this fledgling technology.

 


Via dromius, Guogen Yang
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Methods in Enzymology Vol 546 - The Use of CRISPR/Cas9, ZFNs and TALENs in Generating Site-Specific Genome Alterations

Methods in Enzymology Vol 546 - The Use of CRISPR/Cas9, ZFNs and TALENs in Generating Site-Specific Genome Alterations | Plant Genetics, NGS and Bioinformatics | Scoop.it
This new volume of Methods in Enzymology continues the legacy of this premier serial with quality chapters authored by leaders in the field. Methods to assess mitochondrial function is of great interest to neuroscientists studying chronic forms of neurodegeneration, including Parkinson's, Alzheimer's, ALS, Huntington's and other triplet repeat diseases, but also to those working on acute conditions such as stroke and traumatic brain injury. This volume covers research methods on how to assess the life cycle of mitochondria including trafficking, fusion, fission, and degradation. Multiple perspectives on the complex and difficult problem of measurement of mitochondrial reactive oxygen species production with fluorescent indicators and techniques ranging in scope from measurements on isolated mitochondria to non-invasive imaging of metabolic function.Continues the legacy of this premier serial with quality chapters authored by leaders in the fieldCovers research methods in biomineralization scienceProvides invaluable details on state-of-the-art methods to assess a broad array of mitochondrial functions

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Making designer mutants in all kinds of model organisms

Making designer mutants in all kinds of model organisms | Plant Genetics, NGS and Bioinformatics | Scoop.it

Recent advances in the targeted modification of complex eukaryotic genomes have unlocked a new era of genome engineering. From the pioneering work using zinc-finger nucleases (ZFNs), to the advent of the versatile and specific TALEN systems, and most recently the highly accessible CRISPR/Cas9 systems, we now possess an unprecedented ability to analyze developmental processes using sophisticated designer genetic tools. Excitingly, these robust and simple genomic engineering tools also promise to revolutionize developmental studies using less well established experimental organisms.


Modern developmental biology was born out of the fruitful marriage between traditional embryology and genetics. Genetic tools, together with advanced microscopy techniques, serve as the most fundamental means for developmental biologists to elucidate the logistics and the molecular control of growth, differentiation and morphogenesis. For this reason, model organisms with sophisticated and comprehensive genetic tools have been highly favored for developmental studies. Advances made in developmental biology using these genetically amenable models have been well recognized. The Nobel prize in Physiology or Medicine was awarded in 1995 to Edward B. Lewis, Christiane Nüsslein-Volhard and Eric F. Wieschaus for their discoveries on the ‘Genetic control of early structural development’ usingDrosophila melanogaster, and again in 2002 to John Sulston, Robert Horvitz and Sydney Brenner for their discoveries of ‘Genetic regulation of development and programmed cell death’ using the nematode worm Caenorhabditis elegans. These fly and worm systems remain powerful and popular models for invertebrate development studies, while zebrafish (Danio rerio), the dual frog species Xenopus laevis and Xenopus tropicalis, rat (Rattus norvegicus), and particularly mouse (Mus musculus) represent the most commonly used vertebrate model systems. To date, random or semi-random mutagenesis (‘forward genetic’) approaches have been extraordinarily successful at advancing the use of these model organisms in developmental studies. With the advent of reference genomic data, however, sequence-specific genomic engineering tools (‘reverse genetics’) enable targeted manipulation of the genome and thus allow previously untestable hypotheses of gene function to be addressed.


Via Dr. Stefan Gruenwald, Mary Williams
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Unit 1 of English Communication for Scientists | Learn Science at Scitable

Unit 1 of English Communication for Scientists | Learn Science at Scitable | Plant Genetics, NGS and Bioinformatics | Scoop.it

Communication is an integral part of the research you perform as a scientist. Your written papers serve as a gauge of your scientific productivity and provide a long-lasting body of knowledge from which other scientists can build their research. The oral presentations you deliver make your latest research known to the community, helping your peers stay up to date. Discussions enable you to exchange ideas and points of view. Letters, memos, and résumés help you build and maintain relationships with colleagues, suppliers, employers, and so on.

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The top 100 papers: NATURE magazine explores the most-cited research papers of all time

The top 100 papers: NATURE magazine explores the most-cited research papers of all time | Plant Genetics, NGS and Bioinformatics | Scoop.it

The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating — all of these breakthroughs won Nobel prizes and international acclaim. Yet none of the papers that announced them comes anywhere close to ranking among the 100 most highly cited papers of all time.

 

Citations, in which one paper refers to earlier works, are the standard means by which authors acknowledge the source of their methods, ideas and findings, and are often used as a rough measure of a paper’s importance. Fifty years ago, Eugene Garfield published the Science Citation Index (SCI), the first systematic effort to track citations in the scientific literature. To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. (See the full list at Web of Science Top 100.xls or the interactive graphic, below.) The search covered all of Thomson Reuter’s Web of Science, an online version of the SCI that also includes databases covering the social sciences, arts and humanities, conference proceedings and some books. It lists papers published from 1900 to the present day.

 

The exercise revealed some surprises, not least that it takes a staggering 12,119 citations to rank in the top 100 — and that many of the world’s most famous papers do not make the cut. A few that do, such as the first observation1 of carbon nanotubes (number 36) are indeed classic discoveries. But the vast majority describe experimental methods or software that have become essential in their fields.

 

The most cited work in history, for example, is a 1951 paper2 describing an assay to determine the amount of protein in a solution. It has now gathered more than 305,000 citations — a recognition that always puzzled its lead author, the late US biochemist Oliver Lowry.


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Here's Why We Haven't Quite Figured Out How to Feed Billions More People

Here's Why We Haven't Quite Figured Out How to Feed Billions More People | Plant Genetics, NGS and Bioinformatics | Scoop.it
Solving the world's looming food crisis will require big investments in agricultural research, yet public support for that is lagging.

Via Mary Williams, Loïc Lepiniec
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Should we upgrade photosynthesis and grow supercrops? - opinion - 06 October 2014 - New Scientist

Should we upgrade photosynthesis and grow supercrops? - opinion - 06 October 2014 - New Scientist | Plant Genetics, NGS and Bioinformatics | Scoop.it
A long-awaited breakthrough by crop scientists raises some thorny issues for conservation. Michael Le Page proposes a radical solution
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What lives here? DNA sequencing analysis shows what lives in a stream of water

What lives here? DNA sequencing analysis shows what lives in a stream of water | Plant Genetics, NGS and Bioinformatics | Scoop.it

Industry, agriculture and human settlement put a strain on bodies of water; some organisms cannot survive due to the changing conditions in streams and rivers. Accordingly, their existence sheds light on the quality of the habitat. However, the number of experts able to identify the small animals on the basis of their appearance is in decline; only a few junior researchers are active in this field. RUB researchers from the Department Animal Ecology, Evolution and Biodiversity help preserve expert knowledge.


Database with "DNA barcodes"

For this purpose, they are creating a database in collaboration with the "German Barcode of Life Project": in the first step, qualified experts identify the water organisms based on their appearance. Subsequently, a short characteristic segment of the animals' genome – i.e. the barcode – is decoded and fed into the database. Someone who wishes to find out which species are represented in a body of water, takes a water sample, sequences the DNA of the organisms contained therein and matches it against the database. Vasco Elbrecht and Dr Florian Leese have developed an innovative lab protocol which renders this so-called DNA barcoding much faster than hitherto. They are able to identify more than thousand animals within a week after taking the sample. Even now in the development stage, the method identifies more than 80 per cent of the species correctly. It is thus more reliable than species identification based on external characteristics, and the biologists from Bochum are convinced that they will optimise the quota in the near future.


Assessment systems have to be adjusted to the new method

In their study, the Bochum-based biologists have also demonstrated the limitations of DNA barcoding. Using this method, it cannot be determined how many individuals of a certain species can be found in a body of water. The established assessment criteria for water quality, on the other hand, do include such data. "This is a problem for available assessment systems," says Florian Leese. "However, running waters are very dynamic; the frequency of species varies strongly for natural reasons over time. Therefore, it makes sense to record the quality based on conclusive species lists, without focusing too much on frequency.”

 

V. Elbrecht, F. Leese (2015): Can DNA-based ecosystem assessments quantify species abundance? Testing primer bias and biomass - sequence relationships with an innovative metabarcoding protocol,


PLOS ONE, DOI: 10.1371/journal.pone.0130324, http://dx.plos.org/10.1371/journal.pone.0130324


Via Dr. Stefan Gruenwald
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The Science & Education team's curator insight, July 10, 6:13 PM

Again, a good example of how, as Floridi terms it, second generation ICT is transforming our work.

 

Floridi, L. (2014). The 4th revolution. Oxford: Oxford University Press.

 

... and I can also recommend Stefan Gruenwald's 'Amazing Science' scoop.it feed.

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Mutant Crops Drive BASF Sales Where Monsanto Denied: Commodities

Mutant Crops Drive BASF Sales Where Monsanto Denied: Commodities | Plant Genetics, NGS and Bioinformatics | Scoop.it
Crop breeders increasingly are using radiation and gene-altering chemicals to mutate seeds, creating new plant varieties with better yields -- all without regulation.

Via Annals of Botany: Plant Science Research
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Annals of Botany: Plant Science Research's curator insight, November 23, 2013 6:25 AM

IAEA-FAO has had the most every requests to generate mutants - and I am looking forward to better characterization and doing more work with them in many species!

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DNA editing takes a serious step forward -- for better or worse

DNA editing takes a serious step forward -- for better or worse | Plant Genetics, NGS and Bioinformatics | Scoop.it
It's a scenario that has haunted biologists since the dawn of the DNA age: the evil scientist custom-crafting a human being with test tubes and Petri dishes.
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High-throughput functional genomics using CRISPR-Cas9. - PubMed - NCBI

High-throughput functional genomics using CRISPR-Cas9. - PubMed - NCBI | Plant Genetics, NGS and Bioinformatics | Scoop.it

Forward genetic screens are powerful tools for the discovery and functional annotation of genetic elements. Recently, the RNA-guided CRISPR (clustered regularly interspaced short palindromic repeat)-associated Cas9 nuclease has been combined with genome-scale guide RNA libraries for unbiased, phenotypic screening. In this Review, we describe recent advances using Cas9 for genome-scale screens, including knockout approaches that inactivate genomic loci and strategies that modulate transcriptional activity. We discuss practical aspects of screen design, provide comparisons with RNA interference (RNAi) screening, and outline future applications and challenges.

Nat Rev Genet. 2015 May;16(5):299-311. doi: 10.1038/nrg3899. Epub 2015 Apr 9.

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Efficiency of CRISPR-Cas9 Genome Editing Tool is Increased Eightfold

Efficiency of CRISPR-Cas9 Genome Editing Tool is Increased Eightfold | Plant Genetics, NGS and Bioinformatics | Scoop.it
Researchers at the Max Delbrück Center for Molecular Medicine (MDC) Berlin-Buch and the Berlin Institute of Health (BIH) have engineered a more
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Are we ready for back-to-nature crop breeding?: Trends in Plant Science

Are we ready for back-to-nature crop breeding?: Trends in Plant Science | Plant Genetics, NGS and Bioinformatics | Scoop.it

Sustainable agriculture in response to increasing demands for food depends on development of high-yielding crops with high nutritional value that require minimal intervention during growth. To date, the focus has been on changing plants by introducing genes that impart new properties, which the plants and their ancestors never possessed. By contrast, we suggest another potentially beneficial and perhaps less controversial strategy that modern plant biotechnology may adopt. This approach, which broadens earlier approaches to reverse breeding, aims to furnish crops with lost properties that their ancestors once possessed in order to tolerate adverse environmental conditions. What molecular techniques are available for implementing such rewilding? Are the strategies legally, socially, economically, and ethically feasible? These are the questions addressed in this review.

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One hundred important questions facing plant science research - Grierson - 2011 - New Phytologist - Wiley Online Library

One hundred important questions facing plant science research - Grierson - 2011 - New Phytologist - Wiley Online Library | Plant Genetics, NGS and Bioinformatics | Scoop.it

Plant science has never been more important. The growing and increasingly prosperous human population needs abundant safe and nutritious food, shelter, clothes, fibre, and renewable energy, and needs to address the problems generated by climate change, while preserving habitats. These global challenges can only be met in the context of a strong fundamental understanding of plant biology and ecology, and translation of this knowledge into field-based solutions.

Plant science is beginning to address these grand challenges, but it is not clear that the full range of challenges facing plant science is known or has been assessed. What questions should the next generation of plant biologists be addressing? To start to answer this question we set out to compile a list of 100 important questions facing plant science research.

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The amazing decline of global hunger, in one chart

The amazing decline of global hunger, in one chart | Plant Genetics, NGS and Bioinformatics | Scoop.it

hunger is on a major decline in the world. Since 1990, there's been a sustained and massive collapse in the number of people who have difficulty accessing food.


Via CIMMYT, Int.
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Frontiers: The past, present and future of breeding rust resistant wheat (2014)

Frontiers: The past, present and future of breeding rust resistant wheat (2014) | Plant Genetics, NGS and Bioinformatics | Scoop.it

Two classes of genes are used for breeding rust resistant wheat. The first class, called R (for resistance) genes, are pathogen race-specific in their action, effective at all plant growth stages and probably mostly encode immune receptors of the nucleotide binding leucine rich repeat (NB-LRR) class. The second class called Adult Plant Resistance genes (APR) because resistance is usually functional only in adult plants, and, in contrast to most R genes, the levels of resistance conferred by single APR genes are only partial and allow considerable disease development. Some but not all APR genes provide resistance to all isolates of a rust pathogen species and a subclass of these provides resistance to several fungal pathogen species. Initial indications are that APR genes encode a more heterogeneous range of proteins than R proteins. Two APR genes, Lr34 and Yr36, have been cloned from wheat and their products are an ABC transporter and a protein kinase, respectively. Lr34 and Sr2 have provided long lasting and widely used (durable) partial resistance and are mainly used in conjunction with other R and APR genes to obtain adequate rust resistance. We caution that some APR genes indeed include race-specific, weak R genes which may be of the NB-LRR class. A research priority to better inform rust resistance breeding is to characterize further APR genes in wheat and to understand how they function and how they interact when multiple APR and R genes are stacked in a single genotype by conventional and GM breeding. An important message is do not be complacent about the general durability of all APR genes.


Via Kamoun Lab @ TSL
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What is the World's Biggest Cash Crop? - Information Is Beautiful

What is the World's Biggest Cash Crop? - Information Is Beautiful | Plant Genetics, NGS and Bioinformatics | Scoop.it
Rice? Wheat? Maize? Soya? What's the world's biggest cash crop? The answer might surprise you.

Via Mary Williams
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Building agricultural research

Building agricultural research | Plant Genetics, NGS and Bioinformatics | Scoop.it

Nine billion people are expected to inhabit Planet Earth by 2050. Without agricultural research, there is little hope of sustaining this population surge, given that arable land and water supplies are fixed commodities. Yet for decades the agricultural sector has suffered from neglect. If we want to combat new strains of pests that destroy crops, find new crop varieties enriched in nutritional value, improve yields, develop resistance to disease and drought, and provide environmentally sensitive cultivation practices, then agricultural research must be a priority. Why isn't it?

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A faster Rubisco with potential to increase photosynthesis in crops

A faster Rubisco with potential to increase photosynthesis in crops | Plant Genetics, NGS and Bioinformatics | Scoop.it

In photosynthetic organisms, D-ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major enzyme assimilating atmospheric CO2 into the biosphere1. Owing to the wasteful oxygenase activity and slow turnover of Rubisco, the enzyme is among the most important targets for improving the photosynthetic efficiency of vascular plants2, 3. It has been anticipated that introducing the CO2-concentrating mechanism (CCM) from cyanobacteria into plants could enhance crop yield4, 5, 6. However, the complex nature of Rubisco’s assembly has made manipulation of the enzyme extremely challenging, and attempts to replace it in plants with the enzymes from cyanobacteria and red algae have not been successful7, 8. Here we report two transplastomic tobacco lines with functional Rubisco from the cyanobacterium Synechococcus elongatus PCC7942 (Se7942). We knocked out the native tobacco gene encoding the large subunit of Rubisco by inserting the large and small subunit genes of the Se7942 enzyme, in combination with either the corresponding Se7942 assembly chaperone, RbcX, or an internal carboxysomal protein, CcmM35, which incorporates three small subunit-like domains9, 10. Se7942 Rubisco and CcmM35 formed macromolecular complexes within the chloroplast stroma, mirroring an early step in the biogenesis of cyanobacterial β-carboxysomes11, 12. Both transformed lines were photosynthetically competent, supporting autotrophic growth, and their respective forms of Rubisco had higher rates of CO2 fixation per unit of enzyme than the tobacco control. These transplastomic tobacco lines represent an important step towards improved photosynthesis in plants and will be valuable hosts for future addition of the remaining components of the cyanobacterial CCM, such as inorganic carbon transporters and the β-carboxysome shell proteins

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