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.
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”.
[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...
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.
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,
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.
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.
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.
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.
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.
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!
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.”
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.
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
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.”
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).
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.
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.
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.
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.
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
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.
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