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PLOS Biology: Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli

PLOS Biology: Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli | my universe | Scoop.it

The causes and mechanisms of evolutionary diversification are central issues in biology. There is well-established theory that predicts that adaptive diversification can arise because of ecological interactions between individuals, such as competition or predation, but there are no empirical examples in which this process has been observed at the genetic level. We documented the genetic basis of adaptive diversification resulting from competition for resources in populations of the bacterium Escherichia coli. The populations diversified into two coexisting ecotypes representing different physiological adaptations. We found that similar but independently evolved phenotypes often shared mutations in the same gene and, in four cases, shared identical mutations at the same nucleotide position. Timelines of allele frequencies extracted from the frozen “fossil record” of three evolving populations showed parallel evolutionary dynamics, suggesting that mutations causing one type of physiology changed the ecological environment and allowed invasion of mutations causing an alternate physiology. The results provide empirical evidence of adaptive diversification as a predictable evolutionary process.

  
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Rescooped by Norman Warthmann from Plants and Microbes
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Scientific Reports: CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion (2016)

Scientific Reports: CRISPR/Cas9-Mediated Immunity to Geminiviruses: Differential Interference and Evasion (2016) | my universe | Scoop.it

The CRISPR/Cas9 system has recently been used to confer molecular immunity against several eukaryotic viruses, including plant DNA geminiviruses. Here, we provide a detailed analysis of the efficiencies of targeting different coding and non-coding sequences in the genomes of multiple geminiviruses. Moreover, we analyze the ability of geminiviruses to evade the CRISPR/Cas9 machinery. Our results demonstrate that the CRISPR/Cas9 machinery can efficiently target coding and non-coding sequences and interfere with various geminiviruses. Furthermore, targeting the coding sequences of different geminiviruses resulted in the generation of viral variants capable of replication and systemic movement. By contrast, targeting the noncoding intergenic region sequences of geminiviruses resulted in interference, but with inefficient recovery of mutated viral variants, which thus limited the generation of variants capable of replication and movement. Taken together, our results indicate that targeting noncoding, intergenic sequences provides viral interference activity and significantly limits the generation of viral variants capable of replication and systemic infection, which is essential for developing durable resistance strategies for long-term virus control.


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Can Mars' bid to publish genetic maps of historic African crops boost nutrition?

Can Mars' bid to publish genetic maps of historic African crops boost nutrition? | my universe | Scoop.it
Confectionery company says initiative will help breed more drought-tolerant seeds, but critics fear that small-scale farmers will lose out
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IRRI - 50 years of IR8

IRRI - 50 years of IR8 | my universe | Scoop.it
IRRI is a nonprofit research and education center established to reduce poverty and hunger, improve the health of rice farmers and consumers, and ensure environmental sustainability.
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kWIP: The k-mer Weighted Inner Product, a de novo Estimator of Genetic Similarity

Modern genomics techniques generate overwhelming quantities of data. Extracting population genetic variation demands computationally efficient methods to determine genetic relatedness between individuals or samples in an unbiased manner, preferably de novo. The rapid and unbiased estimation of genetic relatedness has the potential to overcome reference genome bias, to detect mix-ups early, and to verify that biological replicates belong to the same genetic lineage before conclusions are drawn using mislabelled, or misidentified samples. We present the k-mer Weighted Inner Product (kWIP), an assembly-, and alignment-free estimator of genetic similarity. kWIP combines a probabilistic data structure with a novel metric, the weighted inner product (WIP), to efficiently calculate pairwise similarity between sequencing runs from their \k-mer counts. It produces a distance matrix, which can then be further analysed and visualised. Our method does not require prior knowledge of the underlying genomes and applications include detecting sample identity and mix-up, non-obvious genomic variation, and population structure. We show that kWIP can reconstruct the true relatedness between samples from simulated populations. By re-analysing several published datasets we show that our results are consistent with marker-based analyses. kWIP is written in C++, licensed under the GNU GPL, and is available from https://github.com/kdmurray91/kwip.

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Could wild mangoes solve the world's chocolate crisis?

Could wild mangoes solve the world's chocolate crisis? | my universe | Scoop.it
A little-known fruit could provide an alternative to cocoa butter.
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Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing : Nature : Nature Publishing Group

Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing : Nature : Nature Publishing Group | my universe | Scoop.it
In 1943, Luria and Delbrück used a phage-resistance assay to establish spontaneous mutation as a driving force of microbial diversity. Mutation rates are still studied using such assays, but these can only be used to examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing, may be skewed by mutational ‘hot’ or ‘cold’ spots. Both approaches are affected by numerous caveats. Here we devise a method, maximum-depth sequencing (MDS), to detect extremely rare variants in a population of cells through error-corrected, high-throughput sequencing. We directly measure locus-specific mutation rates in Escherichia coli and show that they vary across the genome by at least an order of magnitude. Our data suggest that certain types of nucleotide misincorporation occur 104-fold more frequently than the basal rate of mutations, but are repaired in vivo. Our data also suggest specific mechanisms of antibiotic-induced mutagenesis, including downregulation of mismatch repair via oxidative stress, transcription–replication conflicts, and, in the case of fluoroquinolones, direct damage to DNA.
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Rescooped by Norman Warthmann from Ag Biotech News
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New plant engineering method could help fill demand for crucial malaria drug - Max Planck (2016) 

New plant engineering method could help fill demand for crucial malaria drug - Max Planck (2016)  | my universe | Scoop.it

A new and inexpensive technique for mass-producing the main ingredient in the most effective treatment for malaria, artemisinin, could help meet global demands for the drug... Artemisinin is produced in low yields by a herb called Artemisia annua (A. annua)... Researchers... discovered a new way to produce artemisinic acid, the molecule from which artemisinin is derived, in high yields. Their method involves transferring its metabolic pathway... into tobacco, a high-biomass crop.

“Malaria is a devastating tropical disease that kills almost half a million people every year... For the foreseeable future, artemisinin will be the most powerful weapon in the battle against malaria but, due to its extraction from low-yielding plants, it is currently too expensive to be widely accessible to patients in poorer countries. Producing artemisinic acid in a crop such as tobacco, which yields large amounts of leafy biomass, could provide a sustainable and inexpensive source of the drug, making it more readily available for those who need it most”...  

Although further increases in these production levels will be needed if global demand for artemisinin is to be met, the study lays the foundation for much cheaper production of this life-saving therapy in a high-biomass crop, in contrast to a single medicinal plant. It also provides a new tool for engineering many other complex pathways, with the potential to increase production of other essential therapeutic ingredients.


http://www.mpimp-golm.mpg.de/2069723/rbock-malaria-drug-in-tobacco


Underlying article: http://dx.doi.org/10.7554/eLife.13664



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Alexander J. Stein's curator insight, June 15, 2016 5:32 PM
Tobacco is a good target plant: Not a food crop, high yielding, and offering tobacco farmers an alternative source of income than supplying the tobacco industry... 
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The pressure to publish pushes down quality

The pressure to publish pushes down quality | my universe | Scoop.it
Scientists must publish less, says Daniel Sarewitz, or good research will be swamped by the ever-increasing volume of poor work.
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‘Do Not Privatize the Giant's Shoulders’: Rethinking Patents in Plant Breeding: Trends in Biotechnology

‘Do Not Privatize the Giant's Shoulders’: Rethinking Patents in Plant Breeding: Trends in Biotechnology | my universe | Scoop.it
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Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment

Comparative metagenomics reveals a diverse range of antimicrobial resistance genes in effluents entering a river catchment | my universe | Scoop.it
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A Proposal Regarding Best Practices for Validating the Identity of Genetic Stocks and the Effects of Genetic Variants

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NASA: Global Warming Is Now Changing How Earth Wobbles

NASA: Global Warming Is Now Changing How Earth Wobbles | my universe | Scoop.it
NASA: Global Warming Is Now Changing How Earth Wobbles
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Rescooped by Norman Warthmann from Plants and Microbes
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Nature Biotechnology: Plant immunity switched from bacteria to virus (2016)

Nature Biotechnology: Plant immunity switched from bacteria to virus (2016) | my universe | Scoop.it

Each year, staple crops around the world suffer massive losses in yield owing to the destruc- tive effects of pathogens. Improving the disease resistance of crops by boosting their immunity has been a key objective of agricultural bio- tech ever since the discovery of plant immune receptors in the 1990s. Nucleotide-binding leucine-rich repeat (NLR) proteins, a family of intracellular immune receptors that recog- nize pathogen molecules, are promising targets for enhancing pathogen resistance. In a recent paper in Science, Kim et al.1 describe a clever twist on this approach in which the host target protein for the pathogen effector is engineered rather than the NLR protein itself (Fig. 1).


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Direct Measurements of Smartphone Screen-Time: Relationships with Demographics and Sleep

Direct Measurements of Smartphone Screen-Time: Relationships with Demographics and Sleep | my universe | Scoop.it
Background Smartphones are increasingly integrated into everyday life, but frequency of use has not yet been objectively measured and compared to demographics, health information, and in particular, sleep quality. Aims The aim of this study was to characterize smartphone use by measuring screen-time directly, determine factors that are associated with increased screen-time, and to test the hypothesis that increased screen-time is associated with poor sleep. Methods We performed a cross-sectional analysis in a subset of 653 participants enrolled in the Health eHeart Study, an internet-based longitudinal cohort study open to any interested adult (≥ 18 years). Smartphone screen-time (the number of minutes in each hour the screen was on) was measured continuously via smartphone application. For each participant, total and average screen-time were computed over 30-day windows. Average screen-time specifically during self-reported bedtime hours and sleeping period was also computed. Demographics, medical information, and sleep habits (Pittsburgh Sleep Quality Index–PSQI) were obtained by survey. Linear regression was used to obtain effect estimates. Results Total screen-time over 30 days was a median 38.4 hours (IQR 21.4 to 61.3) and average screen-time over 30 days was a median 3.7 minutes per hour (IQR 2.2 to 5.5). Younger age, self-reported race/ethnicity of Black and
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Rescooped by Norman Warthmann from MycorWeb Plant-Microbe Interactions
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Why I Love Genetics: Essay on Occasion of Being Awarded the GSA Medal 2016

Why I Love Genetics: Essay on Occasion of Being Awarded the GSA Medal 2016 | my universe | Scoop.it
The Genetics Society of America (GSA) Medal is awarded to an individual for outstanding contributions to the field of genetics in the last 15 years. Recipients of the GSA Medal are recognized for elegant and highly meaningful contributions to modern genetics, and exemplify the ingenuity of GSA membership.

The 2016 recipient is Detlef Weigel, whose contributions include the identification of the molecular basis for floral patterning; the determination of mechanisms for flowering time; and elucidation of genetic tradeoffs between growth and immunity in natural populations. Notably, his group identified the gene for florigen, a compound made in leaves that induces flowering. Throughout these investigations, Weigel developed multiple resources for the plant genetics community, including activation tagging to create gain-of-function mutants; gathering data and creating a web interface for AtGenExpress, a gene expression atlas for Arabidopsis; and jumpstarting the 1001 Genomes project of Arabidopsis thaliana.

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Genome-wide association study of 12 agronomic traits in peach

Genome-wide association study of 12 agronomic traits in peach | my universe | Scoop.it
Peach is both an economically important crop species and a model for Rosaceae fruit development research.
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Mixing Energy Drinks and Alcohol Mimics Cocaine Exposure

Mixing Energy Drinks and Alcohol Mimics Cocaine Exposure | my universe | Scoop.it
While caffeine is a stimulant and alcohol is a CNS depressant, when the two substances are combined, they don’t cancel each other out. It’s act
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Associations among Wine Grape Microbiome, Metabolome, and Fermentation Behavior Suggest Microbial Contribution to Regional Wine Characteristics

Norman Warthmann's insight:
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Rescooped by Norman Warthmann from Plants and Microbes
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bioRxiv: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016)

bioRxiv: Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae (2016) | my universe | Scoop.it

In February 2016, a new fungal disease was spotted in wheat fields across eight districts in Bangladesh. The epidemic spread to an estimated 15,741 hectares, about 16% of cultivated wheat area in Bangladesh, with yield losses reaching up to 100%. Within weeks of the onset of the epidemic, we performed transcriptome sequencing of symptomatic leaf samples collected directly from Bangladeshi fields. Population genomics analyses revealed that the outbreak was caused by a wheat-infecting South American lineage of the blast fungus Magnaporthe oryzae. We show that genomic surveillance can be rapidly applied to monitor plant disease outbreaks and provide valuable information regarding the identity and origin of the infectious agent.


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Lynne Reuber's curator insight, June 20, 2016 10:53 AM
Molecular epidemiology for plant pathology
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Biden unveiling public database for clinical data on cancer

Biden unveiling public database for clinical data on cancer | my universe | Scoop.it
WASHINGTON (AP) — Vice President Joe Biden unveiled a public database for clinical data on cancer on Monday that aims to help researchers and doctors better tailor new treatments to individuals. Since taking on the cancer issue last year, Biden has repeatedly argued that confining data within institutions has hampered cancer research, with scientists and medical companies reluctant to share proprietary information. [...] cancer research institutions have significant data-sharing arrangements in place, although Biden and other critics say it's too limited and not happening early enough in the process.
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Rescooped by Norman Warthmann from Conservation agriculture
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Modern Industrial Agriculture Is Incompatible With Nature—We Need a New Paradigm Based on Ecology

Modern Industrial Agriculture Is Incompatible With Nature—We Need a New Paradigm Based on Ecology | my universe | Scoop.it
Annual monocultures—corn, wheat, rice—abuse the soil. What if we mimicked nature and grew perennial grains in mixtures instead?

Via CIMMYT, Int.
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The Plan to Rescue Hawaii’s Birds with Genetic Engineering

The Plan to Rescue Hawaii’s Birds with Genetic Engineering | my universe | Scoop.it
There’s a chance to use cutting-edge technology to save native Hawaiian birds from the mosquitoes that are driving them to extinction.
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Parent, carer… #AndAScientist : Naturejobs Blog

Parent, carer… #AndAScientist : Naturejobs Blog | my universe | Scoop.it
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Siemens and Airbus to push electric aviation engines

Siemens and Airbus to push electric aviation engines | my universe | Scoop.it
Siemens and Airbus teamed up today to develop electric and hybrid electric/combustion engines for commercial and private aircraft.
The companies said they would amass a joint development team of about 200 employees that would jointly develop prototypes for various propulsion systems with power classes ranging from a few 100 kilowatts up to 10 and more megawatts, for short, local trips with aircraft below 100 seats, helicopters or unmanned aircraft up to classic short and medium-range flights.
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