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.
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.
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.
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.
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).
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
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.
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.
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.
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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