Engineering plant immunity using crispr cas9 to generate virus resistanceSheikh Mansoor
Targeted genome editing by use of artificial nucleases has the plausible potential to speed basic research as well as plant breeding by providing the means to modify genomes quickly in a specific and predictable manner but advanced CRISPR-Cas9 based technologies first confirmed in mammalian cell systems are quickly being fitted for use in plants. These new technologies increase CRISPR-Cas9’s utility and effectiveness by diversifying cellular capabilities through expression construct system evolution and enzyme orthogonality, as well as enhanced efficiency through delivery and expression mechanisms. RNA-guided genome editing using Streptococcus pyogenes CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats) has renewed the concept of genome editing in plants. CRISPR-associated surveillance complexes are easily programmable molecular sleds that can target any sequence of choice. These complexes offer new opportunities for implementation in biotechnology. Recent studies have used CRISPR/Cas9 to engineer virus resistance in plants, either by directly targeting and cleaving the viral genome, or by modifying the host plant genome to introduce viral immunity. The CRISPR/Cas9 platform could also be used for targeted mutagenesis to identify host factors that control plant resistance and susceptibility to viral infection. Thus, CRISPR/Cas9 technology offers a promising approach for under- standing and engineering resistance to single and multiple viral infections in plants.
With decades of experience in the fields of genomics sequencing, CD Genomics is devoted to providing unprecedented amounts of microbial metatranscriptomic data. Our strong expertise in the informative and unbiased metatranscriptomic sequencing service is guaranteed by state-of-the-art high throughput sequencers, flexible sequencing strategies, and professional bioinformatics pipelines.
Rapid 16S Next Generation Sequencing for Bacterial Identification in Polymicr...Thermo Fisher Scientific
In order to identify prokaryotic species in a sample, it is often necessary to culture the sample for hours or days to increase the abundance of bacteria to assayable levels. This often precludes the rapid identification of infectious species.
Furthermore, some species are not easily culturable. We
have developed a facile research method for identifying
bacterial species by 16S ribosomal RNA sequencing on the
Ion Torrent platform. The Ion 16S™ Metagenomics Kit is
designed to PCR amplify the hypervariable regions of the 16S
gene of bacteria. We used this kit to construct libraries from
15 retrospective samples of synovial fluid with various
bacterial species either spiked in or present at collection.
Libraries were sequenced on the Ion PGM™ system and the
data analysis performed using the Ion Reporter™ workflow
which provides an automated analysis solution. Bacteria
present in the samples were correctly identified in samples
containing a single spiked-in species, mixed-species samples,
and in infected samples. Thus, the Ion Torrent™ platform
provides a mechanism for rapidly identifying bacteria that are
present in research samples without culturing.
Accelerating Scientific Research Through Machine Learning and GraphNeo4j
Miroculus is a molecular diagnostics company that leverages the potential of microRNAs as biomarkers and has created the most easy-to-use and automated platform for their detection. MicroRNAs are small non-coding RNA molecules, whose primary role is to regulate the expression of our genes. Their discovery in circulation of body fluids such as blood plasma/serum, urine and saliva has been followed up by a multitude of studies, providing evidence that detection of specific microRNA molecules can give clues about a person’s health status and may therefore be used as biomarkers for various conditions.
Loom is an up-to-date snapshot of the scientific literature landscape focused on microRNAs that we built to expedite our own research. As of today, there is no compelling way to access much of the microRNA research. By using Loom's easy-to-use, interactive UI, the researcher is able to quickly locate the relevant sentences across many publications relating specific microRNAs with her disease or gene of interest. With this tool, our objective is to provide a visually compelling and complete overview of how microRNAs relate to specific diseases and genes.
At the backend, Loom is comprised of 4 microservices. The first one is a listener that fetches new publications daily that are available in the NCBI databases: PubMed for abstracts and PMC for full-text, open-access publications. Then, a natural language processor scans the publication, breaking them down into their constituent sentences and detecting mentions of microRNAs, genes and diseases.
Within each sentence, a machine learning scorer evaluates the strength and type of relationship on a scale from 0 to 1 and outputs the results in a graph database. The resulting graph database is then queried in real-time by the UI to retrieve the sentences and relationships the user is interested in.
Viral metagenomics is the study of viral genetic material sourced directly from the environment rather than from a host or natural reservoir. The goal is to ascertain the viral diversity in the environment that is often missed in studies targeting specific potential reservoirs.
Next Generation Sequencing for Identification and Subtyping of Foodborne Pat...nist-spin
"Next Generation Sequencing for Identification and Subtyping of Foodborne Pathogens" presentation at the Standards for Pathogen Identification via NGS (SPIN) workshop hosted by National Institute for Standards and Technology October 2014 by Rebecca Lindsey, PhD from Enteric Diseases Laboratory Branch of the CDC.
Application of Whole Genome Sequencing in the infectious disease’ in vitro di...ExternalEvents
http://www.fao.org/about/meetings/wgs-on-food-safety-management/en/
Applications of WGS in industry. Presentation from the Technical Meeting on the impact of Whole Genome Sequencing (WGS) on food safety management -23-25 May 2016, Rome, Italy.
CD Genomics provides viral genome sequencing service within Illumina and PacBio Platforms. We can create high-quality de novo assembly of large viral genomes and highest possible data quality at low cost.
Presentation from the ECDC expert consultation on Whole Genome Sequencing organised by the European Centre of Disease Prevention and Control - Stockholm, 19 November 2015
K-mers in metagenomics
K-mers play a critical role in the exploration of metagenomic data. They have been widely used to assign taxonomic attributions to the short genomic fragments characteristic of shotgun (metagenomic) sequencing. These approaches provide an assembly-free method for profiling microbial communities, and have helped elucidate the factors driving microbial community composition across biogeochemical gradients. Advances in sequencing technology are now making it cost-effective to sequence microbial communities at sufficient depths to allow for the assembly of high-quality contigs. This has made it possible to adopt k-mer based approaches to enable reliable binning of contigs originating from a single microbial population within a community. In this session, I will present both an overview of how k-mers can be used to assign taxonomic attributions to short metagenomic reads, and discuss how these approaches have advanced to a point where population genomes can be recovered en masse from even complex microbial communities.
Design and Evaluation of a 16S-based Integrated Solution to Study Bacterial D...Thermo Fisher Scientific
Analysis of 16S sequences in microbial population gives a quick
overview of the community diversity, and is usually performed by
sequencing one or two hypervariable regions (V-regions), amplified as
a single PCR fragment. We developed a novel approach that
simultaneously surveys multiple V-regions in the 16S rRNA gene.
In the first design of PCR primer pools, V-regions 2, 3, 4, 6-7, 8 and 9
were amplified as individual ~200 bp fragments in one of two multiplex
PCR reactions. The primer pools covered more than 80% of
eubacterial sequences in the GreenGenes database with perfectly
matched primer pairs for at least one V-region. In the second design
the amplicons are longer, 300-400 bp products
Our data analysis module classified individual reads by mapping them
to the reference libraries. With the fragment sizes ranging between
200-300 bp, we achieved genus and, in many cases species level
taxonomic resolution, depending on which V-region was evaluated.
In an initial evaluation we tested the complete solution (PCR
chemistry, workflow and software) on two mock community DNA
samples from BEI resources: HM-276D - even community, with equal
number of rDNA copies for each of 20 bacteria and HM-783D–
staggered community, with variable number of rDNA copies. Several
V-regions were amplified by our primer sets for every organism in the
mock community. The number of classified reads in each V-region for
every bacteria depended on both primer complementarity and ease of
sequencing of the particular PCR fragment. Our approach of
interrogating multiple V-regions and sequencing both amplicon strands
improved system robustness against both PCR and sequencing
biases.
The 314v2 chip achieved 1:100 sensitivity (detection of all organisms
in the staggered mock community with 10^4-10^6 rDNA copies/PCR).
Increased sequencing depth (316v2 and 318v2) increased sensitivity
to 1:1000 (10^3-10^6 rDNA copies).
With human samples, we observed no PCR cross-reactivity with
human DNA and were able to identify and determine characteristic Vsignatures
of several important species. The signatures not only help
to increase the confidence in the organism presence and ID, but may
potentially enable strain differentiation.
Survey of multiple V-regions is useful in monitoring changes in the
microbial community composition
CRISPR-Cas9 is a genome editing tool that is creating a buzz in the science world. It is faster, cheaper and more accurate than previous techniques of editing DNA and has a wide range of potential applications.
RNA-based screening in drug discovery – introducing sgRNA technologiesCandy Smellie
RNA-based screening in drug discovery
Use of X-MAN™ isogenic cell lines in RNAi screening approaches
Comparison of siRNA and sgRNA screening approaches
The challenges of genome-wide CRISPR-Cas9 knockout (GeCKO) screening
Using CRISPR-Cas9 sgRNA for target identification and patient stratification
Moving from screening hit to target validation
sgRNA screening: not just KOs