Sentences with phrase «using deep sequencing»

Grant 1592: Investigation into the Genetics of Scottie Cramp: Sequencing of Associated Chromosomal Regions Dr. Natasha J Olby, VetMB PhD Project Goal: Following up on previous research funded by CHF, the goal of this project is to use deep sequencing techniques to identify genetic mutations associated with Scottie Cramp.

Not exact matches

«This is a story that couldn't have happened five years ago, but with the evolution of deep sequencing, we were able to use the technology at just the right time and harness it with what we've been working on for decades,» he says.

Using mass DNA sequencing, he recently identified resistance genes even in bacteria in pristine permafrost and deep caves.

In this study that used deep DNA sequencing of bacterial specific genes, the guts of both males and females exposed to lead had all of the similar complexity in microbiota as those not exposed.

Roswell Park Cancer Institute (RPCI) researchers used deep T - cell receptor (TCR) sequencing to evaluate the clonal composition of TILs and identify novel prognostic biomarkers in ovarian cancer.

This «deep sequencing» technique has been used to characterize mixtures of microbes living in environments such as oceans and animal guts.

Described in the January 7th issue of Neuron, the technique uses «deep,» highly sensitive whole - genome sequencing of single neurons and a new technology that identifies inserted bits of DNA caused by retrotransposons, one of several kinds of so - called somatic mutations that can arise as the brain develops.

The researchers got around that problem by using deep, next - generation DNA sequencing, allowing them to pick up on even the smallest changes.

Here they photographed organisms from deep - water samples and used technology to sequence the genomes of these single - celled organisms.

They then comprehensively analyzed the changes in the whole genome and epigenome using next generation deep sequencing.

Extracted nucleic acid was amplified using a random PCR method to generate cDNA libraries for Virochip and deep sequencing analyses as previously described [18], [21].

TFUMseq (Temporal FUnctional Metagenomics sequencing) uses shotgun libraries cloned into a recipient bacterial species, tracked over time in gnotobiotic mice by deep sequencing and computational methods.

In this study, the anti-HIV immune responses in immunized llamas were studied via deep sequencing analysis using broadly neutralizing monoclonal HCAbs as a guides.

Using sophisticated statistical analysis of the massive «DNA deep sequencing» data enabled the team to trace the evolutionary forces that shaped these natural Synechococcus populations.

In parallel, we use high throughput sequencing methods to obtain both deep phylogenetic rDNA / rRNA tag data and metagenomic and metatranscriptomic functional profiles from size fractions covering the entire plankton community from viruses to fish larvae (Figure 2B and 2C).

Roswell Park Comprehensive Cancer Center researchers used deep T - cell receptor (TCR) sequencing to evaluate the clonal composition of TILs and identify novel prognostic biomarkers in ovarian cancer.

This has implications for the use of deep sequencing analysis of immunization studies: if the sequence of J3 had been used as a reference to filter the sequences from llama 9 (without prior screening of VHH from llama 9), no J3 - like antibodies would have been found, 3E3 would not have been identified and it would have falsely appeared that the immunization of llama 9 had failed.

To facilitate whole - genome sequencing of TMAdV, we prepared amplified cDNA / DNA libraries for deep sequencing from lung tissue and a lung swab sample from 2 different monkeys using previously published protocols [23], [52].

Our approach uses metagenomic DNA to construct large ‐ scale heterologous expression libraries that are tracked over time in vivo by deep sequencing and computational methods.

In addition, the significant number (> 1000) novel models that came from RNA - Seq that were absent from the zebrafish cDNAs suggests that the deep sequencing offered by RNA - Seq can be used to expand the gene annotation of even well - studied model organisms.

Second, the lab is studying how early life stress impacts both the transcriptome in stress - related brain regions using deep - sequencing methods and the addictive potential of the prescription opioid oxycodone using the drug self - administration paradigm, in male and female rats.

The Ag1000G project is using whole genome deep sequencing to provide a high - resolution view of genetic variation in natural populations of A. gambiae.

We use RNAi screening and deep sequencing to identify components and understand their interactions.

For the XMRV - positive and XMRV - negative prostate cancer samples, randomly amplified cDNA was prepared for deep sequencing using a variation of Illumina's TruSeq protocol (Illumina) as previously described [2], [45].

His contributions include the first use of genetic methods to identify an infectious agent; implication of West Nile virus as the cause of the encephalitis in North America in 1999; invention of MassTag PCR and the first panmicrobial microarray; first use of deep sequencing in pathogen discovery; and molecular characterization of more than 600 viruses.

A consensus sequence based on mapped deep sequencing reads was generated for each of the prostate cancer XMRV genomes and used to correct errors in the previously published sequences, with the requirement of no ambiguity at each discrepant nucleotide position.

In this study, we investigated the putative association between XMRV and prostate cancer using a combination of microarray, PCR, FISH, serological, and deep sequencing approaches.

Raw single reads (and their mate pairs) from deep sequencing libraries corresponding to 3 XMRV - positive samples [VP35, 14,589,296 reads; VP42, 14,573,990 reads; and VP62 (2006), 18,308,352 reads] and 3 XMRV - negative samples [VP10, 5,270,536 reads; VP30, 4,378,204 reads; and VP62 (2012), 3,985,692 reads] were then stripped of adapter and primer sequences and aligned to the CRS mitochondrial genome using BLASTn (word size = 11, E-value = 1 × 10 − 10).

We can leverage the lowering cost of gene sequencing to interrogate cells at a deeper level, and use computational tools to analyze the resulting data.

For example, by deep sequencing bacterial DNAs from diseased and healthy subjects, the inventors propose that features associated with certain microbiome compositional and / or functional features (e.g., the amount of certain bacteria and / or bacterial sequences corresponding to certain genetic pathways) can be used to predict the presence or absence of an autoimmune condition.

Warm up with a flowing sequence of repetitive hip openers, deepen your focus using a block with long - held poses and explore the deep release benefits of pigeon pose.

Use deep conscious breaths as you follow this sequence to lift your mood.

Recall the painful sequence in 2015's «Avengers: Age of Ultron» when Scarlet Witch (Elizabeth Olsen) used her hypnotic powers to push the team into their deepest nightmares?

I prefer the latter from a historical perspective, but what embellishments there are in the 5.1 mix (a more aggressive use of the rear channels — especially in the exterior sequences; deeper rumbles from the subwoofer) prove compelling and thoughtfully - engineered.

Harvard Graduate School of Education will work with the Strategic Education Research Partnership and other partners to complete a program of work designed to a) investigate the predictors of reading comprehension in 4th - 8th grade students, in particular the role of skills at perspective - taking, complex reasoning, and academic language in predicting deep comprehension outcomes, b) track developmental trajectories across the middle grades in perspective - taking, complex reasoning, academic language skill, and deep comprehension, c) develop and evaluate curricular and pedagogical approaches designed to promote deep comprehension in the content areas in 4th - 8th grades, and d) develop and evaluate an intervention program designed for 6th - 8th grade students reading at 3rd - 4th grade level.The HGSE team will take responsibility, in collaboration with colleagues at other institutions, for the following components of the proposed work: Instrument development: Pilot data collection using interviews and candidate assessment items, collaboration with DiscoTest colleagues to develop coding of the pilot data so as to produce well - justified learning sequences for perspective - taking, complex reasoning, academic language skill, and deep comprehension.Curricular development: HGSE investigators Fischer, Selman, Snow, and Uccelli will contribute to the development of a discussion - based curriculum for 4th - 5th graders, and to the expansion of an existing discussion - based curriculum for 6th - 8th graders, with a particular focus on science content (Fischer), social studies content (Selman), and academic language skills (Snow & Uccelli).

There are a sequence of lessons using the wonderful picture book Dougal's Deep Sea Diary alongside the Endless Ocean game.

Highlights of Relevant Experience: Managed matrix team of U.S. and U.K. scientists in first ever large - scale use of US DNA TAP Store integrated liquid handling capabilities to support deep sequencing technology project to generate data for genetic rare variants and for potential asset realignment with project delivery of more than 12,000 samples prepared under extremely tight time lines for GlaxoSmithKline.

We use deep learning to diagnose diseases from radiology and pathology imaging, and to create personalized cancer treatment plans from histopathology imaging and genome sequences.