Category Archives: Transhuman News

CRISPR technology for genome editing - Mandarin
CRISPR, a pioneering genome-editing technique, technology will allow AstraZeneca to identify and validate new drug targets in preclinical models that closely...

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CRISPR technology for genome editing - Mandarin - Video

Britains parliament allows human genome manipulation for first time
Mother #39;s day may be about to get more complicated in the UK after parliamentMother #39;s day may be about to get more complicated in the UK after parliamentCom...

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Britains parliament allows human genome manipulation for first time - Video

Nature lovers are fascinated by the increasing number of singing birds when spring is approaching. Scientists also take advantage of this seasonal phenomenon because they are able to investigate the underlying mechanism; however the evolutionary and molecularbiological background is largely unknown. A team of researchers from the Max Planck Institute for Ornithology in Seewiesen and from the Max Planck Institute for Molecular Genetics in Berlin have now identified the genome of the canary. With these data they were able to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds.

Canaries have been domesticated since the 15th century and are the descendants of the wild canary that lives on the Azores, Madeira and Canary Islands in the North Atlantic Ocean. Like their wild ancestors, domesticated canaries sing stereotyped songs under long-day (breeding) conditions and more variable songs under short-day (non-breeding) photoperiods. The canary has become a preferred model to investigate the neurological changes affecting hormone-dependent song. This is because it has a pronounced reproductive season, with seasonal changes in song and steroid hormone concentrations, and a varying degree of brain plasticity between the breeding and the non-breeding season.

A team of researchers from the department of Behavioural Neurobiology around Manfred Gahr at the Max Planck Institute for Ornithology in Seewiesen and from the Sequencing Core Facility under guidance of Bernd Timmermann from the Max Planck Institute for Molecular Genetics in Berlin together with colleagues from Brazil and the UK now have studied how hormone-sensitive gene regulation has evolved in songbirds. The work resulted in the first high quality assembly and annotation of a female canary genome. In birds, females are the 'heterogametic' sex (ZW) and therefore the analysed genome sequence contained both types of sex chromosomes, says Heiner Kuhl from the Max Planck Institute for Molecular Genetics.

Whole genome alignments between the canary and already identified genomes throughout the bird taxa showed that on a global scale bird genomes are quite similar. However, differences appeared when comparisons were conducted on a finer scale. For example, at the level of the nucleotide there are considerable species differences, which can impact small genetic sequences, such as steroid hormone receptor binding sites. Such differences in these regions might lead to major differences in gene regulation, even between closely related species, says Carolina Frankl-Vilches from the Max Planck Institute for Ornithology.

Following this global analysis the scientists focused on gene networks that had three characteristics -- were showing enrichment or under- representation in the expression profiles of the song control regions HVC and RA, showed seasonality, and were testosterone-sensitive. To verify whether the hormone-sensitive elements among these genes are specific for the canary, they also looked at the genes of the zebra finch because this species did not evolve hormone-sensitive song expression. Among all HVC expressed genes, including the seasonal and testosterone-induced gene pools, many were strictly canary-specific. These analyses reveal specific evolutionary changes in different parts of the song system that control seasonal singing behaviour. Thus, in the canary, those genes that are sensitive for testosterone and estrogen, and are also involved in the rewiring of neurons, might be crucial for re-differentiation of the underlying neuronal substrate, such as HVC, leading to seasonal song patterning. The present study demonstrates the need for high-quality genome assembly to detect the evolution of genes in comparative studies, says the coordinator of the study, Manfred Gahr from the Max Planck Institute for Ornithology.

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The above story is based on materials provided by Max-Planck-Gesellschaft. Note: Materials may be edited for content and length.

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Mapping of the canary genome

New software developed at Nationwide Children's Hospital in Ohio can take raw sequence data on a person's genome and search it for disease-causing variations in a matter of hours, which its creators claim puts it ahead of the pack as the fastest genome analysis software around. They believe that this makes it now feasible to do large-scale analysis across entire populations.

Whereas it took 13 years and cost US$3 billion to sequence a human genome for the first time, senior author Peter White notes that now "even the smallest research groups can complete genomic sequencing in a matter of days." The chokepoint lies in the next step: calibrating and analyzing the billions of generated data points for genetic variants that could lead to diseases.

White and his team tackled the problem by automating the analytical process in a computational pipeline they called Churchill. Churchill spreads each analysis step across multiple computing instances a process its creators call balanced regional parallelization with special care taken to preserve data integrity so that results are "100 per cent reproducible."

Tests showed that Churchill can analyze a whole genome sequence in as little as 90 minutes from a raw FASTQ text-based format through to identifying variant cells at high confidence. An exome, which contains the bulk of disease-causing variants despite being a mere one per cent of the whole genome, can be analyzed in less than an hour. Churchill's performance was validated against the National Institute of Standards and Technology's benchmarks, with scores of 99.7 per cent on sensitivity, 99.99 per cent on accuracy, and 99.66 per cent on diagnostic effectiveness.

While the goal of the research was to create an ultra-fast analysis pipeline, White and his team found an unexpected benefit. Churchill scales efficiently across many servers, which makes it possible to perform population-scale analysis.

They took the first phase of the raw data generated by the 1000 Genomes Project an international research collaboration started in 2008 to establish an extensive public catalog of human genetic variation across the globe and put Churchill to task on all 1,088 whole genome samples across a cluster of computers in Amazon Web Services' Elastic Compute Cloud. Churchill averaged a mere nine minutes per genome in its week-long analysis, which the researchers note compares favorably to a similar analysis performed in 2013 on a Cray XE6 supercomputer.

The Cray supercomputer test analyzed 61 whole genomes in two days, at an average of 50 minutes per genome around five times longer than Churchill required in its cloud test.

"Given that several population-scale genomic studies are underway, we believe that Churchill may be an optimal approach to tackle the data analysis challenges these studies are presenting," White says.

The Churchill algorithm has been licensed to a company called GenomeNext, which adapted the technology for use in a commercial setting. People can get their genome sequenced in a local lab or clinic and then upload the raw data to the GenomeNext system for analysis.

A paper describing the Churchill algorithms and research was published in the journal Genome Biology. The Churchill software is also available, for research purposes only, via its project page.

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Software analyzes human genome in as little as 90 minutes

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One of the most exciting scientific advances made in recent years is CRISPRthe ability to precisely edit the genome of cells. However, although this method has incredible potential, the process is extremely inefficient. Fortunately, scientists at the Gladstone Institutes have discovered a way to enhance the efficiency of CRISPR with the introduction of a few key chemical compounds.

"Currently, there is a trade-off with CRISPR: the technology is very precise, but it is also quite inefficient," says first author Chen Yu, a postdoctoral fellow at the Gladstone Institutes. "We improved this by introducing small molecules that are able to maintain the precision of the technology while boosting its efficiency."

In CRISPR, a protein is delivered into the cell that cuts the genome at an exact specified location. The cell's DNA can then either fuse back together after the faulty gene is removed, or scientists can insert a new gene in the old one's place, substituting bad DNA for good.

Published in the journal Cell Stem Cell, the researchers, in collaboration with co-senior author Lei Stanley Qi, PhD, at Stanford University, successfully identified two small molecules that significantly improve the insertion of new genetic information into a cell's DNA. During their search, the scientists also discovered two compounds that inhibit insertion but enhance deletion of DNA, suggesting the two processes are competitive actions in the cell.

Notably, the researchers were able to accomplish this genome manipulation in several different cell lines, including induced pluripotent stem cells and tissue-specific cells. This is particularly important as it indicates the method can be used in a variety of cell types to create disease models and contribute to the discovery of new disease-specific therapeutics.

Senior author Sheng Ding, PhD, a senior investigator at Gladstone, says that the potential of this discovery extends beyond improving the efficiency of CRISPR. "This study is the first to show that we can successfully manipulate genome engineering using small molecules. This gives us greater capability, enabling us to tune the machinery and also turn it on or off with chemicals, which has important implications for regulating the genome editing process."

Explore further: Bioengineers develop tool for reprogramming genetic code

Biology relies upon the precise activation of specific genes to work properly. If that sequence gets out of whack, or one gene turns on only partially, the outcome can often lead to a disease.

A powerful "genome editing" technology known as CRISPR has been used by researchers since 2012 to trim, disrupt, replace or add to sequences of an organism's DNA. Now, scientists at Johns Hopkins Medicine have shown that ...

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Improving genome editing with drugs