Daily Archives: April 21, 2017

Sandy Maliki, a pure desert dingo and winner of the World's Most Interesting Genome competition, will have her DNA decoded.

Meet Sandy the dingo, owner of the world's most interesting genome.

The wild-born, pure Australian desert dingo recently took first place in the World's Most Interesting Genome competition, and will have her DNA decoded thanks to the Pacific Biosciences SMRT Grant Program. The grant provides genome sequencing for "a particularly fascinating plant or animal."

In a public poll, Sandy secured 41 percent of the votes to beat out a pit viper, a solar-powered sea slug, an explosive beetle and a pink pigeon for the top prize.

Sandy's DNA could offer researchers insight into the process of domestication, according to project leader Bill Ballard, an evolutionary biologist at the University of New South Wales (UNSW). [10 Things You Didn't Know About Dogs]

"Sandy is truly a gift to science. As a rare, wild-born pure dingo, she provides a unique case study," Ballard, who submitted the bid to sequence Sandy's DNA, said in a statement. "Pure dingoes are intermediate between wild wolves and domestic dogs, with a range of non-domesticated traits. So sequencing Sandy's genome will help pinpoint some of the genes for temperament and behavior that underlie the transition from wild animals to perfect pets."

Dingoes were not domesticated by indigenous peoples after being introduced to Australia about 5,000 years ago, according to the UNSW researchers. However, interbreeding with wild and domestic dogs has made pure wild dingoes a rare find.

At 3 weeks old, Sandy, her sister and her brother were discovered in poor health in the Australian desert, and their parents could not be found. The wild pups were taken in by local animal lovers Barry and Lyn Eggleton, who have hand-reared the dingoes since their rescue in 2014.

The sequencing of Sandy's pure-dingo DNA will test of Charles Darwin's 1868 theory on the process of domestication. Darwin theorized that domestication could occur via unconscious selection (a result of nonintentional human influence) and artificial selection (breeding for specific traits).

"This project will reveal the DNA changes between wolves and dingoes (unconscious selection) and dingoes and dogs (artificial selection)," Ballard said in the statement.

Beyond its evolutionary value, sequencing Sandy's genome will give researchers a better understanding of dingo genetics, Ballard said. This could aid conservation efforts to protect the wild canines and improve tests for their genetic purity, he added.

Original article on Live Science.

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This Dingo Has the World's Most Interesting Genome - Live Science

April 20, 2017

Twenty years ago, the protein complex cohesin was first described by researchers at the IMP. They found that its shape strikingly corresponds to its function: when a cell divides, the ring-shaped structure of cohesin keeps sister-chromatids tied together until they are ready to separate.

Apart from this important role during cell-divison, other crucial functions of cohesin have been discovered since - at the IMP and elsewhere. One of them is to help fold the DNA, which amounts to about two meters per nucleus, into a compact size by way of creating loops. "We think that the cohesin-ring clamps onto the DNA-strand to hold the loops in place", says IMP-director Jan-Michael Peters whose team worked on the project.

The chromatin-loops are not folded at random. Their exact shape and position play an important role in gene regulation, as they bring otherwise distant areas into close contact. "For a long time, scientists were mystified by how regulatory elements the enhancers are able to activate distant genes. Now we think we know the trick: precisely folded loops allow enhancers to come very close to the genes they need to regulate", says Peters. Research results point to cohesin as mediator of this process. Jan-Michael Peters and his team have already shown that the cohesin complex accumulates in areas where loops are formed.

Several scientists recently proposed a so-called "loop-extrusion mechanism" for the folding of chromatin. According to this hypothesis, cohesin is loaded onto DNA at a random site. The DNA strain is then fed through the ring-shaped complex until it encounters a molecular barrier. This element, a DNA-binding protein named CTCF, acts much like a knot tied in a rope and stops the extrusion-process at the correct position. Defined genome-sequences that were previously located far apart are now next to each other and can interact to regulate gene expression.

In Nature online this week, IMP-researchers publish data that support the existence of such a mechanism. First author Georg Busslinger, a PhD-student in Jan-Michael Peters' team, showed in mouse cells that cohesin is indeed translocated on DNA over long distances and that the movement depends on transcription, suggesting that this may serve as a 'motor'.

"The loop extrusion hypothesis has opened up a whole new research area in cell biology and we will probably see many more papers published on this topic in the future", comments Jan-Michael Peters. Understanding cohesin-function is also relevant from a medical perspective since a number of disorders, including certain cancers, are associated with malfunctions of the protein-complex.

Explore further: Regulator of chromosome structure crucial to healthy brain function and nerve development

More information: Georg A. Busslinger et al. Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl, Nature (2017). DOI: 10.1038/nature22063

In the nucleus of eukaryotic cells, DNA is packaged with histone proteins into complexes known as chromatin, which are further compacted into chromosomes during cell division. Abnormalities in the structure of chromosomes ...

Researchers at the IMP Vienna discovered that cohesin stabilizes DNA. Jan-Michael Peters and his team at the Research Institute of Molecular Pathology (IMP) found that the structure of Chromosomes is supported by a kind of ...

The cohesin molecule ensures the proper distribution of DNA during cell division. Scientists at the Research Institute of Molecular Pathology (IMP) in Vienna can now prove the concept of its carabiner-like function by visualizing ...

Ten years ago, researchers at the IMP - a basic research institute in Vienna - discovered a fundamental and amazingly plausible mechanism of cell division. They identified a protein complex, which, as a ring-shaped molecule, ...

Protein factors are responsible for organizing chromosomes inside the nucleus in three dimensions (3D), forming a shape like a gift bow, with proteins aggregating as the central 'knot' holding the ribbon-like loops of DNA ...

Within almost every human cell is a nucleus six microns in diameterabout one 300th of a human hair's widththat is filled with roughly three meters of DNA. As the instructions for all cell processes, the DNA must be ...

Scientists at the Centre for Genomic Regulation (CRG) in Barcelona and the Josep Carreras Leukaemia Research Institute and The Institute for Health Science Research Germans Trias i Pujol (IGTP) in Badalona, Spain, have discovered ...

Nematodes are microscopic worms that fall into an often ignored corner of the animal kingdom. While many of them are parasitic, meaning they live inside other organisms, they also help control diseases in humans and kill ...

Gut microbes play wide-ranging roles in health and disease, but there has been a lack of tools to probe the relationship between microbial activity and host physiology. Two independent studies in mice published April 20 in ...

The tobacco hawkmoth Manduca sexta is an important pollinator of the wild tobacco species Nicotiana attenuata; yet hungry larvae hatch from the eggs these moths lay on the leaves. An interdisciplinary team of scientists at ...

Proper nutrition can unleash amazing powers, moms have always assured us, frequently citing Popeye the Sailor Man as evidence. Now, two University of Colorado Boulder scientists have confirmed just how potent some nutrients ...

Researchers have uncovered molecular details of how pathogenic bacteria fight back against the human immune response to infection.

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Looping the genomehow cohesin does the trick - Phys.Org

Thomas Weaver, Ph.D., Chief Executive Officer of Congenica, said: "Sapientia is already used extensively throughout the NHS in the UK as well as by clinical scientists providing reports for the 100,000 Genomes Project. Without a diagnosis, it is difficult to select the most appropriate treatment plan for a patient or make a prognosis of what the likely outcomes may be. Edico shares our vision of transforming healthcare by developing easy to use, highly automated genomics analysis solutions, and by combining our complementary technologies we aim to accelerate the clinician's ability to use genomics to diagnose a patients' disease, and make this available on a global basis."

Edico's DRAGEN Bio-IT processor has been assessed as part of University College London's (UCL) Rapid Paediatric Sequencing Project (RaPs), a pilot aimed at evaluating the use of rapid whole genome sequencing (WGS) for rare diseases in an intensive care clinical setting.

Phil Beales, Professor of Medical and Molecular Genetics at UCL, said: "For children with rare diseases and their parents, answers cannot come quickly enough. Faster answers mean less time finding a diagnosis and more time making decisions about treatment and care. After extensively testing and validating the platforms, we were impressed by the speed, accuracy and cost savings conferred. Initially, we will apply the technology to a number of clinical cases where rapid turnaround is especially critical, and ultimately envisage the solution will be widely used as we scale our efforts."

Added Pieter van Rooyen, Ph.D., Chief Executive Officer of Edico Genome: "As genomics marches towards the clinic, we recognize clinicians and researchers need easy to use, all-in-one solutions that enable genomic data to be analysed and shared quickly, easily, accurately and cost effectively. Congenica has first-hand perspective of the needs of the clinical genomics community from its extensive work with the NHS, including the Genomics England initiative, and through this new collaboration we're able to create an all-in-one, easy-to-use offering that significantly accelerates the ability of hospitals and clinical labs to move from the sequencing of a sample to a clinical diagnosis."

About Congenica

Rapid, accurate and scalable diagnosis of patients with inherited genetic diseases helps accelerate access to the best clinical treatments and prevention strategies. Congenica, a global clinical genetics software company, created Sapientia that offers Clinical Scientists, Hospitals and Clinical Labs an all in one software platform to enable scalable, accurate, fast and flexible genetic diagnostic services. Congenica is a global company, headquartered in Cambridge UK and founded by pioneering researchers from the Sanger Institute.

Clinicians and scientists are using Sapientia, a cloud-based integrated software platform to analyze and interpret genetic data linked to patients' phenotypes. The software is designed to support clinical interpretation workflows and generate professional diagnostic reports. Sapientia handles the main data inputs including BAM, VCF and FASTQ files in many upload formats and the added flexibility to Integrate and manage customer legacy data to enhance diagnostic capabilities.

Find out more about Congenica at http://www.congenica.com or follow @Congenica.

About Sapientia

Sapientia facilitates analysis of genetic data to produce a comprehensive diagnostic report that can be linked to patients' symptoms, supporting clinical decision-making about rare genetic disease. The platform is based on pioneering research from the UK Wellcome Trust Sanger Institute, NHS clinicians and regional genetic testing laboratories, and its underlying technology has been validated by leading independent institutes and clinicians, including Genomics England Ltd.

About Edico Genome

The use of next-generation sequencing is growing at an unprecedented pace, creating a need for easy to implement infrastructure that enables rapid, accurate and cost-effective processing and storage of this big data. Edico Genome has created a patented, end-to-end platform solution for analysis of next-generation sequencing data, DRAGEN, which speeds whole genome data analysis from hours to minutes while maintaining high accuracy and reducing costs. Top clinicians and researchers are utilizing the platform to achieve faster diagnoses for critically ill newborns, cancer patients and expecting parents waiting on prenatal tests, and faster results for scientists and drug developers.

For more information, visit http://www.EdicoGenome.com or follow @EdicoGenome.

About DRAGEN

The DRAGEN platform features optimized algorithms for mapping, alignment, sorting, variant calling and more. Multiple end-to-end, clinical-grade pipelines are available from Edico, including genome/exome, cancer, transcriptome/RNA-seq, structural variant, copy number variant, epigenome/methyl-seq, metagenome/microbiome, joint genotyping and third-party pipelines such as GATK 3.6. The platform is flexible and allows for customization of algorithms and existing pipelines. Best-in-class solutions for onsite, cloud or hybrid cloud analysis have been created through partnerships with top technology companies, includingIntel,IBM,Dell EMC, andAmazon Web Services.

To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/congenica-and-edico-genome-partner-to-speed-analysis-from-dna-to-diagnosis-for-inherited-diseases-300442461.html

SOURCE Edico Genome

http://www.edicogenome.com

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Congenica and Edico Genome Partner to Speed Analysis from 'DNA ... - PR Newswire (press release)

THE VENEMA CHAPTERS

Chapter Two provides us with a useful analogy about the development over time incrementally of a language (e.g. the word treuth becomes truthe and then truth) and the development of a human genetic code. While languages can change rather quickly, biological speciation and change takes place over thousands of years and herein lies another problem: 1) no one is around that long to observe the change, indeed whole civilizations rise and fall in the time it takes for even an incremental change of that sort; 2) no one WAS around when this process began, in fact Venema is clear enough that even the fossil record only goes back 200,000 years max, but evolutionary theory requires a much much longer timeline to account for all the genetic permutations and combinations. Thus, we are talking about extrapolation back in time based on modern science, when the actual empirical observation of the change has not taken place over the time period required. 3) the assumption is that things are operating now, as they always have done according to the modern theories of evolution and natural development. But alas, we have no time machine to go back and check the math and the genetics from long, long ago. Again, no room is allowed for God to tinker with the process along the way, he simply set it in motion and is observing. But what about that language analogy Venema wants to use?

Evolutionary theory can be guilty of the etymological fallacy, assuming that notable similarities between things must be caused by a shared common ancestry. Since Venema uses the analogy with language, I shall do the same at this point. Lets take the English word bare, which in Old English was baer, very close, and having exactly the same letters as bear. Ah ha, you say, these two words must share a common ancestor! Not a bit of it. Bare seems to come from the Dutch baar, and ultimately from the proto-Germanic bazaz. By contrast bear comes from the old word for brown or the brown one; beron in proto-Germanic or in old Norse bjorn, like the current Scandanvian name.

Genetics has done a wonderful job of showing lots of similarities in the letters etc. of the genetic code. Its when they try to explain the similarities that the train comes off the tracks. There are other possible, legitimate explanations for similarities other than they must share a common ancestor.

Imagine two builders who intend to build two different buildings, serving different purposes. But the construction materials are exactly the samecinder blocks, boards, shingles, electrical wires, plumbing and so on. One building is an exercise gym, the other building is an apartment complex. One building is single story, the other is a high rise. Would anyone actually want to say that Building B came from or is an evolved form of Building A, just because they shared lots of common materials or building blocks? No. Similarity of make-up is no proof of derivation.

DNA, genes, genomes, tell us a lot about the building blocks that go into the making of all sorts of creatures on earth. Detailed genetic study can show possible connections based on similar genetic patterns and codes. But we all know the problem of coming up with a very good hypothesis, or even a theory (a hypothesis that provides the best explanation of a particular sort for the known facts on the ground), that does not take into account all the evidence. You can argue consistently and coherently with and within a certain circle of evidence, and be incorrect, because you have not taken into account (or in some cases even deliberately eliminated) some of the evidence.

Continued here:
Adam and the Genome Part Four - Patheos (blog)