Monthly Archives: August 2017

By David Cruz Senior Correspondent

You might just be hearing about it, but this technology has the potential to change pretty much everything and everyone in the world.

CRISPR is a programmable nucleus, so the power of it is. And what makes it work so well for gene editing and some of the techniques we use is this protein can use this small segment of RNA to find a site in the genome and cut it. And by making this DNA break in the genome is what allows us to introduce sequences and repair, explained Peter Romanienko, the managing director of the Genome Editing Core Facility at Rutgers University.

If you think of the genome as a Word document, youre basically cutting and pasting. And its that simplifying of the process that makes the potential for life-saving cures in cancer, HIV or heart disease possible.

You have this linear code of DNA and the CRISPR is programmable, so you can create a segment of this and say I want you to cut here, or I want you to cut there. So you can cut anywhere, and thats the power of it, he added. You can target it to any site in the genome to study any gene.

While Romanienko says the Genome Editing Core Facility at Rutgers University uses CRISPR mainly to study cells to fight disease, it has also raised concerns among some ethicists, who fear that the technology, available pretty much around the world, can fall into the hands of individuals, or states, that would unleash its power towards not so benevolent ends.

One could liken it to nuclear energy in that it serves a great purpose and is, in theory, clean burning energy, but it can also blow up the world.

I think if were smart enough to come up with a technology, I think were smart enough to control it we should be smart enough to control it. And if we cant, we shouldnt use that technology. Its like a cell phone. Its a very great tool, but you cant text and drive, Romanienko said.

But, you know, people text and drive all the time, and while the law in some countries, like ours, prohibits taxpayer funding of testing on human embryos, private funding is available around the world. In fact, a privately-funded team in Oregon did exactly that, editing the DNA of a human embryo to remove the gene for heart disease. Again, sounds like a good thing, but whats to stop anyone from editing embryonic DNA to create, for lack of a better term, a master race.

People have been manipulating genomes for hundreds of years, crossing different plants and animals, livestock, so its nothing new that weve been doing. Its just the precision with which we can do it is the main difference, noted Romanienko. If you can create it, you have to be responsible for it.

Scientists have been changing our world since the ancient Greeks. You could say the world has done OK since then, but Hippocrates never had the ability to edit the genome, and its worth wondering what kind of world this would be if he had.

The rest is here:
Rutgers scientists working on technology that could, literally, change the world - NJTV News

August 9, 2017 The importance of standards is dramatically illustrated when they dont exist or are not commonly accepted. an international team led by DOE JGI researchers has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases. Credit: Zosia Rostomian, Berkeley Lab Creative Services

During the Industrial Revolution, factories began relying on machines rather than people for mass production. Amidst the societal changes, standardization crept in, from ensuring nuts and bolts were made identically to maintain production quality, to a standard railroad gauge used on both sides of the Atlantic. The importance of standards is dramatically illustrated when they don't exist or are not commonly accepted, e.g., Macs, vs. PCs, or even pounds vs. kilograms.

More than a century after the Industrial Revolution, advances in DNA sequencing technologies have caused similarly dramatic shifts in scientific research, and one aspect is studying the planet's biodiversity. Microbes play crucial roles in regulating global cycles involving carbon, nitrogen, and phosphorus among others, but many of them remain uncultured and unknown. Learning more about this so-called "microbial dark matter" involves extracting microbial genomes from the amplified DNA of single cells and from metagenomes. As genomic data production has ramped up over the past two decades and is being generated on various platforms around the world, scientists have worked together to establish definitions for terms such as "draft assembly" and data collection standards that apply across the board. One critical term that needs standardization is "metadata," defined simply as "data about other data." In the case of sequence data, metadata can encompass what organism or cell was sequenced, where it came from, what it was doing, quality metrics, and a spectrum of other characteristics that add value to the sequence data by providing context for it and enabling greater biological understanding of the significance of the sequence.

Published August 8, 2017 in Nature Biotechnology, an international team led by researchers at the U.S. Department of Energy Joint Genome Institute (DOE JGI), a DOE Office of Science User Facility, has developed standards for the minimum metadata to be supplied with single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) submitted to public databases. "Over the last several years, single-cell genomics has become a popular tool to complement metagenomics," said study senior author Tanja Woyke, head of the DOE JGI Microbial Genomics Program. "Starting 2007, the first single-cell genomes from environmental cells appeared in public databases and they are draft assemblies with fluctuations in the data quality. Metagenome-assembled genomes have similar quality challenges. For researchers who want to conduct comparative analyses, it's really important to know what goes into the analysis. Robust comparative genomics relies on extensive and correct metadata."

Categories of Genome Quality

In their paper, Woyke and her colleagues proposed four categories of genome quality. Low-Quality Drafts would be less than 50 percent complete, with minimal review of the assembled fragments and less than 10 percent contaminated with non-target sequence. Medium-Quality Drafts would be at least 50 percent complete, with minimal review of the assembled fragments and less than 10 percent contamination. High-Quality Drafts would be more than 90 percent complete with the presence of the 23S, 16S and 5S rRNA genes, as well as at least 18 tRNAs, and with less than 5 percent contamination. The Finished Quality category is reserved for single contiguous sequences without gaps and less than 1 error per 100,000 base pairs.

The DOE JGI has generated approximately 80 percent of the over 2,800 SAGs and more than 4,500 MAGs currently accessible on the DOE JGI's Genomes OnLine Database (GOLD). DOE JGI scientist and study first author Bob Bowers said many of the SAGs already in GOLD would be considered Low-Quality or Medium-Quality Drafts. These are highly valuable datasets, though for some purposes, researchers might prefer to use High-Quality or Finished datasets. "Single cell and metagenomic datasets vary greatly in their overall quality. However, in cases where a low quality, fragmented genome is the only representative of a new branch on the tree of life, some data is better than no data," he added. "Bringing up the proposed categories will force scientists to carefully consider genome quality before submission to the public databases."

From Proposal to Community Implementation

Moving from a proposal in print to implementation requires community buy-in. Woyke and Bowers conceived of the minimum metadata requirements for SAGs and MAGs as extensions to existing metadata standards for sequence data, referred to as "MIxS," developed and implemented by the Genomic Standards Consortium (GSC) in 2011. The GSC is an open-membership working body that ensures the research community is engaged in the standards development process and includes representatives from the National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI). This is important since these are the main data repositories where the minimum metadata requirements are implemented. By working directly with the data providers, the GSC can assist both large-scale data submitters and databases to align with the MIxS standard and submit compliant data.

"Other key public microbiome data management systems such as MG-RAST, IMG and GOLD have also adapted the MIxS standards," said Nikos Kyrpides, head of the DOE JGI Prokaryote Super Program and GSC Board member. He notes that as part of the DOE JGI's core mission, the Institute has been involved in organizing the community to develop genomic standards. "The GSC has been instrumental in bringing the community together to develop and implement a growing body of relevant standards. In fact, the need to expand MIxS to uncultivated organisms was identified in one of the recent GSC meetings at the DOE JGI."

"These extensions complement the MIxS suite of metadata standards by defining the key data elements pertinent for describing the sampling and sequencing of single-cell genomes and genomes from metagenomes," said GSC President and study co-author Lynn Schriml of the Institute of Genome Sciences at University of Maryland School of Medicine. "These standards open up a whole new area of metadata data exploration as the vast majority of microbes, referred to as microbial dark matter, are currently not described within the MIxS standard."

She described the group and their mission as community-driven. "I think it helps that the people developing standards are the people conducting the studies," she said. "We have a vested interest in the data. Research is growing and expanding and it is critical that we capture this data in a rigorous way. Developing these novel metadata standards enables researchers to consistently report the most critical metadata for analysis. Capturing data using controlled vocabularies facilitates data consistency, thus making the databases richer and reusable." And in the end, it is to be hoped, sequence data accompanied by agreed-on standards for metadata will mean the same thing to everyone who wants to use it.

Explore further: New database of DNA viruses and retroviruses debuts

More information: Robert M Bowers et al, Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea, Nature Biotechnology (2017). DOI: 10.1038/nbt.3893

There are more microbes in, on, and around the planet than there are stars in the Milky Way. Microbes affect food production; air quality; natural breakdown of plants, trees and biomass; soil quality for agriculture; and ...

A new publically available database will catalog metadata associated with biologic samples, making it easier for researchers to share and reuse genetic data for environmental and ecological analyses.

The number of microbes in a handful of soil exceeds the number of stars in the Milky Way galaxy, but researchers know less about what's on Earth because they have only recently had the tools to deeply explore what is just ...

In a series of four articles published in the Database issue of the Nucleic Acids Research journal, DOE JGI researchers report on the latest updates to several publicly accessible databases and computational tools that benefit ...

Single cell genomics and metagenomics are pioneering techniques that have helped researchers assess environmental microbial community structure and function. As projects applying these techniques scale up, however, researchers ...

Massive amounts of data require infrastructure to manage and store the information in a manner than can be easily accessed for use. While technologies have scaled to allow researchers to sequence and annotate communities ...

If you've got plenty of burgers and beers on hand and your own stomach is full, an uninvited guest at your neighborhood barbecue won't put much strain on you.

Researchers at Newcastle University (UK) found that European sea bass experienced higher stress levels when exposed to the types of piling and drilling sounds made during the construction of offshore structures.

Small, seemingly insignificant mutations in fruit flies may actually hold clues as to how a species will evolve tens of millions of years in the future.

Most of us have had the experience of backing away when someone has stepped inside the bounds of our personal space. But, until now, little has been understood about the mechanisms that allow us to determine when someone ...

During the Industrial Revolution, factories began relying on machines rather than people for mass production. Amidst the societal changes, standardization crept in, from ensuring nuts and bolts were made identically to maintain ...

The color of T-shirts people wear affects escape behavior in western fence lizards, according to a study published August 9, 2017 in the open-access journal PLOS ONE by Breanna Putman from University of California, Los Angeles ...

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Defining standards for genomes from uncultivated microorganisms - Phys.Org