Daily Archives: March 6, 2017

Ms. Smith (not her real name) is a freelance writer and programmer with a special and somewhat personal interest in IT privacy and security issues.

Network World | Mar 6, 2017 9:03 AM PT

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DNA is supposed to be the answer for solving cold cases. For example, Wisconsin police have turned to DNA to help solve a 42-year-old cold case of Baby Sarah. Recently in Niagara Falls, cops found the man responsible for a smash and grab robbery committed 11 years ago, in 2006, via DNA which the man had been ordered to submit for unrelated offences. But it takes some state labs a year-and-a-half to process DNA, so some police departments are bypassing the state labs and creating their own DNA databases to track criminals.

The Associated Press reported:

Dozens of police departments around the U.S. are amassing their own DNA databases to track criminals, a move critics say is a way around regulations governing state and national databases that restrict who can provide genetic samples and how long that information is held.

The actual number of police departments maintaining DNA databases is not known, as there is no state or federal oversight, but AP cited Frederick Harran, an early adopter of a local Pennsylvania DNA database, as saying there are at least 60.

To get around the 18-month wait for Pennsylvania state lab to process DNA, Harran said the DNA samples are turned into a private lab which can get the results out within a month. The private lab work is paid for via money from assets seized from criminals. To Harrans way of thinking and justifying the local DNA database, If they are burglarizing and we don't get them identified in 18 to 24 months, they have two years to keep committing crimes.

Catching crooks is not a bad thing, but not all DNA collected comes from people suspected of crimes. AP explained, Some police departments collect samples from people who are never arrested or convicted of crimes, though in all such cases the person is supposed to voluntarily comply and not be coerced or threatened.

The coercion factor may come into play such as when DNA is collected from kids. San Diego cops can collect DNA from kids if a kid will sign a consent form. The ACLU filed a lawsuit against San Diego after police collected DNA samples from minors without first obtaining parental consent or a warrant.

ACLU attorney Bardis Vakili told AP that when cops take DNA samples from kids without a court order, its hard to imagine its anything other than coerced or involuntary. I think they are trying to avoid transparency and engage in forms of surveillance. We don't know what's done other than it goes into their lab and is kept in a database.

A San Diego officer admitted that cops stopped five boys walking through a park not because they were suspected of having been involved in a crime, but because they were black juveniles wearing blue on a gang holiday. The cops told four of the boys that they could go after submitting to mouth swab and signing a consent form. The fifth boy signed and was swabbed as well before being taken into custody on charges which were dropped due to the illegal stop. Yet the cops kept the DNA.

The EFF said that targeting black children for DNA collection is a gross abuse of power and a gross abuse of technology by law enforcement. Some argue that local DNA databases are as well.

University of Arizona law professor Jason Kreig told AP, The local databases have very, very little regulations and very few limits, and the law just hasn't caught up to them. Everything with the local DNA databases is skirting the spirit of the regulations.

Its one thing for DNA to possibly be used to store all of the worlds data in one room and quite another for cops to avoid regulations by maintaining local DNA databases.Sometimes, investigators turn to familial searching searching offender databases with wider parameters to identify people who are likely to be close relatives of the person who may have committed a crime. Its even worse when you consider that some of the DNA is collected in questionable circumstances and stored for who knows how longmaybe permanently?

On the other hand, some people pay to turn in their DNA to sites willing to help trace their ancestors. The cops can just turn to those sites to request the DNA information. As Wired warned, Your relatives DNA could turn you into a suspect.

Ms. Smith (not her real name) is a freelance writer and programmer with a special and somewhat personal interest in IT privacy and security issues.

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Should police departments be able to have their own DNA databases? - Network World

The Oklahoma Genealogical Society Spring Seminar 2017 will be from 10 a.m. to 4 p.m. April 1 at the Oklahoma History Center, 800 Nazih Zuhdi Drive.

A Day with the Genetic Genealogist Blaine Bettinger, Ph.D., J.D. is the theme of the presentation. Bettinger is an intellectual property attorney and a DNA specialist and creator of the website The Genetic Genealogist online at http://www.thegenetictgenealogist.com.

His lectures will include:

Using Autosomal DNA to Explore Your Genealogy used by genealogists about 2010 to reveal hidden information which was not available in Y-DNA or mtDNA. Autosomal DNA had useful ethnicity estimates, helped with finding long-lost cousins and examining genealogical problems. This test is now a must have tool for genealogy.

Using Third-Party Tools to Analyze Your Autosomal DNA DNA testing companies provide their own analysis of test results. Third-party tools allow test-takers to learn more about their genomic heritage. This lecture will focus on some of these tools such as including admixture calculators and the identification of genetic cousins.

Begging for Spit This lecture, which is a challenge for genealogists, will provide ways to encourage family members to participate in the DNA testing.

The Science Fiction Future of Genetic Genealogy although not available now, the future of genetic genealogy will be available soon. This lecture will provide information on how companies are using DNA and genealogies to reconstruct the genomes of ancestors. The program also will provide information on how the information might be used in the future.

Blaine also is the author of books Guide to DNA Testing and Genetic Genealogy and Genetic Genealogy in Practice.

Registration fee is $50 before March 15, which includes the syllabus and lunch. Registration after March 15 is $60. The registration form is available online at okgensoc.org/events/2017SpringSeminar. Send advance registration and fee to Oklahoma Genealogical Society, P.O. Box 12986, Oklahoma City, Oklahoma 73157-2986.

If you wish to join or renew your membership in the Oklahoma Genealogical Society membership, the fee is $25 for an individual or $30 for a family membership.

If you have a question, event, idea or an experience you wish to share, email Sharon Burns at sburns@opubco.com.

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Seminar explores aspects of DNA research - NewsOK.com

Data storage technologies are having a hard time keeping up, as data in the world is doubling every two years, according to a 2014 estimate by EMC. As a result, researchers are looking at various methods to store data as a possible storage medium.

Recently, researchers Yaniv Erlich and Dina Zielinski of the Data Science Institute at Columbia University and the New York Genome Center (NYGC) unveiled a new technique that allows DNA to store more data than ever before. In nature, DNA works by storing information about different forms of life and its characteristics using four base nucleotides: A, G, C and T. DNA has been studied for a while as a possible solution for storing human-generated data.

In essence, DNA works just like your hard drive, but instead of binary ones and zeros to store digital data, it uses a quaternary base to store information about a living organisms genes. DNA is an ideal storage medium because it is ultra-compact and can last hundreds of thousands of years if kept in a cool, dry place, as demonstrated by the recent recovery of DNA from the bones of a 430,000-year-old human ancestor found in a cave in Spain.

DNA wont degrade over time like cassette tapes and CDs, and it wont become obsolete if it does, we have bigger problems, said Yaniv Erlich from Columbia University.

The researchers showed how an algorithm designed for streaming video on a cellphone can unlock DNAs nearly full storage potential by squeezing more information into its four base nucleotides. During their experiment, researchers said they successfully stored six files inside DNA molecules a full computer operating system (KolibriOS), a 1895 French film Arrival of a train at La Ciotat, a $50 Amazon gift card, a computer virus, a Pioneer plaque, and a 1948 study by information theorist Claude Shannoninto 72,000 DNA strands, each 200 bases long.

After this, they retrieved the data using DNA sequencing technology and then a software to translate the code back into binary form so that it becomes readable again. The files were recovered with no errors.

To retrieve the information, we sequenced the molecules. This is the basic process, Erlich said.

Erlich explained how DNA is a better option than the current ones we already have. DNA has several advantages to store information, he said. The first thing is that its very compact. In effect, its about one million times more compact than what you can get when you use a regular digital media.

The storage capacity is massive; it can reach a density of 215 Petabytes per gram of DNA and can last a very long period of time, which can be over a 100 years.

We believe this is the highest-density data storage device ever created, said Erlich.

The main barrier at the moment of bringing this into commercialisation is time and money, as it takes about two weeks to synthesize the DNA sequence, while it costs $7,000 to sequence 2MB of data into DNA, and then another $2,000 to read it.

Despite this, the research team is very optimistic. When questioned how long it would take for this technology to be made available to everyone, Erlich replied that, I would guess more than a decade. We are still in early days, but it also took magnetic media years of research and development before it became useful.

The research has been published in the journal Science.

Excerpt from:
DNA: Is it the hard drive of the future? - Techworm

March 6, 2017 Geographic distribution of biosamples and organisms encompassed by the Genomes OnLine Database. The location where the organism was isolated is marked with pink dots; the location of the biosample is marked with blue dots. Credit: US Department of Energy

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 much more. To work with these microbes, scientists need to learn more about how microbes and viruses interact. Viruses influence microbes' abilities to work. Scientists at the U.S. Department of Energy (DOE) Joint Genome Institute built the largest publicly available database for viruses. This single effort increases the number of known viral genes by a factor of 16. Further, in a series of four articles published in Nucleic Acids Research, DOE Joint Genome Institute researchers report on the latest updates to several other publicly accessible databases and computational tools. These databases and tools will benefit the global community of microbial researchers.

Microbes play key roles in the planet's biogeochemical cycles. Viruses, thought to outnumber microbes by 10 fold, can alter those cycles. Advances in sequencing technologies have generated vast amounts of data about the viruses. Working with the data requires tools to manage and interpret it. The updated database analytical tools offer details on microbes, specifically microbial genomics, and viruses. A new database, available to the public, enables analyses that can help scientists answer questions about the viruses that infect microbes, an interaction that affects countless natural processes and may provide tools for speeding up beneficial (or slowing down harmful) microbial actions. The insights gained from this work are relevant to DOE missions in bioenergy and environment.

Providing high-quality, publicly accessible sequence data goes hand-in-hand with developing and maintaining the databases and tools that the research community can harness to help answer scientific questions. In a recent series of articles published in Nucleic Acids Research, researchers at DOE's Joint Genome Institute, a national scientific user facility, describe a database called Integrated Microbial Genomes with Virus Samples (IMG/VR). IMG/VR is a comprehensive computational platform integrating all the sequences in the database with associated metadata and analytical tools.

IMG/VR follows on the heels of a recent DOE Joint Genome Institute viral diversity report in Nature. Additional articles in the same issue describe updates to several publicly accessible, interactive databases since the last set of reports published in 2014. For example, as of July 2016, there were 47,516 archaeal, bacterial, and eukaryotic genomes in the IMG with Microbiome Samples (IMG/M) system, with researchers noting that number "represents an over 300% increase since September 2013." IMG/M contains annotated DNA and RNA sequence data of archaeal, bacterial, eukaryotic, and viral genomes from cultured organisms; single cell genomes (SCG) and genomes from metagenomes from uncultured archaea, bacteria, and viruses; and metagenomes from environmental, host-associated, and engineered microbiome samples.

Another paper concerns the Genomes OnLine Database (GOLD), a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four-level classification system in the form of a study, organism (for isolates) or biosample (for environmental samples), sequencing project, and analysis project. A fourth paper focuses on the IMG Atlas of Biosynthetic gene Clusters (IMG-ABC). Launched in 2015, IMG-ABC enables researchers to search for biosynthetic gene clusters and secondary metabolites. Their latest update now incorporates ClusterScout, a tool for targeted identification of custom biosynthetic gene clusters across several thousand isolate microbial genomes, as well as a new search capability.

Explore further: Database of DNA viruses and retroviruses debuts on IMG platform

More information: I-Min A. Chen et al. IMG/M: integrated genome and metagenome comparative data analysis system, Nucleic Acids Research (2017). DOI: 10.1093/nar/gkw929

Supratim Mukherjee et al. Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements, Nucleic Acids Research (2017). DOI: 10.1093/nar/gkw992

David Paez-Espino et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses, Nucleic Acids Research (2017). DOI: 10.1093/nar/gkw1030

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 ...

The number of microbes in, on, and around the planet - on the order of a nonillion, or 1030 - is estimated to outnumber the stars in the Milky Way. Microbes are known to play crucial roles in regulating carbon fixation, as ...

The wealth of genomic and metagenomic datasets for microbes, particularly from previously unstudied environments, within the Integrated Microbial Genomes (IMG) system is being applied in a new public database to the search ...

Researchers sequenced 230 diverse archaeal and bacterial genomes to learn more about the roles DNA methylation plays in prokaryotes.

Using a specially designed computational tool as a lure, scientists have netted the genomic sequences of almost 12,500 previously uncharacterized viruses from public databases.

DOE JGI researchers have developed an automated tool called MetaBAT that automatically groups large genomic fragments assembled from metagenome sequences to reconstruct single microbial genomes.

A small team of researchers with members from the University of California and the University of Michigan has found that some personality traits unique to a queen wasp are passed down to her offspring, the worker wasps. In ...

A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research.

Three species and three genera of birdeater spiders are described as new to science in a paper recently published in the open access journal ZooKeys. In their study, the Brazilian spider experts, Drs. Caroline Fukushima and ...

One of the unique and most iconic features of many modern turtles is that they can withdraw their neck and head to hide and protect them within their shells. The group name of species which do this, Cryptodira, even means ...

The scientists who uncovered why zebras have black and white stripes (to repel biting flies), took the coloration question to giant pandas in a study published this week in the journal Behavioral Ecology.

Research by the University of Southampton has found that methods used to predict the effect of species extinction on ecosystems could be producing inaccurate results. This is because current thinking assumes that when a species ...

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New database of DNA viruses and retroviruses debuts - Phys.Org

March 6, 2017 Credit: University of New Mexico

A young company developing technology created at the University of New Mexico (UNM) is on a mission to disrupt the landscape of DNA sequencing.

Armonica Technologies, LLC, is developing a DNA sequencing platform that will sequence a complete human genome in minutes. The company's goal is to make the technology the gold standard for DNA sequencing for precision medicine research applications. Armonica has optioned a portfolio of patented and patent pending technologies from STC.UNM. The technology is called "optical nanopore sequencing" and uses nanochannels to deliver single DNA molecules through nanopores. Nanopores are very small holes with an internal diameter of 1 nanometer (one billionth of a meter). The nanopores slow down DNA translocation enough to produce massively parallel, single-base resolution using optical techniques.

Here's how nanopore sequencing works: when a nanopore is immersed in conducting fluid, voltage can be applied to produce an electric current. The current is sensitive to the size and shape of the nanopore so that if a DNA strand passes through or near the nanopore, the amount of current changes. The change in the current as the DNA molecule passes through the nanopore represents a reading of the DNA sequence.

"There is an unmet need in the fast-growing DNA sequencing market," said Armonica President & CEO Scott Goldman. "Today's standard genome sequencing approach requires extensive library preparation and creates a massive computational and bioinformatics problem related to reassembling the data set. Armonica will resolve these problems by introducing a sequencing instrument that will not require library preparation and will generate reads of up to 50,000 bases, combined with a parallelism of 1 million. This approach will net 50 billion basesmore than sufficient to sequence the entire human genome in minutes."

The innovative nanopore technology was developed by Distinguished Professor Emeritus Steve Brueck, Research Assistant Professor Yuliya Kuznetsova, and Postdoctoral Fellow Alexander Neumann from UNM's Center for High Technology Materials (CHTM) and Professor Jeremy Edwards from UNM's Department of Chemistry & Chemical Biology, in collaboration with Redondo Optics CEO Edgar Mendoza.

"Nanopore sequencing analyzes long DNA strings, with long reads that provide more accurate identification of genome variations," said Brueck. "It is an approach, therefore, that leads to a more thorough, faster, and accurate genomic analysis, allowing researchers to substantially improve the ability to make new discoveries. One of the challenges of nanopore sequencing is to improve the resolution to be able to detect single nucleotides (bases)."

"We believe our nanochannel technology will disrupt the industry because it produces very long reads for higher accuracy, very high parallelism using optical techniques, and high throughput rates for greater processing speed. It will be an affordable tool for researchers," said STC CEO Lisa Kuuttila. "This technology portfolio represents a leap in genomic sequencing technology that could be a huge benefit for the DNA sequencing industry, which is experiencing explosive growth. The company's research and development are currently being done at UNM's CHTM, a research center with a global reputation for inventing disruptive nanoscale technologies and providing outstanding scientific expertise and technical support. We are very excited about the technology's potential and believe in the company's vision."

Explore further: The gene sequencing that everyone can afford in future

DNA sequencing is important to science. While Professor Qian Linmao and his group from Tribology Research Institute, Southwest Jiaotong University, were working on the optimization of the third-generation sequencing technique ...

(Phys.org) U.K. based Oxford Nanopore Technologies has made good on a promise made two years ago to produce an inexpensive genome sequencer that is based on nanopore technology. David Jaffe, with the Broad Institute reported ...

Research published this week in Nature Nanotechnology shows a new method of enzyme-controlled movement of a single strand of DNA through a protein nanopore. The paper, by researchers at the University of California Santa ...

(Phys.org) High-speed reading of the genetic code should get a boost with the creation of the world's first graphene nanopores pores measuring approximately 2 nanometers in diameter that feature a "built-in" optical ...

Scientists at The University of Nottingham have demonstrated for the first time that it is possible to selectively sequence fragments of DNA in real time, greatly reducing the time needed to analyse biological samples.

In a future of personalized medicine, doctors may quickly glean the changes in the DNA sequences of patients that predispose them to specific diseases or determine the most appropriate therapeutic approach simply by analyzing ...

A small team of researchers with members from the University of California and the University of Michigan has found that some personality traits unique to a queen wasp are passed down to her offspring, the worker wasps. In ...

A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research.

Three species and three genera of birdeater spiders are described as new to science in a paper recently published in the open access journal ZooKeys. In their study, the Brazilian spider experts, Drs. Caroline Fukushima and ...

One of the unique and most iconic features of many modern turtles is that they can withdraw their neck and head to hide and protect them within their shells. The group name of species which do this, Cryptodira, even means ...

The scientists who uncovered why zebras have black and white stripes (to repel biting flies), took the coloration question to giant pandas in a study published this week in the journal Behavioral Ecology.

Research by the University of Southampton has found that methods used to predict the effect of species extinction on ecosystems could be producing inaccurate results. This is because current thinking assumes that when a species ...

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Continue reading here:
Pushing the boundaries of DNA sequencing - Phys.Org

The Park Slope Garage Condominium at 845 Union St., where a parking spot is on the market for $300,000. View Full Caption

DNAinfo/Leslie Albrecht

PARK SLOPE The hottest real estate in Brooklyn may be a closet-sized slab of concrete on Union Street.

A parking spot at the 845 Union St. parking garage is on the market for $300,000.

Like other condo properties, whoever buys the parking spot will have to pay monthly charges. In this case it's $240 in monthly maintenance fees, plus an extra$51 in monthly taxes.

But the monthly charges could be worth it if you sell the spot for a tidy profit in a few years. Just four years ago a spot in the same garage sold for a then eye-popping $80,000.

"Even though youre not going to be saving money monthly, its an asset thats increasing in value," said Constantine Valhouli, co-founder of the real estate analytics firm NeighborhoodX.

Parking garages are more in demand than ever as many have been converted to other uses, he said.

Valhouli likened the six-figure price tag for a parking spot to Brooklyn's rising real estate fortunes. The borough was once simply an affordable alternative to Manhattan but now attracts buyers seeking luxury housing.

"It shows how the market is maturing, where people are willing to pay an amount tagged to luxury and convenience rather than to yield," Valhouli said.

The $300,000 price tag is comparable to the asking prices for one-bedroom apartments for people, not vehicles in Rego Park, Spuyten Duyvil or Gravesend, according to a quick perusal of StreetEasy.

Garage owner Howard Pronsky of Berman Realty predicted in 2013 that prices for his parking spots would probably go up, in part because the parking garage directly across the street at 800 Union St. was being converted into condos and retail.

A 4-year-old boy was killed at the garage, which is also known by the address 841 Union St., in 2016 after falling down a 50-foot elevator shaft.

RELATED: Free Park Slope Parking up For Grabs in Lottery at Methodist Hospital

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$300000 Parking Space Could Be Yours in Park Slope - DNAinfo