In 2003, Paul Hebert, researcher at the University of Guelph in Ontario, Canada, proposed “DNA barcoding” as a way to identify species. Barcoding uses a very short genetic sequence from a standard part of the genome the way a supermarket scanner distinguishes products using the black stripes of the Universal Product Code (UPC). Two items may look very similar to the untrained eye, but in both cases the barcodes are distinct.
Until now, biological specimens were identified using morphological features like the shape, size and color of body parts. In some cases a trained technician could make routine identifications using morphological “keys” (step-by-step instructions of what to look for), but in most cases an experienced professional taxonomist is needed. If a specimen is damaged or is in an immature stage of development, even specialists may be unable to make identifications. Barcoding solves these problems because even non-specialists can obtain barcodes from tiny amounts of tissue. This is not to say that traditional taxonomy has become less important. Rather, DNA barcoding can serve a dual purpose as a new tool in the taxonomists toolbox supplementing their knowledge as well as being an innovative device for non-experts who need to make a quick identification.
The gene region that is being used as the standard barcode for almost all animal groups is a 648 base-pair region in the mitochondrial cytochrome c oxidase 1 gene (“CO1”). COI is proving highly effective in identifying birds, butterflies, fish, flies and many other animal groups. COI is not an effective barcode region in plants because it evolves too slowly, but two gene regions in the chloroplast, matK and rbcL, have been approved as the barcode regions for land plants.
Barcoding projects have four components:
1 The Specimens: Natural history museums, herbaria, zoos, aquaria, frozen tissue collections, seed banks, type culture collections and other repositories of biological materials are treasure troves of identified specimens.
2 The Laboratory Analysis: Barcoding protocols can be followed to obtain DNA barcode sequences from these specimens. The best equipped molecular biology labs can produce a DNA barcode sequence in a few hours. The data are then placed in a database for subsequent analysis.
3 The Database: One of the most important components of the Barcode Initiative is the construction of a public reference library of species identifiers which could be used to assign unknown specimens to known species. There are currently two main barcode databases that fill this role:
a) The International Nucleotide Sequence Database Collaborative is a partnership among GenBank in the U.S., the Nucleotide Sequence Database of the European Molecular Biology Lab in Europe, and the DNA Data Bank of Japan. They have agreed to CBOL's data standards (pdf; 30Kb) for barcode records.
b) Barcode of Life Database (BOLD) was created and is maintained by University of Guelph in Ontario. It offers researchers a way to collect, manage, and analyze DNA barcode data.
4 The Data Analysis: Specimens are identified by finding the closest matching reference record in the database. CBOL's Data Analysis Working Group has created the Barcode of Life Data Portal which offers researchers new and more flexible ways to store, manage, analyze and display their barcode data.
Species identifications underpin all of biological research. Existing morphologically-based diagnostic approaches are often both cumbersome to use and are effective only for certain life stages. DNA-based systems promise to revolutionize the task of identification by providing reliable, inexpensive and rapid diagnosis of species identity.
Imagine a day when any living thing can be identified accurately and rapidly to the species level using a hand-held device the size of a cellular phone. A day when the biodiversity of an entire nation can be inventoried and monitored, and thereby better protected. When invasive species, disease agents and their vectors, and agricultural pests can all be identified and tracked with ease, thus saving millions of dollars and improving both human health and that of the natural environment. When pollen grains at a crime scene can be linked to those on a suspect’s shoes, the quality of water analyzed in terms of its living inhabitants as well as its chemical constituents, and endangered or dangerous species crossing national borders immediately recognized – not just by highly trained professional taxonomists, but by anyone. A day when bio-prospectors will be able to collect and rapidly identify thousands of species that may yield new lifesaving drugs, and when the plant and animal ingredients in food products can be assessed with certainty even after processing. Imagine a day when every curious mind, from professional biologists to schoolchildren, will have immediate access to the names and biological attributes of any species on the planet.
To be sure, this still rings of science fiction. But thanks to an ambitious effort by a growing consortium of scientists, it is poised to become reality. The method that will enable this advance is "DNA barcoding", an approach that employs a small fragment of DNA, a portion of a single gene, to provide a unique identifier – a "DNA barcode" – for each living species on Earth. Using these DNA barcodes, it will be possible to identify any organism, be it juvenile or adult, male or female, large or small, from only a tiny piece of tissue. This is vastly more efficient than traditional approaches which are often based on the detailed examination of specific body parts and which typically require interpretation by trained experts. In addition, because DNA barcoding quickly distinguishes new species, it will greatly accelerate the rate of their discovery. Given that it has taken 250 years to describe roughly 15% of life’s estimated diversity and that this diversity is now being lost at an alarming rate, the taxonomic revolution incited by DNA barcoding arrives at a critical time.
If you turn on a light at night in the mountains of Papua New Guinea, says Paul Hebert, you will collect some 2,000 species of moth. Moving up the mountain a bit will net you a different but equally daunting crowd. As a young postdoc in the 1970s, Hebert, now an evolutionary biologist at the University of Guelph in Ontario, spent five years trying to make sense of that fluttering confusion, before finally deciding it was beyond his or any human’s capacity. For two decades after that he retreated to water fleas, of which there are only 200 species. Then in 2003 he did something new. In a paper that year he began by describing the diversity of life as a “harsh burden” for biologists, and proceeded to suggest some relief: Every species on Earth could be assigned a simple DNA bar code, Hebert wrote, so it would be easy to tell them apart.
The bar code Hebert suggested is part of a gene called CO1, which helps produce the energy-carrying molecule ATP. CO1 is so essential that every multicellular organism has it. But there is enough variation in its sequence—each of the 600-odd spots in the bar code region can be filled by any of four different DNA bases—that two species rarely have the exact same one. Such differences in a gene are readily scanned by machine even when the animals themselves might confound an expert; Hebert’s group is now sequencing a thousand specimens a day. They’ve bar coded nearly 40,000 species of moth and butterfly already. The technique has commercial as well as scientific promise. Mislabeling of fish on menus is rampant, it turns out.
(News/Archives)
Biodiversity measures the variation of life shaped through ecology and evolution from genes to species and ecosystems. Genetic variation plays a critical role in the ability of individuals and species to respond and adapt to environmental change while the diversity of species within and between ecosystems provides significant advantages to ecosystem function and resilience. One of the ironies of biological research is that after more than 250 years of dedicated biological science, the total number of species within any country or region remains unknown. While we often have a good idea of the identities and ecological roles of the larger, more charismatic animals (birds, mammals) the truth of the matter is that most of life is small (insects, bacteria, fungi) and currently undescribed. Shedding light onto these lesser known groups is important because all of the larger groups, including ourselves, depend on these smaller organisms for some part of their daily natural history. In order to protect and understand the diversity of life in Ontario, we must be able to know the species and ecosystems upon which humans, and our industry and lifestyle, depend.
iBOL's goal is to capture, using a handheld device, the unique "DNA barcode" of each and every species on earth, and organize that information to be accessible and useful for everyone (sound familiar?). A DNA barcode is a gene sequence that uniquely identifies any species, and iBOL has already barcoded 35,000 of them. There are approximately 10M species on the planet (half of which have yet to be discovered), so there's a long way to go, but the components for success are in place.
During my recent family vacation to Costa Rica I hiked the rain forest, and by the end of the trip could easily identify a toucan, eyelash viper, and three types of monkeys (howling, spider, and Rosenberg offspring). Pretty impressive, right? Then Dr. Janzen showed me a photo of that same rain forest and told me that there were approximately 400 species of animals and plants in that picture, and not a toucan or monkey among them. So it turns out that I'm just as bio-illiterate as everyone else, but Google can do something about this. When we talk about organizing all the world's information, a blueprint of the world's natural biodiversity should be part of it.
In 18 months full human genome sequences will be available under $100 - and in minutes. The $5,000 full human genome was announced to come in 9 months. Is "Big IT" ready for the avalanche of data, to be obtained and processed e.g. while the patient is still on the operating table, to be diagnosed, and how the genomics glitch, that caused a benign or malign tumor, could be compensated for?
Algorithmic approaches are needed to better understand genome regulation, even for the simple reason to deploy most effective data retrieval, data storage and computational means, via both parallel hardware and software, but more importantly for opening entirely new perspectives.
In the 100+ year old Genomics, for over half a Century had us to resign to the fatalistic gloom that we are stuck with any glitches in our inherited genome. Is it true that genomic glitches doom one to "incurable" hereditary diseases?
No longer. Genomics now considers the DNA-RNA-Protein chain not as a thermodynamically closed system, where entropy increases, but as an open system that can be interfered with. There is theoretically sound hope that you are not stuck with your genomic glitches.
After half a Century of sticking to two mistaken axioms of Genomics, the paradigm of recursive genome function must quickly make up for lost time for those (potentially) inflicted with formerly "incurable" diseases. "The Genome baby is left on the doorsteps of Information Technology".
Doctors sent those inflicted with fleece for "debugging". Debugging genome information (by Genome Computers) would be much harder without understanding the algorithms that our natural genome computing operates with.
A DNA molecule consists of millions of different nucleotides that make up the human genome; the blueprint of living organisms.
Next, single strands of DNA molecules that are floating above the microchip are threaded or pulled through the nanopore by an electrical field, which begins the process of reading and sequencing the molecules.
The DNA Transistor device consists of alternating nanometer-sized layers of metal and dielectric. Discrete charges located along the backbone of a DNA molecule get trapped by electrical fields inside the nanopore. By trapping the DNA molecule, scientists will have ample time to measure the molecule structure.
By cyclically turning on and off these gate voltages, researchers have shown theoretically and computationally, and expect to be able prove experimentally, the plausibility of moving DNA through the nanopore at a rate of one nucleotide per cycle a rate that IBM scientists believe would make DNA readable.
Low-cost, yet efficient analysis of DNA data promises to help facilitate the discovery of new healthcare products, and help determine an individual's predisposition to a particular disease or condition.
At the center of DNA barcoding’s rising stock lies the promise of many practical applications. Customs officials could easily identify trafficked, endangered, invasive, or other important species. Animal and plant ingredients in food products could be pinpointed. Biodiversity could be catalogued over large areas to readily identify diversity hotspots for conservation.posted by barnacles at 8:47 PM on July 14, 2010 [4 favorites]
Not everyone shares the vision. A growing opposition to DNA barcoding has emerged from within the ranks of evolutionary biology. And many of the sharp volleys in the debate are sounding from labs here at UC Berkeley.
Asked whether species can be said to have barcodes, Berkeley integrative biology professor, Brent Mishler was unequivocal. “No.” Mishler, an evolutionary biologist who studies mosses and serves as director of the University and Jepson Herbaria on campus, argues that DNA barcoding borrows from a dangerously false view of biological diversity. Barcoding “makes some sense for some systems, like screws in a warehouse,” he says, “but not for an evolving system.”
Products in a warehouse maintain a uniform level of difference from one another that can accurately be tracked by a barcode. But species are not discrete and unchanging units. They are aggregations of individual organisms that collectively constitute the present-day representatives of an evolving lineage. The conditions that drive the evolution of these lineages act on organisms, not on singular characteristics like fur color or particular genes. A single trait, like a gene, might distinguish species within a group of organisms with a common evolutionary history. But any single characteristic is insufficient a priori and on its own to diagnose and classify the whole of biotic diversity. “Contrary to their posturing as cutting-edge,” Mishler argues, “DNA barcoders are returning to an ancient, typological, single-character approach, and are maintaining a pre-Darwinian view of species.”
In fact, studies have shown that the family trees of particular genes do not always correspond to the family trees of the organisms that harbor those genes. And empirical studies of barcoding projects have used the same data as barcode proponents to reveal the absence of a one-to-one relationship between mitochondrial barcode variation and species variation. For Daniel Rubinoff, associate professor of Entomology at the University of Hawaii and former UC Berkeley PhD student and postdoc, the reasons for these shortcomings come down to a simple fact. “A dynamic process like speciation can’t be modeled by a procedure as rigid as barcoding.”
...once you're in the neighborhood, if we're really getting close to these super cheap whole genome sequences, why not do the whole thing.Yeah, endeavors like Genome 10K (a plan to sequence over 10,000 vertebrate genomes in five years) will largely take the place of barcoding, I predict.
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The broader applications of DNA barcoding, however, are undeniable. The Feather Identification Lab at the Smithsonian Institution, working with the Federal Aviation Administration (FAA) and the U.S. Air Force, is using the tool to identify bird species that collide with aircraft, a phenomenon the FAA estimates costs about US$345 million every year. But “snarge,” a Feather Lab term for the goop wiped from an aircraft following a bird strike, is often anatomically unrecognizable. Being able to identify a species allows airfields to implement appropriate habitat management programs, as well as warn crews of particular bird dangers and help engineers design better airplanes.
(Bonus Snarge) and Recently.
SNARGE:
Wired
snarge.net
in battle on birds, air force deploys a secret weapon
identifying the bird when not much bird is left
audubon snarge
CSI for Birds: Scientists Use Forensic Techniques to Improve Airport Safety
Taxonomy isn't black and white(PDF), By Nick Atkinson
Why DNA barcoding works
Rob DeSalle [PDF] An excellent review of the involved issues, topics, considerations, applications, and understandings
Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied Arthropods in a high-throughput context: the example of Collembola
Using DNA barcodes to connect adults and early life stages of marine fishes from the Yucatan Peninsula, Mexico: potential in fisheries management
Morphological, ecological, reproductive and molecular evidence for Leptodiaptomus garciai (Osorio-Tafall 1942) as a valid endemic species
A new cryptic species of Leberis Smirnov, 1989 (Crustacea, Cladocera, Chydoridae) from the Mexican semi-desert region, highlighted by DNA barcoding
Barcoding endangered Sea Turtles
15 New Bird Species-SciAm
Hundreds of new sea creatures found on Australian reefs
The Walter Reed Biosystematics Unit (WRBU) is a unique national resource. Its mission is to conduct systematics research on medically important arthropods and to maintain the U.S. mosquito collection.
Freaky New Bats Found by DNA Barcoding
Teenage DNA sleuths expose New York fish fraud
Mercury in Tuna Sushi Higher at Restaurants than Groceries
DNA 'Barcodes' Surface Fishy Impostors on Menus
Previously Mefi: Apples
Third International Barcode of Life Conference, Session 2A: Karen James-
Education
This has very real uses.
Next-gen barcode application
A Canadian study shows even if you don’t swallow the worm at the bottom of a bottle of the Mexican liquor mescal, you may not have avoided the worm’s DNA.
In these studies, COI sequences accurately identify bdelloid rotifer species, further demonstrating the robustness of DNA barcoding.
-“this refutes the idea that sex is necessary for diversification into evolutionary species.”
Early in Michael Crichton’s 1990 novel Jurassic Park, Dr. Henry Wu, chief scientist at Jurassic Park Research Insitute, showing visitors around his facility, displays ”the actual structure of a small fragment of dinosaur DNA“. Astute readers pointed out Dr. Wu’s dinsosaur genetic resuscitation project was unlikely to succeed, as the sequence in Crichton’s novel was a fragment of the bacterial plasmid pBR322.
DNA Barcoding of Bushmeat - Cameroon
Life Behind Bars, UCSanDiego
Rockefeller Barcode Blog
posted by infinite intimation at 8:42 PM on July 14, 2010