This Biotech Basics is an assembly of the most important findings of 2010. These findings were originally published in the Biotechnology Discoveries and Applications guidebook, an easy-to-use resource that keeps life science educators and their students on the cutting edge. Research highlights in this article are culled from the eight-page New Findings section of the guidebook, summarizing major discoveries from the past twelve months. For links to more information about each new finding, visit the guidebook online (see link at end of article).

Highlights:

• The recent genetic sequencing of King Tut and other mummies offered insight into the royal family tree as well as providing new details about Tut’s cause of death.
• The FDA is currently discussing whether to approve the first genetically modified animal for human consumption – Atlantic salmon that possess a growth hormone gene that allows them to grow three times as fast as unmodified salmon.
• The Neanderthal genome was sequenced. It was discovered that humans and Neanderthals coexisted at one point in history.
• New genomes published this year include apple, corn and wheat.

And now, 2010 in biotechnology:

Infectious disease
Antibiotic treatment increases bacterial mutation rate
Recent research has shown that treating bacteria with low concentrations of antibiotics increases the mutation rate in the bacterial cells. Many bactericidal antibiotics work by disrupting the bacterial cell’s DNA, proteins and lipids. Researchers treated Escherichia coli bacteria with low doses of three antibiotics: ampicillin, kanamycin and norfloxacin. With all three treatments the mutation rate of the bacterial cells increased up to eight-fold. Similar results were observed with a different E. coli strain as well as Staphylococcus aureus. These findings provide important insight into the increasing problem of drug-resistant bacteria and suggest that antibiotics themselves could be a key player in this resistance.
REFERENCE: Kohanski, M.A., DePristo, M.A. & Collins, J.J. Sublethal antibiotic treatment leads to multi drug resistance via radical-induced mutagenesis. Molecular Cell 37, 311-320 (2010)

King Tut’s DNA
Using genetic testing to unravel an ancient family pedigree
Genetic testing on several mummies buried in Egypt’s Valley of the Kings has allowed Egyptian scientists to unravel the tangled family tree of Tutankhamun, the boy-king who ruled Egypt from 1333-1323 BC.

The genetic information was used to identify family relationships among the mummies. A previously unidentified mummy was confirmed to be King Akhenaten, the father of Tutankhamun. Additional mummies were identified as Tutankhamun’s mother and his probable wife. The DNA fingerprints also revealed that Tutankhamun’s parents were siblings. Marriage among close relatives was a common occurrence among Egyptian royalty, but such relationships increased the likelihood that recessive mutations would be passed to a child. Medical imaging suggests Tutankhamun was born with a clubbed foot and partial cleft palate, both potentially the result of genetic defects.

Tutankhamun’s mummy was also tested for traces of infectious disease. DNA from the parasite Plasmodium falciparum was found, indicating malarial infection at the time of death. An unhealed broken leg was discovered in an earlier analysis. It has been speculated the malaria may have weakened his immune system, leaving him susceptible to complications from the leg injury and resulting in his early death.
REFERENCES: Hawass Z. King Tut’s Family Secrets. National Geographic 2010.
http://ngm.nationalgeographic.com/2010/ 09/tut-dna/hawass-text
Hawass Z, et al.. Ancestry and Pathology in King Tutankhamun’s Family. JAMA 303 (7): 638-647 (2010)
JAMA and Archives Journals (2010, February 17). Study examines family lineage of King Tut, his possible cause of death.
Science-Daily www.sciencedaily.com

Synthetic biology
The first “man-made” genome
This spring, researchers announced the creation of the first bacterial cell with a genome designed by a computer and made entirely in the lab. The scientists synthesized the 1.08 million base pair genome from Mycoplasma mycoides, a bacteria that often infects goats, but is not dangerous to humans. The genome was created by synthesizing DNA fragments of chemicals in the laboratory, assembling fragments into an entire genome and inserting it into a host Mycoplasma cell whose own DNA was destroyed. When the host cells grew and divided, they did so under the direction of the synthesized genome.
REFERENCES: Gibson, D. G., Glass, J. I., Lartigue, C., et al. Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome. Science 329(5987):38-9. 2010
Khali, A. Collins J.J. Synthetic biology: applications come of age. Nature Reviews Genetics 11, 367-379 (2010)

Agriculture
From field and stream to the kitchen table
The genomes of several plants have been published this year including apple, corn and wheat. Knowing the genome sequences of these organisms aids in understanding plant characteristics and developing genetically modified organisms with enhanced traits. For example, it may be possible to produce apples with higher levels of antioxidants or soybean crops with increased oil production for use in alternative fuels. In addition to soybean, other organisms are currently being genetically engineered as potential sources for biofuel, including algae, Escherichia coli and eucalyptus trees.

AquaBounty super salmon
The FDA is currently discussing the approval of the first genetically modified animal created for human consumption. GM Atlantic salmon contain a growth hormone gene from a Chinook salmon that is linked to a genetic on-switch (a promoter sequence) from a distant relative of the salmon known as an ocean pout.

Salmon do not typically make growth hormone in cold weather, limiting their growth to warmer months. The on-switch from the pout maintains hormone production year round. As a result, the salmon grow to market size in 16 to 18 months instead of 36. These large fish are unable to reproduce, preventing the GM version from interbreeding with the wild salmon population. The outcome of this FDA meeting will be one to watch as it sets the precedent for the future approval of other GM animals.
REFERENCES: Neuman, W. & Pollack, A. Farmers Cope With Roundup-Resistant Weeds. The New York Times 3 May 2010 www.nytimes.com
Neuman, W. ‘Non-GMO’ Seal Identifies Foods Mostly Biotech-Free. The New York Times 29 August 2009 www.nytimes.com
Schreck, S. GM Salmon Up For Debate. Food Safety News 30 August 2010
www.foodsafetynews.com
Soybean Genome Sequenced: Analysis Reveals Pathways for Improving Biodiesel, Disease Resistance, and Reducing Waste Runoff ScienceDaily 14 January 2010
www.sciencedaily.com

Studying the genome to understand the sequence
1000 Genomes Pilot Project
The 1000 Genomes Project has released data from its first three pilots. The ultimate goal of the 1000 Genomes Project is to build a detailed database of human genetic variation that helps researchers understand human diversity and genetic contribution to human disease. To achieve this goal, the project will sequence the genomes of 2,500 people from 27 populations worldwide. The 1000 Genomes Project, when complete, will produce an extraordinary amount of data. The pilot project data alone encompasses nearly 8 trillion base pairs of DNA – more than 50,000 gigabytes of space.
 REFERENCE: Wood, L, et al. 1000 Genomes Project Releases Data from Pilot Projects on Path to Providing Database for 2,500 Human Genomes. 1000 Genomes Project 21 June 2010
www.1000genomes.org

Genetic Information Nondiscrimination Act
Claim of genetic discrimination tests new law
In 2009, the Genetic Information Nondiscrimination Act went into effect, prohibiting employment discrimination based on genetic information. The first test of GINA has been raised, pitting a natural gas and electricity provider against an employee who claims she was fired after revealing that she carried a high-risk breast cancer mutation.
REFERENCE: Vorhaus, D. GINA in Action: Woman alleges genetic test led to firing. Genomics Law Report
www.genomicslawreport.com

DNA sequencing
Exploring microbial populations
Bacteria and archaea live in all environments capable of sustaining life (and in some extreme environments are the only forms of life). There are an estimated 5×1030 of these organisms present on Earth. Metagenomics – the thorough study of the genomes of uncultured microorganisms – is helping researchers better understand their function and influence on animals, crops and humans. The first microbial genome was sequenced in 1995.  Thanks to advances in sequencing technology, there are now more than 1,200 such genomes stored in the Genbank genetic database. The Human Microbiome Project seeks to characterize and understand the way microbes contribute to human health and disease. Microbes on the skin, gut and elsewhere outnumber human cells by about 10 to 1. Differences in bacterial populations present in the digestive system have recently been linked to obesity, metabolic syndrome and inflammatory bowel disease.
REFERENCES: Wooley JC, Godzik A, Friedberg I A Primer on Metagenomics. PLoS Comput Biol 6(2): e1000667. (2010)
Flintoft L. Human microbiome: A gut feeling for disease. Nature Reviews Genetics 11, 237 (2010)

Comparative genomics
Neanderthal draft genome published
Researchers published the draft genome sequence of the Neanderthal, using DNA collected from the bones of three Neanderthal females who lived in Croatia more than 38,000 years ago. Neanderthals are estimated to have separated from the ancestors of modern humans between 270,000 and 440,000 years ago, but coexisted with modern humans initially in the Middle East and later in Europe. When the genomes were analyzed and compared, several interesting findings emerged. Between 1 – 4 percent of the genomes from individuals of European and Asian ancestry are Neanderthal in origin, yet Africans have no Neanderthal segments. These findings suggest that a low level of interbreeding occurred between Neanderthal and modern day humans, but only with populations that had migrated out of Africa.
REFERENCE: Green, R. et al. A Draft Sequence of the Neanderthal Genome. Science 328, 710 (2010)

– Dr. Neil Lamb
director of educational outreach
HudsonAlpha Institute for Biotechnology

For more information:
www.hudsonalpha.org/education/resources/guidebook
Genetics, genomics and biotechnology are fast-paced and ever-changing fields with new discoveries occurring every day. To help educators stay up to date on these discoveries and how to bring them into the classroom, the HudsonAlpha education outreach team publishes an annual biotechnology guidebook.   Of specific interest to the general public is the first few pages of New Findings. Read more about the discoveries listed here in the 2010 guidebook – available at hudsonalpha.org.