Showing posts with label Genetics. Show all posts
Showing posts with label Genetics. Show all posts

Monday, July 22, 2013

Sciobeantown at Midsummer Nights' Science

On July 17, Sciobeantown headed over to the Broad Institute in Cambridge, MA to join in on their four week lecture series: Midsummer Nights' Science. Members of Sciobeantown took to Twitter with the hashtags #broadtalks and #sciobeantown to livetweet the event, which featured a talk from cancer genomics researcher Levi Garraway.*

If you missed the event, a video of the talk called, "Exploring the genome's dark matter** what frontiers of genomic research are revealing about cancer" is now online. You can also check out Sciobeantown's contribution to the Twitter discussion with this Storify of the event by Amanda Dykstra. Thank you to the Broad Institute for setting aside space at this event (which filled the room to capacity) so that Sciobeantown could participate!

*Dr. Garraway is a researcher at the Dana-Farber Cancer Institute, in addition to his work at the Broad Institute and Harvard Medical School. I do cover his melanoma work as part of my job at Dana-Farber. 
**Using dark matter as a metaphor for the non-protein coding portion of the genome has been the subject of some science writer snark (possibly from me...okay, from me) but the title of the talk is the title of the talk, folks. 

Sunday, January 20, 2013

Media Consumption 1/13/13-1/20/13

Once again just sharing a few things that I read last week that stuck out to me... as always, let me know if you have a favorite story that you want to share!

Pick 1: Cancer/Medicine Coverage
Study Highlights the Risk of Handing Over Your Genome – Susan Young MIT’s Technology Review
With genome sequencing for biomedical research on my mind, I think this is a really interesting story for all of us to be paying some attention. A new study showed that researchers were able to deanonymize genomic data – essentially take genetic information that had been made anonymous and figure out whose data it was using information that was publicly available on the Internet. It raises a lot of questions about regulations, and questions of security for people who allow their genomes to be sequenced for research.

Pick 2: Scientific Study
Ebola virus: PLoS Pathogens
Thomas W. Geisbert, Boston University School of Medicine
Now Where Did I Put That Ebola? – Helen Shen for Nature
“In the first study of its kind, the US Center for Disease Control and Prevention (CDC) unveiled statistics on problems related to the handling of hazardous biological agents, such as Ebola, SARS, and anthrax, at hundreds of academic and government research centers.” Forget Outbreak or Contagion, this one will make you want to break out the hazmat suit – unless of course the “inadvertent release” of pathogens isn’t as horrifying to you as it is to me.

Pick 3: Writing Pick
Should You Be a Writer or an Editor? Part One: The Writers and Part Two: The Editors – Christie Aschwanden for The Open Notebook
This was a really great two part article, which tackles an issue that I think all writers face at some point in their careers – is what you are best at and what you should be doing to write or is it to edit? The natural career progression goes from writer to editor, but if you just want to write or just want to edit? How do you tell what fits for you? Some great writers and editors weigh in with their experiences. Also, if you’ve never heard of The Open Notebook, take the time to explore the site a little. I can’t stress enough what a great resource for writers it is. 

Bonus Pick:
Sherlock Holmes and the Infamous Brain Attic – Maria Konnikova on BoingBoing
Partly chosen because I have a recent fascination with Sherlock Holmes, but also chosen because Konnikova is an awesome science/psychology writer (you can normally catch her over at Scientific American writing the Literally Psyched blog) and I’ve really been looking forward to her first book “Mastermind: How to think Like Sherlock Holmes” which is out this month.

Monday, November 5, 2012

SFSYO Scientist of the Month: Philipp Schiffer

Science For Six-Year-Olds (SFSYO for this school year) is a recurring segment on Science Decoded for Mrs. Podolak's first grade class at Lincoln-Hubbard elementary school. This year the posts are inspired by #iamscience (also a Tumblr) and #realwomenofscience two hashtags on twitter that drove home for me the importance of teaching people who scientists are and what they really do.

Hello first graders! I hope you are all okay and back at school after hurricane Sandy. Now that it is November we have a new scientist of the month. I am so excited to introduce you to Philipp Schiffer who is finishing up his PhD at school in Cologne, Germany. Like I did with Dr. Penny, I asked Philipp a bunch of questions to find out more about what he does. I hope you will enjoy learning more about him. Below you can read my interview with Philipp, and if you'd like to ask him any questions, be sure to leave them in the comments!
***
At work in the lab. Courtesy of Philipp Schiffer.
Erin: What type of scientist are you?

Philipp: I'm an evolutionary biologist [this means he studies genetics, DNA, and how different living things came to be,] currently I've morphed into a computer geek but I'm hoping to move away from the computer screen a bit more in the future. 

Erin: What did you study in school, and where did you go?

Philipp: I studied Biology, majoring in Zoology with minors in Genetics and Palaeontology. I did most of my studies at the University of Cologne, Germany with some time in Australia studying and catching wombats.  I'm currently finishing my PhD thesis in Cologne, but I've also studied at the University of California Riverside where I was learning about nematodes. I also got to spend some time in Edinburgh in Scotland. 

Erin: Where do you work and what does a typical day at work entail?

Philipp: It's called the Cologne Biocenter, in the middle of Köln am Rhein. At the moment I am spending most of my working hours in front of my computer, doing science in-silico, which means I am analyzing data from the genome sequencing assays I conduct. In between I hop over to the lab to study the nematodes, look at their DNA or run some other experiments. 

Erin: Why did you decided to become a scientist?

Philipp: I have always liked to think about things. I guess when I was in the 9th or 10th grade I wanted to tackle the big problems/questions like finding a cure for diseases. Now of course, I do something totally different, which I actually like better!

Out of the lab! Courtesy of Philipp Schiffer.
Erin: What is your favorite thing about your job?

Philipp: There is a new and intriguing question to answer every day, more than one on most days. That is the main thing, I am really interested in answering questions about life - why it is the way it is and how did it become like that? Why are species different and how does it happen. There is a woo hoo! moment when things finally click into place and make sense, which is really cool. It is also really nice to work with people around the world - I like the exchange of thoughts and ideas in different cultures. I enjoy talking to colleagues very much, and working with students. It is also fun to be able to listen to music when working, and so much more. 

Erin: What is something about your job that might surprise us?

Philipp: There is no magic in science, actually most ideas or experiments don't work the way you think they will, and once something really works the main thing is to wonder why did it work this time? So there is a lot of frustration in being a scientist, but then there is also a lot of fun. Still, the first thing is the most important, science is hard work. 

Erin: What are your favorite things to do for fun?

Philipp: Science IS fun. I also like wind surfing and sailing, I like rugby too and wish I had more time to do that. I also read about history, politics, and the world in general as much as I can. I very much enjoy chatting with friends over coffee.
***

What do you think first graders? I think Philipp has a pretty cool job, and he's gotten to go to school in so many different places, can you find them all on a map? If there is anything you'd like to know about his research, make sure to ask him questions in the comments. 

For any of my regular (adult) followers you can catch Philipp on Twitter @evolgenomology. If you'd like to be featured as a scientist of the month send me an email or DM me on twitter, I'd love more volunteers and thank you Philipp for lending us your time to share what you do!

Sunday, June 24, 2012

Book Review: Jurassic Park

I'm about two decades late to the party with this book review, but considering I was two years old when Jurassic Park was first published my interest in dinosaurs, genetics, etc. needed a little more time to develop. I have finally read Michael Crichton's iconic Jurassic Park, and not really surprising anyone I loved it. I have been exposed to the cultural premise of Jurassic Park my whole life, but I'd never read the book or seen the movie, so really it was like my first exposure to the story in its entirety. I found my Dad's old copy from back when it was first released and decided to rescue it from the book donation bin. I'm glad I did.

In case you live under a rock and are thus unaware the premise of Jurassic Park is that scientists develop a way to pull dinosaur blood samples out of mosquitoes fossilized in amber. The blood is used to decode the genetic sequence for a variety of dinosaurs and they are then grown and hatched in a lab. An eccentric billionaire funds the project because he believes he can make billions by using the dinosaurs as the main attraction in a theme park. What could go wrong genetically recreating dinosaurs for a modern day tourist attraction? Everyone involved in the project thinks nothing could go wrong, yet things do go awry on the island where the theme park is built causing much dinosaur related havoc.

I can only speculate what reading the book when it was first published must have been like and how I would have perceived the ideas and lessons in the context of early 90's technology. Still, even in our current age of high speed genome sequencing I think the warnings in Jurassic Park continue to hold true. Things go wrong because the people working on the dinosaur project don't give nature enough credit. They think there can't possibly be a way for their fail-safe measures (creating only female dinosaurs and making them lysine dependent) to be overcome by the dinosaurs. They doubt the intelligence of the life forms they create and their ability to adapt. They also don't appreciate that they have created something new instead of just recreating the past.

The desire to profit off the dinosaurs is the main priority, leading to a lack of understanding about them and the process that created them. Living in an age of even more advanced scientific ability, I think remembering that there can always be unexpected outcomes with any scientific experiment is important.   I am a firm supporter of genomic research, but the key word there is research. Creating a profitable enterprise like the one in Jurassic Park shifts the priority from understanding to economics. Understanding should always be the goal with scientific inquiry and processes, because if we are going to use technology to manipulate, change, or create we need a firm grasp on the what and the how.

Ultimately I think what I took away from Jurassic Park was a sense of respect for science and nature. We can't take ability for granted. Ethics are important. Why we do things matters as much if not more so than just our base ability to do them. While I know (obviously) that Jurassic Park is a work of fiction, I think it gives a reader a lot to think about regarding research and real-world applications, even after so many years. It is also pretty entertaining, the plot is great but the characters are also well developed and it is definitely action packed. I now need to find the time to watch the movie, and read The Lost World. I'm totally hooked. Have you actually read Jurassic Park? Just seen the movie? How old were you? What did you think? I'd love to know what other people thought when they first encountered the story.

Tuesday, July 19, 2011

Polar Bears Have The Luck Of The Irish

I recently learned that I share a trait with my absolute favorite animal, the polar bear, in that we can both trace our ancestry back to Ireland. For people who follow this blog, or have at least looked back through the archives a bit, you'll see that I find it impossible to pass up a good polar bear story. I've written about animal healthcaremysterious death, and the polar bear's status (or lack thereof) as an endangered species. So it should come as no surprise that I can't pass up the opportunity to talk about this new research that shows an ancient Irish connection to modern day polar bears.

via Wikimedia Commons
A team of researchers led by Beth Shapiro of Penn State University and Daniel Bradley of Trinity College (Dublin) has identified a common ancestor of polar bears (Ursus maritimus) and brown bears  (Ursus arctos) that lived in Ireland before the peak of the last ice age some 20,000 to 50,000 years ago. The researchers concluded that all modern day polar bears can trace their lineage back to this ancient female brown bear. The specific lineage of the brown bear that shared their mitochondrial DNA with polar bears went extinct around 9,000 years ago, but the research still shows that the modern species are related.

Despite significant differences between polar bears and brown bears (size, coloring, fur type, tooth shape, swimming ability vs. climbing ability, etc.) scientists have suspected for some time that the species have closely connected histories. The polar bear is known to have mitochondrial DNA (the part of the genome contributed by the mother) that traces back to the brown bear. But how modern polar bears acquired this brown bear DNA was a bit of a mystery.

via Wikimedia Commons
The two species are known to interbreed, and have been studied in captivity in addition to being spotted in the wild. An example of a polar bear/brown bear hybrid, jokingly nicknamed grolar bear or pizzly, was found in the wild Canada in 2006. But, even with the knowledge that the two species can co-mingle scientists were still perplexed about the history of these different species. The long standing theory about how polar bears evolved from brown bears had their history traced to the ABC Islands (the Alaskan Islands of Admiralty, Baranof, and Chichagof) around 14,000 years ago. But the bears' genomes tell us a different story.

The research team led by Shapiro and Bradley found that the hybridization of polar bears occurred much earlier than would have been possible on the ABC Islands through a genetic analysis of the bears. The study analyzed 242 samples from polar bear and brown bear mitochondrial DNA spanning 120,000 years and several different geographical regions. The researchers found that the fixation of the mitochondrial genome in polar bears likely occurred closer to 50,000 years ago in the area of present-day Ireland.

According to Shapiro, in addition to genetic evidence, the interconnected history of the polar bear and brown bear is also supported by climate events. One example of this is the British-Irish ice sheet, which reached its maximum range around 20,000 years ago. At this time parts of Ireland would have been difficult to inhabit, pushing bears from the warmer areas toward ice shelves and land exposed by lower sea levels. This would have brought the bears into close contact with their northern neighbors, showing how the animals that became two different bear species could have started out in the similar location, sharing their genes.

The polar bear is currently considered a threatened species, and future conservation efforts may be aided by this new understanding of its genetic history and its ability to hybridize with the brown bear. The research is described in the paper, "Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline" in the journal Current Biology.

Sunday, March 6, 2011

History Remains a Mystery: DNA Can't Confirm Remains Are Amelia Earhart

I use Science Decoded for class and have assignments that require me to post in certain ways. This week I'm ATTEMPTING to write in a diamond structure (writers will know it but that means really specific- big issue- really specific.) I'm going to try to do so by tackling Amelia Earhart and the role of DNA analysis in identifying her possible remains, a subject I previously mentioned in the post What Happened to Amelia Earhart?

Today she is the topic of book reports, the namesake of streets, schools and scholarships, and even the subject of a major motion picture starring actress Hilary Swank. But in 1937 when she decided to fly around the world, Amelia Earhart - famous though she was - was also something unheard of at the time. She was a woman shattering convention – simply because she wanted to.

Amelia Earhart broke her first world record at the age of 24 on October 22, 1922 when she flew her airplane to an altitude of 14,000ft. The highest altitude then recorded for a female pilot. By April 8, 1931 she would beat her own record soaring to 18,415ft. She set four records for speed from 1930-1933, and in 1932 she was the first woman to fly solo across the Atlantic Ocean, five years to the day after Charles Lindberg first accomplished the feat. She wrote a book about the trip called “For the Fun of It.”

Earhart became a champion for women’s rights by being an outspoken female figure in a male dominated field. In 1932 she helped form, and was elected president of the Ninety Nines a club for women aviators.

According to the website operated by the estate of the famous aviator, Amelia Earhart is quoted as having said, “One of my favorite phobias is that girls, especially those whose tastes aren’t routine, often don’t get a fair break. It has come down through the generations, an inheritance of age-old customs which produced the corollary that women are bred to timidity.”

Source: Wikimedia Commons
Earhart was the first person to fly solo from Los Angeles to Mexico City, the first person to fly from Mexico City to Newark nonstop, and the first person to fly across the Red Sea to India. Not just the first woman. She was the first PERSON to complete these milestone trips.

Having accomplished all of this it is no surprise that on June 1, 1937 when she was 39-years-old Earhart set out to become the first woman to fly around the world. She almost succeeded. On June 29th, Earhart and navigator Fred Noonan arrived in Lae, New Guinea with only 7,000 miles of the trip left. On July 2nd Earhart and Noonan took off for their next checkpoint at Howland Island. 

It is here that the story of a strong female aviator, a role model for men and women alike becomes a mystery. She was sucked into the vortex of the Bermuda triangle. She flew to Rio to live a life of secrecy. She was abducted by aliens. Although the theories about why Earhart never arrived at Howland Island are many, truly no one knows what happened to her, Noonan, or their twin engine Lockheed Electra airplane. Although the most likely scenario is that Earhart and Noonan were unable to find Howland Island and then ran out of fuel.

With clouds obscuring the stars, Noonan’s ability to navigate would have been heavily compromised. The failure of their radio transmissions would have left Earhart and Noonan unable to ask for help. Landing in the ocean or on one of the South Pacific’s islands may or may not have killed the aviator. She was declared dead, but some say she could have survived the landing and lived for awhile as a castaway. This theory was buoyed in 2010 by the discovery of three bone fragments that might be a human finger on Nikumaroro (formerly known as Gardner Island) in the Republic of Kiribati.

It was on Nikumaroro in 1940 that a British Naval officer found 13 bones including a skull believed to belong to a castaway. The bones were sent to Fiji for analysis where they were later misplaced. A connection was never made to Earhart because at the time the bones were analyzed and believed to belong to a man. American officials were never officially notified of the discovery.


The International Group for Historic Aircraft Recovery (TIGHAR) took up the mystery of what happened to Earhart and Noonan and the possibility that the 1940 Nikumaroro bones were either the aviator or her navigator in 1988. An analysis of records from Fiji conducted by TIGHAR forensic anthropologists based on new computerized technology indicate that the initial analysis was wrong and the remains belonged to a white female.

TIGHAR conducted new searches of the island in 2001, 2007 and 2010. The search in 2010 turned up the three bone fragments, reportedly in the same area that the original 13 misplaced bones were found. TIGHAR recruited the help of Cecil Lewis of the University of Oklahoma’s Molecular Anthropology Laboratories to analyze the bone fragments. Last week TIGHAR announced that Lewis’ findings were inconclusive. It is possible that the bones are a human finger bone, but bones could also belong to a sea turtle. Other organisms like birds and fish have been ruled out due to the structure of the bone.

Nikumaroro Map. Source: Flickr.
The initial test for the presence of human mitochondrial DNA conducted by Lewis was positive, but subsequent tests did not replicate that result. Because the process of extracting DNA damages the bone, further attempts to determine the bone’s origin would use up the rest of the sample. Doing so would make independent replication – a crucial part of the scientific process in which other scientists conduct the same experiment to make sure that the results are valid – an impossibility.

A mitochondrial DNA profile on Earhart has been compiled from a female relative. Mitochondria are an organelle – a small part of a cell. Mitochondria are involved in creating energy to power the cell. Unlike the rest of the cell, mitochondria contain DNA that is directly passed between mother and child, meaning that it is the same for all individuals on the maternal side of the family lineage.

TIGHAR has decided to shelve the DNA testing of the 2010 Nikumaroro bone fragments to ensure that in the future when DNA analysis technology improves to the point where less material is needed to discover if the bones are human (and if they are Earhart’s) there will still be enough of the bones left to test. But, when the bone is able to be tested for human DNA, the mitochondrial DNA profile of Earhart will be used to confirm if the bones are hers.

Other artifacts recovered from the Nikumaroro site (including what may be fecal matter, a freckle cream jar, and evidence of meals being cooked) are still being analyzed for direct evidence of Earhart or Noonan. Another expedition to Nikumaroro is scheduled for the summer of 2012 – to mark the 75th anniversary of Earhart's flight and disappearance. The new expedition will focus on finding the remains of her Lockheed Electra, believed to be deep down on the slope of the reef on the Island's west end.

The identification of Earhart’s remains (if they are hers) would be a triumph of scientific technology. As her story becomes intertwined with science, it becomes ever more ironic that Earhart didn’t view the information gathered from her flights as science. “I lay no claim to advancing scientific data other than advancing flying knowledge,” she said. “I can only say that I do it because I want to.”

If Earhart has a scientific legacy it is not to be found in her bones. Earhart believed women should never stop trying to excel in fields dominated by men. She busted the boys club of aviation, and paved the way for women to do the same in other fields. Female scientists who have broken into their own boys club, and penetrated the historically male dominated research fields embody Earhart’s determination to succeed.

Whether or not science will one day be able to tell if Earhart met her end on Nikumaroro Island, her legacy to science, and all of society, is in encouraging women to break with convention.

“Now and then women should do for themselves what men have already done – occasionally what men have not done – thereby establishing themselves as persons, and perhaps encouraging other women toward greater independence of through and action. Some such consideration was a contributing reason for my wanting to do what I so much wanted to do.”

Wednesday, February 16, 2011

Humans Contaminate DNA Databases

Interesting research has been published in the online journal PLoS One, describing a problem with contamination in non-human DNA databases. DNA databases are libraries of genetic information about specific species. When a species has its genome sequenced, its genetic data goes into a database so that other research can be conducted based on that known genetic information.

When a DNA database becomes contaminated it means that there is other information that has corrupted the data stored in the database. In the new PLoS One paper the researchers (from the University of Connecticut) evaluated human contamination of databases that were supposed to contain other species - like the zebrafish. So contamination occurs when human DNA gets incorporated into the database for another species. When researchers go to work with the data about the zebrafish for example, they are actually working with human data without knowing it.

The University of Connecticut researchers looked for human contamination in NCBI genome databases, the University of California Santa Cruz (UCSC) databases, and the Joint Genome Institute databases. They found human DNA where it shouldn't have been in a total of 492 of 2,749 evaluated databases.

This contamination issue is extremely problematic because research conducted based on contaminated information can not be trusted to be accurate. It can also be very difficult to track down which databases are contaminated unless the resources (time, money, etc) are spent to evaluate databases for clarity - as was done in this new research.

Database contamination is a relatively new issue brought to light be the massive influx of new genetic information made possible by improved genome sequencing technology. A similar issue that has existed for decades is cell line contamination which occurs when cells that are suspended in culture (alive outside of the body) are contaminated with cells that aren't supposed to be there.

No regulatory body has stepped up and put a stop to cell line contamination in the last thirty years. I just hope that database contamination doesn't follow suit.

To learn more, read the paper about Database contamination, or read an article I wrote for BioTechniques about cell line contamination. As taxpayers we spend a lot of money to fund scientific research, so it is important to know what problems (like contamination) exist in the research community.

Sunday, February 6, 2011

Sequencing Genomes to Save Species

For this post I’m trying something a little different. I mentioned a few weeks ago that I’m using Science Decoded for class, and as a part of that we were assigned to write a post in the form of a list.

*****
All living organisms are made of DNA, a series of nucleotide bases (Adenine, Guanine, Cytosine, and Thymine) contained in chromosomes. Genome sequencing is an analysis of DNA, conducted by “reading” the different patterns of nucleotides A-G-C-T for differences between species, and abnormalities within a species. Researchers around the world are working to sequence the genomes of a variety of organisms, including those on the endangered species list.

1. Orangutan (Pongo abelii) – In January 2011 the National Institutes of Health (NIH) announced the publication of the orangutan genome sequence. Funded by the NIH, researchers from Washington University School of Medicine in St. Louis, MO and Baylor College of Medicine in Houston, TX sequenced the genome of a female Sumatran orangutan, five additional Sumatran orangutans, and five Bornean orangutans (Pongo pygmaeus.) The research shows that orangutans share 97% of their DNA with humans, but compared to humans and chimpanzees, orangutans have evolved much slower leading to fewer mutations (variations in the code between individuals of a species). (Read more

2. Tasmanian Devil (Sarcophilus harrisii) – Fifteen years ago a facial cancer was identified in tasmanian devil populations. The cancer has ravaged the species, resulting in an 80% decline that has forced the species to the brink of extinction. This cancer is transmissible, which means that biting the face of an infected animal passes it between individuals. In September 2010 researcher from the Wellcome Trust Sanger Institute and the genome sequencing company Illumina announced that they sequenced the tasmanian devil genome in an attempt to learn more about the cancer and how to stop it from wiping out the species. (Read more)

3. Giant Panda (Ailuropoda melanoleuca) – Arguably one of the cutest endangered species, the giant panda is a prominent symbol of China, where it lives in a restricted mountain area. According to the Beijing Genomics Institute (BGI) the number of giant pandas left in the wild is estimated between 1600-3000. In December 2009, BGI published the complete sequence of the giant panda genome. With the information obtained by the genetic analysis researchers hope to learn more about the genetic and biological factors that shape this species behavior to assist in disease control and conservation efforts. (Read more)

4. Tibetan Antelope (Pantholops hodgsoni) – Listed by the United Nations as an endangered species since 1979, the Tibetan antelope could hold the key to understanding the pathogenesis of chronic plateau sickness. The species calls China’s Qinghai-Tibet Plateau home, making them ideal for studying the evolution of species that thrive in environments characterized by extreme cold and low oxygen levels. The genome sequence of the Tibetan antelope was announced in December 2009 by researchers from BGI and Qinghai University. (Read more)

5. Coral Reefs (Acropora millepora) – Coral reefs are among the world’s most diverse ecosystems, yet according to the Genome Center at Washington University it has been predicted that in the next 50 years between 40%-60% of the world’s coral reefs will die. In 2005 the NIH funded the sequencing of the coral A. millepora (which is not an endangered species, though coral reefs as a whole are endangered ecosystems) to serve as a “lab rat” for studies of the environmental factors (light, sediment load, or acidity) that can cause coral death. (Read more)

Not quite endangered & not fully sequenced:
6. Polar Bear (Ursus maritimus) – Recently removed from the list of endangered species recognized by the United States, researchers at BGI are still working to sequence the polar bear genome. The polar bear sequence is a part of a three-pronged project to sequence the Tibetan antelope (completed in 2009) and emperor penguin genomes.

7. Emperor Penguin (Aptenodytes fosteri) – One of the most recognizable penguin species, the Emperor Penguin is found in Antarctica. The emperor penguin is currently under consideration for inclusion under the Endangered Species Act, due to the effects of climate change. The genome sequencing project is being conducted by researchers from BGI in conjunction with sequencing the polar bear, and Tibetan antelope genomes. (Read more)

8. Snow Leopard (Uncia uncia) - In October 2009 researchers from Oregon State University, the Western University of Health Sciences, and the Miller Park Zoo (IL) announced plans to sequence the genome of the snow leopard (which is on the Endangered Species list). According to Oregon State, the snow leopard is prone to diseases that do not plague other big cats including pneumonia, enteritis, hip dysplasia, and papillomaviruses. Sequencing the genome could help researchers identify what makes the snow leopard susceptible to these disorders. (Read more)

Genome sequencing technology continues to develop, making it easier and cheaper to sequence the genomes of various organisms. While an endangered species has yet to be saved due to the information obtained by sequencing its genome, what researchers learn will help them gain a better understanding of endangered species, which is a step in the right direction towards improving conservation efforts. 

Friday, January 28, 2011

Revising Taxonomy

Very few people in the United States give a damn about the Egyptian Jackal. While I have nothing to offer as proof of this, I stand by my hunch that this specific canid isn't high on the list of most popular animals, because really, who has even heard of it before? (I hadn't until today...)

Golden Jackal. Source: Wikimedia Commons.
Why then should people care that genomic analysis has revealed that the Egyptian Jackal is actually a wolf, not a jackal at all? Well, because even if you don't find the power of genomic analysis fascinating (like I do) this revision of current taxonomy (the classification of species based on how they are related to each other) is a great example of how science is a fluid thing that continually changes as new things are discovered. I think that understanding how even accepted scientific information can change is a hurdle that many people have to clear before they can really start to follow science in the news.

For years, the Egyptian Jackal (Canis aureus lupaster) was believed to be a subspecies of the Golden Jackal (both species that call parts of Africa home.) Researchers from the University of Oslo (Norway) noticed physiological differences (ie: differences in the way it looked) between Egyptian Jackals and other Golden Jackals, which led them to pursue a genetic analysis.

Sequencing the Egyptian Jackal's genome has shown that it is a closer evolutionary relative to wolves found in India and the Himalayas (even to the United States' Grey Wolf) than to Golden Jackals. Revising the taxonomy could have important impacts on conservation efforts. If Canis aureus lupaster (now renamed the African Wolf -- and the only wolf now known to live in Africa) is a distinct species, an evaluation needs to be done to see how many members of this species there are, to determine if it is endangered.

I like this story because its a great example of how scientists are constantly revising accepted information the more they learn. However, I think when you tell people that science is constantly changing it is important to distinguish between making a revision and being flat out wrong. Scientists weren't just wrong in their taxonomy. The Egyptian Jackal/African Wolf is a canid, so that part of the taxonomy was and still is correct. The genetic analysis enabled research to put the species into an even more specific category.

So when we say that science changes, we mean that it gets more specific and thus more accurate. But that doesn't mean that the scientists who came before had everything all wrong. Often when scientists revise information their predecessors/colleagues were close, but didn't have the necessary tools to learn enough to get things exactly right. There is always more that scientists can learn, and as they do, they fine tune, which is the case with the Jackal/Wolf taxonomy.

For more on the Jackal/Wolf revision, the research paper was published in PLoS One.

Wednesday, January 19, 2011

To Test, Or Not To Test: A Regulatory Question

My internship with BioTechniques dumped me headfirst into the world of genome sequencing. One of the hottest (and by that I mean most talked about, funded, and hyped up) biotechnology fields, genome sequencing has a lot of power. The media loves genome sequencing because it attracts a lot of public interest, so its no wonder the technology is a headline maker.

For those who are unfamiliar with the term, genome sequencing is a process by which a machine takes a sample of your DNA (from saliva or blood) and "reads" it by identifying the nucleotide bases (Adenine, Guanine, Cytosine, or Thymine) that make up your personal DNA sequence. By comparing this sequence to the human draft sequence (a previously "read" and studied human DNA strand) researchers can tell if anything in your DNA sequence is out of place, indicating a chance for genetic disease.

I tried looking into personal genome sequencing companies for an article for my J800 class last semester. While I did come up with an article eventually, I decided not to pitch it on the grounds that none of the personal genome sequencing companies would make a representative available to talk to me, therefore my article was slightly off kilter. Apparently, no one wants to bother with helping a student, and if you don't have a definite place to publish you just aren't important enough for the corporate world to give a damn.

But, I still find personal genomics incredibly interesting, which is why the New York Times article Heavy Doses of DNA Data, With Few Side Effects caught my eye. The article takes a look at research from the Scripps Translational Science Institute that shows that people who pay money to have their genome analyzed often did nothing with the data, and even when the results indicated a higher risk for disease people didn't feel any extra anxiety.

The results are interesting because they go against what you would think the common reaction to obtaining your genetic data would be. There has been controversy about public access to genetic information on the grounds that people won't understand it and will thus act rashly or misunderstand their results. The new research shows that most people either didn't do anything with the information they obtained, or consulted a medical professional before acting.

The new research doesn't close the door on the issues surrounding personal genomics by any means. The idea that the technology and service should be regulated, and by who, and how strictly are all still prominent concerns. However, the study could serve to help policy makers decide how to regulate the industry.

Thursday, January 13, 2011

The Plant That Took Over America

Sphagnum subnitens. Source: Wikimedia Commons.
It grows, it spreads, it takes over North America... its peat moss. Now I know that peat moss isn't exactly the most exciting of topics, but the article Single peat moss plant 'conquered America' stood out to me for a few reasons.

I have written a lot about genome sequencing and genetics, and this research sequenced the genome of the peat moss Sphagnum subnitens, and found that all the samples they collected were genetically identical. This means that there is a common ancestor for the peat moss that spread prolifically throughout North America. 

The research was conducted by teams from Ramapo College in New Jersey (another reason why this article caught my attention,) Binghamton University in New York, and Duke University in North Carolina.  The different types of peat moss vary in color and are found in distinct locations, which makes the 100% genetic match all the more amazing. 

The moss species reproduces sexually, but a single plant can make both the necessary sperm and eggs so its offspring are genetically identical, without being asexually reproduced clones.

Wednesday, January 5, 2011

BioTech's New Hot Shot

There was an interesting article in the New York Times today (yes, I was magically granted access to their website again, not sure why but I'm glad) by Andrew Pollack. Taking DNA Sequencing to the Masses takes an in-depth look at the work of Jonathan M. Rothberg.

Dr. Rothberg is the founder of the genome sequencing company Ion Torrent. The article looks at Ion Torrent's role in providing cheap (under $50,000) sequencing technology with the launch of their Personal Genome Machine. The technology isn't intended for the general public, but will make obtaining a sequencing system more feasible for smaller universities and clinics that can't afford larger machines.

The article draws a parallel between Rothberg and Apple founder Steve Jobs on several occasions. Pollack paints Rothberg as a bit of a rebellious nerd, who certainly has high hopes for his company and the technology they are developing.

Pollack ends the article with Rothberg saying that he believes that genome sequencing will become as useful for medical applications as imaging (like X-rays, CAT Scans, etc.) I like this article because statements like that aren't blown out of proportion. I think that for an article that is focused on what can be achieved in the future the ideas all stay grounded in what is really feasible, which can sometimes be difficult in a science technology article.

Wednesday, December 22, 2010

Elephant Species

Source: Wikimedia Commons.
Photographer: Johnny Liunggren.
Researchers have put an end to debate about whether the African Elephant is one species, or two. New findings published in the journal Public Library of Science Biology show that the African Elephants that dwell in the savannah are a distinct species from those that dwell in the forests.

Loxodonta africana, the savannah dwellers, are much larger and in some cases twice as heavy as Loxodonta cyclotis, the forest dwellers. The debate about whether the elephants were separate species has been going on for at least a decade. The research shows that the two species diverged from their common ancestor around the same time that humans and chimpanzees evolved. How long ago the species split was a surprise for the researchers.

Thursday, October 28, 2010

1000 Genomes Project

For as long as I can remember my parents have been telling me that I'm special (in a good way, not in the derogatory way the kids are using the term these days). Most of us start life out thinking that we're unique and the more we learn about life, and the more it kicks out asses we become so disillusioned that we cease believing we're really all that special.

But, new data generated by the 1000 Genomes Project recently confirmed that our parents have been right all along. The 1000 Genomes Project is an effort to sequence the genes of 2,500 people from around the world in an attempt to fill the gaps in the draft sequence of the human genome left by genetic variation. 

The draft sequence was established in 2000 by teams led by J. Craig Venter and Francis Collins. While that was a breakthrough moment in the field of genetics because it enabled the study of diseases caused by changes in our DNA, it only took us so far. 

Genetic variation refers to the differences in the human genome between individuals (ie: if my code is AGTCAGTC, yours might be AGCCAGTC). That kind of a difference can have a huge impact on how disease manifests itself, therefore studies looking for treatments for genetic-based disorders (Alzheimer's, Parkinson's Disease, Cancer, etc.) are hindered by these variations. 

The new data obtained by the 1000 Genomes Project, is a 95% map of human genetic variation. The results of the study show that each individual person has an average of 75 variations (single nucleotide polymorphisms, or SNPs, which are changes in the code like I described above). These variations are essentially what makes each of us different from everyone around us. My parents were right, I am special, but something tells me they weren't referring to my genes. 

This is exciting for a few reasons:
1. Millions of dollars have been invested in this project, it is good to see something actually come of it. 
2. A better understanding of variation can enable more progressive research on genetic disease, from causes to treatments. 
3. Genome sequencing technology is advancing quickly, and making interesting research like this a reality. Expect more projects like 1000 Genomes, it's definitely about to get ambitious in here. 
4. A project like this sets important standards for open access information and data sharing among researchers for genetic studies at this scale. 

Read more: 

Monday, October 18, 2010

Rare Variants

My article from the October issue of BioTechniques is out! I reported this one back in August right as I was moving to Madison. It is exciting to finally be able to see it in print. It is also available online, which means you should be reading it right now.

Many thanks to the scientists who spent so much time talking to me about rare variants, and to the editorial staff at BioTechniques for editing, and editing, and editing some more. 

Posing with the October issue!
Before you dive into the article, I'm sure you are asking yourself what is a rare variant, and why do I care? Well - rare variants are specific mutations in the genome that only happen in a few individuals, in some cases even just a single person. These variants are important because any time that something is amiss in your genome, it has an effect on you. At times these effects include causing disease. So, studying rare variants can tell doctors important things about disease and possibly help come up with new treatments. But, studying these rare variants is extremely difficult. To learn why, read the article!

Thursday, September 30, 2010

Historical Documents

I consider letters historical documents. I think that when you put words down on paper, even in the casual form of a personal letter it becomes a piece of history. It records what you were thinking at a specific time and place, sealing a bit of history onto paper. I love seeing an envelope in my mailbox, so in the age of email I am lucky to have a few friends that love mail as much as I do, and so write me letters in exchange for me filling their mailboxes.

I just got a letter today from my friend Cassi, and have been wanting to write a reply all day, but have been tremendously distracted by my paper on the American Red Cross, among other things. The paper is for J620 my International Communication class -- we are studying the media of humanitarian movements, which has nothing to do with science writing but as far as electives go I'm learning a lot. It is due tomorrow and my brain is totally tapped out so I'm taking a break from editing to blog (although blogging isn't exactly relaxing for my brain.)

Anyway, I was already thinking about letters and how much I love and appreciate all of my letters, when I saw the article "Rivalry Among DNA Sleuths Comes Alive In Letters," by Nicholas Wade for the New York Times. I am very tempted by the field of science history, if I were ever to turn academic instead of professional I would definitely be interested in exploring the history of science journalism, which in my opinion would include correspondence between scientists (if it becomes part of public record of course.)

The authors of biographies of Watson and Crick (the scientists credited with discovering the double helix structure of DNA) told Wade that the newly found letters from Crick's personal documents don't really add anything new to the historical record of the research that led up to the double helix discovery, but do add personal anecdotes to the rivalry that existed between the researchers at the time.

The correspondence also added a bit to the sympathy that I feel for Rosalind Franklin. She is a researcher who was working on finding the structure of DNA, and she had done all the research and documented everything that she needed to unravel the structure -- she just didn't realize the significance. Watson and Crick are the ones that took Franklin's basic research and realized that DNA has a double helix structure. I've always felt that Franklin got gypped when they were giving out the Nobel Prizes, so I feel for her, she was so close! The snippets from the letters in Wade's article just reminded me of that.

Thursday, September 16, 2010

Chocolate Genes

Source: Wikimedia Commons
A science news story that has been circulating in the media this week is the sequencing of the chocolate genome. I know I've already talked about genome sequences and why I think some are more important and interesting than others so I won't bore you with that. But, I did want to put up links to a couple of different articles on the subject because I think it is interesting to compare and contrast the headlines and leads in terms of who went for the cheesy chocolate jokes, who worked the chocolate in a subtle way, and who went for a strictly hard news angle.

There is value to all of the approaches, so my mind isn't made up yet on what I favor. I think if I had to choose I'd go for middle of the road approach (which is usually a pretty safe place to be) and say that you have to work the chocolate in, in some way because its what makes the story fun, but that you don't have to get ridiculous with yourself and lose the science and the purpose of the story.

CNN: Sweet scientific discovery in the world of chocolate
ScienceDaily: Sequencing of cacao genome to help chocolate industry, subsistence farmers
GenomeWeb: Consortium Using 454, Illumina Sequencers to Decode Cacao Genome
US News and World Report: A Taste of the Chocolate Genome
SiFy News: Cacao genome sequencing a boon to chocolate lovers
CBS News: Sweet Science Cacao Genome Map Completed
Scientific American: Candy-maker releases cacao (coco) genome sequence online
Reuters: Scientists Unlock Coca Genome, Release to Public Domain
New York Times: Rival Candy Projects Both Parse Cocoa's DNA
AOL News: Wunderbar! Scientists Crack Chocolate's DNA Code

Overall, I think that all these articles (which are just a sampling of what is out there) have interesting differences in the way they handle the headlines and even the rest of the body of the story. It might all be about chocolate, but each news organization definitely puts on their own spin.

Sunday, September 5, 2010

J. Craig Venter: Portrait of a Businessman

The New York Times' Andrew Pollack just published an interesting article on J. Craig Venter, the scientists and businessman who became a household name (at least around geneticists' dinner tables) by competing with Francis Collin's federally funded team to complete the Human Genome Project.

Venter's company Synthetic Genomics created a sensation in May when they announced the creation of the first synthetic organism. I covered the finding for BioTechniques: Venter Creates First Synthetic Life. Recently Venter has focused on his efforts to use algae as a biofuel. Despite receiving funding from companies like Exxon Mobil and BP, Venter's algae efforts have generated far less of a media frenzy.

The article takes a look at why Venter's more industrial aims haven't generated the kind of success that his research and science based work has. It also gives some interesting insight into Venter himself.

Thursday, August 26, 2010

Wheat Genome Adds to Available Draft Sequences

Scientists have released the draft sequence of the wheat genome. There are new draft sequences being released all the time as genome sequencing capabilities have increased. While they are all important because they increase researchers' overall knowledge of the organisms that have been sequenced and how all organisms interact and are interrelated, some sequences have a far greater impact than others.

I've written about a few genome sequences that were released in the last year for BioTechniques, but I thought the wheat genome was worth mentioning because of the obvious impact it will have on the food industry. Whenever a staple crop is sequenced it adds to researchers abilities to tackle issues like world hunger by making super foods, but that is an issue which is controversial in and of itself. The more we learn, the more we can do. But just because we can make genetically modified foods that thrive in unconventional climates, should we?

Also just a note about why it is called a draft sequence and not just the sequence: every genome that is sequenced starts as a draft, when researchers sequence a genome there are parts of it that they either don't understand the function of, or that they haven't been able to unravel. So, the working genome that researchers use is a draft, it is what researchers will use compare their own sequencing work with that organism, to check for accuracy. But it is just a draft, drafts can be amended later if need be. Essentially, it goes back to the main nature of scientific exploration: researchers are constantly building on their knowledge base, which is why most scientific findings are left open to be improved upon as researchers learn even more.

Draft sequences I've reported on in the last year:
Horse Genome
Corn Genome
Hydra Genome
HIV Genome
King Tut's Genome

Thursday, August 19, 2010

Junk DNA & A Wisconsin Update

I saw this article in the New York Times today, and it got me thinking about how misleading the concept of "junk DNA" is for the general public. It isn't really a good descriptive term because junk signifies that the DNA isn't needed, when really researchers just don't yet know what that DNA does. It isn't part of the exome (part of the genome that codes for proteins - which make all the substances of your body) but that doesn't mean that it doesn't have a role. I think its a term that people should avoid using because I think it causes more confusion than it does good.

In other news, today was my first full day in Wisconsin. I saw my apartment and met my roommate Francis, and she seems really awesome so that was exciting. I spent all day waiting for my boxes to come from UPS (which arrived at 6:45pm and ripped open, of course) but they finally came so that made me happy. Tomorrow we'll try to actually set up the apartment since my stuff is literally just dumped out all over the place. There is a definite lack of storage so we'll have to try to fix that, but overall the apartment is really nice and in a great location.