Warm as a fish in the sea

No one can accuse the opah, Lampris guttatus, of being a cold fish. Nor could one call it a cold-hearted fish. Even if it were the most emotionally distant and bitter of all fish, the opah is in fact a warm fish. That is to say, the opah is a warm-blooded fish.

Warm-bloodedness, or endothermy, provides many distinct advantages to an organism, including quicker reaction times and increased muscle power. As endotherms are able to move between very cold and very hot environments, they also see increased habitat expansion. Endotherms can conserve heat generated by metabolic processes and maintain their body at temperatures above or below that of their surrounding environment. Endotherms that live underwater, such as whales and dolphins, have adapted to the challenges of retaining body heat in water, which has a particularly high heat capacity, by employing thick layers of blubber. Continue reading

May 2015 SWAC Seminar: Mark Derewicz

mark_derewicz_7092web

Mark Derewicz

Speaker: Mark Derewicz, Science Communications Manager at UNC School of Medicine/UNC Health Care

Date: May 26th, 2015

Time: 5:30 PM

Location: Bondurant Hall, Room G030

Event Link: https://swac.web.unc.edu/event/mark-derewicz-seminar/

Last month, SWAC hosted a very successful first seminar featuring Lauren Neighbours, PhD, RAC, from Rho, Inc., a contract research organization in Chapel Hill. This month we are switching gears from medical writing and regulatory affairs to writing about science for a non-scientific audience.

Our featured speaker will be Mark Derewicz, Science Communications Manager at the UNC School of Medicine and UNC Health Care. Mark’s main role at UNC is to write press releases and feature stories on both basic science and clinical research ongoing at the university. He also manages relations between UNC and local, state, and national media. Additionally, Mark was formerly a writer and editor for UNC Endeavors, an online magazine profiling research efforts at UNC, where he pitched several stories to NPR. Mark is especially skilled at making high-level scientific concepts accessible, an ability that is currently more valuable than ever with the advent of social media and increased interactions between scientists and the general public.

If you are interested in learning to better communicate about science with a broad audience, please come to SWAC’s Monthly Seminar on Tuesday, May 26th at 5:30 PM in Bondurant Hall (Rm. G030) and hear what Mark has to say.


PEER EDITED BY Dan Albaugh AND JONATHAN SUSSER

Follow us on social media and never miss a SWAC Seminar Announcement:

This article was co-published on the TIBBS Bioscience Blog.

NCI Ras Initiative: Let’s get together and drug RAS!

Non-scientist friends and relatives often ask me whether I am “curing” cancer, and question why the cure for cancer doesn’t already exist following decades of funding for research. Worse, some social media conspiracy theorists are irrevocably convinced that the cure for cancer already exists, but, for monetary gain, the government only allows companies to treat patients with subpar chemotherapeutics that will only  prolong the disease, not cure it. When faced with such conversations, which are usually a testament to the poor public science education in this country, I tell people about the complex nature of cancer and the difficulty of cancer drug development. I try to explain that cancer is different in every person. I discuss the heterogeneous nature of tumors, and how different sections of a single tumor are genetically distinct from one another. I explain that it is incredibly difficult to identify a therapeutic window where a compound can selectively target and kill tumor cells and not healthy cells, because tumor cells are just corrupted versions of your own healthy cells. I even quote my graduate research mentor, Dr. Channing J. Der and say, “Cancer drug design is not for the faint of heart.” Then, I usually tell people the story of the RAS proteins.

 Over thirty years ago, the RAS proteins were implicated as oncogenes, which are genes that have the potential to lead to cancer when not properly regulated. Today, we know that activating mutations in the three RAS isoforms, N-RAS, H-RAS, and K-RAS, are present in nearly one-third of all human cancers. Additionally, these mutations actively drive some of the most aggressive and deadly tumor types, including lung, colon, skin, and pancreatic cancer. These discoveries sparked decades of unfruitful efforts to design inhibitors of RAS as a means to selectively target and eliminate tumor cells that are dependent upon RAS signaling for growth and survival, while avoiding damage to normal cells. After three decades, and an unthinkable amount of money and effort, no pharmaceutical company or academic institution has been successful in targeting RAS proteins with any clinical efficacy.

RAS-image

Continue reading

Naturally GMO, the sweet potato way

Contrary to scientific consensus, the public at large continues to harbor concerns over the consumption of foods containing  Genetically Modified Organisms, or GMOs. To make matters worse, scientists have now discovered we have unknowingly been eating GMO foods for more than 10,000 years. Indeed, it seems our overambitious ancestors may have even selected for crops with these controversial modifications.

Copyright Bailey PeckWhile performing small RNA-sequencing on sweet potatoes, Tyna Kendt et al. (PNAS, 2015) stumbled upon reads with sequence similarity to genes found in Agrobacterium. This genus of bacteria is commonly used by plant biologists for genetic engineering as it has the ability to transfer DNA from its own genome to plants. In fact, Continue reading

Move over, Mendel

Recently featured in Science, Valentino Gantz and Ethan Bier have developed a novel genome editing method that subverts traditional heritability. Termed the mutagenic chain reaction, this process  can insert new mutations in the genome that automatically spread themselves to neighboring chromosomes. Thus, homozygous mutants are generated after just one generation, instead of the two generations normally required under Mendelian rules of heritability.Gregor_Mendel_frownsauce

To successfully impart mutations, the system uses CRISPR/Cas9 technology. CRISPR/Cas9 consists of two parts: a bacterial protein (Cas9) that cuts DNA and a guide RNA (gRNA), which determines where cutting will occur. When expressed together in cells, Cas9 cuts DNA at a site in the genome specified by the gRNA. The CRISPR system can be used to silence genes or to insert new genetic material into the genome. In this report, the researchers use genes encoding CRISPR components as their insert. This powerful and potentially dangerous improvement led to creation of homozygous mutants in fruit flies after only one generation.

First, genetic material encoding CRISPR components is injected into a fruit fly embryo. After being expressed in the injected flies, the CRISPR components find and cut the DNA at the gRNA-specified site. After the DNA is cut, the chromosome must be repaired through a process called homology-dependent repair. This is a process by which DNA sequences are exchanged between identical or similar DNA molecules to repair the damaged DNA. If there are extra genes included in one of those sequences, they will be inserted as well. As you might guess, the genetic material that was originally injected carries the aforementioned identical DNA sequences, leading to permanent incorporation of the CRISPR components into the genome.

Next, the process begins again. The second target sequence, residing on the second copy of the chromosome, is cleaved, and the identical DNA sequences from the first chromosome are incorporated. The end result is a genome, previously unedited, that possesses two copies of brand new DNA. Traditional models of heritability dictate that homozygous mutants should take at least two generations to be present in the genome. The mutagenic chain reaction can achieve this effect in only one generation.

MCR Figure

The implications of this research are a double-edged sword. The mutagenic chain reaction has tremendous potential in expediting the creation of model organisms. Additionally, scientists could modify mosquitoes and other human disease carriers, reducing their potential to spread disease. However, once an edit is in the wild, its effects, good or ill, are irreversible. Discoveries such as this are exciting, but must be carefully controlled. The authors acknowledge this fact, and went to great lengths to ensure that their engineered flies never made it out of the laboratory. The flies were kept inside three layers of containment, and were only ever handled by one researcher in secure biosafety areas. The authors even suggest having another major molecular biology conference, similar to the 1975 Asilomar conference on recombinant DNA, to set guidelines for future use of genome editing technology.

Technology like CRISPR and the mutagenic chain reaction hold potential to fundamentally change how humans interact with nature, for better and for worse. Already, much knowledge has been gained from CRISPR. For one, we now know better than ever that rules—even 150 year-old ones—are made to be broken.

edited by Rachel Cohen and Erinn Brigham

Gantz and Bier Article: Valentino Gantz and Ethan Bier, “The mutagenic chain reaction: a method for converting heterozygous to homozygous mutations”. DOI: 10.1126/science.aaa5945

Follow us on social media and never miss a science news article:

This article was co-published on the TIBBS Bioscience Blog.

Mr. Turtle

In 2012, I was working at the Cooperative Oxford Lab in Oxford, Maryland, when we were notified of and rescued a stranded sea turtle. Sadly, the turtle was so sick that it died. An intern performed the necropsy (an autopsy on animals) and found that the turtle’s stomach was full of plastic trash and even a belt buckle and a hair comb. I never got  the image of the dying turtle out of my head.

Meanwhile, besides mourning plastic-choked sea turtles, I was also feeling bewildered and upset by the constant talk from overseas outlaws, urging us Muslims living in the west to commit destructive acts. I decided I needed to do something to protest such talk, and it suddenly hit me that I could teach myself how to make animated videos declaring my love for the exquisitely lovely country of Sweden, where I used to live, and my darling home state of North Carolina. Little did I know that this commitment would eventually serve me in many more ways.

It took a few years, but a light bulb finally went off in my head, and I put two and two together: why not use my new animation skills to shed light on environmental concerns?  Even better, why not do this as a project with children? This is how the animation “Mr. Turtle Gets Sick” came to be.

SAMSUNG

Teaching children how to animate!

A second grade teacher at Northside Elementary, right here in Chapel Hill, graciously allowed me into her classroom last October through December. Along with help from my little brother, two fellow geology students, and especially my brother’s roommate, we first taught the children sea turtle ecology, let them draw illustrations, and recorded each child’s voice for the narration.

2014-12-04 12.28.12

The crew of “Mr. Turtle Gets Sick.”

After this, we began animating. We first taught this to the whole class and then worked with each child individually. We provided the oversight and structure while letting the kids decide on the different actions and take the helm of doing the actual computer work. For example, if a child wanted to show Mr. Turtle swimming, then he or she specified Mr. Turtle’s position at both his start and end point, and the amount of time it took him to move that far. The fact that there was a “timeline” component meant that, in addition to the reading, artwork, and animation involved, the kids even practiced their math skills by learning how to space the actions out evenly. The illustrations the kids had drawn served as the background scenery.

 

At the unveiling, the children saw the finished product for the first time, and all the parents were invited for the viewing. The parents were thrilled! Afterwards, I contacted a local sea turtle expert, and he came to the classroom and did a follow-up presentation. He told the kids about sea turtle nests on North Carolina’s beaches, how sea turtles get caught in fishing nets, and how actually not all species of sea turtles eat jellyfish. The kids had so many questions that we kept going right until it was time to go to lunch.

Working with children was a beautiful experience, especially after being around academics all day. If anyone is interested and would like to be involved in future similar activities, please email me!

Animation: “Mr. Turtle Gets Sick”

Credits: Sharla Coleman’s second grade classroom at Northside Elementary, Mejs Hasan, Sean Catangui, Ali Hasan, Elsemarie deVries, Theo Jass

Software used: Blender, a free, open-source 3D modeling and animation program.

See ‘Mr. Turtle Gets Sick’ and other animations by Mejs here:

Mr. Turtle Gets Sick: http://youtu.be/ierH4oUaqO4

Dear Foreigner: http://youtu.be/jW99oPD3gK4

Freedom: http://youtu.be/H4inZuEF4ZM

Peer edited by Suzan Ok and Leanna Gentry.

Follow us on social media and never miss an article:

Arctic Tales of Icy Trails

Far out in eastern Russia, deep in the Siberian Plateau, lies one of the great waterways of the world. 

The Lena is the eleventh longest river on Earth. For thousands of treacherous kilometers, she makes her way through forests and across tundra, eventually delivering her waters into the icy cradle of the Arctic Ocean. The power of these frigid landscapes is such that for six months out of the year, the surface of the Lena is completely frozen.

The freeze starts with the deepening chill of October and extends through black December twilights and a solemn New Year.

Even when fresh springtime breezes arrive, melting the ice, the Lena pays a terrible price for her freedom. The sheets of ice do not yield peacefully, drop by drop, in a quiet surrender to the warmth. Instead, the process is rife with violence. As some parts of the ice destabilize, the flow of the river increases suddenly, and before the ice has a chance to melt, it sweeps downstream, displacing and spilling water over the banks and causing major flooding. This process is called “ice break-up.”

Very few people live along the vast plain where the Lena alternates between flow and ice. Near the Arctic Circle, a lonely station is the last shivering wisp of human life before the river dissolves into its northern grave.

Sarah Cooley in the lovely Scandinavian dream of Iceland, just one of the countries where she has pursued her polar studies as a UNC student.

Sarah Cooley in the lovely Scandinavian dream of Iceland, just one of the countries where she has pursued her polar studies as a UNC student.

Records made at this station over several decades indicate the precise date in spring when the Lena breaks free of her icy grip – the precise date when the ice crumbles and the entire river flows again. Over the past years, this date on which the ice breaks has crept earlier and earlier.

Thousands of miles away, in an office at UNC, sits Sarah Cooley. She has never been to Russia, nor seen the Lena with her own eyes, so she cannot tell you about its beauty, or ferocity, or chill. However, she has seen the Lena plenty through images. These are not images captured by a camera, but rather images captured by satellites, whose falcon-like eyes see much from their distant orbits. Can careful mastery and manipulation of these images tell us something about ice break-up on the Lena, something beyond the comprehension of a single station outpost?

It was August 2014, and Sarah was preparing to start her senior thesis. She wanted to focus on glaciers and satellites, so she went to find Dr. Tamlin Pavelsky, a professor in the geology department, whose earlier research focused on ice break-up in Arctic Rivers. However, Dr. Pavelsky completed his project in 2004, during the infancy of the newly-launched Terra and Aqua satellites. These satellites carry onboard quite a remarkable instrument called MODIS.

Although its name makes every aspiration at modesty, MODIS has much of which to be proud. Since 2000, the MODIS sensor has snapped images of the entire planet, every day. That means hundreds of thousands, if not millions, of images dedicated just to Arctic rivers like the Lena are available, free of charge, on a NASA website.

Now that MODIS is fifteen years old, her idea was to recreate Dr. Pavelsky’s project, incorporating the many extra years of data into the study. The first step required Sarah’s full familiarity with the NASA LAADS website, from which she had to download over 16,000 satellite images.

“It might be the most images anyone’s ever ordered before,” Sarah explains. The four Arctic Rivers she studied stretch out over 18 MODIS scenes. For each of those 18 scenes, Sarah downloaded 60 days’ worth of images over the fifteen years of MODIS’ existence. The sixty days were centered on March, April, and May, since that is the window in which the ice break-up occurs. Eighteen scenes on sixty days for fifteen years added up quickly!

It took Sarah three months to acquire her full library of images. The ordering process is not too difficult, “but then you have to wait for it, and when you get it, it’s not always what you expected, it might have errors, or wrong dates and be the wrong place.”

These images from MODIS show the progression of ice break-up on the Lena River of Russia. Where the river shows white, it is frozen ice. The white slowly overtaken by black water indicates that the ice is disappearing.

Nevertheless, after a Christmas break spent watching Sherlock and trying the utter patience of the NASA LAADS website, Sarah eventually was ready to proceed with her analysis of those thousands of images.

The thing to know about satellite images is that they are not precisely like the pictures we might snap, with ambitions of posting to Facebook and getting 100 likes.

A satellite image is a record of how much light is being reflected off the surface of the Earth – and not just the ordinary, commonplace lights like blue light, red light, and green light. Satellites also venture into the realms of light humans can’t see, such as near-infrared light, and short-wave infrared light, and all sorts. The falcon eyes of MODIS captures these wavelengths of light, then translates its findings into simple numbers that computers and brains can interpret and analyze.

Sarah was sitting on a trove of 16,000 MODIS images of near-infrared light. But can near-infrared light actually tell us anything about ice in Arctic rivers? This is where Sarah had to experiment.

She found that when the Lena was frozen, it reflected almost all near-infrared light that reached it. On the other hand, when the river was an unshackled tumult of free-flowing water, its reflectance was very low. And when the river was a mix of ice and water, its reflectance value was somewhere in between.

Sitting in her warm office thousands of miles away, Sarah started watching the progression of ice break-up on the Lena by using near-infrared light as the key to unlock her satellite images.

With her reflectance data in hand, Sarah sliced her northern rivers into ten kilometer slabs. Then, like a child playing with its food, each slab was cut into impossibly tiny 250 meter pixels. For all her MODIS images, Sarah counted up which of her tiny pixels crossed the threshold that equaled ice; which lay in the range of water; and which belonged to the brew that denotes a mixture of ice and water.

On the day that 75% of the tiny pixels in a given slab passed the threshold that implies water, that slab was declared to have undergone its spring melting. This method finds the exact date that each slab of river melted, allowing detailed analysis of melting time on a year to year basis. It means that instead of a single date of ice break-up provided by a lonely station near the Arctic Circle, Sarah can now produce an estimate of when ice break-up is happening along the entire river.

It’s a very straightforward approach, and that’s one of the things Sarah likes about MODIS. “I really enjoy the simplicity, and it being daily is great. You can really do a lot with it.”

Of course, Sarah did not count all of the pixels and separate them into categories by hand. Instead, she wrote a series of computer scripts that did the work. The first part of her script classified the MODIS images into land, water, ice, and ice and water mixture. Then, all clouds were removed. Finally, computers calculated the amount of ice melt in each 10-kilometer slab. These scripts took three hours to run per river, much preferable to the hundreds of tedious hours it would take to do by hand. Now the scripts can be passed on and used by others, absorbing the newer images that MODIS keeps adding to its archives.

It is quite an achievement, especially compared to how Sarah felt when she first arrived at UNC as a freshman and saw older classmates doing sophisticated projects.

She remembers vividly thinking: “Oh my gosh, I can never do that. Now I realize I can do so many more things than I ever thought I could. And I realize that learning all those things isn’t something that happens overnight, it’s something you learn by taking classes, doing research, working in the lab. And now I’m never intimidated by coding. I love coding and seeing the things I can do with it.”

We are now in the waning days of April, and Sarah will soon graduate from UNC Chapel Hill. She and Dr. Pavelsky are finalizing a paper on their results.

After UNC, Sarah is moving to England to complete a Masters of Philosophy degree in Polar Studies at Cambridge University as a Gates Cambridge Scholar. Showing a persistent interest in Arctic ice, she plans to focus on glacier flow in Greenland.

Sarah fell in love with Greenland and wanted to pursue polar science ever since she studied abroad in Denmark and visited the Greenland ice sheet. “It’s really cool being out there, and there’s people, wildlife. Some people like to study polar science in Antarctica, but to me, it seems so empty. I like how in the Arctic everything feels connected to the people and the land.”

Meanwhile, the Lena still succumbs to the bleak icy thrall that envelops her every October, from which she cannot relax until the spring ice break-up, which every year creeps earlier in the calendar. Signs of climate change are everywhere.

Will the river change its melting patterns? Will its ice break-up involve more flooding in the future, or will it occur in irregular patches that do not progress linearly down its Siberian route? All of these are questions that satellites, ground station data, and scientists like Sarah can help to answer.

Peer edited by Chris Givens and Chelsea Boyd. 

Follow us on social media and never miss an article: