CreatureCast – Tangled String

posted by Sophia Tintori / on December 31st, 2010 / in Cell Biology, Podcast

This video is about the enzymes that, for me, first turned cells into little toy chests full of delightful tiny gadgets.

All of the mechanical things that our bodies do, like keeping other things out, or seeing, can be described by somewhat abstract functions. For example, ‘the skin makes a protective sheet’ or ‘the lens focuses light’. But then all of those abstract functions can be broken down again into mechanical motions of the small molecules inside the cells, complete with hinges and springs, making them seem tangible once more, at least to my mechanism-oriented mind: The outside of each skin cell is littered with little molecules that hold on to the same types of molecules on the next cell in a strong handshake, forming a tight, grime-proof layer, while lens cells pack hundreds of copies of a single type of protein up tight against each other, forming almost a crystal, and then jettison all of things in the cell that would scatter light, like DNA or mitochondria, in order to let light pass cleanly through the cell.

This story in this video is about a problem that all living things have — how long and thin DNA is, and how easy it would be to get it all tangled. Not only is there a huge amount of DNA in each cell (around two meters in each human nucleus, for example), but also every time a cell divides into two, the two strands of all of that DNA have to be untwisted from each other to be copied. Think about pulling the fibers of a length of twine apart; the wound end gets tighter and tighter and then twists up on itself, making it impossible to move forward. Thankfully there are these little enzymes, called topoisomerases, that are there to iron out the wrinkles.

Video and narration by Sophia Tintori, with an original score generously provided by Amil Byleckie. The video is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

Waiting for the bus (…in the wild)

posted by Stefan Siebert / on December 22nd, 2010 / in Birds

A couple of days ago when waiting for the bus at Kennedy Plaza near Burnside Park in downtown Providence, I witnessed an episode of urban wild life. Luckily I had my camera at hand. While waiting at the bus stop I started looking into the trees and suddenly spotted a proud red-tailed hawk which just had caught a pigeon and was about to start its meal. I was not the only one who was amazed by the scene. While trying to find a good angle, I bumped into Peter Green, who was also on the hunt for good shots. As I learned, Peter devotes a great part of his free time to the hawks and falcons of the city. Beside the red-tailed these also include Cooper’s hawks and Peregrine Falcons, arguably the fasted animals on the planet, with speeds over 200 mph. If you want to see more of raptor life in Providence visit Peter’s website (or visit Burnside Park). I ended up missing my bus, and the next two as well, but I will definitely keep my eyes open the next time I am downtown.

Pictures by Stefan Siebert

Practical Computing for Biologists

posted by Casey Dunn / on December 7th, 2010 / in Books, Technology

I’m happy to announce the release of Practical Computing for Biologists, a book I wrote with my friend Steve Haddock. Here is a flyer with more information. The book is available directly from the publisher, Sinauer Associates, and from Amazon.

We wrote this book because computational tools are becoming increasingly important across all of biology, but few biologists have training in general tools for handling and analyzing data. There are many reasons for the growing role of computers in biology, even in fields that were adequately served by an Excel spreadsheet and a piece of scrap paper just a decade ago. First and foremost, datasets are now just too large to reformat or analyze by hand, and there is increasing interest in analyzing different types of datasets in combination. Both tasks require custom tools.

Biologists are facing larger datasets for a couple reasons. There is a growing number of public data archives where biologists can deposit raw data from their studies, and these archives enable large analyses across datasets. In addition, instruments now generate far more data than they used to. Improved imaging tools scan organisms at very high resolution, DNA sequencers generate 100,000 times more data than they did a few years ago, environmental sensors can log temperature and humidity at sub-second intervals for months, and physiological instruments are growing more precise. Gone are the days when a young scientist can find refuge from statistics, mathematics, and computer programming in the basement of a Natural History museum, the forests of Halmahera, or a developmental biology lab.

But the changes are happening so fast right now that university curricula haven’t kept up, and biologists that were trained even a few years ago now find that they need to learn computer skills that weren’t covered in any of their coursework or prior research training. There is wide recognition that these are critical problems in biology. There are a couple of possible solutions. First, biologists can work to get computer scientists interested in the problems they face and collaborate with them on solutions. Second, biologists can become more proficient with computational tools. Both need to happen.

Many interesting problems in biology are also interesting computational problems, and there is a strong history of close collaboration that has produced software tools that biologists can use even if they don’t have a computer science background. Many of the day-to-day computational challenges that biologists face, however, are not particularly interesting to computer scientists. These include reformatting the output of one program so that it can be used as the input to another program, automating the download of weather data from several field sites, and writing a script to automatically shuttle data through a series of analyses that require multiple programs and some novel calculations. It is highly unlikely that computer scientists would solve these many routine problems for many biologists, and the challenges are so varied that no one piece of software could take care of them all.

This is where our book comes in. We provide a grounding in time-tested general-purpose tools for handling data, including regular expressions, the Unix command line,  Python, and  image editing tools. An emphasis on general-purpose technologies rather than particular analysis programs enables biologists to build a skillset that can be used to face a far larger set of problems. We hope that the book will be useful to established scientists, as a companion book in courses that have a computational component, and as a stand-alone textbook.

The bird sculpture on the cover is by Ann Smith.

CreatureCast – The Stomatopod Strike

posted by Sophia Tintori / on December 7th, 2010 / in Arthropods, Biomechanics, Podcast (Student Contribution)

This podcast comes from Nati Chen, a sophomore in Casey Dunn‘s Bio 0410 Invertebrate Zoology class here at Brown University. In this video, Nati describes how this crustacean is able to move its appendages faster than could possibly be accounted for by muscles alone.

All of the artwork and edited was done by Natividad Chen, and many of the sound effects are real recordings of stomatopods, provided graciously by the Patek lab at University of Massachusetts at Amherst. The video is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

CreatureCast – Moray Eel

posted by Sophia Tintori / on December 1st, 2010 / in Podcast (Student Contribution), Vertebrates

Here is the first of this semester’s creaturecasts from the students in Casey Dunn‘s Bio 0410 Invertebrate Zoology class here at Brown. Students in this class have the option of making a creaturecast episode for their final project. This one from Phil Lai introduces the Moray Eel and describes the amazing way they eat.

This video was drawn and edited by Phil, and  is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

Enjoy!

Gone Fishing

posted by Sophia Tintori / on October 29th, 2010 / in Jellies, lab, molluscs

This video was taken by a submarine sent down into the ocean to collect deep sea animals. While you’re watching it, pretend you’re driving it remotely from a dark room that’s swaying back and forth, on a boat 600 meters above the submarine, and you’ve been watching marine snow fly by like stars for the last several hours.

One of the perks of working with jellyfish is going to sea to collect them. The Dunn lab occasionally gets the chance to join our friends from the Haddock lab, at the Monterey Bay Aquarium Research Institute (MBARI), on a week-long excursion out into the Pacific Ocean.

About nine scientists from different labs, about five submarine pilots, and a full boat crew leave from Moss Landing aboard the Western Flyer. Once we reach deep water, we stop driving and drop the submarine into the ocean. The submarine that lives on this boat is called Doc Ricketts. It is about 7 feet tall, has propellors, cameras, lights, collecting buckets, spatulas, and measuring instruments. A crane lifts Doc Ricketts off the floor, the floor opens up to reveal the surface of the sea, and the machine is gently lowered into the water.

This is not the type of submarine that people can travel in. Rather, it has a 2.5 mile umbilical connecting it to the boat, where the pilots are driving it around remotely from the control room, while watching a live, high-definition video feed of what the submarine is seeing.

The control room is a dark little cave on the boat. If you are not driving, controlling the camera, or keeping records of the animals, you can sit in the back and watch the marine snow fly by on the screen as the boat rocks deeply back and forth. When someone spots a shadow that looks like an animal, they shout ‘stop!’ and the pilots drive closer to it. Sometimes it turns out to be a decaying blob of sea-lint, but with any luck it’s an intricate radiolarian, or an elusive vampire squid, or some other beautiful creature. After getting a couple of minutes of close-up footage, which is sometimes the only record of the animal as it exists in the wild, we will either collect it in one of the buckets on the submarine, or keep on flying.

By the end of the night, the pilots have brought the submarine back into the boat, hopefully with all 20 collecting buckets full of interesting animals in their native water. Every one lines up and passes the buckets into one of the labs on the ship, and begins sorting through them and looking for their animals. Amidst the excitement, renowned scientists can be heard saying things like ‘Look at this, have you ever seen anything so magenta in your life?’

Some folks will put their animals in the lab’s walk-in refrigerator (with lids, so they don’t slosh out of their bowls with the rocking of the boat) to look at another day. Some will stay up until the wee hours at their microscopes, processing the samples as quickly as they can while the boat speeds through the night to the next destination. In this photograph, Dr. Claudia Mills is gently taking a Paraphyllina out of one of the sampling buckets (from a depth of 2360 meters), so she can draw it and take notes before sunrise, when the submarine will be lowered into the water again.

All of these photographs were taken by Sophia Tintori during a research cruise last year, except the control room photograph, which was taken by Stefan Siebert on a cruise earlier this month. The video of the humbolt squid is also from this recent cruise and it provided graciously by the Monterey Bay Aquarium Research Institute. All photos are released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

Perspective of a bird

posted by Sophia Tintori / on October 11th, 2010 / in Birds, optics

Male bower birds boast an architectural prowess, it is true. They also have a discerning eye when it comes to the color palette for their homes. It turns out that, if that weren’t enough, these birds also use forced perspective, arranging stones in their court in size order to create an optical illusion for the female who is shopping around for a mate.

This is a bower from the one of the avenue species of bower birds — those who build a long avenue out of sticks, with a court at the end made of stones, shells, bones and bits of colored plastic. The female stands outside the avenue (where the photographer was lying to take this picture) and looks through it to the male bower bird who is dancing around on the stones at the back. The funny thing about this picture is that to us the stones look like they are all a similar size, but they are actually arranged with the largest ones in the back, and the smallest ones in the front. If you switch the positions of the stones, as Endler, Endler and Door (Current Biology, 2010) did in this photograph…

… the males will move them back into the opposite size gradient within three days.

The males are creating variation of an Ames room, sort of like this one:

The trick in this picture is that the room is actually much deeper and taller on the left side, and so the leftmost suited guy looks really tiny, whereas the suit on the right is standing closer downstage, on the smaller side of the irregularly shaped room, which makes him look huge. One caveat of this illusion is that it only works if the viewer is standing at one particular point, but this is guaranteed of the female bower bird because she has to look down the long narrow avenue of twigs to see the court. One of the possible reasons the male bower bird creates this Ames court might be to make himself look bigger in the front of the court when compared to other objects placed in the back next to the bigger stones, like the suit on the right.

The bower photographs are from the research of Endler et al, which can be found in this paper from September. The Ames room photograph was grabbed from this blog. More on bower birds and female chosiness can be found in an earlier video of ours on picky females.

Know Your New England Bioluminescants

posted by Sophia Tintori / on September 27th, 2010 / in Arthropods, Comb Jellies, Dinoflagellates

Towards the end of the summer the waters around southern Rhode Island get quite sparkly at night. I’ve wondered for a while what exactly the sparkling things might be, but it wasn’t until recently that I remembered to bring a bucket with me and look at its contents in the light of day.

When I went out to the ocean a couple of weeks ago, I noticed three distinct sizes of glowing creatures; the tiny specks that make a cloud when you kick the water, the medium ones that look like a pair of triangles, and the big circular ones, that stay glowing for a second or two.

Steve Haddock, one of our friends at the bioluminesence lab at the Monterey Bay Aquarium Research Insitute, helped characterize some of these organisms. Here’s what I found.

The larger circular ones are comb jellies.

We get a lot of comb jellies called Mnemiopsis around here. By the end of the summer there are sometimes so many that it feels like swimming in a giant bubble tea. This seems to be a very young Mnemiopsis, not quite mature yet. Comb jellies don’t have any stinging cells, and are not technically jellyfish– corals and anemones are more closely related to jellyfish than these creatures are, even though these look similar. For more about the psychedelic rainbow colors pulsing down the side of this animal, check out Brown undergrad Lee Stevens’ podcast on comb jellies.

According to Dr. Steve Haddock, bioluminesence correspondent, the smallest size of glowing thing is most probably a bunch of single celled organisms called dinoflagellates.

The last glowing group I found seems to be these copepods, a type of small crustacean.

The appendages at the very back of their bodies are long and thin, but move back and forth so fast that they look like little paddles. These thin appendages whipping around are probably what looked little triangles underwater.

These videos and photos were taken by Sophia Tintori, and released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license. Thanks to Steve Haddock for his help. If you see jellies in the water, you should let Steve know at Jellywatch.org. Thanks to Mickey Zacchilli for helping with the video. If you enjoy watching the pulsating comb rows of a comb jelly, here is another clip for you.

Jellyfish Capsule Hotel

posted by Sophia Tintori / on September 11th, 2010 / in Arthropods, Jellies, Parasites, Siphonophores

These little pinkish crustaceans have set up house inside the muscular pulsating swimming parts of the colonial jellyfish, Nanomia. Out in the deep sea, there are few solid structures to call home, so living things will often take shelter in or on other animals.

Fish or bugs often hang around the tentacles of jellyfish because the jellies catch food there and are likely to drop pieces that can be salvaged. But these crustaceans are taking a different approach. They are living inside of swimming bells that are nowhere near where food is caught and eaten. These powerful little pods contract to push the colony through the water. The amphipods are likely to be taking refuge in the sturdy tissue, and feeding off the jellies flesh from the inside of the swimming bell.

Stefan Siebert, a post-doc in the Dunn lab, took this photograph of a Nanomia that he caught on a collecting trip in California. The gas-filled gland that keeps the colony afloat is hanging off the left side of the page. Three swimming bells for jet propulsion (with one amphipod crustacean in each) are seen in the middle. The part of the colony that feeds, reproduces, protects, and more, starts in the bottom right corner of the photograph. These amphipod crustaceans happen to be very similar to the ones we just made an animation about, that live on the fried egg jelly.

Here is a video from Casey Dunn of some other colonial jellyfish, to get a sense of how this close up photograph fits into the context of the whole colony, and to see how the swimming bells pulsate.

This photograph, by Stefan Siebert, is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

CreatureCast – Siphonophore Snacks

posted by Sophia Tintori / on August 23rd, 2010 / in Jellies, Podcast, Siphonophores

Here’s a short episode featuring Trisha Towanda, of the fried-egg jelly story. If you’ve ever wondered what a siphonophore taste like, it’s spicy.

Puppetry and editing by Sophia Tintori, with slightly modified music by Anita. Sea snow from deep sea footage courtesy of Dr. Steve Haddock at the Monterey Bay Aquarium Research Institute. This video is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.