2014 Koch Institute Image Award Winners

Last fall, we featured The Koch Institute Image Award galleries in several Cell Picture Shows. This Show furthers the collaboration, as we showcase this year’s winning submissions. Both the Koch Institute Public Galleries and the Cell Picture Show share a similar ethos: recognition and dissemination of the extraordinary imagery produced through life science research. On March 4, 2014, these winning images were unveiled at MIT’s Koch Institute for Integrative Cancer Research in Cambridge, MA. 

We congratulate the 2014 Image Award Winners and are excited to continue to the collaboration between MIT and Cell Press. This collection of stunning images offers a window into the fascinating worlds opened to us by microscopy and other biomedical imaging techniques.

Biopolymer in Bloom

Julio D’Arcy, Erik Dreaden, and Paula Hammond

Hammond Laboratory

MIT Koch Institute

A New Environment for Studying Cell Growth. Measuring cancer cells’ real-time response to external influences can be challenging. Here, engineers have created biocompatible plastic structures onto which cells can adhere and develop as they would inside the body. The electrically conductive nature of the scaffolds allows researchers to measure the properties of the growing cells. By changing the environment or introducing new substances into the system, researchers can figure out which factors promote or discourage cell growth.

Image: This image, taken with a scanning electron microscope, shows the micro- and nano-scale structures of this device

The More the Messier

Kristin Knouse

Amon Laboratory

MIT Koch Institute

Understanding Complicated Cell Division. The mitotic spindle is an array of tracks that partitions chromosomes during cell division. Most normal cells form bipolar spindles, which segregate chromosomes equally into two daughter cells. However, many cancer cells form multipolar spindles, which cause chromosome mis-segregation and genomic instability.

Image: Like many cancer cells, liver cells also form multipolar spindles during cell division. Shown here is a liver cell with a multipolar spindle (green) pulling the chromosomes (blue) in many directions. Further research into cell division in the liver could indicate how this process is exploited or disrupted in cancer, revealing novel avenues for cancer therapy.

Target Practice

Omar F. Khan and Edmond W. Zaia

Langer and Anderson Laboratories

MIT Koch Institute

Improving Gene Therapy with Nanotechnology. How can we turn off the genes that promote the development of cancer? Using specially designed nanoparticles as genetic patches, engineers can deliver customized payloads to a cell’s gel-like cytoplasm, where most cellular activity occurs, and mitigate the effects of cancer-causing genes in the cell’s nucleus.

Image: This image shows nanoparticles (red) in the cytoplasm of cervical tumor cells (green). As researchers learn more about how cells respond to these therapies, they will continue to tweak the patches to determine the appropriate distribution of synthetic and genetic material to best target different types of cancer.

Blood, Heat, and Tumors

Alex Bagley, Jeff Wyckoff, and Sangeeta Bhatia

Bhatia Laboratory

MIT Koch Institute

Improving Drug Delivery with Gold Nanorods. Blood vessels are highways through the body. They can transport drugs to cancer cells, but finding the appropriate ramp to exit the vessel can be tricky.

Image: This image shows a network of blood vessels (green) and collagen (purple) infused with gold nanorods (yellow) inside of a living tumor. When researchers heat the particles with near-infrared light, the blood vessels become leaky, making it easier to deliver a therapeutic cargo to its final destination. Because blood vessels provide a universal transport system, such combination therapy has widespread implications for treatment, regardless of cancer type or specific drug needed

The Bad Seed

Mandar Deepak Muzumdar 

Jacks Laboratory

MIT Koch Institute

Modeling the Growth of a Tumor. Small changes have big effects. Although scientists know that certain gene mutations trigger tumor formation, the subsequent cellular events that drive cancer progression are not well understood. Cell-specific fluorescent marking allows researchers to track mutated cells over the entire course of cancer development.

Image: This image shows mutated (green) and nonmutated (red and yellow) cells in a pancreas. Over time, the green cells will multiply dramatically and form a solid tumor, while the others will not. Comparing properties and behaviors of the different cell types will set the stage for earlier diagnosis, better treatment, and even chemoprevention of deadly cancers.

Rainbow Connections

Zeynep Saygin

Kanwisher Laboratory

MIT Department of Brain & Cognitive Sciences

Mapping Neural Pathways in the Brain. The human brain is massively complex. Neuroimaging techniques such as MRI provide a noninvasive tool for studying its inner workings.

Image: This image shows pathways of nerve fibers through the brain in three dimensions: up/down (blue), front/back (green), and left/right (red). By comparing these maps of connectivity with maps of neural function, researchers can begin to predict how individual brains will respond to different stimuli. That will eventually help them to understand healthy brain development and will enable earlier diagnosis and interventions for conditions such as autism and dyslexia.

Silencing Echoes

Soheil Feizi, Steven Lee (Artist), Daniel Marbach, Muriel Medard, and Manolis Kellis Computational Biology Group

MIT Computer Science and Artificial Intelligence Laboratory

Cleaning Up Networks. Are all connections meaningful? This image visualizes a new algorithm (known as "network deconvolution") for determining important relationships in complex networks. Like a filter on a camera lens, it reveals which links (lines) between interconnected elements (points) are most essential. As the lens passes over each network area, indirect links disappear and direct links become visible. Already tested on large networks mapping gene regulation, protein folding, and academic co-authorship, network deconvolution can be used to identify key drivers of biological, social, and technological systems.

Ganglion Style

Alex Norton for EyeWire

Seung Laboratory

MIT Department of Brain and Cognitive Sciences and MIT Media Lab

Crowdsourcing Science through Online Games. It's all fun and games until somebody maps a neuron! Then it’s time to move on to the next one. The online game EyeWire challenges players, most of whom have no background in neuroscience, to create virtual 3D models of actual neurons using real laboratory data.

Image: The reconstruction seen here shows ganglion cells in the retina. By comparing this gamer-generated map to previously collected data about the neurons’ firing activity, neuroscientists can create a functional model of how vision works. With more than 100,000 players, EyeWire has already helped researchers to uncover how the eye helps us perceive moving stimuli.

Something Fishy

Annie Cavanagh and David McCarthy

School of Pharmacy

University College London

The Secret Lives of Zebrafish. Humans and fish have more in common than you might expect. Since the 1970s, a tropical freshwater minnow known as the zebrafish has been used to study the genetic and physiological development of living organisms. By mapping the zebrafish genome and studying irregularities in their development, researchers have been able to create robust models of how vertebrates develop and identify genetic conditions that lead to diseases such as cancer.

Image: This image shows a false-color scanning electron micrograph of a zebrafish embryo. It appears in the Koch Institute Public Galleries as part of a partnership between the Koch Institute and Wellcome Images.

Collateral Damage

Aprotim Mazumder, Jennifer A. Calvo, and Leona D. Samson

Samson Laboratory

MIT Koch Institute, Department of Biological Engineering, Department of Biology, and Center for Environmental Health Sciences

Investigating the Side Effects of Chemotherapeutics. How much is too much? When treating cancer, it is important to balance a drug’s effectiveness at killing tumor cells with its toxicity to healthy cells elsewhere in the body.

Image: This image of brain tissue shows cerebellar granule neurons (pink), which sustain significant damage when exposed to certain DNA-damaging therapeutics, and surrounding Purkinjee cells (orange), which do not. Researchers are studying these responses to determine the cell properties and repair mechanisms that make different cell types more or less vulnerable to chemotherapy.

ORIGINAL: Cell

Andy Lomas Lets Digital Systems Bloom In "Morphogenetic Creations" Exhibit

Andy Lomas, a digital artist and mathematician, likes to let the virtual world spin out of control. Using software code to creates very basic rules, Lomas then sits back and watches his digital “growth systems” bloom, fractalize, shape-shift, and otherwise behave in organic and emergent ways.

Yesterday, at the Los Angeles Center for Digital Arts (LACDA), Lomas’s Morphogenetic Creations opened, giving digital art enthusiasts the opportunity to see his dynamic virtual systems up close. The exhibit includes work from the Aggregation, Flow, and Cellular Forms series. To coincide with the exhibit, Lomas uploaded a view of these digital growth videos to Vimeo. Startlingly beautiful to behold, they’re a bit like Ernst Haeckel’s Art Forms of Nature animated with a cyberpunk edge.

I recently rang up Lomas, who lives in the United Kingdom, to talk about Morphogenetic Creations. We talked about his background in mathematics, his early fascination with D’Arcy Wentworth Thompson’s On Growth and Form, and how his work as a computer-generated effects artist for film (The Matrix sequels and Avatar), where highly-predictable outcomes and stability predominate, served as a springboard for the more random digital forms he now creates.

The Creators Project: What can people expect to see at the Morphogenetic Creations exhibit at LACDA?

Andy Lomas: There will be four animation pieces from the Cellular Forms series in the windows, but also then some 44x44-inch big prints of new and old work. They’re ridiculously high-resolution at 12,000x12,000 pixels.

Another thing I have at LACDA for the Aggregation series are picture frames with these old, Victorian-style stereo viewers to create a 3D effect. The frame only contains two pictures, but through the stereo viewer it really looks like this three-dimensional thing. I believe they’re going to pull those out for this exhibit as well.

Is Cellular Forms the most recent series?

The two Cellular Forms videos are the most recent. They’re almost exactly the same date because they’re basically differently rendered versions of the same thing. That would be Cellular Forms and Cellular Forms (X-Ray version).

What I quite like is the idea that there are two things: the creation of these three-dimensional data structures, where the goal is to create the most organic things possible with very simple rules; and that there is no one correct way of doing that. One shows you everything solid, while the other gives you an x-ray that reveals what’s actually going on inside. Neither is the original, if you like. They’re just different views into the data.

And you wrote the software code for this series?
Yeah, I wrote the software for Cellular Forms. I’m a code junky. I write it for my own pleasure. There are two main parts to the code. 

• One is what I call the simulation engine, which is the thing that is actually almost like running a growth process. It starts with a sphere or ball of cells, with rules for how they divide and have forces between them, how it moves, changes shape, and grows over time.  
• Then there is the rendering stage, which takes the data produced by that simulation and turns it into something you can see. It produces pixel data out of cell data, if you like.

Did you use this code in your film work, or did you build it on the side for this specific purpose?
It’s completely built on the side. It’s very much a labor of love. When I worked on The Matrix sequels for this company I was working with then, another person there used a much simpler version of what’s called Diffusion Limited Aggregation for some of the effects work. It was used for when Agent Smith was turning other people into other Smith’s with these tendril things. DLA inspired the code I wrote.

When you’re doing things for films, you have to construct things in a very different way—you have to make things very controllable and directable. Whatever you do, when the director or visual effects supervisor looks at it and says, “That’s great, but can you change this and modify that,” that is what you spend most of your time doing. One of the things I like about my own work is that it is trying to be almost exactly the opposite. You’re hoping for the things which are unexpected.

It’s almost like growing plants; you don’t know exactly how a plant is going to grow. But, you start to learn that if you cross-breed that with that, then it might do something interesting. Maybe nine of the plants end up really uninteresting, but one does something really interesting and maybe different than what you thought it would. People talk about emergence, where things emerge that you didn’t expect, which you almost can’t use in professional production.

Do you prefer the lack of control that your solo work affords you?
I’ve got to say that I prefer the lack of control. As soon as things become digital, people think that they can control everything. When you get to a certain level of complexity, you can explore it more than control it. I prefer the things where 99% of the time it doesn’t produce anything interesting, but that 1% of the time is like, “Wow, that’s really cool.” I’m not a control freak director. I actually want the work to surprise me instead of do exactly what I thought it was going to do.

What specifically might have influenced Cellular Forms and your other series?
I’ve always been fascinated by sculpture and form. I also used to scuba dive and look at coral. To my mind, organic things go from really hideous to incredibly beautiful, whereas most engineered things go from ugly to something quite interesting. In organic forms, there is a very visceral reaction. Trees look beautiful and mold looks ugly, and things like that.

My original background is in mathematics, which I studied as an undergraduate. One of the main areas I got interested in is what’s called Dynamical Systems, which is sort of the math behind Chaos Theory and Complexity Theory—the math of how things change over time when you almost reapply the same rule again and again and again. So, the combination of those two, it’s almost like how simple could the rules be to make something that is as beautiful as a tree or coral or something like that. So, those two have always been like two germs working together. And, to my mind, computers are the things that allow you to actually try that out.

Any other critical influences in your work?
There was a Scottish mathematician named D’Arcy Wenthworth Thompson, who wrote a book about a hundred years ago now called On Growth and Form, which is basically him talking about the constraints of the real world. When you think about how things grow, are the sorts of forms that you see in the real world just the results of almost the only things that can grow? With a computer we can actually test that. Often, it doesn’t work quite how you expected.

For more of Lomas' work, head over to his website here.

@djpangburn

ORIGINAL: The Creators Project

By DJ Pangburn
Jan 10 2014

Popular Scientist. Aydogan Ozcan (LUCAS Inventor)

ORIGINAL: UCLA MAGAZINE
By Robin Keats
Apr 1, 2013


UCLA Associate Professor of Electrical and Bioengineering Aydogan Ozcan is one of the world's "Brilliant 10" scientists, as proclaimed by Popular Science magazine. Ozcan is the director of the Bio-and Nano-Photonics Laboratory at the UCLA Henry Samueli School of Engineering and Applied Science, where he leads a team of students in creating breakthrough—and inexpensive—technological devices that bring the frontiers of medicine to ordinary individuals.

Photo by: Clara Richmond.

We could begin with any one of more than a dozen startlingly original inventions to frame the contributions of Aydogan Ozcan, but let's start with the crowd-sourced bio-game he and his team of researchers created to diagnose malaria. One thousand online gamers from around the world were directed to identify, then "kill" or "bank," infected red-blood cells that appeared on their screens as electronic images. Their success rate at identifying the disease was very comparable to that of medical experts. This decidedly non-expert methodology is designed for use in developing nations where hugely expensive diagnostic equipment is unavailable.

And then there is BigFoot, the name Ozcan gave to the monitoring software he pioneered that allows diabetes patients and others with chronic foot ailments to track their conditions at home using a conventional flatbed scanner and a PC.

These are just two of an apparently endless lineup of incredible ideas that spring from the mind of the 34-year-old scientist who already holds 22 patents, with more than 15 pending, for inventions in wide-field and lens-less imaging, nonlinear and fiber optics, critical coherence tomography and nanoscopy.

Ozcan's self-described "prize child," though, is LUCAS, an acronym for "Lens-less, Ultra-wide-field blood Cell monitoring Array platform based on Shadow imaging." It turns a cell phone into a diagnostic device by clipping on a gadget that combines an LED light, a spatial filter and a slot for a medical slide. Information is gathered by the device, which sends it off to diagnosticians anywhere in the world. Bring LUCAS into the jungle where people get little or no medical attention, and voila! Expert diagnosis.

Through the device, millions of people in such remote areas as sub-Saharan Africa who would otherwise go undiagnosed will be screened or monitored for malaria, and eventually for tuberculosis and HIV. It will also help prevent waterborne illnesses that kill about 5 million people a year. And the cost to clip LUCAS onto your cell phone? Five to 10 bucks.

No 'Aha' Moment
Ozcan was born in Istanbul, Turkey, in 1978. His father was a government worker, his mother a housewife. His education began in the small, Black Sea city of Sinope, which also gave the world Diogenes, founder of Cynic philosophy. "My family moved around a lot," he says. "Five different schools for the five years of elementary school we have in Turkey ... I think those moves caused me to develop skills that have helped me quickly adapt to things."

Ozcan went to Bilkent University in Ankara for his bachelor's degree. He earned a master's degree and Ph.D. at Stanford University, followed by two years in Boston on the research faculty of Harvard Medical School's Wellman Center for Photomedicine. Ozcan joined UCLA as an assistant professor in 2007.

What turned him onto scientific innovation? "There was," he says, "no 'aha' moment." But as early as his freshman year in high school, "the idea of proving something and learning the framework of proofs was so unique," he recalls. "That's when I said 'I love it' [and] thought I'd be in a profession that allows for the creation of useful things." 

Add caption

For his breakthrough medical diagnostic inventions, Ozcan has been honored by NASA, the U.S. Department of State, the Gates Foundation, National Geographic and Popular Mechanics, among other institutions and publications. In the photo above, he is holding a prototype of his LUCAS device in his lab.

Teaching Invention "Being a scientist and going to the frontier of knowledge requires a lot of dedication, a lot of small things put together," he says. "I insist that my students know that those who are successful in this profession are the ones who learn how to cope with failures. You improve from rejection; you write a new manuscript; you try again. Some people would say, 'It's enough.' I won't play that game."

It has to be that way, Ozcan says of his role as an educator. "Within the school of engineering, the function of a professor is to create new information and new technologies. You also have to train the next generation of engineers and scientists, so that new know-how is continually created to make life simpler."

Ozcan adds, "The definition of engineering, for me, is to make life simpler and better. That's the most important thing that differentiates an engineer's mind from that of a physicist. A physicist is looking at interesting questions, but not how a combination of disciplines could be applied to create things that will enhance life. That's the intersection of science and engineering and I want to be, professionally, at that juncture. Engineers need to be very multidisciplinary. That's what I stress in my lab."

Creating Invention
The man whose world involves complex technologies like optics, photonics and imaging has a simple vision of his own future as an innovator. "It's like a single picture," he says. "You can give yourself 10 or 15 years to paint it, but then it's going to be something you can admire. That's how I take my career. I'm in the middle of that picture now [with] the expansion of the cell phone into an array of telemedicine tools."

Cell phones, he points out, have better graphics processors than IBM supercomputers had in the late 1980s. "There are already 5 billion cell phones in use," he explains. "We manufacture 2 billion of them every year … There will be more of them everywhere on the planet."

With this phenomenal global network of smart gadgets, he points out, computation is almost free.

"Because cell-phone use is so ubiquitous and inexpensive," he adds, "I can rely on it … to design new microscopes and micro-analysis tools that look at bodily fluids using technology attached to the cell phone or running on it."

The "Nano Internet" and Beyond
The young scientist's next challenge is already obvious to him. He foresees spending the next decade or so building the "Nano Internet," which he describes as "the development of these personal micro-analysis tools [that] give us something more valuable than the tools themselves."

What he envisions are millions of his tiny devices interconnecting and streaming personal health information in real time, from brainwaves to blood-pressure counts.

"If my lab and others like it do our work well," he predicts, "then we'll have this kind of Nano Internet. The opportunities that lie ahead of us, with our eyes, with our information, channeled into the micro and Nano worlds."

These and other trails yet unimagined will be blazed from Westwood. "UCLA maintains and extends such vision," says Ozcan. "It's got everything I need to fulfill whatever I dream."

Biology Basics: What’s the deal with Epigenetics?

ORIGINAL: OBR Review
Written by Brian Abraham

January 17, 2013

Photo credit: © WGBH Educational Foundation

Why do we care?
With few exceptions, namely functionally variable regions in the immune system and in disease, all of a person’s cells have the same DNA sequences and genes. Yet the variety of cells in terms of shape and function is vast. How is it that a muscle cell and a blood cell have the same genes yet do such strikingly different things?

In short, not every gene is being used or transcribed by all cell types: There are certain genes that are essential for blood cells that muscle cells don’t express (transcribe) or use. For example, genes making proteins that recognize foreign bodies would be useful for an immune blood cell but would be a waste of a muscle cell’s energy. The burgeoning fields of epigenetics and epigenomics investigate these patterns of on/off genes and what regulates their expression. Epigenomics refers to the genome-wide application of epigenetics, which generally refers more to single-gene analyses.

Where does it apply?

“Epigenetic” as an adjective refers to heritable traits that are not changes to the DNA sequence itself. Heritability can be across both cell divisions as well as trans-generational. When a fat cell replicates and both daughter cells retain fat cell traits, inheritance is referred to as divisional/replication inheritance. When offspring retain traits of their parents, the inheritance is termed trans-generational inheritance.

A famous example of such trans-generational epigenetic inheritance is the Dutch Hongerwinter. In 1944, the Dutch in areas of the Nazi-occupied Netherlands were starving as the result of a blockade. Fetuses that developed in the wombs of mothers surviving the famine showed a number of characteristic traits of nutrient deprivation themselves, including glucose sensitivity. Later biochemical analyses demonstrated epigenetic marks on genes regulating insulin-like growth factors– characteristics of nutrient deprivation– despite no change in the DNA of these genes. Further tests of second-generation offspring may show that these marks and traits acquired in response to starvation are inherited across multiple generations.

Before Darwin’s famous description of evolution by natural selection, Jean-Baptiste Lamarck proposed the idea that traits acquired by the parent can be passed down to offspring. For instance, a giraffe’s neck is long because its parents had to stretch to reach higher trees. When On the Origin of Species elegantly explained population shifts by survival, the idea of heritability of acquired traits lost popularity. The theory was further buried when Mendelian genetics demonstrated the mechanism of genetic inheritance. It has lain dormant until a recent resurgence in interest implicating epigenetics as a plausible explanation for trans-generational inheritance of acquired traits.

How does it work?

Roughly 3 meters of DNA sequence is stored inside every nucleated human cell; the condensation and packaging of the DNA sequence is essential to regulation of gene expression. In general, uncondensed genes are expressed more readily than condensed genes. Following is a discussion of the various methods by and degrees to which genes are condensed into “chromatin”– the name given to the DNA/condensing protein complex.

Developmentally Programmed Nuclear Destruction during Yeast Gametogenesis (PND) Michael Eastwood/Dr. Marc Meneghini Video Abstract

ORIGINAL: Cell Video Abstracts

Francesca Peri - Developmental Cell Sieger/Peri Video Abstract

Radiación de los móviles es causa del TDAH en ratones de laboratorio [ESTUDIO]

ORIGINAL: Mashable

Marzo 17, 2012

KateFreeman

Foto cortesía de iStockphoto 

Mujeres en embarazo tengan cuidado: es posible que desee agregar los teléfonos celulares a la lista de  de las cosas de las cuales debe mantenerse alejada de durante el embarazo.

Los investigadores de la Universidad de Yale estudiaron los efectos de la radiación de los móviles de las crías de ratones embarazadas y la exposición a determinados podría dar lugar a discapacidades de desarrollo como el TDAH (Transtorno de Déficit de Atención e Hiperactividad), su estudio señala que en el 15 de marzo emisión de informes científicos.

Se colocó un teléfono móvil silenciado en el modo de llamada activa encima de una jaula de ratonas embarazadas. Otro teléfono móvil totalmente inactivo se colocó encima de otra jaula de ratones embarazadas para actuar como un control. Las ratonas en ambas jaulas tuvieron crías, que se dejaron crecder. A continuación, los investigadores realizaron una serie de pruebas para medir la actividad cerebral en los ratones adultos que habían estado expuestos a la radiación, como fetos. Las pruebas mostraron que los ratones tenían una menor capacidad de memoria y eran más hiperactivos que el grupo control. Las áreas del cerebro que controlan estas funciones se han visto afectados por la radiación, dicen los investigadores. Llegaron a la conclusión de que la radiación de los celulares impacta negativamente en el desarrollo del cerebro de las crías, y potencialmente podría causar discapacidades en el desarrollo como el TDAH .

El estudio es el primero de su tipo en vincular radiación de los móviles de los trastornos del desarrollo en los hijos, de acuerdo con el Dr. Hugh S. Taylor, jefe de la División de Endocrinología Reproductiva e Infertilidad en la Universidad de Yale Medical School.

"Hemos demostrado que los problemas conductuales en ratones que se parecen al TDAH son causados por la exposición a radiación de telefonía celular en el útero", dijo Taylor a Science Daily. "El aumento de los trastornos de conducta en los niños humanos puede ser en parte debido a la exposición del feto al celular de irradiación de teléfono."

Los ratones se gestan durante un tiempo mucho más corto que los seres humanos (sólo 19 días) y nacen con cerebros mucho menos desarrollados que los seres humanos, dijo que el primera co-autor del estudio, Tamir Aldad. Se necesita más investigación para demostrar los posibles riesgos de radiación de los móviles a los fetos humanos.

los teléfonos celulares se han vinculado como causantes de mucho, desde la muerte masiva de colonias de abejas a su disposición a sacrificar la propia vida sexual y las relaciones. Docenas de estudios y los investigadores han debatido la cuestión de si o no la radiación de los teléfonos celulares causan cáncer. Es un tema todavía en debate.

Delfines encallados fueron salvados por la comunidad (en Brasil)