Wednesday, December 19, 2012

It's The Most Wonderful Time Of The Year!

This is my favorite time of year (November-December), and so in keeping with the magic of the holiday season, it seems appropriate to show some of the most 'magical' images of the microscopic world!

Confocal image of Polypodium Virginianum spore filled sporangia and paraphyses (specialized protective hairs). 2012 Olympus Bioscapes International Digital Imaging Competition. Image credit: Dr. Igor Siwanowicz, HHMI Janelia Farm Research Campus

"Brainbow": cerebral cortex of mouse brain. Individual neurons express different colors to permit researchers to distinguish between and follow the path of each neuron. Image Credit: Mr. Pierre Mahou, Dr. Emmanuel Beaurepaire, Dr. Karine Loulier. Laboratory of Optics and Biosciences(Mahou, Beaurepaire) Institut de la Vision (Loulier)

Pollen in hazel catkin section. 2012 Olympus Bioscapes International Digital Imaging Competition. Image credit: Mr. Michael Gibson, Northampton, UK

Beech cross section. 1994 Nikon Small World Photomicrography Competition. Image credit: Jean Ruegger- Deschenaux, Zurich, Switzerland

And finally...happy holidays, everyone!
Collage of stained mammalian cells, Nikon Small World 2011 Photomicrography Competition. Image credit: Dr. Donna Stolz, University of Pittsburgh

Friday, December 14, 2012

New Species Of Slow Loris Discovered In Borneo

Slow lorises are small, furry, and utterly adorable. But don't let their cute'n'cuddly appearance fool you- slow lorises also have the distinction of being one of the few mammals that have a toxic bite.

In a study published recently in the American Journal of Primatology, researchers reported finding a new species of slow loris, Nycticebus kayan, lurking in the jungles of Borneo. Nycticebus, derived from ancient Greek, translates to 'night monkey'. The species was named for the mostly nocturnal habits of its members, a trait which can make finding and studying members of the genus Nycticebus difficult.

To classify the different species of slow loris, researchers focused on differences in the loris' furry 'facemasks'. Their findings have raised the slow loris species count by three. What started out as a single species (N. menagensis) and two subspecies (N. bancanus and N. borneanus) are now recognized as three distinct species, while N. kayan is an entirely new addition.

Tuesday, December 11, 2012

Immune Cells, Attack! T Cells Genetically Engineered To Target Tumor Cells

In this video, T cells (purple) are vigorously attacking cancer cells (red). T cells have very important functions in the immune response. These immune cells are 'trained' to identify and respond to foreign invaders in our bodies. Cancer cells are typically included in their repertoire, as most cancer cells are abnormal enough that they are recognizable as a distinctly foreign population of cells among healthy cells; in many cancers, however, T cells lose the ability to recognize cancerous cells and fail to fight off the growing tumor.

Researchers at Adaptimmune, a company specializing in T cell therapy, extracted T cells from thirteen people with multiple myeloma, a type of cancer. Engineered genes encoding receptors that would better recognize the proteins NY-ESO-1 and LAGE-1 were then added to the extracted T cells, which were then re-injected into the patient. All thirteen patients were simultaneously given a standard treatment for multiple myeloma.

Monday, December 10, 2012

H. Pylori's Achilles Heel, In 3D

According to folk wisdom, being under extreme stress is enough to give someone an ulcer. As it turns out, stress has little do with peptic ulcer diseases and gastritis (inflammation of the stomach): the real culprit is the bacterium H. Pylori. Over 90% of all cases of peptic ulcer disease and gastritis are the product of infection with H. Pylori. The stomach bug gained notoriety after it was discovered that individuals infected with the microbe had a six times higher risk of developing gastric (stomach) cancer than unaffected individuals. Since then, H. Pylori has been vilified for its pathogenic qualities. (To be fair, colonization of this stomach critter may have some redeeming qualities: later studies have indicated that H. pylori infection may reduce the risk of esophageal adenocarcinoma, another type of cancer).

Helicobacter Pylori. Image credit:

The notion that a bacteria could live and thrive in the stomach took some getting used to among scientists and doctors. The environment in the human stomach is extremely harsh and acidic, making it inhospitable to many micro-organisms. H. Pylori has adapted by cleverly developing a way to neutralize the stomach's acidity by secreting an enzyme which breaks down urea, a naturally occurring waste product in human fluids. The enzyme, urease, chops up urea into its component parts, ammonia and carbon dioxide. Ammonia, which is basic, then neutralizes the acid in the stomach.

H. Pylori is shaped like a corkscrew and possesses a long whip-like tail, or flagella. These properties are exploited to allow it move efficiently through the liquid environment in the stomach aided by the flagella and to burrow into the lining of the stomach as a corkscrew would spiral into a wine cork. After settling into the stomach lining, H. Pylori infection may be asymptomatic in some individuals or may contribute to the development of ulcers or gastric cancer. It is not yet clear why the bacteria is pathogenic in some individuals and harmless in others. To test for the bacteria, a simple blood test for antibodies against H. Pylori or testing for urease in patients' breath is often sufficient to diagnose H. Pylori infection.

H. Pylori in stomach tissue retrieved during a gastric biopsy. Image credit: Wikipedia

 After infection has been confirmed, infected individuals are typically given a round of antibiotics to fight off the bacteria. Researchers at the DOE's SLAC National Accelerator Laboratory at Stanford University wanted to find a new, more efficient way of eliminating the ulcer- and cancer-causing bacteria. They managed to find a chink in the microbe's armor- by disabling the mechanism which permits neutralization of stomach acid, they realized, the microbes would then become vulnerable to and unable to survive the extreme acidity of the stomach.

H. Pylori takes in urea from its environment through small channels and chops it up before releasing neutralizing ammonia and carbon dioxide, the byproducts of this activity. A team of researchers led by Hartmut Luecke reported in a paper which was published online in Nature on Dec. 9th that they had managed to solve the structure of these channels by x-ray crystallography.

The first step in solving a protein structure by x-ray crystallography is to actually getting the protein of interest to crystallize in a neat, well-ordered pattern- a task which is notoriously difficult with membrane proteins. Proteins are finicky enough as it is, and even slight changes in pH, salinity, temperature, and other variables can cause a protein to change or lose its shape. Membrane proteins are especially problematic because they need to be carefully extracted from the membrane in a way that won't disrupt the actual shape of the protein; after removal from the membrane, moreover, certain parts of the protein that are normally hidden from water and tucked away within the membrane may be exposed, causing the protein to change shape. All told, experimenting with 'growing' conditions for protein crystal samples is often time and labor intensive.

Luecke and his team stated in a press release that they screened thousands of crystals before finding the right one for their experiment. Once they had the urea channels crystallized, they determined its structure by x-ray crystallography, bouncing x-rays off of the protein and measuring the scatter of the rays to create a 3D map of the protein (I know that explanation isn't really doing the process any justice, so imagine tossing thousands of tennis balls at a statue and carefully recording and measuring the angles and directions they bounce back in...then, from that mountain of data, figuring out where they must have initially struck and bounced back from to reproduce the image of the statue- in other words, its complicated).

Understanding the structure of these channels makes it easier to identify potential drug targets or therapeutic ways of interfering with these channels activity. Disrupting the movement of urea into the cell would compromise the microbe's ability to neutralize its environment, rendering the bacterium unable to survive in the extremely acidic human stomach. Instead of relying on antibiotics as a catch-all treatment for H. Pylori infection, which may sometimes harm the 'good' bacteria in our gut, solving the structure of the microbe's membrane urea channels may permit for the design of a more specific and reliable way of targeting the bacterium in the stomach.

Thursday, December 6, 2012

Can Homicides Be Contagious?

A new study which appeared in the most recent issue of the journal Justice Quarterly suggests that homicides may be just as contagious as the flu. 

The study was led by April Zeoli, an assistant professor in the School of Criminal Justice at Michigan State University. Zeoli and her team studied homicide rates in Newark, NJ between 1982 and 2008 by entering the time and location of each murder into software typically used to monitor infectious disease. They found that the program could be used to predict and model the spread of homicides in a manner similar to the movement of infectious diseases throughout a population. 

In the 26 year period encompassed within the study, the homicide rate in Newark was on average three times higher than the national average. The homicide 'epidemic' originated from central Newark after a rise in homicide cases in that area before spreading to the southern and eastern wards of the city. As a number of homicide cases cropped up in the areas outside of central Newark, homicide rates in central Newark dropped. This pattern was maintained as homicide cases spread throughout the city, with rises in homicides spreading to neighboring 'susceptible' areas before dwindling back down at the source. Zeoli hypothesized that gangs and firearms acted as the infectious agents which were the vehicle for the spread of homicides throughout Newark.

Certain areas of the city, however, remained unaffected throughout the 26 year period, similar to the resistance observed in certain populations when tracking the spread of infectious diseases. By studying these areas, Zeoli suggests, law enforcement officials may be able to identify the variables which confer 'resistance' to a given population and devise ways to encourage similar qualities in at-risk population. Identifying vulnerable populations- typically in poor, low-income areas- which the homicide 'epidemic' is most likely to spread to next may also serve as a useful tool for law enforcement officials to predict the spread of homicides and intervene when possible by directing their resources to those areas.