Tuesday, October 23, 2012

Monocyte Fashion

Hyperbolic Blood Cells,
by Cyberxaos; Feb. 2008 
Monocytes play a role in infection-fighting and in inflammation. However, they are only one type of cell that run the body's immune system. But they do it with style.

Each monocyte has different abilities to react to and release chemokines (chemicals that cause action), and each has a different surface, a surface decorated with different types of CD molecules. There are three basic types of monocyte: classicnon-classic or patrolling, and intermediate. They are categorized by their CD molecules, their fashion.

The classic monocyte sports relatively a lot of CD14 and no CD16 molecules. Tim Gunn refers to them as CD14++CD16-; at least he would if he wrote about the fashion of monocytes. These are the monocytes we mainly think of, the divas or warriors that go to sites of infection and differentiate further into macrophages and dendritic cells. If the body does not need all of them, they are sent back to the bone marrow fitting room where their fashion is altered...they get down-regulated to CD14+CD16++ and become patrolling monocytes.

Different cells within blood
from Wikipedia
The CD14+CD16++  non-classic patrolling monocytes hang out on the lining of blood vessels and in the spleen, but also participate in general, not-too-inflammatory, wound healing. These monocytes are the least inflammatory of the bunch.

Of course, there are monocytes in the middle: the intermediate, pro-inflammatory ones. They secrete tumor necrosis factor and other chemokines to keep inflammation going. They have been linked to atherosclerotic activity. The fashion for this function is CD14++CD16+, in between the classic and non-classic patrolling design.

Most fashion is superficial, but the surface of monocytes determines their actions and how they react to their environment. And we have only touched the surface of monocytes. Other posts will convey how they develop, how they are trafficked within the body, and how they function in trauma and infections.

Source: Pamer EG, Shi C. Monocyte recruitment during infection and inflammation. Nature Reviews/Immunology. November 2011; 11:762-74.

This is the third post of a series: Inflammatory Language. The series will briefly emphasize aspects of inflammation, mainly in response to microorganisms, but not always. You can contribute to this column by submitting a 300-400 word piece to me by email, along with byline.  If deemed appropriate (it can be serious, political, scientific, or funny as long as it pertains to inflammation), we'll publish it here and not use it for anything else--thank you. At some point, I may be able to offer compensation, but can only now offer the warm fuzzy feeling you get when you post something for people to read.

Friday, October 19, 2012

Short Story Science: Stone Link

Red Granite Stones at Braewick Beach
A section of a photograph by Mike Pennington

Richard usually liked staring out the window, but not this evening. His neighbor, Mrs. Gerkart, was standing still at her door, with her key in her hand. Richard didn’t like what he saw. He ran to her, but she disappeared. A small red granite stone lay on the stoop as her substitute.

“Okay. That was not real. No more coffee so late in the day,” he stuttered to no one but Sam, his red Persian. Sam looked at him as he would any other day, and returned to the house, to his nap on the couch.

Richard had had Sam only a month. He had followed Richard home from a walk. It was Don, his best friend at the college, who said he should keep Sam. “Give him a chance. You’ll be less lonely,” he had said while tapping Richard on the shoulder. Richard never learned where Sam had come from, but they settled in nicely together. Sam liked the food, warmth, and occasional attention that Richard gave him.

That night in bed, as he lay thinking about gorgons, Richard got an awful headache. He opened his eyes, and in front of him was a man in sandals carrying a large bag. The man wasn’t standing; he was two feet off the ground. Richard couldn’t breathe. The bag was familiar. He heard hissing—perhaps it was his fan. Sam leapt from the bed, making a most uncharacteristic sound for a cat, and ran out. Within a few moments, there was nothing, the room empty, and the fan was off. His headache was gone.

Richard blinked into the dark. Perhaps he had had too much salt at dinner. Sleep was now out of the question, so he went downstairs to make coffee. Mrs.Gerkart’s porch light was on. With no worries, but in need of distraction, he went back upstairs with his mug to the den, to work on a work-in-progress, Mythology and Modern Man. He taught ancient history at UW, but found mythology and its link to modern life fascinating and was slightly obsessive about it.

A half hour into his work, he noticed that Sam as nowhere around. Finding this strange, he went back down stairs—in  his slippers, untucked USC t-shirt, Green Bay Packers pajama pants, and hair channeling Einstein—to look for him. Standing three feet from the stairs was Sam—stiff and staring.

“What’s wrong Sam?”

Sam didn’t move.


For only an instant, the headache returned and he saw the head of Medusa in Perseus’s hands. Perseus knew what he was doing.

Richard hardened and fell to the floor.


“Richard, I got worried about you when you didn’t attend the Spartan webinar with us last night,” Don was at Richard’s bedside at the hospital.

“Oh. I guess I forgot. What happened to me?”

“The doctors say you have toxoplasmosis. You probably got it from Sam. Your arthritis medicine weakened your immune system, and you got a brain infection. They have you on medications, so you’ll be okay now.”

Richard wasn’t too sure. “But Perseus had Medusa’s head.  He was there, Don. And Sam and I were turned to stone." He knew Don wouldn't believe this. "Where’s Sam?”

Don knew Richard was confused, but toxoplasmosis could cause confusion, and Richard had been working too hard. “He’s at home, fine—eating tons and frisky as anything.” Sam was different, but okay.

“It seemed real. Mrs.Gerkart too, the neighbor. How is she?”

“I don’t know. She wasn't home when I went over there. Probably at her daughter’s house in, where was that? Michigan?” He looked unsure. “Get some rest now. I’ll be late for class if I don’t get going. Be back later.” He saw Richard’s upturned gaze. “It’s okay Richard. It wasn’t real.”

Richard was not too sure. There was a chill in the room, and the smell of water and rocks entered his sleep. 

Don did not return later.

Tuesday, October 16, 2012

Petroplague: Oil-eating Microbes

For the most part, I prefer walking along rows and rows of books in bookstores to online shopping. Ebooks, not being on real bookshelves, don’t currently have much of a chance with this non-nook, non-kindle, non-ipad, I-want-to-turn-an-actual-page reader. However, I may need to change. Many great science ebooks and many works of fiction with science are available only in digital format, and Petroplague has gotten my attention. There are no zombies. There is gas and a petrol-feasting organism that jeopardizes the way we live. This was a different plague. I read…<gasp>…PDF.

The title didn’t grab me, nor did the cover art. But the author did. Here is my disclaimer: I’ve corresponded with Amy Rogers, so there may be bias. 

I started my correspondence with her (or her with me) because of our shared passion and enthusiasm for science and science writing. It drips off her. It runs through her website and into her support of other authors. I’m sure the enthusiasm runs into her home-life too, into her family and children—they will benefit immensely from her.

So, because of Amy and her enthusiasm, I read. I found great microbial science, oil-eating microbes running amuck, a well thought-out Los Angeles landscape, children’s stories and songs, references to art, and  characters who grew with knowledge.  Here is what Amazon says about her:

Amy Rogers, M.D., Ph.D., began her writing career in elementary school by (unsuccessfully) submitting anecdotes to Reader's Digest in hopes of earning twenty-five bucks. By junior high her real passion was science, especially microbiology. In the bedroom of her home in rural southern Minnesota, she kept Petri dishes of bacteria in an egg incubator and won purple ribbons in science fairs. That passion led her to study biochemistry at Harvard, and ultimately to earn a doctorate in immunology. Wee beasties animated her years of teaching microbiology at the university level. More recently, micro-critters inspired her to write novels and short stories that highlight their amazing powers.

Amy's thrilling science-themed novels pose frightening "what if?" questions. Compelling characters and fictionalized science--not science fiction--make her books page-turners that seamlessly blend reality and imagination. Relentlessly curious, Dr. Rogers works for scientific literacy and nature education for kids.

This author loves dim sum, Ted Drewes, redwood forests, Minnesota lakes, Hawaiian beaches, and cats. She lives in Northern California with her husband and two exceptional children who believe she has an unreasonable tolerance for mysterious things growing in her refrigerator.

What is not to like?

File:USA tar bubble la brea CA.jpg
From Wikipedia: La Brea tar pits
In Petroplague, Syntrophus, a microbe, escapes experimental confines and begins to eat up oil-derived chemicals like the tar in the La Brea tar pits, the gasoline in cars around the Los Angeles area, and the oil within California’s geological structure. Big problems result (understatement).

Within the text, there is an exhibition of contagion theory and the growth of microorganisms…

“Christina cordoned off her grief and started to work. She picked up a bacterial culture needle—a thin platinum wire mounted on a pencil-like handle—and lifted the wire into the hottest part of the burner flame until the metal glowed red. After allowing the wire to cool in the air, she plunged it into a flask of cloudy yellow liquid:  an old culture of the photosynthetic E. coli bacteria. Then she dipped the tip of the wire into a tube of fresh sterile broth. To the naked eye the wire looked clean, but Christina knew it was covered with thousands of invisible bacteria that would slip off into the fresh food and begin to grow vigorously, doubling in number every half hour. Only a touch was all it took to spread bacteria from one liquid to another.”

And Petroplague outlines well in the following three scenes how microorganisms can potentially spread and lead to disaster:

“He poured about a half cup into the borehole, and the plague-infected fuel disappeared into the depths. Jack expected to repeat this process all the way to Mission by looping back east across the valley floor to the city of Bakersfield and to the Kern River oil field where he knew pump jacks covered the arid plain as thick as paparazzi around an A-list celebrity.

The rod on the contaminated pump jack rose and fell, rose and fell as Manley and Jack strolled away.”


“When unfolded, the gauge stick was twelve feet long. Ronny lowered it through the port and dipped it into the gas. The overfill alarm was right; the tank was nearly full. He refolded the stick and kept it handy because he’d be using it at the stations he visited next. Then he sealed the access port, packed up the gas hose, and wheeled his tanker tuck back on the road.”

And this scene in which a mechanical “pig” is used to run through fuel lines to check their integrity:

“Did you bring the pig, Al?” Ken asked.

“Wouldn’t be doing my job if I didn’t,” Al replied. “I’m the pig keeper.”

They both smiled at his joke.

“These smart pigs are my babies,” Al continued. “The one in the truck is new. I used it for the first time yesterday. Worked like a charm.”

”Which in-line inspection did you use it for?”

“We ran the pig through the gasoline delivery pipelines. Got data on the integrity of all the 87 and 89 octane pipes, from storage tanks to trucks.”

”Then I expect the pig will do a good job again today. We’ll run it through the jet fuel pipelines from here to LAX. Program the pig to record information on metal loss and corrosion, and temperature and pressure in the pipe. Of course if there are any early signs of fracture, I want to know. Get pictures, if you can.”

”It’s as good as done,” Al said.

Uh oh. Insert ominous music here. Christina, the main character—a PhD. student and Dr. Chen, her mentor, are working out the details:

They would get more details from the DNA tests and the chemical analysis of the gasoline, but Christina could no longer deny the facts. Her bacteria were eating L.A.’s gas.

Just before dawn, Christina and her boss shared their data with each other. In laboratory science, results were often ambiguous or conflicting, but their efforts tonight had produced clean data and an inescapable conclusion. Dr. Chen looked defeated, his shoulders sagging and his face wooden.

“I have to contact the authorities. If the infection spreads…” He paused, and shuddered. “The oil-eating bacteria mush not escape the L.A. basin. The city must be quarantined.”

Is there a solution? Dr. Chen leads Christina to a potential cure, but is it?

“…an antibiotic that seems to affect Syntrophus.”

“I thought we tested all the antibiotic classes and none of them worked.”

“This is a new substance. I don’t have a clue what it is, I just know that it’s produced by one of the microbes in our collection”

“From an oil field?”

“Yes. Presumably these bacteria compete with each other in the wild, and one species evolved to make an antibiotic that kills the other.”

Of course, there are twists that I can not divulge. It is a thriller with disaster at every turn. And aside from the wonderful science, the characters grow throughout the story. 

Even the assumingly thick boyfriend of Christina’s cousin can grow—from a man who places grilled chicken on the same platter as the uncooked pieces—to a curious conversationalist regarding mutated bacteria.


“Not exactly. More like, they learned a new skill from some friends.”

“We’re talking about itty bity microbes here, right?” Mickey said.

 “We are, but even bacteria have ways of sharing information. The information is in the form of genetic material. Bacteria can actually give some of their DNA to each other in a process called horizontal gene transfer. It happens in the wild. Last night I found DNA in my Syntrophus that wasn’t there before. The new DNA codes for aerobic survival.”

Don’t worry. Aerobic is explained, but not pendantically. The story will show you what it is. 

File:Hieronymus Bosch - The Garden of Earthly Delights - Prado in Google Earth-x4-y1.jpg
A section of Hieronymus Bosch's dark and
disturbing work;from Wikipedia
Also well placed within the story are details of microbiology experiments, details of what bioremediation is, description of bacterial predators, growth of microorganisms, PCR, and DNA hybridization and ELISA analysis, lateral genetic transfer…whew! It is not, however, written with the PhD in mind. It truly is written for all readers from high school on up (some middle schoolers may enjoy it too). Humor and references to children’s songs and stories and to artwork (nod to Hieronymus Bosch) added interest as well.

For the curious-minded who wish to learn more, end notes on various topics (i.e. collapsitarianism and lateral gene transfer) are provided. This is where Dr. Rogers explains how the real science was used in the story.

In short, the science of the book holds high honors, channeling the work of Craig Venter and numerous bioremediation scientists. Petroplague explores what happens when the products of great and interesting science get into the wrong hands of ecoterrorists (and a greedy businessman).

I think Petroplague and the idea behind it is fantastic. And it can now sit on your bookshelf, or occupy space on your favorite ereader. 
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