Stories tagged Cells

May
12
2009

Yes, this is on the list too
Yes, this is on the list tooCourtesy tsweden
Check it out: it turns out that women have more powerful immune systems than men. (I include myself in the “men/boys” group.)

So, let’s see… if we’re arranging the list in terms of the order in which I’ve realized each one, then this new development falls at the end, right after “better resistance to sunburn” and “less likely to get testicular cancer.”

If the list is alphabetical (how nice and neat!), it goes between “more powerful backstroke” and “more powerful interpersonal skills.”

Despite my rabbit-killing-strength grip and my powerful stammer (each unlikely to be beaten by women as a whole), the bite of each item on the list burns like jalapeño scorpion stings.

It’s nice, then, that this new fact isn’t quite so painful to accept. See, I like getting sick. I want to get sick. In particular, I want to get the swine flu. My great-grandfather was beaten (i.e. killed) by the swine flu back in 1920 or so, and I’ve been aching for a rematch. Swine Flu vs. JGordon Round II: The Final Showdown: This Time it’s Personal: A Century-Old Family Feud Comes to Blows: To the Death!

Sure, I don’t actually want to die at all, but this disease needs to at least get a foothold in my system if we’re finally going to see who’s the bigger man. (Me, duh.)

If I were what we often call a “lady,” my powerful immune system would make the flu showdown less likely. So thank goodness that that’s not the case. My female body would be producing estrogen left and right, and that estrogen would be blocking the production of an enzyme called Caspase-12. Caspase-12, precious Caspase-12, is needed in my body, because it blocks my inflammatory processes. Inflammation is one of the body’s primary defenses against infection. Blood flow increases at the site of an injury or infection during inflammation, beginning the healing process and delivering structures that kill and absorb pathogens. And I don’t want that. I mean, if every time Evander Holyfield approached Mike Tyson’s boxing ring a flood of blood and plasma crushed Holyfield and washed him away, how would The Dynamite Kid ever have gotten the chance to prove who’s tougher? I want to let the swine flu into my ring, and then I want to bite its ear off and threaten to eat its children.

I’m leaving it up to my frail male body to arrange this fight.

Apr
11
2009

Amazing nano factories known as proteins

Protein structure: three representations of the protein triose phosphate isomerase.
Protein structure: three representations of the protein triose phosphate isomerase.Courtesy Opabinia regalis
Understanding proteins and how they work is very useful. One type of protein called an enzyme is like a nano sized factory that can take apart molecules or build new molecules out of smaller parts.

Plant cellulose can be turned into ethanol fuel. Oil slicks could be digested into non-pollutants. Custom designed proteins will soon allow "living" factories that can manufacture almost anything we can imagine. Protein "hackers" are creating synthetic antibodies — proteins designed to bind tightly to specific targets, such as tumor cells, which can then be destroyed.

The Defense Advanced Research Projects Agency

To accomplish this goal, DARPA is investing in the development of new tools in diverse areas such as topology, optimization, the calculation of ab initio potentials, synthetic chemistry, and informatics leading to the ability to design proteins to order. At the conclusion of this program, researchers expect to be able to design a new complex protein, within 24 hours, that will inactivate a pathogenic organism. Protein Design Processes (DARPA)

The Protein Data Bank and Rosetta@Home

Proteins are made from a complex chain of amino acids. Several resources are helping to illuminate the complex relationship between the sequence of a chain of amino acids, the shape into which that chain will ultimately fold, and the function executed by the resulting protein.

The Protein Data Bank is an ever growing data bank of detailed schematic protein information. Another program that is helping to understand how proteins are shaped is the Rosetta@Home project which allows thousands of home computers to determine the 3-dimensional shapes of proteins being designed by researchers.

Try protein folding

"Would you like to play a new computer game and help scientists analyze protein chemistry -- at the same time? Here is a fun and interesting computer puzzle game that is designed to fold proteins -- the objective is to correctly fold a protein into the smallest possible space." Grrlscientist

Watch this video to learn how to "fold-it"

Apr
06
2009

What if your doctor could prescribe a pill that would erase any and all of your worst memories instantly?!

Rather than reliving it every single day, you could simply forget the time in 6th grade when you farted while doing sit-ups in gym class, and the day that your beloved cat Pookie was run down by your mother's Buick, and the boyfriend who broke your heart when he ran off to join the circus.

Rather than dwelling on bad memories, you could forget about them and move on to live the rest of your happy sunshiny life.

While it may sound like the plot of a certain indie film, brain scientists at a lab in Brooklyn are working on a scientific breakthrough that may make all of this possible. They've discovered that a chemical in the brain called PKMzeta acts like a speed dial to all of our worst (and best) memories. When a drug called ZIP is injected directly into the brain, memories are blocked and viola! No more dwelling on the painful, embarrassing, traumatic past.

Nevermind that it isn't quite that simple, or that this method has only been tested on rats, or that it involves a chemical being injected directly into the brain. It's from Brooklyn, so you know it'll be on the gifts & novelties table at Urban Outfitters just in time for the holidays. In fact, I can already see the marketing campaign involving lots of waifish models who apparently forgot to eat.

While this kind of 'made to order' miracle memory eraser won't be hitting the shelves anytime soon, there is a whole lot of money being spent on research that aims to better understand how memory works inside our brains. The reason that scientists want to know how memory works is that memory is so important to our emotions, our ability to learn, our spatial knowledge, our motor skills and much much more. When it isn't working as it should be, all kinds of problems can result.

For some people, painful and traumatic memories can wreak havoc on their emotional and social lives. Post-Traumatic Stress Disorder and Depression are examples of diseases that involve the unconscious recall of frightening or upsetting memories. If these memories could be blocked, patients might experience a dramatically improved quality of life. Bad habits are also tied to our memories, since addictive behaviors are learned. If memories of experiences with drugs and alcohol could be blocked, some addicts might stand a better chance of recovery. And for those who suffer from Alzheimer's or Dementia, improvements in the understanding of memory could lead to new methods of memory enhancement, helping to reduce the impact of these diseases.

While plenty of good things will come from this kind of research, it also raises ethical questions. Any drug that can dramatically improve or block selected parts of our memory will inevitably find a commercial market among people who may not suffer from any disease at all. Students who can afford them might start taking memory enhancing drugs right before an exam, criminals might use memory blockers to short circuit the moral questions that arise from their behavior and ordinary people might be tempted to use memory blockers to forget painful or embarrassing moments, rather than learning from them.

To top it all off, since our good and bad memories are not neatly sorted for doctors to target, erasing painful memories would probably mean getting rid of some of the good ones as well. Sometimes it's hard to tell which is which, since good or bad, your memories make you who you are today.

Source: New York Times

Mar
29
2009

Plasmid genetic transfer
Plasmid genetic transferCourtesy Mike Jones

Stem cells from skin via virus transfer feared carcinogenic

Embryonic stem (ES) cells are like blank cells that give rise to every type of cell and tissue in the body.

In Nov., 2007, scientists reprogrammed human skin into stem cells. That technique used cancer causing viruses which remained in the created stem cells.

Such genetic baggage posed safety concerns for potential therapies like cell transplants, and confounded work in the lab, as the introduced genes sometimes spurred mutations that interfered with the normal function of induced cells.

Stem cells produced with no viral remnants

Now, by using a plasmid rather than a virus, James Thompson and Junying Yu have converted adult skin cells into pluripotent stems cells that are completely free of vector and transgene sequences.

The resulting cells, says Thomson, are remarkably similar to embryonic stem cells and show the same capacity to proliferate indefinitely in culture and diversify into all the cell types of the human body. Univ of Wisconsin News

Stem cells for tissue regeneration coming soon

This is a major advance toward safely reprogramming cells for clinical use. The new viral vector-free iPS cells will be available to researchers almost immediately through the International Stem Cell Bank at the WiCell Research Institute.

Research paper abstract in Science:
Human Induced Pluripotent Stem Cells Free of Vector and Transgene Sequences

Mar
20
2009

Result of massive hoax: Don't try this at home. Why bother?
Result of massive hoax: Don't try this at home. Why bother?Courtesy Mark Ryan
Every dang time the vernal equinox comes around (like today) people everywhere raid their refrigerators and stupidly try to balance raw eggs on smooth surfaces. Why? I don't know. I suppose because all the forces of the solar system are somehow magically aligned today and it's one of two days (the other being the autumnal equinox) it's actually maybe possible to do. I'm a sucker for this kind of crap, so I decided to try it myself. That was a mistake. After wasting most of the morning trying to get the damn egg to stay upright I have to report that my experiment was a dismal failure as can be plainly seen in the accompanying photo. Stupid egg.

Thanks to the Internet I was able to check out the validity of this so-called "Equinox Miracle" and to tell you the truth I wasn't really that surprised to learn that it's all a bunch of pseudo-scientific hooey. The equinox offers no "special conditions" for balancing eggs. If you're patient enough it can be done any day of the year (yeah, sure), and you don't have to have a PhD in physics - anyone can do it. Except me evidently. (yes, yes - I should have Googled before doing the experiment but that's neither here nor there at this point). Oh well, you can read about it yourself here and here.

But you know what? Why should I be acting like I have egg on my face? You should be thanking me; think of all the time I've saved you. Consider it my gift to you on this first day of Spring.

Jan
09
2009

Influenza virus: Negative-stained transmission electron micrograph (TEM) depicting the ultrastructural details of a number of influenza virus particles, or “virions”.
Influenza virus: Negative-stained transmission electron micrograph (TEM) depicting the ultrastructural details of a number of influenza virus particles, or “virions”.Courtesy pingnews.com
Every time flu season comes around there seems to be concern whether the current flu shot vaccine will be able to stave off the viral attack. That’s because viruses and bacteria have a habit of mutating, which subsequently makes a particular vaccine against them ineffective. So each year the medical profession comes up with a vaccine they think will be an effective counterattack against the invading virus. Our own natural antibodies do something similar.

"We've known for a long time that our antibody-forming system adapts itself to every microbe we encounter," said Gerald Weissmann, M.D. He’s Editor-in-Chief of the FASEB Journal where a new study on the subject appears. “What we didn't understand fully is exactly how this happens,” he added.

When viruses or other microbes attack us, our body’s defense system goes into action - via evolution - figuring out ways to create antibodies that will successfully neutralize the invader. There’s two ways our bodies do this: either by mutation of a single cell or mutation of a cluster of cells.

New research out of Detroit’s Wayne State University shows how clusters of our cells quickly customize themselves to fight new forms of attacks. It has to do with how our genes code for antibodies. When a RNA polymerase replicates DNA it moves across it like a scanner. If the scan is smooth, a single mutation (or none at all) takes place. But if the RNA is stalled over the DNA then in some cases multiple mutations occur. The process allows for rapid deployment of tailor-made antibodies to attack the invader.

Why is this important? Well, according Weissmann, as our climate warms the ranges of parasites and microbes expand, making more people vulnerable to infectious diseases than they have been in the past.

“Now that we know [how cluster mutations occur], we can begin to find ways to manipulate this process so illnesses can be prevented or made significantly less dangerous."

LINKS
Science Daily report
DNA from the Beginning (good primer)
Explanation of the polymerase chain reaction

Dec
12
2008

Cold sore afflicted: Most of us are infected by the herpes simplex virus-1 during childhood.
Cold sore afflicted: Most of us are infected by the herpes simplex virus-1 during childhood.Courtesy andrewjthomas
Researchers have found a link between the virus that causes cold sores and Alzheimer’s disease. This isn’t good news for me. I’ve suffered from cold sore outbreaks (aka fever blisters) since I was a kid. These nasty things - which usually erupt on or around your mouth - come from being infected with HSV-1 (Herpes Simplex Virus 1) and are contagious, spreading easily via direct contact. HSV-2 (Herpes Simplex Virus 2, is generally known as genital herpes. Both are similar skin infections (and are related to Herpes zoster, also known as shingles which anyone who's ever had chicken pox can get). The difference between the two versions of HSV is essentially the site of preference for each. HSV-1 prefers the oral area, while HSV-2 prefers the genitalia, although either can occur in both places. You could say oral HSV-1 is just more socially acceptable. The Buzz had previous posts about HSV-2 here and here so I won't go into that now.

Regarding HSV-1, the virus infects something like 90% of the adult population, but only 20-30% of those ever present symptoms. Otherwise the invader lays dormant within nerve cells of the host. When an outbreak does occur it begins as an itching or tingling on the skin. A day or two later painful fluid-filled blisters form in the region. These eventually burst leaving open ulcers. During this time the virus is very contagious. But that’s not a big deal since the likelihood of anyone wanting to be near you, let alone look at you is extremely low at this time in the cycle. However, despite common belief, the virus is communicable at any time – even when no symptoms are present. But since most of us are already infected - who cares? Eventually the ulcers dry up, scabs form, flake off and reform, and the virus become inactive again. The cycle runs anywhere from a week to ten days. Several things are known to trigger outbreaks, including common colds, stress, and even exposure to sunlight.

Two of my 4 siblings get outbreaks, and we probably inherited the virus from our dad who used to get them but no longer does since he’s retired. I suppose I’ve passed the affliction on to my sons because my youngest experienced his first outbreak just last year over his eyelid rather than around his mouth. The outbreaks can take place anywhere on your face (I’ve had them on my nose) and although they can occur on either side of the face they usually only appear on one side at a time during any one outbreak.

As if I’m not suffering enough, now researchers at the University of Manchester in England are saying they have DNA evidence that HSV-1 is present in 90% of the plaque found in the brains of Alzheimer patients. The research, led by professor Ruth Itzhaki, appears in the recent Journal of Pathology.

The same researchers, in a previous study, linked production of beta myloid - the primary component of protein plaque deposits - to HSV-1 infections of nerve cells in mice. Together, the two studies make a strong case that the dementia in Alzheimer’s sufferers is caused by the same virus that triggers cold sores.

"We suggest that HSV1 enters the brain in the elderly as their immune systems decline and then establishes a dormant infection from which it is repeatedly activated by events such as stress, immunosuppression, and various infections," said Professor Itzhaki.

The virus destroys the nearby brain cells causing them to release and deposit amyloid proteins that form plaque deposits on brain tissue.

The one good thing about this disturbing development is that anti-viral medications used now to treat cold sores could lead scientists toward prevention or even a cure of Alzheimer’s disease.

LINKS

ScienceDaily story
Physorg.com story
The truth about herpes
Alzheimer's disease linked to junk food
Snoring linked to Alzheimer's

Oct
13
2008

A display on adult stem cells, here at the SMM: In fact, this exhibit features Catherine Verfaillie herself.    (Good looking out, BK)
A display on adult stem cells, here at the SMM: In fact, this exhibit features Catherine Verfaillie herself. (Good looking out, BK)Courtesy bryankennedy
Following the results of an evaluation by a panel of experts at the University of Minnesota, the magazine New Scientist published an article last week announcing that some of the data used in a groundbreaking study on adult stem cells had been falsified.

The study, performed at the University of Minnesota under the supervision of Catherine Verfaillie, is part of a line of research that seemed to indicate that adult stem cells, taken from bone marrow, are pluripotent—that is that they have the potential to develop into any type of cell. Previously, only embryonic stem cells were thought to be pluripotent, and Verfaillie’s research looked like it could eventually offer an alternative to the ethically complicated use of embryonic cells for research (which requires the destruction of an embryo).

Unfortunately, other scientists had trouble replicating Verfaillie’s results, which were published in the journal Nature. New Scientist began examining the research done by Verfaillie and her team, and found that key images in the research appeared several times in papers for different experiments, and, in the case of a related study in the publication Blood, were used twice in the same paper, but had been visually altered slightly, and flipped 180 degrees. New Scientist reported their findings to the University, which began a formal investigation of the matter.

The University just recently completed the investigation, and found that data in the blood article had indeed been falsified (the images in particular), by a former PhD student of Verfaillies’, Morayma Reyes. The University and Catherine Verfaillie have asked Blood to redact the study.

Verfaillie has stated that she was unaware of the problems with the published study, and while she didn’t believe that the data was deliberately falsified, she takes ultimate responsibility for the errors.

Reyes, who now works as an assistant professor at the University of Washington, denies that the images represent deliberately altered data, and blames the errors on inadequate supervision and training. She claims that she had neither the equipment (photo editing software) nor knowledge required to alter the images. The differences in the reoccurring images were likely the result of the inadvertent use of the image adjusting tools built into lab equipment, she says, and the duplication of a figure within the Blood paper was accidental. Reyes also feels that she has been treated unfairly by the University, and that the expert panel in the investigation demonstrated a clear “lack of expertise” in the field of stem cell biology.

Reyes’ full position can be read here. The University’s response can be found here.

The altered images, Reyes asserts, shouldn’t change the results of the paper, but the whole incident brings up some interesting issues on the process of vetting science. While the errors in the paper never should have made it past Verfaillie and the rest of her team, the process of peer review should have caught them anyway. Generally, before research is published in a scientific journal, the editors select several scientists in the particular field of the paper to evaluate and comment (often anonymously) on the paper. The review panel is meant to confirm that the methodology of the experiments and the interpretation of the results are sound. Research can then be recommended (or not) for publication.

Publishing research essentially formally submits it to the scientific community, and it’s common for other scientists to attempt to replicate experiments, especially if a study makes particularly striking claims (like adult stem cells being pluripotent). The work of other scientists in replicating results is, obviously, essential to the scientific method—in this case is was what finally drew attention to some of the irregularities in Verfaillie’s team’s work.

Reproducibility can be a tricky thing, though—difficulty in repeating results doesn’t necessarily mean that they aren’t reproducible. (Here’s a good article on repeating and reproducing results.) But the problems in reproducing these results drew attention to the questionable data, which brought up another aspect of scientific vetting: the University’s investigation into academic misconduct. If the problems with reproducibility seem to come from data being changed, added, or omitted to strengthen a conclusion, then there could be a serious problem. This sort of misconduct undermines scientific progress, and can call into question the reputation of the institution it came out of and the validity of other research performed there. And if Morayma Reyes seems a little extra defensive in her letter, it’s understandable, because being accused of academic misconduct is a big deal, and no good for your career and future work.

The subject of the research further complicates the situation—this isn’t the first time issues of academic dishonesty have come up with regards to stem cell research. In 2006, a Korean scientist’s claims that he had cloned human embryos (thereby eliminating the need to destroy new embryos for stem cells) turned out to be based on lies. There’s a fear that the potentially huge medical payoff of stem cell research, as well as the ethical debate surrounding the use of human embryonic stem cells, could lead to science that is less than completely thorough, or even situations like the Korean controversy. And that’s bad for science in general. There’s also the thought that errors that are unintentional (as may be the case with Reyes’ images) could be the result of “pathological science,” where results are steered in a particular direction by scientists because of “subjective effects, wishful thinking, or threshold interactions.” It doesn’t have the same ethical problems, but pathological results aren’t a whole lot better for science than straight-out misconduct, and it’s a serious potential pitfall with the benefits of stem cell research waiting out there as temptations.

So there you go. It looks like things are, for the most part, being handled appropriately in this situation, but it’s an interesting window into scientific process.

Any thoughts? Does it seem like the vetting process of science is lacking in some way? Or is it maybe too thorough? Professor Reyes, I imagine, would argue that too much has been made of this situation, and there are many who argue that the process of peer review limits the communication and dissemination of scientific ideas.

Or, even better, does it seem like I got something wrong here?

Let’s have it, Buzzketeers.

Oct
10
2008

A modern blacktip shark: living a modern life on her own.
A modern blacktip shark: living a modern life on her own.Courtesy Albert Kok

*The original headline here was "Immaculate conception observed. In a shark." However, it was pointed out to me that "immaculate conception" and "virgin birth" really aren't the same thing. I changed it, but I resent the implication that I don't know the difference. Just because I get things wrong all the time, it doesn't mean that I was wrong about this. Not, you know, necessarily.

It looks like lady sharks have won another battle of the sexes. The sex war had been fought to a standstill, a stalemate siege, if you will, with the male army relying on the “well, you’ll need us eventually” tactic.

Apparently this isn’t necessarily the case. Deep inside the female Fortress of Celibacy, a devious plan was being hatched: virgin birth.

(Many types of sharks, it should be noted, give live birth, like mammals, instead of laying eggs.)

There have, in fact, been two documented cases of ladies-only shark reproduction. The first was in the Omaha Zoo, where a female hammerhead shark unexpectedly gave birth to a baby shark (called a “pup”) in her tank. Unfortunately, some of the other sharks (of a different species) in her tank immediately ate the pup. Whoops. But DNA tests were done on the… leftover chunks of the pup, I guess, and they showed that the baby did not have a father.

The other case happened in May of last year, with the research results being released this last week (hey, sometimes science stays out all night and gets up late, so give it a break). A blacktip shark named Tidbit had been living at the Virginia Aquarium and Marine Science Center for the last eight years, with no contact with males sharks of her species. When Tidbit died mysteriously last May, an autopsy revealed her nearly full-term pregnancy (the stress-related complications of which were probably what did her in). The shark pup had died as well—and aquarium staff believed that it would have been eaten by the tiger sharks in the same tank anyway had it actually been born—but genetic testing revealed it to be Tidbit’s child, and Tidbit’s alone.

Scientists studying the bizarre pregnancies believe that the pups got all the required chromosomes when the mother’s egg split, and then reunited—a process called "parthogenesis.”

Single-sex reproduction, it’s believed, might be an adaptation to situations when there are too few male sharks in a wild population. It’s rare enough, however, that it would be very unlikely that sharks could survive through pathogenesis alone. The process results in a lack of genetic diversity as well, which could leave individuals vulnerable to congenital disorders.

So, ladies, I salute your ingenuity, but you’re not rid of us yet.

Oct
08
2008

Old-school smeller: This is how we process smells today. With new advancements in receptor protein cell development, we might someday have artificial noses to help with that work.
Old-school smeller: This is how we process smells today. With new advancements in receptor protein cell development, we might someday have artificial noses to help with that work.Courtesy LHOON
That old beak on the front of our face might be in for some serious competition in the future.

Our nose has held exclusive rights on sniffing out the multitude of odors that swirl around us. But with this latest scientific breakthrough, it might be given a run for its money.

Researchers at MIT have figured out how to mass produce the receptor proteins that make up the cells that work in as the receptors in our nose that begin the process of the sense of smell. With further development, these receptor cells could be used in the development of artificial noses. Taking that futuristic thinking a few steps further down the line, an artificial nose could have applications in area like law enforcement, where they could be used to sniff out illegal drugs or explosives. In home security, an artificial nose could be helpful in identifying natural gas leaks or the start of an unintended fire.

Here are the full details of the research. But it’s got me thinking, what other good purposes might there be for artificial noses? Let’s get the ball rolling right here on the Buzz. Share your thoughts with other readers.