Wednesday, November 28, 2007
Monday, November 26, 2007
The data to data do indeed suggest that if you have rotavirus induced diarrea probiotics may definitely be helpful. And collegenous colitis, which is difficult to treat, may be slightly relieved with probiotics. And a big one, irritable bowel syndrome (IBS) may be treatable using B. infantis (that is the bacteria that are largely found in the intestines of human infants)
Unfortunately since bacteria are pretty easy to make, and they are already in your food like yogurt and other fermented milk, anyone can make something and call it probiotic. And of course it is suggested that we all need it and that it is a general 'cure all'. For instance this manufacturer states that:
• Chlorinated drinking water
• Stress, aging and disease
• Born by caesarean section
• Alcohol consumption
• Bacterial infections
• Traveler's bugs
• Antibiotics in food production or prescription medications
So maybe probiotics are great for some conditions and maybe we should all be eating more yogurt but I don't know if eating a bunch of lyophilized bacteria is going to make me 'feel better.'
Wednesday, November 21, 2007
Nature, 302, 21 (April 1983): 652.
Tuesday, November 20, 2007
"Because of their avid adaptation to growth in tissue culture plates, HeLa cells are sometimes difficult to control. For example, they have proven to be a persistent laboratory "weed" and they can contaminate other cell cultures in the same laboratory, interfering with biological research. The degree of HeLa cell contamination among other cell types is unknown, because few researchers test the identity or purity of already-established cell lines. It has been demonstrated that a substantial fraction of in vitro cell lines - approximately 10%, maybe 20%, are actually HeLa cells, due to the fact that the original cells in the cell culture have been overwhelmed by a rapidly growing population derived from HeLa contaminant cells. Stanley Gartler in 1967 and Walter Nelson-Rees in 1975 were the first to publish on the contamination of various cell lines by HeLa."
And recently the TE-7 which have been used for over 20 years as an esophageal cancer model, were found to be a completely different cancer. This has led to the proposal that all cell lines be continuously tested:
"He said the best way to get scientists to comply would be to withhold research grants and publication in scientific journals unless their research used authenticated cell-lines. This verification can be achieved using a technique of DNA profiling which compares the cell-line with a list of known contaminants and can cost as little as £180 per sample. "
Paranoid or justified?
Monday, November 19, 2007
More interestingly, we recently had a great journal club about the evolution of paralogous histone-modifying enzymes in yeast. The paper examined the evolutionary balance between redundancy and diversity of function in duplicate gene pairs, and showed that functionally distinct (non-redundant) paralogues can compensate for their partner when, and only when, the other is deleted. Presumably then, a similar evolutionary dynamic could be at play in the evolution of ribosomes and the regulation of translation in general.
Speaking of histones, if there's no such thing as histone code, maybe it's more of a universe. The complexity of chromatin structure is unbelievable. What's even cooler is that it's dynamic. So not only is chromatin complex, it's ALIVE. At least that was the impression I took away from a recent talk by Ottawa chromatin mapper Marjorie Brand. Check out her lab's latest paper on how spreading of chromatin-associated MLL protein mediates communication between a distal upstream activator element and the B-globin promoter during differentiation.
Another random factoid that was mentioned in the first paper, and news to me: the yeast (S. cerevisiae) arose from a massive whole-genome duplication, but eventually all but 10% of duplicated genes were lost. Weird. Was the initial duplication event selection-neutral for the original yeast cell it occurred in? Hard to imagine, since I would think two genomes take longer to replicate than one, not to mention the structural instability associated with having all that homologous DNA around. So what's the advantage? Not much, if most duplications were eventually lost. Doesn't this say there was indeed a fitness cost to having extra copies of all those genes if they were ultimately weeded out by selection? The only thing that makes sense to me is if the cost/benefit of duplicate genes has varied over yeast evolutionary time. So it was advantagenous to have backup gene copies back sometime in ancient history, but then became unnecessary or cumbersome more recently. Maybe the environment or the yeast's response to it changed. For example, maybe at one point gene inactivation via radiation-induced DNA damage was a big problem for yeast, so it was often useful to have a backup genome copy around. Then, either environmental radiation diminished or yeast evolved a system for preventing or repairing DNA damage, and they no longer needed to keep the backup genes around. I suppose another possibility is that it has something to do with the role of sexual reproduction..........
Alas, I rant like a raving lunatic. Someone set me straight.
(Above figure is from Volkin and Astrachan, Virology, v2 pg. 149 (1956).
The culmination of this series are the 10 rules to do your best research:
- Drop modesty (strive for excellence)
- Prepare your mind (luck favors the prepared minds)
- Age is important (research strategies should be different depending on your age, although I'm not sure I agree with that one)
- Brains are not enough, you also need courage (I assume this means taking risks)
- Make the best of your working condition (don't let your environment limit you, but exploit the advantages you have)
- Work hard and effectively (all the successful scientists I know are workaholics)
- Believe and doubt your hypothesis at the same time (so be skeptical and accept data for what it is, but don't give up on ideas before you test them)
- Work on the important problems in your field (work on something interesting and relevant, no matter what the current trends are)
- Be committed to your problem (because it might take a looong time to solve it)
- Leave your door open (interact as much as you can with other people, you never know where the insights might come from)
Friday, November 16, 2007
"Delays and setbacks are built into the scientific process no matter where it occurs, but researchers in Iran face an additional burden imposed, largely, by politics. Cell biologists lack even the machines that sort cells by surface-protein markers because the necessary US-made equipment cannot be imported. They cannot perform many experiments that we consider routine, but rely on collaborators who have the necessary equipment. Even when equipment has been procured, Iranian researchers face logistics that prevent them from getting on with their experiments.
It seems to me that these restrictions are not in anyone's interest. Scientists themselves exacerbate the situation, fuelled by misinformation that they put themselves at personal risk by travelling to Iran. Of course, people who would not be able to refrain from political discussion or dress as expected would be wise not to go. But the vast majority of scientists would find themselves surrounded, as I was, by courteous, hospitable, well-informed men and women who relish interaction with other scientists. Unfounded apprehensions about the risks of travelling to Iran effectively add a scientific embargo to the politcal one.
I think it's commendable that Jaenisch has the guts to take positions that powerful people in his country might disagree with, rather than bury his head in the sand alongside many of his colleagues.
I love it. There is a bit of conjunctivitis (aka pink eye) making it's way through the lab in which the bay is a part of. It may be that it is from microscope eyepieces, so I wanted to see what I could find on other experiences with this, but I couldn't really.
I did find one person on a forum who said they have encountered pink eye contaminated eyepieces, not once but twice.
I also found out that breast milk cures pink eye. I'm skeptical.
I think one of the reasons I think it's funny is because it's such a childhood thing and one of the funny scenes from "Knocked Up" indicates it can be caused from farting on someone's pillow.
I'm sure I'll think it's funny until it infects someone in the bay.
Wednesday, November 14, 2007
In the fine tradition of marrow rum and in keeping with the season, a pumpkin was chosen as the fermentation vessel of choice. On Hallowe'en night, a small hole was bored into the top of the pumpkin and it was inoculated with a package of baker's yeast, some sugar and a healthy dose of spookiness. The pumpkin was then filled with water and left to ferment at room temperature.
One week later, on the notably less spooky 7th of November, the pumpkin brew was deemed, by arbitrary measure and impatience, ready for tasting.
Tapping the keg: AC makes the first cut
The usually clean Rob, splattered with a mix of pumpkin and baby vomit
Once the pumpkin was cracked open, the yeasty aroma of our brew and the foul stench of evil filled the air. What does evil smell like? As one bystander put it: "It smells like cheese beer." Spectators were simultaneously turned away in disgust and drawn to the spectacle.
Pumpkin ale, or portal to hell?
The resulting liquid
Filtering out the filth
The liquid inside the pumpkin was deemed too 'chunky' to swig fresh from the fruit, so it was put through a coffee filter before tasting. While AC and Rob argued over safety (and who would drink first), I took a sip of the filtered brew. It passed the first test: I didn't keel over. Despite the stink, it was drinkable. It was what I imagine watered down dough put through a blender would taste like. Slight pumpkin overtones. It didn't taste good enough to drink enough to get a buzz given the low alcohol content. This was more bread than beer.
Rob and an uncowardly Coward contemplate the pumpkin ale
Anonymous Coward reacts as Rob takes a healthy swig, while a bystander looks on in disgust
Rob was unsatisfied with the weakness of the drink, so he braved drinking the unfiltered swill. My recommendation for Pumpkin Project 2.0: skip the water, let the natural pumpkin liquids provide the base and let it ferment longer. Of course we still wanted to see what the inside of the pumpkin looked like, so we cracked it right open and let its full bouquet permeate the Bay.
The pumpkin innards and remaining brew
A handful of the resulting goo
Most of the pumpkin innards had pulled away from the shell of the fruit and partially liquefied. Have we stumbled upon a quick and easy way to clean a pumpkin for carving? the inner surface of the pumpkin had softened and was covered with yeasty growth. All drinkers survived the experience, but adjustments need to be made for a successful recipe.
**The Bayblab encourages attempting this experiment at home and posting the results here but takes no responsibility for any injury or illness - physical or mental - that may occur.
"Imagine, if you will, a load of horseshit. And we’re not talking just your average load of horseshit; no, we’re talking colossal load of horsehit. An epic load of horseshit. The kind of load of horseshit that has accreted over decades and has developed its own sort of ecosystem, from the flyblown chunks at the perimeter, down into the heated and decomposing center, generating explosive levels of methane as bacteria feast merrily on vintage, liquified crap. This is a Herculean load of horseshit, friends, the likes of which has not been seen since the days of Augeas."
Tuesday, November 13, 2007
This man has some kind of mutation which rendered his immune system unable to control the warts growing as a result of an HPV infection. Another reason to get the HPV vaccine! The doctors have proposed to use high doses of vitamin A to stop the warts, and remove the rest by surgery.
This 7ft tall 12 year old, had all his teeth by 4 months and was already has big as a 12 year old by the time he got to kindergarden. This is not a case of gigantism, which occurs because of pituitary tumours excreting too much growth hormone, rather this seems to be a new kind of mutation. Joining the 50 or so different genetic syndromes which cause excessive growth such as:
"Extra sex chromosomes (beyond the normal two) with therefore extra copies of the SHOX gene (beyond the normal two) usually results in enhancement of height growth. The most common of these karyotypes are 47,XXY (Klinefelter syndrome), 47,XYY, and 47,XXX. The added height increment is usually modest.
A very rare but more extreme version of "eunuochoid" tallness occurs when a mutation of the estrogen receptor reduces the response of the bones to estradiol. Estradiol is a byproduct of testosterone in both males and females, and is the most potent accelerator of bone maturation and closure known. If a person fails to respond to estrogen, growth can continue until late-20s or longer, and the affected person can reach 8 feet or more in height. Estrogen resistance is the only other endocrine condition that can rival growth hormone excess in producing gigantism. In contrast, the tallness associated with the more common androgen insensitivity syndrome averages only a few inches, as estradiol is not produced directly but rather through conversion from androgens by aromatase.
Marfan syndrome is an uncommon genetic disease due to an inherited defect of connective tissue. In addition to moderate tallness, persons with this condition usually have a slender body build with unusually long fingers (arachnodactyly). Many can also develop a dislocaton of the lens of the eye or, more seriously, a progressive deterioration of the walls of the aorta which can result in sudden death in adulthood. It is usually inherited as an autosomal dominant trait.
Sotos syndrome resembles acromegaly in its mild distortion of facial growth. In addition to tallness, the chief characteristics are large head size, slow development, and autosomal-dominant inheritance."
Monday, November 12, 2007
Next up will be Science Friction: Where the Known Meets the Unknown, by Skeptic editor Michael Shermer. This one also promises to be a doozy, kicking it off with the following gem of an opener:
"It is in the vacuum of such will-nilly whencing and withering that we humans are so prone to grasp for transcendent interconnectedness. As pattern-seeking primates we scan the random points of light in the night sky of our lives and connect the dots to form constellations of meaning. Sometimes the patterns are real, sometimes, not. Who can tell?"
So many ideas, so little time. I'll go so far as to recommend both before even reading them. Or, check back at the bayblab for periodic updates and (what I think) are the coolest memes therein.
One last bonus - since I find myself reviewing the arts - I have to recommend Feist for great music to write or read to. Funky enough to stave off depression and keep you alert, soft enough not to be distracting. I've been checking out "Let it Die" and "The Reminder", and there's not a non-kick-ass track to be found on either. Big up to Amherst, Nova Scotia. Maybe she'll sit in with the spineless Kevin-Z one of these days. Hey, I could see it...
Saturday, November 10, 2007
Thursday, November 08, 2007
"I don't think we're for anything, we're just products of evolution. You can say 'Gee, your life must be pretty bleak if you don't think there's a purpose' but I'm anticipating a good lunch."
- from a BBC interview with Richard Dawkins
Posted by Bayman at 5:21 PM
Wednesday, November 07, 2007
The method is simple: cut the stalk off a fresh marrow (a marrow is a squash, similar to a large zucchini) and scoop out the seeds leaving as much flesh behind as possible. Pack the resulting opening with sugar (most recipes use Demerara - or raw cane - sugar). Replace the top, puncture the bottom and suspend over a bowl or some other receptacle. Most recipes I've seen depend on natural yeasts entering the marrow and fermenting the fruit, but I suspect adding yeast may be required. Some call for the addition of chopped ginger or raisins to add flavour. Fermentation time seems to range from a week up to several months, depending on the recipe!
A sample recipe:
Whether the ensuing brew is a tasty potable, or instead something worthy of its British cooking heritage is unclear but it seems like a good candidate for the next bayblab project. Perhaps other fruit would make good candidates for recipe adaptations.
Pair ladies' nylon stockings
Slice the top off the marrow and scoop out the seeds, but leave as much of the flesh as possible, and don't puncture the skin. The seeds are attached to the inside of the marrow with little strings: one way to detach obstinate seeds is to fill the marrow with water and shake well. Fit a stocking onto the marrow, and pack the marrow tightly with Demerara sugar. Stand upright in a large vase or similar and leave for a day. Osmosis will draw fluid from the marrow into the sugar, dissolving some and leaving a gap below the end of the marrow. Add a teaspoon of ginger (finely chopped fresh ginger root if available, otherwise dried ginger) and pack more sugar on top. Replace the marrow upright in the pot, and cover to ensure nothing can fall into the pot or the end of the marrow. Pulling the second stocking down over the top of the marrow and pot is a good way to do this. Leave in a cool dark place for at least two weeks, and if possible, four. Inspect at intervals.
The idea is that the sugar ferments, generating an alcoholic liquor which gradually eats its way through the bottom of the marrow and collects in the pot. It takes three or four weeks to reach full strength, during which time the marrow becomes very floppy. The stocking filters the liquor and also provides much-needed surgical support. I have tried this recipe three times, twice with marrows and once with a Turk's Head Turban gourd, also from Elder Stubbs. One week's fermentation gives a liquor which has a pleasant taste but is not very strong - after three weeks, it has a noticeable punch. The ginger adds pungency to counteract the blandness of the marrow, giving the rum a pleasant warmth.
Tuesday, November 06, 2007
When thinking about it a little more it didn't surprise me that reproductive organs would contain the ligand, since they are known to express the receptors:
"With respect to reproductive organs, cannabinoid receptors and/or endocannabinoids have been detected in the pituitary gland, testis, Leydig cells, epididymis, prostate, sperm cells, ovary, uterus, oviduct, preimplantation embryo, placenta, embryo, fetus and neonates"
It is thought that in sperm, the anandamide prevents the acrosome reaction, therefore preventing the sperm from activating before it reaches the female tract and also preventing polyspermy during fertilization. The question is, how much anadamide (AEA) is there in reproductive biological fluids?
"We detected AEA, OEA, and PEA in human seminal plasma, mid-cycle oviductal fluid, and follicular fluid analyzed by HPLC/MS"
And the sequela, how much of that stuff do you need to feel a buzz?
"Oral administration of AEA and 2-AG to mice can produce psychotropic effects, suggesting that these endocannabinoids reach the brain ( Di Marzo et al., 1998)."
A quick survey of the literature suggest that 5.8mg/kg is the ED50 of AEA to impair working memory performance (i.e. get a mouse high). So a rough approximation of the dose of milk for an infant to feel the effects is 20,209 L of milk, or for a woman to get high of seminal fluid she would need to chug a good 62,142 L. Notice that calculating the converse would be morally reprehensible.
I suppose the fact that it's so dilute is a good thing for the baby since: "Newborn humans, that had been exposed to marijuana prenatally, exhibit increased tremors, exaggerated responses to stimulation, and spend less time sleeping quietly ( Fried and Smith, 2001).".... but it fails to explain why babies have such munchies...
Sunday, November 04, 2007
"If everyone is thinking alike, someone isn't thinking",
is apparently a classic Patton line.
While I'm not sure to what extent independent thinking is valued in the army, it certainly is useful in science. Here are a few more Patton gems that might be useful advice for the scientist:
- "It is only by doing things others have not that one can advance."
- "Never tell people how to do things. Tell them what to do and they will surprise you with their ingenuity."
- "Pressure makes diamonds."
- "Success is how high you bounce when you hit bottom."
- "Few men are killed by the bayonet, many are scared by it. Bayonets should be fixed when the fire fight starts."
Pretty smart for an army grunt, even if he was
Clearly NK cells are well-trained Christian soldiers.
"Onward Christian soldiers marching as to war
With the cross of Jesus going on before.
Christ, the royal master leads against the foe
Forward into battle, see His banners go"
Sounds like inspiration for a new tune from our friend Kevin-Z. I'm hearing a Led-Zepplinesque epic about God's NK and CTL armies battling Satan's tumor cells and their pro-inflammatory macrophage minions. What say you KZ? Do you have the backbone for holy immunology?
Friday, November 02, 2007
cancer biologyWenchypoo presents Meet “Epi”—the Ghost in Your Genes posted at Wisdom From Wenchypoo's Mental Wastebasket, saying, "How everything we experience, eat, drink, and take affects our family tree for three generations.". Epigenetics holds a special place in my heart since I've been secretly trying to figure out the histone code while pretending to work on reproduction. I'm especially interested in transgenerational effects such as those explained by Wenchypoo in this post. Indeed you may not be only getting bad genes from your parents, but also transcriptional memory that was imprinted during their lifetime.
CAD presents VWXYNot?: On the Origin of Tumours by Means of Natural Selection posted at VWXYNot?, saying, "The gradual evolution from normal to malignant cells illustrates a very simple natural law. If an individual produces a number of offspring via an imperfect copying mechanism, the result will be a mixed population of individuals with slightly different characteristics. If one of the variants is able to produce offspring faster than its peers, then those offspring will be over-represented in subsequent generations. ". Is transformation then a kind of speciation event?
prevention & managementAlvaro Fernandez presents 10 Highlights from the 2007 Aspen Health Forum posted at SharpBrains, saying, "Check out this overview of the Health and Science trends discussed in this recent policy event.". While cancer was on the agenda, it's interesting to see how it fits in the global health perspective. Many topics are touched, including how successful patient advocacy groups have been in raising money for cancer research, and the importance of lifestyle and prevention for a healthy population.
Colon update: the red bit is cancer… posted at Dodgeblogium. Andrew shares with us the impact of his diagnosis along with a picture of his colon! It just shows how simple diagnostic methods, such as colonoscopies have drastically changed cancer prevention and diagnosis.
psychologyKamel presents Depression in cancer survivors and their partners posted at Bayblab. Kamel highlights the emotional aspects of coping with a cancer diagnosis and death. Sometimes depression doesn't come from the contemplation of your mortality but rather the loneliness.
Tiffany Washko presents Crazy Sexy Cancer posted at Natural Family Living Blog. This book comes from a recommendation from Oprah, so you know it must be good. Mostly personal tips for people with the disease.
That concludes this edition. Submit your blog article to the next edition of cancer research blog carnival using our carnival submission form. Past posts and future hosts can be found on our blog carnival index page. Contact us if you are interested in hosting the next edition...
I don't know the validity of that statement, but I can certainly imagine that terminal patients with a strong support group of family and friends cope better than those without. This study in the Lancet suggests patients participating in weekly support group therapy do fare better. But what about cancer survivors? How do they cope with a shift back to 'normal' routine?
Cancer survivors face unique challenges: Fear of recurrence, self-conciousness about appearance (weight change, hair loss or even loss of a limb), loneliness (if you feel others can't understand what you've been through) and even guilt about survival (when so many others don't make it) are all emotional issues that need to be dealt with on an ongoing basis post-treatment. These overwhelming emotions can lead to anxiety and depression and require support of family and friends. Sometimes that's not enough, and outside support groups (consisting of other cancer survivors who know what you're going through) are necessary. However the Mayo clinic offers the following caution when choosing a support group:
- Promises of a sure cure for your disease or condition
- Promises of quick solutions to your disease, condition or life situation
- Meetings that are predominantly "gripe" sessions
- A group leader or member who urges you to stop medical treatment
- A charismatic group leader who demands cult-like allegiance
- High fees to attend the group or having to purchase products or services
The Canadian Cancer Society offers peer support for cancer survivors and people living with cancer but there are many others out there.
It's not just cancer patients and survivors that need support. Friends and family are often bearing an emotional load themselves. Recent studies have shown that the social circle of cancer survivors, particularly partners, are also at risk for depression. In some cases, the mental health of partners was rated lower than the survivors themselves, and they were less likely to receive mental health treatment or support. This can put a great strain on relationships and magnify anxiety and depression in these pairs. This study was restricted to bone marrow transplant recipients and their partners, but the literature suggests it could be broadened to other cancer types.
Cancer is a complex disease, with complex issues lingering once clinic visits are finished. Support needs to extend outside the treatment room and is an ongoing process for patients and their loved ones even after treatments are finished and cancer is beaten.