Molecular Biology
worldsfair | May 15, 2007"The rapidity of this folding reaction tells us something about the mechanism of protein folding. We know that folding is rapid and spontaneous because proteins can be purified then unfolded by treating them with certain chemicals that cause them to become denatured or unfolded. These denatured proteins can then be allowed to re-fold when the chemicals are removed."
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worldsfair | May 15, 2007"Collagen is the major protein component of the connective tissue of vertebrates; it constitutes about 25% to 35% of the total protein in mammals. Collagen molecules have remarkably diverse forms and functions. For example, collagen in tendons forms stiff, ropelike fibers of tremendous tensile strength; in skin, collagen takes the form of loosely woven fibers, permitting expansion in all directions."
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grrlscientist | May 10, 2007tags: bipolar disorder, manic-depressive illness, mental health, molecular biology
Bipolar disorder depends upon small, combined effects from variations in many different brain genes, none of which is powerful enough by itself to cause the disease, according to a new genome-wide study. Despite this revelation, this new study shows that targeting one enzyme produced by one of these altered genes could lead to development of new and more effective medications.
The research, conducted by Amber E. Baum, Francis J. McMahon, and their colleagues, is the first study to genetically scan thousands of…
grrlscientist | May 4, 2007tags: evolution, birds, orioles, Icterus, research
"Oriole."
Image appears here with the kind permission of the photographer, Pamela Wells.
[Larger image].
I often think about differences in morphological and behavioral traits in closely-related species and wonder whether the speed and character of changes in these traits reveal anything about the evolutionary relationships between taxa. For example, in birds, both visual and auditory cues, such as plumage and song patterns, are essential for identifying members of their own species. However, these phenomena have rarely been systematically…
pharyngula | May 4, 2007Way back in the early 19th century, Geoffroy St. Hilaire argued for a radical idea, that vertebrates and most invertebrates were inverted copies of each other. Vertebrates have a dorsal nerve cord and ventral heart, while an insect has a ventral nerve cord and dorsal heart. Could it be that there was a common plan, and that one difference is simply that one is upside down relative to the other? It was an interesting idea, but it didn't hold up at the time; critics could just enumerate the multitude of differences observable between arthropods and vertebrates and drown out an apparent…
evolgen | April 26, 2007
The recent Scientific American article on junk DNA (discussed here) has instigated a quite a furor in the bioblogosphere. Here is a collection of links:
ERV linked with a tone of disgust.
I restated my frustration with the term junk DNA.
JR Minkel, the author of the Scientific American article, responded to my criticisms.
Ryan Gregory replied to Minkel's SciAm blog post, introducing the term "junctional DNA" to replace junk DNA describe sequences with unknown function. Gregory also tells us how a genome is like an onion (let me count the ways), or something of the sort wonders why onions…
evolgen | April 24, 2007Would I write about junk DNA? No. Never. Not me. Not even when Scientific American publishes sub par articles on junk DNA. Well, they're at it again.
The most recent junk DNA article describes a study by Gill Bejerano of Stanford University which I can't find published anywhere (neither can ERV). Is Scientific American describing unpublished research on their website? Either way, they're doing it poorly. The study described in the article identified non-coding sequences that were conserved across all sequenced mammalian genomes but missing from the chicken genome. Five percent of the…
pharyngula | April 19, 2007There is considerable interest in a recent paper in PNAS that purports to have found some rather substantial homologies in the proteins that make up the bacterial flagellum. That would be extremely interesting if it were true, but it looks like there are massive methodological problems in the work. Matzke has put up a preliminary criticism; the gang at PT are working on a much more detailed analysis, and if half of what I'm hearing about the paper is true … well, it's going to be rather thoroughly sunk.
If you are arguing against ID's favorite example, the flagellum, do not use the data in…
evolgen | April 11, 2007Those of us who work on non-human systems often grumble about the total disregard human geneticists (that's geneticists who study humans, not humans who are geneticists) have toward non-human research (that's research on non-humans, not non-humans doing research). I get the feeling that plant biologists have the same attitude toward non-plant researchers, and I imagine there is some unwritten chain of superiority wherein you must pay respect to the researchers working on a system "above" you and ignore the research done on a system "beneath" yours -- and, yes, I realize the higher and lower…
grrlscientist | April 11, 2007tags: bipolar disorder, mania, manic mouse, psychiatric research
Some of you, like me, suffer from bipolar disorder or might know someone who does, so I thought I'd take this opportunity to write a little about the creation of a mouse model to study the genetics that are thought to underlie the manic phase of bipolar disorder -- a phase that has not been well understood so far.
Bipolar disorder, or manic-depressive illness, is a psychiatric condition that affects a person's moods. Typically, a person who suffers from a classical bipolar disorder (Also known as bipolar affective disorder,…
pharyngula | April 6, 2007Jonathan Wells apparently felt the sting of my rebuttal of his assertions about Hox gene structure, because he has now repeated his erroneous interpretations at Dembski's creationist site. His strategy is to once again erect a straw man version of biologist's claims about genetic structure, show that biologists have refuted his dummy, and claim victory. The only real question here is whether he actually believes his historical revisions of what we've known about Hox genes, in which case he is merely ignorant, or whether he is knowingly painting a false picture, in which case he is a malicious…
pharyngula | April 3, 2007This evening, I am watching an episode of that marvelous and profane Western, Deadwood, as I type this; it is a most excellently compensatory distraction, allowing me to sublimate my urge to express myself in uncompromisingly vulgar terms on Pharyngula. This is an essential coping mechanism.
I have been reading Jonathan Wells again.
If you're familiar with Wells and with Deadwood, you know what I mean. You'll just have to imagine that I am Al Swearingen, the brutal bar-owner who uses obscenities as if they were lyric poetry, while Wells is E.B. Farnum, the unctuous rodent who earns the…
pharyngula | March 29, 2007The mammalian tree is rooted deeply and branched early!
(click for larger image)All orders are labelled and major lineages are coloured as follows: black, Monotremata; orange, Marsupialia; blue, Afrotheria; yellow, Xenarthra; green, Laurasiatheria; and red, Euarchontoglires. Families that were reconstructed as non-monophyletic are represented multiple times and numbered accordingly. Branch lengths are proportional to time, with the K/T boundary indicated by a black, dashed circle. The scale indicates Myr.
That's the message of a new paper in Nature that compiled sequence data from 4,510…
evolgen | March 19, 2007Both Carl Zimmer and Larry Moran have posts on the gene content in the human genome. Carl points out that the estimate of the total number of genes in the human genome is decreasing, but we still don't know what a whole bunch of those genes do (according to the one database he searched). Larry's post deals with what he considers a misconception regarding the historical estimates of gene content in humans. He argues that, while the estimates of the number of protein coding genes have decreased over the years, they haven't really decreased as much as some people seem to think (from about 40,000…
pharyngula | March 13, 2007
What do you know…just last week, I posted an article dismissing a creationist's misconceptions about pharyngeal organization and development, in which he asks about the evidence for similarities between agnathan and gnathostome jaws, and what comes along but a new paper on the molecular evidence for the origin of the jaw, which describes gene expression in the lamprey pharynx. How timely! And as a plus, it contains several very clear summary diagrams to show how all the bits and pieces and molecules relate to one another.
The short summary is that there is a suite of genes (the Hox and Dlx…
grrlscientist | March 2, 2007
The effect of the myosin inhibitor blebbistatin on the localization of Borealin.
Human embryonic kidney cells were treated with a myosin inhibitor for 3.8 hours. Confocal microscopy shows Borealin in green and microtubules in red.
Image: Kaur et al., BMC Cell Biology 2007, 8:5 [PDF].
As long as you send images to me (and I hope it will be for forever), I shall continue to share them with my readership. My purpose for posting these images is to remind all of us of the grandeur of the natural world and that there is a world out there that is populated by millions of unique species. We are a…
grrlscientist | February 21, 2007I think I've posted this before, but thought that some of you might not have seen it yet. This video shows how 6 feet of DNA is packaged into the microscopic nucleus of a cell and also how DNA is replicated.
grrlscientist | February 19, 2007Swedish researchers claim that it may be possible to read a person's personality by analyzing their irises. They studied 428 people and correlated iris patterns with warm-heartedness and trust or neuroticism and impulsiveness. The researchers looked at crypts (pits) and contraction furrows (lines curving around the outer edge of the iris), which are formed when pupils dilate.
It was found that those with more crypts were likely to be tender, warm and trusting, while those with more furrows were more likely to be neurotic, impulsive and give in to cravings.
The researchers suggest that a…
grrlscientist | February 15, 2007Awhile ago, I linked to an article about acetaldehyde (pictured), which is the toxic ethanol metabolite that gives people a hangover when they drink too much. This week, I read an article in the New Scientist about acetaldehyde. It turns out that acetaldehyde is found in more substances than you probably ever thought possible. Not only is it a metabolite of ethanol breakdown by the liver, but it is also found in tobacco, vehicle exhaust fumes, coffee, and ripe fruits; it is often used to create a fruity flavor in yogurt; and it is produced by certain mouth bacteria.
For many years,…
evolgen | February 15, 2007Some bio-bloggers are atwitter over an article by Wojciech Makalowski on Scientific American's website about Junk DNA. I'm a little late to the game because, well, I've been really busy looking at sequences to determine if they are junk DNA. Is it irony? Is it coincidence? Who cares? It's an opportunity to discuss semantics, and I love semantics.
Those of you who have hung around here for a while know this topic often comes up at evolgen (remember this, this, and this . . . hell, here's what a search for Junk DNA turns up). Long story short, I can't stand the term junk DNA, but I do agree…