genetics
pharyngula | March 11, 2012Good news! The gorilla genome sequence was published in Nature last week, and adds to our body of knowledge about primate evolution. Here's the abstract:
Gorillas are humans' closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation…
pharyngula | February 23, 2012I was going to talk about a cool recent paper that described the evolution of novelties by way of modifying modular gene networks, but I started scribbling it up and realized that I was constantly backtracking to explain some fundamental concepts, so I stopped. I was concerned because one of the most common sources of confusion I've found in my students in the past was difficulty in distinguishing phenotypes from the complexities of the underlying genotype, and I have to be slow and thorough in setting up those differences early on until it sinks in, a habit I'm continuing here. It's so easy…
jeure | February 17, 2012No one credits heavy drinking with making people smarter - the mind-numbing effects are well documented. Odds are that if you haven't experienced this personally, you've witnessed it in the foolish antics of others. The clear correlation between rapidly diminishing intelligence and rising alcohol consumption is no secret.
But the long-term effects may go deeper than a morning headache or a need to wear sunglasses inside. A new study conducted at Brookhaven National Laboratory reveals that genetic factors can make some individuals more susceptible than others to lasting neurological damage…
pharyngula | December 19, 2011I've been guilty of teaching bean-bag genetics this semester. Bean-bag genetics treats individuals as a bag of irrelevant shape containing a collection of alleles (the "beans") that are sorted and disseminated by the rules of Mendel, and at its worst, assigns one trait to one allele; it's highly unrealistic. In my defense, it was necessary — first-year students struggle enough with the basic logic of elementary transmission genetics without adding great complications — and of course, in some contexts, such as population genetics, it is a useful simplification. It's just anathema to anyone…
milhayser | September 2, 2011
Greg Laden reports that scientists have sequenced the genome of the Tammar Wallaby, which boasts "the longest period of embryonic diapause of any known mammal, highly synchronized seasonal breeding and an unusual system of lactation." The new research "provides a hitherto lacking understanding of marsupial gene evolution and hopes to have identified marsupial-specific genetic elements." Dr. Dolittle shares more amazing research on Life Lines, telling us seals can cool off their brains while diving to conserve oxygen. They do this by shunting blood "to large superficial veins allowing heat…
mikethemadbiologist | August 22, 2011
There's some good news and bad news regarding E. coli surveillance in meat products. The good news:
The pathogenic Shiga toxin-producing Escherichia Coli (pSTEC) serotypes known collectively as the "Big Six" will soon be banned from U.S. meat, a top expert told a meat industry conference Thursday.
Action to declare the six non-O157:H7 serotypes as adulterants in meat could come as early as next week, according to Mohammad Koohmaraie, chief executive officer for the meat division of IEH Laboratories & Consulting Group based in Lake Forest Park, WA.
For certain, he says, the Big Six --…
pharyngula | July 7, 2011I found a recent paper in Nature fascinating, but why is hard to describe — you need to understand a fair amount of general molecular biology and development to see what's interesting about it. So those of you who already do may be a little bored with this explanation, because I've got to build it up slowly and hope I don't lose everyone else along the way. Patience! If you're a real smartie-pants, just jump ahead and read the original paper in Nature.
A little general background.
Let's begin with an abstract map of a small piece of a strand of DNA. This is a region of fly DNA that encodes a…
mikethemadbiologist | June 13, 2011Note that I said cranky, not mad. Mad is reserved for moral degenerates who cut funding to assist people with cerebral palsy. But cranky? Yes. Recently, I've come across a couple of papers that describe interesting collections of E. coli. For example, one paper isolated a bunch of E. coli from soil and water in Hawaii to determine if there is a dominant point source of fecal contamination and if there are sustainable populations of E. coli in Hawaiian soils (which would mean we can't use simple counts of E. coli to determine if a water source is contaminated by feces). Another paper…
mikethemadbiologist | June 9, 2011Or maybe wild-ass speculation. As the data continue to come in about the E. coli outbreak in Germany caused by E. coli O104:H4 HUSEC041 (well, everything but the public health and epidemiological data which are a contradictory, incoherent mess), it appears that one of the things that has made this strain so dangerous is its ability to make Shiga-like toxin--a compound that stops cells from making proteins cells--the mechanism is similar to that of the biowarfare agent ricin (Note: there are several different Shiga-like toxins; for clarity, since it's not germane to this post, I'll lump…
tsmith | June 3, 2011...when it contains a weird gene conferring methicillin resistance that many tests miss.
Methicillin-resistant Staphylococcus aureus (MRSA) has become a big issue in the past 15 years or so, as it turned up outside of its old haunts (typically hospitals and other medical facilities) and started causing infections--sometimes very serious--in people who haven't been in a hospital before. Typically MRSA is diagnosed using basic old-school microbiology techniques: growing the bacteria on an agar plate, and then testing to see what antibiotics it's resistant to. This can be done in a number of…
mikethemadbiologist | May 26, 2011A seminal discovery of modern biology was Joshua Lederberg's demonstration that bacteria can swap genes through a process known as bacterial recombination. Not only is recombination the mechanism by which antibiotic resistance genes are transferred, but it's also been turned into a useful tool for genetically manipulating E. coli, which has led to so many things, including the industrial synthesis of insulin; it's also a key tool--and at one time--the key tool for molecular genetics.
So while working my way through Population Genetics of Bacteria: A Tribute to Thomas S. Whittam, I came…
pharyngula | May 12, 2011Inbreeding is bad. It increases the frequency of homozygosity for deleterious traits.
There's this little thing called pleiotropy. Selection is a powerful tool, but traits can have multiple effects, and extreme selection for peculiarities can have unpleasant side effects — you may think a pug's curly tail is adorable, but it comes with all kinds of spinal ailments. And cute little doggies with cute little heads may have skulls too small for their brains, leading to syringomyelia.
If you've got an hour, this video is worth watching. Add pedigree dog shows to puppy mills as examples of animal…
pharyngula | May 4, 2011Oh, yeah…didn't you know it was a crack team of Darwinist commandos who took out bin Laden, all to protect our secrets? David Klinghoffer doesn't go quite that far, but he does demonstrate just how insane the gang at the Discovery Institute have gotten. After all, he does claim that Obama delayed the raid on Osama in order to promote creationism.
President Obama is said to have known the whereabouts of Osama bin Laden since September but chose to wait until May to authorize action against him. Why the delay? Could it perhaps have been to provide a super-timely news hook for the rollout of…
pharyngula | April 27, 2011
I've been giving talks at scientific meetings on educational outreach — I've been telling the attendees that they ought to start blogs or in other ways make more of an effort to educate the public. I mentioned one successful result the other day, but we need more.
I give multiple reasons for scientists to do this. One is just general goodness: we need to educate a scientifically illiterate public. Of course, like all altruism, this isn't really recommended out of simple kindness, but because the public ultimately holds the pursestrings, and science needs their understanding and support.…
milhayser | April 2, 2011
To judge by its name, cancer may seem like a monolithic disease. But a recent study which sequenced the genomes of seven prostate cancers reveals just how staggeringly complex the disease can be. The sequencing revealed not only DNA mutations, but rampant rearrangements of the chromosomes themselves. As ERV explains, "we arent talking a mutation here, a tiny deletion there—we are talking huge chunks of DNA in the wrong place." Once a cell becomes cancerous—which is no simple transition—it no longer functions as part of a bodily community. Instead, it founds its own community of cellular…
mikethemadbiologist | March 24, 2011Because we are human after all. Jason Collins at Evolving Economics, in response to my post about one economist's misunderstanding of biology, asks a very good question:
On the flip side, did Dawkins or Gould (or their respective supporters) ever concede to the other side that they were wrong and substantially change their world view?
I agree with Razib about what happened:
My own attitude is that both Richard Dawkins and Stephen Jay Gould retreated from maximalist positions when it came to the gradualism vs. punctuated equilibrium arguments of the 1970s substantively. But rhetorically they…
mikethemadbiologist | February 21, 2011A couple of weeks ago, I found a post, "Is HIV 'fingerprinting' junk courtroom science?", which argues:
But calling the comparison of HIV strains' genes "fingerprinting" -- calling to mind the more-familiar matching of human suspects' DNA to blood at a crime scene -- is dangerously misleading, they warn.
"By calling such investigations HIV fingerprinting, scientists raise unrealistic expectations" about the method's accuracy among juries and judges, the write. "Unlike for (human) DNA fingerprinting, where a likelihood can be calculated for a full match between the evidential DNA and the…
heathero | February 18, 2011I got to spend last week in sunny California. I forgot how wonderful it is to sit and eat lunch outside! I was participating in a workshop held at the Department of Energy's Joint Genome Institute (JGI). The workshop was entitled Microbial Genomics and Metagenomics. Basically I spent the week learning about different tools that are available to help biologists deal with the data flood that has come out (and continues to flow faster and faster) of sequencing technologies that continue to get faster and cheaper.
Since microbes are not exactly easy to observe with ones eyes,…
sa smith | February 11, 2011A neat paper was just published in Nature, where they did complete genome sequencing of the prostate cancer tumors from seven advanced/aggressive prostate cancer patients.The genomic complexity of primary human prostate cancer
Why did they want to do this? They hoped to identify some new features of aggressive prostate cancer that could be exploited for treatment purposes. A mutation obliterates Gene X? Maybe administering Protein X helps. A chromosomal rearrangement plops a strong promoter in front of Gene A? Maybe administering inhibitor of Protein A helps. Heck, maybe everyone has a…
gregladen | January 19, 2011Bedbugs (Insects of the Cimicidae family, commonly Cimex lectularius) are annoying, might carry diseases (though this is unclear, so probably nothing importat1, and are apparently becoming more common in the US. Interestingly, there has been very little study done of their genetics. A new study just out in PLoS ONE looks at the bedbug genome in an effort to better understand pesticide resistance in these pesky critters.
The current working hypothesis is that pesticide resistance in bedbugs results from point mutations in certain genes, though there may be another explanation. Bedbugs…