I’ve recently been preparing some new courses which have given me the opportunity to browse through the literature from the dawn of molecular biology. And in the process I came across a 43 year old paper entitled “Studies of Polynucleotides XCVI. Repair replication of short synthetic DNA’s as catalyzed by DNA polymerase.” by Kleppe and Khorana in the Journal of Molecular Biology. Its an elegant manuscript that describes how DNA polymerase can replicate a DNA strand but only if there is a section of duplex DNA, known a as primer, from which it can start.
So Klepper et.al. started off with a bit of DNA that looked like this:
and after incubating with DNA polymerase ended up with a DNA sequence with the gaps filled in, like so.
Well isn’t that nice?
But the really intriguing bit is the last paragraph of the discussion.
.. the DNA duplex would be denatured to form single strands. This denaturation step would be carried out in the presence of a sufficiently large excess of the two appropriate primers. Upon cooling, one would hope to obtain two structures, each containing the full length of the template strand appropriately complexed with the primer. DNA polymerase will be added to complete the process of repair replication. Two molecules of the original duplex should result. The whole cycle could be repeated, there being added every time a fresh dose of the enzyme. … After every cycle of repair replication, the process of strand separation...
If you’re a man and you live in Scotland do not drink tea. According to a BBC report >7 cups a day give you a >50% greater chance of developing prostrate cancer than “normal” tea drinkers. This was the result of a study over 37 years involving 6000 volunteers aged between 21 & 75 years of age. I’m surprised they didn’t choose whisky and/or beer (they have probably been checked at some point in distant past). This is in direct contrast to a National Cancer Institute report which suggests the opposite, at least for green tea.
What’s next I wonder, coffee is already on the black list, as well as fatty foods smoking, no doubt sex will also rear it’s ugly head in the list of cancer producing agents, water is also dangerous, fish swim in it and you can drown as well.
Wiki tells us the exact opposite to the results reported by the Glasgow study. Tea is actually beneficial for you in all sorts of ways.
So what’s in tea that makes it so harmful or so good for you? Well there is theanine and caffeine, making up about 3% of its dry weight up to 90mg per cup, depending upon the tea. Theanine moves across the blood brain barrier (quite distant from the prostrate) and has a synergistic effect with caffeine, high doses even providing a neuroprotective effect. Caffeine is a stimulant and the author of the Wiki page suggests that it may even have moderately protective effect against certain cancers.
There are also things like theobromine (or should it be...
Professor Rahul Sarpeshkar and colleagues at MIT have created an implantable fuel cell which relies on glucose as its fuel. The device could potentially be used as a power source for the computers needed to decode brain signals and manipulate prosthetic or perhaps paralyzed limbs. The article was published in PLos ONE.
There are many layers of cool in this story. Implantable glucose fuel cells have been invented before – back in the 70s – but contained enzyme-based anodes which degraded over time and needed to be replaced. Because of this, implants like pacemakers rely on lithium ion batteries – which also drain over time, but have a much longer lifespan. This design utilizes a platinum anode to oxidize glucose ultimately to gluconic acid, liberating 2 electrons. The cathode is a matrix of single-walled carbon nanotubes which reduce dissolved oxygen to water.
What strikes me as the coolest part of this story, the fuel cell is fabricated on a silicon chip and would be placed in the cerebralspinal fluid next to the brain. Platinum is already known for being fairly biocompatable, but placing the chip in the cerebrospinal fluid is beneficial as there are very few white blood cells in the CSF to trigger an immune response and potential rejection. The CSF contains roughly the same concentration of glucose as plasma, and is not predicted to consume enough glucose fuel so as to impair brain function.
via DOI:10.1371/journal.pone.0038436
To avoid short circuiting the...
Tonight, we make soap.
Matt over at Sciencegeist is organizing this blog carnival in an effort to reclaim the word chemical from the hands of ignorant people who blindly assume anything with ‘chemicals’ in it must be evil. This is not a moment too soon. I’m not exactly sure how the pendulum of public opinion swung from products being advertised as ‘Better living through chemistry’ to products being advertised as ‘chemical free’ (whatever that means). Soaps and other skin care/beauty products are certainly in the cross-hairs of the ‘chemical free’ crowd, but that’s not what I’m talking about today.
As the tallow renders, you skim off the layer of glycerin. If you were to add nitric acid, you got nitroglycerin. If you were to add sodium nitrate and a dash of sawdust, you’d have dynamite.
This is my first post here so imagine my excitement when I came across this attention grabbing title from the JACS press room “Could “advanced” dinosaurs rule other planets?”. Something cool to write about on my first day! Excellent.
So of I trotted to look at the paper that was the bases of the press release. It has the more mundane title “Evidence for the Likely Origin of Homochirality in Amino Acids, Sugars, and Nucleosides on Prebiotic Earth”.
What’s this got to do with dinosaurs I thought? Best delve a little deeper into the paper.
The paper describes how the homochirality of sugars and amino acids in life on Earth may have originated from a small excess of L-amino acids and D-sugars in meteorites. These then seeded early life, leading to their near total dominance in life as we know it.
Sorry, still no idea what this has to do with dinosaurs. The paper is pretty interesting in it self, but I still don’t get the press release. I’d best read a little further .
Ahh, it turns out that astronomers think that neutron stars may act like cyclotrons and produce circularly polarized light. And if this light has enough energy it could account for the deracemization of amino acids on asteroids.
Still no dinosaurs.
OK, maybe the link with dinos will be clearer in the conclusions.
“An implication from this work is that elsewhere in the universe there could be life forms based on D amino acids and L sugars depending on the chirality of circular polarized light...
Welcome back to CLT! Had my employer-sponsored annual health screening today. Reminded me of this one.
See more CLT humor!
via Bloomenkraft
Enjoy!
This is the third time I’ve written a How Does It Work column (homemade chloroform and Coors Light cold-activated bottles). It’s a lot of fun (and a lot of work) to write these columns, and I’m really enjoying writing them. I have two more ideas for upcoming How Does It Work columns (forest fire fighting, microwave panini “grilling”), but if you’ve always wondered how something (chemical) works, let me know and I’ll try to work it into the queue! On to Fruit Ripening: How Does It Work?!
via Westwood Banana
Have you ever wondered what causes fruit to ripen? Why do we store some fruits in the refrigerator and some on the counter? Why do we have a special fruit crisper drawer in the fridge?
The answer has to do with a plant growth hormone. One plant growth hormone is primarily responsible for the complex transition we call ‘Fruit Ripening.’ So what would you guess that growth hormone looks like? Do you think it looks more like the protein-based human growth hormone (HGH) or bovine growth hormone (BGH)? Like the synthetic hormone zearalanol, or like other plant hormones like auxins? Or none of the above? Answer below the jump.
What does the Fruit Ripening Hormone look like???
Before I tell you the answer, let’s look at the physical changes that occur when a fruit ripens. Before the fruit is ripe enough to eat, the unripe fruit is green, immature, and not as tasty. It is hard, sour, not fragrant, and...
Sincere apologies for not writing regularly on the blog. My chemical career trajectory has recently taken an unplanned turn and has required me to learn an other new skill set to succeed. I am now the CTO for my PI’s biotechnology company, which sounds cool to say, but isn’t as much fun as discussing science. My duties have now switched to making sales pitches, finding investors, writing SBIR grants, and making sure projects are progressing, I still found a little time to sneak in some science experiments last week. So lets get down to pretty pictures.
I xenografted some mice in the lab a few weeks ago for a collaborative project that didn’t go anywhere. Last week, the tumors grew past the point of no return, and at UCLA once they hit 1.5 cm we are mandated to euthanize the mice. Last week I also found myself with a little extra time and with the help of a fellow chemist we made some fluorescent molecules that “potentially” have interesting tumor targeting properties. As I had mice with tumors too big, and molecules that target tumor cells, I pretty much said what the hell and injected this molecule into the mice (Yes, I had ARC approval). A picture of the results is below with the control mouse on the left, injected mouse on the right. Areas colored red have the highest intensity, areas colored dark blue have the lowest intensity.
It is a result like this that makes me happy for working at the crossroads of Chemistry and Biology. I love being able...
Fathi Moussa
Lon Wilson
Last year I covered Khodakovskaya et al.’s paper regarding the benefits of growing tomatoes in carbon nanotubes (CNT).[CB] At the time I was concerned with the potential health risks associated from eating carbon nanotubes, but today in ACS Nano my concerns are alleviated. A paper from Lon Wilson’s and Fathi Moussa’s research groups discusses the effects from administering oral doses of carbon nanotubes (concentrations as high as 1g of CNT per kg body weight) to Swiss mice.[ACS Nano] The authors summarize their work the best.
CNT materials did not induce any abnormalities in the pathological examination. Thus, under these conditions, the lowest lethal dose (LDLo) is greater than 1000 mg/kg b.w. in Swiss mice.
So feel free to eat all the CNTs you want in lab, assuming they are not functionalized, you do it only once, and you limit yourself to single walled carbon nanotubes. I think partly because the results of the oral administration of CNTs went without any interesting side effects to present, the authors also looked into what happens when you inject CNTs into the peritoneal cavity of mice.
The image on the left is the control while the image on the right is 14 days after injecting mice with CNTs at a concentration of 1g CNT per kg of mouse. Although it looks sickly, the mice injected with the high concentration of CNTs did not die. Well…, not from the CNTs anyways.
Link to paper: In Vivo Behavior of Large Doses of Ultrashort...
Mariya Khodakovskaya
Alexandru Biris
There has been a lot of concern over the health effects arising from the burgeoning field of nanotechnology, David Barden covered one such paper focusing on nanotube production in Highlights in Chemical Science earlier this month.[HCS] What hasn’t been as discussed are the potential health benefits of carbon nanotubes (CNTs). In a paper released yesterday in ACS Nano, Mariya Khodakovskaya & Alexandru Biris (+coauthors) found that tomato seeds grown in a medium of carbon nanotubes germinated and grew more efficiently than their control group brethren.[ACS Nano] This result is spectacularly seen from the image below.
After 27 days of growth.
The tomatoes grown in carbon nanotubes weighed more, grew longer stems, and matured faster. The authors reason this is due to the carbon nanotubes facilitating water intake, however the evidence provided doesn’t prove this beyond a reasonable doubt. Although I wouldn’t recommend eating these tomatoes just yet, one could still use the increase in plant biomass and efficiency for biofuels and related projects.
Link to paper: Carbon Nanotubes Are Able To Penetrate Plant Seed Coat and Dramatically Affect Seed Germination and Plant Growth
Mitch
For as long as artificial sweeteners have been used, there has been a varying level of controversy over the safety of their use; both for humans and the environment in general. Saccharin and Aspartame have been plagued by health concerns raised by researchers for decades. Most studies have shown that only in very high concentrations are they dangerous, however few long term (>10 years) studies have been completed, so lower dose, chronic exposure has yet to be rigorously investigated. Currently, most diet sodas use aspartame and saccharin, including my favorite, Coke Zero. Another very popular sugar substitute, sucralose has begun to steal the spotlight away from aspartame in recent years, taking over popular drinks like Crystal Light, Tim Horton’s and Starbucks coffee.
The chlorinated sugar substitute called sucralose (commercially marketed as Splenda (TM)) was first synthesized in 1976, as part of a collaboration between Queen Elizabeth College in London and the Tate and Lyle Chemical Company. It is manufactured by the selective chlorination of sucrose, in which three of the hydroxyl groups are replaced with chlorine atoms. Supposedly the graduate student, Shashikant Phadnis, working on the synthesis misunderstood his professor’s request to test the chemical as a request to taste the chemical. Just goes to show, sometimes to make a lucrative discovery, a chemist must take the ultimate test!
Whatever happened, it has been found that Sucralose is approximately...
A while ago I blogged about a paper where a set of structures analogous to estrogen were made. Now a follow-up paper has appeared in Protein Engineering, Design and Selection. The aim was actually not to make simple analogues of estrogen, but to use the compounds to create specific receptor proteins.
Starting from the human estrogen receptor α, the authors employed directed evolution: they changed the residues in proximity of the ligand by mutagenesis, screened the resulting mutants, and selected the best receptor mutants for the next round. After the third round of directed evolution, they came up with an optimized mutant that bound to CV3320 with an EC50 of 55 nM, while the affinity to 17β-estradiol was reduced by a factor of 10 (4 nM).
While the authors admit that the selectivity over 17β-estradiol could still be improved, it still is a nice piece of work that demonstrates the power of directed evolution. This way, a protein receptor for a substrate that does not occur in nature can be made. Such a receptor can be used to make biological switches.
