Madoff a Mac

I guess it should come as little surprise that a person capable of bilking thousands of people out of billions would gravitate towards a company that does the same. Not to overly irritate rabid mac fans, ( I don't consider my iphone a bilk), but one can only imagine how his computing style might have contributed to his greed.... If he were a PC would the average number of BSDs per day have minimized his fraudulent trades? Unlikely since he never made any. The mac wasn't mentioned in the story, but obviously channel 7 spends a lot of time watching him in his penthouse jail.

Marijuana and Cancer - NYAS

Interesting (still controversial) finding by Maura Gillison's group at Ohio State. You can keep checking her blog, which at least talks about HPV cancers in men. Increased marijiana use is correlated with increased suseptability to oral cancer with HPV etiology. The major factors of head and neck cancers that are HPV unrelated are tobbacco and alcohol use. Smoking and drinking has no effect on HPV related cancers (which make up about 99% or tonsilar cancers). However HPV related cancers are correlated with increased number of partners for oral sex, and interestsingly marjiuana use. Her current hypothesis involves endocaniboid receptors that are present in high concentration in tonsils. Its known in mice that marjiuana can locally supress immune response, which may mean that if you are exposed to HPV and marijuana you risk can increase. (Gillison, et. al. 2008 Journal of the National Cancer Institute 100 (6), pp. 407-420 )

Family Recipe - Homestyle Competent cells

I've been getting a lot of random good feedback about my cells. People I haven't even made them for keep asking for them, and quite a few have said they are better than what they have purchased commercially. I think its because I really do make each aliquot with love. The only thing I can think of that I really don't see other people doing is keeping things cold. I make them in the cold room, and aliquot them into tubes that are already in liquid nitrogen. Also, you can keep them in TFB1 longer than 90 min ( I have certainly left them overnight). Maybe I will post the results from this latest batch of ccdb survival cells vs. Invitrogen's, which sell for $189 per ten transformations. I made enough for 100 transformations, essentialy free (1 box =~ $1890 worth of cells) when you borrow all the reagents (just don't borrow everything from the same lab). If they really are that good, I should sell (barter) them for other things I need around the lab, or for my lab courses taught in the city.

Competent cells

Adapted from QIAexpressionist 07/97

TFB1 (Cold) 500ml

100mM RbCl 6g

50mM MnCl_2• 4H₂O 5g

30mM CaCl_{2 •} 2H₂O 0.7g

30mM KAc 1.5g

15% glycerol 75g

pH5.8 w/ 10%HAc

TFB2 (Cold) 500ml

10mM MOPS 1g

10mM RbCl 0.6g

75mM CaCl_{2 •} 2H₂O 5.5g

15% glycerol 75g

pH 8.0 Autoclaved or pH6.8 Sterile Filtered

5M KOH

1. Streak out cells on plate with appropriate antibiotic, incubate 37^oC overnight.
2. Pick a single colony and inoculate 10ml of LB-Antibiotic overnight at 37^oC.
3. Add 1ml overnight culture per 100mL of pre-warmed LB broth containing antibiotic and shake at 37^oC until an OD₆₀₀ of ~0.5 in reached.
4. Cool culture on ice (at least 5 min depending on size), and transfer to sterile round bottom centrifuge tube.
5. Collect the cells by centrifugation at low speed (5 min, 4000x g, 4 ^oC)
6. From this point keep everything cold and on ice!
7. Discard the supernatant and resuspend the cells gently in ICE COLD TFB1 buffer (30mL TFB1 per 100ml of culture). Incubate 90 min on ice.
8. Collect the cells by centrifugation at low speed (5 min, 4000x g, 4 ^oC)
9. Discard the supernatant and resuspend gently in ICE COLD TFB2 buffer (4ml per 100ml culture).
10. Aliquot in 100-200 μl portions in cold sterile microfuge tubes, and freeze in liquid nitrogen.
11. Store cells at -70 ^oC

Tip: Make them with love, and keep them cold, i.e. I hold them next to my heart.

Unfinished Thought #1 HIV therapy

I have been wondering how to post my unfinished thoughts, hence fulfilling the name of the blog. For instance, given the recent chimpanzee attack, how could a team of chimpanzee's be harnessed to commit bank robberies? More on that later...

Regarding the elimination of HIV by antiretroviral therapy. In a recent New Scientist article it was proposed that if everyone infected was on antiretrovirals, there would be essentially zero transmission of HIV. Putting everyone of these drugs, given the expense is impossible. Not to mention getting them to take them, and eventual mutations that would eventually emerge.

Nevertheless, the idea for a solution I have is linked to another unfinished thought to be posted later. What if everyone (at least the infected) were implanted with a chip that synthesized and dosed the medication as needed?

The synthesis would have to be based on microorganisims (bacteria, ect) that had been altered to produce a drug along a particular pathway. The implant would maintain the level of these organisims, controlling their reporduction, fuel them by collecting nurtients from the blood, all the necessary things. The chip could then adjust the dosage so that little to no user imput was needed.

This would be a good way to administer many if not all drugs. It would be a bit ironic since we would be trying to coax organisims into doing our chemistry instead of trying to go the other way round.

Inside Cancer (upgrade!)

Traveled to Chicago for our first workshops of the year on cancer ( www.insidecancer.org ). It was well attended with various college and HS faculty and overall went well. Traveling outside NY is always an interesting traipse into culture shock. I am not sure where to begin about how strange the customs of the locals were, but that's because I find most people strange. I tried to look at the clues, like the way their subway is organized, or the perponderance of Stop signs on what I thought were streets in the middle of downtown Chicago. The main thing about going on a trip like this is getting as much for free as possible. We stayed at the Allerton hotel, where I left my workmates to their cots, and asked for and got the free upgrade. Twin flat screen TVs, living room, nice views, ect. I only manged to use one of the TVs as I was only in for one evening.

We supped at le whatever, I don't remember the name, but it was supposed to be french-thai fusion. The waiters had some uniforms inspired by the chinese army in the time of Chairman Mao (that was the french part?). The food was Thai, and ranged from acceptable - good.

The workshop went well, it was at Illinois Tech. We had breakfast at the hog and cow, or elephant and something. The pancakes were good, although had we actually run into the Danish ambassador, I would have managed a pastry or two.

23 and Me

I am coming as close today to having my genome sequences as is feasible for a few hundred bucks ( at least for the next few years) using the SNP genotyping service provided by 23andme. 23 and me examines nearly 600,000 SNPs for under $400. Of course only a few of these SNPs have verified (or at least published) medical, phenotypic, or other interesting qualities. I am certainly interested about what this will reveal about my ancestry. I have almost zero ethnic affiliation (typical for schizoid personalities I understand); but it should be interesting.

I am at many times frugal, passing on some of the other toys I want, but this was an exception. First of all, it is illegal (or possibly illegal) for me to have this genotyping done in New York State. Apparently there are various ethical/legal issues that upset NY's Attorney General, and there was/is the fear that NY residents might not be able to use this service at all. So rather than wait for the 23 and me service to be off-limits, I cashed in my 5-gallon dH20 jug of coins ($412 + dollars) and was off to New Jersey, where anything goes.

I decided to make a day of it, and took the ferry from the world financial center to Hoboken; a frontier town on the wrong (?) side of the genetics Mason-Dixon Line, and the closest I could get to not being in New York, while not venturing too deep into the Jersey wilderness.

I apprehensively boarded the floating ferry dock, which was part circus tent and part rusted out dumpster. As the waves buffeted the heap, I was partly comforted that once I had provided a sample of my DNA, it would be recorded and could live on if I didn't make it back. Crossing the icy Hudson, it was a quick trip to the other side. To find the Fed-Ex Kinko’s, where I would send back the pre-paid envelope.

"Inside the beast"

Ignoring the Fed-Ex drop-off boxes (decoys from the NJ eugenics ministry??? Not sure, but I could not sense any malevolent thoughts from the locals), I found the Kinko's a block away, where I felt sure my sample would make it safely to the lab.

Spitting into a tube on the open street and placing into a biohazard bag and mailer was at once undignified, and possibly suspicion arousing. So from the local park, I produced a saliva sample (as I approached way points along my route, the ferry, the train stations, the Kinko’s, I felt it increasingly easy to salivate) and mixed it with the preservative provided. Into the mailer, and into the Kinko’s drop-box.

A few weeks from now, I will be getting my results which I hope to share and make into lesson plans. Getting home was now an easy task, though belabored. The NY Waterway calls themselves the “civilized commute,” and boasts surprise free commutes. Due to the ice, the boat (the Peter R. Weiss, whoever that was) was late, and when it did arrive was unable to dock back at the WFC due to ice. They said they would send a larger boat, and fortunately the Senator Frank Lautenberg raced into port at a speed it I was sure would push the dock off its moorings. The senator promptly left without taking on a passenger. The Weiss eventually transported us to some other NJ station, where finally we boarded the Empire State which saw us all home. Now to wait for the results.

"looking over into the NY police state"

P.S. New York may be a police state, but the Financier Patisserie at the WFC has make a great "Opera" torte.

Discrimination / Species profiling - Hudson river plane crash

Fortunately no one was killed or seriously injured in the recent Hudson river plane crash. But unfortunately I can't believe the easy handed species profiling the Media is engaging in by accusing Canadian geese for the accident. No mention, of "alleged", or "suspected", not even evidence that a Canada goose did this. I can't speak to the moral turpitude of every Canada goose (the same can be said about people), but I find the type of profiling unwarranted. While some reporters are saying a flock of "birds" its clear what they are inferring. Computer animated images clearly show a Canada goose, implicating it in the accident. We don't know this for sure people! I thought innocent until proven guilty still carried weight.

I am glad the damage was minimal, but could we be more careful about our reporting. I don't know what the potential impact (no pun intended) on the goose community will be, but be sure to check out canadageese.org these next few weeks for action alerts.

Why the species profiling, did they have to draw in a Canada goose?