10 themes of a stem cell biology comprehensive exam

Stem cell biology – regenerative medicine

1. basic concepts: stem cell, kinds of stem cells (embryonic, placental, adult), uni-, multi-, pluripotency, stem cell markers, niche, regeneration, tissue engineering

I (scientist) desperately need a one click Reprint Request widget!

Just like other scientists, I guess, who are sending thousands of email reprint requests to other colleagues when the pdf of the paper is not available online.

The Regeneration Station – a biotech blog by Aastrom’s Jon Rowley

Jon Rowley is a senior manager at Aastrom Biosciences with a long experience in the not too old Regenerative Medicine field. I am pleased to introduce here his new blog The Regeneration Station as one of the first biotech – regmed blog written by an industrial expert who will share with us his insights on stem cells therapies, biomaterial-based devices, tissue engineered products and … biotech stock options i.e. all the things that are shaping the face of a young industry. According to Jon: Early adopter companies form and often fail, but they do succeed in removing some risk from the technology. As risk decreases, large companies try to figure out how to play in the new technology sandbox that is littered with small companies. Today, even Baxter is running a cell therapy clinical trial for cardiac regeneration, PerkinElmer is buying up cord blood banks, Celgene is dabbling in placenta-derived cells, and Teva Pharmaceuticals has an autologous MSC long bone trail underway.

There is another thing why more academic science bloggers should read Regeneration Station. Jon will definitely show us the “time and money” gap between science and the translation of it: “I do not want to undermine the importance of the great work that was done in generating pluripotent stem cells from adult skin cells, but the only thing I think about when hearing this news is TIME and MONEY. I know I will be fielding questions from my friends and relatives over Thanksgiving weekend on whether or not Aastrom (my employer) is doing this type of work or if we have to change our business model. I will have to explain that this type of research is at such an early stage, that it will not be impacting what is going on in Biotech for 20 years, if not more. It is challenging enough to manufacture and distribute an autologous cell product

Unofficial and hypercritical peer review of a paper on p53’s role in hESC regulation

Once I wrote shortly about the following peer review paper which was popped out of my PubMed feeds to draw some attention to it: Han Qin, Tianxin Yu, Tingting Qing, Yanxia Liu, Yang Zhao, Jun Cai, Jian Li, Zhihua Song, Xiuxia Qu, Peng Zhou, Jiong Wu, Mingxiao Ding, Hongkui Deng
Regulation of apoptosis and differentiation by p53 in human embryonic stem cells.
J Biol Chem. 2007 Feb 23;282(8):5842-52 doi:10.1074/jbc.M610464200

Now I got a very thorough comment on this paper by an author nicknamed “wolf” which systematically goes through the paper and gives a highly critical peer review of it. So I just publish the comments and next ask the authors (the first or the last) of the criticized paper and give them the possibility to defend their experiments and statements. My role here is the role of the blog”publisher”.

Comments re Qin paper p53 and hESC apoptosis by “wolf”:

This paper starts with making a fundamental mistake in not determining the kinetics of UV induced apoptosis and therefore missing the modulation of p53 target genes.
Subsequently they attempt to explain the absence of this by using transient transfections and analysing the cells at timepoints when half of the cells (mainly the undiff cells) are already dead and then interpret the data of the differentiated transfected (more resistant) hESC as if they were undiff hESC. The paper then desperately tries to come up with explanations for their own contradictory results). The data set further lacks controls (lentiviral mock transduced cells, no isotype controls etc), uses the wrong assays (such as PI staining to assess apoptosis, morphological assessment of differentiation by surface area) and lacks insight into the mechanisms controlling apoptosis (no cyt c release, no idea how p53 by itself might trigger mitochondrial apoptosis, etc).

Specifically;

Materials and Methods

Page 2: The authors use mainly one line of late passage hESC (p42-p68) grown in KSOR, which are highly CD30 positive leading to alterations in apoptosis regulation. We use three hESC lines at passages before p12 only.

Page 3: endoderm differentiation occurs in 4 days after Activin addition ? This is very quick with >80 % of hESC expressing sox17 after 100 ng/ml activin ?

Page 3: In immunostaining no antibody controls were used instead of isotype control with identical concentrations. We use isotype controls for all our immunos.

Let’s vote now for the 10 Finalist Lab Websites at The Scientist!

Ladies and gentlemen of science! You can now rank the 10 finalist websites from 1 to 10 (1 being the best) at the Laboratory Website and Video Awards hosted by The Scientist. Please do not hesitate, judging is a lot of fun and this is a big issue: figuring out the parameters of the labsite of the future based on the plus and minus features of current laboratory web pages! Some comments of the judging panel were published, just scroll over the judges’ photos. Winners will be announced in December. As a member of the judging panel my comments were chosen and published by the editors too, according to the selection I was rather critical (screenshots). Quick reminder: The LaWVas awards is the one that grew out of my unofficial lab website competition idea. The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

And 2 more:

inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa?

Have you ever asked any important but infrequently asked questions? Have you ever heard about the first personal genome service by the biotech startup 23andMe? Here is an inF.A.Q. addressed to this company:

According to the cool 23andMe genetics educator:

According to the peer review literature this is not necessarily the case and sometimes (rarely I admit) things in your cells can happen otherwise or more scientifically (mitochondrial recombination can occur):

When 23andMe’s Maternal Ancestry Tree service is tracing the genetic path of their customers, the microarray employees are identifying their haplotypes based on the differences in the mitochondrial DNA. The company is using SNPs (single nucleotide variants) unusually both from genes in the compact mitochondrial coding region (around 15.5kb) as well as within the circa 1kb large hypervariable region to give a detailed ancestry assignment. 23andMe examines few thousand places (over 2000 says Mr. Bettinger) on the mitochondrial DNA out of the total 600,000 SNPs.

But.

In the above case the 28 year old man’s blood and muscle differed at 18 positions which allowed assignment of the two sequences to separate European mtDNA haplogroups, H and U5, former being the same as the mother’s haplotype, while the haplotype of the patient’s muscle mtDNA was identical to that of his father’s and uncle’s blood. I wonder whether 23andMe’s Illumina chips can help make things clear in cases like this. (solution: let’s sequence the whole mito genome instead of a couple thousand basepairs). So as the first step in my mission to support the mission of 23andMe to support the mission of academic research I’d like to suggest putting a short tail on the possibility of paternally inherited mtDNA in the cool 23andMe genetics education material.

What is your (science) blogging writing style, Chris Patil?

I have to interrupt my 23andMe streaming cause there are more interesting things are goin’ on. Chris Patil of Ouroboros has already been a blogterviewee (Part 1, 2, 3) on Pimm. He then shared his detailed views on aging and life extension technologies, but I always wanted to ask Chris about his approach on blogging as it was obvious from the launch of Ouroboros that he has a style and angle on the aging literature that goes far beyond the usual and sometimes dead boring “this journal published this and that journal published that” science blogging subgenre. We all need to find new and experimental ways in science blogging to make it more than just simply echoing the peer review literature and a sharp focus, good arguments and neat English definitely helps, so below you can read the secrets of Chris in blue. I also encourage you to try to mimic him to the amount of one blog post as a blogging homework. (The picture was made by Bora of the Clock fame at Berkeley, California this August when there was a science blogger party one day before the SciFoo Camp. Chris is on the left. The other guy is an unidentified science blogger.)

It’s a challenging question. Like speech mannerisms or your own personal walk, style is something that emerges from a lot of little decisions that happen below the level of explicit consciousness. As I’m writing this, I’m wondering, ‘Is this in my style?’ It’s like listening to my own voice on tape. Nonetheless, I shall try:

My own history in science writing goes back to college, when I wrote a weekly Q&A column for the Stanford Daily (‘The Science Bug’; I had inherited it from an earlier staffer and passed it along to someone else when I left; years later, my younger brother took up the job). The audience was mostly other students, i.e. bright and educated but not necessarily scientists, so the main challenge was providing necessary factual and conceptual background without sounding like a lecturer — the readers were getting enough lectures in their coursework, and I knew that an overly didactic style would turn them off.

Unlike a reporter, I had a great deal of freedom to explore different styles, and eventually I found one that really felt like me which is not to say I didn’t have influences. I worshipped Cecil Adams (of the famous syndicated Q&A column The Straight Dope) at times perhaps veering across the line into outright imitation. From him I learned that questions don’t really want “answers”; they want “stories“, with a beginning, middle and end. You have to take the reader somewhere, from familiar ground to unfamiliar ground (and, sometimes, safely back again).

Pan-galactic experience: the 23andMe “official launch” webcast

Wow, what an all web experience it was: Linda Avey and Anne Wojcicki co-founders presenting their slides on the just launched personal genome service of their company 23andMe, then answering questions. The whole webcast will be available later on their website.

Here is a very short account of their webcast based on my texting and ears: Of course, they are planning to launch a blog later, they are in close contact with F.D.A. people to get things right, the genetic data on the 23andMe are belonging to customers, Google Health connection: not any right now, but open to work with anybody to empower individuals’ advance research, consumers are parts of the research process via answering surveys (so this is not really user-generated content in a Wikipedian way).

Some of my questions were connected to 23andMe’s mission to support academic research, a mission I wanted to put to the test:

- Do they plan to launch PhD programs and setting up a wholly functional research lab? Answer: a little laugh after this question and Linda Avey said something like that “oh, no, maybe later, who knows?”.

- Do they plan to organise research conferences to support research? Answer: “It’s something that we have and plan.”

My third accepted question (with a terrible English) was (the unaccepted ones were of course more intertesting.

The answer was the usual “yeah, later”.

23andMe on Pimm:

Web entrepreneurs and biotech: strangers from distant lands

23andMe: “official launch” webcast by co-founders Avey and Wojcicki

23andMe’s mission: connecting all people on the DNA level or social networking XY.0

The new faces of Silicon Valley: biotech-savvy co-founders Avey-Wojcicki

The life extension bonus effect of personal genome services: +10 years?

Spit a big in a tube, search with Genome Explorer: the 23andMe way

23andMe: the early bird of web based biotech startups

Update: Berci Meskó of Scienceroll has also been a webwitness of the Webcast.

Web entrepreneurs and biotech: strangers from distant lands

Elrond: Strangers from distant lands, friends of old you have been summoned here to answer the threat of Mordor. Middle Earth stands upon the brink of destruction, none can escape it. You will unite or you will fall. Each race is bound to this fate, this one doom. Bring forth the ring, Frodo.
[Frodo puts the ring on a stand for all to see]
Boromir: So it is true. In a dream, I saw the Eastern sky grow dark. But in the West, a pale light lingered. A voice was crying, “The doom is near at hand, Isildur’s Bane is found.”
[Reaches for the Ring]
Boromir: Isildur’s Bane…
Aragorn: Boromir!
Gandalf: speaking the words engraved on the Ring] Ash Nazg Durbatuluk, Ash Nazg Gimbatul, Ash Nazg Thrakatuluk, Agh Burzum-ishi Krimpatul.
[the light darkens and the air rumbles; Boromir backs away from the Ring]

Let us form the first real alliance of BT folks and IT people through personalized genomics (and later with regenerative medicine as I hope so), but take care, biologists and geneticists have way too powerful tools and web entrepreneurs are greedily looking for new territory with their unconceivable computational and storage capacity and perpetual hunger! Go, go, push, push! (Of course, there is no such thing as an outside threat of Mordor in this situation, the real threat (the other side of the reward coin) as in every revolutionary case is the shared ambition of tech people to make formerly impossible things possible).

The following words are from David Ewing Duncan’s Welcome to the Future:

Some analysts predict that the genetic-testing market 23andMe is entering could be worth a staggering $12.5 billion by 2009. Naturally, this has attracted the interest of Web entrepreneurs. They see an industry that is largely unregulated (so far) and costs only a few million dollars to enter—the price of a few brilliant programmers, a website, and marketing—and are betting that people will pay to test their own DNA directly. One indication of the potential market is that online medical-information companies are starting to make real profits. WebMD, for instance, attracts 40 million users a month and expects to net more than $30 million this year, mostly from ad sales. “I’m convinced there is an early-adopter market here,” says Sue Siegel, former president of Affymetrix and now a venture capitalist at Mohr Davidow. “Millions of people are used to getting health-care information online.”

23andMe: Genetics brings people together, rather than differentiate

“We are all from the same seed” – Kara Swisher summarizes what she heard from Linda Avey, co-founder of web based personal genome service 23andMe in the video interview below. Linda and the other founder Anne Wojcicki just talked about the company’s ancestry, genetic comparison and similarity seeking services, the ones that will technologically turned into a social networking service later based on shared genotypes backed by the genetical connectedness of all people (in this case all 23andMe customers). I called this idea the social networking XY.0 yesterday.

Linda’s thought was the following: “If genetics has the basis to bring people together, rather than differentiate them, that’s gonna be really interesting.” (Thanks Deepak for finding the videos)

In a recent Nature report by talented journalist Erika Check Hayden called So similar, yet so different we can find the following expert opinions on the very same topic that is commercialized and envisioned now by 23andMe (citing lengthy here, emphasis by me): In his 2000 State of the Union Address, President Bill Clinton chose to emphasize something he had recently heard from a genome researcher: that humans are all, irrespective of race, 99.9% the same genetically. “Modern science,” he told his country’s legislators, “has confirmed what ancient faiths have always taught: the most important fact of life is our common humanity.” Seven years on, and four years after the final publication of the sequences from the Human Genome Project, new technologies and larger data sets are allowing genome biologists to answer a conundrum embodied in that unity-inspiring percentage: if our DNA is so similar, why do we seem different in so many ways?

23andMe: “official launch” webcast by co-founders Avey and Wojcicki

From the press release: The co-founders of 23andMe, the first, web-based personal genome service, Linda Avey and Anne Wojcicki will hold a webcast media briefing on Monday, November 19, 2007 at 11:00 am PST/2:00 pm EST. (via The Genetic Genealogist)

23andMe’s mission: connecting all people on the DNA level or social networking XY.0

In these days, tech companies with MISSIONS are flourishing. I guess you’ve already heard about the company, whose mission is to organize the world’s information and make it universally accessible and useful. The newly launched, Mountain View based 23andMe seems similar in the mission respect. 23andMe is the first (already successful) and web (or rather Google) – based biotech company offering personalized genome service to its customers including interpreted and highly probabilistic information on the health risks of the customer’s genetic profile. But 23andMe has much more to offer in these early days and I think that mainly the biggest mission behind the company will be to show how different people are irreversibly connected and similar through their genetic material and variants. The company’s Global Similarity Map based on the comparison of the evaluated SNP (single nucleotide polymorphism) variants amongst customers and the Ancestry Service based on the by and large maternally inherited mitochondrial DNA. They will make this mission more explicit by introducing a social networking service around shared genotypes or as it claimed in the Wired article on 23andMe:
This is also where a novel use of social-networking tools comes in. Wojcicki envisions groups of customers coming together around shared genotypes and SNPs, comparing notes about their conditions or backgrounds and identifying areas for further scientific research on their own. “It’s a great way for individuals to be involved in the research world,” Wojcicki says. “You’ll have a profile, and something almost like a ribbon marking participation in these different research papers. It’ll be like, How many Nature articles have you been part of?’” (Social networking will be included in version 2.0 in a matter of months, Avey says.)

The idea of social networking based on genetic similarities and vulnerabilities: this is social networking XY.0 and the challenge

The new faces of Silicon Valley: biotech-savvy co-founders Avey-Wojcicki

After Jobs-Wozniak, Yang-Filo, Brin-Page, it’s time to memorize the names of the co-founders of 23andMe, the first personalized genome service, who are turning the tech establishment into a biotech mode.

The new faces of Silicon Valley: the age of Blue Jeans/Black T-Shirt co-founder computer nerds is over, welcome to the era of stylish, well-dressed genetics-savvy co-founder business ladies! According to the about page of 23andMe:

Linda Avey has over 20 years of sales and business development experience in the biopharmaceutical industry while the other founder, Anne Wojcicki brings to 23andMe a 10-year background in healthcare investing, focused primarily on biotechnology companies.

23andMe is probably the most well-connected startup in the history of Silicon Valley with an unlimited amount of networking and server capabilities thanks to Wojcicki and board member Esther Dyson.

The life extension bonus effect of personal genome services: +10 years?

After all, what customers can really expect of personal genome services that companies like 23andMe can offer beyond knowing whether they have a perfect pitch or not? If the service can really help in minimizing the risk of life threatening diseases, than the real expectation is to live longer by using those personalized/commercialized genome data. The future will answer this question, but it seems pretty sure that robust life extension (more than, say 100 extra productive and healthy years) is not within range just by knowing your predisposed genetic makeup in details. At the present moment the life extension bonus effect for using those services cold be around a decade and this guess is coming from Thomas Goetz’s article in Wired on 23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics:

And, yes, we will know whether our children are predisposed to certain traits or talents — athletics or music or languages — and encourage them to pursue certain paths. In short, life will become a little more like a game of strategy, where we’re always playing the percentages, trying to optimize our outcomes. “These are enormously large calculations,” says Leroy Hood, a pioneer of genomic sequencing and cofounder of the Institute for Systems Biology in Seattle, who suggests that if we pay attention and get the math right, “it’s not a stretch to say that we could increase our productive lifespans by at least a decade.”

Spit a big in a tube, search with Genome Explorer: the 23andMe way

Detailed article in the New York Times on the early experience of decoding the genetic code and interpreting the customers’ DNA via the service of 23andMe. The buzz name of the project: personalized genetics/genomics. Although other companies are mentioned briefly, the focus is clearly on 23andMe. The basics: get rid of a thousand bucks (sorry, just $999 per person) by build your order online, spit a big (2.5 mls) in a plastic tube in the postal delivered Saliva Kit, FedEx your saliva back to Mountain View (plus shipping and handling cost), wait a couple of weeks for an email and then use the company’s in-built Genome Explorer to find out the surprising details of your genetic makeup online.

From the NYT article: I soon found that I might well be sight impaired during those extra years. According to the five SNPs for macular degeneration I fed into the “Genome Explorer,” I was nearly 100 times more likely to develop the disease than someone with the most favorable A-C-G-T combination.

Other links:

Wired by Thomas Goetz: 23AndMe Will Decode Your DNA for $1,000. Welcome to the Age of Genomics

bbgm by Deepak: Your personal health: Consumer genomics becomes reality

Scienceroll by Berci Meskó: Personalized Genetics: Still Rising

Tit in the webcam and lifecasting for animals

A lifecasting and human free video streaming channel for animals could easily be a lot more interesting than Justin.tv. An early video tracking system based on miniaturized, animal-borne video cameras was developed for studying the undisturbed behavior (capturing lizards, using tools, flying) of new Caledonian crows and published in Science. Of course the online supporting material in this case is obviously the main stage so enjoy the online birdwatching. Some technical details on the setup: We designed tail-mounted camera units that do not interfere with movement and ensure safe shedding of the tag with regular molt. Units transmit a color video signal with sound to custom-built receivers and incorporate very high frequency (VHF) radio tags for simultaneous positional tracking. We deployed cameras on 18 different crows (12 males) in our dry forest study site (21°33′50”S, 165°19′27”E), capturing 451 min of analyzable video footage from 12 subjects (38 ± 5 min per bird, mean ± SE; maximum of 60 min). Hey, Makers, it’s time to set up your homemade animal videocams and install them on the Rats in the front room, roaches in the back and the racoons at the backyard. The tit picture was made with a webcam in Szentgotthárd, Hungary.

Who is afraid of ribosomal RNA?

This is from an Affymetrix technical note on The Human Exon 1.0 ST Array: “On average, the 18S and 28S ribosomal RNAs account for approximately 90 percent of any eukaryotic total RNA sample whereas the messenger RNA population makes up less than 2 percent in a given sample.” (I just wanted you to know.)

Puzzle: Which institute belongs to the following job titles?

Is it by accident that both Google first ladies are biologists?

Or is it the strongest personal indication of the future of technology? No, it’s not my job to answer this question, but I could be optimistic about the consequences of it. By now the story of Anne Wojcicki, Sergey Brin and 23andMe is a commonplace in the blogosphere. While Anne is graduated with a BS in Biology from Yale, Larry Page’s future wife Lucy Southworth happens to be a biology (genetics) grad student at Stanford interested in aging research too.

Learning new things from your partner is the most effective way of quickly acquiring ordered, contextual and practical knowledge. A good example is Aubrey de Grey who learned biology from his wife, experimental drosophilist and fine-tuned scientist of chromosomal mechanics Adelaide Carpenter.

For instance here is how Lucy explains nerve structure and Multiplex sclerosis: Look, Larry you’re familiar with this…

Many nerves are like an electric cord. An electric cord usually contains a thin metal wire covered in plastic that insulates the metal. The plastic layer keeps the electricity from leaving the wire. This can both speed up the electrical flow and keep nearby objects safe from the electricity.

But this could be interesting for you too: The metal wire in a nerve cell is called the axon. This is the part that carries the electrical signal. The insulation on a nerve cell is called myelin. Like in the electric cord, the myelin keeps the electrical signal from leaving the nerve.

As I said, in MS a patient’s immune system attacks the myelin destroying it. This affects a patient’s nerves like stripping the insulation off an electric cord does. Some of the electricity will short out causing the nerve to not conduct electricity as well any more. Also the electricity might jump off the axon and affect other nerves.

IT friendly explanation, isn’t it? Now I can imagine an average conversation amongst Lucy and Larry on how to solve the following problem:

Interdisciplinarity explained: “Eclectic others, who are smart and fun to have around”

I’ve found the following perfect quote in Paul Smaglik’s NatureJobs report on the current human brain mapping efforts of scientists all around the world (emphasis by me): Interdisciplinary groups are trying to combine imaging approaches and analyse them with statistics, and computational and mathematical modelling. Nikos Logothetis, a professor in physiology and cognitive processes at the Max Planck Institute for Biological Cybernetics in Tübingen, Germany, has combined data from fMRI and electrophysiology and wants to do both approaches simultaneously, then use “lots and lots of mathematics” to build circuit diagrams.

Karel Svoboda, a group leader at the Howard Hughes Medical Institute’s Janelia Farm campus, says that all 15 neuroscience groups there take a similar approach, but concentrate on specific regions of the cerebral cortex. Janelia plans to add 10–15 more leaders, says Svoboda: investigators examining neural circuits who use imaging tools; physicists, engineers and computational scientists who are building tools; and “eclectic others, who are smart and clever and fun to have around”.

Finally I understood the essence of interdisciplinarity in a sentence fragment. Thanks, Karel Svoboda.

What is your (science) blogging writing style, Maxine Clarke?

I met Maxine online first when she commented my post on the The problem of online “supporting information” in peer-review articles and then interviewed her on Nature policies concerning the same problem. Then I met Maxine offline in London and learnt a lot on how every issue of Nature is born and other insights I hope I can share with my readers here later. The following is Maxine’s answer to my stylish question and I would also like to offer her culture rich personal bookblog, Petrona.

My professional blogs (Nautilus, Peer to Peer and From the Blogosphere) are addressed to a particular group of people: scientists who read, review and publish, or would like to publish, in our journals. Therefore, the style I try to achieve is helpful, informative and stimulating, yet not didactic or dull. I aim to highlight the benefits of publishing at Nature Publishing Group and provide assistance to those wishing to do so, in a way that is not too directly promotional, but which is constructive to authors and interesting to them and other readers, as well as encouraging their feedback. Therefore I write about news concerning journal policies and format, as well as announcements of new journals, projects, conferences and online tools of interest to authors and reviewers. I also highlight when journal content is free for some reason, because this means that the authors of those articles are achieving greater “reach” for their articles (as well as making it possible for more people to read them, by my announcement). I also highlight news from the wider world of science communication, for example about quality indicators (citations tools and impact factors, for example), ethics, peer-review and so on, in the hope of stimulating community discussion of these issues, as this can help us decide on our journals’ evolution. Finally, I blog to provide an approachable forum for potential authors to ask questions about our publication policies, and to have them answered quickly in a way that can also benefit others, as they can see the responses.

Next blogterviewee is the number one scientific aging blogger, Chris Patil of Ouroboros.

Earlier:

Deepak Singh

me

“Give One Get One” starts today at the One Laptop per Child project!

I’ve just ordered 2 more laptops, although we already have 3, why? Because starting today you (in the U.S. or Canada) can donate an XO laptop to a child in the developing world and receive one for $399+24.95 for shipping. And Anna, the better half of my family in New Orleans, alarmed and convinced me to participate in the program. Lastly, I’ve played with one XO laptop at the SciFoo camp (picture on the right) and I loved it, the concept, the implementation and the intuitive interface. The “Give One Get One” program is the best way ever to persuade geeks to donate.

Here are the details:

From all of us at One Laptop per Child, thank you for your interest in our mission. Today marks the first day of our limited-time “Give One Get One” program. Starting today, when you donate an XO laptop to a child in the developing world, you’ll receive one for the child in your life. The price for the two laptops will be $399, $200 of which is tax-deductible. Additionally, T-Mobile is offering donors one year of complimentary access to T-Mobile HotSpot locations throughout the United States, which can be used from any Wi-Fi-capable device, including the XO laptop.

Please visit www.laptopgiving.org to participate in Give One Get One and discover more about the revolutionary XO laptop. You can also donate by calling toll-free 1-877-70-LAPTOP (1-877-705-2786). This is the only time

The birthplace of America’s first superhero: downtown Budapest

It’s weekend which means I am not just about biology and biotech blogging and can allocate a little time to spend on other projects like visiting the nearest Barnes & Noble at Metairie (it is a shame that there are no big bookstores in Uptown New Orleans except the Tulane Campus) and buying new books for entertainment like the one called The Secret Life of Houdini: The Making of America’s First Superhero by William Kalush and Larry Sloman. I slowly got interested in Houdini due to the account of my friend Csaba on the Houdini figure in the book Ragtime by Doctorow. Another indirect hint was Chabon’s The Amazing Adventures of Kavalier & Clay

Guess where was Houdini born: Anne Fleischmann was urging Cecilia Weisz on, alternately wiping her brow and giving her some ice chips to suck on. On March 24, 1874, the small room at Rákosárok utca 1. sz. had been emptied, the three young boys sent out to play. Only a few neighbors were there as Anne expertly cradled the baby’s head and turned it slightly to allow the shoulders to emerge. She gently grabbed the baby’s chest as the rest of the bloody body was expelled from the womb.

Of course, a newborn meant another mouth to feed, and another warm body to share this typically small “room-and-kitchen” flat in the predominately Jewish section of Pest, part of the newly consolidated town of Budapest, Hungary. That made four sons now for Mayer Samuel Weisz, who had recently graduated law school. One could only assume that Mayer Samuel would make a very eloquent solicitor if the story of the courtship of his future wife was any indication.

Ok, let’s move with our Google weapons to figure out exactly where is this location in present Budapest:

Search 1: Rákosárok utca Budapest

What is your (science) blogging writing style, Deepak Singh?

Actually the idea of asking science bloggers about their style came to my mind reading one email remark of Deepak on the writing style. Deepak is the guy behind business/byte/genes/molecules and he was a Sci Foo camper this year. He is one amongst the few bloggers who are standing at the intersection of science and technology and being the founder of Bioscreencast he is actively experiencing the life of a bioweb entrepreneur.

My style is a heady mix of spontaneity, continuous partial attention, a total lack of time, the random connection of ideas formed at different times, semi-formal essay-style writing, attempts at humor, deep thought, tempered enthusiasm, and unbridled passion.

Today’s top story on Blogrunner Science from 2 days ago

Why? Oh, it’s the TierneyLab.

It’s now judging time at The Laboratory Website Awards…

and I really like it. The nominations for the best laboratory websites are now closed at the Laboratory Website and Video Awards hosted by The Scientist. Now it’s the job of the judging panel (and I am one of them) to make our scores and review the nominees and then turn the voting back to you. The winning sites as selected by the editorial team, judging panel and the readers will be announced in this December.

Why do I like it? Well, I learn many new things by scanning through the sites, exploring second order links, realizing new ways the same thing (intorducing lab members, research topics, cooperations…) can be done and I am more and more convinced that this Awards is about to delineate the proper, uptodate frames of the lab site culture and accumulate a lot of new clues on how to make cool and useful future laboratory web stations.

On the other hand I ran into out of time features. For instance, remember that in the 90s, early 2000s, lab sites included links (not in-built customized search boxes) on the so called web search engines for the readers, if for some reason they are not familiar with how to search on the Internet? Believe or not, that are still laboratory websites with a separate category for search engines and links to Google, Yahoo, AltaVista or whatever.

Collect and FedEx menstrual stem cells with the C’elle kit: the next flow

It is a somewhat very positive idea that human tissues previously considered as waste products (after filling their essential role in the human body) like the placenta and the umbilical cord are radically reinterpreted as valuable sources of prospective therapies due to the current results of stem cell research and regenerative medicine. Exactly this reinterpretation is taking place now with the cells of the regularly produced menstrual blood flow as the first commercially available menstrual stem cell service, C’elle was launched by cord blood banker Cryo-Cell.

The user friendly process in a nutshell: Upon ordering, you’ll receive an attractive, discreet C’elle collection kit by FedEx delivery. Inside, you’ll find everything needed for you to collect and send your C’elle menstrual stem cells for processing and preservation, including a menstrual cup, collection tubes, prepaid FedEx airbill for return shipment to Cryo-Cell, and comprehensive instructions for use.

There are 3 plans and pricings available: annual plan for $499 includes processing & first year’s storage, semi-annual plan for collecting two specimens instead one, and quarterly plan for four specimens, and you have to pay for the annual storage thereafter in the range of hundreds of dollars/year.

Unfortunately we’re short of strict scientific details (summary here) as of this moment, but a peer review article will be published this winter. Scientists involved: Amit Patel, Gerald Elfenbein, Stephen J. Noga, Paul R. Sanberg. What we could know: The characteristics of these menstrual stromal cells are similar of the human endometrial stem cells derived from the endometrial lining of the uterus, but their collection is non-invasive and pain free. Let’s take a look on the table left in which menstrual stromal cells are compared to the more established mesenchymal stromal cells from the bone marrow. I’d like to highlight 2 differences:

Blogrunner Science vs. Scienceblogs vs. Postgenomic?

Alien vs. Predator like stupid question for the weekend: Which do you think is the best source when it is about interesting and quality science content: the Techmeme clone Blogrunner (here it’s the science channel of Blogrunner), that is the newly launched automated online news service and blogs aggregator by the New York Times or Scienceblogs or Postgenomic? Which model is the best?

And what do you think about the tons of Eurekalert Press Releases on Blogrunner? Do you like to read press releases?

Watch science videos on the iPhone with vTap beyond YouTube!

So far science videos on the iPhone were restricted to YouTube and subscribed, previously downloaded science-related vlogs on iTunes due to the lack of Flash, Windows Media Player, etc. support. But now with a new web app called vTap a bigger range of (science) videos are available and can now be played in the iPhone’s native QuickTime player in a good quality (screenshots made on a MacBook, the iPhone view is different.) I wonder when can we watch say JoVE or SciVee videos on the iPhone…

From the iPhone Atlas: Dubbed “vtap,” the service lets you search for videos from around the Internet, then — get this — encodes them on the fly and puts them in a format that can be played on the iPhone (H.264). vtap searches YouTube, MySpace, Dailymotion, news sites like the Associated Press and Reuters, even ESPN.

SciPhone links:

Science on the iPhone, is it a good SciPhone? Aspects for a test series

Making notes in a seminar with an iPhone: in progress (SciPhone Test)

Last minute, low budget Halloween costume: Mr. Evil Google

Components from top to bottom:

Insulated Test/Jumper Leads

wig

blue ethernet cable

original Google T-shirt (I got mine at the Euro Maker Faire)

badge (actually I used my SciFoo badge just inside out, there was a modified Google Search Box on the other side with an “I am feeling Evil” button)

components desperately needed, but I haven’t had the time to make them: horns and Google spiders for crawling (the arachnid-centric names for the Web are ideal for Halloween reasons)

assumed background knowledge to recognize Mr. Evil Google: Google’s corporate motto

Problem: For a Halloween costume to be cool it should be targeted for the local Halloween audience and New Orleans is not the geek but the freak capital of the world, so almost nobody recognized me.

P.S. Actually I wanted a dead Google employee costume, but then Grady came out with the idea of Mr. Evil Google

Disclaimer: I am not a Google employee yet.

Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things

As a biotech geek blogger and occasionally Make contributor, who stands at the intersection of science and technology with a (life) science bias, it is more and more exciting to see how the attractive brands of the 2 sides are building the bridge and creating a shared channel. So far, the biggest manifestation of this shared channel was the SciFoo Camp, organized by Nature and O’Reilly, hosted by Google. Now Tim O’Reilly, a native of Cork, Ireland turned Californian tech publisher visited the Nature Headquarters and talked about his angle on the web and tech publishing (giving me an incentive to finish the story of my earlier visit at Nature at September). You can read the informal account of Timo Hannay on the meeting at Nascent (picture: my shot on Tim and Timo summarizing the SciFoo experience at the Googleplex).

One thing seems more visible to me: Tim is bored about his original business and industry and is looking for some new which he seems to find in…. science (see Craig Venter and Tim O’Reilly chat: when 2 worlds meet).

The computer industry was a very exciting place, and then it became boring, because it became consolidated. ..There is going to be a lot of consolidation, the man will take over (he might be idealistic like google), it is going to get a lot more boring. The interesting question is what will happen when google’s growth slows down?
But you have to have a belief in people’s ability to find new things. There are going to be a lot new areas coming out of science, one thing we can do is to help to birth the future.

or: What happens when folks from synthetic biology meet hedge fund hackers meet roboticists and makers?

Tim’s boreness is really good (not the burned out part) for scientists like me. For instance, one of my ideas (an idea briefly communicated to Phil Torrone at the Austin Maker Faire) is to collect enough bioDIY projects like the “Make stem cells from the placenta at home” together, that is enough to set up an exclusive “sciencey” BioMaker Faire.