Thesis live: 1.1 Turnover or Every cell has a lifespan

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

1.1 Stem cells and regenerative medicine: basic concepts

/turnover: cellular turnover/

The concept of biological turnover (rate) can be interpreted on many levels: molecules, molecular pathways (signaling), organelles, cells, tissues, organs. The turnover rate by which a biological entity is replaced can be quantified by measuring its half-life. /In abstract form “the half-life of a quantity whose value decreases with time is the interval required for the quantity to decay to half of its initial value” (Wikipedia) I have to check whether it is problematic to explicitly use a Wikipedia entry – I am sure it is used implicitly – in a PhD thesis/ The concept of half-life refers to the time required for an initial quantity of entity E to decay half of its initial value. According to Caplan [reference]: “Every cell in the body has a specific half-life; every cell comes to maturation and will, predictably, drop dead in due course.” For instance erythrocytes have half-lives of 60-90 days and the turnover rate of hepatocytes is 1-2 times/year. On Figure 1 from Caplan the lineage development of a differentiated cell and its replacement cell is delineated. The relative position of these two curves to one another defines growth, steady-state, or atrophy depending on when the first cell dies and when its replacement, the second cell, comes online. /I am not sure here how to solve the problem of legends in the case of figures coming from the literature but I figure it out, here is/

caplanturnoverfigure

Continue reading

Thesis live: 1.2 tissue/stem cell introduction scheme

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

When producing a text, a post my building strategy is not linear, but heavily non-linear (I wouldn’t say it’s circular): I’d like to jump to the part of the story where there is something instantly to write/edit; be it the beginning, middle or end. In case of scientific articles frequently the first part to be build are figures/methods, which forms the bulk, the middle of the story after introduction, before discussion.

1.2. Tissues, organs with different turnover and regenerative potential

In order to discuss the different adult tissues in a unified manner, from a systemic point of view, I use the following tissue/stem cell introduction scheme where data are available: development of particular tissue, number of cell types, bioenergetics (high/intermediate/low energy demand), turnover (high/intermediate/low), regenerative potential (high/intermediate/low), resident stem cells, niche, markers, cell sources from other tissues that can contribute to the particular tissue during normal turnover or chronic/acute injury.

Thesis live: 1.1 Basic concepts: Let’s roll!

In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential.

After the Introduction draft it’s time to actually start to fill in the text and that’s really the hard part. In the text I mix complete sentences, paragraphs (source code, object language) with fragmented metacomments (labeled as /draft, comments are here/) as a GTD technique. Used literature, links come after the text in a reference form like: Rando TA. Stem cells, ageing and the quest for immortality. Nature 2006;441:1080-1086. or Rando TA. (2006) Stem cells, ageing and the quest for immortality. Nature 441:1080-1086. (maybe I should check the official rules here)

Figures, diagrams will be included and I don’t promise to figure out brand new ones (but promise to find good ones), but that’s not a necessary job for thesis writers.

Expect me to start with a low quality (including older texts of mine) material and progress toward something more valuable.That is a trend people usually would like to follow throughout their professional careers.

1.1 Stem cells and regenerative medicine: basic concepts

Looking for the exact definition of stem cell is sometimes the source of endless semantical debates, but at least we do know two generally accepted criteria: stem cells are able to renew themselves and could differentiate into other type of cells. First, they are unspecialized, mitotic cells that renew themselves for any (i.e. long) periods through series of cell divisions, which result in similar unspecialized stem cells. This is the so called and overstated “immortality” characteristics. Continue reading

Oxygen control of stem cell niches and cell fates

Did you know that physiological normoxia generally falls in the 2-9% O2 (14.4-64.8 mm Hg) range for most adult cells in vivo? 3 remarkable exceptions are thymus, kidney medulla and most importantly bone marrow which can exist at 1% O2 (7.2 mm Hg). On the other hand, stem and progenitor cells are frequent residents of hypoxic niches and low O2 regulates their differentiation. Conclusion?

Although most cells are maintained in culture conditions at 21% O2, this is unlikely to be optimal for maintaining their normal proliferative or developmental state. The derivation of novel stem and undifferentiated cell populations should therefore be enhanced by culture in the range of 3–5% O2.

More on this very important and usually neglected oxyphsiological angle on stem cells, development and culture in the very uptodate review: The role of oxygen availability in embryonic development and stem cell function by Simon@Keith in Nat Rev Mol Cell Biol. 2008 Apr;9(4):285-96.

stemnicheoxydiff

Some stem cells (such as those in the endosteal bone marrow compartment) occupy extremely low O2 microenvironments (<0.5% O2) Continue reading

Ward Cunningham – What If Bacteria Designed Computers?

cunninghamcartoonportraitThere is a pattern of successful technological innovations I can summarize the following way: there is a nerd engineer who actually invents something and builds the first functional prototype, and there is a geeky enough yo who recognizes the value of the prototype and makes the bigger money/fame/other beneficiaries out of it by turning it into a commercial product: the archetypal nerd/geek pair in this respect is Wozniak/Jobs. In case of the wiki software the programmer/inventor was Ward Cunningham, while Jimmy Wales became the official Mr. Wiki due to Wikipedia.

Recently I discovered Cunningham on Twitter and I learnt that for coding he takes inspiration from life’s processes ranging from cell signaling to cultural evolution. His coming speech: Continue reading

Friday Gumbo Journal Club: hESC line differences and a killer MSC review

It’s Friday, that is a lunch heaven for a Gumbo loving biogeek at Tulane:

gumbojournalclub

Stem Cell Express: Copy Number Variant Analysis of Human Embryonic Stem Cells from the Teitell Lab (It’s good to see that CIRM funded results and papers are coming out): Continue reading

Mitowheel now helps you design PCR primers for mitochondrial DNA!

mitowheelallelebarsGábor Zsurka, scientist and developer made another upgrade on our favorite human mitochondrial DNA visualization tool, MitoWheel: this time allele frequencies at polymorphic positions are included in the sequence bar in the form of a gray bar above or below a nucleotide representing the number of individuals carrying the SNP.

This is really cool as it is a definite step to turn MitoWheel into a tinkering, engineering, mtDNA hacking tool besides its core science mission:

“This can help you to design reliable PCR primers for the human mitochondrial genome. After all, you don’t want your primer’s 3′-end sitting right on a very frequent polymorphism (risking that under certain conditions you will not be able to amplify a PCR fragment from a subset of individuals).” Source: MitoWheel Blog.

Blow your Brain Explorer out with the Human Allen Brain Atlas!

At the SciFoo Camp last year at the Googleplex I suggested a little unconference session (ok, there were some slides ready on my MacBook) and one participant was Chinh Dang (another was this inventor) Technology Director of the Allen Institute for Brain Science who made a little intro to the work of the Institute to the 9-10 attendees after this slide of mine:

SciFoo Brain Atlas

Paul Allen is the likable, Steven Wozniak-type co-founder of Microsoft, but I guess a bit richer (once we estimated with a friend of mine that he could buy all the Budapest condos circa 180 times or sg like that).

But instead of doing that he provided $100M – amongst others – in seed money to fund the Allen Brain Atlas.

Continue reading

Thesis live: Introduction, “contents” draft

From now on I start every “thesis live” post with the standard introduction: In the live thesis building blogxperiment I edit (digest, compile, write, rewrite, delete) my ongoing doctoral thesis in blog posts and put the parts together on thesis live. The title: The physiologic role of stem cells in tissues with different regenerative potential

I am not aiming any perfection, my focus is clearly on getting things (the PhD) done here. Anyway, I found the idea of “writing” a complete, lengthy and formal thesis outdated and inefficient (after all, scientists should conduct nice experiments and publish their results in short, inforich and accessible research papers in order to share it ASAP with the research community, not in book-length, otherwise unaccessible PDFs) and so I try to keep myself motivated by

- doing this “thesis live” series as an open science experiment and getting useful feedback from my fellow scientists and readers

- trying to include as many systemic, whole body level material into it that could be relevant for systemic regmed approaches

- reminding myself every day that without a PhD it is hard to move further in science officially (that’s the least motivating factor though as it is official)

After the blah-blah let’s start with the planned introduction points:

1. Introduction:

1.1 Stem cells and regenerative medicine

1.2. Tissues, organs with different turnover and regenerative potential

Gut epithelium,
Blood – hematopoietic system
Epidermis,
Mammary epithelium,
Vascular endothelium,
Continue reading

Biotech DIY for aging/life extension research: the double future?

“The best way to predict the future is to invent it.” – said Alan Kay, computer legend in 1971.

Recently I had a comment dialogue with Chris on whether state-supported research or industrial business enterprises can (or should) lead to big progress in robust and healthy life extension technologies. Besides the government and corporation coin the research breakthrough could come from an aging focused foundation like the non-profit Methuselah Foundation behind the SENS approach, which supports research projects (like MitoSENS and LysoSENS) and scientists (like Mark and John) through cooperation with university labs. And finally, there is going to be another option to contribute:

agingbioDIYtoast

Imagine the following future scenario: biotech DIY is becoming an accepted home activity so geeks are setting up private labs and conduct basic in vitro (but not in vivo) research. Continue reading

Mitowheel upgrade: phylogenetics in motion

mitowheel creating groupsGábor Zsurka has built some killer functions into Mitowheel, the human mitochondrial DNA visualization tool:

- compare GenBank‘s circa 3000 fully sequenced human mitochondrial genome to the revised Cambridge Reference Sequence mutation by mutation

- by harnessing the power of the colorful group view and using the +, – mutation operators (see detailed introduction) you can dig deeply into phylogenetics and haplogroups

- navigation became more sophisticated

PITTCON, 2008: bioDIY questions, RFVials, and Science’s new web hirings

pittconchildAs a local New Orleans face (my colleagues just call me Mitoman in the lab) I had the chance to just simply walk into the grandiose PITTCON exhibiton at the Ernest N Morial Convention Center and I liked it. In addition to getting answers to some strictly lab related questions concerning filters and fuges (nevermind), I satisfied my 2 major side interests: the older bioDIY and the brand new RFID.

1. I surprised every biotech vendor - some of them laughed, others were meditating a bit - with the question: ok, but what is the cheapest gadget you have for somebody who wants to set up his basic DNA private lab at his backyard?

In my coming series to help launch a grassroots biotech DIY movement I’ll put together concrete suggestions on what to buy, but according to the experts:

- the price of a new benchtop centrifuge (6-8000 x g) is $800-1200, but the manufacturer is simply not interested in individual service and recycle used machines for low-throughput hobbyist end-users

- liquid nitrogen: 24 liter tank around $5000 (you can get it lower), LN itself is not that cheap but it’s worth storing your cells in a local repository bank instead, at least an expert guy told me

- a laminar hood for sterile work with cells is also around $5000, way too much for garage biofreaks, but you can still build your own out of a household air purifier

2. Have you ever thought of tracking, reidentifying your eppendorfs and tiny PCR tubes in the lab instead of the almost impossible hand marking? Well, we are not there yet, but Baytek developed an RFID kit for glass GC or HPLC vials. Continue reading

The conditions of a mass biotech DIY movement

jobswozniakPCR

The idea of doing biological experiments with current biotechnological methods and conducting research projects at home is quite new. There are already many names in use referring to the same concept: bioDIY, home biology, biotech DIY, garage biology.

We have a detailed case example which can be considered as the first registered, high profile biotech DIY activity starting the era of useful garage biology: Recently Hugh Rienhoff amplified his daughter’s DNA at home to help doctors figure out her genetic disorder. From the Nature cover article:

“So he bought a used PCR machine, a microcentrifuge, some small-volume pipettes and a brand new gel box. All told, the equipment cost him about $2,000. With these simple tools and some sequence-specific DNA primers of his own design, he could pick the relevant genes out of his daughter’s genome and amplify them enough for sequencing. Freezing the samples and packing the tiny tubes on ice, Rienhoff sent them off for sequencing at about $3.50 a pop. He prepared upwards of 200.”

Another suggested project was the How to isolate amniotic stem cells from the placenta, at home! but so far I haven’t heard of anybody who really did that at home and I only isolated the cells at the lab.

In my coming series I’d like to examine the following conditions of a mass biotech DIY movement: acquiring skills, affordable kits, tools, hardware, motivations, business opportunities and impact.

acquiring the how to skills:

- good education tools, protocols, videos, howto-s on the web

- short intensive academic or industrial lab courses available for every citizen

- self-education in community: forming Homebrew Biotech Clubs

available, affordable tools, hardware:

- cheap kits: based on the Rienhoff example, a very basic home lab can be set up out of 2-3000 dollars, which is the price of a good laptop.

says Mr. Rienhoff in an email: I bought all the equipment used from a local vendor who buys equipment at auction and from universities. All the gear is at least ten years old so it was very used and low throughput. But given that my project was incredibly focused I did not need the more sophisticated equipment.

- used equipment network: Continue reading

How much data is produced by a life scientist/day?

3TBThe current operational idea behind Google’s Palimpsest Project is to ship 3TB (terrabyte= 1.0995 x 1012 bytes) drive array (Linux RAID-5) for scientists, who upload their data and FedEx the hard drives back to Google. Google then make those data publicly available and manageable. This file transfer method was heavily criticized by Dai Davies in Ars Technica. “This is a bit like using Flintstones technology in the Internet era.” although there are arguments behind this choice, see Jon Trowbridge’s 11th slide. Forget about this uploading/updating problem to the amount of this post. Here I only care about the end-user, the scientist who is provided with whatever tool to upload 3TB of research, measurement data on behalf of her research facility. While for an astronomer hundreds of gigabytes/day can seem as a normal output my angle is on how a life scientist and his data fits to this 3TB equation and eventually to the Palimpsest Project. Accordingly, my question is this:

How much data is produced by an average wet lab scientist, biomedical researcher/day?

I try to come out with a rough guess in the hope of subtle corrections from the commenters: I assume the following (rather busy) daily production of data by our average scientist in an average lab:

running a gel – making a gel photo 300 KB .tiff

preparing 5 samples for sequencing at the core facility, output: 500 KB – 1MB ab1, seq files

FACS sorting of different cell populations: 1 MB of special FACS files and 100 KB pdf out of it

Continue reading

Let’s compile a Biotech for IT folks book and publish it!

IT people are the dominant high tech tribe today and especially on the web. But biotechnology (BT) is the next infotech so no wonder that the IT crowd is growingly curious about everything biotagged on the one hand, while they are usually not too savvy in DNA-RNA-protein-organelle-cell-tissue-organ-organism related matters on the other hand. Check for instance Tim O’ Reilly at Nature: science meets bored tech-savvyness to find new things.

And what can biotech bloggers do in order to meet the growing demands: well here is a little conversation from my twitter channel in the last 20 minutes:

Biotech for IT folks

‘The horror of closed-access publishing’ according to Jonathan Eisen

Jonathan Eisen is the new Academic Editor-in-Chief of PLoS Biology and wants to build a world in which Open Access and “top tier” can go hand-in-hand:

jonathaneisen

So I accepted the invitation and became an Academic Editor. But I confess that I was not yet a true convert to OA or to PLoS Biology. So I decided to do what any good scientist should do in such a situation—I planned a publishing experiment. I’d had many papers in Science and Nature before. And so I convinced my collaborators on a high-profile paper to submit it to PLoS Biology, to see how this new high-profile OA journal would compare.

But then, while finalizing the paper, a two-month-long medical nightmare ensued that eventually ended in the stillbirth of my first child. While my wife and I struggled with medical mistakes and negligence, we felt the need to take charge and figure out for ourselves what the right medical care should be. And this is when I experienced the horror of closed-access publishing. For unlike my colleagues at major research universities that have subscriptions to all journals, I worked at a 300-person nonprofit research institute with a small library. So there I was—a scientist and a taxpayer—desperate to read the results of work that I helped pay for and work that might give me more knowledge than possessed by our doctors. Continue reading

Understanding Aging Conference in L.A.: de Grey, Conboy, Wagers and many others…

UABBA conference, 2008

Looks like the scientist coalition behind healthy life extension is widening. In line with that the question Why was life extension ruled out of the 14 Grand Engineering Challenges? is fading away.

Here is an Aubrey de Grey message from my mailbox:

All details, including forms for abstract submission and
online registration, are at the conference website:

http://www.mfoundation.org/UABBA/

The preliminary program already has over two dozen confirmed
speakers, all of them world leaders in their field. As for previous
conferences I have [co-]organised, the emphasis of this meeting is on
“applied biogerontology” — the design and implementation of
biomedical interventions that may, jointly, constitute a
comprehensive panel of rejuvenation therapies, sufficient to restore
middle-aged or older laboratory animals (and, in due course, humans)
to a youthful degree of physiological robustness. The list of
scientific sessions and confirmed speakers is as follows:

DNA damage, telomeres, cancer
Adam Arkin, Lawrence Berkeley National Laboratory; Jan Vijg, Buck
Institute for Age Research; Jerry Shay, U. Texas Southwestern;
Claudia Gravekamp, Pacific Medical Center Research Institute; Zheng
Cui, Wake Forest University School of Medicine; Rita Effros, UCLA

The cell niche
Irina Conboy, U. California Berkeley; Judith Campisi, Lawrence
Berkeley National Laboratory and Buck Institute; Leanne Jones, Salk
Institute; Ken Muneoka, Tulane University; Kevin Healy, Stanford
University
Continue reading

The human mitochondrial consensus genome sequence by Robert Carter

For historical reasons the standard human mitochondrial sequence, the Revised Cambridge Reference Sequence (rCRS) is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. That’s why many times a usual mtDNA sequence alignment must appeal to phylogenetic historical reconstructions. The rCRS nevertheless provides a uniform nucleotide numbering scheme (0-16569). On the other hand, as there are thousands of high-quality, full-length mitochondrial sequences are now available, Robert Carter thought that it is time to construct and analyze a comprehensive human mitochondrial consensus sequence and published his efforts in Nucleic Acid Research, March, 2007: Mitochondrial diversity within modern human populations The sequence itself available as a supplementary material but with the permission of the author I copy it into this post below.

According to Robert Carter:

So far, all feedback has been good. By introducing the idea of “poly-x” sites (see later), I successfully created a technique that avoids all pre-conceived ideas about genetic history. This also allows one to effectively deal with indels, something that many authors have avoided in the mtDNA literature.

Briefly, 827 sequences were used, a master sequence alignment was created in BioEdit and BioPerl was used for all calculations using the rCRS as a template for nucleotide numbering. Continue reading

The New York Times advertises itself with stem cell research

I’ve just noticed a New York Times paid “stem cell research” Google Adwords ad in my gmail inbox besides the automated Rejuvenation Research Vol. 11, No. 1, Feb 2008 is now available online” mail. That said, The New York Times is ranking the “stem cell” buzzword high and fishes for layman readers interested in the whole regmed topic for its own stem cell site both in the search results and next to articles (in the content network – explains Anna, my online marketer wife, next to me). I wonder for how long they have been paying for these ads? Other mainstream journals have similar ads, like The Washington Post. C’mon folks, let’s spend a part of those ad dollars to real stem cell research too!!!

NYTstemcellad

Healthy life extension is not 1 out of the 14 Grand Engineering Challenges…

…that can be realistically met, most of them early in this century according to the Committee on Grand Challenges for Engineering with members such as Larry Page, Dean Kamen, Craig Venter, Robert Langer and …lifestyle life extensionist, nanovisionary Ray Kurzweil. There is a challenge though called Engineer better medicines and the essay behind looks as if it had been hacked together by Kurzweil and Venter themselves during a sunny Californian Soy Beer Baby Boomer Beach Party. It is about personalized medicine in large and the only hint – I was able to find – to a recent discipline named regenerative medicine is: Continue reading

Warda speaks: “We say the truth, I not burrow any sentences from others.”

The Warda-Han-Proteomics saga continues and finds its way to the show/entertainment business. We’ve already listened to Han, now it’s time for Warda to speak, which he did in an email to James Randerson over at the Guardian Science blog, which makes think (indeed ‘rethink’ as W suggests) that the Warda-Han pair is probably the Laurel and Hardy of the science showbiz.

WardaGuardian

Continue reading

Genome Technology launches MethodShare beta!

Genome Technology, the heavy trafficked New York based biotech website (also a printed monthly magazine) just launched the beta version of MethodShare as “a place for people to discuss methods and tools, recommend methods papers to one another” according to Ciara Curtin, senior editor. The site will be coming out of beta soon.

How the site can position and maintain itself in the narrow space between the professional Connotea reference manager on the one hand and the versatile high end methods site ranging from Nature Protocols to JoVE on the other hand is a really open question at this point. This won’t be a simple game and good luck to them.

Methodshare by Genome Technology

The Warda-Han-Proteomics scandal: fingerprints of plagiarism, too

We have now a well-developed and sad case example of irresponsible scientific editing and publishing: the Warda-Han advanced online paper by the academic journal Proteomics: Mitochondria, the missing link between body and soul: Proteomic prospective evidence. What started as an abstract-based hunch and question about the quality of a recent review, addressed to and amplified by the the scientific blogosphere may probably end as a piece of investigative journalism in the mainstream media with serious consequences and conclusions on scientific publishing. Right now, the real investigation takes place at the comment section of the PZ Myers post A baffling failure of peer review over at Pharyngula. The story there is quickly unfolding thanks to the smart and open-eyed (Google-savvy) contributors who figured out amongst others that Warda and Han significantly reduced their review writing efforts by borrowing many sentences from other colleagues’ papers. Here I’d like to mention and cite only 3 comments: Continue reading

The fingerprints of a mighty creator in Proteomics, impact factor >5

wardahanCreationism/intelligent design is not really an issue for me as I am a biologist working with mitochondria and stem cells, also a life extension supporter, whose angle on things and projections are based on the recent advancements in science and technology. As far as I know, creationism/ID neither suggests any new experiments or heuristic solutions in my research field, nor does it help to plan&build new technologies to extend healthy lifespan. From my point of view, thinking about creationism is a waste of valuable scientific/technological processor time.

But I am not used to encounter with explicit creationism and the fingerprints of a mighty creator as an explanatory force behind a natural phenomenon in scientific peer-review journals. That’s exactly what happened to me in a recent review published online by the Wiley journal, Proteomics (ISI Impact Factor 2006: 5.735) by Mohamad Warda and Jin Han, entitled Mitochondria, the missing link between body and soul: Proteomic prospective evidence.

Last week when I wrote the post Can you tell a good article from a bad based on the abstract and the title alone? on the review I had only 10 minutes for figuring out the post between 2 experiments in the lab during lunchtime. The only thing that came into my mind reading the abstract – popped out of PubMed feeds – was that something stinks here. Now it’s Mardi Gras day and I have a couple of minutes more to address this issue and hopefully no more.

Myrmecologist and blogger Alex Wild picked one sentence from the paper in a comment, and here is the complete paragraph:

Alternatively, instead of sinking in a swamp of endless debates about the evolution of mitochondria, it is better to come up with a unified assumption that all living cells undergo a certain degree of convergence or divergence to or from each other to meet their survival in specific habitats. Proteomics data greatly assist this realistic assumption that connects all kinds of life. More logically, the points that show proteomics overlapping between different forms of life are more likely to be interpreted as a reflection of a single common fingerprint initiated by a mighty creator than relying on a single cell that is, in a doubtful way, surprisingly originating all other kinds of life.

This is the closing paragraph of the section Mitochondrial integrated function disproves endosymbiotic hypothesis of mitochondrial evolution. The mitochondrial part of the well established evolutionary endosymbiotic theory claims that ATP-producing mitochondria were ancient prokariotic invaders of host prokariotic cells eventually turned out to be the common ancestors of eukaryotic cells. I always found this hypothesis one of the most fruitful scientific concepts as it constantly suggest new ideas and warns that current eukaryotic cells are the products of an evolutionary, accidental and instable alliance between the mitos and their hosts. As the endosymbiotic theory is the mainstream academic theory of mitochondrial evolution it is a challenge for scientists to attack it with counterarguments and that’s what Warda and Han are aiming for in that section. What they are doing seems like a legitimate discussion of a scientific theory but ends with the logically unacceptable jump to the fingerprints of a mighty creator as an alternative explanation.

Before I cite the section in question in full length and recommend to my readers to analyze it, I also like to suggest the detailed comment of D. Spencer saying amongst others:

If Wiley and the journal Proteomics allow this into print (it is currently only “published” online) they can kiss goodbye to any hope that Proteomics will ever again be regarded as a serious scientific publication.

Here is the complete section by Warda and Han without references that could be found in the full text: Continue reading

Can you tell a good article from a bad based on the abstract and the title alone?

Many times people only have access to the abstract of peer-review articles, and nothing more. There are different abstract styles (sometimes they’re going too far or on the contrary) in the literature and I’d be curious to hear about your opinion on the following review abstract and title. I became interested and suspicious reading these lines especially the one highlighted in bold.

Mitochondria, the missing link between body and soul: Proteomic prospective evidence. Continue reading

MitoWheel 1.0: the human mitochondrial genome just got visual!

MitowheelYour 16569 basepair long human mitochondrial genome does a lot for you and tells a lot about you. It encodes protein subunits playing crucial role in the production and conversion of ATP, the body’s main chemical energy currency. On the other hand the actual sequence of one’s mitochondrial DNA in a particular tissue or cell population gives a lot of health associated (mitochondrial diseases, aging) and ancestry information.

So far users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA. But now with MitoWheel version 1.0 (yes, it is beta) the situation is about to change. From now on you can spin MitoWheel and play MitoRoulette (details on the game later)! MitoWheel is a graphical representation of the circular human mitochondrial genome, hence the name. The sequence used is the standard Revised Cambridge Reference Sequence. The 3 main components of the app is: a search box, a sequence bar and the wheel.

MitoWheel is the brainchild of Gábor Zsurka, a human mitochondrial geneticist we’ve already met in the post on The power links of the mitochondriologist. Gábor has been doing 100% of the programming too. Disclaimer: With some suggestions and testing I qualified myself to become a member of the developer team! The wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript , a scripting language designed specially for Flash.

What are the basic things you can do with MitoWheel, if you are a scientist in the lab or a student in the seminar or just a tech geek eager to learn biology?

- spin the wheel: browse the genome by clicking the left and right arrows in the sequence bar

mitowheel sequence bar

- search for a nucleotide position or sequence in the search box with numbers: input: 15450 output: T

Continue reading

induced Pluripotent Stem cells from a 69 year old human: the hidden story?

HFLSiPSThe successful reprogramming (dedifferentiation) of differentiated human somatic cells into a pluripotent, embryonic stem cell-like state called induced pluripotent stem cells (iPS) using just 4 (and recently 3) introduced transcription factors is the biggest news of current stem cell biology. In the paper published in Cell by the Yamanaka group (Takahashi et al.) the iPS clones derived from the facial dermis of a 36-year-old Caucasian female were highlighted. Out of 50 000 retrovirally transduced fibroblasts 10 hES cell-like colonies were observed. But what I found really thought provoking (and poorly discussed in the blogosphere) is that with the same approach iPS cells were generated from the synovial tissue of a 69-year-old Caucasian male. Interestingly out of 50 000 modified cells 17 hES cell-like colonies were found. This finding could easily be relevant from a stem cell aging point of view.

During ageing there is an overall decline in tissue regenerative potential, but it is not clear whether it is due to the intrinsic exhaustion of the adult tissue stem cells or the diminished functionality of the stem cell niche or a change in the systemic milieu. Answers could be different – tissue by tissue.

But if a terminally differentiated connective tissue cell, like the synoviocyte above could be completely reprogrammed from a 69 year old, otherwise health individual into a pluripotent state….well it could it be interpreted as an argument against the cell-intrinsic genetic aging program in adult and aged connective tissues with some cautions.

Caution 1: What if the source of the iPS cells were not really terminally differentiated, but undifferentiated stem or progenitor cells coexisting in fibroblast culture. This problem has been discussed in the paper and forms the Achilles’ heel of it.

Caution 2: The reprogrammed iPS cells from an aged person are behaving the same way as the iPS cells from a younger person with no additional cellular aging characteristics.

As the critical tail of almost every peer-reviewed paper used to say: Further study is needed.

Here is the paragraph on the synoviocytes and the tables and figures are in the supplemental data. Continue reading

Craig Venter and the life extension drive: blogterview questions

venterpimmOne strategy (call it Life Extension Gets Personal) to raise awareness for the idea and technology of healthy life extension is to publicly encourage life extension “coming outs” on behalf of mainstream celebrities. In order to get an academic legitimacy for LE (which is one of the most important aim of Pimm) I am interested specially mainstream or at least well established scientific celebrities. To accomplish this project a man needs to identify target persons to interview (finding hints that the person is positive about LE), contacting these persons and publish the final piece somewhere.

As a first target Craig Venter, the genomics pioneer seemed unconventional and free minded enough to approach with the idea of a LE blogterview. On the other hand I found definite signs of his interest in longevity and life extension suggesting that if Craig Venter had been given a technological-medical chance to extend his healthy lifespan significantly he would definitely not like to die due to accumulating functional declines associated with aging within the next, say hundred years. Maybe I am wrong here, maybe I am not but to figure this situation out I translated these signs into the following blogterview questions and tried to contact him in early December, 2007. So far I reached only his nice and diplomatic PR agent, who said that maybe we have a chance to get the blogterview done in the near future. Till we get there below please find my targeted questions to Craig Venter:

1. Once I’ve read somewhere but was unable to recall later that one particular motivation behind the sequencing of your own genome was your serious life extension commitment and the belief that genomics has something to say about life expectancy. Is it true? If yes, what is the story of your life extension commitment? Is it a commitment for moderate or maximum life extension? In A Life Decoded I’ve found only one paragraph in your molecular biography explicitly on Long Life about the I405V of the CETP gene but no more hint on this important topic.

2. What do you think about Aubrey de Grey’s SENS approach? You’ve been one of the judges on the The SENS Challenge Prize organized by the Technology Review in 2005 for those “who could prove that SENS was “so wrong that it is unworthy of learned debate.” ? Who got the point there?

3. What do you think about the mitochondrial theory of aging? I was a little surprised when I’ve found that your circa 16.5kb mitochondrial DNA sequence was not published in the PLOS Biology paper: The Diploid Genome Sequence of an Individual Human Obviously it is not part of the diploid genome but I expected it at least as an appendix as those 37 genes and D-loop region can give important genetic information. Have your mitochondrial genome been sequenced already?

4. In a recent Rolling Stone interview you are saying that “There is probably nothing more important to study about human biology than stem cells.” What do you think about regenerative medicine’s role in a robust and healthy life extension technology? Continue reading

Out of 8 embryo cells: if 1 turned to an ES cell, 7 could still become a child

chungetalblastomereAt least I know how to start my stem cell comprehensive exam tomorrow (The trick is to use blastocyst medium supplemented with laminin and fibronectin):

Human Embryonic Stem Cell Lines Generated without Embryo Destruction

Young Chung, Irina Klimanskaya, Sandy Becker, Tong Li, Marc Maserati, Shi-Jiang Lu, Tamara Zdravkovic, Dusko Ilic, Olga Genbacev, Susan Fisher, Ana Krtolica, and Robert Lanza

“To date, the derivation of all human embryonic stem cell (hESC) lines has involved destruction of embryos. We previously demonstrated that hESCs can be generated from single blastomeres (Klimanskaya et al., 2006). In that ‘‘proof-of-principle’’ study, multiple cells were removed from each embryo and none of the embryos were allowed to continue development. Here we report the derivation of five hESC lines without embryo destruction, including one without hESC coculture. Single blastomeres were removed from the embryos by using a technique similar to preimplantation genetic diagnosis (PGD). The biopsied embryos were grown to the blastocyst stage and frozen. The blastomeres were cultured by using a modified approach aimed at recreating the ICM niche, which substantially improved the efficiency of the hESC derivation to rates comparable to whole embryo derivations. All five lines maintained normal karyotype and markers of pluripotency for up to more than 50 passages and differentiated into all three germ layers.”

Legend: “(A) Stages of derivation of hES cells from single blastomere. (a) Blastomere biopsy, (b) biopsied blastomere (arrow) and parent embryo are developing next to each other, (c) initial outgrowth of single blastomere on MEFs, 6 days, and (d) colony of single blastomere-derived hES cells.”

Context link: Wired: Embryonic Stem Cells Created Without Harming Embryo, for Real This Time

Startup recipe: collect hair at the barber, isolate keratin, regenerate nerves

hairbobbyBiotech entrepreneurs and wantrepreneurs, here is a tip for Ya to launch a regmed business (and don’t forget to market the product as recycled and green) :

Winston-Salem Journal: Human hair could hold key to regeneration of nerve tissue, Wake Forest research shows

The study, published in the current issue of Biomaterials, found that the protein keratin found in human hair enhances nerve regeneration and improves nerve function – compared with current treatment options – in animal research.

As part of the study, the scientists used hair cut at a local barber shop and chemically processed it to remove the keratin. The keratin protein was purified and used to form gels that filled the nerve guidance conduits.
Continue reading

The first human genome project: mitochondrial DNA, 16.6kb, 1981, Cambridge

Andersonetalscreenshot1When I had worked on my MSc thesis in biology on the relation of human mitochondrial mutations and aging the paper I used most frequently was Sequence and organization of the human mitochondrial genome by Anderson et al. published in Nature, 1981. The reason was simple: it is more of a database than a hypothesis driven article with the published 16.569 base pair sequence of the circular human mitochondrial genome (L-strand) containing 37 genes and a bigger non-coding, regulatory region. Throughout my work I had to use it as a basic reference. The sequence is a reconstruction of a single European individual’s mtDNA and contains several rare alleles. Nice figure isn’t it?

Andersonetalscreenshot2

It was once modified and corrected by Andrews et al in Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA in 1999 so today it is called the Revised Cambridge Reference Sequence and are used by mitochondriologists worldwide.

I’ve just realized with the help of genomics pioneer and warrior Craig Venter’s recent molecular autobiography Life decoded, that the brilliant two time Nobel laureate, sequencing urfather Frederick Sanger is also a coauthor of the paper. Here comes Venter: Continue reading

Biogeekipedia: collecting raw materials

RNAigeekipediaentryWired’s Geekipedia is marketed as “People, places, ideas and trends you need to know now“. As such you can find biology and biotech related terms in it (part of the current hip and tech-savvy culture) like ‘stem cells‘, ‘RNAi‘ or ‘brain implants‘, explained. But you won’t find the terms ‘Natureplex’, ‘executable cell biology’, ‘Open Notebook Science’, ‘SciFoo Camp’, ’23andMe’ or ‘Pharyngula’ in it. The idea of building a Geekipedia (call it Biogeekipedia) specialized to the life sciences (biology, biotech, biomedical sciences, bioengineering, biobloggers…) seems pretty straightforward. (Or you can expand it to all natural sciences, but that is not my concern here.) So here I’d like to ask my readers to suggest entries for this Biogeekipedia, exotic, rare, but cool niche terms, buzzwords, good phrases, sentences, ideas and people within the biotech realm (web included) we all need to know. Use your imagination instead of your tag cloud. I start with my own embyronic list right now on the top of my head without links and explanations (Intensive work hours are inversely correlated to the number of quality blog posts). Needless to say it is more of a joke than a serious adventure. (List updated with the suggestions of Mr. Gunn, Jon Rowley and Matthew Oki O’ Connor.)

23andMe

Adie, Euan

aging

ATP/ADP

biobase

biogerontology

biomaterials

biotech DIY (DIY biology, bioDIY, home biology , garage biology, Homebrew Molecular Biology Club)

cancer immunoediting

cell fusion

Chemical Blogspace

CIRM

Connotea

convergent medical technologies

Craig Venter

deCODE

Easton, Alf

embryome

executable cell biology

FACS

Geekipedia

Genentech

genetic reprogramming

Google First Ladies

Google Palimpsest Project

Continue reading

23andMe on the biparental inheritance of mitochondrial DNA and more

23andMelogoIn my former blog post inF.A.Q. for 23andMe: what if I have mitochondrial DNA from Pa? I meditated on 23andMe‘s capability of detecting paternal mitochondrial DNA in their customers’ saliva with their Illumina microarray chips scanning around 2000 mitochondrial single nucleotide variants. Published here the initial answer of the 23andMe Editorial Team to this fairly technical, but nevertheless crucial question with permission granted. Besides, I am happy to report that I am working on a blogterview with one of the key member of 23andMe’s Research Team. Hopefully I’ll be able to get back to you with some first-hand information on the science and technology behind the personal genome service of 23andMe and on how 23andMe can facilitate academic research.

Dear Attila Csordas,

Thank you for your interest in 23andMe’s research mission. The question of paternal inheritance of mtDNA is a fascinating one, and the debate in the literature has continued over the past couple of decades. Currently, there is little evidence for paternal inheritance of mtDNA, outside of isolated individuals. However, the array platform lets us resolve multiple SNP states independently. 23andMe’s technology and throughput may indeed provide a novel way to address the question. We will include the question in our consideration of research projects. In the meantime, here are a couple of articles discussing the subject:

Bandelt et al., “More evidence for non-maternal inheritance of mitochondrial DNA?”
Chinnery, “The Transmission and Segregation of Mitochondrial DNA in Homo Sapiens” in Human Mitochondrial DNA and the Evolution of Homo Sapiens.

Sincerely,

The Editorial Team at 23andMe

The question is crucial for a personalized genetics company like 23andMe providing Maternal Ancestry Tree service for the customers based on the exclusively maternal inheritance of mitochondrial DNA. As one of my correspondent partner wrote: Continue reading

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

abstractQin

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. Continue reading