Changing the game: absolute protein quantification by relating histone mass spec signals to DNA amounts and cell numbers

One thing system biologists want is to have by and large absolute protein concentrations or copy numbers per cells available cheaply for their models leveraging all sorts of omics data. Looks like such results can now be easily delivered based on a study published on the 15th of September by the Mann lab in Molecular & Cellular… Continue reading Changing the game: absolute protein quantification by relating histone mass spec signals to DNA amounts and cell numbers

Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 17 December 2013

1. DNA methylation age of human tissues and cell types by Steve Horvath: This is the type of relevant data mining study most bioinformaticians are dreaming of: you pull together a large body of publicly available datasets (CpG methylation) that are not too heterogeneous (Infinium type II assay on Illumina 27K or Illumina 450K array platform), derive robust… Continue reading Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 17 December 2013

Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 8 December 2013

1. Is aging linear or does it follow a step function? A good & simple question on Quora that surprised even Aubrey de Grey. If you are a bioinformatician out there – looking for a new pet project – go pull together some data & try to plot it! Let me know if you have something.… Continue reading Three links in Aging, Regenerative Medicine & Healthy Lifespan Extension: 8 December 2013

LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

The LavaAmp is a portable PCR thermocycler that has the potential to become the default garage biology (home biology, bioDIY, DIYbio) tool once it hits the market. Think of Apple II for personal computing or MakerBot for 3D printing. The 1st LavaAmp prototype was shipped this week from Biodesic to Gahaga Biosciences and the process… Continue reading LavaAmp: cheapest pocket PCR thermocycler dreamed for DIY biologists

Sage Bionetworks Update: building an OA standard for human disease biology

Sage Bionetworks is a not-for-profit organization developing an open-access “pre-competitive” platform for networked and annotated models of human disease. It’s a huge and unparalleled bioinformatics enterprise: starting with an anonymous $5 million donation and soon making high throughput, large-scale human and mouse biological data (largely from Merck) available in the range that’s already in the… Continue reading Sage Bionetworks Update: building an OA standard for human disease biology

Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Nature’s Journal Club column is usually a good & always a short read providing exciting angles on scientific topics/papers from good researchers. Recently ‘neuroscientist’ Dave Featherstone argued for a broader approach to brain mapping by not restricting it only to the connectome between neurons. Neurons are making up less than 10% of the human brain… Continue reading Mapping neurons without glial cells ~ SNP genotyping w/o whole sequencing?

Bright cells, big city: Cellular images hit Broadway

Surprise email from Conor McKechnie, GE Healthcare proving the aesthetics of science and the value of blogging: A while (!) back you posted an inspiring piece linking to Harvard’s BioVisions inner life of the cell – it was 2006…It got me thinking that we could do something similarly inspiring with actual cellular images entered into… Continue reading Bright cells, big city: Cellular images hit Broadway

Practical DNA: Hugh Rienhoff’s got a story to tell

After the Nature cover article Hugh Rienhoff and the story of My Daughter’s DNA is now covered by Wired magazine. I wrote about Hugh (a fellow SciFoo Camper) as an example of any future bioDIY effort in The conditions of a mass biotech DIY movement and now the Wired piece gives us more context and details… Continue reading Practical DNA: Hugh Rienhoff’s got a story to tell

Nature Insight: The complex trait of quantitative genetics

Nature’s newest issue has a Quantitative genetics supplement with 3 free access pieces included out which I find this review the most interesting: Reverse engineering the genotype–phenotype map with natural genetic variation by Matthew V. Rockman. There’s a lot information to digest and many patterns to understand in this background field in order to approach… Continue reading Nature Insight: The complex trait of quantitative genetics

Vadlo, the beta biomedical search engine wants to scale up!

forwarded, nonpersonal mail from Maya Kennard (you might get that email too): Resource link/Story suggestion for your website:Title: VADLO – Biomedical Search Engine Description: Vadlo is a search engine for the biology/biomedical scientists, educators, clinicians and reference librarians. References Also check the Daily cartoons! The idea is that we feed them with searches and links and… Continue reading Vadlo, the beta biomedical search engine wants to scale up!

Nature Personal Genomics Very Special

The newest Nature issue concentrates on personal genomics and its consequences via many types of articles some of them with free access. I only read 1 piece so far by Erika Check Hayden, who has the exclusive freedom at Nature to always pick the best stories and write on any of them, but being a… Continue reading Nature Personal Genomics Very Special

Green fluorescent protein wins the Chemistry Nobel Prize!

Green fluorescent protein (GFP) is something really familiar for many biologists, now it will be familiar for the whole world for a period via the Chemistry Nobel Prize: From the Nobel Press Release: The remarkable brightly glowing green fluorescent protein, GFP, was first observed in the beautiful jellyfish, Aequorea victoria in 1962. Since then, this… Continue reading Green fluorescent protein wins the Chemistry Nobel Prize!

Science X2 signals: big pharmas, stem cells, mobile MRI

The Institute for the Future‘s X2 project is all about tracing future trends in science and technology As the steward of the Biomedical Sciences and Biotechnology Group I collect signals in these fields on which some forecasts can be based later on. Here are some issues I found future sensitive enough recently: GlaxoSmithKline collaborates with… Continue reading Science X2 signals: big pharmas, stem cells, mobile MRI

Sergey Brin, Gly2019Ser & a real chance against Parkinson disease/aging!

It was already known that amongst the Google top people Sergey Brin is the one who is most interested in pushing biotechnology and the biomedical sciences: in his Stanford years he was interested in biology courses according to The Google Story, he married Anne Wojcicki (who graduted from biology at Yale), Google invested $4.4 million… Continue reading Sergey Brin, Gly2019Ser & a real chance against Parkinson disease/aging!

My personalized genetics: 2 ml saliva FedExed to 23andMe!

As the second operation of building my genetically well informed future yesterday (2 days after completing the order) I collected 2 ml of my saliva with the help of 23andMe’s Oragene DNA self-collection kit manufactured by DNA Genotek. First operation has been the sequencing of the D-loop of my mitochondrial DNA out of 5 ml… Continue reading My personalized genetics: 2 ml saliva FedExed to 23andMe!

BioBarCamp: we have room for 55 plus Campers!

BioBarCamp is due in circa 3 weeks and we have now 45 BioBarCampers signed up on the list of attendees and our host the Institute For The Future has the capacity for around 55 more campers, roughly for 100 people in general. We already have a very valuable mix: researchers, biologists (grad, postdoc, PI), coders-engineers-bioinformaticians,… Continue reading BioBarCamp: we have room for 55 plus Campers!

Hourglass, a blog carnival devoted to the biology of aging

Finally Chris over at Ouroboros came up with the idea and the quick implementation of Hourglass, a blog carnival devoted to the biology of aging/biogerontology.  For some reason I am not an explicit supporter of blog carnivals – many of my posts were chosen by carnival editors but I never hosted one -, but Hourglass… Continue reading Hourglass, a blog carnival devoted to the biology of aging

The decellularized matrix hack: skipping many steps in tissue engineering

The concept of decellularizing complex organs in cadavers and reseeding the remaining matrix structure with differentiated, stem or progenitor cells, growing in a bioreactor and transplanting back to the organism could turn out to be a real technological shortcut in the field of tissue engineering. It is not a brand new story on the web,… Continue reading The decellularized matrix hack: skipping many steps in tissue engineering

Petabyte Age Wiredesque lesson on what science can learn from Google

I argued many times here that biology based biotechnology is the next information technology but in order to do so, biotech should harness good IT patterns and mimic its massive computing practices to handle the enormous amount of constantly accumulating data. Often this trend could be summarized in a simple way: keep your eye on… Continue reading Petabyte Age Wiredesque lesson on what science can learn from Google

UCSF Memory & Aging Center channel on YouTube & ‘Fight for Mike’

Even tech people in Silicon Valley need to join their powerful forces and sources when it is about aging related neurodegenerative diseases and help research and the clinic. UCSF Memory and Aging Center channel on YouTube  Om Malik: A Personal Note: Pause & Read via John Battelle  

Future stop: California health officials against personal genetics risk-takers

It’s official: The California Department of Public Health wants practicing physicians (many of them prehistorically, sorry, traditionally trained) to be the patres familias in issues between personal genetic test takers and direct-to-consumer personal genetic testing start-ups while declining the test takers’ right to get familiar with their own genetic makeup and risks by their own.… Continue reading Future stop: California health officials against personal genetics risk-takers

Understanding Aging Conference on FriendFeed!

The “Understanding Aging: Biomedical and Bioengineering Approaches” conference will be held from June 27-29, 2008 at UCLA organized by Aubrey de Grey, Irina Conboy and Amy Wagers. I like to call it UndertsEnding Aging in myself and I am excited to go to LA and meet new people also people from SENS3. Yesterday I created… Continue reading Understanding Aging Conference on FriendFeed!

The Biogerontology Research Foundation receives charitable status, UK

Just landed in my mailbox, emphasis added by me: Dear Attila, I would like to provide you with a copy of the press release to be distributed via press release distribution sites on Wednesday. We will also put it on our site within a few hours after this email so you can confirm its authenticity.… Continue reading The Biogerontology Research Foundation receives charitable status, UK

The Sergey, Larry, Eric test by Anne & Linda: 23andMe at home

“We really think that we can change Health Care…I want to change it in 5 years…it has to change and that’s we all are about” – says Anne Wojcicki, 23andMe co-founder, in the Google Tech Talk on Googling the Googlers’ DNA: A Demonstration of the 23andMe Personal Genome Service. Also a good presentation by Linda… Continue reading The Sergey, Larry, Eric test by Anne & Linda: 23andMe at home

BioBarCamp: August 6-7, The Institute for the Future, Palo Alto

When I wrote about BioBarCamp for the first time, it was just an idea to organize an unconference for biogeeks, people interested in life scientists around SciFoo Camp time. Now thanks to Alex Soojung-Kim Pang, Science X2 project leader, we have a date and a venue: August 6-7, The Institute for the Future, 124 University… Continue reading BioBarCamp: August 6-7, The Institute for the Future, Palo Alto

What path would you follow: Shumway or Barnard?

Monya Baker has an excellent Q&A with the authors of the recent Nature Insight: Regenerative Medicine over at The Niche blog. Ken Chien, the author of Regenerative medicine and human models of human disease – see earlier post – recalls the paradigmatic story of heart transplantation and the 2 main surgeons behind, Norman Shumway and… Continue reading What path would you follow: Shumway or Barnard?

Synthetic morphology: what kind of animal is that?

As far as I understand synthetic morphology = develompental biology +synthetic biology + tissue engineering + anatomy to create new cellular patterns. Jamie A. Davies: Synthetic morphology: prospects for engineered, self-constructing anatomies “This paper outlines prospects for applying the emerging techniques of synthetic biology to the field of anatomy, with the aim of programming cells… Continue reading Synthetic morphology: what kind of animal is that?

Problem: embryonic stem cell lines vary & iPS lines too

Finally I started to digest all the articles (usually on the streetcar on my way to work and home) from the recent Nature Insight: Regenerative Medicine and I try to pick up some stories for you (& interesting enough for me) from that, in case you are not lucky enough to have an available copy.… Continue reading Problem: embryonic stem cell lines vary & iPS lines too

What’s your current science related desktop image?

Desktop background images are important parts of people’s everyday lives in terms of unintended staring time. Usually they are picked up for the eyes (sg spectacular & cool and/or sexy) and hearts (family members), but why not use them for information uptake and learning? So I’d like to ask: What’s your current science related desktop… Continue reading What’s your current science related desktop image?

Puzzle: Which Wired article is cited in Nature Biotechnology?

Nature Biotechnology is the (peer review) journal for me: it’s geeky, fresh and it takes into account more than just one point-of-view, that of the scientist-academist’s: technology & business are hand in hands also. (Recommending Nat Biotech makes a niche sense here while recommending Nature, which is actually the only science journal I’m reading issue… Continue reading Puzzle: Which Wired article is cited in Nature Biotechnology?

How overrated is phosphorylation? – an opinion

David Secko writes: “Today, it is thought that one third of the proteins present in a typical mammalian cell are covalently bound to phosphate (i.e. they are phosphorylated at one time or another)” Well I haven’t checked what kind of measurement the above 1/3 estimation is based on but if true it is no wonder… Continue reading How overrated is phosphorylation? – an opinion

BioBarCamp in the Valley before the SciFoo Camp!

It seems that my favorite ever unconference, the SciFoo Camp will be aroundunconferenced by a BioBarCamp this year. The whole idea of the BioBarCamp is based upon the SciFoo Camp, so it is by no means a competitive but a complimentary event. From the BarCamp wiki: “The BioBarCamp is an idea (fed by the tweets… Continue reading BioBarCamp in the Valley before the SciFoo Camp!

Human proteome project: 21000 genes/1 protein, 10 years, $1 billion?

In order to have the slightest change to design a robust, systemic life extension technology, we need to accumulate every systemic macromolecular, cellular, tissue- and organ level data of the normal, physiological human body, connect the trillions of nodes with scalable software algorithms and suck out the draft of the proper sequence of consecutive treatment/regeneration… Continue reading Human proteome project: 21000 genes/1 protein, 10 years, $1 billion?

Thesis live: 1.2 Liver, regeneration and stem/progenitor cells

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. 1.2. Tissues, organs with different turnover and regenerative potential /bioenergetics data missing/ Liver… Continue reading Thesis live: 1.2 Liver, regeneration and stem/progenitor cells