Monday, August 11, 2008

The DNA Network

The DNA Network

Healthcare revolution begins [ScienceRoll]

Posted: 11 Aug 2008 03:10 PM CDT

Jay Parkinson and his collegues now are totally ready to revolutionize healthcare as Hello Health is up and running.

I’m excited about it and can’t wait to see how it goes and when it becomes a worldwide franchise.

Further reading:

Feeling Better! [The Gene Sherpa: Personalized Medicine and You]

Posted: 11 Aug 2008 12:28 PM CDT

Thank you to all the well wishers out there. Your encouragement has gotten me through a pretty tough time. But I am up and running again. I hope you spread the word to other listeners.....The Sherpa...

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Finding Information: Factors that improve online experiences [ScienceRoll]

Posted: 11 Aug 2008 12:00 PM CDT

On, there is a recently published study focusing on factors that can improve online experiences. The authors (Sathish Menon and Michael Douma) tried to find out what kind of factors readers look for in blogposts and articles.

Some key findings:

  • Easy access to complete information is key to visitor enjoyment.
  • Good visual design and up-to-date information are critical.
  • Visitors want information fast. Web site visitors are looking for simple, accurate, fast, and easy to navigate web sites - preferably with links to information they seek.
  • Visitors want a broad range of topics. Relative to designers and organizations, visitors more strongly believe that a broad range of topics is important.
  • Visitors still need handholding.
  • Visitors point to the lack of breadth and depth of site content as causing an "Information Gap." Although over 90% of visitors say that they are able to find the information they are looking for, over 50% report that there is a gap between what they are looking for and what typical web sites provide, and 60% think that a personal guide would help them navigate web sites.

So if you are a medical blogger,

  • write short posts
  • use microblogging services (Twitter or Friendfeed)
  • cover interesting topics and help your readers in several ways:
  • let them see full articles in your RSS feed (do not force them to go to your site by providing only titles in the feed)
  • create collections for them about the most important posts you have ever had
  • highlight short sentences that can summerize the content of an article

Shameless Self Promotion # 200: Are We Alone [The Tree of Life]

Posted: 11 Aug 2008 10:56 AM CDT

Just a little quick link here. People might be interested to check out the "Are we alone" Radio Show from July 21, 2008 (Are We Alone). A direct MP3 link is here. Here is there summary of the show from that date:
Remember Mr. Potato Head? You changed his look by snapping in plastic mustaches, googly eyes and feet. Now imagine doing the same with a living cell: inserting the genes you want to create the organism you want. Welcome to the world of synthetic biology. It has potential to create new bio-fuels and life-saving drugs. It also ushers in a host of ethical and safety concerns. We examine both when we discuss this emerging science of mix and match genes. Plus, does doing an end run around Mother Nature challenge the essence of life itself?

This show is produced by the SETI institute and has some interesting topics on different science things.

Genetic regulation of cortical structure in the pediatric brain demonstrated by landmark twin study [biomarker-driven mental health 2.0]

Posted: 11 Aug 2008 09:54 AM CDT

Like most parents, I enjoy watching my children develop and marvel at the many similarities they bear to myself and my wife. The reshuffling of physical and behavioral features is always a topic of discussion and is the definitive icebreaker during uncomfortable silences with the inlaws. In some cases, the children are blessed with the better traits, but in other cases, there’s no option but to cringe when, “Look - wow, he really has your nose - hmmm”, is muttered. Most interesting, is the unfolding of patterns of behavior that unfold slowly with age. Differences in temperament and personality can instill great pride in parents but also can be a grating source of friction. One of my F1’s has recently taken to sessions of shrill, spine rattling, screaming which I hope will pass soon.

Why ? Many parents ask. “Have WE been raising him/her to do this ? - surely that’s what the neighbors must think”. “Is it something in the family ? I heard Aunt Marie was a bit of a screamer as a child - hmmm.”

In one of several of their landmark studies on the genetic regulation of pediatric brain development, Jay Giedd and colleagues, now provide in their recent paper, “Variance Decomposition of MRI-Based Covariance Maps Using Genetically-Informative Samples and Structural Equation Modeling”, a core framework on the relative contribution of genes vs. environment for the developing cortex. The paper is part of an ongoing longitudinal study of pediatric brain development at the Child Psychiatry branch at NIMH. Some 600 children participated - including identical twins, fraternal twins, siblings and singleton children.

The team used an analytical approach known as MACAAC (Mapping Anatomical Correlations Across the Cerebral Cortex) to ask how much does the variation in a single part of the brain co-vary with other parts ? Then the team used structural equation modeling to explore how much this co-variation might differ across identical twins vs. fraternal vs. siblings vs. age-matched singleton children. In locations where there is an high genetic contribution to co-variation in cortical thickness, identical twins should co-vary more tightly than fraternal twins or siblings etc. In this way, the team were able to parse out the relative influence of genes vs. environment to the developing brain.

In general terms, the team reports that a single genetic factor accounts for the majority of variation in cortical thickness, which they note may be consistent with a major mechanism of development of cortical layers involving the migration of neurons along radial glia. Genetic co-variances across separate locations in the brain were highest in the frontal cortex, middle temporal gyrus and left supramarginal gyrus. Interestingly, when environmental covariations were observed, they were usually restricted to just one hemisphere, while genetic covariations were often observed bilaterally.

Figure 5 of this paper is really incredible, it shows which areas of the cortex are more influenced by genes vs. environment. If I can just find the areas involved in screaming, the next time one of my neighbors looks askance at my F1, I’ll be able to explain.

Handling research animals: taking courses and learning how to be kind [Discovering Biology in a Digital World]

Posted: 11 Aug 2008 09:00 AM CDT

The first lab mouse I touched had soft white fur and a light pink tail. It looked cute enough to snuggle and take home as a pet and I was smitten. As my hand into the cage, thinking the mouse would respond like my pet gerbils or my brother's pet rat. As my hand closed around it's belly, that sweet little mouse sunk it's teeth deep in my thumb. I screamed and shook my hand, smashing the mouse on the cement floor and killing it in an instant.

Read the rest of this post... | Read the comments on this post...

Sciencebase Science Portal [Sciencebase Science Blog]

Posted: 11 Aug 2008 07:00 AM CDT

Sciencebase isn’t just a blog, oh no, it’s a vast empire. A huge hulk of a beast with many arms, various outposts, and more to the point lots of pages that you may not have spotted if you only watch the site via the free-to-grab newsfeed. So, in an effort to tame the hulk, here are a few links to other sections of Sciencebase that may be of interest:

Watch with Sciencebase - As the name would suggest this is the site’s video section, lots of science videos here, including links to many more and at the moment featuring the inimitable Martyn Poliakoff playing with his dog chews.

Learn with Sciencebase - Resources for younger readers in education, including downloadable science projects, chemistry homework help. - Also does what it says on the tin, bringing you the latest science and space headlines direct from National Geographic

Science Extra - This microblogging section is a space where you can catch up on some of the odder science stories or get my take, in as few words as possible, on some of the breaking science news.

Sciencebase Reading List - This page is offsite, but very much part of Sciencebase, flagging up papers, articles, posts, and other stuff of interest - everything from science geekery and tech news to blogging and browsing tips and tricks.

Social Media - Speaking of offsite resources, there are a whole load of places you can connect with Sciencebase across the blogosphere, through social bookmarking sites, and in social networking hangouts. Here are a few LinkedIn, StumbleUpon, Facebook, Plurk, Sciencebase Flickr photos, FriendFeed.


Sciencebase Science Portal

Medicine 2.0 Carnival at SharpBrains [ScienceRoll]

Posted: 11 Aug 2008 01:11 AM CDT

Tips on Restriction Digests [Bitesize Bio]

Posted: 10 Aug 2008 11:47 PM CDT

Restriction digests are simple. But underestimate them at your peril. Restriction digests and screens are the cornerstone of many procedures in molecular biology so getting them right, and knowing how to tell if they are going wrong, is an essential skill.

This quick guide to setting up and troubleshooting restriction screens will tell you what you need to know.

Step by step guide to designing a restriction screen

Step 1. Make a list of the available enzymes

Every lab tech and his dog has a stock of restriction enzymes available at his disposal so why not use what's available? Write down (in alphabetical order) a list of the restriction enzymes you have. Identify any potentially mischievous restriction enzymes and try to avoid them (I put an asterisk* next to them). Problematic enzymes could be those inhibited by methylation, those that require incubation at temperatures other than 37C or just enzymes that are unfriendly for whatever reason.

Step 2. Identify sites in your insert

Identify restriction sites in your insert. If you can identify two sites in your insert that will produce a good sized band that's great because this will increase the power of your screen by including an insert-only band.

Step 3. Identify sites in your vector

See if the restriction sites being used in the insert are also present in the vector and determine what sized bands will be produced. Then choose as many restriction sites in the vector that are required to digest the vector on the 5` and 3` sides of the MCS and around the vector. Choose restriction sites that will produce good-sized, indentifiable bands in your restriction screen.

Step 4. Perform the restriction screen

Try the screen! And hopefully it will work. If not, analyse why it might not have worked; go back to your plan and work out what sites could be present in the clone to give you the result you obtained. Perform a second screen with different enzymes to confirm the results of the first screen.

Hopefully this process will take you onto better and more informative restriction screens so that when that stumbling block does come along you can hop straight on over it and continue of your merry post-cloning way.

Troubleshooting restriction digest

Restriction digests can produce undesirable results or fail for a variety of reasons. Here is a checklist:

• the restriction enzymes have lost their activity
• the restriction enzyme is blocked by methylation (some restriction enzymes are blocked when their recognition sequence is methylated - link)
• enzyme was incubated at an incorrect temperature
• an incompatible buffer was used
• too much DNA or too much enzyme was in the reaction (this produces a ladder)
• vector or insert has a deletion
• incomplete digestion (enzymes not fully functional)
• a restriction site has been added or removed
• the vector prep is dirty
• too much enzyme, high ionic strength or high glycerol caused star activity
• the clone is actually a negative, damn

A good practice when a restriction screen fails is to setup another digest with a different set of enzymes. Much like the supervisor without morning coffee, restriction screens can be difficult to interpret at times and a second set of bands can really help work out what's going on.

When a clone fails in a restriction screen, it's important to question your data and be sure you know it really is a negative. Sometimes apparently negative clones are actually positive and the cloning Gods are just playing hardball.

Setting up the most informative digest possible, and going through the checklist above should help you with this and could save invaluable time and resources by avoiding either repeating the same mistakes or re-cloning the insert when you already have the clone you want!

What tips do you have for performing restriction screens?

Solving the Cell: Will the Future of Biology be Boring? [adaptivecomplexity's column]

Posted: 10 Aug 2008 11:30 PM CDT

How do you know when a scientific problem is finished? Biologists have been cracking open the cell and studying its molecular insides for a very long time now. How much more is there to learn? Perhaps it seems obvious that we are still missing much: we can't cure cancer very well, for example. On the other hand, one could ask, what's really keeping us from curing cancer, a lack of basic understanding or insufficiently developed technology? Nowhere is this problem of defining a scientific endpoint more obvious than in the community of scientists who are focused on some of the most basic questions in cellular and molecular biology - the community of yeast biologists. Yeast biologists now have to figure out what human biologists will be asking in the decades to come: what does it mean to solve a cell? Are there any big questions left in molecular biology?


Neanderthal mitochondrial genome sequenced [HENRY » genetics]

Posted: 08 Aug 2008 05:38 PM CDT

Green et al in today’s edition of Cell publish a complete mitochondrial genome from a Neandertal:

A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small.

ScienceDaily has some more info.

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