Owner: Bitesize Bio. The Molecular Biology Blog URL:http://www.bitesizebio.com Join Date: Tue, 28 Aug 2007 17:43:53 -0500 Rating:0 Site Description: Technical tips, updates and comment for molecular biologist. The tricks for getting the best out of PCR, plasmid cloning, oligos, ligation. Site statistics:Click here
Science, Ethics and Controversies 2007-11-29 06:02:16 An essay in today’s issue of Nature struck a contentious cord at the intersection of modern science and politics: that of the ethical regulation of science. The context of ethics and science was succinctly summed up:
When in 1978 the first baby was born by in vitro fertilization (IVF) it was inevitable that there would be calls for the procedure to be prohibited. That science develops too fast for morality had become the cliché of the twentieth century.
Focusing on IVF in Britain, this essay by Mary Warnock is narrow in scope. The same principles can be applied to the use of recombinant genetics and embryonic stem cell research, to name a couple more. The instant that these breakthroughs hit the world stage, they have sparked uproars from “moral authorities,” but in the end, it is largely the scientists that regulate themselves. (the National Academies of Science
have been the ones to issue the ethical guidelines on the conduct of all of the above forms of biomedi Read more:Controversies
, Ethics
Enzyme Commission (EC) Numbers 2007-11-28 06:14:40 In the early 1950’s so many new enzymes were being discovered in the burgeoning field of biochemistry that enzyme nomenclature was in danger of getting out of hand. With no guidelines on how to name enzymes, researchers simply chose their own. Some enzymes were given names, like diaphorase or Zwischenferment, that conveyed nothing about the reaction they catalyzed and enzymes with similar function were given names that implied they were different. It was all very confusing and clearly if the situation continued it would be disastrous for our attempts to study enzymes. (more…)
Read more:Numbers
, Commission
, Enzyme
Please, don’t take Bitesize Bio “on Faith” 2007-11-28 05:53:28 Science is an endlessly fascinating, challenging, and intellectually-satisfying endeavor. So it saddens me any time that I see someone mistakingly make claims about taking science on faith. This isn’t the forum for taking on religion - if you want that, more of my thoughts on that can be found at Migrations.
I have one request though, for us here at Bitesize Bio, and in particular, on our discussions of interesting and ground-breaking scientific studies:
Don’t take us on faith. Instead, ask questions. Scrutinize. Check out the data for yourself. Be skeptical. Be analytical. And reach your own conclusions. Catch me making a mistake, and demonstrate how a mistake was made. (more…)
Read more:Faith
, Please
Thinking Microbes 2007-12-10 13:05:45 Cognition is a term frequently used in several loosely related ways to refer to a faculty for the human-like processing of information. Signal transduction networks certainly fit that bill, as the mediate adaptive changes in gene expression to specific sensory inputs. Melinda Baker and Jeffry Stock, in the recent issue of Current Biology, elaborate on modalities of such cognition in bacteria: Networks and integrated circuits in bacterial cognition.
Of course, they’re not quite circuits in the electrical engineering sense either. Think chemical networking, where each biomolecule in a signaling network can interact with a variety of other molecules, with varying interaction kinetics, and where each interaction has the potential to impact additional outcomes. Coupled with the selection of functions in the micro-environmental milieu, cellular networks ended up organized in efficient ways to control motility, metabolism, growth, and eventually higher processes.
But just suppose fo
At last - an easy backup solution 2007-12-10 06:29:43 When I was writing up my PhD thesis I was paranoid about data backup
. Years of hard work - pictures, data-files, notes, publication lists not to mention the thesis manuscript itself - all stored on one hard drive. Copying onto CDs or detachable hard drives was fine, but what if I lost those, or they became corrupt?, or what if my house burnt down? - all my work would be gone. (more…)
Around the Blogs 2007-12-07 05:31:33 10 interesting posts on cell and molecular biology, and the scientists involved, starting off with…
My paper in PLoS Biology is out today - The signal sequence coding region promotes nuclear export of mRNA - Alex gives us an author’s summary on his blog. Congrats on getting the paper published! (more…)
Read more:Blogs
There’s No Need To Be Paranoid About RNA Purification 2007-12-06 06:45:26 RNA purification may be a common procedure in molecular biology but it is by far the one that people fear most.
Why? Dreaded RNase.
It’s everywhere… all over your bench and pipettors, and floating in the air, waiting for the chance to creep into your prep, shred your RNA into nucleotides, and ruin a day’s work.
Well, not really. It’s true that extra precautions need to be taken for RNA preparation, but as long as you follow some basic good laboratory practices, RNase contamination need not a problem. In contrast to Nick’s paranoid outlook, I suggest a more relaxed approach to RNA purification. (more…)
Myosin Isoforms: Duplication and Divergence 2007-12-06 05:59:09 Myosin II functions as a molecular motor which facilitates contraction of the actin cytoskeleton during migration, resides outside of protrusions at the front of motile cells, and acts at a distance to impact cell protrusion, signaling, and maturation of nascent adhesions. So clearly myosin II is a protein that is of great importance for understanding cell migration.
But Myosin II is not just one protein. There are actually two isoforms of this protein that are not identical, just very very similar. I’m not familiar with where in the natural history of cells the genes for these two proteins diverged, but they’re clearly derived from a single ancestral gene. And beyond that, there are quite a few other myosins which are more distantly similar (the list easily goes into double-digits)1.
Vicente-Manzanares et al.2, in their paper, determine the divergent functions of myosin IIA (MIIA) and MIIB, and find that these isoforms have become suited to spatial and functional nic
Personal Genomes and Modern Eugenics 2007-12-05 09:55:29 As genetic screening becomes increasingly advanced and personal genomes become more commonplace, the potential for genetic engineering and modern eugenics is becoming a reality. “Designer babies” may not be science fiction forever, creating an ethical dilemna on the horizon.
Hsein-Hsein keeps us informed on personalized sequencing companies that are coming out, including 23andMe, deCODEme, and Navigenics, and now the first whole genome squencing company, Knome. The goal for some is to one day sequence genomes for $1000, putting it within the reach of average consumers.
(more…)
Read more:Personal
, Modern
An Easy Lysis / Homogenization Method for Any Sample 2007-12-05 06:41:53
Lysis of some microbes is easy, but for others its much more difficult - I think due to differences in the make-up of their cell wall.
At the moment, one of my colleagues is preparing hundreds of cell-free extracts from microbes isolated from the environment to screen for interesting enzyme activities. Since she is processing a wide range of microbes she has to use a method that will lyse all of them - even the most difficult ones.
Unfortunately that means using glass beads and a lot of vortexing to mechanically break the cells. I say unfortunately because not only does it take her a very long time to process all of her samples, but she has a very noisy vortex mixer, which is driving me crazy!
Yesterday I came across something that could be the answer to both of our prayers. (more…)
Read more:Sample
The Basics: How Ethanol Precipitation of DNA and RNA Works 2007-12-04 09:31:04 Ethanol precipitation is a commonly used technique for concentrating and de-salting nucleic acid (DNA or RNA) preparations in aqueous solution. The basic procedure is that salt and ethanol are added to the aqueous solution, which forces the nucleic acid to precipitate out of solution. The precipitated nucleic acid can then be separated from the rest of the solution by centrifugation. The pellet is washed in cold 70% ethanol then after a further centrifugation step the ethanol is removed, and the nucleic acid pellet is allowed to dry before being resuspended in clean aqueous buffer. So how does this work? (more…)
Read more:Basics
, Works
miRNAs Get Flipped 2007-12-04 06:12:29 On a couple other blogs, a study published in Science by Joan Steitz1 is being called “One of the biggest findings of the year,” and “If it turns out to be true, this finding just flipped the whole field on its head.” Bitesize Bio would be greatly remiss to not mention to so hot a story, joining in with The Daily Transcript and One Random Scientist.
The abstract, from Switching from Repression to Activation: MicroRNAs Can Up-Regulate Translation: (more…)
Happy Holidays… 2007-12-20 09:39:19 The Bitesize Bio team will be taking a well-earned rest over the holidays and we would like to wish our readers a very merry Christmas. Myself, Dan, Suzanne and Terry have really enjoyed bringing you the best of molecular and cell biology tips, journal articles, news, comment and other stuff over the last four months since the blog started and we are looking forward to bringing you even more information and entertainment-packed articles, as well as some excellent new features, in 2008. We will be resuming our daily article schedule on Jan 2nd.
For our final post of the year, we present a paper written by Larry Silverberg on the science behind Santa Claus. We hope you enjoy it.
Thanks for reading and supporting Bitesize Bio, and see you next year!….
ON THE TECHNICAL EXPLANATION FOR SANTA CLAUS’ ABILITY TO DELIVER PRESENTS WORLDWIDE IN A SINGLE NIGHT
Larry Silverberg
Professor of Mechanical and Aerospace Engineering Raleigh, NC
November 12, 1997
The Premise: To explain t Read more:Happy
, Holidays
, Happy Holidays
The Big Story of 2007: Cellular Alchemy 2007-12-19 16:08:17 Amid the political controversy and obstructions to conducting stem cell research, scientists this year managed to turn lead into gold… Genetically manipulating fibroblasts to become ESC(embryonic stem cell)-like sort of sounds like alchemy in a way, doesn't it? The product of these papers, inducible pluripotent stem (iPS) cells, were created by transfecting four factors into fibroblasts, Oct3/4, Sox2, c-Myc, and Klf4, and they found that the epigenetic, morphological, and proliferative characteristics resembled those of embryonic stem cells. (more…)
Read more:Alchemy
Salesman Stories 2007-12-19 00:10:45 Have you ever had a sales person suggest just the right new kit or enzyme that makes your life a whole lot easier? Or on the flip side, how about when a sales person doesn't get the hint that you are in the middle of keeping track of setting up a 96 well plate of PCR reactions and can't stop what you're doing?
Being a sales rep is a really tough job, requiring a thick skin, good interpersonal skills and the ability to handle rejection and a lot of pressure. I’m sure many of you have had the experience of sales people who were very good, as well as those of the more clueless variety so thought it would be fun for us to discuss our experiences, both good and bad. Here are some questions we could look at:
1- What makes a good sales person ?
2- What are the worst qualities in a sales person you have observed that should be avoided at all costs?
3- What is your funniest or best sales rep story? (Please, no company names, unless you are giving kudos!)
So here are my answ Read more:Stories
The Challenge of the Two-Body Problem 2007-12-18 09:19:13 This is a rather personal post for me, as I’m getting set to follow my wife abroad, while still seeking a research or lecturing position of some kind, whatever may happen. The situation is sometimes known in academia as the “two-body problem,” and is occasionally lamented as a fact of life for the challenging life of a researcher.
In searching for stories that I could relate to, given my situation, I came across one in the Chronicle of Higher Education. Helen Atwood (a pseudonym) mentions many of the emotional and stressful points of my situation, although the details are of course different. I don’t know whether my story will turn out as well as hers did, but I would rather take the chance than lose my marriage.
Atwood offers some advice, that I’ll try to follow, and others might be interested in as well: (more…)
Read more:Problem
, Challenge
Get Inside A Molecular Biologist's Imagination 2007-12-17 23:57:30 I’ve always thought that it takes a good imagination to study molecular and cell biology since we never actually see much of the molecular processes we study, dissect and hypothesize on every day. Think about the mental models you have of the processes of cytoskeleton polymerization/ de-polymerization or DNA translation for example. Aren’t they amazing?
Biovisions, a Harvard animation company have come up with an animation of cellular processes that is probably the closest thing to an external representation of a molecular biologist’s imagination you can get. (more…)
Read more:Molecular
BioChemWeb: Virtual Library for the Molecular Biologist 2007-12-17 12:55:34 Wikipedia gets quite a bit of attention, and the student of the molecular biological sciences regularly needs a more in-depth information resource. There’s Bruce Alberts et al.’s Molecular
Biology of the Cell, Harvey Lodish et al.’s Molecular Cell Biology, and David Nelson’s Lehninger Principles of Biochemistry if you have the textbooks handy. An online compilation or virtual library is extremely useful too.
Fitting that bill for the biochemist or cell and molecular biologist is BioChemWeb. With such a resource, I’m surprised that I don’t hear many of my colleagues mention it, ever. In it, everything from tutorials to protocols to multimedia to a Who’s Who listing can be found there.
Check it out, if you haven’t already. (more…)
Read more:Library
The Easier Way to Write a PhD Thesis 2007-12-17 00:45:57 For most scientists, writing their PhD thesis will be one of the most time consuming and complicated individual tasks they ever undertake. In my experience, the most common approach taken by students is to bury their head in the sand, get on with the research and only start thinking about the thesis when they absolutely have to, as the end of their PhD approaches. This obviously works, but it generally leads to a very stressful few months (yes, months) of writing. But it doesn’t have to be that way, with the right approach you can make the whole process much easier - here’s how: (more…)
Read more:Write
, Thesis
Keeping up on the journals 2007-12-14 10:20:37 As scientists, we have to keep up with new research coming out and follow the journals. We all have our preferred way of doing so though. Sporadic searches on Pubmed are one way, or weekly email updates on specific search terms (also offered by Pubmed) are another. Alternatively, there’s Hubmed for RSS of Pubmed updates, and many more options besides.
Using search terms narrows your attention however, so I prefer simply browsing around my favorite journals online. I get a broader sampling of current research that way - which may not be of concern for the average scientist, but for a blogger, it’s often more productive for finding topics to blog on in the peer-review literature.
Some of my favorite journals, below the fold (feel free to add to the list in the comments!): (more…)
Around the blogs 2007-12-13 23:54:19 There was some great stuff in the molecular and cellular biology blogosphere this week - here are my favorites… (more…)
Protein Sociology: Collective Interaction Behaviors 2007-12-13 09:29:25 As always, it’s these odd conjunctions of things that don’t go together that catches the eye. In this case, molecular and sociology. The actual article1 is much more mundane and true to the correct science jargon, and included in a special section of the most recent Nature on “Proteins to Proteomes.” It’s also a nice article that examines a broad array of topics in molecular biology.
Of greater interest and with a slightly less catchy title, is another article on the section: Reaching for high-hanging fruit in drug discovery at protein-protein interfaces2. The abstract: (more…)
Read more:Interaction
, Collective
, Sociology
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