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Model Organisms in Biomedical Research
2008-01-22 12:32:00
The term “model organism” is often used in research, to describe species that are extensively studied to understand particular biological phenomena. We say “model,” because there is usually the expectation that discoveries made in the organism model will be representative of related taxonomic groups. In particular, model organisms are widely used to explore potential causes and treatments for human disease when human experimentation would be unfeasible or unethical. For instance, a it may be difficult or impossible to visualize cellular processes in mammalian embryos; and the manipulation of human subjects is tightly regulated for obvious reasons. This strategy is made possible by the common descent of all living organisms, and the conservation of metabolic and developmental pathways and genetic material over the course of evolution. (more…)
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Preps in the Zyppy: How I Changed my DNA Miniprep, Gel Extraction and Conce
2008-01-21 10:47:00
After years of loyalty, our relationship was becoming stale - things just weren’t the way they used to be. I was putting in more than I was getting back and complaining about it didn’t seem to help. I just got the same old answer thrown back at me… “it’s not our problem, it’s yours”. Then things ...
More About: Services , Kits , Reagents , Prep

Around the Blogs
2008-01-18 14:38:00
It’s Friday again, and time to recap some recent and relevant posts around the rest of the blogs:
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BioPop: 10 Songs That Should Be On Every Biologist?s iPod
2008-01-18 07:56:00
The late Francis Crick once said that “Trying to determine the structure of a protein by UV spectroscopy was like trying to determine the structure of a piano by listening to the sound it made while being dropped down a flight of stairs.” But, if you thought that protein structure determination was the closest that biologists ...
More About: Songs , Ipod

In Which I Agree with the Corporations
2008-01-17 13:03:00
In Deserting the hungry?, a Nature essay argues today that “Monsanto and Syngenta are wrong to withdraw from an international assessment on agriculture.” The assessment, titled the International Assessment of Agricultural Science and Technology, is an ambitious, 4-year, US$10-million project that aims to do for hunger and poverty what the Intergovernmental Panel on Climate ...
More About: News , History , Corporations , The Corporation

Ligation Independent Cloning Protocol
2008-01-17 10:43:00
A while back I wrote a post on a T4 DNA polymerase dependent ligation independent cloning method. In the comments, Max asked if anyone had a protocol. Since there does not appear to be a simplified protocol available on the web, I thought I would post mine for reference. It is adapted from a 2006 Organic ...
More About: Independent , Protocol , Cloning , Proto

Deserving of More Media Attention
2008-01-16 16:14:00
It’s no secret that science journalism is, with a few notable exceptions, very lackluster in general. It seems to a lot of biologists whom I speak to that cell and molecular biology, genetics, and related fields, are especially underrepresented in the press. Yesterday, Alex vented a bit on this, reflecting on the capacity ...
More About: Media , Communication , Attention

Who Else Thinks Biology Teaching Methods are Wrong?
2008-01-16 10:27:00
I shudder to think of the way I was taught about metabolic pathways as an undergrad. Lists of mysterious names connected by arrows - all to be memorized, with little reference to how the processes actually worked on a chemical basis. Even worse - and perhaps embarrassingly for me - I was almost at the end ...
More About: Biology , Teaching , Learning , Methods , Wrong

Closer to the Genetic Roots of Autism
2008-01-15 18:36:00
To go with this past Friday’s post on Alzheimer’s, recent progress is being made in understanding Autism . That’s the claim coming from an initial identification of a gene called CNTNAP2, which when mutated, this gene indicated a predisposition to autism in a specific population of Old Order Amish children from Pennsylvania. Three separate ...
More About: News , History , Roots , Closer

No more white elephants! - consider this before buying a real-time PCR cycl
2008-01-15 07:48:00
Does your lab have a closet full of white elephants; once expensive instruments that are no longer fit for purpose, or have broken down? In many cases, all of that wasted money and resource could have been saved if the buyers had made smart choices about matching the instrument more closely to their needs. A real-time ...
More About: Buying , Time , White , Real , Real Time

Seeing Bacterial Bones with Cryo-EM Tomography
2008-01-14 13:32:00
Until this decade, the notion that bacteria had cytoskeletons that maintained their cylindrical morphologies was not seriously considered. “People more or less thought the bacterial cell was a swimming pool and the chromosome was this ball of spaghetti,? says Stanford microbiologist Lucy Shapiro. The lack of apparent internal organization to bacteria supported this ...
More About: News , History , Bones , Tomo

Work Smarter With The Molecular Biologist?s Toolbar
2008-01-14 13:06:00
To (hopefully) make the life of molecular biologists everywhere a little easier, I have put together a Molecular Biologist’s tool-bar for Firefox/IE, which you can download here. It’s main feature is the multi-search box from which you can search Google, Pubmed, Scirus, Wikipedia, SwissProt and others directly, saving you from navigating to the individual sites every ...
More About: Software , Work , Toolbar

Curing Alzheimer?s through TNF?
2008-01-11 18:09:00
One of the more dreaded diseases that plague our elders is Alzheimer ’s disease, which robs the afflicted of not just their memories, but their dignities as well. Research on the role of cytokines in disease progression has illuminated a therapy with great potential, according to a recent study. Edward Tobinick and Hyman Gross, ...

Around the Blogs
2008-01-11 15:59:00
Here’s my take on the most interesting blog posts of the last week:
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PlasMa DNA: Free, cross-platform plasmid mapping and analysis software
2008-01-10 18:03:00
If you are looking for some free plasmid manipulation and analysis software, then you need look no further than PlasMa DNA. It’s packed with features, user friendly and looks great. Best of all, it is a cross-platform application - it works on both PC and Mac, and the files produced on one operating system can ...
More About: Software , Plasma , Analysis , Free , Cross

The Math of Free Will
2008-01-10 11:13:00
One of the common arguments from religionists against scientific determinism is that of Free Will. Clearly, we humans possess the capacity for making choices, and have some influence over the direction of our lives. Our cells, too, possess the capacity for choice, as do bacteria and even molecules. For us, our choices ...
More About: Books , Math , Free will

Meiosis and Mitosis Tutorial
2008-01-09 08:53:00
I recently caught wind of Openlearn, at Open University, which is a UK university that is dedicated to distance learning. Apparently started in 1969, and hosting part-time students who will received real degrees, the OU’s teaching quality was listed as the fifth best in the UK. “Now anyone can access free ...
More About: Tutorial , Mitosis

Keeping Your Eyes On The Prize
2008-01-09 06:35:00
It?s easy to get bogged down in the day-to-day of producing experimental results but as a scientist it is your job to do the exact opposite - a good scientist has to think about their work on all levels. Here is a light-hearted reminder of the importance of large scale, small scale, ?out-of-the-box?, lateral and ...
More About: Eyes

Get Your Clone 90% Of The Time with Ligation Independent Cloning
2008-01-08 14:36:00
Are you stuck in cloning hell?, Tired of doing ligations that don?t work? Want a faster, more efficient cloning procedure?… You should try ligation independent cloning. A growing number of researchers swear by ligation independent cloning methods because they are simpler and more efficient than conventional cloning and as a recent convert to their ranks, I’d ...
More About: Time , Clone , Independent , Cloning , The Time

New Journal Ranking Tool
2008-01-07 11:39:00
Thompson Scientific is great for gaging the impact factors of various journals, but it has had a bit of a monopoly on journal rankings. As with any ranking scheme, there can be more than one valid way of comparing alternatives. Enter a new ranking tool - that’s free - the SCImago Journal ...
More About: News , History , Tool , Ranking

Free Mind Mapping Software
2008-01-07 09:46:00
Mind mapping is an extremely useful technique for note-taking, brainstorming and learning. In the past I often tried to use mind-mapping, but the neat-freak in me was never satisfied with the messy maps I would create. However, now there is an alternative to scribbling out mind maps on paper, with the availability Free Mind, a ...
More About: Software , Mind , Mind mapping , Mapping

Around the Blogs
2008-01-04 11:30:00
Time for the first ‘Around the blogs’ for the new year! Let’s see what discussions are going on related blogs*…
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Kinase Structures and Autoinhibition
2008-01-03 09:36:00
Here’s a comment on work published about 6 months ago that was relevant to me, given my graduate studies on FAK with Jun-Lin Guan. The relations between protein structures and evolution are quite interesting indeed. As more structures are being solved for multimodular signaling proteins, the regulatory kinetics (on, off, and everything in between) is ...
More About: Structures

Alternative Careers For Scientists
2008-01-03 08:12:00
What happens when you finally get the degree you worked so long for and then realize you really don?t want to spend the rest of your life in the lab? Or you get tired of working long hours with few results and low pay? or you succumb to any of the other reasons that might ...
More About: Alternative , Careers , Scientists , Alterna

5 Ways to Get More Results This Year
2008-01-02 13:22:00
Happy New Year to all of our readers! We are back, refreshed and raring to go after our holidays and hope that you are too. In the coming year we hope that Bitesize Bio will be your indispensable companion, bringing you articles that keep you informed on the best literature, products, tech tips, news and ...
More About: Results

Relating to Historical Contingency in Biology
2008-01-02 13:16:00
Two blog posts recently collided for me. First, in a blog discussion on Macroevolution vs. Microevolution, Allen MacNeill clarified some issues for me (thanks to TUIBG for bringing it back up): Add the newly emerging fields of evo-devo and epigenesis to the foregoing, and it is increasingly clear that macroevolution (i.e. cladogenesis) follows different rules ...
More About: Biology , Historical , Contingency

Happy Holidays?
2007-12-20 16:39:00
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 ...
More About: Holidays , Happy Holidays , Happy

The Big Story of 2007: Cellular Alchemy
2007-12-19 23:08:00
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 ...
More About: Story , Alchemy , Cellular , The Big Story

Salesman Stories
2007-12-19 07:10:00
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 ...
More About: Stories , Careers , Salesman

The Challenge of the Two-Body Problem
2007-12-18 16:19:00
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 ...
More About: Body , Careers , Problem , Challenge , Halle