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Pin-pointing DNA Ligation Problems
2007-11-20 14:01:00
In any experimental procedure, getting the controls right can save you a lot of work when things go wrong by allowing you to pin-point the source of the problem. DNA ligation is no different. In this article I look at how to set up a ligation reaction with a complete set of controls, and use ...
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Across the Comparative Oncogenomic Landscape
2007-11-20 13:09:00
“How many genes are mutated in a human tumor?” That’s the question that a team of researchers at Johns Hopkins posed, and took a comparative genomic approach. By analyzing the sequences of 20,857 transcripts from 18,191 human genes, in 11 breast and 11 colorectal cancers, Wood et al. were able to generate a ...
More About: Landscape , Acro

Aptamer-DNA Chimeras
2007-11-19 12:58:00
One of the neat tools in molecular biology is the ability to recombine parts of two proteins to create fusion or chimeras. They’re often extremely useful for simple experiments, some of the time for targeting protein domains to subcellular sites, or to isolate a structural component of a protein. The functional information is ...

Gene Genie #20
2007-11-19 01:04:00
Here at Bitesize Bio we are very proud to have the chance to host our first ever blog carnival. Gene Genie brings together blog articles from an array of perspectives within the area of human genes, genetics and diseases. It has been a pleasure and an education reading through all of these great articles and ...

Genes Linking Aging and Cancer
2007-11-16 13:39:00
This month’s Nature Genetics has an article introduced with the catchy title Aging and cancer: killing two birds with one worm. That’s referring to using C. elegans as a model organism, of course, due to its utility as a model organism for genetic research. Pinkston-Gosse and Kenyon follow a C. elegans-ortholog of FOXO ...
More About: Cancer , Linking , Genes

Around the Blogs
2007-11-16 12:25:00
Here’s my round-up of the best from around the blogs this week:
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Choosing a Post Doc Position
2007-11-15 16:38:00
After all that hard work, you finally have your PhD. Now what? If your career choice is academic research, your first post-doc position beckons. The choice of where, and with whom, to take up a post-doc position is a very important one as it is at the post-doc stage where publications are required to move ...
More About: Post , Careers , Position

Online Data and Project Management
2007-11-14 13:24:00
During a research project, how do you record your data, conclusions and the samples you produce? What about ideas, insights and thought-trains? It would be very useful to have a good system to easily store all of these valuable products of your work and retrieve them when you need to look at your data ...
More About: Communication , Project Management , Management , Data , Project

Population Genetics Mechanisms on a Genomic Scale
2007-11-14 13:16:00
Three papers from UC Davis have appeared on the PLoS journals in the past few days that bring together population genetics and genomic sequencing to address questions of importance to evolutionary biology. Their discussions of divergence in coding versus non-coding, and adaptive versus neutral shifts, are what caught my eye. Collectively, they’re three ...
More About: Genetics , Scale , Pula

Rookie Researcher Disasters
2007-11-13 16:30:00
Wide eyed and wet behind the ears, the rookie researcher steps into the lab for the first time. Armed with several years’ knowledge mined from text books, lectures and undergrad labs he feels ready to take his place amongst the worldwide legions of scientists who battle daily in the pursuit of knowledge. Little does he ...
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What to Look for in a Good Mentor
2007-11-13 13:01:00
For every half-way decent mentor or adviser that an aspiring scientist comes across, it sometimes seems as though there is another lurking, who is simply a jerk*. Let’s face it - scientists aren’t consistently “people-persons.” Maybe they had bad mentors, and inadvertently end up passing on the karma. Or maybe science just ...
More About: Communication , Mentor , Careers , Good

10 Tips For Better DNA Gel Extraction Results
2007-11-12 14:31:00
What is it about gel extraction of DNA that makes it a pain? Maybe it?s poor product yields or maybe it?s because the process uses harsh chemicals (chaotropic salts, ethidium bromide, ethanol, heat) that will damage or denature DNA and potentially decrease cloning success. In this article I share some tips, both from experience ...
More About: Tips , Results , Extract

Error Bars in Biology
2007-11-09 16:57:00
….statistics. The very word strikes fear into the heart of many a biologist (including me). In an article published earlier this year, Cumming and co-workers of La Trobe University, Melbourne gave a very useful rundown of common mistakes made when using statistical error bars in biology and suggested a number of rules that should be ...
More About: Biology , Bars , Error , The Basics , Biol

Around the Blogs
2007-11-09 13:01:00
For a survey of 10 interesting articles posted recently, out there in the molecular and cellular blogosphere…
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Science Writing: Selling Your Research
2007-11-08 13:02:00
Browsing around on the Nature Network blogs, I came across one interesting discussion from a couple weeks ago that few researchers actually spend much time thinking about (I think). Martin asked, “I was wondering how much, if at all, the quality of the writing of a submitted paper is considered in the peer review ...
More About: Science , Selling , Writing , Communication , Research

Re-Think PCR and Win an IPhone
2007-11-08 00:40:00
Robert, a Bitesize Bio reader sent me an e-mail to tip me off about a fun little contest being run by BioRad at www.rethinkpcr.com. You are invited to say how you would “re-think” PCR. At first I thought this was a technical contest, seeking real suggestions on how PCR could be improved but actually you just ...
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The Basics: How Alkaline Lysis Works
2007-11-07 13:50:00
Alkaline lysis was first described by Birnboim and Doly in 1979 (Nucleic Acids Res. 7, 1513-1523) and has, with a few modifications, been the preferred method for plasmid DNA extraction from bacteria ever since. The easiest way to describe how alkaline lysis works is to go through the procedure and explain each step, so here goes. 1. Cell Growth and Harvesting The procedure starts with the growth of the bacterial cell culture harboring your plasmid. When sufficient growth has been achieved, the cells are pelleted by centrifugation to remove them from the growth medium. (more…)
More About: Works , Basics , The Basics , Kali

Gene Regulatory Networks during Development
2007-11-07 13:02:00
Gene regulatory network (GRN) circuits are collections of DNA segments in a cell which interact with each other (indirectly through their RNA and protein expression products) and with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA. A lot of research has gone into (a) identifying components of GRNs and (b) developing mathematical models describing their dynamic spatial and temporal interactions. Molecular and cell biologists have a lot to offer in explaining embryonic development from the former perspective. Eric Davidson’s lab at Caltech has been working on this for a few years, with a recent http://www.sciencemag.org/cgi/content/abs tract/318/5851/794">paper in Science on such findings in sea urchin embryos. (more…)
More About: Networks , Development , Gene , Regulatory

10 Reasons NOT to be a Scientist
2007-11-06 17:56:00
Ok, this week has been a bad week in the lab so far. A few weeks ago I wrote a post describing 15 reasons to be a scientist. Today I am in the mood to cross over to the dark side and give you 10 reasons NOT to be a scientist! Strangely I could only think of 10. If you have any more, please feel free to add them in the comments section below. (more…)
More About: Scientist , Reasons

A Missing Post-translational Modification
2007-11-06 13:13:00
Eukaryotic cells possess a surveillance mechanisms that identifies aberrantly processed mRNA precursors and prevents their flow to the cytoplasm by tethering them near the site of transcription. Termed post-translational modification, this process includes the distinct events of 5′ capping, 3′ polyadenylation, and intron splicing. During processing, nascent mRNA assembles together with RNA binding ...
More About: Post , Missing , Modification , Tran , Missi

Spare a Thought for Tech Support Reps
2007-11-05 17:27:00
Have you ever called technical service departments for advice and help in troubleshooting or choosing a product? Depending on the reason for the call, the experience can vary from positive and helpful all the way to torture for both people. Working in technical service can feel like a very unrewarding job as you are handling ...
More About: Tech , Careers , Support , Thought , Tech Support

History of Cell Biology
2007-11-05 15:09:00
The cell theory, or cell doctrine, states that all organisms are composed of similar units of organization, called cells. The concept was formally articulated in 1839 by Schleiden & Schwann and has remained as the foundation of modern biology. The idea predates other great paradigms of biology including Darwin?s theory of evolution (1859), Mendel?s laws ...
More About: Cell Biology , News , History , Biology , Cell

Around the Blogs
2007-11-02 17:16:00
Here’s what I’ve been reading around the blogs this week…
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Fluorescent Neurons Over the Brainbow
2007-11-02 14:59:00
Site-specific recombinases have, for the past 20 years, been one of the most powerful tools in studying the functions of all sorts of genes. Most widely used as the Cre/lox-based system for inserting or deleting genes in mice, transgenic analyses have told us volumes about animal development1. For instance, mouse genetic knockouts are ...
More About: Fluorescent , The Brain , Rainbo

Ubiquitination Isn?t Just for Recycling Anymore
2007-11-01 16:52:00
Ubiquitin is a small protein, which can be attached to other cellular proteins - a post-translational modification called ubiquitination. Discoveries in the ’80s illuminated ubiquitin as a label for degradation and recycling of the modified protein. Recent studies however, are suggesting more nuanced roles for ubiquitin in signal transduction and cellular function.
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10 Ways to Work RNase Free
2007-11-01 16:51:00
Working with RNA? What fun! Those little, nearly indestructible RNases are everywhere - on your skin and mucous membranes, in the water and (some of the) enzymes you use, on lab surfaces, even in airborne microbes! Here are 10 ways to keep the RNases at bay, and keep your precious samples safe:
More About: Work , Free

The Basics: How Does DNA Ligation Work?
2007-10-31 16:02:00
It takes a real effort to keep your basic knowledge of molecular and cell biology fresh, in addition to everything else you have to do. Wouldn’t it be great to if there was a place where you could find easy-to-read articles that allow you to brush-up on those basics in just a couple of minutes? …I ...
More About: Work , Basics , The Basics

Cells - This Side Up
2007-10-31 15:56:00
Perhaps the most fundamental aspect of migration of any kind is, how do you know which way to point yourself? Heck, this isn’t just about migration, it’s about how something is oriented in its immediate environment. For orientation, there’s magnetic North, gravity, or any conceivable cue that you might choose to face towards. ...
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Arthur Kornberg, Biochemist
2007-10-30 15:41:00
In memorandum of one of the pioneers of molecular biology, who was awarded a Nobel Prize in medicine for the discovery of DNA polymerase. What molecular biology blog would this be if we didn’t honor his memory? Larry Moran presents a fine eulogy, as does the NYTimes: Dr. Arthur Kornberg, a biochemist whose Nobel ...
More About: News , History , Chemist , Chem

?Loss of Function?
2007-10-30 15:40:00
Now for a bit of light entertainment of the biological kind. Wash out your mind - I don’t mean that kind of biological entertainment
More About: Loss , Function