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
Heterologous Gene Expression Problems? 2007-10-09 10:41:33 When heterologous gene expression goes wrong it can be a real headache. Here’s my checklist for the steps to take when you encounter problems with this dark art.
Check the construct by sequencing the expression cassette to make sure that everything is as you expect. A lack of expression could result from a stray stop codon. (more…)
GFP Beach Scene 2007-10-05 09:42:58 Just a bit of fun for a Friday… I’ve often thought that some of what we molecular biologists do with staining and things could easily pass for artwork, but I’ve never seen anything like this fantastic agar plate artwork posted on Wikipedia. It shows a San Diego beach scene drawn on an agar plate using an eight color palette of bacterial colonies expressing fluorescent proteins. (more…)
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Bitesize Bio Welcomes Dan Rhoads 2007-10-19 10:06:42 Regular readers may have noticed that the number of articles published on Bitesize Bio has been quite low. Despite this apparent lack of activity, this has been a period of big changes with next Monday seeing something of a re-launch of the site
I’ve been searching, nay hunting, for an accomplished writer to join me for about a month now, looking for someone who could offer a different perspective and style to my own to bring our readers an even greater variety of articles and insight. Enter Dan Rhoads, author of the popular Migrations blog (well worth checking out). Dan is a real mine of information, an avid reader of all things science and a really slick writer.
Between us we have been re-defining the site somewhat. From next week you can expect coverage of both molecular and cell biology topics and techniques as Dan’s more cell biology-orientated background comes to the fore. We will also have more journal club and news articles to keep you abreast of the latest developm
How to: Keep your data organized 2007-10-16 11:00:40 Talented, enthusiastic scientist required. Must have good organizational skills.
Do you fit the bill? With the pace of molecular biology and biochemical research quickening year on year, the importance of good organization and planning skills for researchers is becoming increasingly important. Here are 5 ways to ensure that your data is organized and easily analyzed, samples are safe and accessible and your project is carried out efficiently. (more…)
History of Molecular Biology 2007-10-24 09:09:46 As a freshman biology major in undergrad, I was introduced to molecular biology with the following description: Molecular
biology represents the intersection of genetics, biochemistry and cell biology. Some people, it turns out, add microbiology and virology into the mix. So molecular biology is often used as a catch-all, to describe a wide breadth of interests. (more…)
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, Molecular Biology
The Invention of PCR 2007-10-24 09:08:49 Few technical breakthroughs that have changed the face of their field like the Polymerase Chain Reaction (PCR). Gene cloning, sequencing of complex genomes, DNA fingerprinting and DNA-based diagnostics are just some of the techniques that were either inefficient, crude or plain impossible before PCR. The technique has revolutionized biological research and biotechnology to such an extent that it can be considered as one of the major reasons for the boom the field has experienced over the last 20 years or so. (more…)
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Histone Methylation Determines Cell Fate 2007-10-23 08:48:36 Gene expression is controlled at all sorts of levels in eukaryotic cells, and one of the hot areas is that of histone modifications and how they influence transcriptional accessibility on chromosomes - epigenetic regulation, as it’s called. Think of it as an analog annotation system for the cell’s genome, where each gene is wrapped up in such a way that it’s either accessible to transcriptional machinery or not. There are enzymes that add these annotations, and enzymes that remove them, which determine cell fate on one level in a sort of gene expression balancing act. (more…)
10 Tips on Writing a Research Poster 2007-10-23 08:48:17 Poster presentations are a great way to show off your hard work, especially if you are just starting out in research. They are much less stressful than oral presentations, but still provide great networking opportunities and valuable practice at talking about your work. Follow these simple tips to create an attractive poster that will draw readers in and get people talking (to you!)
Choose your content wisely. The information you can get across on a poster is very limited. Choose a single aspect of your research that you think you can explain fully in a small amount of text and graphics and focus on that alone. (more…)
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, Poster
Modeling Tertiary Structure 2007-10-22 09:18:31 Predicting and modeling protein structure, making protein crystallography somewhat obsolete, has been an elusive science to date. Since Linus Pauling and others determined that the most favorable secondary structures are the alpha helix and beta sheet, molecular and structural biologists have sought a set of rules with which to predict a protein’s structure from its amino acid sequence.
Structure
prediction is still more guesswork than anything however, even with the power of 21st century supercomputers. It is based on comparisons to previously solved structures, not on reductionist rules and laws of chemistry.
Except maybe not. (more…)
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10 Links: Cell and Molecular Biology Podcasts 2007-10-22 09:03:39 Podcasts are great. I listen to podcasts every day during my commute and find them a great way to pick up information, whether it’s to learn about a new subject, brush up on something I have studied before or keep up with the news. Here are 10 molecular and cell biology related podcasts that I hope you will find useful. (more…)
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, Molecular Biology
, Podcasts
Firefox Add-ons for Molecular and Cell Biologists 2007-10-29 11:22:04 Firefox
is the most popular browser on the web. This in large part due to the vast array of free add-ons that allow you to customize the browser and add features that will help your everyday work. And molecular and cell biologists are not left out. In this article I have compiled a list of Firefox add-ons for bioscientists. Some specifically help with things like bioinformatics and information searches, while others provide more general support with PDF downloading and unit conversion and the like. Here they are: (more…)
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IRESs and Negative Data 2007-10-29 10:17:00 Nature Precedings represents a step forward for disseminating experimental results in the internet age. Especially ‘negative’ results, that might not have gotten published otherwise, but is extremely helpful to other researchers in trying to avoid making the same mistakes. Refutation of a hypothesis, while not a discovery, is the goal of the well-planned experiment in the trenches of science.
An outstanding example of such a Preceding can be found in the manuscript Internal ribosomal entry site lacks secondary structure by Xuhua Xia of the University of Ottawa’s Department of Biology.
(more…)
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Around the Blogs 2007-10-26 09:24:53 10 links to some popular blogs of the molecular and cellular biosciences:
Bacillus? Acinetobacter? Thermus?!? - Rosie takes us through her thought process in developing an experiment on growth conditions, while she considers what organism to use.
These Cells are Left-Handed - Some comments on the influence of chirality on cell polarity.
Chlamydomonas Swims Across the Line - The plant that swims gets its genome sequenced.
TRPV1 Ion Channels - A student answers his professor’s question about a ligand-gated ion channel, and what was done to test its interactions with anesthetics.
Microcosm: Unveiling the New Book (Or At Least Its Cover) - Here’s teaser on a new book on the horizon.
MicrobeWorld: what have you done? - Sandra catches a bunch of microbiologists mistaking a bacterium for a virus.
Do Bacteria Age? - Well, do they?
A Fever for Enzymes - Explanations of how temperature relates to enzymatic reaction rates, sparked by one of our posts.
The Nobel Prize in Chemistry 194 Read more:Blogs
Time to Think 2007-10-26 06:48:20 Spare a thought for your poor over-worked neurons. In the information age, they are bombarded with input from the moment they are dragged into consciousness by the radio alarm clock each morning then throughout the day by e-mail, Google searches, RSS feeds, mobile phones, newspapers, books, blogs and more. In the post genomic era, it’s even worse if you are a bioscientist. The amount of data available literally at your fingertips via BLAST searches and the like is staggering. In this environment it’s easy for your mind to become overloaded, and an overloaded mind is no good for the logical and creative thought processes that are essential for effective science. (more…)
Open Access to Science 2007-10-25 09:21:11 The Public Library of Science
(PLoS) defines the issue of Open Access
Publication as:
An Open Access
Publication[1] is one that meets the following two conditions:
1. The author(s) and copyright holder(s) grant(s) to all users a free, irrevocable, worldwide, perpetual right of access to, and a license to copy, use, distribute, transmit and display the work publicly and to make and distribute derivative works, in any digital medium for any responsible purpose, subject to proper attribution of authorship,[2] as well as the right to make small numbers of printed copies for their personal use.
2. A complete version of the work and all supplemental materials, including a copy of the permission as stated above, in a suitable standard electronic format is deposited immediately upon initial publication in at least one online repository that is supported by an academic institution, scholarly society, government agency, or other well-established organization that seeks to enable open access, unr
5 Ways to Clean Up A DNA Sample 2007-10-25 09:20:25 One of the most common tasks in molecular biology is cleaning up DNA from aqueous solutions to remove buffer salts, enzymes or other substances that could affect downstream applications. Examples include cleaning up PCR reactions, digests or other enzymatic treatments and cleaning up genomic or plasmid DNA contaminated with cellular proteins/debris. There are several ways to approach DNA clean-up, here are five of them. (more…)
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, Sample
Around the Blogs 2007-11-02 11:16:44 Here’s what I’ve been reading around the blogs this week… (more…)
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Fluorescent Neurons Over the Brainbow 2007-11-02 08:59:08 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 routinely the most convincing method available to determine the most vital function of a given gene product.
In some tissues however, imaging of intricate cellular structures is very difficult. In the brain, for instance, it can be difficult to distinguish one cell from the next in a synaptic circuit, and even more challenging to render a map of neural connections that include divergence and convergence of synaptic relays between many neurons. Fluorescent
labels and other staining techniques have been used, to limited effect, but ‘connectomic’ maps of many or all neurons has been beyond the reach of available methods.
(more…)
Ubiquitination Isn’t Just for Recycling Anymore 2007-11-01 10:52:17 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. (more…)
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10 Ways to Work RNase Free 2007-11-01 10:51:44 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…)
The Basics: How Does DNA Ligation Work? 2007-10-31 10:02:42 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 hope you said “yes”, because this is the aim of my “The Basics
:” series of articles, which I will be bringing to you periodically (Feel free to let me know whether you think this is a good or bad idea either in a comment or by hitting the “contact” button above). This article explains the basics of DNA ligation. I hope you find it useful. (more…)
Cells - This Side Up 2007-10-31 09:56:05 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. How do cells orient themselves, however?
One of the primary ways in which cells orient themselves is by labeling regions of the cell membrane - by phosphorylating a type of lipid called phosphatidyl-inositol(4,5)bisphosphate [PI(4,5)P2] (green), so that it becomes [PI(3,4,5)P3] (purple), as shown by the image (Comer and Parent, 2007). As this reaction invovles the phosphorylation of the ‘3′ site of the inositol ring of carbon atoms, the enzyme which catalyzes this reaction is called PI-3 Kinase. (kinase = phosphorylating enzyme)
(more…)
“Loss of Function” 2007-10-30 09:40:48 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…)
Arthur Kornberg, Biochemist 2007-10-30 09:41:03 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 Prize-winning discovery of how DNA is assembled helped ignite the biotechnology revolution, died on Friday in Stanford, Calif. He was 89 and worked in his laboratory at Stanford University until a few days before his death.
The cause was respiratory failure, a spokesman for Stanford said.
(more…)
The Basics: How Alkaline Lysis Works 2007-11-07 06:50:35 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…)
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, Works
Gene Regulatory Networks during Development 2007-11-07 06:02:49 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 paper in Science on such findings in sea urchin embryos.
(more…)
Read more:Regulatory
, Development
10 Reasons NOT to be a Scientist 2007-11-06 10:56:49 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…)
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A Missing Post-translational Modification 2007-11-06 06:13:17 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 proteins into ribonucleoprotein particles (mRNPs). Failure to successfully complete any of these maturation steps results in the retention in the nucleus and trigger the mRNA’s degradation. RNA polymerase II is thought to facilitate recruitment of several proteins essential for pre-mRNA processing - the C-terminal domain (CTD) of the largest subunit of RNA Pol II in particular.
(more…)
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Spare a Thought for Tech Support Reps 2007-11-05 10:27:32 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 complaints most of the time. However, an experienced technical service scientist can not only help solve your problems but can also become a trusted resource and friend.
As a technical service representative for almost 5 years at a major biotech company, it would amaze me what people can do wrong with a simple kit. (more…)
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, Support
, Tech Support
History of Cell Biology 2007-11-05 08:09:42 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 of inheritance (1865), and the establishment of comparative biochemistry (1940).
(more…)
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