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
Error Bars in Biology 2007-11-09 09:57:23 ….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 adhered to when presenting data in this way, especially in publications. The article provides a quick taster of their advice, which helps to make things seem a little less scary.
Two types of error bars are commonly used in biology. Descriptive error bars used to describe a data set and inferential error bars used to determine which conclusions can be justifiably drawn from a data set. These are summarized in the table on the right, which is taken from the paper. (more…)
Around the Blogs 2007-11-09 06:01:24 For a survey of 10 interesting articles posted recently, out there in the molecular and cellular blogosphere… (more…)
Read more:Blogs
Science Writing: Selling Your Research 2007-11-08 06:02:48 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 process?” A fair number of people agreed that the quality of the writing in the end doesn’t really influence the decision to accept or reject a paper. But good writing, especially in the first paragraph, certainly helps. (more…)
Read more:Science
, Research
, Science Writing
Re-Think PCR and Win an IPhone 2007-11-07 17:40:53 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 have to complete a sentence starting with “I think” in a PCR-related manner. Most people seem to have gone for some sort of PCR-related pun or joke. Here are a few of my favorites: (more…)
Genes Linking Aging and Cancer 2007-11-16 06:39:26 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 transcription factors, DAF-16, to phenotypes of manipulated lifespans and cancer susceptability. The pathway stems from the respective ortholog of insulin/insulin-like growth factor 1 (IGF-1) receptors, and FOXO transcription factors turn on genes involved in p53-dependent apoptosis, cell cycle arrest, and cellular stress resistance.
(more…)
Read more:Genes
, Linking
, Cancer
Choosing a Post Doc Position 2007-11-15 09:38:33 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 to the next level (tenure-track) and where your research direction is determined. Whether you will publish or perish is drastically affected by your choice. How do you make sure you choose wisely? Here is some advice I wish someone had given me when I was making the decision. (more…)
Around the Blogs 2007-11-16 05:25:01 Here’s my round-up of the best from around the blogs this week: (more…)
Read more:Blogs
Online Data and Project Management 2007-11-14 06:24:12 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 or your thoughts on a particular problem weeks, months, or years later. (more…)
Read more:Project
, Management
Population Genetics Mechanisms on a Genomic Scale 2007-11-14 06:16:57 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 very densely packed studies, providing a fountain of info that only bioinformatics can process. (more…)
Read more:Population
, Genetics
, Mechanisms
, Scale
Rookie Researcher Disasters 2007-11-13 09:30:51 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 suspect the pitfalls that lie ahead, the classic mistakes and unknown dangers lie in his path.
Here are four rookie researcher disasters. All are true stories that I have witnessed (and one that I made myself - I’ll let you guess which). Each of you will likely have your own tales to tell, please share them in the comments section below and let this serve as a guide, helping rookie researchers of the future avoid the mistakes of others.
1. Pipette inferno. A pristine set of micro-pipettes hang in their holders above the bench. Tools of precision, and of considerable value. Filled with anticipation, the rookie is performing his first ever culture inoculation. Read more:Rookie
, Researcher
, Disasters
What to Look for in a Good Mentor 2007-11-13 06:01:54
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 attracts a higher-than-average number of socially inept individuals - who knows. (more…)
Read more:Mentor
10 Tips For Better DNA Gel Extraction Results 2007-11-12 07:31:37 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 and from helping people with the procedure, to help maximize yields of high quality DNA from the gel extraction process. I hope these suggestions help you to obtain high yields and purity of double-stranded DNA.
1. Trim the gel slice as much as possible. Get rid of all the excess gel including in front of or behind the DNA. Most people cut out a square around the gel but don’t think to stand it up and trim the gel on front and back. If you poured a thick gel, there will be a lot more gel to remove. The more you can remove encasing your DNA, the higher the yields. (more…)
Read more:Extraction
Free, Publication Quality Plasmid Annotation 2007-11-21 06:29:26 I just came across an extremely nice piece of plasmid mapping and annotation software that I’d like to share with you. PlasMapper is a web-based application, created by staff from the University of Alberta, that automatically generates fully annotated plasmid maps from your raw sequence input.
Using a database containing the sequences of hundreds of features (replication origins, antibiotic resistance cassettes etc), as well as restriction enzymes, the program identifies each of the features in your inputted plasmid and renders them in a publication quality graphical or text map. The image on the right shows some examples of the output of the application - click the image to view a larger version. (more…)
Read more:Quality
Microtubules at the Membrane in Apoptosis 2007-11-20 18:15:07 Apoptosis, or programmed cell death, is an evolutionarily conserved and neatly orchestrated process important for tissue remodeling and safe elimination of severely damaged cells. Conducted by a caspase-mediated proteolytic cascade, the cell death program results in a series of cellular changes distinct from cellular necrosis. And one of the critical aspects that distinguish apoptosis from necrosis is that intracellular components of apoptotic cells are isolated, preventing membrane permeability and release of inflammatory molecules.
Just how do dying cells keep themselves from spilling out their materials into the surrounding tissues? And what role do the cytoskeleton components have in this process? Those are the questions that José Sánchez-Alcázar and colleagues1 asked in a paper in July’s issue of the journal Apoptosis. (more…)
Read more:Membrane
Pin-pointing DNA Ligation Problems 2007-11-20 07:01:24 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 them to pin-point the cause of your ligation problems. (more…)
Across the Comparative Oncogenomic Landscape 2007-11-20 06:09:51 “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 topographical representation of gene mutations. The average number of mutations per tumor was approximately 80, but ranged from 39 to 193.
(more…)
Read more:Across
, Landscape
Aptamer-DNA Chimeras 2007-11-19 05:58:34 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 often quite interesting.
One manuscript recently in Nature Precedings used the chimeric molecule approach slightly differently. John Rossi and coworkers describe a aptamer conjugate for delivering anti-HIV siRNA specificially to infected cells. The aptamer in question is a gp120-interacting molecule. The envelope glycoprotein gp120 is expressed on the surface of HIV-1 infected cells, allowing binding and interalization of the whatever is conjugated to the aptamer, in concept. In this case, Rossi et al. have conjugated the chimera to an siRNA that releases an anti-tat/rev siRNA, which in turn inhibits HIV replication. (more…)
Gene Genie #20 2007-11-18 18:04:49 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 I’d like to thank all of the authors for contributing, and Gene Genie founder Berci Mesko for allowing us to host the carnival. So lets get to the articles…. (more…)
10 Simple Rules For Doing Your Best Research 2007-11-27 06:24:19 Last month, Thomas C. Erren and colleagues published an editorial in PLoS Computational Biology entitled 10 simple rules for doing your best research, according to Hamming. The article provides some great philosophical guidance on setting out to do great research, drawing on advice given by the mathematician Richard Hamming during a Bell Communications Research
Colloquium Seminar in 1986. (more…)
Read more:Rules
, Simple
, Simple Rules
The Biased Choices of Cells 2007-11-27 06:24:03 Here’s one of my favorite journal articles from the past year - an elegant study by Natalie Andrew and Robert Insall published in Nature Cell Biology: Chemotaxis in shallow gradients is mediated independently of PtdIns 3-kinase by biased choices between random protrusions. From the introduction:
We have made detailed, quantitative observations of Dictyostelium cells chemotaxing in shallow gradients, which contradict current models in several ways (see Supplementary Information, Fig. S1): first, new pseudopods are made in spatially restricted sites by splitting of the leading edge; second, the timing and direction of these new pseudopods are random, so they cannot correct the cell’s direction; and third, the survival and retraction of pseudopods are spatially controlled, suggesting an alternative mechanism of chemotaxis.
This model is very similar to the mechanism of growth cone guidance, where random protrusions are constantly exploring the cell’s surroundings, &lsqu
Ribosomal Paralogs not Redundant Afterall 2007-11-26 06:14:59 In the budding yeast Saccharomyces cerevisiae, 59 of the 79 cytoplasmic ribosomal proteins are encoded by two genes, stemming from an ancient genome duplication event. Komili et al. (2007) now report that these paralogous genes are not functionally equivalent, suggesting the possible existence of a “ribosome code.”1
Yeast and mammalian genomes are riddled with apparently duplicated genes, differing in only a few amino acids from one paralogue to its clone. Because they’re so nearly identical, most researchers assume some degree of redundancy in such circumstances, and attempt to ascertain the function of only one of the two. If there is any difference in function between two paralogues, the difference might be unimportant, or just too difficult to tease apart experimentally.
As we gain more and more insight into how the cell works, such minutiae might be a curious area to study up on. In the case of the yeast S. cerevisiae, it turns out that 59 of their 78 ribosomal prot
Newborn Screening. Saving Lives the Molecular Way 2007-11-26 06:07:50 As a product manager, one of my responsibilities is to exhibit at various scientific conferences to promote and advertise products for genomic DNA extraction. Less than three months into the job, I attended the American College of Medical Genetics (ACMG) conference to promote a new product we had just launched for DNA extraction from blood and cells. After hours of talking to people about the features and benefits of my fancy new kit, a gentleman walked by my booth, looked at the demo on the table, and asked me to explain how it worked. Excited that I finally found an interested scientist, I enthusiastically went into my spiel, but as it turned out, I was the one who did most of the listening.
(more…)
Read more:Newborn
, Screening
, Saving
, Lives
, Molecular
Around the Blogs 2007-11-23 06:23:53 A few articles from around the blogosphere, relating to the molecular biology of the cell and the conduct of science.
Confocal Image of Cochlea Wins Art Prize - Stunning micrography!
Microbial Sociology - Detailed post on the molecular mechanisms of microbial communication.
The Selfish Gene Drives an Operon - What does horizontal gene transfer look like from the gene-centered view of evolution, or “selfish gene” model of evolution? Operons anyone?
The Growth Cone - Kickoff post to a short series on the neuron structure of the same name. Growth Cones are a fascinating topic for me, relating to both the brain’s wiring and how cells move.
The Origins of Genome Architecture - A review of Michael Lynch’s book, which reportedly could have been subtitled “Why R.A. Fisher was wrong.”
Authorship on Scientific Papers - Discussion of the rules of authorship, and handling disputes equitably.
Bringing Your Research Lab’s Web Site into the 21st Century - Sci Read more:Blogs
Get Involved With Bitesize Bio 2007-11-22 07:46:53 We’d like to invite you, our wonderful, talented readers to get more involved with this blog. Here’s a few ways you can do so:
Suggest a topic you’d like us to write an article on (click here to do this)
Share your knowledge… write an article for the blog. Whether have one technical tip you are burning to share, or you’d like to write more regularly, your contributions are very welcome. (Mail your article to nick {at} bitesizebio{dot}com or contact me at the same address if you’d like to be a regular contributer)
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If you are a blogger, write a guest article that we can post he Read more:Involved
The Best of: Tech Tips 2007-11-22 06:16:13 Bitesize Bio has gained a lot of new readers over the past few months so I thought it would be a good idea to highlight some of the articles newer readers may have missed. I’ll do this periodically to make sure none of our readers miss any of our great content. So, here are the best of our tech tips articles so far: (more…)
20 Ways to Increase your Productivity 2007-12-03 06:05:30 No matter how efficient you are, it’s always possible to improve your productivity and improving your productivity means that you get more of the rewards you are trying to obtain: results, publications… or dare I say it, money.
Here are 20 ways to improve your productivity. Some are focussed toward improving the productivity of bench research, but most are applicable in many other jobs. This list is based on much longer general list that can be found at Steve Pavlina’s excellent personal development website. (more…)
Read more:Productivity
Entosis: Cellular Canabalism 2007-12-03 05:44:22 There might be more to cell death besides apoptosis and necrosis. In a paper that sounded a bit fishy to me, Michael Overholtzer, Joan Brugge and coworkers1 introduce “Entosis”: A non-apoptotic cell death process, that occurs by cell-in-cell invasion.
As Eileen White2 described:
Upon examination of mammary epithelial cell lines in suspension, Overholtzer et al. noticed the presence of cells within other cells. Further investigation of this phenomenon revealed that detachment of mammary epithelial cells from the ECM initiates a new pathway of nonapoptotic cell death called entosis in which one cell invades into another.
(more…)
The Limits of Horizontal Gene Transfer 2007-11-30 10:17:19 Looking at the tree of life, descent with modification is an obvious theme, where genes are passed on through ‘vertical’ lines of ancestry. It so happens though that genes can jump from one lineage to another, by a process called ‘horizontal gene transfer’ (HGT). Naked DNA uptake (transformation), viruses (transduction), and plasmids (conjugation) are the mechanisms by which the genetic units of heredity need not be inherited in the usual sense. HGT appears to blur the boundaries of what a species is, particularly for the bacterial domain of life. So the study published by Rotem Sorek, Edward Rubin et al.1 on the determination of barriers to HGT is interesting from a couple different perspectives. (more…)
Read more:Horizontal
, Limits
Around the Blogs 2007-11-30 06:52:22 Here are the highlights of what I’ve been reading around the blogs this week: (more…)
Read more:Blogs
Electroporation on a (96 well) Plate 2007-11-29 06:30:26 I just came across a neat device now being offered by BioRad that may interest those of you who do a lot of electroporation of difficult-to-transfect mammalian cells, where tedious optimization of the electroporation protocol itself is required. (more…)
Read more:Plate
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