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If you’re reading our Microscopy and Imaging Channel here on BitesizeBio, you might have heard about the new techniques which fall under the umbrella of ‘Super-Resolution Microscopy’. In her recent article, Cynthia introduced us to the limits of resolution and how this can be overcome. Question time You may have more questions; In this introduction…
Discover interesting facts about Congo red and it can help us understand Alzheimer’s disease.
Unlike Nick Oswald I think I can multitask in the lab. If I organize my day efficiently and perform lots of experiments and other tasks in parallel, I get more done. But there is a school of thought – the one described in Nick’s article – that says no-one can really multitask, that our brains…
Why do I see a cloud? When you are looking at protein localization within a cell, have you ever wondered why you see a cloud of fluorescence rather that several individual fluorescent points? Well, light microscopy has a theoretical resolution limit of 200 nm. This means that in theory, to resolve two points as being…
You have spent days, if not weeks, at the bench setting up the treatment and control samples for that crucial experiment. You submitted your cDNA library for sequencing and after a few weeks of waiting anxiously you get back a list of differentially expressed genes. Hooray?! Hold on- not quite yet! There is something you…
RNases are like the baddie super-heroes amongst laboratory enzymes. They are omnipotent, destructive and seemingly indestructible. This is because they were created by evil overlords, for the sole purpose making life difficult for the brave scientists who battle every day to produce high quality, intact RNA preps. Ok, I’m joking about the overlords part. But…
Mammalian cell culture can easily deplete grant funds. Sometimes you can alter protocols to use expensive reagents sparingly. Here are a few tips!
Acid-fast stain (AF) is a special staining technique used in the histology lab. Discover which bacteria this stain detects, the history behind it, and how it works.
There is no such thing as “junk” DNA Until recently, vast areas of the genome had been denounced as “junk” DNA, because they do not encode proteins. However, it has become clear that these regions have a large diversity of other functions, from transcriptional and translational regulation to the protection of genes and genome integrity….
Personal Protective Equipment (PPE) such as your lab coat and gloves are an essential piece of kit when working in a laboratory; however, it is important to know when it is inappropriate to use PPE. 1) Don’t wear your lab coat, gloves or other PPE in offices or dining areas. They may have become contaminated…
Gomori’s methenamine silver is a special histology stain for detecting fungi. Find out how and why you might want to use this stain in the lab.
You can really tell when Honours Project students start working in the lab on their projects: the pH meter probe is suddenly floating in water and the weighing area is a mess, because nobody had time to explain “the weighing etiquette”. Fret no more! We will spell it out and you can print it out…
You’ll give me an (enzymatic) complex! Following on from Part 1 of this article, let’s start by having a look at the two most popular enzymatic ‘sandwich’ methods; A step ahead of your competition In my opinion gaining an understanding of different detection systems and how they can be applied can give your research an…
MicroRNAs (miRNA) are short, non-coding RNAs involved in post-transcriptional silencing of gene expression. miRNAs can be associated with exosomes and can function as cancer-specific biomarkers. This, coupled with the fact that they are stable in plasma and serum makes them valuable diagnostic tools, as long as they can be reliably isolated from the serum and…
In a recent article, I gave some tips about how to obtain good results with sequencing DNA after bisulfite conversion (it contains some tips that apply to the approach described in this article, too). Bisulfite sequencing is a very useful technique if you want to know the methylation status of every CpG in your genomic…
In my last article, I explained that plasmid DNA recovered from a plasmid prep consists of few different species; supercoiled, nicked, linear and single stranded circular, and how you can distinguish them on a gel. Supercoiled DNA is the desired form of plasmid DNA; it performs better in downstream applications such as automated sequencing and…
In my previous article I covered different immunohistochemical staining techniques at a superficial level. In the following articles I will start to explain these technologies in a bit more detail and in which situations they should be applied. All of the following will involve additional stages when applying them, for example- serum blocking, protein blocking,…
For those of you who print out the results that you have acquired from the Flow Cytometer to stick in your lab book, did you know that inkjet printers and cytometers have a shared history? Flow Cytometry is less than 50 years old and machines today still use some of the same principles as the…
Comparing and measuring gene expression is certainly an integral part of research—gene expression patterns continue to show us how different cell networks are regulated, and point to new biological pathways and possible treatments for disease. But one crucial part of gene expression lies in making sure that differences in gene expression are due to gene…
Alternative splicing is a highly orchestrated process that uses a multitude of regulatory mechanisms. Splicing specificity involves a precise interaction between cis- and trans-acting regulatory elements, and factors that disrupt these interactions can result in aberrant splicing. There are multiple ways in which mutations can affect splicing fidelity: Global analysis of alternative splicing is essential…
Conserved elements are stretches of DNA sequence that are under purifying selection. That means mutations leading to a change of function in this part of the DNA are detrimental to the organism and will not become fixed in the genome, but rather discarded by natural selection. The level of conservation between species gives an idea…
A commonly used technique in epigenetics is Chromatin Immunoprecipitation, or ChIP for short. This technique can show you whether a certain protein (e.g. transcription factor or histone modification) binds to DNA, when in its native conformation, namely chromatin. Insightful, but difficult This information can be very insightful, but difficult to obtain. Most protocols and suggestions…
The ELISA (enzyme-linked immunosorbent assay) is a rapid method used to detect the amount of a protein of interest in clinical and experimental samples. There are a number of ELISA formats to choose from, depending on your research needs. These include direct ELISA, indirect ELISA, competitive ELISA and sandwich ELISA. We have previously covered the…
According to the International Society for Stereology, the area of scientific study encompassed by this term is that which analyzes solids. If that all sounds a bit too much like materials science, then for us microscopists, it’s really about the review of three-dimensional objects (mainly tissues) by making horizontal and vertical incisions. Stereology can be…
In her article How to Get Perfect Protein Transfer in Western Blotting, Emily Crow recommends Coomassie staining your gel after transfer to the membrane to check the quality of the transfer. A good transfer should not leave behind proteins and PVDF membrane, stained by 0.1% Ponceau S in 5% phosphoric acid and destained with water…
The importance of epigenetics in biology is increasingly acknowledged (if you’re not convinced yet, read my crash course). One commonly studied epigenetic mark is CpG methylation: cytosines that are directly followed by a guanine nucleotide (indicated by CpG), can be methylated, unlike non-CpG Cs. Since attachment of a methyl group to a cytosine can affect…
Sanger sequencing is still a workhorse of most molecular biology labs. Even with the advent of next-generation sequencing we still need to sequence our clones and PCR products. In this article I have listed some of the tips and tricks we used in our Sanger services. (1)Dilution of BigDye: I’d expect this to be a…
The Basic Local Alignment Search Tool (BLAST) algorithm is at the heart of a free suite of online resources available through the National Center for Biotechnology Information (NCBI). While most researchers are aware of BLAST as a sequence alignment tool, NCBI’s BLAST suite offers so much more! I’ll cover in-depth how to use these resources…
The last two decades have seen a dramatic increase in the number of publications using immunohistochemistry (IHC) as a research tool to identify the spatial location of proteins of interest within cells, tissue sections and whole-mount preparations. Grinding and binding The advantages over ‘grind and bind’ methods are apparent, but the very best results will…
Finding a good primary antibody can often feel like playing Russian roulette. Nothing is more disappointing than buying a $300 antibody that doesn’t work for your use. There are some steps you can take, however, to increase your likelihood of success. Scout out Other Labs Before you buy, ask if anyone around you or in…
Calculations can be the bane of laboratory work. Fortunately, there are many easy methods to help you do the maths you need in the lab. Here, we tell you about the different ways to calculate primer concentration depending on the starting material. For all calculations, let’s assume we have 22 nmol of a DNA primer…
Alternative splicing events often occur in a spatiotemporal manner, and some are regulated by alternative splicing regulators, with striking variation across tissue types and developmental stages. Alternative splicing events are often differentially regulated across tissues and during development, as well as among individuals and populations, suggesting that individual isoforms may serve specific spatial or temporal…
Of all the words you write to prepare a manuscript, too often the most important ten or so are left as an afterthought. You’ve slaved for weeks to finish your manuscript. Through draft and re-draft, you managed to shoehorn hundreds of man-hours of careful lab work into the word limit designed to be precisely 300…
Anyone who is involved in DNA sequencing in one form or fashion knows there are multiple ways to skin a cat: Sanger-based, next generation (NGS), and of course the new ion torrent sequencing technology. Which technology you use is usually dependent on the questions you’re trying to answer – and how fat your wallet is….
Anyone who has spent any amount of time in a cell or tissue culture lab will have experienced contamination at some point. You might not admit it, or want to admit it, but you know you have! I performed my graduate work in a basement university lab with an out-of-service emergency exit door in the…
It is a truth universally acknowledged that free cheese exists only in a mousetrap, and even there it’s free only to the end user. So it’s no wonder that the traditional system of most scientific publications through publishing houses seems to be fair. A publishing house (PH) employs editors as well as technical personnel to…
The correct documentation and storage of your laboratory samples may be a tedious process, but it will make your life a lot easier in the long run. The last thing any scientist wants when trying to complete a key last experiment for a publication is not being able to find or identify a critical sample….
Need to stain Gram-negative organisms? You should consider the Warthin-Starry stain.
I have been fortunate enough that in my career to date I have rarely experienced the problem of other people stealing my reagents. However, one PI told me of her experiences working in a US laboratory where things had got so bad people brought their reagents home at the weekends! Working in a research laboratory…
Parents of small children attending nursery know that the period of time from September to June is a succession of colds and flues for the whole family – children with their underdeveloped immune system exchange viruses, creating new potent strains. Well, that’s probably how bacteria feel all the time in the natural environment teeming with…
The eBook with top tips from our Researcher community.