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BioHalloween Top Ten

10/31/2013

With the Halloween holiday upon us, the editors at BioTechniques thought it would be interesting to look back in our archives and compile a Halloween-themed Top Ten. From ghost cells to monster cloning, we hope you enjoy our SPOOKY Top Ten list!

1. Ghost Peaks

“Locking of 3’ends of single-stranded DNA templates for improved pyrosequencing performance” by Utting et al.

Ghost peaks or signals can be a problem in many molecular biology applications. This article from 2004 by Utting et al. demonstrated how using modified 3’ single stranded templates (generated by specifically modified primers) can be used to eliminate those ghost peaks in pyrosequencing.


2. Ghost Cells

“Flow cytometric analysis of the cell cycle in transfected cells without cell fixation” by Pestov et al.

From ghost peaks to ghost cells (permeabilized cells that retain green fluorescence) --- this article generated ghost cells through the use of 0.02% digitonin for flow cytometric analyses of the cell cycle.


3. Glass Knives

“High-resolution three-dimensional reconstruction of a whole yeast cell using focused-ion beam scanning electron microscopy” by Wei et al.

High-resolution reconstruction of yeast cells is important, and methods advances such as the one described by Wei et al. have the potential to enhance our understanding of cellular anatomy as well as the intricate relationships amongst proteins and organelles. To accomplish their yeast reconstruction here, the authors used a glass knife to cut thin slices off a cured resin block of yeast cells.


4. Phantom Zones

“Quantification of DNAse type I ends, DNAse type II ends, and modified bases using fluorescently labeled ddUTP, terminal transferase, and formamidopyrimidine-DNA glycosylase” by Baskin et al.

Substituting fluorescently labeled ddUTP for dUTP in the TUNEL assay permitted quanitification of fluorescent signals, enabling the levels of modified DNA bases to be interrogated in tissues and fixed cells. To examine fluorescence, the authors utilized labeled tissue “phantoms” for quantification of microscopy fluorescence.



5. Ancient bodies

“Beyond ancient microbial DNA: nonnucleotidic biomolecules for paleomicrobiology” by Tran et al.

Understanding plagues and epidemics of the past requires detection of pathogens from buried individuals. The field is called paleomicrobiology, and this 2011 review examines the techniques used by researchers in this discipline to study the diseases of the dead.




6. Live Cells?

“Automated image analysis of Live/Dead staining of the fungus Aureobasidium pullulans on microscope slides and leaf surfaces” Nelson et al.

Live/Dead stains are common now, but this 2000 article by Nelson et al. took things a step further – the authors developed a program to make telling live cells from dead ones even simpler for scientists. Zombies beware.

7. Dead Cells?

“Spatial manipulation of cells and organelles using single electrode dielectrophoresis” by Graham et al.

Here, a simple dielectrophoretic device is described that can be used to locate and pick out single cells for replating. And just like the program from our number 6 entry, this device can tell the difference between a living and a dead cell since dying cells lose resistance to passive ion leakage. But what about zombie cells?


8. Suicide Vectors

“Conjugal vectors for cloning, expression, and insertional mutagenesis in Gram-negative bacteria” by Lauro et al.

Lauro et al. detail a design for conjugal suicide vectors that works in Gram negative bacteria. A multi-purpose system, the vectors can be used for cloning, mutagenesis, or expression studies.




9. Out from Darkness

“Using photoactivatable fluorescent protein Dendra2 to track protein movement” by Chudakov et al.

With a little light, photoactivatable fluorescent proteins can spring to life – from a dark state to a brightly fluorescent one. This 2007 article details how the Dendra2 fluorescent protein can be used in protein localization studies.


10. Monster Cloning

“Swapping of functional domains using a chimeric monster deletion mutagenesis strategy” by Yang and Zweib

Monsters, chimera, and swapping of functional domains --- I’m seeing geek Halloween heaven written on this one! Happy Halloween to all!

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Keywords:  Top Ten Halloween