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Recent Articles

Picking The Right Functional Imaging Probe

Picking The Right Functional Imaging Probe

By: Heather Brown-Harding, PhD

As biologists, we study the process of life, however, it’s intricacies cannot be captured by a snapshot in time. Generally, the easiest imaging experiments are those where the samples are stained, fixed, and imaged within a few days of procurement, but that too doesn’t capture the dynamic processes common in cells and organisms. Live cell imaging when combined with reporters serves as a powerful tool to provide solid imaging data. Cameleon —one of the first reporters— was developed in 1997 in Roger Tsien’s lab.  Cameleon is a green fluorescent protein (GFP) that undergoes a conformational change in the presence of…

Essential Concepts in Gene Prediction and Annotation

Essential Concepts in Gene Prediction and Annotation

By: Deepak Kumar, PhD

After genome assembly (covered in my previous blog) comes the vital step of gene prediction and annotation. This step entails the prediction of all the genes present in the assembled genome and to provide efficient functional annotation to these genes from the data available in diverse public repositories; such as Protein Family (PFAM), SuperFamily, Conserved Domain Database (CDD), TIGRFAM, PROSITE, CATH, SCOP, and other protein domain databases. It is imperative to understand that prediction and annotation of non-protein-coding genes, Untranslated Regions (UTR), and tRNA are as vital as protein-coding genes to determine the overall genetic constitution of the assembled genome. …

Brightness Is In The Eye Of The Detector - What To Consider When Designing Your Panel

Brightness Is In The Eye Of The Detector - What To Consider When Designing Your Panel

By: Tim Bushnell, PhD

The heart and soul of the flow cytometry experiment is the ‘panel.’ The unique combinations of antibodies, antigens, fluorochromes, and other reagents are central to identifying the cells of interest and extracting the data necessary to answer the question at hand. Designing the right panel for flow cytometry is essential for detecting different modalities. The more parameters that can be interrogated will yield more information about the target cells. Current instruments can measure as many as 40 different parameters simultaneously. This is exciting, as it allows for more complex questions to be studied. Panel design is also valuable for precious samples,…

7 Key Image Analysis Terms For New Microscopist

7 Key Image Analysis Terms For New Microscopist

By: Heather Brown-Harding, PhD

As scientists, we need to perform image analysis after we’ve acquired images in the microscope, otherwise, we have just a pretty picture and not data. The vocabulary for image processing and analysis can be a little intimidating to those new to the field. Therefore, in this blog, I’m going to break down 7 terms that are key when post-processing of images. 1. RGB Image Images acquired during microscopy can be grouped into two main categories. Either monochrome (that can be multichannel) or “RGB.” RGB stands for red, green, blue – the primary colors of light. The cameras in our phones…

5 Essential Concepts In Genome Assembly From NGS data

5 Essential Concepts In Genome Assembly From NGS data

By: Deepak Kumar, PhD

The main goal for researchers, clinicians, and students who perform Next Generation Sequencing (NGS) and produce sequenced data for diverse projects involving human samples is to find biomarkers or variants to make diagnoses; and deduce the genetic anomalies that could be responsible for the disease they are conducting research on. Most projects (academic or non-academic) constitute the prior ideology on deciphering the “unknown.” There are well-versed computational protocols and pipelines formulated by labs across the world in determining what the “unknown” variants are. The fact that we have the “reference” human genome available – thanks to the Human Genome Project – plays…

Tools to Improve Your Panel Design – Determining Antigen Density

Tools to Improve Your Panel Design – Determining Antigen Density

By: Tim Bushnell, PhD

When a researcher chooses to use flow cytometry to answer a scientific question, they first have to build a polychromatic panel that will take advantage of the power of the technology and experimental design. When we set up to use flow cytometry to answer a scientific question, we have to design a polychromatic panel that will allow us to identify the cells of interest – the target of the research.  To identify these cells, we need to build a panel that takes advantage of the relative brightness of the fluorochromes, the expression level of the different proteins on the cell,…

The 5 Essentials To Successful Spectral Unmixing

The 5 Essentials To Successful Spectral Unmixing

By: Heather Brown-Harding, PhD

In an ideal world, we would be able to use fluorophores that don’t have any overlap in emission spectra and autofluorescence wouldn’t obscure your signal. Unfortunately, we don’t live in such a world and often have to use two closely related dyes – or contend with fluorescent molecules that are innately part of our sample. Fluorescent molecules include chlorophyll, collagen, NADPH, and vitamin A.  One example that I recently encountered was developing a new probe for lipids. The reviewers requested a direct comparison of the new dye to Nile Red in the same sample. Both dyes would localize to the…

The Essential Dos and Don'ts of NGS (Next Generation Sequencing)

The Essential Dos and Don'ts of NGS (Next Generation Sequencing)

By: Deepak Kumar, PhD

Next Generation Sequencing (NGS) is a rapidly evolving and widely used method worldwide in both academic and non-academic settings. One of the most valuable aspects of NGS is producing millions of sequenced reads with diverse read lengths from small amounts of input DNA. NGS methods are extremely versatile; producing reads as short as 75 bp, as seen in SOLiD sequencing, to long reads ranging upwards of 1000bp in the case of Pyrosequencing.  Both long and short reads fill a unique niche for researchers. Longer reads generated from NGS are excellent for genomic rearrangement and genome assembly projects; especially when there…

The 5 Fundamental Methods For Imaging Nucleic Acids

The 5 Fundamental Methods For Imaging Nucleic Acids

By: Heather Brown-Harding, PhD

There are 4 major ways to sort cells. The first way can use magnetic beads coupled to antibodies and pass the cells through a magnetic field. The labeled cells will stick, and the unlabeled cells will remain in the supernatant. The second way is to use some sort of mechanical force like a flapper or air stream that separates the target cells from the bulk population. The third way is the recently introduced microfluidics sorter, which uses microfluidics channels to isolate the target cells. The last method, which is the most common––based on Fuwyler’s work––is the electrostatic cell sorter. This blog will focus on recommendations for electrostatic sorters.

This Is How Full Spectrum Cytometry Works

This Is How Full Spectrum Cytometry Works

By: Tim Bushnell, PhD

There are 4 major ways to sort cells. The first way can use magnetic beads coupled to antibodies and pass the cells through a magnetic field. The labeled cells will stick, and the unlabeled cells will remain in the supernatant. The second way is to use some sort of mechanical force like a flapper or air stream that separates the target cells from the bulk population. The third way is the recently introduced microfluidics sorter, which uses microfluidics channels to isolate the target cells. The last method, which is the most common––based on Fuwyler’s work––is the electrostatic cell sorter. This blog will focus on recommendations for electrostatic sorters.

My Proven 5-Point Fast Track To A Career In Flow

My Proven 5-Point Fast Track To A Career In Flow

By: Tim Bushnell, PhD

There are 4 major ways to sort cells. The first way can use magnetic beads coupled to antibodies and pass the cells through a magnetic field. The labeled cells will stick, and the unlabeled cells will remain in the supernatant. The second way is to use some sort of mechanical force like a flapper or air stream that separates the target cells from the bulk population. The third way is the recently introduced microfluidics sorter, which uses microfluidics channels to isolate the target cells. The last method, which is the most common––based on Fuwyler’s work––is the electrostatic cell sorter. This blog will focus on recommendations for electrostatic sorters.

Up Your Stain Game With These 7 Non-Fluorescent Histology Dyes

Up Your Stain Game With These 7 Non-Fluorescent Histology Dyes

By: Heather Brown-Harding, PhD

There are 4 major ways to sort cells. The first way can use magnetic beads coupled to antibodies and pass the cells through a magnetic field. The labeled cells will stick, and the unlabeled cells will remain in the supernatant. The second way is to use some sort of mechanical force like a flapper or air stream that separates the target cells from the bulk population. The third way is the recently introduced microfluidics sorter, which uses microfluidics channels to isolate the target cells. The last method, which is the most common––based on Fuwyler’s work––is the electrostatic cell sorter. This blog will focus on recommendations for electrostatic sorters.

Top Technical Training eBooks

Get the Advanced Microscopy eBook

Get the Advanced Microscopy eBook

Heather Brown-Harding, PhD

Learn the best practices and advanced techniques across the diverse fields of microscopy, including instrumentation, experimental setup, image analysis, figure preparation, and more.

Get The Free Modern Flow Cytometry eBook

Get The Free Modern Flow Cytometry eBook

Tim Bushnell, PhD

Learn the best practices of flow cytometry experimentation, data analysis, figure preparation, antibody panel design, instrumentation and more.

Get The Free 4-10 Compensation eBook

Get The Free 4-10 Compensation eBook

Tim Bushnell, PhD

Advanced 4-10 Color Compensation, Learn strategies for designing advanced antibody compensation panels and how to use your compensation matrix to analyze your experimental data.