Want to see more videos like this? View our collection of customer interviews here.

Our first interview is with Dr. Xiao-Ning Zhang at St. Bonaventure University. Watch the video below to learn about Dr. Zhang’s RNA splicing research, and hear how her lab uses DNASTAR Lasergene for genomics, transcriptomics, and structural biology. Then check out our full collection of customer interviews here!

Microscopic view of the Ebola virus

The Ebola epidemic in West Africa has proven to be a devastating reminder that humans as a race are not immortal- we are not exempt from catastrophic biological diseases capable of wiping out entire villages.

In 2014 Kent Brantly and Nancy Writebol were helping patients in Liberia when the two Americans were infected with Ebola. That is where Dr. Michael Pauly and Mapp Biopharmaceutical, Inc. stepped in with ZMapp™. ZMapp™ is an experimental drug for treating Ebola, which at the time, had only been tested on animals. With no better alternative, Brantly and Writebol were given the drug cocktail, comprised of three antibodies. Both patients recovered fully after the drug was given. Today, ZMapp™ is in clinical trials in West Africa.

I sat down with Dr. Michael Pauly to learn more about this experimental drug, his company’s response to the Ebola epidemic, and his experience using DNASTAR software.

Tell us a bit about your recent work with ZMapp™:

A series of events came together, in terms of our development and the current outbreak. We joined forces with a group in Canada screening combinations of antibodies and generated some good animal data.  One of the antibody combinations appeared to be unusually efficacious in animal trialing. It was quite an unusual event that all happened about a year ago, coincident with the increase of this outbreak.

How exactly does ZMapp™ work to fight the virus?

A lot of information is still being found out. The three antibodies in ZMapp™ interact directly with the virus. The degree to which they interact with different epitopes or proteins on the surface of that virus, and exactly how they interact, whether they are directly neutralizing, or whether they enhance the secondary immune response that people have, is still unclear. Something we’ve seen in the primate data, and something so interesting about cocktails, is that by themselves, the individual antibodies don’t show anywhere near the kind of effectiveness that they do in combination. The whole idea of antibody cocktails has really been bolstered as a part of this result.

What was it like to be involved with the Ebola crisis? It’s been very dramatic, as you said, and pretty devastating.

Ultimately for most everybody, it’s just tremendously motivating. Nobody has any trouble working all day and all night when faced with those sorts of issues. You’re just trying to make an effective product and that part makes your work life and the rest of your life pretty simple. Your work becomes very personal and in that way, quite meaningful. It gives everybody an extra added boost to work hard and make something that works.

What are some of the unique challenges you face in your work?

We are always trying to relate antibody structure to function, and we spend a lot of time trying to figure out what makes an antibody express well or perhaps not so well. Another set of challenges is related to speed and throughput. We’re screening a lot of antibodies and reagents, and anything we can do to increase that throughput and, in the case of DNASTAR software, anything we can do to more effectively model and screen a sequence in order to understand structure function is helpful.

How does DNASTAR software help you with those challenges?

We use the DNA side of your software all the time. We use it daily for DNA analysis. We have our own particular database of all the sequences we’ve made, and almost all the protein sequence that we currently use is in DNASTAR- based format.

For a long time scientists just made antibodies in cell lines without knowing what the sequences were; they just purified the antibodies and used them as reagents. There are still cell lines going back ten years or more that are making good antibodies, but people don’t know the sequences of them. We sequence cell lines that express antibodies we don’t know the sequence of, so we use degenerate primer pools to try to retrieve the antibodies that are being expressed by the cell line. We use SeqMan Pro to assemble traces, make contigs, and try to find what look to be antibody sequences that are being expressed by various cell lines.

Another thing we have always appreciated is DNASTAR has good support. You can call somebody and get help easily.

Would you like to see your organization featured on the DNASTAR Blog? Contact thomase@dnastar.com to schedule an interview. We love learning about the important work of our customers!

Tell us about your work!

I work at the Stored Product Insects and Engineering Research Unit at the ARS Center for Grain and Animal Health Research, Manhattan, KS. Our mission is to find better, safer ways to control insect pests found in and around food storage areas, including grain storage and processing facilities and warehouses. I use a functional genomics approach to identify vulnerabilities in stored product pests that can be exploited for the development of control products based on biological pesticides (proteins, RNAi, etc). Our primary focus is on coleopteran storage pests, including the red flour beetle (the genetic model for coleopterans), yellow mealworm (a biochemical model), and lesser grain borer. We have a sequenced genome for the red flour beetle, and we are working with Australian collaborators to sequence the lesser grain borer genome. We have transcriptome projects in all three insects. Our challenges have been how to store, transfer, and analyze data with minimal resources.

How has DNASTAR software helped you?

 We’ve developed a computer infrastructure based on in-house MacPros and iPlant for data storage and transfer (and some analysis programs). However, our workhorses have been ArrayStar for transcriptome analysis (differential gene expression), and Lasergene Genomics Suite for genome assembly. We’ve also used MegAlign for evolutionary analysis and Lasergene’s Structural Biology Suite for tertiary structure predictions of proteins lacking a crystal structure. We find that the customer support is unparalleled and has been critical in designing workflows and working within our existing computer infrastructure.

What does DNASTAR software do best, in your opinion?

 As I said, ArrayStar has been instrumental in providing detailed analysis of differentially expressed genes in a transcriptome analysis. With minimal effort, the output immediately provides you with scatter graphs, tables, and statistical analysis, and options of such features like Venn diagrams and heatmaps, all publication quality. I was able to analyze a dataset and compare it to an analysis by a bioinformaticist and determine that genes of interest were not included in the latter analysis. Basically I know what I am looking for and can vary the parameters to more accurately reflect the biological processes in the insect. We’ve also found that SeqMan NGen, the assembler in Lasergene, provides better assemblies with data from some platforms, including Ion Torrent PGM.

Can you speak to DNASTAR’s support for you and your work?

 The technical support is instrumental to our success in analyzing transcriptome and genomic data. In the beginning we needed more support in project design, “tweaking” analysis, or data interpretation. For example, with assembly projects, we match our data to the amount of RAM and processors; sometimes it is necessary to either split data into multiple files, or prefilter using ArrayStar (Thank you Matt, who taught me how to do this). Now, we share that information with other lab members and colleagues. We find that support is quick, usually the same day.

Is there anything else you’d like to share?

Without DNASTAR, we would not have been able to progress in the analysis of our high throughput sequencing data. Resources for bioinformatics are not yet available through ARS. We have purchased multiple licenses and usually have them fully engaged. Thank you for this valuable resource!

Tell us about your work! What are your research goals?

Currently, I am working on identifying the molecular mechanisms causing male infertility in Cstf2t knockout animals. The Cstf2t gene encodes τCstF-64 that is a testis-expressed paralog of CstF-64. CstF-64 is a polyadenylation protein that stimulates the cleavage of nascent mRNAs and the subsequent polyadenylation of the upstream cleavage product. τCstF-64 participates in the cleavage and polyadenylation of the mRNAs during spermatogenesis, while CstF-64 expression is meiotically inactivated.

What kinds of data are you working with?

In our laboratory, we use several high-throughput sequencing techniques: RNA-seq, A-seq, and CLIP-seq.

What are some data analysis challenges you face?

The biggest challenge working with next-generation sequencing data is the amount of data. Even the latest hardware of a stand-alone computer has trouble processing the data in a reasonable time (less then an hour). However, huge progress in this regard has been made in the past several years. Another challenge is the integration of the various data sets in a meaningful biologically relevant model.

How has DNASTAR software helped you?

DNASTAR offers a user-friendly interface, relative short time of data processing for RNA-seq data sets using SeqMan NGen and ArrayStar, and customizable gene list searches.

What does DNASTAR software do best, in your opinion?

I have been using DNASTAR software packages since the beginning of my scientific carrier. Definitely, the best part of the DNASTAR applications is how user-friendly they are.

Can you speak to DNASTAR’s support for you and your work?

DNASTAR support team is always available with specific answers to all of my questions.

Tell us about your work!

My research has primarily focused on the molecular and cellular biology mechanisms of rare pediatric diseases, neuroinflammatory pain and neuromuscular development. Quantifying mRNA expression levels across a broad range of genes has been a critical component within my projects. I use the Lasergene software to optimize everything from primer selection to analysis of our sequence data. The biggest challenges are linking the species-specific genetic and protein information to various pathways.

How has DNASTAR software helped you?

The Lasergene software has really helped us with our bioinformatic-driven projects. We are constantly exploring both novel drug targets and working to gain a better understanding of current targets of interest. Particularly when working on physiological and pharmacology experiments, we need to have a high degree of confidence in our molecular work. The Lasergene software gives that to us, especially with gene sequence and protein analysis.

What does DNASTAR software do best, in your opinion?

Data analysis, especially with sequence alignment and working with results from the sequencer. I have also come to appreciate the flexibility of the software with primer design. I have also recently started working with Protean 3D and find it to be extremely helpful with understanding poorly published proteins of interest.

Can you speak to DNASTAR’s support for you and your work?

While at the Medical College of Wisconsin I managed a large departmental network because of my familiarity with the program. While things typically ran smoothly, any questions I had were answered same-day, which made my work incredibly easy.

Tell us about your work!

Currently, we do a lot work in Africa with specific focus on Mycobacterium tuberculosis (MTB) detection and next-generation sequencing (NGS). We develop molecular reagents and products that simplify and enhance molecular detection from the point of sample collection, detection, and DNA sequencing. We also do work with influenza viruses and have recently done some whole-genome MRSA sequencing as well.

How has DNASTAR software helped you with your research goals?

In 1999, I established the U.S. Air Force’s molecular influenza strain surveillance program and was first introduced to DNASTAR by the CDC. Since then, I’ve never let go. I prefer DNASTAR over other bioinformatics software because it’s so simple to use. I have observed and participated in the evolution and maturation of DNASTAR software from simple gene alignments of DNA off automated slab gel sequencers to today’s cutting edge, multimillion read NGS assemblies! DNASTAR continues to mature alongside rapid advances in sequencing technologies.

What does DNASTAR software do best, in your opinion?

Since we do a lot of barcoding/indexing of patient isolate samples, I like the ease with which I can perform a multi-patient analysis within a single SeqMan NGen assembly-the software enables you to quickly switch within barcoded/indexed patients. I also like that with SeqMan NGen I can quickly input a reference gene or gene panel of interest against a full genomic library file to quickly assess for mutations in genes of interest. Sometimes you just want to look at specific genes and you don’t always need/want the hassle of dealing with an entire 4.2 million bp MTB genome!

Can you speak to DNASTAR’s support for you and your work?

The DNASTAR team works closely with Life Technologies and Illumina to simplify the analysis of NGS data for the everyday scientist. Most scientists are good at empirical experimentation and molecular biology testing but a bit intimidated by the size of raw data output and the bioinformatics aspects of NGS. DNASTAR bridges the gap between 2-3 gigabytes of raw NGS sequence data and a thorough genetic analysis containing graphical alignments, mutational reports, and phylogenies.   For example, from incredibly large raw MiSeq data files containing 24 indexed MTB genomes I can easily use the tools in DNASTAR to assemble contigs and analyze TB isolates for mutations in antibiotic resistance genes. From here it’s simple to generate SNP reports, multiple sequence alignments, and phylogenetic trees.

Is there anything else you’d like to share with us?

When I get into trouble I find it easy to contact DNASTAR technical support. Matthew Keyser and his team are always available for troubleshooting and resolving user issues.