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A Brief Interview with Dr. Blaine Fritz

A Brief Interview with Dr. Blaine Fritz

Chronic diseases like lower extremity wounds, which prevail in diabetic patients, are expensive to treat and cause reoccurring trauma to patients. Diabetic-related foot ulcers (DFUs) are also highly prone to infections, which increases the risk of hospital admission and amputation. Therefore, properly classifying infection severity in lower extremity ulcers is essential to guide appropriate treatment.

Presently, clinicians and researchers use subjective classification systems to stratify lower extremity ulcer infections for treatment and research. These classifications are based on guidelines that combine clinical data and wound observations. To better understand the relationship between infection severity and clinical classifications, a study by Fritz et al. (2022) focused on obtaining host and bacterial RNA sequences from infected human tissues using dual, host-pathogen RNA sequencing. The objective of this approach was to see whether these clinical classifications reflect the ulcer’s transcriptome. The results of the experiment (*SPOILER ALERT*) suggest that indeed stratification of infection status based on a transcriptomic fingerprint may be an objective method to categorize infection severity.

For more details results, you can read the full article here.

Now more on the scientist behind the research, Dr. Blaine Fritz (pictured on the right) is a post-doc working at the University of Copenhagen in the Department of Immunology and Microbiology. He is part of the Costeron Biofilm Center and has a background in studying host-pathogen interactions. We asked him a few questions to get to know more about him, his research and his motivation 😊.

1. What is it about bacteria that interests you the most?

The most interesting thing about bacteria, for me, is the huge role that they play in our everyday lives, which we are just beginning to discover. The advent of computational and molecular tools for understanding bacterial communities has allowed us a much deeper look into these microbial communities and their function.

  1. When did you start studying ulcer infections treatment and research?

I started studying bacterial infections in ulcers and various other diseases during my master and PhD work at the University of Copenhagen in 2014. Prior to that, I also worked with bacterial biofilms, but in an industrial rather than a clinical setting.

  1. How does RNA sequencing and thus gene expression in ulcer tissue and infecting bacteria help provide valuable information?

Our application of dual RNA sequencing allows an insight into physiology of both human cells and infecting bacteria as they are directly in an infection. This gives a picture of how the immune system responds to bacterial infection and vice versa.

  1. What is the direct impact your latest research findings will have on patients with chronic lower extremity wounds?

We hope that these results will help researchers and physicians understand the major factors of host response to bacterial infections during chronic ulcers. Though this is basic research, the methods and data are publically available for others to work further on this and eventually develop methods or targets for mitigating these chronic bacterial infections.

  1. What tools are key in your methodology?

Several things – including the preparation of the sample for RNA-sequencing and the bioinformatics processing of the data are essential for our methodology. For example, a high sequencing depth in combination with performing ribosomal RNA depletion (in this case we used a mix of 10:1 Human:Pan-Prokaryote riboPOOLs) rather than poly-A enrichment is a key step to obtaining also bacterial RNA sequences from infected human tissues.

  1. What fascinates you the most about your job?

What fascinates me most is the incorporation of advanced technologies for sequencing data in combination with our increased access to high-performance computing in order to solve complex biological problems and ultimately improve patient livelihood. I think that the application of these technologies and others are just beginning to be explored.

  1. If you would have not been a scientist, what other profession would you have chosen?

I think, had I not become a scientist, I would have become an engineer. I am also interested in music, so I also thought about becoming a sound engineer or a professional musician.

  1. What is the best career advice you have gotten?

I think one of the best pieces of advice to remember is that it is YOU who is the asset. Always remember that you possess specialized skills. So, remember that it is not what you can do for your employer, but rather what your employer can do for you in order to make your working life enjoyable. Never get stuck in a career which doesn’t make you happy!

Image: Biofilm aggregates in an infection (provided by Dr. Fritz).

The creation of the siFractor- an interview with Dr. Jan Medenbach

The creation of the siFractor- an interview with Dr. Jan Medenbach

siTOOLs latest device, the siFractor is a game changer for any application involving the fractionation of centrifugated samples. Its applications include isolation of protein complexes and RNPs, purification of extracellular vesicles and ribosome profiling (Ribo-Seq). We sat with the co-creator of the siFractor, Dr. Jan Medenbach and asked him how the siFractor works, its benefits and what led him to co-create this device.

  1. Could you tell us briefly about yourself

My name is Jan Medenbach.  I’m a Group Leader at the University of Regensburg in Bavaria, Germany and I’ve been working in RNA Biology for more than 20  years now.

  1. What is siFractor and what it is for?

It’s a device meant for fractionation of samples from ultra-centrifugation tubes so you basically insert your tube and the device itself is hooked up into a host system, an FPLC machine, which allows you to fractionate the sample from the tube and to monitor simultaneously different parameters such as UV absorption and conductivity of the sample. The whole system gives you utmost control about fractionation of the sample.

  1. What led you to co-create siFractor?

I was doing many ultra-centrifugation runs in the past and I wasn’t happy with the available equipment for fractionation. It was error prone and results were not very reproducible. The detectors were not very sensitive and essentially, I lost many samples which was very frustrating. So, I had to come up with a better solution.

  1. How does siFractor work?

The underlying principle is quite simple and it’s very old. A needle is used to pierce the ultra-centrifugation tube and to deliver a dense chase solution which will then displace your sample and push it through the FPLC machine for analysis and fractionation.

It can be hooked up to this whole system which gives you great control of over fractionation at the same time it’s meant to operate at higher pressure giving you high flow rates for fractionation so you can also save a lot of time while being able to monitor with very sensitive detectors your sample while it’s pushed through the machine.

5. Where can you find information on the siFractor?

For more information you can visit the siTOOLs Biotech website. 

🎥: To watch the video of the interview visit our YouTube channel.

siTOOLs Biotech sponsors Argonautes Conference 2022

siTOOLs Biotech sponsors Argonautes Conference 2022

MUNICH, GERMANY – siTOOLs Biotech GmbH, a young, research-driven biotech company based in Munich/Martinsried and rapidly growing in the field of functional genomics and Next-Generation RNA sequencing, today announced its support for the upcoming Argonautes Conference 2022 at University of Regensburg as lead sponsor.

The conference, organized by Prof. Gunter Meister from University of Regensburg, and Prof. Martin Simard of CHU de Québec-Université Laval Research Center, will be held from 24th to 27th August 2022.

The conference’s scientific program will focus on Argonaute, the core protein of the RNAi mechanism: and how mutations in the Argonaute gene can lead to rare genetic disorders.  The program starts with sessions dedicated to the diverse roles of prokaryotic Argonaute proteins (pAgo), and the functions of Argonaute in plants. It will then move to new insights in the structure of Argonaute proteins, touch on the role of Argonaute in the silencing of transposable elements and show how Argonaute is involved in animal development. The conference will finally come to the 4 human Argonaute proteins and their role in disease.

Andrew Walsh, bioinformatician at siTOOLs Biotech is one of the confirmed speakers of the event. He will show how large-scale RNAi screening datasets can be used to study the molecular behavior of human Argonaute proteins. Other highlights include a keynote lecture by Dr. Leslie Gordon, who drove the development of a treatment for a rare disease Progeria, and a panel with affected families sharing their experiences.

“We are excited to sponsor the Argonautes Conference,” said Michael Hannus, Founder and Managing Director of siTOOLs Biotech. “As an RNA company, our mission has always been to support and facilitate RNA research to help accelerate scientific breakthroughs. We are sponsoring this conference to promote the research and drive awareness of Argonaute related diseases. Hopefully the conference can contribute to finding solutions for the life of children and families impacted by AGO2 (Lessel-Kreienkamp/Leskres) syndrome.”

Are you doing RNAi research, arrayed RNAi screens, or CRISP validations?

Come by and ask us any questions regarding your experimental setup, methods or bioinformatics analysis.

Connect with us through this link to receive updates and meeting opportunities for siTOOLs Biotech at the conference. We will be setting up a booth at this event where you can meet our team of scientists!


Featured image: Regensburg, from mojolo/Adobe Stock

A brief interview with Dr. Mar Martinez Pastor

A brief interview with Dr. Mar Martinez Pastor

Dr. Mar Martinez Pastor is a microbiologist from Valencia, who currently works as a senior Research Scientist in the Schmid Lab (leader Dr. Amy Schmid) at Duke University. She is a specialist in microbial response to abiotic stress. At the Schmid lab her research is focused on the transcriptional regulation of iron homeostasis in halophilic archaea.

Halophilic archaea are salt-loving archaea, which can be found in hypersaline environments like the colorful salt pond pictured above in San Francisco Bay, California. Because halophilic archaea thrive in environments of extreme pH, temperature and salinity they are considered extremophiles. As the name suggests, studying how they cope under extreme conditions can also be extremely tricky and never boring.

In hypersaline environments iron availability can rapidly fluctuate. Thus, how different species of halophilic archaea control iron homeostasis relies on the role of certain transcription factors from the DtxR family that regulate the expression of hundreds of genes to facilitate the adaptation (Martinez-Pastor et al., 2017). To have an insight of the archaeal transcriptome changes as a consequence of the stress response, proper sequence coverage of mRNA is necessary. However, in prokaryotes the high rRNA:mRNA content (80-90% : ~10%) has been an obstacle in obtaining the desired information about the mRNA sequences.

In her latest article, Dr. Martinez compares and tests the efficiency of rRNA removal kits in the hopes of obtaining the “cleanest” mRNA sequences. Her results show the ribosome depletion kit from siTOOLs Biotech: Pan-Archaea riboPOOL was able to efficiently deplete >90 % of rRNA among Halobacterium salinarum (pictured left, image provided by Dr. Martinez), Haloferax mediterranei and Haloarcula hispanica. Likewise, the custom-design riboPOOL for the species Haloferax volcanii was highly successful in rRNA depletion (Martinez Pastor et al., 2022). 

In conclusion, we could say it’s the ideal time to study transcriptomics in extremophiles like salt-loving archaea. ??

Our Pan-Archaea riboPOOLs are ready, efficient and pleased to help “break” through the bottleneck in the study of genome-scale gene expression in archaea. We can’t wait to read what Dr. Martinez and her colleagues will find out next.

Lastly, besides learning about Dr. Martinez research we wanted to know more about her journey in science, her hobbies and what she enjoys. So here it goes:

Six questions for Mar (which means sea ? in Spanish):

1. What is the most interesting part of studying archaea?

Archaea are ancient microorganisms that colonize all kind of environments, from the most common to the weirdest. By shape and structure, they look like bacteria; however, there are some other features as the transcriptional machinery, that resembles to a simpler version of Eukaryotes. And even more, other traits make them to be unique (as their cell membrane structure). Using Archaea as a model organism makes me feel that I am studying the midpoint of life, and any discovery could be pointing in any direction, could explain evolution and adaptation, could be giving us insight from the past and lightening the future!

2. What is the most challenging part of studying iron homeostasis in halophilic archaeal species?

There is not a “starting point”! I started my scientific career investigating with the yeast Saccharomyces cerevisiae as a model organism, and every hypothesis was based on the bibliography, however, working with iron imbalance adaptation in Archaea I realized that different species, even those that are closely related, behave differently in response to iron stress! Also, I had to face many experiments that weren’t previously described in the bibliography (as for siderophore detection or for using kits as riboPOOLs for the first time!)

3. What drew you to study iron homeostasis?

I have been always curious to know more about how cells respond to abiotic stress. I am so thrilled to unravel the mechanism by which cells detect a change in the environment and trigger an adaptative response.

4. How important is it to have a mentor, and what advice do you give young scientist which are part of a lab that is not as supportive?

I was very lucky to join the Schmid lab. Dr. Schmid provides all the tools to learn science from different sides (wet biology, system biology, bioinformatics…), she is supportive and gives us plenty of opportunities to teach, to present our work in conferences and meetings, to attend courses and complement our formation, in summary, to grow as a complete scientist. Young scientists have more needs beyond learning technics. A mentor should be a model. My advice for young scientist is to learn as much as they can from their current mentor, but if this is not enough, to rush looking for the next one to learn from.

5. What would you do if you had more time?

In lab, long term experiments: growing cells for longer periods in changing conditions and check what transcriptional mechanisms they use to adapt. In life, I would like to get back to activities that I abandoned, or I do now with limited time. I would like to read novels, walk the dog or go swimming without thinking that every single minute that I am spending on a hobby is stolen from a “more important” activity!

6. Which is your favorite place in the world?



Featured image: Salt ponds with pink colored Haloarchaea on the edge of San Francisco Bay, California; photo by Kenneth Lu, 2013 available through Flickr.


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