Author: Laura Leiva

A Brief Interview with Patrick Hörner on Malaria and insecticide resistance

A Brief Interview with Patrick Hörner on Malaria and insecticide resistance

Malaria, a devastating disease that has plagued humanity for centuries, continues to take a heavy toll on vulnerable populations worldwide. Caused by the Plasmodium parasite, this disease is primarily transmitted through the bites of infected female Anopheles mosquitos. Malaria exacts a staggering toll, particularly in sub-Saharan Africa, where it remains a leading cause of morbidity and mortality. Its symptoms, which range from high fevers to severe anemia, can incapacitate individuals and, if left untreated, can be fatal.

One of the major obstacles to eradicating this global health threat lies in the growing problem of insecticide resistance among its primary vectors, particularly the Anopheles mosquitos. These resilient insects have evolved to withstand the very agents intended to control them. In Anopheles gambiae, resistance to insecticides arises through a complex interplay of five distinct mechanisms: 1) behavioral shifts, such as alterations in host-seeking behavior; 2) cuticle thickening, which fortifies the mosquito’s exoskeleton; and at a molecular level, 3) alterations to target sites, 4) detoxification processes, and 5) insecticide binding.

However, amidst these challenges, researchers like Patrick Hörner, a PhD student at Dr. Victoria Ingham’s lab in the Heidelberg University Hospital focus on investigating the impact of insecticide resistance phenotype on Plasmodium development in vivo.

Patrick Hörner, PhD student at the Heidelberg University Hospital

For his research, Patrick uses a combination of bioinformatics and molecular biology (e.g. RNAi) to identify the pathways and genes that influence vector competence and insecticide resistance status. To gain deeper insight into Patrick’s PhD research project, his motivations, the challenges he faces, and his aspirations in the global fight against malaria, we had the opportunity to interview him:

What initially sparked your interest in studying malaria and its vector mosquitos?

I have always been aware that malaria is a devastating disease and responsible for the death of many people, especially children in Africa. What triggered me to do my PhD in that field was actually a field trip to Namibia during my masters in 2019 though. I always had the urge to help people in some kind of way and I’m fascinated by the lifestyle of parasites, in particular in the interaction with their host species. So I did my master’s thesis project on the dog tapeworm Echinococcus granulosus at the University of Hohenheim and had the privilege to collect field samples in Namibia. When we collected our samples during the trip in this beautiful country, we were fortunate to get to know many very nice people in small villages in the so-called Caprivi strip in the north of the country. While we explained our research aims, most people only answered by asking in turn why we’re not researching malaria and they told us many stories about their encounters with the disease. You could really sense that malaria is one of the biggest threats they face.

Could you briefly tell us about your PhD research project?

My project deals with the problem of insecticide resistance of African malaria vectors and how we could overcome this major obstacle for the elimination of the disease. I’m particularly focusing on one major mechanism, that we think is related to resistance to insecticides and in the immune response against Plasmodium parasites. We try to find solutions on how we can manipulate mosquitos to either circumvent resistance or even tackle the malaria parasite inside the mosquito vector. The advantage of targeting the mosquito stages of Plasmodium has the advantage that they harbor the parasite’s life cycle stages where the lowest numbers are present, which is called the bottleneck.

Some of the techniques you use are RNAi, what are some challenges or limitations you’ve encountered while working with RNAi in mosquitos?

We are using RNAi to knock specific genes down in the mosquito by either injecting long dsRNAs or since the start of our collaboration with siTOOLs also siRNAs pools (siPOOLs). We look at how such knockdowns affect the development of the malaria parasites or the resistance status of the vector itself. Obviously, the first challenge is always to keep the mosquitos alive when you puncture them with a needle and inject the RNA into their thorax. That means you have to be very cautious and do a lot of practice sessions before you can actually do the experiments. The second obstacle is that you need a very high concentration of your RNA to effectively knock the genes down when you use “naked” RNA as we usually do, because a lot of it gets degraded before reaching the target.

How does your research on Anopheles gambiae tie into broader malaria control and prevention strategies?

Our research focuses on helping to improve vector control tools that are applied in field settings, like insecticide-treated bednets or new up-and-coming tools e.g. attractive targeted sugar baits. We also test the efficacy of currently used substances on such tools against mosquitos and parasites, especially the widely used pyrethroid insecticides. These insecticides have been causing widespread resistance in sub-Saharan Africa but are still applied on all insecticide-treated bednets, due to a lack of alternatives.

Are there any particular milestones or breakthroughs you’re aiming for in the near future within your research area?

I guess as a scientist you’re always aiming for breakthroughs but in the end, it’s very hard to define what that actually means. Probably there won’t be one specific breakthrough that eliminates malaria in the near future, as this parasite is very complex and adapts quickly. We’re always aiming to contribute to the pool of knowledge and tools in the fight against the disease because only the interplay of all existing measures, like vaccines, drugs, and vector control have a chance to keep the disease in check and eventually reach the common goal of eradication.

What precautions do you take when working with mosquitos?

When you’re doing experiments on uninfected mosquitos, we normally knock them down on ice first, so they can’t fly away. Of course, you get bitten here and there but that is just the nature of the work. It gets obviously trickier when you work with malaria-infected mosquitos. In this case, we have to keep them in a BSL-3 lab in humidified incubators and sort the ones we need for our experiments out, and kill them right away in a secured glass glove box. When you take those out of the BSL-3 you carry them in a sealed tube and inactivate the parasites at -80°C before you start your experiments.

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

Although I’ve been playing and coaching soccer for my whole life, I’m an even bigger American football fan and an exchange semester to Penn State University during my bachelor’s only increased my love for the game. I would have always liked to go into coaching there, because of the high complexity of the game with endless individual and team tactics and techniques to explore for your team.


Working with mosquitos? We have reagents for RNA inteference (siPOOLs) as well as ribosomal RNA removal kits (riboPOOLs) for Aedes albopictus and Anopheles gambiae.  Request a quote here.

Image: Anopheles gambiae mosquitos (provided by Patrick Hörner).

Our Team’s Favorite RNA Molecules🧬

Our Team’s Favorite RNA Molecules🧬

At siTOOLs we are celebrating RNA day (Aug. 1st) the entire month with a focus on all things RNA and a promotion on siPOOLs and riboPOOLs.

RNA day is celebrated the 1st of August, since the RNA codon that initiates protein synthesis is made of the following nucleotides: adenine (A), uracil (U), and guanine (G). AUG codes for the amino acid methionine (Met) in eukaryotes and formyl methionine (fMet) in prokaryotes.

RNA is one of the most versatile biomolecules in existence and the focus of siTOOLs research, so we asked the siTOOLs team which is their favorite RNA molecule.✨

1. Dr. Michael Hannus – Founder and Managing Director:

2. Dr. Nicola Conci – RNA-Seq Specialist & Bioinformatician:

3. Matthias Weiss- Head of Production:

4. Kevin Wobedo – Scientific Sales & Marketing:

5. Dr. Laura Leiva – Scientific Marketing:

6. Jessie Midgley – Junior Sales Manager:

A journey into the gut microbial control center: small RNA’s influence on Bacteroides thetaiotaomicron’s metabolism

A journey into the gut microbial control center: small RNA’s influence on Bacteroides thetaiotaomicron’s metabolism

The gut model organism Bacteroides thetaiotaomicron

Bacteroides thetaiotaomicron is a commensal bacterium that inhabits primarily the human large intestine and is considered one of the most important members of this microbial community. B. thetaiotaomicron is a highly versatile microbe, capable of utilizing a wide range of carbohydrates including those that are indigestible by human enzymes. It breaks down complex polysaccharides from plant cell walls and other dietary sources, producing short-chain fatty acids (SCFAs) that are an important energy source for humans. Furthermore, it has also been shown to play a crucial role in our immune system development, through the production of regulatory T-cells that help prevent autoimmune disorders.

It’s no wonder Bacteroides thetaiotaomicron has been chosen as a model representative of the gut microbiota. B. thetaiotaomicron is widely spread in human populations and relatively easy to grow and study under laboratory conditions. In a study by Ryan et al. (2020), differential RNA sequencing (dRNA-Seq) was used to generate a single-nucleotide resolution transcriptome map of B. thetaiotaomicron. High-resolution RNA-sequencing served as a tool to explore the role of small RNA molecules in regulating metabolism in the gut bacterium Bacteroides thetaiotaomicron.

By comparing different laboratory growth conditions, the researchers identified various small RNA molecules that exhibited differential expression patterns. These small RNAs were found to be associated with the regulation of key metabolic pathways in the bacterium. The authors suggest that these findings could have implications for understanding the interactions between gut microbes and the host and for the development of new therapies for metabolic diseases. Overall, the study highlights the importance of transcriptome mapping in uncovering novel regulatory mechanisms in bacterial metabolism. Furthermore, the results shed light on the intricate regulatory networks within this gut microbe and provide insights into its adaptation to different nutrient environments.

Note: Our Pan-Prokaryote riboPOOL played a small but significant role in this study. Prior to RNA sequencing, the Pan-Prokaryote riboPOOLs kit was used for ribosomal RNA depletion. Our Pan-riboPOOLs are a versatile solution that allows for simple mono- and multitranscriptomic studies using a single-step rRNA depletion for a phylogenetic group (e.g., bacteria, fungi, or mammals).

A Brief Interview with Dr. Daniel Ryan

Dr. Daniel Ryan, postdoc at the Helmholtz Institute for RNA-based Infection Research

We interviewed the first author of the study: “A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron”. Dr. Daniel Ryan is a postdoc at the Helmholtz Institute for RNA-based Infection Research located in Würzburg, Germany. He is a member of the Westermann Lab and his research focuses on non-coding RNAs and RNA-binding proteins in the human gut commensal Bacteroides thetaiotaomicron.

He further explained the process of generating a high-resolution transcriptome for Bacteroides thetaiotaomicron and the exciting parts of being an RNA research scientist.

  1. Can you briefly explain the main findings of your research and what motivated you to study small RNA regulation in Bacteroides thetaiotaomicron?

The gut microbiota has recently attracted significant attention from the scientific community due to its impact on human health and physiology. Various diseases, including inflammatory bowel disease (IBD), diabetes, colon cancer, and depression, have been linked to an imbalanced microbiota, also known as dysbiosis. Furthermore, a healthy gut microbiota plays a crucial role in preventing invasive pathogens from gaining a foothold and establishing infections. My research at the Westermann Lab aims to understand the diverse interactions between gut microbes and their host. To achieve this goal, we utilize the gut model organism Bacteroides thetaiotaomicron (B. theta), an anaerobic, non-spore forming predominant member of the healthy gut microbiota.

My foray into small RNA biology started during my Master’s thesis work at the KU Leuven, Belgium where I investigated the regulatory networks of sRNAs in E. coli. I came to appreciate the immense regulatory potential of these non-coding molecules in governing rapid responses to diverse environmental cues. A few years later, during my PhD research at KIIT University, India, I had the opportunity to delve into the roles of sRNAs in regulating acid stress survival and virulence programs in Salmonella, the pathogen responsible for causing typhoid. Having gained extensive experience in studying sRNAs and their intricate regulatory networks, I shifted gears to the gut microbiota as the focus of my postdoctoral research. After more than a decade of involvement in the field of sRNAs, I remain highly enthusiastic about uncovering novel sRNAs and investigating their intricate interactions within diverse organisms. Ultimately, my aim is to reveal regulatory cascades and pathways that can be harnessed to improve human health.

  1. What tools were necessary to create a high-resolution transcriptome map for Bacteroides thetaiotaomicron, and what challenges did you encounter during this process?

In order to construct a high-resolution transcriptome map of B. theta, it is crucial to extract RNA of high quality from representative and diverse conditions that effectively stimulate gene expression. This is easier said than done, since one of the main challenges of working with gut microbes is their anaerobic nature and often cumbersome culture conditions. To ensure optimal anaerobic conditions, all media and equipment used for bacterial culture must be degassed to remove oxygen, which can be toxic and inhibit growth. Once robust and reproducible growth can be achieved, RNA is extracted, sequenced and analyzed to obtain a single nucleotide resolution of the transcriptome. I then employed a suite of bio-informatics tools to annotate the transcriptome and subsequently manually validate and edit each feature. Although this final step is time-consuming and labor-intensive, it is essential for obtaining a high-quality and reliable result.

  1. Were there any unexpected or surprising findings in your research?

I was delighted to discover that the number of potential sRNAs in B. theta was similar to that of other model organisms, such as E. coli and Salmonella. Moreover, the vast majority of these sRNAs had no known homologs in these well-known species. This suggests that B. theta has undergone functional adaptations specific to its niche, which is primarily the human large intestine. Consequently, I anticipate a wealth of novel biological insights, potentially revealing new modes of interaction and target regulation.

  1. Are there any potential applications or implications of your research for human health, such as developing targeted therapies or interventions for gut-related disorders?

In order to develop effective targeted therapies, it is crucial to first and foremost “know your target”. Going in blind is never a good strategy and this is where I see the potential of this work. With this high-resolution transcriptome and the “Theta-Base” browser, we have provided a framework to discover and identify novel genes and sRNAs that can further be investigated as potential targets to regulate or modulate activity. These newly identified targets whether coding or non-coding can be exploited to modulate B. theta to achieve specific functions for instance, they could be used to exclusively metabolize a particular carbon source or prevent the consumption of a specific metabolite. While this example is simplistic, several laboratories are already conducting pilot studies in this area, offering promise for the future of targeted medicine.

  1. What would you say are some of the challenges or gaps in knowledge that need to be addressed in the field of gut microbiota research?

One of the overarching challenges in gut microbiota research is distinguishing between correlative and causative effects. It is therefore imperative to develop protocols and methodologies that delve into various phenomena at a detailed level before drawing reliable conclusions.

There are also specific challenges to address, particularly regarding the creation of microbial consortia that accurately reflect the composition of the gut microbiota.  This is not easy considering the vast numbers of bacteria and their complex interactomes that make up a healthy microbiota. Moreover, models representing the human intestinal niche, which harbor these diverse microbial communities, need further refinement to better reflect this complex environment.

  1. Finally, what is your favorite part of being an RNA research scientist?

As an RNA research scientist, what I find most fascinating is the varied range of roles that this molecule can play. From intricate structural scaffolds to subtle enzymatic and regulatory functions, RNA displays a multitude of capabilities, and witnessing these firsthand is truly captivating.


Differential RNA sequencing (dRNA-Seq) is a technique used to identify transcriptome features and define overall transcriptomic architecture, such as transcription start sites, terminators, non-coding RNAs, coding RNAs, promoters, etc.

A transcriptome map is a comprehensive profile or catalog of all the RNA molecules (transcripts) produced by an organism or a specific cell type under particular conditions. It provides a snapshot of the active genes and their expression levels within the cells or tissues being studied.

The Hidden World of Microbiomes and Their Impact on Our Lives

The Hidden World of Microbiomes and Their Impact on Our Lives

Microbiomes are the diverse communities of microorganisms that inhabit different parts of our bodies, as well as the environment around us. In recent years, research has revealed the vast and complex hidden world of microbiomes and their impact on our lives, from influencing our digestion and immune system to potentially affecting our mood and behavior. Advances in technology have enabled scientists to study microbiomes in unprecedented detail, leading to new insights into their diversity and functions. Understanding the microbiome and its role in human health and disease has the potential to transform how we approach medicine, nutrition, and the environment.

Staph, can be both good and bad for humans

With high diversity, you also get a combination of characters, the human microbiome is consequently no stranger to the good, the bad and the ugly.

There are good microorganisms, then nasty ones, and then good ones that might turn into bad ones.

One of the most famous good/bad bacteria is Staphylococcus aureus commonly known as Staph. It’s generally found on the skin and in the nasal passages of healthy individuals, where it can play a beneficial role in preventing colonization by other, potentially harmful bacteria. However, S. aureus can also cause a range of infections, including skin infections, pneumonia, bloodstream infections, and heart infections. Some strains of S. aureus are antibiotic-resistant, making them particularly difficult to treat. Thus, understanding what triggers the switch from a peaceful commensal bacterium inhabiting our noses to a virulent pathogen is key to identifying potential therapeutic targets.

A study by Wittekind et al. (2022) provided further insight into the mechanisms behind the expression of virulence genes in S. aureus. The research describes the discovery of a novel protein, ScrA (which stands for S. aureus clumping regulator A), in Staphylococcus aureus (SaeRS). ScrA interacts with the SaeRS two-component system (TCS), which is known to regulate the expression of virulence genes in S. aureus. The results show that ScrA plays a key role in the regulation of virulence gene expression by the SaeRS system, and that deletion of the ScrA gene results in a significant decrease in virulence in a mouse infection model. Thus, ScrA could be a promising target for the development of new therapies to treat S. aureus infections.

One of the key methods in Wittekind et al. (2022)  experiment was RNA-sequencing to get a glimpse of the gene expression profile of S. aureus. The global view provided by RNA-Seq helped pinpoint one of the S. aureus two-component systems that showed higher expression when ScrA was overexpressed.

Since rRNA accounts for 80-90% of the transcriptome limiting the detection efficiency of desired RNAs by RNA-Seq. The removal of ribosomal RNA (rRNA) before RNA-Seq greatly improves and economizes RNA-Seq. In this study, ribosomal RNA depletion was performed using the Staphylococcus aureus– specific riboPOOL rRNA removal kit.

Marcus busy in the lab. 👨🏻‍🔬

A Brief Interview with Dr. Marcus Wittekind

To have further insight into the process, challenges of studying human microbiomes, and the most interesting findings related to small RNAs (sRNAs) we interviewed Dr. Marcus Wittekind.

Marcus is a research scientist at Ohio University and is a member of Dr. Ronan Carroll’s Lab. His research is focused on bacterial pathogenesis and the role RNA molecules play in the bacterial cell. Meet one of the scientists behind the research:

  1. What inspired you to pursue research on human microbiomes?

I have always had an interest in how microbes interact with their host. Staphylococcus aureus is particularly interesting to me in that it is found in ~30% of the population as a human commensal and just sits in the nose without any issues. Yet, when S. aureus migrates to other areas you can get devastating disease. It’s fascinating how S. aureus is able to make this transition and switch from a relatively passive existence to a virulent pathogen. Along with S. aureus, it’s astounding how little we actually know about the microbiome and how it influences our health. It’s exciting to live during a time when we’re uncovering these connections.

  1. What are the most interesting findings from your latest research on the commensal bacteria Staphylococcus aureus?

My findings about S. aureus have focused primarily on a single small protein ScrA. Although my research has been focused on a single protein, I think it can serve as an example of just how much we have left to learn. I found ScrA to act as a sort of link between two well-studied regulatory systems in S. aureus. While this is an interesting subject in its own right, I think where this story comes from is particularly interesting. My mentor Ronan Carroll originally identified the scrA gene, which was at the time called tsr37, as a small non-coding RNA. However, we later came to find out that some of these small RNAs actually encoded small proteins. Now this isn’t surprising, we already know of a toxin encoded on a small RNA. However, it makes me wonder how many more proteins are we overlooking as being just small RNAs? Some of my studies also suggest that ScrA is really only important when S. aureus is infecting the heart. In laboratory conditions we don’t really see any changes when we delete scrA, which would normally lead to us just moving on without discerning the function of ScrA. Only due to marked phenotypes when we overexpress ScrA did we even become interested in its function. How many more genes play a vital role in virulence but are being overlooked because we can’t see anything in the lab? I think ScrA serves as a reminder of how unassuming genes can actually have a larger role than what we see on the benchtop.

  1. What are some of the biggest challenges researchers face in the field of microbiomes?

The sheer complexity of the interactions between pathogens and their host. For me, this has manifested as finding the exact conditions in which ScrA is activated and carries out its function. All I really know is that scrA plays a role in infecting the heart. However, the question still remains as to what triggers scrA production. Nutrient abundance? Immune system components? Temperature? Host signals? At this point, I can only guess. For me I only have to focus on a single organism. The complexity drastically increases when you consider environments with multiple organisms such as the digestive system, skin, or wounds. While the complexity is fascinating it is also difficult to wrap your head around exactly what is taking place.

  1. What technologies and methods are key for your research?

There are many different technologies and methods that are essential for my work. However, a few stand out to me. I went into this project with no idea what was causing the phenotypes. So, we decided to cast a wide net and see what was being altered in the cell. RNA-sequencing actually gave us our first hint of what was going on. We saw global changes in gene expression; however, we were able to pick out one system in particular that showed promise. One of the two-component systems in S. aureus (SaeRS) showed higher expression when we overexpressed ScrA. Thanks to the global view we can get by using RNA-seq we were able to identify a potential mechanism with one experiment as opposed to screening individual regulators.

On the same note, mass spectrometry allowed us to get a global view of protein changes. This was particularly useful when we were identifying what host factors were being bound when we overexpress or delete scrA. We were able to “shave” the surface of the cells with immobilized trypsin and identify the exact proteins present, and more importantly what proteins could be accessed by the trypsin. Being able to quickly sort through all the different components was essential to forming a working model for ScrA mediated aggregation.

Finally, we can’t ignore how essential animal models are for studying virulence. While it would be great and I look forward to a day when we no longer need to perform animal experiments, right now they are absolutely vital to understanding these pathogens. We utilized a mouse model of systemic infection to determine if scrA was essential for virulence. Not only was I able to show that scrA is needed for virulence, but I was also able to show that scrA is primarily needed for heart infections. This is something we wouldn’t have known without animal models. When we delete scrA and use it in our in vitro experiments, we see limited effects and only under specific conditions. However, we saw a drastic decrease in virulence in a mouse model.

  1. What are some potential applications of your research on human health?

One of the primary reasons I want to understand S. aureus virulence is to identify potential therapeutic targets. It’s well known that antibiotic resistance is on the rise and at some point, we are going to need alternative treatments. S. aureus is interesting because in most cases it just sits in the nose and doesn’t cause disease. If we can understand what triggers that switch from a passive carry to an aggressive infection, we might be able to force S. aureus to stay in a passive state or at least limit its virulence. I’ve shown ScrA is needed for effective heart infection by S. aureus. It may be possible to target ScrA and inactivate it, reducing its ability to infect the heart. This could be useful in people undergoing heart surgeries, especially in cases with indwelling medical devices, which may introduce S. aureus into the heart.

  1. What advice would you give to someone interested in pursuing a career in Bacteriology?

Bacteriology is a wide field, take your time to explore different aspects and find something that really interests you. The sheer volume of information can be overwhelming when you get started, but as time goes on it becomes more familiar. The best way to see what really interests you is to get involved in research. Reach out to people whose research interests you and find opportunities to get involved. I know how intimidating this idea can be (I started researching as an undergraduate) but many professors are happy to have interested people join their lab regardless of experience. Most importantly don’t feel obligated to stick with the first thing you start studying. One of the things I love about bacteriology is how much there is to learn. If you don’t like what you’re studying, there is always something else you can try. It’s important to find your niche and what you enjoy. Being passionate about your work is an important part of this field.


Two-component systems (TCSs) are signaling pathways that allow bacteria to sense and respond to changes in their environment. A TCS consists of two proteins: a sensor histidine kinase and a response regulator. The sensor histidine kinase detects a specific environmental signal and transfers a phosphate group to the response regulator protein, which then activates or represses the expression of specific genes.

Small RNAs (sRNAs) are short, non-coding RNA molecules that typically range in size from 50 to 500 nucleotides. They are important regulators of gene expression in bacteria, archaea, and eukaryotes, and play diverse roles in cellular processes such as stress response, metabolism, and virulence.

Microbiome May Blog Series

Microbiome May Blog Series

Hi there and welcome to our May blog series inspired by microbiomes🧫👾!

We’re excited to announce that we will be launching a new blog series on microbiomes, featuring topics ranging from skin microbiomes to gut microbiomes. Our riboPOOLs kits have been used in numerous studies exploring the intricacies of microbiomes, and we’re thrilled to share our knowledge with you.  Additionally, as May is the month of microbiomes, we are offering a 15% discount on all of our microorganism riboPOOLs kits and probes (24 and 96 reactions). Request a quote.

Microbiomes are communities of microorganisms (such as bacteria, viruses, fungi, and archaea) that live in and on various organisms and environments. These tiny organisms play a crucial role in maintaining the health and well-being of living organisms and their ecosystems.

Nevertheless, human microbiomes may also harbor commensal bacteria, such as Staphylococcus aureus. Which, depending on their location in the human body or the prevailing environmental conditions, can potentially lead to aggressive infections.

More on this topic in our next blog post:

The Hidden World of Microbiomes and Their Impact on Our Lives


A Brief Interview with Marcus Wittekind

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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