<figure class="image image-style-align-left"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/Ivan_Tomic_350x304_e1a6e9d186.jpg"><figcaption>Ivan Tomic, Research Computation Specialist, Atomic lab</figcaption></figure>The CEIRR Network is proud to spotlight Ivan Tomic, a research computing specialist in <a href="https://atomic-lab.org/team/" target="_blank" rel="noopener noreferrer">Dr. Adriana Tomic’s lab</a> at Boston University, part of Johns Hopkins CEIRR (<a href="https://www.ceirr-network.org/centers/jh-ceirr#Adriana%20Tomic" target="_blank" rel="noopener noreferrer">JH-CEIRR</a>). Tomic was awarded “Outstanding Poster” in Poster Session B of the <a href="https://www.ceirr-network.org/news/ceirr-annual-network-meeting-2024" target="_blank" rel="noopener noreferrer">CEIRR Annual Network Meeting 2024</a> for his poster titled “Immunoaut: Decoding Immune Response Patterns After Influenza Vaccination Using Machine Learning”.&nbsp;&nbsp;Tomic was inspired to go into science by his “fascination with technology and a drive to make tangible contributions to human health” and was drawn to systems immunology specifically because it “offered the perfect synergy between [his] technical expertise and the potential to impact lives.” His award-winning poster focused on using the Artificial Intelligence (AI) driven platform Immunoaut to help elucidate factors that contribute to the protective immunity that vaccines afford us. One of the ultimate goals of his research is to create tailored vaccination strategies aimed at improving vaccine effectiveness and personalizing influenza prevention.&nbsp;&nbsp;In addition to giving us insight into his research, Tomic also spoke about his appreciation of the collaborative and innovative nature of the CEIRR Network through “ensure[ing] [researchers] access to a wealth of resources, enabling impactful discoveries.” He said he appreciates how CEIRR “encourages the integration of advanced tools like artificial intelligence to unravel complex biological systems and push the boundaries of immunological research.”&nbsp;The iDPCC also gained more insight into Tomic himself through a series of thought-provoking questions:&nbsp;&nbsp;1. What are your plans following your training?A. I see my future at the forefront of computational immunology, leading initiatives that revolutionize how we understand and manipulate immune responses. Atomic Lab has set the stage for this, and I plan to continue contributing to its mission while expanding its technological reach. My goal is to develop platforms that empower scientists globally, make data-driven medicine accessible, and inspire the next generation of researchers to embrace computational approaches.&nbsp;2. Do you have advice for other trainees??&nbsp;&nbsp;A. For trainees, my advice is to embrace technology wholeheartedly as it is the future of biology. Don’t shy away from learning computational tools and integrating them into your research. At Atomic Lab, we thrive at the intersection of disciplines, and I’ve seen firsthand how this multidisciplinary approach leads to breakthroughs. Be curious, seek mentorship, and always push the boundaries of what’s possible.3. What is your favorite lab technique?A. My favorite technique is building and implementing AI models for immune data analysis. It’s not just about crunching numbers; it’s about uncovering patterns that redefine our understanding of the immune system.&nbsp;4. Do you have any hobbies or special interests that you'd like to share?A. When I’m not immersed in code or immunology, I’m often found sailing or exploring tech-driven hobbies like building custom computational systems. Sailing teaches me to navigate challenges with precision, much like working in the ever-evolving field of computational biology. These hobbies fuel my creativity and help me stay grounded, complementing my work at Atomic Lab.&nbsp;

Spotlight

JH-CEIRR

Conferences

Awards

Vaccine

Modeling

Outstanding Poster Awardee Ivan Tomic gives insight into how he utilizes AI to improve vaccine research and how technology shapes his everyday life.

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Ivan Tomic Speaks About His Passion for Leveraging Technology to Make Impactful Contributions to Vaccine Research 

<figure class="image image-style-align-right"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR_Presentation_Schneider_400x533_d5401ea3cd.png?updated_at=2025-01-10T16:40:09.019Z"><figcaption>Cosette Schneider presenting her award-winning poster during the CEIRR Annual Network Meeting 2024.</figcaption></figure><img><img>The CEIRR Network proudly spotlights Cosette Schneider, a Ph.D. Candidate and trainee in&nbsp;<a href="https://www.medschool.umaryland.edu/profiles/coughlan-lynda/" target="_blank" rel="noopener noreferrer">Dr. Lynda Coughlan’s Lab</a>, part of&nbsp;<a href="https://www.ceirr-network.org/centers/cript" target="_blank" rel="noopener noreferrer">CRIPT</a>. Schneider was awarded first place for her poster titled, “The characterization of cellular and humoral immune respons<img>es to influenza A virus” at the&nbsp;<a href="https://www.ceirr-network.org/news/ceirr-annual-network-meeting-2024" target="_blank" rel="noopener noreferrer">CEIRR Annual Network Meeting 2024</a> in New York City, NY.Schneider enjoys training in the CEIRR Network because of the program’s emphasis on collaboration, “which have greatly supported [her] thesis research.” Prior to her Ph.D. training at the&nbsp;<a href="https://www.medschool.umaryland.edu/" target="_blank" rel="noopener noreferrer">University of Maryland School of Medicine</a>, she developed mRNA- and protein nanoparticle-based vaccines for malaria as an&nbsp;<a href="https://orise.orau.gov/index.html" target="_blank" rel="noopener noreferrer">ORISE</a> Postbaccalaureate Research Fellow at the&nbsp;<a href="https://wrair.health.mil/" target="_blank" rel="noopener noreferrer">Walter Reed Army Institute of Research</a>. This fellowship helped her “identify vaccinology and antigen engineering as [her] primary research interests.” As she progresses through her Ph.D. program and continues her research, Schneider is “motivated by the fact that [her] research informs the development of vaccines for a virus of pandemic potential because [she] firmly believe[s] in the importance of preventative measures for infectious diseases and the role of vaccines as ‘weapons of mass protection.’”The iDPCC also asked Schneider to answer some thought-provoking questions:1. Who/what inspired you to go into science in general?A. I attended a small liberal arts college, so my undergraduate studies were quite diverse, including an emphasis on French and international politics and policy, in addition to the life sciences. Although my educational background is multidisciplinary, I continued to pursue the sciences in my graduate studies because scientific knowledge is always evolving at such a rapid pace, which, to me, is ideal for lifelong learning.2. What is one thing on your bucket list?&nbsp;&nbsp;A.&nbsp;I want to travel to 30 countries by the time I am 30. I have travelled to 17 countries in the past 5 years, and I have 5 more years to go! Hopefully, some international conferences will help me achieve my goal!3. What was your childhood dream job?A. My dream job was something new every day! Some longer-lived dream jobs included a firefighter, veterinarian, pilot, forensic scientist, and pediatric oncologist.4. What are your plans following your training?A. After I complete my Ph.D., I want to pursue postdoctoral training in an academic lab focused on structural biology, antigen and vaccine platform engineering, and/or rational vaccine design.&nbsp;5. What is your favorite mundane lab chore?&nbsp;&nbsp;A.&nbsp;My favorite mundane chore is to update our lab’s notice board with colorful, cheesy flyers about our lab’s accomplishments.<img>

CRIPT

Influenza

Poster presenter awardee and Ph.D. Candidate, Cosette Schneider, highlights the role of vaccines as “weapons of mass protection” and her educational journey to vaccinology and antigen engineering.

Headshot of Cosette Schneider, PhD Candidate and Trainee in CRIPT

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Cosette Schneider Provides Insight on Her Influenza Research and Multi-Disciplinary Background

The development of the COVID-19 vaccines was nothing short of a triumph of modern medicine. However, the one weakness of the shots was the inability to stop the spread of the virus. St. Jude Children’s Research Hospital CEIRR (<a href="https://www.ceirr-network.org/centers/sjceirr" target="_blank" rel="noopener noreferrer">SJCEIRR</a>) researchers from Washington University in St. Louis (WashU) may have found a way to combat this shortcoming by targeting the virus’s point of entry — the nose and mouth. The study evaluating this vaccine candidate was recently highlighted in a <a href="https://medicine.washu.edu/news/nasal-covid-19-vaccine-halts-transmission/" target="_blank" rel="noopener noreferrer">WashU Medicine article</a>.<figure class="image image-style-align-right image_resized" style="width:50%;"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/Nasal_COVID_19_Vaccine_Article_Image_24d878a892.jpg?updated_at=2024-12-18T19:25:07.051Z"><figcaption>Artistic rendering of SARS-CoV-2 virions, the virus that causes COVID-19.</figcaption></figure>Why is targeting the nose and mouth so integral to preventing transmission? Viruses such as influenza virus, SARS-CoV-2, and respiratory syncytial virus (RSV) multiply rapidly in the nose, allowing them to spread from person to person within the first few days of exposure. Intramuscular vaccines generate a less potent immune response in the nose than in the bloodstream, leaving the nose and mouth vulnerable against fast-spreading viruses.&nbsp;Although it seems that targeting the nose and mouth will limit viral reproduction more efficiently, gathering the evidence necessary to prove that mucosal vaccines reduce transmission is trickier than one would expect, underscoring the importance of animal models in biological research. To address this gap, <a href="https://infectiousdiseases.wustl.edu/people/jacco-boon/" target="_blank" rel="noopener noreferrer">Jacco Boon, Ph.D.</a>, <a href="https://infectiousdiseases.wustl.edu/people/michael-s-diamond/" target="_blank" rel="noopener noreferrer">Michael Diamond, M.D., Ph.D.</a>, and other researchers developed and validated a model that mimics community transmission of SARS-CoV-2 in hamsters, which was then used to assess the efficacy of mucosal vaccination on SARS-CoV-2 spread. The study compared hamsters vaccinated with a <a href="https://medicine.washu.edu/news/washus-nasal-covid-19-vaccine-approved-for-use-as-booster-in-india/" target="_blank" rel="noopener noreferrer">nasal COVID-19 vaccine</a> to those vaccinated with an intramuscular COVID-19 vaccine—the vaccine approved for use in humans—to evaluate the impact of both vaccines on airborne infection and transmission. &nbsp;The study showed that hamsters that were vaccinated with the nasal vaccine and went on to develop SARS-CoV-2 infections did not transmit the virus to vaccinated or unvaccinated hamsters. In direct contrast, when hamsters were given an intramuscular COVID-19 vaccine, spread of the virus still occurred. In summary nasal vaccination—but not intramuscular vaccination—broke the cycle of transmission in hamsters.&nbsp;&nbsp;These results have immediate and direct implications as the world prepares for a possible avian flu epidemic. Currently the avian flu virus is causing an outbreak in dairy cows and could adapt to humans. An intramuscular vaccine for avian influenza already exists, but a team of researchers at WashU, that includes Dr. Boon and Dr. Diamond, are harnessing these results to work toward a nasal vaccine for avian influenza.&nbsp;Read the full press release:&nbsp;<ul><li><a href="https://medicine.washu.edu/news/nasal-covid-19-vaccine-halts-transmission/" target="_blank" rel="noopener noreferrer">Nasal COVID-19 Vaccine Halts Transmission</a>&nbsp;&nbsp;</li></ul>Read the article in Science Advances:&nbsp;<ul><li><a href="https://www.science.org/doi/10.1126/sciadv.adp1290" target="_blank" rel="noopener noreferrer">Darling TL et al. (2024) Mucosal immunization with ChAd-SARS-CoV-2-S prevents sequential transmission of SARS-CoV-2 to unvaccinated hamsters. Sci. Adv. 10(31): eadp1290</a>.&nbsp;</li></ul>

In The News

SJCEIRR

SARS-CoV-2

Study of a nasal COVID-19 vaccine shows promising results in limiting airborne transmission in hamsters indicating targeting the nose and mouth may be key to controlling the spread of respiratory infections.&nbsp;

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SJCEIRR Researchers Find Nasal COVID-19 Vaccine Halts Transmission

<figure class="image image-style-align-right"><a href="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR_Avian-Infobyte_08262024.pdf" target="_blank" rel="noopener noreferrer"><img src="https://ceirr-public-website-static-prod.s3.amazonaws.com/CEIRR_Avian_Infobyte_Final_Draft_750x971_3794527f51.png?updated_at=2024-09-11T14:53:18.132Z"></a><figcaption>“Wild Bird Surveillance: Influenza Movement on Flyways” Infobyte. To view a full-size PDF version, click the image above.</figcaption></figure>Conducting influenza surveillance in wild and domestic animal hosts is part of the CEIRR Network’s core mission to study respiratory viruses with pandemic potential. Wild birds, especially shorebirds and waterfowl, represent a significant reservoir of influenza viruses in part due to their migration patterns allowing viruses to spread over large geographic regions quite quickly. Researchers from St. Jude Children’s Research Hospital CEIRR (<a href="https://www.ceirr-network.org/centers/sjceirr" target="_blank" rel="noopener noreferrer">SJCEIRR</a>), <a href="https://vet.uga.edu/person/david_e-_stallknecht/" target="_blank" rel="noopener noreferrer">David Stallknecht, Ph.D.</a> and <a href="https://vet.uga.edu/person/poulson-rebecca/" target="_blank" rel="noopener noreferrer">Rebecca Poulson, Ph.D.</a>, lead avian influenza surveillance in wild bird populations at the University of Georgia (UGA). The main goals of these efforts aim to understand the 1. ecology and epidemiology of avian influenza viruses in a wide range of avian hosts, 2. viral persistence in wild bird populations, 3. how these viruses move with wild animal hosts, and 4. the significance of highly pathogenic (HP) H5N1 in wild bird populations.Since 2014, the CEIRR Network (and previous iteration called <a href="https://www.ceirr-network.org/about/the-legacy-of-ceirs" target="_blank" rel="noopener noreferrer">CEIRS</a>) has sampled nearly 260,000 wild birds for avian influenza viruses. Surveillance efforts cover much of North America with sampling in all four major migratory patterns, called flyways: the Pacific, Central, Mississippi, and Atlantic. These loosely defined and overlapping migratory zones extend well-beyond North America, as well. All four flyways stretch into South America (not shown) where many waterfowl migrate during the North American winters; notably the Atlantic flyway overlaps with flyways in Europe (not shown). The vast geographic area that migratory birds cover highlights the importance of researching the pandemic potential of avian influenza A viruses (IAVs) in spurring the next outbreak. Multiple types of IAVs could be present in a migrating bird population at the same time. Some gene segments of these viruses can mix, often termed viral reassortment, leading to new strains of influenza. Birds traveling with these IAVs can spread the virus to other bird species, or even to land animals and mammals. To understand the impact of avian influenza on wild bird populations, Drs. Stallknecht, Poulson, and others in the field surveilled IAVs in <a href="https://www.ceirr-network.org/resources/publications?keyword=36105667" target="_blank" rel="noopener noreferrer">bald eagles</a>, <a href="https://www.ceirr-network.org/resources/publications?keyword=27309076" target="_blank" rel="noopener noreferrer">snow geese</a>, <a href="https://www.ceirr-network.org/resources/publications?keyword=31131568" target="_blank" rel="noopener noreferrer">mallards</a>, and <a href="https://www.ceirr-network.org/resources/publications?keyword=33105913" target="_blank" rel="noopener noreferrer">ruddy turnstones</a>, among other species. In an interview with the iDPCC, Drs. Stallknecht and Poulson shared more about how they got involved in studying avian influenza in wild birds, the importance and impact of their research, and how their work challenges paradigms to expand our understanding of avian influenza dynamics in wild birds.&nbsp;How Did They Start Studying Influenza in Wild Birds?Both Dr. Stallknecht and Dr. Poulson are faculty at the Southeastern Cooperative Wildlife Disease Study at the College of Veterinary Medicine at UGA, and both had serendipitous entries into the field of avian influenza in wild birds. Dr. Stallknecht, Professor Emeritus at UGA, started working with flu in the 1980's as a wildlife biologist working on a USDA task force assigned to an outbreak of HP H5N2 in poultry in Pennsylvania. There he met and worked with a renowned avian flu expert from St. Jude Children’s Research Hospital, <a href="https://www.stjude.org/directory/w/robert-webster.html" target="_blank" rel="noopener noreferrer">Robert Webster, Ph.D.</a> This was followed by graduate work on influenza in wild blue-winged teal at Louisiana State University, and he’s been studying influenza ever since, including his involvement in the CEIRR and CEIRS Networks from the beginning.Dr. Poulson, who’s now an Assistant Professor, began studying influenza after she moved to Georgia. She applied for a research technician role in Dr. Stallknecht’s lab and quickly fell in love with the field, eventually completing her Ph.D. with Dr. Stallknecht. Dr. Poulson loves that the avian influenza field is “so constantly changing and there are so many underexplored and unanswered questions.” Giving a personal reason why she’s stayed in the field, “Ruddy turnstones also, separately, are very charismatic.”&nbsp;Importance of Wild Avian Surveillance and ResearchDrs. Stallknecht and Poulson focus on the future to inform present conservation efforts in wild birds. They value wildlife and aim to keep these natural resources “front and foremost” in their research. Dr. Poulson always advocates for wildlife to be an “equal member at the table” when discussing health: “The health and well-being of these animals and their populations is critically important to entire ecosystems. And sometimes I feel like that gets lost in conversations.” Their group views their research from the wild bird perspective: working to understand the wildlife reservoir, how viruses persist, and when and where they’re capable of entering into that reservoir.When Drs. Stallknecht and Poulson started detecting infections of a new strain of influenza (HP H5N1) in North American wild birds, they also saw increases in mortality in many wild bird species: eagles, condors, ducks, and more. The fieldwork became emotionally taxing. However, when they began investigating snow geese, and applying antibody tests not normally applied to wild bird surveillance, they found that many infected birds including black vultures, condors, eagles, and even mammals, actually survive infection. This was encouraging to learn and provided much need information to understand possible impacts on wildlife populations.The iDPCC dove deeper into the health and safety of animal populations to better grasp the risk of influenza transmission from wild birds to mammals. Dr. Stallknecht notes that the risk is nearly impossible to quantify in the wild, but described three major scenarios where avian influenza transmits to another species:<ol><li>Most wild bird infections are caused by low pathogenic avian influenza (LPAI), which can but rarely pass to wild or domestic mammals. These viruses do “spill over” to domestic poultry on occasion and can cause severe problems.&nbsp;</li><li>In contrast, highly pathogenic avian influenza (HPAI) infections have a higher risk to “spill over” into wild mammals because they often kill their bird host. Wild mammals and predatory birds may come across weak or deceased birds and eat the carrion. Direct contact with HPAI is the main factor in determining whether a wild animal will acquire an infection.</li><li>With HPAI, infections also have been detected in domestic mammals (cats, dairy cows) but direct transmission from wild birds is rare, and these problems are usually associated with human error, such as not providing an adequate barrier between wild birds and these animals.</li></ol>Because of the potential death toll and transmission to other species, detecting positive cases of HPAI rings the alarm bells. Their group quickly studies the characteristics of the virus and assesses the risk to wildlife. Unfortunately, this presents a series of challenges. “Basically, we're dealing with a problem right now that we don’t know where it’s going, and we don’t know how bad it will be, and this type of event will happen again, even if we get beyond this one,” explains Dr. Stallknecht. While these viruses of concern present complex issues, Drs. Stallknecht and Poulson focus on understanding the trajectory of the virus and what may be possible, so they can devise strategies to keep wildlife safe and impacts low.&nbsp;Challenging Paradigms in Shorebird MigrationThe paradigm in North America holds that shorebirds migrate from South America in early spring towards their Arctic breeding grounds and stop in Delaware Bay via the Atlantic flyway. The birds fuel up on horseshoe crabs before continuing their journey to the Arctic. This sparked an intuitive site for influenza sampling efforts that are still <a href="https://www.ceirr-network.org/news/influenza-surveillance-efforts-in-north-american-shorebirds-is-the-start-to-understanding-and-anticipating-threats-posed-by-a-h5-n1" target="_blank" rel="noopener noreferrer">ongoing by SJCEIRR</a> researchers. The Network has learned a lot about the wildlife and virus dynamics within Delaware Bay over the years. A major problem lies in what happens outside of the bay. Dr. Poulson notes, “It’s hard to pinpoint where the viruses detected at Delaware Bay come from.”To start teasing apart the inputs of influenza into the Delaware Bay ecosystem, Drs. Stallknecht and Poulson leveraged their proximity to the southeastern US coastlines. They increased sampling on South Carolina, Georgia, and Florida coasts over several years to interrogate shorebird species in different times of year to understand how these viruses are maintained, and then subsequently moved to new locations. Using nano-tag telemetry on ruddy turnstones in the southeast, they tracked virus and bird movement over time and space. They found that many birds stop in the southeast US and can bypass Delaware Bay on their way to the Arctic. They’re starting to tie together movement and maintenance of viruses at different times of year based on genetic similarity. They found genetic similarity of IAV in the southeast during winter and detected similar genetic signatures in IAV at Delaware Bay months later. Dr. Poulson highlights the utility of this “multi-pronged approach [of] linking telemetry, viral movement, and genetic data to better understand the role of shore birds in disseminating viruses to different locations.”To wrap up our discussion, Dr. Poulson recalls a common phrase in the field: “The more we learn about flu, the less we know.” There are many open questions and challenges when studying wild populations, but Drs. Stallknecht and Poulson’s passion for the health of these ecosystems drives them to maintain their effort. However, they’re not alone in this effort. Dr. Poulson noted, “Lots of dots on that map, right? And lots of collection efforts. But in fact, that is representative of just a handful of dedicated groups historically having collected all those data. That’s a small but mighty and critically important effort.” Drs. Stallknecht and Poulson are proud to belong in the CEIRR Network community for so many years and look forward to researching influenza’s role in these dynamic, wild bird ecosystems.<hr>To read more about this topic, check out:<ul><li><a href="https://www.ceirr-network.org/resources/publications?keyword=36105667" target="_blank" rel="noopener noreferrer">Alkie TN, et al. (2022) A threat from both sides: Multiple introductions of genetically distinct H5 HPAI viruses into Canada via both East Asia-Australasia/Pacific and Atlantic flyways. Virus evolution. 8(2): veac077.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=27309076" target="_blank" rel="noopener noreferrer">Wong JK, et al. (2016) Antibodies to Influenza A Viruses in Wintering Snow Geese (Chen caerulescens) in Texas. Avian diseases. 60(1 Suppl): 337–340.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=31131568" target="_blank" rel="noopener noreferrer">Hollander LP, et al. (2019) Prevalence of Influenza A Viruses in Ducks Sampled in Northwestern Minnesota and Evidence for Predominance of H3N8 and H4N6 Subtypes in Mallards, 2007-2016. Avian diseases. 63(sp1): 126–130.</a></li><li><a href="https://www.ceirr-network.org/resources/publications?keyword=33105913" target="_blank" rel="noopener noreferrer">Poulson R, et al. (2020) Influenza A Viruses in Ruddy Turnstones (Arenaria interpres); Connecting Wintering and Migratory Sites with an Ecological Hotspot at Delaware Bay. Viruses. 12(11): 1205.</a></li><li>Additional CEIRR publications on <a href="https://www.ceirr-network.org/resources/publications?keyword=wild%20bird" target="_blank" rel="noopener noreferrer">influenza in wild birds</a> or <a href="https://www.ceirr-network.org/resources/publications?keyword=flyway" target="_blank" rel="noopener noreferrer">influenza in flyways</a>.</li></ul>

iDPCC

Surveillance

Infobyte

SJCEIRR researchers study the movement of avian influenza in wild bird populations for pandemic preparedness and research response.

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