In this episode, Dr. Aaron Cypess discusses the future of brown adipose tissue (BAT) and white adipose tissue (WAT) research at the NIDDK, focusing on three pillars: integrative physiology, noninvasive imaging, and clinical trials. First, there's integrative physiology, where scientists use cell lines to dig into how fat cells work, how they burn energy, and how they respond to obesity treatments. Then there's noninvasive imaging—think PET-CT and MRI—which helps researchers actually see where fat is in the body and how active it is. And finally, clinical trials are testing treatments like mirabegron to see if they can activate brown fat and boost metabolic health. Dr. Cypess highlights the importance how taking this combined approach to studying BAT and WAT physiology can open doors to real, meaningful benefits to patients.
In this episode, Dr. Aaron Cypess discusses two pivotal moments that led him to change his approach to research. Initially planning to major in biology, he was encouraged to study chemistry, which provided a strong foundation in precision and quantitative analysis. During his endocrinology fellowship, Dr. Cypess shifted his focus to clinically relevant research, leading to his entry into the Clinical Investigator Training Program. This program allowed him to leverage his dual MD and PhD training to study human brown adipose tissue (BAT). Dr. Cypess also reflects on the pressures of being a physician-researcher and how the supportive environment at the NIH's NIDDK has enabled him to continue his impactful research. He highlights the benefits of the NIH's collaborative environment and resources, such as the NIH Clinical Center and the post-baccalaureate fellowship program, which have been instrumental in his research on BAT and its implications for human health.
In this conversation, Dr. Aaron Cypess discusses his research on brown adipose tissue (BAT), an organ that burns fat to generate heat. Initially thought to be present only in small mammals and young children, functional BAT was discovered in adult humans in 2009, spurring global research into its potential for treating obesity and metabolic diseases. Dr. Cypess explains the differences between BAT and white adipose tissue (WAT), and how BAT communicates with other tissues through hormones. Dr. Cypess then focuses on BAT's role in diabetes and obesity, highlighting the collaborative environment that supports his research.
In this episode, David Yarmosh and Briana Benton discuss the future of the ATCC Genome Portal, focusing on upcoming data types and platform enhancements. Benton reveals that by the end of 2025, researchers will gain access to methylation data for the bacteriology collection with future plans to annotate virology genomes, integrate antimicrobial susceptibility data, and enable advanced search features such as taxonomy browsing and gene-based queries. As the portal evolves into a dynamic “digital twin” platform, it will offer more than genome sequences, incorporating valuable metadata like microscopy images and QC results. Benton underscores the pivotal role of customer feedback in driving these innovations and highlights ATCC’s Supporting Membership, which expands data accessibility to researchers beyond those purchasing physical products. With a vision to establish the portal as a trusted, comprehensive reference for authenticated microbial data, ATCC continues to advance reproducibility and innovation in biological research.
In this episode, David Yarmosh and Briana Benton revisit the origins and evolution of the ATCC Genome Portal, tracing its journey from an ambitious research concept in 2017 to a groundbreaking resource for high-quality, traceable genomic data. Benton shares how early internal research proposals—including her push for long-read sequencing and Dr. Marco Riojas’ vision for sequencing ATCC’s collection—laid the foundation for the portal. Their work, along with challenges in microbiome research where public genome assemblies failed to match known inputs, underscored the need for a reliable genomic resource. Launched in 2019 with just 250 genomes and basic sequencing tools, the portal has since expanded to over 5,500 genomes, backed by automation, a larger team, and advanced sequencing capabilities. The portal is continually evolving and now includes data from bacteriology, virology, mycology, and protistology collections, all accessible via a secure REST-API. Looking ahead, ATCC plans to enhance the portal with methylation data, expanded annotations, and additional QC-related metadata, striving to create a comprehensive “digital twin” of each organism to reinforce scientific reproducibility and informed decision-making.
In this episode, Briana Benton presents the ATCC Genome Portal, which was launched in 2019 to offer researchers high-quality, traceable genome data directly associated with physical materials in the ATCC collection. Benton explained that each genome published on the portal is produced entirely in-house, adhering to ISO 9001 standards from strain cultivation to final genome assembly. With over 5,500 genomes currently available and new additions made quarterly, the portal aims to eventually encompass ATCC’s entire collection. The portal’s distinctive value lies in its unparalleled traceability, including documentation of storage conditions and equipment used, which ensures scientific reproducibility and reliability. While the portal does not provide analytical tools, Benton emphasized that ATCC’s mission is to supply authenticated, reproducible data, enabling researchers to utilize their preferred tools for analysis.
In this episode, Dr. Nilay Chakraborty discusses the newly launched MicroQuant portfolio by ATCC, which consists of quantitated microbial reference materials designed to simplify quality control testing. These materials are essential for ensuring the safety and efficacy of products across various industries, including food, cosmetics, and pharmaceuticals. The portfolio includes 12 products that meet stringent regulatory requirements, focusing on ease of use and delivering consistent results in terms of colony-forming units (CFU). They highlight the importance of regulatory guidelines and how the portfolio addresses both known pathogens and adventitious agents. The conversation emphasizes the engineering innovation behind MicroQuant, which reduces preparation time from two weeks to less than a minute, offering significant cost savings and logistical benefits. The portfolio is designed to reduce genetic drift risks and ensure consistency in QC testing, with potential for future expansion based on customer input.
Dr. Chakraborty continues his discussion on cryobiology, focusing on the innovative ThawReady™ Assay Ready Cells that his group developed. He explains that traditional cryopreservation methods cause cellular injuries that manifest when cells are thawed, leading to delayed functionality. ThawReady™ Assay Ready Cells are designed to minimize these injuries, allowing immediate use after thawing and reducing the time and effort required for cell culture. Dr. Chakraborty goes on to discuss the strategic approach ATCC took, leveraging advanced omics technologies to understand and mitigate cellular injuries. The conversation also covers the broader implications of this technology, including cost savings and enhanced efficiency. Dr Chakraborty concludes the discussion by highlighting the importance of compatibility with new characterization technologies and the need for standardization.
In this episode Dr. Nilay Chakraborty, head of the Cryobiology Research and Development Department at ATCC, explains his group's focus on creating innovative technologies and products involving ATCC's organisms and cell lines. Dr. Chakraborty stresses the overall aim to improve the delivery and format of these materials to better serve customers. He then discusses the challenges of managing ATCC's extensive catalog and the importance of cryopreservation in maintaining the bioactivity of biological materials. The conversation highlights the complexities of cryopreservation, the need for different preservation recipes, and the expansion of their R&D unit to include specialized manufacturing. Dr. Chakraborty then explores the intricacies of freezing biological materials and opportunities for improving preservation processes. He also shares his background in engineering and its application to cryobiology, emphasizing the development of platform technologies and the importance of understanding biology at a deeper level for more effective preservation solutions.
In this episode, Dr Jesse Boehm relates his inspiring journey into the world of translational research. Dr Boehm focuses on how his laboratory engineered solutions to complex biological problems, particularly cancer. He stresses the importance of working alongside cancer patients, sharing a very personal story and the impact it had on his perspective. Thanks to this perspective, Dr. Boehm encourages cancer scientists to consider urgency and patient impact of their research.
In this episode, Dr. Jesse Boehm discusses the importance of collaboration in cancer research. Dr. Boehm touches on some of the partnerships that he has been involved in, such as the large collections of organoids and cell models in the Human Cancer Models Initiative. Although logistical and bureaucratic can challenge these cross-institutional partnerships, Dr. Boehm shares the key ingredients that make collaboration more feasible. Dr Boehm also notes that the urgency seen during the recent pandemic should be applied to cancer research to drive significant progress.
In this episode, David Yarmosh and Tasha Santiago-Rodriguez delve into their unexpected journeys into bioinformatics and data science. Tasha shares her transition from wet lab work to data science, emphasizing the importance of reproducibility and proper experimental controls in microbiome research. Finally, Tasha reflects on her work with ancient DNA and microbiomes, viewing it as a way of revealing history and making history by uncovering details about ancient cultures.
Here, Nick Greenfield discusses the evolution of One Codex from a microbiome analysis company to an integrated end-to-end provider. Greenfield brings up a few ideas that he has been incubating, particularly around large language models and data visualization. In a discussion about the future of One Codex, Greenfield shares upcoming changes to his organization’s business model. He also remarks on the challenges of maintaining and updating their database due to the constant changes in taxonomy.
In this episode Nick Greenfield, the founder of One Codex, discusses his transition from a background in environmental studies and international relations to establishing a microbiome company. He touches on his experience entering a contest by the Defense Threat Reduction Agency in 2013, aimed at developing better metagenomics algorithms. Despite not winning, the positive feedback on their prototype’s ease of use revealed a market gap. This led to the creation of One Codex. Greenfield further expostulates on the challenges and lessons learned during the construction of the first metagenomic database for One Codex.
In this episode Nick Greenfield, the founder of One Codex, describes his organization’s evolution from a microbiome analysis company in 2014 to a full-service microbial company. Mr. Greenfield shares his transition from CEO to board chair, reflecting on the early days of One Codex when there was no market. He also emphasizes the company’s focus on reducing complexity for the user, providing a high-quality result, and making new types of data more accessible for a large audience. Mr. Greenfield then shares some of One Codex’ positive contributions to the biological community and the general market.
In this episode, James Crill delves into the future of microbial forensics, emphasizing the importance of fully vetted databases for microbial forensics and the impact of rapid technological advancements. Mr. Crill discusses the evolution of sequencing technologies, from large laboratory equipment to more mobile and efficient technologies. He underscores the urgency for data validation and authentication due to the influx of diverse data and the ongoing changes in sequencing technologies. Crill closes by discussing the importance of studying microbial forensics and microbial communities, emphasizing the need for continued research and development of new techniques in this field.
In this episode, Jamie Crill discusses his research focus of microbial forensics, particularly the origins of bacteria and yeast. Join us as we engage discussion about how to use microorganisms to determine if a crime was a biological one, or if these microbes can clarify when and where a person has been recently. Additionally, Dr. Crill will discuss what the current methods are for determination, and what it's like to teach these skills to graduate students.
In the third episode in this series, Dr. Birgitt Schuele shares her insights on the current state and future directions of this field, from diagnosis and care to mechanisms and treatments. She also tells us about her own work on using machine learning to study mouse behavior in the dark, and creating 3D organ models from stem cells to simulate drug responses. She explains how these technologies can help us understand our own biology better, and reduce the need for animal models and human trials. She also discusses the challenges and limitations of creating a simulated human that can capture the complexity and diversity of individual biology.