Model learns how individual amino acids determine protein function

Phys.org | March 25, 2019

A machine-learning model from MIT researchers computationally breaks down how segments of amino acid chains determine a protein's function, which could help researchers design and test new proteins for drug development or biological research. Proteins are linear chains of amino acids, connected by peptide bonds, that fold into exceedingly complex three-dimensional structures, depending on the sequence and physical interactions within the chain. That structure, in turn, determines the protein's biological function. Knowing a protein's 3-D structure, therefore, is valuable for, say, predicting how proteins may respond to certain drugs. However, despite decades of research and the development of multiple imaging techniques, we know only a very small fraction of possible protein structures—tens of thousands out of millions. Researchers are beginning to use machine-learning models to predict protein structures based on their amino acid sequences, which could enable the discovery of new protein structures. But this is challenging, as diverse amino acid sequences can form very similar structures. And there aren't many structures on which to train the models.

Spotlight

It has been well documented that genetic studies of human disease, especially large-scale ones, have not captured the level of diversity that exists globally, as they are predominantly based on populations of European ancestry (Popejoy and Fullerton, 2016). The under-representation of ethnically diverse populations impedes our ability to fully understand the genetic architecture of human disease and exacerbates health inequalities.


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MEDICAL

Slingshot Biosciences, Inc. Partners With Cambridge Bioscience to Distribute Synthetic Cells Throughout United Kingdom and Ireland

Slingshot | June 16, 2022

SLINGSHOT BIOSCIENCES, INC. the makers of synthetic cells that bring consistent precision and accurate control to replace inconsistent blood and tissue controls for use in flow cytometry and other biotech markets, today announced they have extended their distribution channel through a new agreement with Cambridge Bioscience, a UK-based specialist distributor of life science research tools. The agreement entitles Cambridge Bioscience to the right to distribute and resell Slingshot Bio’s products in the United Kingdom and Ireland. Through Cambridge Bioscience’s network of customers, Slingshot Bio will be able to establish its presence in the United Kingdom and Ireland market with the well-established presence and expertise of Cambridge Bioscience which has been selling into flow cytometry for many years. Cambridge Bioscience’s network will provide us with the market penetration needed to reach our full sales potential. Slingshot Biosciences has considered many distribution partners and we are confident that Cambridge Bioscience’s extensive knowledge in the field, prominent presence, and large customer base will help us leverage our position in the flow cytometry market.” Jeffrey Kim, CEO & Founder. About Slingshot Biosciences, Inc. Founded in 2012, Slingshot Biosciences is a fast-growing life sciences company with a platform technology and paradigm-shifting mission to make synthetic cells the gold standard for all cell-based applications—including diagnostics, and adoptive cell therapy development and instrument calibration.

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CELL AND GENE THERAPY

Mission Bio Announces Pharma Assay Development Services for Solid Tumor Research

Mission Bio | July 18, 2022

Mission Bio, Inc., the pioneer in high-throughput single-cell DNA and multi-omics analysis, announced the launch of solid tumor assays through its Pharma Assay Development (PAD) services. The availability of this new service offering will help to accelerate the development of cancer therapeutics by reducing the time and cost associated with the characterization of solid tumor cells. Precision therapeutics for solid tumors have been historically bottlenecked due to technical challenges associated with the ability to deeply profile thousands of individual cells for a rich characterization of tumor evolution and heterogeneity. This must be done at a much higher resolution compared to bulk next-generation sequencing to enable detection of rare events, at a much earlier stage before progression. Utilizing Mission Bio's Tapestri™ platform, the company's PAD services for solid tumors partner with researchers to provide high-resolution data to unmask the underlying genetic diversity across cell populations. Insights into the clonal landscape and co-occurrence of mutations enable improved patient stratification for clinical trials and the identification of druggable targets for precision therapeutics. Researchers can also monitor treatment resistance by analyzing the acquisition of rare mutations driving tumor progression over the course of treatment. The expansion of Mission Bio's PAD services to solid tumor research comes just three months after the launch of the Solid Tumor Solution on the Tapestri™ Platform, demonstrating Mission Bio's commitment to continuously developing innovative single-cell technologies for its pharma customers. "We have seen tremendous uptake and interest from top-tier pharma companies for our blood cancer Pharma Assay Development program, and we expect the same momentum for our solid tumor services. With our solid tumor services, Mission Bio partners with pharma customers to elucidate the mechanisms of drug resistance through mutation acquisition, determine how cells transform from benign to malignant states, and reveal the genomic changes enabling cancer cells to metastasize – without having to bring single-cell technology or resources in-house. From a customer's perspective, it is as easy as shipping out samples and getting a fully analyzed report back." Todd Druley, MD, PhD, Chief Medical Officer of Mission Bio Mission Bio's PAD services deliver comprehensive support across the therapeutic development process. The company has a dedicated team that works with researchers to develop assays, identify high-impact samples, and analyze the data. As part of the service, pharma partners have access to Mission Bio's innovative technology, assay development team, R&D organization, and bioinformatics support. About Mission Bio Mission Bio is a life sciences company that accelerates discoveries and cures for a wide range of diseases by equipping researchers with the tools they need to better measure and predict our resistance and response to new therapies. Mission Bio's multi-omics approach improves time-to-market for new therapeutics, including innovative cell and gene therapies that provide new pathways to health. Founded in 2014, Mission Bio has secured investment from Novo Growth, Cota Capital, Agilent Technologies, Mayfield Fund, and others. The company's Tapestri™ platform gives researchers around the globe the power to interrogate every molecule in a cell together, providing a comprehensive understanding of activity from a single sample. Tapestri™ is the only commercialized multi-omics platform capable of analyzing DNA and protein simultaneously from the same sample at single-cell resolution. The Tapestri™ Platform is being utilized by customers at leading research centers, pharmaceutical, and diagnostics companies worldwide to develop treatments and eventually cures for cancer.

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INDUSTRIAL IMPACT

Persephone Biosciences Closes $15M Seed Financing Round

Persephone Biosciences | July 20, 2022

Persephone Biosciences Inc., a synthetic biology company reimagining patient and infant health through the development of microbiome-based medicines, today announced that it has closed a $15 million seed financing round. The round was co-led by First Bight Ventures and Propel Bio Partners, and included investments from Y Combinator, Fifty Years, Susa Ventures, American Cancer Society’s BrightEdge Fund, Pioneer Fund, and ZhenFund among others. “This financing is a significant milestone for Persephone and the culmination of years of thoughtful engagement with forward-thinking investors and individuals who are committed to the vast potential of our platform and technology. We plan to deploy this capital to further expand our research and clinical programs across a range of therapeutic areas, as well as pursue new collaborations. With our ARGONAUT study ramping up, it is an exciting time for us. We are grateful for the support of all our stakeholders and their commitment and confidence in our vision.” Stephanie Culler, CEO and Co-founder of Persephone Biosciences Persephone was founded to leverage a unique understanding of the microbiome as a therapeutic approach for a number of indications, including infant health and oncology. The company’s ARGONAUT trial (NCT04638751) is the largest study ever conducted in the U.S. to identify biomarkers for cancer treatment and prevention by mapping the gut-immune axis. In December 2021, Persephone announced that Janssen Biotech, one of Janssen Pharmaceutical Companies of Johnson & Johnson, would collaborate with the company on the colorectal cancer patient arm of ARGONAUT, and on an arm of additional healthy individuals with varying cancer risk. Then in April 2022, Persephone announced a collaboration with Ginkgo Bioworks to enable the synthetic biology tools needed to develop the next generation of microbial therapies. About Persephone Biosciences Persephone Biosciences is pioneering the use of synthetic biology for the development of microbial products that impact patient and infant health. Persephone is building an end-to-end platform to industrialize the development of engineered cells that restore health to damaged human ecosystems. The company was founded in the summer of 2017 by synthetic and metabolic engineering pioneers, Stephanie Culler, Ph.D., and Steve Van Dien, Ph.D.

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MEDICAL

MediKarma Selects 1upHealth as its Interoperability Partner to Help Patients Acquire Their Medical Records from Hospital EMRs

1upHealth | June 07, 2022

MediKarma, Inc, a global leader in an AI-based patient engagement, education and navigation platform, has selected 1upHealth, the market leader offering healthcare's most complete FHIR® data platform, as its interoperability partner to help patients request and acquire their medical records through FHIR-based APIs. Fast Healthcare Interoperability Resources (FHIR®) is the future of healthcare that brings together claims and clinical information in one common standard to drive innovation. MediKarma, Inc. intends to upend the healthcare market by providing a consumer-focused platform with personalized human body visualization, a dynamic health score and an AI voice companion that answers the important, recurring question, "What do I do next?" By integrating seamlessly into a consumer's lifestyle and leveraging data from multiple sources, MediKarma reduces friction within the healthcare journey and provides the best next action, which enables an improved healthcare experience. The interoperability partnership between MediKarma and 1upHealth solves two significant user challenges: one, helping patients quickly access all of their medical and EMR records from multiple sources, and two, helping patients make sound decisions about the best way to enable continuous improvements in their personal healthcare. MediKarma's AI-enabled healthcare coach and daily health scores provide easy-to-access and Next Step information for the consumer. Finding a vendor with an accurate, easy-to-navigate records collection capability was paramount when selecting 1upHealth as an interoperability partner, The 1up|Health History app is easy to navigate and enables complete user health history to be integrated into the Medikarma workflow in under an hour." Kris Narayan, CEO of Medikarma. 1upHealth is leading healthcare's conversion to FHIR®, a standard that is based on the same web technologies that have transformed other industries such as retail, travel and finance, We purpose-built a modern data architecture to rebuild how healthcare accesses, stores, analyzes and shares data using a scalable, serverless environment." Joe Gagnon, CEO of 1upHealth. The 1up|Health History application enables individuals to connect and request their health data from the company's integrated network of 10,000+ clinical and payer endpoints. The disparate data is then ingested and conformed into clean FHIR® that is more timely, usable, and computable.

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Spotlight

It has been well documented that genetic studies of human disease, especially large-scale ones, have not captured the level of diversity that exists globally, as they are predominantly based on populations of European ancestry (Popejoy and Fullerton, 2016). The under-representation of ethnically diverse populations impedes our ability to fully understand the genetic architecture of human disease and exacerbates health inequalities.

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