Dina Buitrago Silva

This is fun, a pending Illumina patent (US20240158849A1) that describes a completely new way to do sequencing (surfaced by Nava Whiteford on the ASeq discord). Inventors are Rico Otto and Hayden Black. My interpretation (maybe the inventors will chime in to correct🤪): - Build a chip with pairs of electrodes on it, each pair of electrodes fitted with a circuit [160] that measures very small electrical changes (e.g. current) between the electrodes. - Assemble a long polymer bridge between the two electrodes. - Here's where it gets crazy: coat the bridge in gold 👑 so it's electrically connected at each end to an electrode, and etch the gold off the middle of the bridge (what could do wrong 😳) so there is an exposed detector [113] - Mix up a soup of bases like A [123] that have a conductive tail [133]; each base gets its own version of the tail, and each of the four tails is electrically different e.g. has a different resistance. - Send a polymerase [105] chunking along the DNA strand to be sequenced [150], incorporating bases like [123] to form a complementary strand [140] - Each time a base is incorporated into [140] its conductive tail [133] somehow (😳) flops onto the bridge detector [111] so changes the electrical properties of the bridge which can measured by the detector circuit. Easy peasy, sequencing squeezy! Patents shows some scanning tunneling microscope pictures that may or may not show this working 🤷‍♂️ Why do this? If this works in practice (big if around any sequencing technology) it's pretty cool as it's a single (maybe CMOS) chip with no light source, optical detectors, integration time, nanopore (organic or otherwise). As the investors write, it "is robust, reproducible, sensitive, accurate, works in real time, detects single molecules, and has high throughput." Anyway, nice to see there's some greenfield research going on at Illumina 👏👏👏

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Single-cell and spatial transcriptomics friends: it'd be tremendously helpful to our team if you could briefly chat about your current unmet needs in this quickly-evolving space (no pun intended!) and gauge the value of the technologies we're developing. Please DM if you'd like to participate!

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You're a scientist finishing grad school and you want a job in biotech. When should you apply? Do you need to do a postdoc? What about industry postdocs? Here are my answers to these 3 common questions: 𝗤𝘂𝗲𝘀𝘁𝗶𝗼𝗻 𝟭 How long before graduation should I start applying to jobs in biotech? 𝗔𝗻𝘀𝘄𝗲𝗿 𝟭   Start applying 4-6 months before graduation. It can take 1-2 months to get into the groove of applications and to get the traction you need for your first interview. Once you get your interview it can take anywhere from 1-3 months for the hiring process to finish (depends on size of company). Note: small startups tend to want you to start working right away. Large pharma companies tend to be more willing to wait 4-6 weeks. 𝗤𝘂𝗲𝘀𝘁𝗶𝗼𝗻 𝟮 Do I need to have postdoc experience? Does it help me? 𝗔𝗻𝘀𝘄𝗲𝗿 𝟮 It depends on your skills. If you meet all of the skills in a high demand field, you don’t need to do postdoc (ie coding + lab, gene editing crispr/cas9, CAR-T, bioinformatics). If you want to go to industry the purpose of a postdoc is to upskill. 𝗤𝘂𝗲𝘀𝘁𝗶𝗼𝗻 𝟯 How does industry view academic postdocs vs industry postdocs? 𝗔𝗻𝘀𝘄𝗲𝗿 𝟯 Industry postdocs are the best choice for individuals who want to pursue the postdoctoral path. You'll get to upskill, while gaining experience that is considered "industry experience". Just make sure you do your postdoc at a big name, reputable pharmaceutical company (ie BMS, Merck, J&J, Genentech, Lilly) 𝗠𝗮𝗶𝗻 𝘁𝗮𝗸𝗲𝗮𝘄𝗮𝘆? Plan ahead and focus on building out skills that are in high demand. #biotech, #biotechjobs, #scientist PS - what other questions do you have about getting your first (or next) biotech job? Comment below.  

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Will synthetic biology ever launch? 🚀 An opinion piece arguing that synthetic biology is all hype and no product (link below) was published coincidental with this week’s SynBioBeta conference (surely not a coincidence tho). It’s a heavy accusation but not one that should be dismissed out of hand. One of my favorite panel questions from the audience this week echoed the charge - the questioner had spent 30 years in this field himself and was still waiting to see commercial proof of its promise. Will we ever make products, he asked? I’ve thought about this question a lot this week through the conference. As a first time attendee to SynBioBeta, I was expecting it to be a bit of a “scene,” but what I found instead was a community grappling (transparently and honestly) with a fundamentally new technical paradigm that is HARD for very real reasons (e.g. petroleum is cheap!) - but that also has the potential to unlock a step change in how our society looks and feels. It’s easy to forget that technical revolutions take time. The first commercially-relevant steam engine was launched in 1712, a full century before the Industrial Revolution it enabled was fully and obviously in operation. Will lots of early companies burn mountains of cash and go out of business in the process of discovering and trying to solve the biggest challenges? Yup. And while searching for technoeconomic and business models that make sense in this field? Yup. Will it take more than one investment cycle to see the full evolution and deployment of this field? Yup. The evaporation of easy money and thinning patience for big promises will winnow the current synthetic biology startup landscape, but the field (and the people and their experience) will remain - and the next generation of companies will be wiser, more disciplined, more focused - and more successful. One of the big themes this year was that synthetic biology companies need to SHIP. As confident as I am that the next 12 months will bring more company “failures” in this space, I’m just as confident we’ll see real, durable progress on launching focused, valuable products - and that this will create concrete and convincing steps towards unveiling the potential we all know this field has. #syntheticbiology #bioengineering #future #molecularfarming #foodtech #synbiobeta #synbiobeta2024

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I'm excited to attend the #SynBYSS Symposium hosted by the J. Craig Venter Institute at the University of Hawaii at Manoa. This event will delve into the latest advancements in synthetic biology, covering a diverse range of topics that are shaping the future of the field. Key areas of focus include: - Fundamentals and Scientific Discovery: Exploring the origins of life, synthetic cells, new mechanism discoveries, and the design of minimal genomes. - Human Health and Translational Medicine: Advancements in synthetic biology for novel medicines, engineered microbiomes for health, and applications in mammalian systems. - Sustainability and Innovation: Progress in biofuels, biomaterials, agricultural applications, and addressing biosecurity and ethics with computational tools and multi-omics approaches. Looking forward to engaging with experts from academia and industry. https://lnkd.in/dy__A8Du #SyntheticBiology #Biotechnology #SynBYSS #EngineeringBiology #Genomics #LifeSciences #Biosecurity #Sustainability

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The GLP1 story illustrates the "academic-industrial valley of death”. What is interesting is how/why the eventual winners (Novo/Lilly) succeed. Ie not through novel target biology but meaningful iterations on delivery, safety, efficacy etc. 2x-daily exenatide to weekly semaglutide to oral semaglutide = masterclass in persistence of development. PCSK9 inhibitors - target ID was some amazing work, but the real change came from solving manufacturing challenges, optimizing dosing schedules, finding right patient populations etc. PD1/PDL1 - Merck wasn't first, but Keytruda dominates through trial design and execution informed by others' stumbles. When the market is so massive coming in 2nd/3rd no longer matters. ☠️ For smaller markets these dynamics reverse = Economics of coming in 2nd look very different, recruitment is a complicated mess, so are the costs, market is 30-60% smaller after the first one; and you just do not recover from suboptimal trial design.

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🔬 A crucial discussion unfolded at #AAPSPharmSci360, as industry leaders tackled the FDA's transformative laboratory-developed test (LDT) proposed rule and its implications for biomarker testing at last month's conference in Salt Lake City.   The high-impact session, moderated by our Chief Scientific Officer, Dr. Lauren Stevenson, brought together expert perspectives from Stephen Piccoli (Sun Pharma), Patrice Hugo (IQVIA Laboratories), and Mark Ma (Rallybio).   The session revealed critical insights into the FDA's April 2024 LDT Final Rule, fundamentally reshaping how diagnostic and exploratory biomarker tests are regulated. Under this new framework, LDTs will transition from their current enforcement discretion policy to being regulated as medical devices.   The implications are significant: industry data suggests 200-400 clinical studies could face delays over the next three years, potentially affecting 30,000-45,000 patients. We're proud to see Immunologix Laboratories contributing to these vital industry discussions.   Read the full article by Bioanalysis Zone here: https://lnkd.in/eTvyRRgY   As a specialized bioanalytical CRO, we understand firsthand how these evolving regulations will reshape pharmaceutical development. Our expertise in this space allows us to offer strategic guidance to sponsors through:   💠 Sophisticated biomarker strategies coupled with depth of regulatory expertise 💠 Custom biomarker assay development and validation 💠 Method transfer and optimization for context of use 💠 PK/PD analysis This regulatory evolution presents both challenges and opportunities for our industry. As we look ahead, our scientific team remains committed to delivering innovative, compliant solutions that advance drug development programs and ultimately benefit patients.   Thank you to AAPS for facilitating these critical conversations that help shape the future of our industry!   #Bioanalysis #DrugDevelopment #Biomarkers #CRO #PharmaceuticalScience #RegulatoryScience #ImmunologixLabs

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An important paper that shows how nextgen anti-CTLA-4 in combination with anti-PD-1 can make a big difference in MSS CRC patients without liver metastasis!

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I think we're seeing a whole new Illumina strategy for defending the mid-market from Element Biosciences competition. I for one was thinking too narrowly to see this - figured it was all about Aviti vs NextSeq. But I think we're starting to see a clever three-pronged Illumina strategy: (1) Times are hard, why buy a mid instrument for $400K when you can just skip that and send your samples out to someone with an X? (2) High throughput is where it's at, here's a cheap NovaSeq X, why not stretch a little for that and be able to hang with the cool kids? (3) Have you seen our new MiSeq i100? Here take this Lego one. It's just $100K, you can most of your stuff with that, and just send out for the big stuff. Sure, kills NextSeq sales too, but that's easy pain for Illumina to bear, but existential for Element. Here's Illumina CFO Ankur Dhingra spelling it out for Wolfe's Doug Schenkel: "...customers, because of the macro [economic/grant] issues, have been transitioning their sample volume to high throughput. And a lot of our mid throughput customers who are constrained by that macro environment are resorting to sending their samples to either core labs or other sequencing providers." "...the constrained environment is making people take decisions on what are they going to invest in their lab or until money frees up, they're going to take advantage of the lower high throughput [X-based sequencing as a service] pricing that is available externally." "I do think there are additional two factors that are coming our way from an Illumina perspective. We have said we will be launching a slightly lower throughput version of NovaSeq X with a single flow cell. And that is at a price point which is well below 1 million. So, there is a potential that some of our mid throughput customers may see some value there. And also, the higher end of the new MiSeq i100 that we have launched has capabilities that can seep into some of the mid throughput kind of requirements as well. So, it's [Element?😳] going to get squeezed from a little bit from both the directions as well."

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From their abstract: Since the discovery of the enediyne polyketide synthase cassette in 2002, genome sequencing has revealed thousands of distinct enediyne biosynthetic gene clusters, each harboring the conserved enediyne polyketide synthase cassette. Here we report that (1) the products of this cassette are an iodoheptaene, a diiodotetrayne and two pentaynes; (2) the diiodotetrayne represents a common biosynthetic intermediate for all known enediynes; and (3) cryptic iodination can be exploited to increase enediyne titers. These findings establish a unified biosynthetic pathway for the enediynes, set the stage to further advance enediyne core biosynthesis and enable fundamental breakthroughs in chemistry, enzymology and translational applications of enediyne natural products.

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Pharmaceutical Reflections on the Nobel Prize - David Baker and his protein design lab. In 2014, I spent a delightful day with David Baker and his lab members, when I was sent to evaluate his lab's synthetic protein engineering technology, and application to pharmaceutical assets, such as enzymes, binders, and drug delivery systems [molecular cage]. At that time, the Baker lab was already famous for creating a software program that allowed the building of protein structures. This program used starting blocks of peptides that self assembled like viruses, into a complex 3D structure predicted in silico. It could also be used to modify and propose alternative structures, for example, a pH resistant enzyme to digest gluten [PvP biologics] for celiac patients, akin to the concept of lactase for those who are lactose intolerant. All this was done computationally, yet without the use of current day AI / LLM software. It is interesting to note that despite in silico prediction, self assembly to desired super structure, or modified enzymes needed to be tested in real life. Multiple variations would still need to be test synthesized on the bench. So it was remarkable that the validation part was the protein fabrication lab that could test, in small scale, thousands of designs to find the winners that would yield the desired functional properties of the protein macromolecule. As applied to pharma, synthetic peptide sequences carry a high risk in eliciting an immune response, so such structures would be best suited for vaccination programs, where a an immune response from a new cage can be paired with antigen delivery [Icosavax VLP spin out]. In the case of pH resistant glutenase, this protein is orally ingested and thus apart from direct circulation. Clinical testing would still need to be performed EXTREMELY carefully to ensure potency and patient safety in tackling celiac disease [PvP acquired by Takeda]. Unlike lactose intolerance where the malady is based on osmotic imbalance in the bowel, celiac disease is based on an immune / allergic response to peptide components of gluten that may be damaging at miniscule levels. Thus the dose of recombinant glutenase has to match (exceed) the gluten intake and complete digestion in the stomach before reaching the intestines. Such a system would surely benefit from a gastric retention drug delivery system to keep glutenase in stomach as long as possible, and resist wash out by coincidental gastric emptying. The work of David Baker and his Institute for Protein Design lab is truly remarkable, and indeed worthy of a Nobel Prize. I look forward to the day when AI can reliably create functional synthetic peptide structures that can evade the adaptive immune system, and usher in a new era of pharmaceutical products.

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There will be ~500 posters per full day at ASGCT. I've spent hours combing through them. Here are 5 from each day I think you should look at: (This one is focused on gene therapy, but a cell therapy-focused one is coming later this week!) Wednesday: #450: Anellovectors expand the payload capacity of Anellovirus-based vectors, promising more robust gene therapy applications. #485: AAV-RoBERTa enhances AAV efficiency with machine learning, setting new standards in predictive biology tools. #493: Investigating adhesive phenolic molecules for dual AAV vector delivery—potentially a game-changer in gene therapy. #562: Engineered cell lines could be the key to reducing AAV production costs and increasing efficiency. #570: Demonstrating how Design of Experiments methods can significantly boost AAV yields. Honorable Mention: #526: Claire Marasco will be showcasing the potential of global regulatory harmonization in gene and cell therapy. Thursday: #927: Engineering solutions to mitigate risks associated with ex vivo lentivirus applications. #1043: Showcasing how at-line amino acid measurements can optimize scalable rAAV production. #1044: Leveraging high-throughput virology and Design of Experiments for rapid AAV production optimization. - Andrea is a great former colleague, this poster is worth your time! #1048: Advanced sensors for in-line and on-line monitoring optimize cell and gene therapy processes. #1206: A new protein language model predicts cell surface proteins, enhancing genomic therapies. Honorable Mention: #979: Engineered AAV capsids show improved transduction efficiency and reduced immunogenicity. Friday: #1437: An improved helper plasmid with E2a and E4 gene deletions increases AAV productivity and lowers costs. #1453: GUAAVA, an AI tool, designs highly manufacturable AAVs to cut production costs. #1465: AI designs synthetic AAV capsids that may escape pre-existing immunity, expanding the serotype frontier. #1467: Multiscale computational techniques provide insights into the Parvoviridae family's inner capsid structures. #1505: A high-throughput screen identifies targets that enhance AAV9 production without compromising potency. Honorable Mention: #1557: Innovating with Extracellular vesicle-associated AAV (EV-AAV) to avoid innate immune responses. See you on the poster floor! #genetherapy #aav #biotechnology #ai #innovation

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New gene editing technique?! This isn't my area of science (I'm a medchem nerd!), but it sure does sound pretty cool - and just like CRISPR, I'm sure it'll be a tool that will be used in a lot of amazing new research! Getting started with your RNA-based research? At NBS Scientific USA, we have a few GenTegra LLC products that can help to stabilize RNA for up to TWO WEEKS. Message or email me for more information! https://lnkd.in/dDfnFRAP https://lnkd.in/dAQQM9A9 #gentegra #rna #CRISPR #BridgeRNA #science #nerds #scienceiscool #biology #research

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Excited to announce the 2025 Gordon Research Conference (GRC) on Protein Engineering, this second GRC on Protein Engineering will be held at Bryant University in Smithfield, RI from July 27th to August 1st 2025 https://lnkd.in/g-763SeF. please come join us if you would be interested in this exciting field. Different fields have experienced a transformative expansion in research distinction and capabilities. There now exists a strategic opportunity for protein engineering to take the lead and spearhead the integration of this joint effort, reflected by The Nobel Prize in Chemistry 2024. We believe that this GRC conference will create a gateway for the next generation of engineers and researchers, and will be a vehicle toward future development in the midst of an amazing convergence of multiple cutting-edge areas in protein engineering and its applications. Confirmed speakers include the Nobel Laureate Prof. Frances Arnold and distinctive scientists showing below: 1.            Fundamental Principles of Protein Engineering Possu Huang (Stanford University)/Frances Arnold (CalTech, Nobel Laureate)/Huimin Zhao (University of Illinois at Urbana-Champaign) 2.    Biosensors and Imaging Jennifer Prescher (UC Irvine)/Jin zhang (UC San Diego)/Robert Campbell (Tokyo University)/Nathan Shaner (UC San Diego) 3.    Rational Design of New-to Nature Proteins Jiri Damborsky (FNUSA-ICRC & Masaryk University, Czech Republic)/Joelle Pelletier (University of Montreal)/Sílvia Osuna (University of Girona & ICREA, Spain)/Koga Nobuyasu (Osaka Univ, Japan) 4.    AI for Protein engineering Zhongyue John Yang (Vanderbilt University)/ Jennifer Listgarten (UC Berkeley)/Doug Barrick (Johns Hopkins University) 5.    Biocatalysis and Industrial applications Carlos Martinez (Pfzer)/ Stephanie Galanie (Merck)/Zhi Li (National University of Singapore, Singapore)/Brent Dorr (Ginkgo Bioworks) 6.    Protein Engineering for Synthetic Biology Pimchai Chaiyen (Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand)/Weixin Tang (University of Chicago)/Jay Keasling (University of California, Berkeley) 7.    Directed Evolution for Enzyme Optimization Yang Yang (University of California Santa Barbara)/Leilei Zhu (Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, China)/Miguel Alcalde (Institute of Catalysis, CSIC, Spain)/Chang Liu (University of California, Irvine) 8.    Protein engineering for Immunotherapy and other diseases Anna Wu (Beckman Research Institute, City of Hope)/Xue Gao (University of Pennsylvania)/Bingfei Yu (University of Southern California)/Wilson Wong (Boston University) 9.    Repurposing Protein for Novel Chemistry and Applications Stefan Lutz (Codexis Inc)/Xiongyi Huang (Johns Hopkins University)/Xiaojing Gao (Stanford University)

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🌟 Best of #ASMS2024 🌟 Fintiede Solutions is thrilled to share the groundbreaking advancements unveiled by Evosep at the #ASMS2024 conference in Anaheim! Evosep continues to push the boundaries in the field of proteomics, introducing innovations that are set to transform research and clinical diagnostics. 🔬 Key Innovations Announced: Fully Automated Workflows: - Capable of processing over 500 plasma samples per day. - Maximizes efficiency and minimizes manual intervention. - Ideal for accelerating drug discovery and supporting large-scale translational research. - Reduces cost per sample and environmental impact. Whisper™ Zoom Methods: - Enhances scalability and sensitivity for detailed and accurate proteomic analyses. - Unlocks the ability to detect low-abundant proteins and identify novel biomarkers. - Facilitates deeper biological insights into disease pathways. Evosep Biolabs: Center of Excellence for High Throughput Proteomics: - Specializes in high-throughput proteomics with automated sample preparation. - Offers access to state-of-the-art LC-MS/MS workflows and expert assay development. - Provides scalable capacity for outsourcing proteomics research projects. 🏆 Impact and Vision: Evosep's innovations are designed to make clinical proteomics 100x more robust and 10x faster, revolutionizing the landscape of proteomics research. These advancements are particularly aimed at accelerating drug discovery and enhancing proteomics-based diagnostics, ultimately improving patient care. We are proud to be part of this journey and look forward to the incredible breakthroughs these technologies will enable in the near future. #Evosep #Proteomics #ASMS2024 #ScientificInnovation #DrugDiscovery #TranslationalResearch #Biomarkers #ClinicalDiagnostics #automation #whisper

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🚀 Top 3 Tips to Expand Your Biotech Network on LinkedIn 🌐 As a senior at UC San Diego pursuing my undergraduate degree in #communications, I wrote a paper on #Madonna — yep, you heard that right — strike a pose! I've been fascinated by her commitment to and quest for reinvention, and I will never stop reinventing myself. Lately, I've found myself diving deep down the Alice in Wonderland rabbit hole of researching the #psychedelictherapeutic space! If you’re as passionate about the cutting-edge developments in the psychedelic therapeutic space as I am, you know how crucial it is to have a robust professional network. Recently, I’ve been diving deep into this exciting field, researching new companies and connecting with like-minded professionals. I even wrote an opinion piece on the Lykos Therapeutics ad comm results. Here’s how to leverage your LinkedIn presence to expand your life sciences network with real-world tips from my experience! 1. Optimize Your Profile for Discovery 🔍 2. Engage With Your Connections Regularly 💬 3. Join and Participate in LinkedIn Groups 👥 Expanding your biotech/biopharma network on LinkedIn takes time and effort, but the rewards are worth it. By #optimizing your profile, engaging with your connections, and participating in groups, you'll build a robust professional network that supports your career growth in biotech, rare disease, oncology, psychedelic therapeutics, or whatever you choose. Remember, you have the power to create your own opportunities. So strike a pose — keep pushing boundaries, stay curious, and never stop connecting! 🤝 Read the full post on our blog: https://lnkd.in/grYcg2fB #LinkedInTips #BiotechNetworking #CareerGrowth #ProfessionalNetworking #Biotech #PsychedelicTherapeutics #TuesdayTip

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When I made the transition from the broader world of Capital T Tech into Biotech—specifically gene and cell therapy via. OspreyBio—I was shocked by how much of the field still feels ‘archaic’. For example, you mean to tell me that scientists still use razor blades to cut DNA out of gels? Or that, more often than not, when researchers need a vector, they just send out their designs to a third-party company to build it for them? And if they can’t build it then that project is just over? This isn't a rare occurrence. In fact, this lack of control over the process has become so commonplace that it's shaping the entire industry—from the way research is done in the lab, to how educational programs are structured, to how therapeutics are ultimately brought to market. At first, this was a bit surprising to me. From DNA purification to cell culturing, so much of the work is hands-on, and often pretty straightforward. But here's the catch: while this simplicity is awesome, it also feels like we’re hitting a ceiling. A lot of DNA engineering knowledge is being sidelined, and the burden of innovation is being shifted to external companies that handle everything from vector design to DNA synthesis to manufacturing. In other words, the discovery process is getting boxed in. A lot of today’s biotech tech is embedded within the genetic material itself, but the tools around it—tools that could open up new possibilities and unlock new discoveries—are left to the service providers. This limits the creativity and flexibility that researchers can apply to their work. Simply put: if your vector design is constrained by what a service supplier can build, you’re only able to explore within those boundaries. This is exactly why I’m so excited about the work we’re doing at OspreyBio. Yes, we offer a service that can make almost anything—but we’re also building a platform for DIY innovation. Our BoP (Bird of Prey) platform is designed to empower scientists with new, novel tools to enhance and expand the process. We want to put more control back in the hands of researchers and help unlock the full potential of genetic engineering. I’m happy I get to help push this forward, and I’m very enthused about what we will be accomplishing in the next few quarters. 

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Amgen IPP strikes again! Led by the talented Dhanusha Nalawansha and P. Ryan Potts, Ph.D., our team has developed a novel promixity induced modality called LYMTACs. LYMTACs are heterobifunctional small molecules that recruit proteins of interest to the lysosome by co-opting lysosomal resident proteins. This technology is especially effective for membrane targets and offers a "double whammy" mechanism of action: it degrades the target of interest or relocates and traps it to the lysosome. Learn how we applied LYMTACs to target mutant KRAS where we showcase the benefit of this novel approach over traditional modalities. Congrats to all co-authors and collaborators. https://lnkd.in/gN_jxAGQ

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