Stemloop, Inc.

???Feature Friday: Spotlight on Dr.?Marie M. Daly?? Dr. Marie M. Daly’s legacy in biochemistry is profound and inspiring. As the first African American woman to earn a Ph.D. in Chemistry in the United States???, her achievements laid critical foundations in science and broke down barriers???. After earning her undergraduate degree from Queen’s College and her Ph.D. at Columbia University, Dr. Daly delved into research that would change how we understand the chemistry of life???. Her doctoral work, under Mary L. Caldwell, investigated digestive enzymes like amylase, setting the stage for a lifetime of scientific contributions that spanned across fields. Dr. Daly made groundbreaking discoveries in cholesterol metabolism, showing its role in cardiovascular health????by identifying how high cholesterol contributes to artery blockage. This early work was essential in developing our current understanding of heart disease and preventive healthcare???. Her insights into lipid metabolism and cell membrane structures advanced our knowledge of cellular health and disease???. But Dr. Daly’s research went beyond cholesterol—she was equally fascinated by the cell nucleus, working to decode the mysteries of nucleic acids and histones, proteins that help structure DNA and influence gene regulation???. Her early studies on nuclear molecules laid the groundwork for modern epigenetics, influencing research into diseases like cancer. Beyond her research, Dr. Daly was a passionate advocate for diversity in science, championing opportunities for underrepresented groups. She taught and mentored at institutions like Howard University and the Albert Einstein College of Medicine????, encouraging minority students to pursue careers in STEM. Dr. Daly also established scholarship programs to help students from diverse backgrounds access higher education?????????????, building pathways for future scientists and leaders. Today, her pioneering work continues to impact areas from lipid research to gene regulation and protein synthesis. As we celebrate her contributions, let’s also honor Dr. Daly’s commitment to knowledge and inclusion in science—a legacy that lives on in the researchers inspired by her remarkable achievements??????. #MarieDalyLegacy #WomenInScience #BiochemistryPioneer #DiversityInSTEM #TrailblazingChemist #STEMHistory

??Stemloop Reads: Challenges for AI Protein Design AI is transforming protein design, offering exciting prospects for creating bespoke proteins. But we’re not there yet! Sara Reardon’s latest piece in Nature highlights five key challenges that stand in the way: Binding: Although binding algorithms between proteins have been successful, predicting binding with small molecules remains challenging. ?? New catalysts: Designing enzymes for new functions is challenging since structure doesn’t always correlate directly with function. ?? Modeling conformational changes: Proteins change shape, making it hard to capture all active forms computationally. ?? Complex Protein Structures: Designing multifunctional proteins or machines is limited by data on known molecular structures. ?? Learning from Design Failures: AI often “hallucinates” invalid structures, with few mechanisms to learn from design errors. ?? ??Read more about these challenges and potential solutions here: https://lnkd.in/gKvz4gHM #ProteinDesign #ArtificialIntelligence #Biotech #Innovation

???Zombie Genes: The Secrets of Life After Death!???♂?? Spooky but true: some genes don’t seem to know when to quit! Zombie genes actually “wake up” after death, showing a strange surge in activity in tissues like the brain and liver. As other cells go quiet, these genes start switching on, and researchers are still uncovering exactly why. ? Less than a decade ago, researchers discovered that gene expression doesn’t stop at death! Some genes, dubbed "zombie genes," awaken and start functioning days later, often mirroring those active during early development.????♂??? ? These genes play crucial roles in cell survival, stress responses, and even cancer. One key player is the hypoxia-inducible factor (HIF), a transcription factor that regulates hundreds of genes in response to low oxygen—a vital part of embryonic development and cellular survival. ? But why do these genes come alive after death? The phenomenon, known as the thanatotranscriptome, might help us in fields like forensics (predicting postmortem intervals) and organ transplantation (improving donor-recipient matches).??? ? In honor of Halloween, it’s a fitting time to ponder these “living” secrets of the dead.????So, what’s the takeaway? Zombie genes may hold the molecular keys to understanding the continuum of life and death. What do you think—can science illuminate the mysteries beyond the veil???????Share your thoughts below! ? Link to full article ? https://lnkd.in/gm28mcay #ZombieGenes??#GeneExpression #TranscriptionFactors??#Forensics #OrganTransplant #CellBiology?#ScienceMysteries #Biotechnology

Stemloop Reads: Cell-Free Protein Synthesis ?? Last month, Zachary Sun of Sepia Biosciences shared a fascinating look into Kangma Healthcode, a company in China focused on revolutionizing cell-free protein synthesis. They claim to have solved two major challenges: synthesizing complicated proteins and scaling production. As a eukaryotic organism, yeast is able to produce more complicated proteins than traditional E. Coli systems. Previously, others have had difficulty getting a good yield from these systems, but Kangma has reported yields up to 1 mg/mL! As for scaling, Kangma has reported hitting 100,000 L scale production in 2024, with apparent GMP-like processes. This far surpasses the typical Western standard of 1,000 L scales. Here at Stemloop, we are excited by this news out of China on developments in the cell-free protein synthesis space! We are also excited to read more from Zachary, so be sure to check out his post below! ??: https://lnkd.in/g_c2P9Zb #Innovation #CellFree #Yeast #Biotechnology?

???eDNA Sensors: Changing How We Monitor Wildlife????? Environmental DNA (eDNA) is a game-changer for wildlife conservation! Instead of using time-consuming methods like camera traps, scientists can now simply collect samples from water, soil, or even air to detect the DNA that animals leave behind—such as through skin, hair, or waste[1]. By analyzing these environmental traces, researchers can identify which species are present in an ecosystem without needing to physically capture or observe them. This non-invasive approach makes it easier to track rare or endangered animals while minimizing human impact on their habitats.?? Real-World Applications of eDNA??? eDNA has already helped conservationists identify species that are hard to monitor, like fish in the Amazon and Orinoco rivers. Scientists have been able to detect?near-threatened?fish like the giant catfish (Sorubim) and?vulnerable?species such as the arapaima, one of the world’s largest freshwater fish[2]. By using eDNA, researchers can better understand how these species are distributed across ecosystems and help inform conservation strategies to protect them. This method is crucial for saving biodiversity without disturbing the animals or their environments!????? Biosensors in eDNA: What’s Next???? While eDNA is already making a big impact, biosensors are set to take things to the next level! Scientists are developing sensors that can detect the DNA of harmful species, like crown-of-thorns starfish (COTS), which damage coral reefs. By using a special DNA probe, this sensor detects COTS before they can wreak havoc on coral, providing an early warning system to prevent outbreaks[3].??????Another project is even using CRISPR-Cas technology to improve eDNA detection for species like Atlantic salmon, making it easier to monitor endangered animals in real time[4]. The future of biosensors in wildlife monitoring is bright, and these innovations could be key to saving vulnerable ecosystems!?????? #eDNA #WildlifeConservation #Biodiversity #Innovation #Biosensors #ConservationTech #CRISPR [1] https://lnkd.in/es7M6fY [2] https://lnkd.in/gynkJrxu [3] https://lnkd.in/gmsdCe2m [4] https://lnkd.in/gnJCai8Q

Stemloop Reads: Energy and AI ???? Several of the Nobel Prize announcements earlier this month involved applications of AI and machine learning to scientific research. Although this technology presents exciting possibilities across numerous fields, there are also concerns about its impact on the environment. ?? In an article posted to Nature this month, Katherine Bourzac discusses this issue and potential solutions. It is an issue faced by computer scientists previously; in the 1990’s, they were able to address energy efficiency challenges by shifting to multicore processors. Today, innovators around the world are seeking a similar solution to the energy crisis presented by AI. This includes further improvements in chip design, adjusting how databases are accessed, and innovations in photonics.?? Here at Stemloop, we are excited by the emerging applications of AI, especially when it comes to protein design and structure determination. As a company who values using science as a positive force in our world, we are grateful for those working to improve the environmental impact of these processes! ??Read more here: https://lnkd.in/dYvcfRFE #AI #Innovation #Sustainability

???Feature Friday: Spotlight on?Dr.?Ernest Everett Just??? This week, we honor Dr. Ernest Everett Just, a trailblazing African American biologist whose research transformed our understanding of cell biology and development???. Graduating?magna cum laude?from Dartmouth in 1907 and earning his Ph.D. from the University of Chicago in 1916???, Dr. Just was one of the first African American men to achieve this milestone. His summers at the Marine Biological Laboratory (MBL) refined his expertise in marine invertebrate fertilization, unlocking groundbreaking discoveries. ???Dr. Just’s major contribution? He discovered the "wave of negativity" that sweeps across a sea urchin egg after fertilization. Once a sperm enters, this electrical wave prevents any other sperm from entering—a process called?polyspermy. He identified two mechanisms that help block additional sperm: a?fast block?that acts instantly to stop more sperm and a?slow block?that changes the egg’s structure over time, sealing it off?[1]. His work revealed how eggs ensure they are fertilized by just one sperm, a key discovery for cell biology! Despite facing systemic racism, which limited his opportunities at major universities, Dr. Just continued his work at Howard University and co-authored the textbook?General Cytology?in 1924, shaping the future of biology. ???In Europe, Dr. Just thrived, conducting research at Italy’s renowned zoological station Anton Dohrn and becoming the first American invited to the Kaiser Wilhelm Institute, a hub for Nobel Prize-winning research. ???At Stemloop, we draw inspiration from Dr. Just’s legacy of resilience and dedication. His pioneering work in cellular biology serves as a reminder of the importance of inclusivity and diversity in science. ??Dr. Just’s work laid the groundwork for modern biology, and his discoveries continue to inspire scientists in the fields of developmental biology and beyond. His dedication to science and education remains a beacon of excellence for future generations. [1]?https://lnkd.in/gkY4K3nS #ErnestEverettJust #CellBiology #DevelopmentalBiology #Innovation #FeatureFriday #STEM #ScientificLegacy #Biosensors #Education #DiversityInSTEM

Stemloop Reads: Engineering Transcription Factors ?? Earlier this month, two of our scientific cofounders, Michael Jewett and Julius Lucks, collaborated with others on a paper in ACS Synthetic Biology, detailing the process of engineering transcription factors for greater sensitivity, selectivity, and dynamic range. By using automation and cell-free workflows, they were able to screen over 100 variants in less than 48 hours! This article starts with an investigation into optimal parameters for using Echo Acoustic Liquid Handlers, including reaction volume, fluid composition, and plate uniformity. Using these findings, they set up 3,682 unique reactions to characterize 127 MerR and 134 CadR variants! Here at Stemloop, we are energized by the idea of integrating more automation into our existing workflows! Seeing this idea come to fruition with allosteric transcription factors has been greatly inspiring! ??Read the full article here: https://lnkd.in/gf-PPsmg #SyntheticBiology #Automation #Biosensors #Innovation #Biotech

???Celebrating Nobel Excellence in Science!??? This year’s Nobel Prize winners in?Physics,?Chemistry, and?Physiology or Medicine?have made groundbreaking contributions that are shaping the future of technology, biology, and medicine. Let's take a moment to applaud their incredible achievements!???? ???Physics: John J. Hopfield & Geoffrey E. Hinton Awarded for pioneering work in?machine learning with artificial neural networks—the foundation of modern AI!??? Fun fact: Hinton's work helped spark the development of AI that can?teach itself?by learning from data, just like the human brain!????? ???Chemistry: David Baker, Demis Hassabis & John M. Jumper Recognized for their game-changing advancements in?computational protein design?and?protein structure prediction. Their discoveries are revolutionizing how we understand proteins and biology! Fun fact: Thanks to AlphaFold, we now have 3D structures for nearly all (98.5%) of the human proteome???. Of these, 36% are predicted with very high accuracy??, and another 22% with high accuracy??? ???Physiology or Medicine: Victor Ambros & Gary Ruvkun Honored for their discovery of?microRNA?and its crucial role in regulating gene expression—paving the way for innovations in disease treatment and understanding gene regulation. Fun fact: MicroRNAs were once thrown aside as insignificant, but they turned out to be essential regulators of gene expression!???? #NobelPrize #Innovation #ScienceForTheFuture #MachineLearning #ProteinDesign #MicroRNA

???Citrate Series: Week 2 - Citrate’s Biochemical Superpowers & The TCA Cycle Welcome back!????This week, we’re diving into why citrate is not only vital for your body’s energy???but also a key player in industries like biotech and biomanufacturing. Citrate’s Biochemical Superpowers??? Citrate, a negatively charged molecule??, interacts with other substances in powerful ways. In your body, it fuels energy production, supports strong bones???, and helps make fatty acids and cholesterol. But it’s also a star in industries like pharmaceuticals????and food preservation, thanks to its ability to stabilize products and control acidity. The TCA Cycle – The Heart of Cellular Energy??? Here’s something cool: every time you breathe????, the TCA cycle (or Krebs cycle) is turning your food into energy!??Inside your cells’ mitochondria???, citrate is the first molecule created, sparking a chain reaction that converts nutrients into the energy you need for everything—from a workout to your daily tasks. Why Citrate is a Big Deal for Industry??? Beyond human metabolism, citrate plays a major role in industrial applications. In biomanufacturing???, measuring citrate levels helps optimize processes like fermentation, while in medical diagnostics , it can help detect metabolic disorders. Whether it’s improving bio-based products????or advancing healthcare, citrate is at the core of it all. Want to see the TCA cycle in action?????Check out this animation that breaks down each step! ? https://lnkd.in/ebaNyax6 Missed last week’s intro to citrate??Catch up on Week 1 and see why citrate is everywhere—from your body to the products you use every day! Citrate Series: Week 1 ? https://lnkd.in/e_HZtRXn #Citrate #TCAcycle #KrebsCycle #Metabolism #Biosensors #EnergyProduction #Biotech #Innovation #IndustrialInnovation