TowardPi’s Post

Scientists at Sanford Burnham Prebys have found that small extracellular vesicles (sEVs) traveling between Christine S. Liu the brain carry more complete instructions for altering cellular function than previously thought. Main Takeaways: 🪩 Neural sEVs contain full-length poly-adenylated mRNAs with diverse and novel isoforms. 🪩 Neural sEV mRNA composition is distinct from bulk brain and includes L1Hs sequences. 🪩 Neural sEVs are selectively packaged by Alzheimer’s disease state and cell type. 🪩 Neural sEV-enriched mRNAs contain RNA-binding protein motifs Congratulations to Linnea Ransom, Christine S. Liu, Emily Dunsmore, Carter Palmer, Juliet Nicodemus, Derya Degirmenci Ziomek, Nyssa Williams, and Jerold Chun! Their work can be accessed here: https://lnkd.in/e5Q3GBVb #nanoparticles #exosomes #vesicles #mRNA #RNA #innovation #research #education #pharma #science #biology #molecularbiology

✨ Excited to share our latest publication in Nature Communications! This is my second coauthored paper in Nature Communications! 🎉 The study, "Vasculogenic skin reprogramming requires TET-mediated gene demethylation in fibroblasts for rescuing impaired perfusion in diabetes," investigates innovative strategies for improving vascular repair in diabetes. You can read the full article here: https://lnkd.in/gRH6wdeq. A special congratulations to the first authors, Dr. Sujit K. Mohanty and Dr. Kanhaiya Singh, and to Dr. Chandan K. Sen, the PI and mentor leading this work, for their outstanding vision and dedication. I’m proud to have contributed, among others, to this work by conducting single-cell RNA sequencing experiments for 7 samples using the 10x Chromium device, including GEM production, cDNA synthesis, DNA cleaning, library construction, and cDNA/library quality checks, in the Indiana University ICRME (Indiana Center for Regenerative Medicine and Engineering), which is part of the Department of Surgery, where I started my single-cell RNA sequencing adventure. 🔬 Transitioning from hands-on single-cell experiments to 💻 bioinformatics codes, functions, and algorithms, I’ve learned how to connect the 🧬 cells I see under a microscope to the numbers and patterns revealed through data analysis. This dual perspective has allowed me to understand and approach problems from both sides, bridging experimental and computational biology. #NatureCommunications #SingleCellRNAseq #10xGenomics #Bioinformatics #DiabetesResearch #RegenerativeMedicine #Collaboration #CellChat #UMAP #DotPlot #VlnPlot

https://lnkd.in/eD59nwt8 I'm excited to share the main chapter of my PhD dissertation, now published in Genes!  For the first time, we investigated how transfer RNA levels are fine-tuned during brain development in fruit fly ( Drosophila) - neurobiology's favorite model organism. Key finding: Neural stem cells and neurons maintain different tRNA expression profiles to optimize the production of cell-type specific proteins. Using transcriptome-wide "omics" approaches - hydro-tRNAseq, (m)RNAseq, cell-type specific mRNA decay measurements - our model supports that differential tRNA abundance during Drosophila neurogenesis likely serves to shift optimal translation from proliferation toward a subset of differentiation associated transcripts (especially RNA-binding proteins and kinases). Intriguingly, we didn't observe any widespread 'anticodon buffering' in the Drosophila nervous system as compared to previous reports in the mammalian CNS - where changes in individual tRNA genes don't affect the overall anticodon pool. We think this difference reflects the shorter timescale of invertebrate neurogenesis compared to mammals, creating selection pressure to evolve quick-acting post-transcriptional regulatory mechanisms such as unbuffered tRNA changes to modulate translation of existing mRNAs. Grateful to my PhD advisors Michael Cleary and David Ardell. Special thanks to my former Cleary Lab mate Josephine Sami, PhD for generating the mRNA decay data.

🌟 Exciting Research Update! 🌟 Our latest study on Alzheimer’s disease (AD), a devastating neurodegenerative disorder affecting millions worldwide, has been published in Nature’s Scientific Reports. 🧠✨ In this research, we explored how static and oscillating electric fields can disrupt the harmful Aβ fibrils associated with AD. Using molecular dynamics simulations, we specifically examined a polymorphic fibrillar complex of the Aβ1–40 peptide with the Osaka mutation (E22Δ), which is known for its toxicity and stable structure. Our findings reveal that applying a 0.3–0.4 V/nm electric field at a 0.20 GHz frequency can effectively disrupt these toxic fibrils, potentially offering a novel therapeutic approach to combating AD pathology. This is a promising step forward in understanding and addressing Alzheimer’s disease. 🔬⚡ A huge thank you to Dr. Artyom Baev, Dr. Erkin Kurganov, and my dedicated MSc student Mukhriddin Makhkamov for their valuable contributions to this work. Read the full paper here: https://lnkd.in/ddSvPmmS #AlzheimersResearch #NeurodegenerativeDisorders #MolecularDynamics #Therapeutics #ScientificReports #ElectricFields #ResearchInnovation #ADPathology

🌟 Exciting Advances in Sonogenetics and Sonopharmacology! 🌟 It started in 2021 with the first publication in #NatureChemistry and since then a lot has happened around the fields of #Sonopharmacology and #Sonogenetics at DWI... In their recent publication in the journal #AdvancedAdvanced Materials, Aman Ishaqat, Johannes Hahmann, Cheng Lin, Xiaofeng Zhang, Chuanjiang He, Wolfgang H. Rath, Pardes Habib, Sabri E. M. Sahnoun, Khosrow Rahimi, Rostislav Vinokur, Felix M. Mottaghy, Robert Göstl, Matthias Bartneck, and Andreas Herrmann transferred the conceptual framework of polymer mechanochemistry to in vivo applications, specifically immunostimulation, using medically approved imaging ultrasound. They also validated the sonogenetic function of their system by achieving gene knockdown in mammalian cell cultures. This proof of concept paves the way for broad therapeutic applications across various diseases. If you would like to find out more, you can find the publication (open access) here: https://lnkd.in/eEgyXhQr We also recommend the current review by Johannes Hahmann, Aman Ishaqat, @Twan Lammers and Andreas Herrmann in #AngewandteChemieInternationalEdition. The authors highlight the potential of sonogenetics – a cutting-edge technique that uses ultrasound to control and monitor cellular functions. Combining genetic engineering with ultrasound, this approach offers non-invasive and precise manipulation of cells. From imaging to therapy, sonogenetics surpasses the limitations of optogenetics and magnetogenetics, offering deep tissue penetration and high spatiotemporal control. The review can be found here (open access): https://lnkd.in/eS4df6rg We are curious to see what else is coming... This research work is funded and supported by Deutsche Forschungsgemeinschaft (DFG) - German Research Foundation, Werner Siemens-Stiftung, and Max Planck School Matter to Life, among others.

How to Use Immunohistochemistry (IHC) for Developmental Biology Immunohistochemistry (IHC) is a valuable tool in developmental biology to study protein expression and localization at various stages of organismal growth and differentiation. It provides spatial and temporal insights into developmental processes and their underlying molecular mechanisms. The following is a guide on how to use IHC in developmental biology: 1. Tissue preparation Collect tissues from embryos or developmental stages at key time points. Fix samples using an appropriate fixative (e.g., paraformaldehyde) to preserve tissue architecture and proteins. Embed tissues in paraffin or OCT for cryosectioning, depending on the desired resolution and antibody compatibility. Cut tissues into thin sections (5-10 µm) and mount on slides. 2. Dewaxing and antigen retrieval For paraffin-embedded samples, remove paraffin with xylene and rehydrate sections in graded alcohols. Use heat-induced epitope retrieval (HIER) to restore antibody binding sites that were masked during fixation. 3. Blocking Incubate tissues with blocking solution (e.g., normal serum or BSA) to reduce nonspecific antibody binding. 4. Primary Antibody Incubation Apply primary antibodies against developmental markers such as transcription factors (e.g., Sox2, Pax6), signaling molecules (e.g., Wnt, BMP), or differentiation markers. Optimize incubation time and temperature for specific markers. 5. Secondary Antibodies and Detection Use secondary antibodies conjugated to enzymes (e.g., HRP) or fluorophores for visualization. Apply chromogenic substrates for enzyme-based detection or fluorescent imaging for multi-marker analysis. 6. Counterstaining and Imaging Counterstain with hematoxylin or nuclear stains for structural context. Analyze protein expression and localization under light or fluorescence microscopy. IHC enables researchers to study cell differentiation, tissue patterning, and molecular pathways in developmental biology, providing a deeper understanding of the growth and development of an organism. Reference [1] Adam Packard et al., PLOS One 2016 (https://lnkd.in/e9Xu93Qe) #IHC #DevelopmentalBiology #ProteinExpression #MolecularBiology #TissueAnalysis #BiomedicalResearch #Immunohistochemistry #ResearchTechniques #CellDifferentiation

How to Use Immunohistochemistry (IHC) for Developmental Biology Immunohistochemistry (IHC) is a valuable tool in developmental biology to study protein expression and localization at various stages of organismal growth and differentiation. It provides spatial and temporal insights into developmental processes and their underlying molecular mechanisms. The following is a guide on how to use IHC in developmental biology: 1. Tissue preparation Collect tissues from embryos or developmental stages at key time points. Fix samples using an appropriate fixative (e.g., paraformaldehyde) to preserve tissue architecture and proteins. Embed tissues in paraffin or OCT for cryosectioning, depending on the desired resolution and antibody compatibility. Cut tissues into thin sections (5-10 µm) and mount on slides. 2. Dewaxing and antigen retrieval For paraffin-embedded samples, remove paraffin with xylene and rehydrate sections in graded alcohols. Use heat-induced epitope retrieval (HIER) to restore antibody binding sites that were masked during fixation. 3. Blocking Incubate tissues with blocking solution (e.g., normal serum or BSA) to reduce nonspecific antibody binding. 4. Primary Antibody Incubation Apply primary antibodies against developmental markers such as transcription factors (e.g., Sox2, Pax6), signaling molecules (e.g., Wnt, BMP), or differentiation markers. Optimize incubation time and temperature for specific markers. 5. Secondary Antibodies and Detection Use secondary antibodies conjugated to enzymes (e.g., HRP) or fluorophores for visualization. Apply chromogenic substrates for enzyme-based detection or fluorescent imaging for multi-marker analysis. 6. Counterstaining and Imaging Counterstain with hematoxylin or nuclear stains for structural context. Analyze protein expression and localization under light or fluorescence microscopy. IHC enables researchers to study cell differentiation, tissue patterning, and molecular pathways in developmental biology, providing a deeper understanding of the growth and development of an organism. Reference [1] Adam Packard et al., PLOS One 2016 (https://lnkd.in/e9Xu93Qe) #IHC #DevelopmentalBiology #ProteinExpression #MolecularBiology #TissueAnalysis #BiomedicalResearch #Immunohistochemistry #ResearchTechniques #CellDifferentiation

𝗜𝗺𝗽𝗼𝗿𝘁𝗮𝗻𝗰𝗲 𝗼𝗳 𝗰𝗲𝗹𝗹 𝗺𝗼𝗱𝗲𝗹𝘀 𝗶𝗻 𝗽𝗿𝗲𝗰𝗹𝗶𝗻𝗶𝗰𝗮𝗹 𝗿𝗲𝘀𝗲𝗮𝗿𝗰𝗵 🧬🔬 As biomedical research advances, cell models are transforming the landscape, guiding us towards more ethical and precise science. Moving beyond the traditional animal models, 2D and 3D cell models have become indispensable tools, offering reliable alternatives paving the way for personalized medicine. Innovations like CRISPR and induced pluripotent stem cells (iPSCs) have revolutionized our ability to study human diseases in a dish. Human iPSCs, in particular, are a game changer, offering a viable alternative to primary cells. They replicate native cell behavior, are available in large quantities, and are of human origin. Our cutting-edge platforms for automated patch clamp, cell analytics, and membrane biophysics are at the forefront of research and drug discovery. Our systems allow researchers to screen ion channels with unmatched flexibility and scalability, explore complex cellular behaviors, and study membrane dynamics with precision and depth. 🔍 Curious to learn more? Explore our iPSC profiling solutions: https://ow.ly/gee350T11PJ #iPSC #CellModels #CellAnalytics #Electrophysiology #PatchClamp #APC #MembraneBiophysics

How to Use Immunohistochemistry (IHC) for Cellular Localization of Proteins Immunohistochemistry (IHC) is an important technique to determine the cellular localization of proteins within tissues. By visualizing specific proteins in different regions (e.g., nucleus, cytoplasm, or cell membrane), IHC provides important insights into protein function and cellular mechanisms. Here is a step-by-step guide: 1. Tissue preparation Collect tissue samples and fix them in formalin to preserve protein structure and tissue morphology. Embed the samples in paraffin, cut them into thin sections (3-5 µm), and mount them on slides. 2. Dewaxing and antigen retrieval Remove paraffin using xylene and rehydrate tissue sections with graded alcohol solutions. Perform antigen retrieval (e.g., heat-induced epitope retrieval) to restore accessibility to epitopes that were masked during fixation. 3. Blocking Block endogenous peroxidase activity with hydrogen peroxide (if using enzyme-based detection). Use a blocking buffer (e.g., BSA or normal serum) to reduce nonspecific binding of antibodies. 4. Primary antibody incubation Incubate tissue sections with a specific primary antibody against the protein of interest. For example: (1) Nuclear proteins: antibodies against transcription factors. (2) Cytoplasmic proteins: antibodies against signaling proteins or enzymes. (3) Membrane proteins: antibodies against receptors or adhesion molecules. Optimize antibody concentration and incubation time for precise localization. 5. Secondary antibodies and detection Apply secondary antibodies conjugated to enzymes (e.g., HRP) or fluorophores. Use chromogenic substrates (e.g., DAB) for light microscopy or fluorescence imaging. 6. Counterstaining and visualization Counterstain with hematoxylin to obtain structural context and visualize sections under light or fluorescence microscopy. 7. Applications: (1) Study cellular processes and protein functions. (2) Identify mislocalized proteins associated with diseases. (3) Explore dynamic protein changes during cell signaling. IHC provides precise spatial information about protein localization, advancing cell biology and pathology research. Reference [1] KTH Royal Institute of Technology, PHYS.ORG 2017 (https://lnkd.in/ebspubQv) #IHC #ProteinLocalization #CellBiology #BiomedicalResearch #MolecularBiology #Pathology #TissueAnalysis #Immunohistochemistry #ResearchTechniques

Organoids offer potential for applications such as developmental biology research, drug screening, and companion diagnostics. However, capturing high-resolution images of living organoids without pre-treatment, like staining or fixation, has been a challenge. We recently published a paper showcasing high-resolution, label-free imaging and analysis of live intestinal organoids using holotomography. This work was made possible through a collaboration between the IBS team led by Director Koo Bon-kyung, organoid culturing expertise, TOMOCUBE, INC.’s the 2nd generation holotomography HT-X1 and software development, and measurement and analysis by Dr. Manjae Lee's Biomedical Optics Lab at KAIST. You can read more in the paper here: https://lnkd.in/g36-BNU4 While we’ve made progress, new challenges have emerged. For organoids thicker than 150 µm, blurring caused by multiple scattering becomes an issue. Overcoming this will allow us to apply holotomography to larger organoids. Additionally, the ability to analyze cell types and states directly from holotomography images would be a new research direction. Exciting times ahead for organoid research! #Organoids #Holotomography #BiomedicalInnovation #DrugScreening #LifeScience #Tomocube #KAIST #IBS