Zhang Cathy’s Post

Source: Folia microbiologica Protein profiling and immunoinformatic analysis of the secretome of a metal-resistant environmental isolate Pseudomonas aeruginosa S-8. The secretome was characterized using bioinformatics and mass spectrometry, with 1088 proteins identified. The secreted proteins were categorized based on their subcellular localization and functional pathways. The study also identified immunodominant epitopes from the secretome that could be used as vaccine targets. Overall, this research has implications for diagnostics and vaccine development. PMID: 38457114 | DOI: 10.1007/s12223-024-01152-5

In case you missed the news late last year, Tome Biosciences has been making waves in the biotech space with more than $200 million in investments from major VCs. While those numbers are impressive, what’s driving that interest is more exciting: the use of #CRISPR technology to insert new genes in a process called programmable genomic integration (PGI). This new approach modifies the CRISPR process – which up until now has been primarily used to edit existing genes – and combines it with enzymes that can insert entirely new genetic code into DNA. This could give doctors and scientists far more control over genetic therapies and open the door for new treatments and even cures for genetically driven diseases. The basis of the PGI research comes from this fascinating paper in Nature Biotechnology: https://lnkd.in/ekqRGnBn Figure 1 shows the schematic of the novel Cas fusion protein that is enabling this new technology. The team behind this work wrote a paper about it two years ago and I’m eager to see what the Tome team does with that foundation as they move towards a commercial launch. Perhaps #HPLC chromatography and #lcms mass spectrometry will play a role in characterizing and performing release testing on future drug substances and products. #LifeatWaters #WatersInnovation

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Associate Professor Yarin Gal and former doctoral student Pascal Notin have had an article published in Nature Biotechnology on 'Machine learning for functional protein design'. Recent breakthroughs in AI coupled with the rapid accumulation of protein sequence and structure data have radically transformed computational protein design. The article discusses the new capabilities and outstanding challenges for the practical design of enzymes, antibodies, vaccines, nanomachines and more are discussed, and also highlights trends shaping the future of this field. Read the article here: https://lnkd.in/de78MinZ  #compscioxford

🎯 Targeted sequencing allows us to focus time, expenses, and data analysis on specific areas of interest. Microbial genomics greatly benefits from high-throughput analysis of phylogenetic marker genes, functional genes, and antimicrobial resistance genes for profiling community members and determining functional diversity. But how do we identify who is doing what? Linking phylogenetic markers with functional genes can answer that question. ➡️ Atrandi Biosciences | Droplet Genomics developed a workflow that involves cell encapsulation into semi-permeable capsules, multiplex PCR, amplicon concatenation, and long-read sequencing. This results in a '1 read = 1 cell' data interpretation. Notably, achieving #singlecell resolution doesn't require any barcoding! Furthermore, the workflow can be performed on thousands of cells in parallel in a single tube, thanks to the properties of semi-permeable capsules! What scientific questions can you tackle with this approach? 👉 Which microbes carry antimicrobial resistance genes (link 16S rRNA with AMR genes); 👉 Which microbes carry a specific functional gene (link 16S rRNA with functional gene sequence); 👉 Which microbes are interacting with fungi (link 16S rRNA with fungal ITS); 👉 and others. ⏬ Download the application note to learn more about barcoding–free single–cell targeted sequencing: https://lnkd.in/dHzkAjGG Did you know? Encapsulating cells has never been easier! Try the Flux platform for semi–permeable capsule generation: https://lnkd.in/eDV5nC_E

I am thrilled to share that our work on FLiP–MS, a novel structural proteomics workflow for globally monitoring protein complex dynamics, has just been published! 🎉 In this research, we developed FLiP–MS, a cutting-edge method that probes changes in protein–protein interactions with high throughput and peptide-level structural resolution. By generating a library of peptide markers, FLiP–MS enables comprehensive monitoring of protein complex dynamics. Applying this approach to Saccharomyces cerevisiae, we uncovered links between Spt-Ada-Gcn5 acetyltransferase activity and the assembly state of several complexes, providing both global and molecular insights into cellular responses to DNA replication stress. A heartfelt thank you to all the amazing co-authors, but especially to Cathy Marulli for the incredible collaboration. Working alongside my fantastic co-first author was an absolute joy! We shared countless memorable moments, from brainstorming sessions to late-night data analyses. Even during the tough times without lab access due to the pandemic, we kept each other motivated and turned challenges into opportunities. Also, a big thank you to Paola Picotti for believing in us and encouraging us to pursue this high-risk project, even when the initial results weren't the most promising. Her unwavering support made this achievement possible. This journey has been a testament to teamwork, perseverance, and passion for science. Excited to see where this leads next! #Proteomics #TeamScience #PPI #ETHZ #PicottiLab #Gratitude Read the full article here https://lnkd.in/diUmT8Zm

So I think I may be a smidge late on this but still worth discussing Genentech's recent publication on scRNA-seq technologies, here were my key takeaways but interested to hear what others thought! - If you're looking for higher MT percentages, BD Rhapsody was the best kit of the bunch. - 10x Genomics FRP had a great showing with steep saturation curves, high UMIs, and the highest number of attainable genes. But FRP had fairly low MT percentages and RP content potentially due to the loss of cytosolic transcripts due to the fixation & permeabilization process this kit shares with Parse Biosciences & Scale Biosciences. - Combinatorial kits generally had lower correlation among replicates in pseudobulk quantitative expression profiles. - BD Rhapsody came out in front on the cost-effective balance of performance and expense per cell, but did have the lowest cell recovery of the group. - Notably Singleron Biotechnologies had a 244% cell recovery (with high variation across samples) which could suggest an issue with the cell counting or cell calling. Additionally, there was a linear correlation between observed cell count and sequencing depth. Final takeaway: If your research gravitates toward metabolism & immune cell activation and high sensitivity isn't a priority, BD Rhapsody seemed to be the best cost-saving option. For those looking at subtle transcriptional changes, mapping cellular trajectories, and characterizing rare cell populations, 10x's FRP kit in particular seems to come out on top.

Enhance your biobanking research with microarray solutions that enable large-scale molecular profiling of biological samples, giving researchers a comprehensive view of genetic variations. Dive into the ways it can advance your biobanking studies: - High-throughput Analysis: Enables simultaneous analysis of thousands of genes, SNPs, or other markers in a single experiment. - Comprehensive Molecular Profiling: Provides insights into molecular mechanisms, underlying disease, drug responses, and other biological processes. - Discovery of Biomarkers: Serves as a diagnostic tool for early disease detection, progression, or predictors for treatment efficacy. - Long-Term Storage Stability: Is compatible with archived biobank samples, allowing researchers to retrospectively analyze samples years after collection. - Quality Control and Standardization: Offers standardized protocols that help to facilitate meta-analyses and large-scale collaborative research. - Integration with Omics Data: Produces data that can integrate with genomics, transcriptomics, and proteomics data for comprehensive understanding. From personalized medicine to understanding complex diseases, microarrays drive biobanking forward, fueling breakthroughs for a healthier tomorrow: https://hubs.ly/Q02w9k3-0 #ClinicalResearch #Diagnostsics #BioBanking

Unlock Insights with Protein-Protein Interaction Networks Creative Proteomics specializes in detecting protein-protein interactions through advanced methods like Yeast Two-Hybrid, Co-Immunoprecipitation (CO-IP), and Bio-Layer Interferometry (BLI). Our services allow for qualitative and quantitative analysis, crucial for understanding molecular interactions in various biological contexts. Why Choose Us? Diverse Methodologies: We offer both in vivo and in vitro techniques tailored to your experimental needs. Custom Assay Development: Our team can develop specific protocols and validate assays on custom samples. Comprehensive Data Analysis: Receive detailed reports and guidance on future research directions. Let us help you navigate the complexities of protein interactions to enhance your research outcomes! 🔗 Learn more and get started: https://lnkd.in/gY5Vh4BC #Proteomics #Biotechnology #ProteinInteractions