Andressa Dias Costa, M.D.

The Si lab at CMU is hiring postdocs to discover how cellular organizations determine fitness in various conditions using multidisciplinary tools. Postdoctoral Position in Cell Biophysics Experiment Carnegie Mellon University See the full job description on jobRxiv: https://lnkd.in/dPd8JsVA #bioengineering #biophysics #microbiology #microfluidics #quantitative_biology

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💡 Exciting insights from recent research at University of Catania on predicting antimicrobial resistance in Klebsiella pneumoniae using machine learning! This study used the Watchmaker DNA Library Prep Kit with Fragmentation and emphasizes the critical role of genomic data in addressing the issue of antibiotic resistance. 🦠 Read the full article for more details: https://ow.ly/AXYo50U84mT #AntimicrobialResistance #Genomics

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🆕New in #JEV 🆕 A novel multiplexed immunoassay for surface-exposed proteins in plasma extracellular vesicles Emma Tordoff, Jillian Allen, Katya Elgart, Ahmed Elsherbini, Vrinda Kalia, Haotian Wu, Erden Eren, Dimitrios Kapogiannis, Olesia Gololobova, Kenneth Witwer, Olga Volpert, Erez Eitan Small membranous extracellular vesicles (EV) incorporate proteins and nucleic acids from the parent cell. Proteins exposed on EV surface are dictated by cellular origin and biogenesis pathway. To better understand the EV origin and function, it is important to develop methods that reveal surface protein composition of heterogeneous EV populations in culture supernatants and in biofluids. Tetraspanins CD9, CD63, and CD81 are common and abundant EV markers. However, their relative enrichment (profile) on EVs of specific cellular origins is not fully elucidated. We introduce LuminEV, a novel version of the Luminex assay for the multiplexed analysis of EV surface proteins. Optimized LuminEV reagents enable direct, specific, and sensitive measurements of EV markers in biofluids and in culture supernatants, bypassing EV isolation step. LuminEV assay for CD9, CD63, and CD81 was validated by comparing simplex and multiplex measurements, establishing linearity, spike-in recovery, inter- and intra-assay precision, and reproducibility between operators. LuminEV measurements of CD9, CD63, and CD81 in conditioned media from 15 cell lines revealed strong variations between cell types and showed high sensitivity, which enabled EV detection without prior concentration. Using tetraspanin levels as a readout, we noted suppression and induction of EV release from the cultured cells by GW6869 and monensin. Measurement of EV CD9, CD63, and CD81 in blood plasma from 70 disease-free donors showed respective abundance of 72, 16, and 12%. CD63 displayed weak, albeit significant, negative correlation with age and was slightly lower in female samples. The assay was then used to detect cell type-specific EV surface markers, including CD235a (erythrocytes), GAP43 (neurons), and CD68 (macrophages), and to detect differences in tetraspanin profiles between healthy and diseased donors. In summary, LuminEV offers robust and sensitive approach for multiplexed assessment of EV surface proteins, to facilitate the research into EV biology, biomarker, and therapeutic applications. https://lnkd.in/eUsJWDZQ

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📣 📣 Newly Published Article: Advances in #radiomics applications for #intrahepatic #cholangiocarcinoma: a comprehensive review and future directions ✔ Full text: https://lnkd.in/g5dcNSuB 📚 Radiomics was first introduced by Lambin et al. in 2012, and since then, research in this field has grown rapidly. Researchers have shown great interest in developing efficient methods for automatically extracting a large number of quantitative features from medical images, aiming to enhance diagnostic accuracy and predictive capability. Although there has been a rise in Radiomics studies focusing on intrahepatic cholangiocarcinoma (ICC) in recent years, comprehensive reviews are still relatively scarce. This study explores how Radiomics technology can be utilized in modeling analyses to predict lymph node metastasis, microvascular invasion, and early recurrence of ICC, as well as the application of deep learning in these analyses. This paper provides a brief overview of the current state of Radiomics research and offers references for future studies. Your kind sharing will always be appreciated! Aly Strauss Mar Miserachs William Karnes Laxmikant Desai Gale Fiarman Tamneet Basra, MD Jose Noguera Vian Azzu Eric Gochanour Natasha Von Roenn Orestis Sidiropoulos Norah Terrault Thomas Leventhal Adriaan van der Meer      

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Community resource: Systematic synthesis and identification of monolignol pathway metabolites Chung-Ting Kao, et al. 📖 https://ow.ly/loI650TMq7N Community resources are designed to provide a detailed methodological overview of a topic or to report a project or dataset that will be of significant use and interest to the plant science community. Find all of our Community resources here: https://ow.ly/joIz50TNmU6

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🚀 Streamline Omics Data Analysis with Firehose 🚀 Analyzing large-scale cancer genomics and proteomics datasets is easy with Firehose, the Broad Institute's powerful suite of tools and pipelines. 🔹 What Sets Firehose Apart? End-to-End Workflows 🔄 From raw data processing to downstream analysis, Firehose has you covered. Multi-Omics Capabilities 🧬 Integrate data across genomics, transcriptomics, and proteomics. Reproducible Results ✅ Standardized pipelines ensure consistent analyses. Simplify your omics research with Firehose today! #BigData #CancerGenomics #DataAnalysis #TCGA

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Don't miss our poster presentations at Discovery on Target in Boston, MA! 📃 "Identification and characterization of small molecules inhibiting RNA targets: miRNA" 🏷 Session A, poster A39 📆 October 1st to 2nd a.m. 👩🏼‍🔬 Paola C., PhD, Director Alliance Management Abstract: RNA plays a key role in transcription and translation: gene regulation, proliferation, apoptosis, and development. The biological function is linked to the unique secondary and tertiary structures. Many diseases are associated with dysregulation of RNA functions, so there is a growing interest in RNAs as drug targets for novel therapies or targeting undruggable proteins. The most used modalities are antisense oligonucleotides (ASOs), CRISPR gene editing, and more recently small molecules. [...] Discover more about our approach that demonstrates a miRNA targeting platform that could be applied to other oncogenic miRNA targets: https://lnkd.in/edM4ecJj For more questions and details, come and meet our team at our booth 508! #DrugDiscovery #Biophysics #RNA #SPR #microRNA #DiscoveryOnTarget #BostonDOT24

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New paper citing #proteinimager entitled "Allosteric Modulation of the YAP/TAZ-TEAD Interaction by Palmitoylation and Small-Molecule Inhibitors" In their recent study, researchers investigated the dynamics of the YAP/TAZ-TEAD interaction, a critical component of the Hippo signaling pathway implicated in cancer development. Previous research suggested that TEAD's autopalmitoylation affects YAP/TAZ binding, but the precise mechanisms remained unclear. Through molecular dynamics simulations, the researchers provided detailed insights into these interactions, revealing that the studied inhibitor impacts YAP and TAZ binding to TEAD differently. Their findings offer valuable implications for the design of future cancer therapeutics targeting this interaction. The paper: https://lnkd.in/d5Ke9kMu Try Protein Imager: https://lnkd.in/dc8yQfy #science #scienceillustration #scientificpaper #structuralbiology #HippoSignaling #CancerResearch #MolecularDynamics #YAP #TAZ #TEAD #Palmitoylation #SmallMoleculeInhibitors #simulation

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📍 Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues Bai et al. presented Patho-DBiT by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. Highlights ✔️ Patho-DBiT enables spatial whole transcriptome sequencing in clinical FFPE tissues ✔️ It permits spatial co-profiling of gene expression, splicing, and non-coding RNAs ✔️ Genome-wide detection of spatial SNV distribution distinguishes malignant subclones ✔️ It dissects spatiotemporal dynamics of lymphomagenesis at the single-cell level. ➡️ More details: https://lnkd.in/ewHDeVpn #YaleUniversity #spatialomics #spatialbiology #singlecellanalysis #singlecell

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Next-generation sequencing (NGS) technologies continue to open new frontiers in #biology. This article, written by RJ Mackenzie for Technology Networks, explores how the latest advances in #NGS have helped researchers explore areas of the #genome that were previously dismissed as uninformative. https://lnkd.in/evhVknZ3

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🚀 Exciting Publication Alert! The HESI eSTAR Committee's latest review explores how transcriptomic points of departure (tPODs) can revolutionize toxicological safety assessments. 🧬 🔑 Key Highlights: • Efficiency & Innovation: Faster, health-protective assessments with reduced reliance on long-term animal studies. • Bioinformatic Framework: A nine-step workflow for tPOD derivation, including data processing and normalization. • Research Priorities: Addressing gaps in study design, platform standardization, and uncertainty quantification. • Regulatory Impact: Insights into integrating tPODs into regulatory toxicology with tools like EPA’s ETAP and BMDExpress. This open-access article is a must-read for toxicologists, regulatory scientists, bioinformaticians, and anyone in molecular toxicology. 📖 Read the full article here: https://ow.ly/t02450U7TmS #Toxicology #NAMs #Bioinformatics #RegulatoryScience

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📑Check out the #Article "Evaluation of Hi-C sequencing for the detection of gene fusions in hematologic and solid pediatric cancer samples" 📌Access the full paper here: https://lnkd.in/d2vED2n7 👏by Dr. Anthony Schmitt et al. Arima Genomics 1. What are the main findings? • Hi-C sequencing, which looks for structural variation by preserving the 3D conformation of the genome, was 100% concordant with clinical diagnostic testing workflows for detecting clinically significant genomic rearrangements in pediatric leukemia and rhabdomyosarcoma specimens. • Hi-C also detected clinically significant genomic rearrangements not previously detected by prior clinical cytogenetic and molecular testing. • Hi-C performed well with archived non-viable and viable frozen leukemic cell samples as well as archived formalin-fixed paraffin-embedded tumor tissue specimens. 2. What are the implications of the main findings? • Hi-C sequencing could provide additional diagnostic, prognostic, and therapeutic value by identifying clinically significant genomic rearrangements potentially missed by current clinical diagnostic testing workflows. • The genome-wide, partner-agnostic nature of the Hi-C approach helps it overcome the limitations inherent to targeted FISH- and RNA-sequencing panels. • The DNA-based nature of Hi-C allows it to be less dependent on RNA and the presence/absence of a fusion transcript and thus potentially better able to detect promoter swap or enhancer-hijacking-type rearrangements.

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