NanoImaging Services’ Post

Artificial Intelligence for Organ Tissue Equivalents? Our latest paper explains how we analyze the response of human lung organ tissue equivalents to viruses. The study reveals potential biomarkers indicative of specific viral infections and offers profound insights into the host’s defense mechanisms and viral manipulation strategies. #AI #OTE Wake Forest Center for Artificial Intelligence Research Wake Forest University School of Medicine Wake Forest Institute for Regenerative Medicine Mostafa Rezapour https://lnkd.in/djJEXn38

The virus manuscript is now out on bioRxiv!! It's been years in the making, and I feel incredibly lucky to have worked with an amazing team of scientists with diverse areas of expertise. A few key results: - We expanded the open-source (C++) transcriptomic data pre-processing tool kallisto to perform translated alignment of nucleotide sequences to an amino acid reference. ✨ To date, this is the only software tool capable of translated alignment while retaining single-cell resolution. ✨ - We used translated alignment to identify viral RNA in bulk and single-cell RNA sequencing data based on highly conserved motifs, thereby overcoming limitations due to the lack of viral reference genomes. ✨ We can detect up to 10^12 (!!!) viral species. ✨ - We leveraged the single-cell resolution to train logistic regression models that can successfully predict the presence of novel viruses in individual cells based on host gene expression. ✨ This approach revealed previously unknown viruses whose presence perturbed host gene expression. ✨ - We also describe and validate eight different workflows for masking host sequences and find that most viruses have at least some sequences that also align to the host genome and/or transcriptome. We provide a complete, albeit nuanced, answer to the currently unsolved problem in the field of how to deal with such ambiguity. As usual, our approach is efficient (max. 1.5 min for 1 million sequences), open-source, well-documented, can be executed in three lines of code, and can be run from a laptop. I presented this project at the Cold Spring Harbor Laboratory Biology of Genomes conference last May, and you can view the recording here: https://lnkd.in/gSDwVgNR Which viruses do you have in your sequencing data?

🦠🧬 New research uncovers the genetic evolution of SARS-CoV-2, focusing on the repeated knockout of ORF8. The study suggests that positive selection drives this genetic alteration, indicating its potential importance in the virus's adaptation and survival. Understanding these genetic changes can provide insights into the virus's evolution and transmission dynamics, aiding in the development of targeted therapeutic strategies. #SARSCoV2 #GeneticEvolution #COVID19Research 🧪🔍🦠 https://lnkd.in/dGDJ4aDZ

😆 Excited to share the RNA Special Issue! Five insightful articles! 📓 Special issue topic: RNA World in Health and Disease 🎓 Guest editors: Dr. Marco Ragusa, Dr. Cristina Barbagallo 🔎 Find more at https://lnkd.in/epQv5C66 📚 Published Articles: 1️⃣ Bioinformatics evaluation of the circRNA–miRNA–mRNA axis in cervical squamous cell carcinoma 🔗 https://lnkd.in/gSWayjyJ 2️⃣ The coevolution of Covid-19 and host immunity 🔗 https://lnkd.in/ggnKVCxf 3️⃣ Self-replicating RNA viruses in vaccine development 🔗 https://lnkd.in/gnabjv4M 4️⃣ RNA-RNA competitive interactions: a molecular civil war ruling cell physiology and diseases 🔗 https://lnkd.in/gHUYqdEj 5️⃣ m6 RNA methylation: an emerging common target in the immune response to cancer and severe acute respiratory syndrome-coronavirus-2 infection 🔗 https://lnkd.in/gWSGK5UY #miRNAs #lncRNAs #circRNAs #epigenetics #cancers

Happy Monday everyone! It's that time of the week again, and we have the latest news from the genomics world for you all in one place. Top stories from Week in Brief include: 🧬As part of the Human Cell Atlas, researchers have used single-cell technology to map the body’s response to COVID infection. The work explains why some individuals appear not to get the disease following exposure. 🧬Scientists have developed a low-cost, CRISPR-based test for the flu, which can be used to differentiate between different strains of the virus. 🧬Researchers have developed a new technology that can determine the precise sequence and length of telomeres on individual chromosomes. Read the full article here: https://lnkd.in/ep2fusmc

Working on the #Viral Load bench has been very knowledgeable. And here, I’ll talk about a few things I’ve learnt so far. NB: Particularly, I’ve been working on HIV-1 Viral Load. Viral Load Laboratory is primarily focused on quantifying the amount of virus present in a given blood sample. This quantification is used for monitoring infections as well as evaluating treatment for patients. The activities carried out in a viral load laboratory are: ▪️Sample Preparation For easy and unambiguous identification of samples, we do #barcoding. Barcoding is attaching unique barcode labels to sample containers, such as test tubes, for accurate identification, tracking, efficiency, error reduction and traceability. After barcoding, the next thing we do is manual #aliquoting. Aliquoting is process of dividing a larger volume of a sample into smaller, equal portions. The main purpose of this is standardization for consistent and reliable results. ▪️Sample Transfer This is done using The Roche COBAS 6800/8800 system which is highly effective, precise and consistent. In this stage, the samples in primary collection tubes are placed into the system’s input rack and are placed into the designated loading area of the COBAS 6800/8800 system. In the machine, the robotic arm scans the barcode of each sample for easy identification. Then the system aliquots and then transfers to the processing area within the system. ▪️Sample Processing While processing samples, Automated Nucleic Acid Extraction, and PCR Setup and Amplification are carried out. First, the COBAS system extracts the viral RNA from the plasma samples ensuring high purity.Then, the extracted RNA is transferred to reaction wells where the PCR amplification will occur. During the PCR Amplification, the system prepares the PCR master mix and distributes it into the reaction wells along with the extracted RNA. Then, the system performs real-time PCR amplification and quantification of HIV-1 RNA, using fluorescent probes ▪️Sample Analysis Here, the system analyzes the fluorescence data to determine the viral load for each sample. Then the results are uploaded and the reports are generated for review. #viralload #virology #hivresearch #researchassistant #virology #genomics

Giardia duodenalis, a major cause of waterborne infection, infects a wide range of mammalian hosts and is subdivided into eight genetically well-defined assemblages named A through H. However, fragmented genomes and a lack of comparative analysis within and between the assemblages render unclear the molecular mechanisms controlling host specificity and differential disease outcomes. To address this, we generated a near-complete de novo genome of AI assemblage using the Oxford Nanopore platform by sequencing the Be-2 genome. We generated 148,144 long-reads with quality scores of> 7. The final genome assembly consists of only nine contigs with an N50 of 3,045,186 bp. This assembly agrees closely with the assembly of another strain in the AI assemblage (WB-C6). However, a critical difference is that a region previously placed in the five-prime region of Chr5 belongs to Chr4 of Be-2. We find a high degree of conservation in the ploidy, homozygosity, and the presence of cysteine-rich variant-specific surface proteins (VSPs) within the AI assemblage. Our assembly provides a nearly complete genome of a member of the AI assemblage of G. duodenalis, aiding population genomic studies capable of elucidating Giardia transmission, host range, and pathogenicity. https://lnkd.in/eyRNg9Ft

The study delves into the mechanisms behind SARS Coronavirus RNA ribose 2′-O-methylation by the nsp16/nsp10 protein complex, shedding light on viral RNA cap modification crucial for stability, translation, and immune evasion. 💡🦠 #SARSCoV #RNAmodification #proteincomplex

🦠 Unlock new insights into COVID-19 research! Our latest blog delves into a cutting-edge protocol for detecting SARS-CoV-2 viral proteins in formalin-fixed, paraffin-embedded tissues. This highly sensitive and specific method, using ProSci’s affinity-purified antibodies, is key to understanding virus distribution and load in COVID-19 patients across all common variants. Highlights from the summary: ◉ High Sensitivity & Specificity: The protocol effectively detects SARS-CoV-2 nucleocapsid and spike proteins, providing a reliable method for studying viral distribution and load in COVID-19 patients. ◉ Broad Applicability: The protocol works across all common SARS-CoV-2 variants, ensuring utility in diverse research and clinical settings. ◉ Strong Correlation with RNA Levels: IHC-detected nucleocapsid protein levels closely match viral RNA levels, validating the accuracy of this method. Discover how this research can elevate your studies in viral pathogenesis and beyond. Read more: https://lnkd.in/g5q2zwBU #ProSciCustomAntibodyService #SingleDomainAntibodies #SARSCoV2 #COVID19Research #Pathology #Immunohistochemistry #ViralDetection #GeneseeScientific

📍 Immune system compartmentalization under symbiosis in the stony coral Oculina arbuscula    Valadez-Ingersoll et al. used a multiomic approach to characterize symbiotic states of the facultatively symbiotic coral Oculina arbuscula by generating genotype-controlled fragments of symbiotic and aposymbiotic tissue.     Key findings  📍No difference in bacterial communities between symbiotic states  📍Differential abundance of proteins related to immunity, consistent with immune suppression during symbiosis  📍Diverse cell clusters within six cell types across symbiotic states  📍High expression of nitrogen cycling and sugar transport genes in the gastrodermal cell cluster containing algal-hosting cells from symbiotic tissue   📍Low expression of genes involved in immune regulation in gastrodermal cells from symbiotic tissue. ➡ More details: https://lnkd.in/ejrc8qxT #BostonUniversity #spatialomics #spatialbiology #singlecellanalysis #singlecell