The paper «Enhancing the reverse transcriptase function in Taq polymerase via AI-driven multiparametric rational» is published in the journal of Frontiers in Bioengineering and Biotechnology. The result is based on the AI models developed in NOVEL and Institute of Artificial Intelligence MSU.
We trained a Ridge regression model to predict multiple enzyme properties in the wild type and mutated Taq polymerase. The model is based on the embeddings of Taq polymerase primary structure generated by a protein language model. Using the regression model we conducted an in silico screen of over 18 million potential mutations, narrowing the field to 16 top candidates for comprehensive wet-lab evaluation.
This approach led to the identification of 18 enzyme variants that exhibited markedly improved reverse transcriptase activity while maintaining a favorable balance of other key properties. Several enzymes validated via this procedure were effective in single-enzyme real-time reverse-transcription PCR setups, implying their utility for the development of new tools for real-time reverse-transcription PCR technologies, such as pathogen RNA detection and gene expression analysis.
Our approach offers a robust framework for designing enzyme mutants tailored to specific biotechnological applications. The full text article is here https://www.frontiersin.org/journals/bioengineering-and-biotechnology/articles/10.3389/fbioe.2024.1495267/full.
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Employees of NOVEL collaborated in the publication of the article "RNAseq profiling of blood from patients with coronary artery disease: "Signature of a T cell imbalance" in the Journal of Molecular and Cellular Cardiology Plus.
The investigation of regulatory T cell dysfunction in CAD is the focus of the article. Researchers have accurately analyzed the biggest sample of gene activity in CAD using cutting-edge sequencing and bioinformatics methods.
It has been demonstrated that transcripts connected to the immunological synapse (interaction) are particularly connected to CAD. T-cells and B-cells can communicate with diverse antigen-presenting and immunomodulatory cells at the immunological synapse, which is contact-dependent. Fibromodulin (FMOD; upregulated 2.8-fold in CAD) is one of the most differentially expressed genes and is known to be associated with atherosclerosis, cardiomyopathy, and iron-dependent programmed cell death.
Moreover, transcripts for proteins connected to the immunological synapse's formation and operation have been found. Nebulette is involved in the binding of actin and desmin for the operation of the cytoskeleton and vesicular movement (increases 2.4 times in CAD). Transcripts that were directly connected to T cell activity and the regulation of differentiation were present in the immunological synapses' signaling pathways. T-cell activation is mediated by butyrophilin, which is elevated 1.7-fold in coronary artery disease.
The paper demonstrates how alternative sequencing technologies (SeqLL and Illumnina) enable the identification of transcripts linked to alterations in T regulatory cells, but with distinctly distinct transcripts linked to CAD.
The full text of the article can be found here: https://www.sciencedirect.com/science/article/pii/S277297612300003X?via%3Dihub
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The III All-Russian Conference "High-performance Sequencing in Genomics" (HSG-2022) was held June 19-24, 2022 in Novosibirsk Akademgorodok. The event brings together such fields as eukaryotic and prokaryotic genomics, metagenomics of microorganism communities, medical genomics, transcriptomics, protein-nucleic acid interactions, and translation.
New methods based on high-performance sequencing and their practical application were discussed at the conference.
Leading experts from Novel participated in this conference.
Mikhail Pomaznoy: "The most important thing at any conference is new contacts. This event is important for us, because NGS Wizard is not yet familiar to everyone. Surprisingly, we managed to make new contacts with people who are working in the neighboring building and did not know about our project. The variety of topics makes the reports interesting, because it allows me to hear about areas that I have nothing to do with. For example, research of bacterial communities of the Barents Sea is something distant, unfamiliar and fascinating for me.”
Maria Starchevskaya: “My report at the conference "High-performance sequencing in genomics" was devoted to metagenomic analysis of Colorado potato beetle genomes. The search for viral genetic sequences is an urgent and challenging task and we developed an analytical software pipeline that performs identification and annotation of viral material in NGS data.”
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