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Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.
mSystems
January 2025
Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland.
Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%.
View Article and Find Full Text PDFIntrinsic Gene Expression Correlates of the Biophysically Modeled Diffusion Magnetic Resonance Imaging Signal.
Biol Psychiatry Glob Open Sci
March 2025
Department of Radiology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin.
Magnetic resonance imaging (MRI) is a powerful tool to identify the structural and functional correlates of neurological illness but provides limited insight into molecular neurobiology. Using rat genetic models of autism spectrum disorder, we show that image texture-processed neurite orientation dispersion and density imaging (NODDI) diffusion MRI possesses an intrinsic relationship with gene expression that corresponds to the biophysically modeled cellular compartments of the NODDI diffusion signal. Specifically, we demonstrate that neurite density index and orientation dispersion index signals are correlated with intracellular and extracellular gene expression, respectively.
View Article and Find Full Text PDFQuantitative magnetic resonance imaging responses in head and neck cancer patients treated with magnetic resonance-guided hypofractionated radiation therapy.
Phys Imaging Radiat Oncol
January 2025
Department of Biophysics, Medical College of Wisconsin, Milwaukee, WI, United States.
Background And Purpose: Quantitative MRI (qMRI) has been explored for detecting tumor changes during radiation therapy (RT) in head and neck squamous cell cancer (HNSCC). Clinical trials show prolonged survival with PD-1 targeted immune checkpoint inhibition. Hypofractionated radiation regimens are being studied to counteract radioresistant clonogen formation.
View Article and Find Full Text PDFBiophysical and spectroscopical insights into structural modulation of species in the aggregation pathway of superoxide dismutase 1.
Commun Chem
January 2025
Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India.
Superoxide dismutase 1 (SOD1) aggregation is implicated in the development of Amyotrophic Lateral Sclerosis (ALS). Despite knowledge of the role of SOD1 aggregation, the mechanistic understanding remains elusive. Our investigation aimed to unravel the complex steps involved in SOD1 aggregation associated with ALS.
View Article and Find Full Text PDFRapid structural analysis of bacterial ribosomes in situ.
Commun Biol
January 2025
Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
Rapid structural analysis of purified proteins and their complexes has become increasingly common thanks to key methodological advances in cryo-electron microscopy (cryo-EM) and associated data processing software packages. In contrast, analogous structural analysis in cells via cryo-electron tomography (cryo-ET) remains challenging due to critical technical bottlenecks, including low-throughput sample preparation and imaging, and laborious data processing methods. Here, we describe a rapid in situ cryo-ET sample preparation and data analysis workflow that results in the routine determination of sub-nm resolution ribosomal structures.
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