Genome3D (http://www.genome3d.eu) is a collaborative resource that provides predicted domain annotations and structural models for key sequences. Since introducing Genome3D in a previous NAR paper, we have substantially extended and improved the resource. We have annotated representatives from Pfam families to improve coverage of diverse sequences and added a fast sequence search to the website to allow users to find Genome3D-annotated sequences similar to their own. We have improved and extended the Genome3D data, enlarging the source data set from three model organisms to 10, and adding VIVACE, a resource new to Genome3D. We have analysed and updated Genome3D's SCOP/CATH mapping. Finally, we have improved the superposition tools, which now give users a more powerful interface for investigating similarities and differences between structural models.
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http://dx.doi.org/10.1093/nar/gku973 | DOI Listing |
Cancer Cell Int
December 2024
Division of Cancer Biology, Laboratory Animal Center, The Fourth Military Medical University, Xi'an, 710032, Shaanxi, China.
Tumor organoids have emerged as powerful tools for in vitro cancer research due to their ability to retain the structural and genetic characteristics of tumors. Nevertheless, the absence of a complete tumor microenvironment (TME) limits the broader application of organoid models in immunological studies. Given the critical role of immune cells in tumor initiation and progression, the co-culture model of organoids and peripheral blood mononuclear cells (PBMCs) may provide an effective platform for simulating the interactions between immune and tumor cells in vitro.
View Article and Find Full Text PDFCommun Chem
December 2024
Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
The PepT transporter mediates the transport of peptides across biological membranes. Despite advancements in structural biology, including cryogenic electron microscopy structures resolving PepT in different states, the molecular basis of peptide recognition and transport by PepT is not fully elucidated. In this study, we used molecular dynamics simulations, Markov State Models (MSMs), and Transition Path Theory (TPT) to investigate the transport mechanism of an alanine-alanine peptide (Ala-Ala) through the PepT transporter.
View Article and Find Full Text PDFIn Vivo
December 2024
Department of Veterinary Medicine, Yanbian University, Yanji, P.R. China;
Background/aim: This study aimed to investigate the safety and efficacy of deferoxamine (DFO) pretreated feline adipose tissue derived mesenchymal stem cells (fATMSCs) for the treatment of inflammatory disorders.
Materials And Methods: fATMSCs were isolated from feline adipose tissue and characterized using flow cytometry for surface marker expression and differentiation assays for adipogenic, osteogenic, and chondrogenic lineages. Different concentrations of DFO were used to evaluate its impact on fATMSC activity.
J Environ Manage
December 2024
Department of Applied Biology, Miguel Hernández University of Elche, Elche, Spain; Centro de Investigación e Innovación Agroalimentaria y Agroambiental (CIAGRO-UMH), Orihuela, Spain.
Offshore wind energy is experiencing accelerated growth worldwide to support global net zero ambitions. To ensure responsible development and to protect the natural environment, it is essential to understand and mitigate the potential impacts on wildlife, particularly on seabirds and marine mammals. However, fully understanding the effects of offshore wind energy production requires characterising its global geographic occurrence and its potential overlap with marine species.
View Article and Find Full Text PDFNeural Netw
December 2024
School of Physical Science and Technology, Lanzhou Center for Theoretical Physics, Key Laboratory of Theoretical Physics of Gansu Province, and Key Laboratory of Quantum Theory and Applications of MoE, Lanzhou University, Lanzhou, Gansu 730000, China. Electronic address:
The human brain exhibits heterogeneity across regions and network connectivity patterns; However, how these heterogeneities contribute to whole-brain network functions and cognitive capacities remains unclear. In this study, we focus on the regional heterogeneity reflected in local dynamics and study how it contributes to the emergence of functional connectivity patterns, network ignition dynamics of the empirical brains. We find that the level of synchrony among voxelwise neural activities measured from the fMRI data is significantly correlated with the transcriptional variations in excitatory and inhibitory receptor gene expression.
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