General principles governing biomolecular interactions between species are expected to differ significantly from known principles governing the interactions within species, yet these principles remain poorly understood at the systems level. A key reason for this knowledge gap is the lack of a detailed three-dimensional (3D), atomistic view of biomolecular interaction networks between species. Recent progress in structural biology, systems biology, and computational biology has enabled accurate and large-scale construction of 3D structural models of nodes and edges for protein-protein interaction networks within and between species. The resulting within- and between-species structural interaction networks have provided new biophysical, functional, and evolutionary insights into species interactions and infectious disease. Here, we review the nascent field of between-species structural systems biology, focusing on interactions between host and pathogens such as viruses.
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http://dx.doi.org/10.3389/fmicb.2012.00428 | DOI Listing |
Bioinform Adv
December 2024
Computer Science Department, Indiana University, Bloomington, IN 47408, United States.
Motivation: Microbial signatures in the human microbiome are closely associated with various human diseases, driving the development of machine learning models for microbiome-based disease prediction. Despite progress, challenges remain in enhancing prediction accuracy, generalizability, and interpretability. Confounding factors, such as host's gender, age, and body mass index, significantly influence the human microbiome, complicating microbiome-based predictions.
View Article and Find Full Text PDFFront Immunol
December 2024
School of Optometry, Jiangxi Medical College, Nanchang University, Nanchang, Jiangxi, China.
Background: Thyroid-associated orbitopathy (TAO) is an autoimmune inflammatory disorder of the orbital adipose tissue, primarily causing oxidative stress injury and tissue remodeling in the orbital connective tissue. Ferroptosis is a form of programmed cell death driven by the accumulation of reactive oxygen species (ROS), iron metabolism disorder, and lipid peroxidation. This study aims to identify and validate the optimal feature genes (OFGs) of ferroptosis with diagnostic and therapeutic potential in TAO orbital adipose tissue through bioinformatics analysis and to assess their correlation with disease-related immune cell infiltration.
View Article and Find Full Text PDFFront Neural Circuits
December 2024
Cognitive Neurophysiology, Brain Research Institute, University of Bremen, Bremen, Germany.
Introduction: A fundamental property of the neocortex is its columnar organization in many species. Generally, neurons of the same column share stimulus preferences and have strong anatomical connections across layers. These features suggest that neurons within a column operate as one unified network.
View Article and Find Full Text PDFEnviron Res
December 2024
Marine College, Shandong University, Weihai, China. Electronic address:
The dark and anoxic environment of ballast tank sediment (BTS) harbors substantial amounts of relic DNA, yet its impact on microbial diversity estimates in BTS management remains poorly understood. This study employed propidium monoazide (PMA) treatment to eliminate relic DNA and used 16S amplicon high-throughput sequencing to characterize both total and viable bacteria. Our findings revealed that relic DNA is abundant in BTS.
View Article and Find Full Text PDFSci Rep
December 2024
MARE-Marine and Environmental Sciences Centre & ARNET-Aquatic Research Network Associated Laboratory - CETEMARES, Av. do Porto de Pesca 30, Peniche, 2520-620, Portugal.
The management and creation of Marine Protected Areas (MPAs) is currently under great focus, with international organisations aiming to protect 30% of our oceans by 2030. The success of MPAs depends on a nuanced understanding of local ecological dynamics and threats, which can significantly influence ecosystem balance. Herbivory can be a stressor for foundation species, namely kelp forests, contributing to their decline in several regions of the globe.
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