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| http://dx.doi.org/10.3343/alm.2017.37.3.293 | DOI Listing |
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Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy.
bioRxiv
October 2024
Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, USA.
In mammalian interphase cells, genomes are folded by cohesin loop extrusion limited by directional CTCF barriers. This interplay leads to the enrichment of cohesin at barriers, isolation between neighboring topologically associating domains, and elevated contact frequency between convergent CTCF barriers across the genome. However, recent measurements present a puzzle: reported residence times for CTCF on chromatin are in the range of a few minutes, while lifetimes for cohesin are much longer.
View Article and Find Full Text PDFThe adsorption-diffusion model and biomimetic simulation reveal the switchable roles of silicon in regulating toxic metal uptake in rice roots.
Chemosphere
April 2024
Ministry of Education Key Laboratory of Environment Remediation and Ecological Health, College of Environmental & Resource Sciences, Zhejiang University, Hangzhou, 310058, China. Electronic address:
Article Synopsis
- * A process-based adsorption-diffusion model was developed to explain silicon's impact on reducing heavy metal stress, evaluated through 28 experiments focused on chromium stress in rice.
- * The study found that while silicon initially aids in chromium adsorption, its primary benefit shifts to blocking diffusion of chromium into plant roots as metal concentrations rise, enhancing our understanding of silicon's role in plant health.
Magnetostriction-Driven Muon Localization in an Antiferromagnetic Oxide.
Phys Rev Lett
January 2024
Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Universitá di Parma, I-43124 Parma, Italy.
Magnetostriction results from the coupling between magnetic and elastic degrees of freedom. Though it is associated with a relatively small energy, we show that it plays an important role in determining the site of an implanted muon, so that the energetically favorable site can switch on crossing a magnetic phase transition. This surprising effect is demonstrated in the cubic rocksalt antiferromagnet MnO which undergoes a magnetostriction-driven rhombohedral distortion at the Néel temperature T_{N}=118 K.
View Article and Find Full Text PDFInsights to HIV-1 coreceptor usage by estimating HLA adaptation with Bayesian generalized linear mixed models.
PLoS Comput Biol
December 2023
Research Group Computational Biology, Max Planck Institute for Informatics, Saarbrücken, Germany.
The mechanisms triggering the human immunodeficiency virus type I (HIV-1) to switch the coreceptor usage from CCR5 to CXCR4 during the course of infection are not entirely understood. While low CD4+ T cell counts are associated with CXCR4 usage, a predominance of CXCR4 usage with still high CD4+ T cell counts remains puzzling. Here, we explore the hypothesis that viral adaptation to the human leukocyte antigen (HLA) complex, especially to the HLA class II alleles, contributes to the coreceptor switch.
View Article and Find Full Text PDFCircadian Vesicle Capture Prepares Clock Neuron Synapses for Daily Phase-Delayed Neuropeptide Release.
bioRxiv
June 2024
Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
sLNv clock neurons release the neuropeptide PDF to control circadian rhythms. Strikingly, PDF content in sLNv terminals is rhythmic with a peak in the morning hours prior to the onset of activity-dependent release. Because synaptic PDF accumulation, rather than synaptic release, aligns with the late-night elevations in both sLNv neuron excitability and Ca, we explored the dependence of presynaptic neuropeptide accumulation on neuropeptide vesicle transport, electrical activity and the circadian clock.
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