Molecular Simulation Studies on the Prion Protein Variants: Insights into the Intriguing Effects of Mutations

Prion diseases, or transmissible spongiform encephalopathies (TSE), are a group of rare fatal neurodegenerative maladies that affect humans and animals. The fundamental breakthrough in TSE research was the discovery of the "prion"\u23afproteinaceous infectious particle\u23af and the verification of the \u201cprotein-only\u201d hypothesis, which states that prions could self-propagate by converting the cellular prion protein (PrPC) into the scrapie form, PrPSc (or prions), and lead to neurodegeneration without using any nucleic acids. The concept of prions may unify neurodegenerative diseases under a common pathogenic mechanism. Indeed, growing evidence shows that TSE may share similar pathogenesis with common neurodegenerative syndromes such as Alzheimer\u2019s disease and Parkinson\u2019s disease, for which there are currently no cure. Today, PrP is one of the most studied models for protein misfolding mechanism and TSE serve as an excellent model for studying many other neurodegenerative diseases. Understanding the molecular mechanism of the PrP misfolding process may profoundly influence the development of diagnostics and effective therapies for neurodegenerative diseases in general. Investigating human (Hu) PrP TSE-linked mutations (more than 50 currently identified mutations, linked to ~15% of the cases) may be very instrumental in this respect, as it can provide hints on the molecular basis of the PrPC\u2192PrPSc conversion. These mutations cause spontaneous TSE, which are likely due to modifications in the native structure of PrPC. They are located all over the structure. Polymorphisms (i.e. non-pathogenic, naturally occurring mutations) in the PrP gene have been found to influence the etiology and neuropathology of the disease in both humans and sheep. In transgenic (Tg) mice, artificial mutations can determine the susceptibility to the infection of different prion strains. Intriguingly, mouse (Mo) PrP containing artificial mutations (denoted MoPrP chimera, hereinafter) have very different effects in vitro: some MoPrP chimera were found to resist PrPSc infection, whereas some others did not; some of the resistant MoPrP chimeras even exhibited a protective effect (known as the dominant-negative effect) over the co-expressed endogenous wild-type (WT) MoPrPC. Most mutations are located in the folded globular domain (GD) while fewer are located in the intrinsically disordered N-terminal domain (N-term). The N-term of PrPC has been suggested to serve multiple functions in vivo, which likely relies on the structural flexibility of this domain. Therefore, characterizing the structural features of the N-term is central for investigating not only the mutations in this domain, but also the physiological role of the N-term. Based on previous studies in our lab, in this thesis we first applied molecular dynamics simulations to studying the impact of all the known Hu TSE-linked mutations in HuPrPC GD. We next applied the same approach to study the GD structure of MoPrP chimeras which contain one or two residues from Hu or sheep PrP sequence. By studying these PrP variants, we aim to identify the structural determinants of the mutants that may play a role in the PrPC\u2192PrPSc conversion. Our calculations discovered that these mutants exhibit different structural features from those of the WT PrP GD mainly in two common regions that are likely the \u201chot spots\u201d in the protein misfolding process. These features can be classified into different types that are correlated to the types of mutants (i.e. pathogenic, resistant or dominant-negative), thus hinting to the molecular mechanisms of PrPSc formation and propagation. We have then predicted the structure of the entire PrP N-term and the impact of the Hu TSE-linked mutations in this domain using a novel Monte Carlo-based simulation approach, PROFASI. PROFASI has already shown to provide structural predictions in a disordered protein such as \u3b1-synuclein. Our results are consistent with available experimental data and therefore firmly allow us to provide the first overview on the structural determinants of all Hu TSE-linked mutations in PrP

Does ESG investment reduce carbon emissions in China?

This study explores the relationship between ESG investments and carbon emissions in China. Our results show that 1% increase in environmental investments would cause 0.246% decrease in CO2 emissions and 0.558% decrease in carbon emission intensity. The impact of ESG investment is heterogeneous across the developed and underdeveloped regions. Environmental investments in the advanced eastern region have significantly improved carbon productivity. In contrast, environmental investments in the central and western regions significantly reduced carbon emissions, but they have little impact on carbon productivity

High-temperature high-sensitivity AlN-on-SOI Lamb wave resonant strain sensor

A piezoelectric AlN-on-SOI structured MEMS Lamb wave resonator (LWR) is presented for high-temperature strain measurement. The LWR has a composite membrane of a 1 μm thick AlN film and a 30 μm thick device silicon layer. The excited acoustic waves include Rayleigh wave and Lamb waves. A tensile strain sensor has been prepared with one LWR mounted on a uniaxial tensile plate, and its temperature characteristics from 15.4°C to 250°C and tensile strain behaviors from 0 μϵ to 400 μϵ of Rayleigh wave and S4 mode Lamb wave were tested. The temperature test verifies the adaptability of the tensile strain sensor to temperature up to 250°C, and S4 mode Lamb wave and Rayleigh wave represent almost the same temperature characteristics. The strain test demonstrates that S4 mode Lamb wave shows much higher strain sensitivity (-0.48 ppm/μϵ) than Rayleigh wave (0.05 ppm/μϵ) and confirms its advantage of strain sensitivity. Finally, for this one-LWR strain sensor, a method of beat frequency between S4 mode Lamb wave and Rayleigh wave is proposed for temperature compensation and high-sensitivity strain readout

Involvement of Lysosome Membrane Permeabilization and Reactive Oxygen Species Production in the Necrosis Induced by Chlamydia muridarum Infection in L929 Cells

Chlamydiae, obligate intracellular bacteria, are associated with a variety of human diseases. The chlamydial life cycle undergoes a biphasic development: replicative reticulate bodies (RBs) phase and infectious elementary bodies (EBs) phase. At the end of the chlamydial intracellular life cycle, EBs have to be released to the surrounded cells. Therefore, the interactions between Chlamydiae and cell death pathways could greatly influence the outcomes of Chlamydia infection. However, the underlying molecular mechanisms remain elusive. Here, we investigated host cell death after Chlamydia infection in vitro, in L929 cells, and showed that Chlamydia infection induces cell necrosis, as detected by the propidium iodide (PI)-Annexin V double-staining flow-cytometric assay and Lactate dehydrogenase (LDH) release assay. The production of reactive oxygen species (ROS), an important factor in induction of necrosis, was increased after Chlamydia infection, and inhibition of ROS with specific pharmacological inhibitors, diphenylene iodonium (DPI) or butylated hydroxyanisole (BHA), led to significant suppression of necrosis. Interestingly, live-cell imaging revealed that Chlamydia infection induced lysosome membrane permeabilization (LMP). When an inhibitor upstream of LMP, CA-074-Me, was added to cells, the production of ROS was reduced with concomitant inhibition of necrosis. Taken together, our results indicate that Chlamydia infection elicits the production of ROS, which is dependent on LMP at least partially, followed by induction of host-cell necrosis. To our best knowledge, this is the first live-cell-imaging observation of LMP post Chlamydia infection and report on the link of LMP to ROS to necrosis during Chlamydia infection. </p

Fast determination of polybrominated diphenyl ethers residues in milk by dispersive solid phase extraction and isotope labeled internal standard-gas chromatography-tandem mass spectrometry

Objective A 13C isotope labeled internal standard-gas chromatography-tandem mass spectrometric (GC-MS/MS) with dispersive solid phase extraction (d-SPE) method was developed for the simultaneous determination of 7 polybrominated diphenyl ethers (PBDEs) residues in milk. Methods After adding13C12 isotope internal standard and extracted with 1% acetic acid acetonitrile, purified with the new Z-Sep+C18 dispersive agent, the analytes in the sample solutions were seperated by DB-5 column (30 m×0.25 mm, 0.25 μm). Operated by electron impact ion source (EI) with multiple reactions monitoring (MRM) mode, the samples were analyzed by gas chromatography-tandem mass spectrometer. The quantifications were performed by the isotope internal standard method with matrix-matched calibration standards. Results Good linearity was obtained for 7 PBDEs in the concentration range of 0.500-100 ng/mL with correlation coefficients (r) above 0.999. Recoveries for 7 PBDEs at three spiked levels of 0.1, 1.0, and 10 μg/kg were in the range of 89.7%-102.9% with relative standard deviations (RSDs, n = 6) of 3.8%-8.3%. The limits of detection and the limits of quantification were in the ranges of 2.4-9.8 and 7.5-30 ng/kg, respectively. Conclusion The established method was simple, efficient and sensitive, and could be applied in the determination of 7 PBDEs in milk

Zebrafish olfactory receptors ORAs differentially detect bile acids and bile salts

The fish olfactory receptor ORA family is orthologous to the mammalian vomeronasal receptors type 1. It consists of six highly conserved chemosensory receptors expected to be essential for survival and communication. We deorphanized the zebrafish ORA family in a heterologous cell system. The six receptors responded specifically to lithocholic acid (LCA) and closely related C24 5β-bile acids/salts. LCA attracted zebrafish as strongly as food in behavioral tests, whereas the less potent cholanic acid elicited weaker attraction, consistent with the in vitro results. The ORA-ligand recognition patterns were probed with site-directed mutagenesis guided by in silico modeling.We revealed the receptors&apos; structure-function relationship underlying their specificity and selectivity for these compounds. Bile acids/salts are putative fish semiochemicals or pheromones sensed by the olfactory system with high specificity. This work identified their receptors and provided the basis for probing the roles of ORAs and bile acids/salts in fish chemosensation. © 2019 Cong et al.1

Unifying view of mechanical and functional hotspots across class A GPCRs

G protein-coupled receptors (GPCRs) are the largest superfamily of signaling proteins. Their activation process is accompanied by conformational changes that have not yet been fully uncovered. Here, we carry out a novel comparative analysis of internal structural fluctuations across a variety of receptors from class A GPCRs, which currently has the richest structural coverage. We infer the local mechanical couplings underpinning the receptors' functional dynamics and finally identify those amino acids whose virtual deletion causes a significant softening of the mechanical network. The relevance of these amino acids is demonstrated by their overlap with those known to be crucial for GPCR function, based on static structural criteria. The differences with the latter set allow us to identify those sites whose functional role is more clearly detected by considering dynamical and mechanical properties. Of these sites with a genuine mechanical/dynamical character, the top ranking is amino acid 7x52, a previously unexplored, and experimentally verifiable key site for GPCR conformational response to ligand binding. \ua9 2017 Ponzoni et al

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Allosteric Na+-binding site modulates CXCR4 activation

G protein-coupled receptors (GPCRs) control most cellular communications with the environment and are the largest protein family of drug targets. As strictly regulated molecular machines, profound comprehension of their activation mechanism is expected to significantly facilitate structure-based drug design. This study provides atomistic-level description of the activation dynamics of the C-X-C chemokine receptor type 4 (CXCR4), a class A GPCR and important drug target. Using molecular dynamics and enhanced sampling, we demonstrate how mutations and protonation of conserved residues trigger activation through microswitches at the receptor core, while sodium ion-a known allosteric modulator-inhibits it. The findings point to a conserved mechanism of activation and the allosteric modulation by sodium in the chemokine receptor family. From the technical aspect, the enhanced sampling protocol effectively samples receptor conformational changes toward activation, and differentiates three variants of the receptor by their basal activity. This work provides structural basis and a powerful in silico tool for CXCR4 agonist design. © 2018 the Owner Societies.1

Features and Evolution of Global Energy Trade Patterns from the Perspective of Complex Networks

As an integral part of economic trade, energy trade is crucial to international dynamics and national interests. In this study, an international energy trade network is constructed by abstracting countries as nodes and representing energy trade relations as edges. A variety of indicators are designed in terms of networks, nodes, bilaterals, and communities to analyze the temporal and spatial evolution of the global energy trade network from 2001 to 2020. The results indicate that network density and strength have been steadily increasing since the beginning of the 21st century. It is observed that the position of the United States as the core of the international energy market is being impacted by emerging developing countries, thus affecting the existing trade balance based on topological analysis. The weighted analysis of bilateral relations demonstrates that emerging countries such as China, Brazil, and Saudi Arabia are pursuing closer cooperation. The community analysis reveals that an increasing number of countries possess strong energy trade capabilities, resulting in a corresponding increase in energy trade volumes