Direct Imaging of Transmembrane Dynamics of Single Nanoparticles with Darkfield Microscopy: Improved Orientation Tracking at Cell Sidewall

Investigation of the cellular internalization processes of individual nanoparticles (NPs) is of great scientific interest with implications to drug delivery and NP biosafety. Herein, by using dual-channel polarization darkfield microcopy (DFM) and single gold nanorods (AuNRs) as orientation probes, we developed a method that is capable of monitoring AuNR orientation dynamics during its transmembrane process. With annular oblique illumination and a birefringent prism to split AuNR plasmonic scattering into two channels of orthogonal polarizations, the AuNR azimuth and polar angles are obtained from their intensity difference and intensity sum. By placing the focal plane of the microscope objective at the elevated cell sidewall rather than at the flat cell top, interference from cellular background is reduced and the signal-to-noise ratio of AuNR orientation sensing is improved significantly, especially for AuNRs inserting into the membrane at a large out-of-plane angle. As a result, we were able to capture the complete membrane-crossing dynamics of single AuNRs. This powerful method could be utilized to obtain valuable insights on NP endocytosis mechanisms of various cells

Understanding the Phosphorylation Mechanism by Using Quantum Chemical Calculations and Molecular Dynamics Simulations

Phosphorylation is one of the most frequent post-translational modifications on proteins. It regulates many cellular processes by modulation of phosphorylation on protein structure and dynamics. However, the mechanism of phosphorylation-induced conformational changes of proteins is still poorly understood. Here, we report a computational study of three representative groups of tyrosine in ADP-ribosylhydrolase 1, serine in BTG2, and serine in Sp100C by using six molecular dynamics (MD) simulations and quantum chemical calculations. Added phosphorylation was found to disrupt hydrogen bond, and increase new weak interactions (hydrogen bond and hydrophobic interaction) during MD simulations, leading to conformational changes. Quantum chemical calculations further indicate that the phosphorylation on tyrosine, threonine, and serine could decrease the optical band gap energy (<i>E</i>_gap), which can trigger electronic transitions to form or disrupt interactions easily. Our results provide an atomic and electronic description of how phosphorylation facilitates conformational and dynamic changes in proteins, which may be useful for studying protein function and protein design

MOESM1 of Microbial community compositions in different functional zones of Carrousel oxidation ditch system for domestic wastewater treatment

Additional file 1: Table S1. Characteristics of the six representative full-scale WWTPs. Table S2: Raw and trimmed reads, Good’s coverage, Chao1, ACE, Shannon, Simpson, and plus numbers of OTUs of the activated sludge samples

Subdiffraction-Limited Plasmonic Imaging with Anisotropic Metal Nanoparticles

We have developed a high-resolution nonfluorescent imaging method based on superlocalization of gold nanorods (AuNRs). By taking advantage of their anisotropic optical property of the plasmonic scattering of AuNRs, selective imaging of only a fraction of AuNRs can be achieved by rotating the sample relative to the linear polarized illumination under cross-polarization microscopy with a high NA objective. The AuNR positions obtained from a series of images could then be used to reconstruct the overall image. Two AuNRs with center-to-center distances of 80 nm were successfully resolved. This simple but deterministic super-resolution imaging technique can potentially be used to fingerprint optically anisotropic metal nanoparticles and their assemblies for labeling, sensing, and encryption applications

Data_Sheet_4_Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study.ZIP

<p>Thermus thermophiles Argonaute (TtAgo) is a complex, which is consisted of 5′-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507–509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.</p

Data_Sheet_2_Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study.ZIP

<p>Thermus thermophiles Argonaute (TtAgo) is a complex, which is consisted of 5′-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507–509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.</p

The 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis Could Classify Systemic Sclerosis Patients at Earlier Stage: Data from a Chinese EUSTAR Center

<div><p>Objectives</p><p>To evaluate the performance of the 2013 ACR/EULAR classification criteria for systemic sclerosis (SSc) in clinical practice in a Chinese patient cohort, and to compare outcomes with the 1980 ACR criteria.</p><p>Methods</p><p>Patients clinically diagnosed with SSc between September 2013 and May 2015 were prospectively recruited from the EUSTAR database of the Peking Union Medical College Hospital. Diagnosis of SSc was based on the evaluation of three experienced rheumatologists. Patients diagnosed with other connective tissue diseases were recruited as disease controls. The 1980 ACR and 2013 ACR/EULAR criteria were applied to the cohort, and patients who fulfilled the criteria were classified as definite SSc patients. Sensitivity and specificity were analyzed for the 2013 and 1980 criteria.</p><p>Results</p><p>A total of 143 SSc patients and 87 patients with other connective diseases were recruited. 41 (28.7%) and 102 (71.3%) cases were diffuse cutaneous SSc and limited cutaneous SSc, respectively. Although the sensitivity of the 2013 criteria (94.4%) exceeded the 1980 criteria (72.7%) (P<0.001), the 1980 and 2013 criteria sets showed no significant difference in specificity (97.7% and 93.1%, respectively, P = 0.278). The sensitivity of the 2013 criteria was significantly higher than the 1980 criteria in some SSc subgroups (e.g., lcSSc, abnormal pattern of nailfold videocapillaroscopy [NVC] and presence of Raynaud’s phenomenon [RP]) compared to others.</p><p>Conclusions</p><p>Relative to the 1980 ACR criteria, in Chinese SSc patients the new 2013 ACR/EULAR criteria had similar specificity and higher sensitivity, especially for patients with mild skin thickening or prominent microvascular diseases.</p></div

Two-Dimensional Carbon Nanosheets for High-Performance Supercapacitors: Large-Scale Synthesis and Codoping with Nitrogen and Phosphorus

Two-dimensional carbon nanosheets codoped with N and P species have been successfully synthesized by a template carbonization method coupled with nitrogenization and phosphorylation processes using trisodium citrate dihydrate, melamine, and NH₄H₂PO₄ as C, N, and P sources, respectively. Dopants of N and P species play crucial roles in the determination of carbon porosities and electrochemical performance; notably, increasing the P content can lead to a decrease in the BET surface area together with a corresponding decrease in the electrochemical performance. For instance, regulating the mass ratio between the C source and the N and P sources to 2:1 results in the maximum BET surface area of 1340 m² g^–1, whereas a ratio of 1:2 results in a decreased value of only 47 m² g^–1. Moreover, the mass ratio of 1:1 results in superior electrochemical behaviors, with a maximum energy density that can reach up to 13.3 Wh kg^–1. The present synthesis method provides an alternative route for producing N- and P-containing carbon nanostructures with two-dimensional features, serving as excellent electrode materials for energy propagation and storage

Integration of Redox Additive in H₂SO₄ Solution and the Adjustment of Potential Windows for Improving the Capacitive Performances of Supercapacitors

Nanoporous carbon material with large specific surface area (2208 m² g^–1) and high pore volume (4.15 cm³ g^–1) has been synthesized by the template carbonization method, using a glucose–zinc nitrate complex as the precursor. Moreover, adding redox-mediated ferrous ammonium sulfate (FAS) to an H₂SO₄ electrolyte and regulating the potential windows in a two-electrode system can result in an ultrahigh specific capacitance of 1499 F g^–1 at 10 A g^–1 and a high energy density of 58.70 Wh kg^–1, which are higher than those of the pristine one without any FAS. These remarkable improvements are attributed to Faradaic pseudocapacitances by the reversible Faradaic reactions of FAS as well as the edge active carbons showing excellent electrosorption toward Fe^2+/3+, NH₄⁺, and H⁺. Furthermore, regulating the potential windows also exerts crucial roles in the capacitive performances. It is revealed that the potential of the −0.5–0.5 V window can lead to optimum capacitance and energy efficiency

Data_Sheet_3_Why Is a High Temperature Needed by Thermus thermophilus Argonaute During mRNA Silencing: A Theoretical Study.ZIP

<p>Thermus thermophiles Argonaute (TtAgo) is a complex, which is consisted of 5′-phosphorylated guide DNA and a series of target DNA with catalytic activities at high temperatures. To understand why high temperatures are needed for the catalytic activities, three molecular dynamics simulations and binding free energy calculations at 310, 324, and 338K were performed for the TtAgo-DNA complex to explore the conformational changes between 16-mer guide DNA/15-mer target DNA and TtAgo at different temperatures. The simulation results indicate that a collapse of a small β-strand (residues 507–509) at 310 K caused Glu512 to move away from the catalytic residues Asp546 and Asp478, resulting in a decrease in catalytic activity, which was not observed in the simulations at 324 and 338 K. The nucleic acid binding channel became enlarged at 324 and 338K, thereby facilitating the DNA to slide in. Binding free energy calculations and hydrogen bond occupancy indicated that the interaction between TtAgo and the DNA was more stable at 324K and 338K than at 310 K. The DNA binding pocket residues Lys575 and Asn590 became less solvent accessible at 324 and 338K than at 310 K to influence hydrophilic interaction with DNA. Our simulation studies shed some light on the mechanism of TtAgo and explained why a high temperature was needed by TtAgo during gene editing of CRISPR.</p