Shanghai Institute of Applied Physics

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Graphene is a monolayer of tightly packed carbon atoms that possesses many interesting properties and has numerous exciting applications. In this work, we report the antibacterial activity of two water-dispersible graphene derivatives, graphene oxide (GO) and reduced graphene oxide (rGO) nanosheets. Such graphene-based nanomaterials can effectively inhibit the growth of E. coli bacteria while showing minimal cytotoxicity. We have also demonstrated that macroscopic freestanding GO and rGO paper can be conveniently fabricated from their suspension via simple vacuum filtration. Given the superior antibacterial effect of GO and the fact that GO can be mass-produced and easily processed to make freestanding and flexible paper with low cost, we expect this new carbon nanomaterial may find important environmental and clinical applications.

Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.

Understanding the origin of high activity of Fe-N-C electrocatalysts in oxygen reduction reaction (ORR) is critical but still challenging for developing efficient sustainable nonprecious metal catalysts in fuel cells and metal-air batteries. Herein, we developed a new highly active Fe-N-C ORR catalyst containing Fe-N(x) coordination sites and Fe/Fe3C nanocrystals (Fe@C-FeNC), and revealed the origin of its activity by intensively investigating the composition and the structure of the catalyst and their correlations with the electrochemical performance. The detailed analyses unambiguously confirmed the coexistence of Fe/Fe3C nanocrystals and Fe-N(x) in the best catalyst. A series of designed experiments disclosed that (1) N-doped carbon substrate, Fe/Fe3C nanocrystals or Fe-N(x) themselves did not deliver the high activity; (2) the catalysts with both Fe/Fe3C nanocrystals and Fe-N(x) exhibited the high activity; (3) the higher content of Fe-N(x) gave the higher activity; (4) the removal of Fe/Fe3C nanocrystals severely degraded the activity; (5) the blocking of Fe-N(x) downgraded the activity and the recovery of the blocked Fe-N(x) recovered the activity. These facts supported that the high ORR activity of the Fe@C-FeNC electrocatalysts should be ascribed to that Fe/Fe3C nanocrystals boost the activity of Fe-N(x). The coexistence of high content of Fe-N(x) and sufficient metallic iron nanoparticles is essential for the high ORR activity. DFT calculation corroborated this conclusion by indicating that the interaction between metallic iron and Fe-N4 coordination structure favored the adsorption of oxygen molecule. These new findings open an avenue for the rational design and bottom-up synthesis of low-cost highly active ORR electrocatalysts.

Compressive surface strains have been necessary to boost oxygen reduction reaction (ORR) activity in core/shell M/platinum (Pt) catalysts (where M can be nickel, cobalt, or iron). We report on a class of platinum-lead/platinum (PtPb/Pt) core/shell nanoplate catalysts that exhibit large biaxial strains. The stable Pt (110) facets of the nanoplates have high ORR specific and mass activities that reach 7.8 milliampere (mA) per centimeter squared and 4.3 ampere per milligram of platinum at 0.9 volts versus the reversible hydrogen electrode (RHE), respectively. Density functional theory calculations reveal that the edge-Pt and top (bottom)-Pt (110) facets undergo large tensile strains that help optimize the Pt-O bond strength. The intermetallic core and uniform four layers of Pt shell of the PtPb/Pt nanoplates appear to underlie the high endurance of these catalysts, which can undergo 50,000 voltage cycles with negligible activity decay and no apparent structure and composition changes.

Methylation at the N6 position of adenosine (m(6)A) is the most abundant RNA modification within protein-coding and long noncoding RNAs in eukaryotes and is a reversible process with important biological functions. YT521-B homology domain family (YTHDF) proteins are the readers of m(6)A, the binding of which results in the alteration of the translation efficiency and stability of m(6)A-containing RNAs. However, the mechanism by which YTHDF proteins cause the degradation of m(6)A-containing RNAs is poorly understood. Here we report that m(6)A-containing RNAs exhibit accelerated deadenylation that is mediated by the CCR4-NOT deadenylase complex. We further show that YTHDF2 recruits the CCR4-NOT complex through a direct interaction between the YTHDF2 N-terminal region and the SH domain of the CNOT1 subunit, and that this recruitment is essential for the deadenylation of m(6)A-containing RNAs by CAF1 and CCR4. Therefore, we have uncovered the mechanism of YTHDF2-mediated degradation of m(6)A-containing RNAs in mammalian cells.

The efficient use of natural gas will require catalysts that can activate the first C-H bond of methane while suppressing complete dehydrogenation and avoiding overoxidation. We report that single iron sites embedded in a silica matrix enable direct, nonoxidative conversion of methane, exclusively to ethylene and aromatics. The reaction is initiated by catalytic generation of methyl radicals, followed by a series of gas-phase reactions. The absence of adjacent iron sites prevents catalytic C-C coupling, further oligomerization, and hence, coke deposition. At 1363 kelvin, methane conversion reached a maximum at 48.1% and ethylene selectivity peaked at 48.4%, whereas the total hydrocarbon selectivity exceeded 99%, representing an atom-economical transformation process of methane. The lattice-confined single iron sites delivered stable performance, with no deactivation observed during a 60-hour test.

Abstract Coupling nanomaterials with biomolecular recognition events represents a new direction in nanotechnology toward the development of novel molecular diagnostic tools. Here a graphene oxide (GO)‐based multicolor fluorescent DNA nanoprobe that allows rapid, sensitive, and selective detection of DNA targets in homogeneous solution by exploiting interactions between GO and DNA molecules is reported. Because of the extraordinarily high quenching efficiency of GO, the fluorescent ssDNA probe exhibits minimal background fluorescence, while strong emission is observed when it forms a double helix with the specific targets, leading to a high signal‐to‐background ratio. Importantly, the large planar surface of GO allows simultaneous quenching of multiple DNA probes labeled with different dyes, leading to a multicolor sensor for the detection of multiple DNA targets in the same solution. It is also demonstrated that this GO‐based sensing platform is suitable for the detection of a range of analytes when complemented with the use of functional DNA structures.

from the atmosphere. Herein, we review innovative technologies that offer solutions achieving carbon (C) neutrality and sustainable development, including those for renewable energy production, food system transformation, waste valorization, C sink conservation, and C-negative manufacturing. The wealth of knowledge disseminated in this review could inspire the global community and drive the further development of innovative technologies to mitigate climate change and sustainably support human activities.

AIMS: To investigate alterations in protein expression associated with deep brain stimulation (DBS) in an attempt to elucidate possible mechanisms of action . METHODS: Cerebrospinal fluid (CSF), obtained from six Parkinson's disease (PD) patients (pre- and post-DBS) and from six normal healthy controls, was studied for differentially expressed proteins. 2-D DIGE, in combination with MALDI-TOF and TOF-TOF Mass Spectrometry (MS) or ESI-MS, was used to identify the changed proteins (3 PD patients and 3 controls). Selected proteins were further studied using western blotting (6 PD patients and 6 controls). RESULTS: Twenty-one proteins were identified after MS and protein database interrogation. Apart from apolipoprotein A-I (apoA-I), the expression levels of complement C4 (C4), IgA, tetranectin, and extracellular superoxide dismutase (EC-SOD), detected by western blotting, correlated well with the 2-D DIGE results. In the follow-up period, the expression levels of C4, apoA-I and IgA were stable whereas EC-SOD and tetranectin were significantly elevated. In addition, when DBS was ceased in one patient due to a suicide attempt, the levels of EC-SOD and tetranectin significantly decreased. CONCLUSION: Our preliminary results suggest that variations in the expression levels of EC-SOD and tetranectin in CSF is related to DBS.

of ~2.8 ± 0.5 at 773 kelvin in n-type tin selenide (SnSe) crystals out of plane. The thermal conductivity in layered SnSe crystals is the lowest in the out-of-plane direction [two-dimensional (2D) phonon transport]. We doped SnSe with bromine to make n-type SnSe crystals with the overlapping interlayer charge density (3D charge transport). A continuous phase transition increases the symmetry and diverges two converged conduction bands. These two factors improve carrier mobility, while preserving a large Seebeck coefficient. Our findings can be applied in 2D layered materials and provide a new strategy to enhance out-of-plane electrical transport properties without degrading thermal properties.

Over the past decade, we have seen rapid advances in applying nanotechnology in biomedical areas including bioimaging, biodetection, and drug delivery. As an emerging field, DNA nanotechnology offers simple yet powerful design techniques for self-assembly of nanostructures with unique advantages and high potential in enhancing drug targeting and reducing drug toxicity. Various sequence programming and optimization approaches have been developed to design DNA nanostructures with precisely engineered, controllable size, shape, surface chemistry, and function. Potent anticancer drug molecules, including Doxorubicin and CpG oligonucleotides, have been successfully loaded on DNA nanostructures to increase their cell uptake efficiency. These advances have implicated the bright future of DNA nanotechnology-enabled nanomedicine. In this review, we begin with the origin of DNA nanotechnology, followed by summarizing state-of-the-art strategies for the construction of DNA nanostructures and drug payloads delivered by DNA nanovehicles. Further, we discuss the cellular fates of DNA nanostructures as well as challenges and opportunities for DNA nanostructure-based drug delivery.

A single-layer MoS2 nanosheet exhibits high fluorescence quenching ability and different affinity toward ssDNA versus dsDNA. As a proof of concept, the MoS2 nanosheet has been successfully used as a sensing platform for the detection of DNA and small molecules.

Abstract Isolated single atomic site catalysts have attracted great interest due to their remarkable catalytic properties. Because of their high surface energy, single atoms are highly mobile and tend to form aggregate during synthetic and catalytic processes. Therefore, it is a significant challenge to fabricate isolated single atomic site catalysts with good stability. Herein, a gentle method to stabilize single atomic site metal by constructing defects on the surface of supports is presented. As a proof of concept, single atomic site Au supported on defective TiO 2 nanosheets is prepared and it is discovered that (1) the surface defects on TiO 2 nanosheets can effectively stabilize Au single atomic sites through forming the Ti–Au–Ti structure; and (2) the Ti–Au–Ti structure can also promote the catalytic properties through reducing the energy barrier and relieving the competitive adsorption on isolated Au atomic sites. It is believed that this work paves a way to design stable and active single atomic site catalysts on oxide supports.

It is of great importance to understand the origin of high oxygen-evolving activity of state-of-the-art multimetal oxides/(oxy)hydroxides at atomic level. Herein we report an evident improvement of oxygen evolution reaction activity via incorporating iron and vanadium into nickel hydroxide lattices. X-ray photoelectron/absorption spectroscopies reveal the synergistic interaction between iron/vanadium dopants and nickel in the host matrix, which subtly modulates local coordination environments and electronic structures of the iron/vanadium/nickel cations. Further, in-situ X-ray absorption spectroscopic analyses manifest contraction of metal-oxygen bond lengths in the activated catalyst, with a short vanadium-oxygen bond distance. Density functional theory calculations indicate that the vanadium site of the iron/vanadium co-doped nickel (oxy)hydroxide gives near-optimal binding energies of oxygen evolution reaction intermediates and has lower overpotential compared with nickel and iron sites. These findings suggest that the doped vanadium with distorted geometric and disturbed electronic structures makes crucial contribution to high activity of the trimetallic catalyst.

Mesoporous TiO2 has gained increasing interest because of its outstanding properties and promising applications in a wide range of fields. Herein, we report the facile synthesis of ordered mesoporous black TiO2 (OMBT) materials, which exhibit excellent photocatalytic hydrogen evolution performances. In this case, the employment of a thermally stable and high-surface-area mesoporous TiO2 as the hydrogenation precursor is the key for fabricating the OMBT materials, which not only facilitate H2 gas diffusion into TiO2 and interaction with their structures but also maintain the ordered mesoporous structures as well as inhibit the phase transformation (from anatase to rutile) and crystal growth during hydrogenation at 500 °C. The resultant OMBT materials possess a relatively high surface area of ∼124 m(2) g(-1) and a large pore size and pore volume of ∼9.6 nm and 0.24 cm(3) g(-1), respectively. More importantly, the OMBT materials can extend the photoresponse from ultraviolet to visible and infrared light regions and exhibit a high solar-driven hydrogen production rate (136.2 μmol h(-1)), which is almost two times as high as that of pristine mesoporous TiO2 (76.6 μmol h(-1)).

Identified charged-particle spectra of ${\ensuremath{\pi}}^{\ifmmode\pm\else\textpm\fi{}}$, ${K}^{\ifmmode\pm\else\textpm\fi{}}$, $p$, and $\overline{p}$ at midrapidity ($|y|<0.1$) measured by the $\mathit{dE}/\mathit{dx}$ method in the STAR (solenoidal tracker at the BNL Relativistic Heavy Ion Collider) time projection chamber are reported for $\mathit{pp}$ and $d+\mathrm{Au}$ collisions at $\sqrt{{s}_{\mathit{NN}}}=200$ GeV and for $\mathrm{Au}+\mathrm{Au}$ collisions at 62.4, 130, and 200 GeV. Average transverse momenta, total particle production, particle yield ratios, strangeness, and baryon production rates are investigated as a function of the collision system and centrality. The transverse momentum spectra are found to be flatter for heavy particles than for light particles in all collision systems; the effect is more prominent for more central collisions. The extracted average transverse momentum of each particle species follows a trend determined by the total charged-particle multiplicity density. The Bjorken energy density estimate is at least several GeV/${\mathrm{fm}}^{3}$ for a formation time less than 1 fm/$c$. A significantly larger net-baryon density and a stronger increase of the net-baryon density with centrality are found in $\mathrm{Au}+\mathrm{Au}$ collisions at 62.4 GeV than at the two higher energies. Antibaryon production relative to total particle multiplicity is found to be constant over centrality, but increases with the collision energy. Strangeness production relative to total particle multiplicity is similar at the three measured RHIC energies. Relative strangeness production increases quickly with centrality in peripheral $\mathrm{Au}+\mathrm{Au}$ collisions, to a value about 50% above the $\mathit{pp}$ value, and remains rather constant in more central collisions. Bulk freeze-out properties are extracted from thermal equilibrium model and hydrodynamics-motivated blast-wave model fits to the data. Resonance decays are found to have little effect on the extracted kinetic freeze-out parameters because of the transverse momentum range of our measurements. The extracted chemical freeze-out temperature is constant, independent of collision system or centrality; its value is close to the predicted phase-transition temperature, suggesting that chemical freeze-out happens in the vicinity of hadronization and the chemical freeze-out temperature is universal despite the vastly different initial conditions in the collision systems. The extracted kinetic freeze-out temperature, while similar to the chemical freeze-out temperature in $\mathit{pp}$, $d+\mathrm{Au}$, and peripheral $\mathrm{Au}+\mathrm{Au}$ collisions, drops significantly with centrality in $\mathrm{Au}+\mathrm{Au}$ collisions, whereas the extracted transverse radial flow velocity increases rapidly with centrality. There appears to be a prolonged period of particle elastic scatterings from chemical to kinetic freeze-out in central $\mathrm{Au}+\mathrm{Au}$ collisions. The bulk properties extracted at chemical and kinetic freeze-out are observed to evolve smoothly over the measured energy range, collision systems, and collision centralities.

Abstract Atomic interface regulation is thought to be an efficient method to adjust the performance of single atom catalysts. Herein, a practical strategy was reported to rationally design single copper atoms coordinated with both sulfur and nitrogen atoms in metal-organic framework derived hierarchically porous carbon (S-Cu-ISA/SNC). The atomic interface configuration of the copper site in S-Cu-ISA/SNC is detected to be an unsymmetrically arranged Cu-S 1 N 3 moiety. The catalyst exhibits excellent oxygen reduction reaction activity with a half-wave potential of 0.918 V vs. RHE. Additionally, through in situ X-ray absorption fine structure tests, we discover that the low-valent Cuprous-S 1 N 3 moiety acts as an active center during the oxygen reduction process. Our discovery provides a universal scheme for the controllable synthesis and performance regulation of single metal atom catalysts toward energy applications.

Abstract The electrochemical reduction of N 2 into NH 3 production under ambient conditions represents an attractive prospect for the fixation of N 2 . However, this process suffers from low yield rate of NH 3 over reported electrocatalysts. In this work, a record‐high activity for N 2 electrochemical reduction over Ru single atoms distributed on nitrogen‐doped carbon (Ru SAs/N‐C) is reported. At −0.2 V versus reversible hydrogen electrode, Ru SAs/N‐C achieves a Faradaic efficiency of 29.6% for NH 3 production with partial current density of −0.13 mA cm −2 . Notably, the yield rate of Ru SAs/N‐C reaches 120.9 , which is one order of magnitude higher than the highest value ever reported. This work not only develops a superior electrocatalyst for NH 3 production, but also provides a guideline for the rational design of highly active and robust single‐atom catalysts.

We report a new search for weakly interacting massive particles (WIMPs) using the combined low background data sets acquired in 2016 and 2017 from the PandaX-II experiment in China. The latest data set contains a new exposure of 77.1 live days, with the background reduced to a level of 0.8×10^{-3} evt/kg/day, improved by a factor of 2.5 in comparison to the previous run in 2016. No excess events are found above the expected background. With a total exposure of 5.4×10^{4} kg day, the most stringent upper limit on the spin-independent WIMP-nucleon cross section is set for a WIMP with mass larger than 100 GeV/c^{2}, with the lowest 90% C.L. exclusion at 8.6×10^{-47} cm^{2} at 40 GeV/c^{2}.