Jilin University

About: Jilin University is a education organization based out in Changchun, China. It is known for research contribution in the topics: Catalysis & Apoptosis. The organization has 101453 authors who have published 88966 publications receiving 1444456 citations. The organization is also known as: Jílín Dàxué.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

Abstract: 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 that there 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 complete process 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 increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most 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 many cases, 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 for reviewers 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 multiple assays 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 autophagy-related 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.

Noble metal-free hydrogen evolution catalysts for water splitting

Abstract: Sustainable hydrogen production is an essential prerequisite of a future hydrogen economy. Water electrolysis driven by renewable resource-derived electricity and direct solar-to-hydrogen conversion based on photochemical and photoelectrochemical water splitting are promising pathways for sustainable hydrogen production. All these techniques require, among many things, highly active noble metal-free hydrogen evolution catalysts to make the water splitting process more energy-efficient and economical. In this review, we highlight the recent research efforts toward the synthesis of noble metal-free electrocatalysts, especially at the nanoscale, and their catalytic properties for the hydrogen evolution reaction (HER). We review several important kinds of heterogeneous non-precious metal electrocatalysts, including metal sulfides, metal selenides, metal carbides, metal nitrides, metal phosphides, and heteroatom-doped nanocarbons. In the discussion, emphasis is given to the synthetic methods of these HER electrocatalysts, the strategies of performance improvement, and the structure/composition-catalytic activity relationship. We also summarize some important examples showing that non-Pt HER electrocatalysts could serve as efficient cocatalysts for promoting direct solar-to-hydrogen conversion in both photochemical and photoelectrochemical water splitting systems, when combined with suitable semiconductor photocatalysts.

DEGseq: an R package for identifying differentially expressed genes from RNA-seq data

Abstract: Summary: High-throughput RNA sequencing (RNA-seq) is rapidly emerging as a major quantitative transcriptome profiling platform. Here, we present DEGseq, an R package to identify differentially expressed genes or isoforms for RNA-seq data from different samples. In this package, we integrated three existing methods, and introduced two novel methods based on MA-plot to detect and visualize gene expression difference. Availability: The R package and a quick-start vignette is available at http://bioinfo.au.tsinghua.edu.cn/software/degseq Contact: xwwang@tsinghua.edu.cn; zhangxg@tsinghua.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.

Highly Photoluminescent Carbon Dots for Multicolor Patterning, Sensors, and Bioimaging

Abstract: Fluorescent carbon-based materials have drawn increasing attention in recent years owing to exceptional advantages such as high optical absorptivity, chemical stability, biocompatibility, and low toxicity. These materials primarily include carbon dots (CDs), nanodiamonds, carbon nanotubes, fullerene, and fluorescent graphene. The superior properties of fluorescent carbon-based materials distinguish them from traditional fluorescent materials, and make them promising candidates for numerous exciting applications, such as bioimaging, medical diagnosis, catalysis, and photovoltaic devices. Among all of these materials, CDs have drawn the most extensive notice, owing to their early discovery and adjustable parameters. However, many scientific issues with CDs still await further investigation. Currently, a broad series of methods for obtaining CD-based materials have been developed, but efficient one-step strategies for the fabrication of CDs on a large scale are still a challenge in this field. Current synthetic methods are mainly deficient in accurate control of lateral dimensions and the resulting surface chemistry, as well as in obtaining fluorescent materials with high quantum yields (QY). Moreover, it is important to expand these kinds of materials to novel applications. Herein, a facile and highoutput strategy for the fabrication of CDs, which is suitable for industrial-scale production (yield is ca. 58%), is discussed. The QY was as high as ca. 80%, which is the highest value recorded for fluorescent carbon-based materials, and is almost equal to fluorescent dyes. The polymer-like CDs were converted into carbogenic CDs by a change from low to high synthesis temperature. The photoluminescence (PL) mechanism (high QY/PL quenching) was investigated in detail by ultrafast spectroscopy. The CDs were applied as printing ink on the macro/micro scale and nanocomposites were also prepared by polymerizing CDs with certain polymers. Additionally, the CDs could be utilized as a biosensor reagent for the detection of Fe in biosystems. The CDs were prepared by a hydrothermal method, which is described in the Supporting Information (Figure 1a; see also the Supporting Information, Figure S1). The reaction was conducted by first condensing citric acid and ethylenediamine, whereupon they formed polymer-like CDs, which were then carbonized to form the CDs. The morphology and structure of CDs were confirmed by analysis. Figure 1b shows transmission electron microscopy (TEM) images of the CDs, which can be seen to have a uniform dispersion without apparent aggregation and particle diameters of 2–6 nm. The sizes of CDs were also measured by atomic force microscopy (AFM; Figure S2), and the average height was 2.81 nm. From the high-resolution TEM, most particles are observed to be amorphous carbon particles without any lattices; rare particles possess well-resolved lattice fringes. With such a low carbon-lattice-structure content, no obvious D or G bands were detected in the Raman spectra of the CDs (Figure S3). The XRD patterns of the CDs (Figure 1c) also displayed a broad peak centered at 258 (0.34 nm), which is also attributed to highly disordered carbon atoms. Moreover, NMR spectroscopy (H and C) was employed to distinguish sp-hybridized carbon atoms from sp-hybridized carbon atoms (Figure S4). In the H NMR spectrum, sp carbons were detected. In the C NMR spectrum, signals in the range of 30–45 ppm, which correspond to aliphatic (sp) carbon atoms, and signals from 100–185 ppm, which are indicative of sp carbon atoms, were observed. Signals in the range of 170– 185 ppm, which correspond to carboxyl/amide groups, were also present. In the FTIR analysis of CDs, the following were observed: stretching vibrations of C OH at 3430 cm 1 and C H at 2923 cm 1 and 2850 cm , asymmetric stretching vibrations of C-NH-C at 1126 cm , bending vibrations of N H at 1570 cm , and the vibrational absorption band of C=O at 1635 cm 1 (Figure S5). Moreover, the surface groups were also investigated by XPS analysis (Figure 1d). C1s analysis revealed three different types of carbon atoms: graphitic or aliphatic (C=C and C C), oxygenated, and nitrous (Table S1). In the UV/Vis spectra, the peak was focused on 344 nm in an aqueous solution of CDs. In the fluorescence spectra, CDs have optimal excitation and emission wavelengths at 360 nm and 443 nm, and show a blue color under a hand-held UV lamp (Figure 2a). Excitation-dependent PL behavior was [*] S. Zhu, Q. Meng, Prof. J. Zhang, Y. Song, Prof. K. Zhang, Prof. B. Yang State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University Changchun, 130012 (P. R. China) E-mail: byangchem@jlu.edu.cn

The photoluminescence mechanism in carbon dots (graphene quantum dots, carbon nanodots, and polymer dots): current state and future perspective

Abstract: At present, the actual mechanism of the photoluminescence (PL) of fluorescent carbon dots (CDs) is still an open debate among researchers. Because of the variety of CDs, it is highly important to summarize the PL mechanism for these kinds of carbon materials; doing so can guide the development of effective synthesis routes and novel applications. This review will focus on the PL mechanism of CDs. Three types of fluorescent CDs were involved: graphene quantum dots (GQDs), carbon nanodots (CNDs), and polymer dots (PDs). Four reasonable PL mechanisms have been confirmed: the quantum confinement effect or conjugated π-domains, which are determined by the carbon core; the surface state, which is determined by hybridization of the carbon backbone and the connected chemical groups; the molecule state, which is determined solely by the fluorescent molecules connected on the surface or interior of the CDs; and the crosslink-enhanced emission (CEE) effect. To give a thorough summary, the category and synthesis routes, as well as the chemical/physical properties for the CDs, are briefly introduced in advance.