Yunnan University

Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms. Proteins, an important class of biological macromolecules, realize their functions through binding to themselves or other molecules. A detailed understanding of the protein-ligand interactions is therefore central to understanding biology at the molecular level. Moreover, knowledge of the mechanisms responsible for the protein-ligand recognition and binding will also facilitate the discovery, design, and development of drugs. In the present review, first, the physicochemical mechanisms underlying protein-ligand binding, including the binding kinetics, thermodynamic concepts and relationships, and binding driving forces, are introduced and rationalized. Next, three currently existing protein-ligand binding models--the "lock-and-key", "induced fit", and "conformational selection"--are described and their underlying thermodynamic mechanisms are discussed. Finally, the methods available for investigating protein-ligand binding affinity, including experimental and theoretical/computational approaches, are introduced, and their advantages, disadvantages, and challenges are discussed.

ADVERTISEMENT RETURN TO ISSUEPREVReviewNEXTFluorescence and Colorimetric Chemosensors for Fluoride-Ion DetectionYing Zhou†‡, Jun Feng Zhang§, and Juyoung Yoon*†View Author Information† Department of Chemistry and Nano Science, Ewha Womans University, Seoul 120-750, Korea‡ Key Laboratory of Medicinal Chemistry for Natural Resource, School of Chemical Science and Technology, Yunnan University, Kunming, 650091, P. R. China§ College of Chemistry and Chemical Engineering, Yunnan Normal University, Kunming 650500, P. R. China*Phone: 82-2-3277-2400. Fax: 82-2-3277-2384. E-mail: [email protected]Cite this: Chem. Rev. 2014, 114, 10, 5511–5571Publication Date (Web):March 25, 2014Publication History Received23 January 2013Published online25 March 2014Published inissue 28 May 2014https://pubs.acs.org/doi/10.1021/cr400352mhttps://doi.org/10.1021/cr400352mreview-articleACS PublicationsCopyright © 2014 American Chemical SocietyRequest reuse permissionsArticle Views18726Altmetric-Citations908LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Absorption,Anions,Color,Fluorescence,Sensors Get e-Alerts

High-quality data are the precondition for analyzing and using big data and for guaranteeing the value of the data. Currently, comprehensive analysis and research of quality standards and quality assessment methods for big data are lacking. First, this paper summarizes reviews of data quality research. Second, this paper analyzes the data characteristics of the big data environment, presents quality challenges faced by big data, and formulates a hierarchical data quality framework from the perspective of data users. This framework consists of big data quality dimensions, quality characteristics, and quality indexes. Finally, on the basis of this framework, this paper constructs a dynamic assessment process for data quality. This process has good expansibility and adaptability and can meet the needs of big data quality assessment. The research results enrich the theoretical scope of big data and lay a solid foundation for the future by establishing an assessment model and studying evaluation algorithms.

In general, the goal of existing infrared and visible image fusion (IVIF) methods is to make the fused image contain both the high-contrast regions of the infrared image and the texture details of the visible image. However, this definition would lead the fusion image losing information from the visible image in high-contrast areas. For this problem, this paper proposed a decoupling network-based IVIF method (DNFusion), which utilizes the decoupled maps to design additional constraints on the network to force the network to retain the saliency information of the source image effectively. The current definition of image fusion is satisfied while effectively maintaining the saliency objective of the source images. Specifically, the feature interaction module inside effectively facilitates the information exchange within the encoder and improves the utilization of complementary information. Also, a hybrid loss function constructed with weight fidelity loss, gradient loss, and decoupling loss which ensures the fusion image to be generated to effectively preserves the source image’s texture details and luminance information. The qualitative and quantitative comparison of extensive experiments demonstrates that our model can generate a fused image containing saliency objects and clear details of the source images, and the method we proposed has a better performance than other state-of-the-art methods.

Abstract By trapping sediment in reservoirs, dams interrupt the continuity of sediment transport through rivers, resulting in loss of reservoir storage and reduced usable life, and depriving downstream reaches of sediments essential for channel form and aquatic habitats. With the acceleration of new dam construction globally, these impacts are increasingly widespread. There are proven techniques to pass sediment through or around reservoirs, to preserve reservoir capacity and to minimize downstream impacts, but they are not applied in many situations where they would be effective. This paper summarizes collective experience from five continents in managing reservoir sediments and mitigating downstream sediment starvation. Where geometry is favorable it is often possible to bypass sediment around the reservoir, which avoids reservoir sedimentation and supplies sediment to downstream reaches with rates and timing similar to pre‐dam conditions. Sluicing (or drawdown routing) permits sediment to be transported through the reservoir rapidly to avoid sedimentation during high flows; it requires relatively large capacity outlets. Drawdown flushing involves scouring and re‐suspending sediment deposited in the reservoir and transporting it downstream through low‐level gates in the dam; it works best in narrow reservoirs with steep longitudinal gradients and with flow velocities maintained above the threshold to transport sediment. Turbidity currents can often be vented through the dam, with the advantage that the reservoir need not be drawn down to pass sediment. In planning dams, we recommend that these sediment management approaches be utilized where possible to sustain reservoir capacity and minimize environmental impacts of dams.

A taxonomic study was performed on strain YIM 31775(T), which was isolated from a soil sample collected from Yunnan Province, China. The isolate was chemo-organotrophic, aerobic and Gram-negative. Cells were short rods and motile, with one or more polar flagella. Growth temperature and pH ranged from 4 to 55 degrees C and 6.5 to 12.0, respectively; the optimum growth temperature and pH were 28-37 degrees C and 7.0-9.0, respectively. Q-8 was the predominant respiratory lipoquinone. The major fatty acids were C(16 : 1)omega7c (42.4 %) and C(16 : 0) (28.1 %). The DNA G + C content was 62.4 +/ -0.3 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain YIM 31775(T) should be placed within the family 'Oxalobacteraceae', in which it formed a distinct lineage. Based on the high 16S rRNA gene sequence divergence and phenotypic characteristics, it is proposed that strain YIM 31775(T) should be classified as representing a novel member of the family 'Oxalobacteraceae', for which the name Naxibacter alkalitolerans gen. nov., sp. nov. is proposed. The type strain is YIM 31775(T) (= CCTCC AA 204003(T) = KCTC 12194(T)).

A Gram-positive, motile, short-rod-shaped strain, designated YIM 004(T), was isolated from a forest-soil sample collected from Lijiang, Yunnan Province, China, and was investigated using a polyphasic taxonomic approach. The isolate contained chemotaxonomic markers that corresponded to those of its phylogenetic neighbour, Georgenia muralis, i.e. it possessed peptidoglycan type A4 alpha with lysine as the diagnostic cell-wall diamino acid, the predominant menaquinone was MK-8(H(4)) and the major fatty acid was ai-C(15 : 0). The G+C content of the genomic DNA was 72.9 mol%. Strain YIM 004(T) exhibited a 16S rRNA gene sequence similarity of 97.3 % and a DNA-DNA relatedness value of 18 % with respect to G. muralis DSM 14418(T). On the basis of the phenotypic and genotypic differences between the isolate and G. muralis, strain YIM 004(T) represents a novel species of the genus Georgenia, for which the name Georgenia ruanii sp. nov. is proposed. The type strain is YIM 004(T) (=CCTCC AB 204065(T)=DSM 17458(T)=KCTC 19029(T)). In addition, an emended description of the genus Georgenia is presented.

In recent years, the concept of combining transition metal catalysis and organocatalysis has emerged as a promising strategy for developing new and valuable reactions, and has attracted considerable attention as it could potentially enable unprecedented transformations not currently possible by use of the transition metal complex or the organocatalyst alone. In this critical review, this strategy is illustrated with several recent outstanding examples, with the aim of shedding light on the synthetic utilities and potentials of this concept as a novel tool in organic synthesis (118 references).

Due to the biological importance of amino acids, the development of optical probes for these molecules has been an active research area in recent years. This tutorial review focuses on recent contributions since the year 2000 concerning the fluorescent or colorimetric sensors for amino acids, and is organized according to their structural classification and reaction types. For reaction based chemosensors, the works are classified according to the mechanisms between sensors and amino acids, including imine formation, Michael addition, thiazinane or thiazolidine formation, cleavage of a sulfonate ester, cleavage of disulfide, metal complexes-displace coordination and others.

Forest restoration is being scaled up globally to deliver critical ecosystem services and biodiversity benefits; however, there is a lack of rigorous comparison of cobenefit delivery across different restoration approaches. Through global synthesis, we used 25,950 matched data pairs from 264 studies in 53 countries to assess how delivery of climate, soil, water, and wood production services, in addition to biodiversity, compares across a range of tree plantations and native forests. Benefits of aboveground carbon storage, water provisioning, and especially soil erosion control and biodiversity are better delivered by native forests, with compositionally simpler, younger plantations in drier regions performing particularly poorly. However, plantations exhibit an advantage in wood production. These results underscore important trade-offs among environmental and production goals that policy-makers must navigate in meeting forest restoration commitments.

Abstract Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action 1,2 . Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment 3,4 . Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

The combination of transition metal catalysis and organocatalysis as a new and exciting research area has attracted increasing attention as it can enable the development of unprecedented transformations that is not possible by use of either of the catalytic systems alone, and can improve the reactivity, efficiency and stereocontrol of existing chemical transformations. In this review, we summarize recent remarkable progress in the field of combined transition metal catalysis and organocatalysis, further highlighting the potential of this new and exciting research area and the many challenges that still remain for the future.

Melatonin is an ancient molecule that can be traced back to the origin of life. Melatonin’s initial function was likely that as a free radical scavenger. Melatonin presumably evolved in bacteria; it has been measured in both α-proteobacteria and in photosynthetic cyanobacteria. In early evolution, bacteria were phagocytosed by primitive eukaryotes for their nutrient value. According to the endosymbiontic theory, the ingested bacteria eventually developed a symbiotic association with their host eukaryotes. The ingested α-proteobacteria evolved into mitochondria while cyanobacteria became chloroplasts and both organelles retained their ability to produce melatonin. Since these organelles have persisted to the present day, all species that ever existed or currently exist may have or may continue to synthesize melatonin in their mitochondria (animals and plants) and chloroplasts (plants) where it functions as an antioxidant. Melatonin’s other functions, including its multiple receptors, developed later in evolution. In present day animals, via receptor-mediated means, melatonin functions in the regulation of sleep, modulation of circadian rhythms, enhancement of immunity, as a multifunctional oncostatic agent, etc., while retaining its ability to reduce oxidative stress by processes that are, in part, receptor-independent. In plants, melatonin continues to function in reducing oxidative stress as well as in promoting seed germination and growth, improving stress resistance, stimulating the immune system and modulating circadian rhythms; a single melatonin receptor has been identified in land plants where it controls stomatal closure on leaves. The melatonin synthetic pathway varies somewhat between plants and animals. The amino acid, tryptophan, is the necessary precursor of melatonin in all taxa. In animals, tryptophan is initially hydroxylated to 5-hydroxytryptophan which is then decarboxylated with the formation of serotonin. Serotonin is either acetylated to N-acetylserotonin or it is methylated to form 5-methoxytryptamine; these products are either methylated or acetylated, respectively, to produce melatonin. In plants, tryptophan is first decarboxylated to tryptamine which is then hydroxylated to form serotonin.

The three tandemly arranged CBF genes, CBF1, CBF2, and CBF3, are involved in cold acclimation. Due to the lack of stable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants deficient in all three CBF genes, it is still unclear whether the CBF genes are essential for freezing tolerance and whether they may have other functions besides cold acclimation. In this study, we used the CRISPR/Cas9 system to generate cbf single, double, and triple mutants. Compared to the wild type, the cbf triple mutants are extremely sensitive to freezing after cold acclimation, demonstrating that the three CBF genes are essential for cold acclimation. Our results show that the three CBF genes also contribute to basal freezing tolerance. Unexpectedly, we found that the cbf triple mutants are defective in seedling development and salt stress tolerance. Transcript profiling revealed that the CBF genes regulate 414 cold-responsive (COR) genes, of which 346 are CBF-activated genes and 68 are CBF-repressed genes. The analysis suggested that CBF proteins are extensively involved in the regulation of carbohydrate and lipid metabolism, cell wall modification, and gene transcription. Interestingly, like the triple mutants, cbf2 cbf3 double mutants are more sensitive to freezing after cold acclimation compared to the wild type, but cbf1 cbf3 double mutants are more resistant, suggesting that CBF2 is more important than CBF1 and CBF3 in cold acclimation-dependent freezing tolerance. Our results not only demonstrate that the three CBF genes together are required for cold acclimation and freezing tolerance, but also reveal that they are important for salt tolerance and seedling development.

As the rapid growth of social media technologies continues, Cyber-Physical-Social System (CPSS) has been a hot topic in many industrial applications. The use of “microblogging” services, such as Twitter, has rapidly become an influential way to share information. While recent studies have revealed that understanding and modelling microblog user behaviour with massive users’ data in social media are keen to success of many practical applications in CPSS, a key challenge in literatures is that diversity of geography and cultures in social media technologies strongly affect user behaviour and activity. The motivation of this article is to understand differences and similarities between microblogging users from different countries using social media technologies, and to attempt to design a Country-Level Micro-Blog User (CLMB) behaviour and activity model for supporting CPSS applications. We proposed a CLMB model for analysing microblogging user behaviour and their activity across different countries in the CPSS applications. The model has considered three important characteristics of user behaviour in microblogging data, including content of microblogging messages, user emotion index, and user relationship network. We evaluated CLBM model under the collected microblog dataset from 16 countries with the largest number of representative and active users in the world. Experimental results show that (1) for some countries with small population and strong cohesiveness, users pay more attention to social functionalities of microblogging service; (2) for some countries containing mostly large loose social groups, users use microblogging services as a news dissemination platform; (3) users in countries whose social network structure exhibits reciprocity rather than hierarchy will use more linguistic elements to express happiness in microblogging services.

Closer matching of the energy levels of transparent electrodes and active materials in organic light-emitting diodes improves efficiency.

The higher ranks of the class Actinobacteria were proposed and described in 1997. At each rank, the taxa were delineated from each other solely on the basis of 16S rRNA gene sequence phylogenetic clustering and taxon-specific 16S rRNA signature nucleotides. In the past 10 years, many novel members have been assigned to this class while, at the same time, some members have been reclassified. The new 16S rRNA gene sequence information and the changes in phylogenetic positions of some taxa influence decisions about which 16S rRNA nucleotides to define as taxon-specific. As a consequence, the phylogenetic relationships of Actinobacteria at higher levels may need to be reconstructed. Here, we present new 16S rRNA signature nucleotide patterns of taxa above the family level and indicate the affiliation of genera to families. These sets replace the signatures published in 1997. In addition, Actinopolysporineae subord. nov. and Actinopolysporaceae fam. nov. are proposed to accommodate the genus Actinopolyspora, Kineosporiineae subord. nov. and Kineosporiaceae fam. nov. are proposed to accommodate the genera Kineococcus, Kineosporia and Quadrisphaera, Beutenbergiaceae fam. nov. is proposed to accommodate the genera Beutenbergia, Georgenia and Salana and Cryptosporangiaceae fam. nov. is proposed to accommodate the genus Cryptosporangium. The families Nocardiaceae and Gordoniaceae are proposed to be combined in an emended family Nocardiaceae. Emended descriptions are also proposed for most of the other higher taxa.

Transition metal-catalyzed cross-coupling reactions have been established as one of the most powerful tools for the construction of C-C and C-X bonds. In this context, the development of novel metal-catalyzed cross-coupling processes that do not require stoichiometric organometallic reagents is particularly attractive. Recently, N-tosylhydrazones have emerged as a new type of versatile coupling partners for transition metal-catalyzed cross-coupling reactions as well as metal-free cross-coupling reactions, and have attracted increasing attention. This tutorial review summarizes recent important developments in this area with N-tosylhydrazones as versatile coupling partners.

Cyclin-dependent kinases (CDKs) are serine/threonine kinases whose catalytic activities are regulated by interactions with cyclins and CDK inhibitors (CKIs). CDKs are key regulatory enzymes involved in cell proliferation through regulating cell-cycle checkpoints and transcriptional events in response to extracellular and intracellular signals. Not surprisingly, the dysregulation of CDKs is a hallmark of cancers, and inhibition of specific members is considered an attractive target in cancer therapy. In breast cancer (BC), dual CDK4/6 inhibitors, palbociclib, ribociclib, and abemaciclib, combined with other agents, were approved by the Food and Drug Administration (FDA) recently for the treatment of hormone receptor positive (HR+) advanced or metastatic breast cancer (A/MBC), as well as other sub-types of breast cancer. Furthermore, ongoing studies identified more selective CDK inhibitors as promising clinical targets. In this review, we focus on the roles of CDKs in driving cell-cycle progression, cell-cycle checkpoints, and transcriptional regulation, a highlight of dysregulated CDK activation in BC. We also discuss the most relevant CDK inhibitors currently in clinical BC trials, with special emphasis on CDK4/6 inhibitors used for the treatment of estrogen receptor-positive (ER+)/human epidermal growth factor 2-negative (HER2-) M/ABC patients, as well as more emerging precise therapeutic strategies, such as combination therapies and microRNA (miRNA) therapy.

microRNAs (miRNAs) are small endogenous non-coding RNAs that function as the universal specificity factors in post-transcriptional gene silencing. Discovering miRNAs, identifying their targets and further inferring miRNA functions have been a critical strategy for understanding normal biological processes of miRNAs and their roles in the development of disease. In this review, we focus on computational methods of inferring miRNA functions, including miRNA functional annotation and inferring miRNA regulatory modules, by integrating heterogeneous data sources. We also briefly introduce the research in miRNA discovery and miRNA-target identification with an emphasis on the challenges to computational biology.