Abstract
With the avalanche of biological sequences generated in the post-genomic age, one of the most challenging problems is how to computationally analyze their structures and functions. Machine ...learning techniques are playing key roles in this field. Typically, predictors based on machine learning techniques contain three main steps: feature extraction, predictor construction and performance evaluation. Although several Web servers and stand-alone tools have been developed to facilitate the biological sequence analysis, they only focus on individual step. In this regard, in this study a powerful Web server called BioSeq-Analysis (http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/) has been proposed to automatically complete the three main steps for constructing a predictor. The user only needs to upload the benchmark data set. BioSeq-Analysis can generate the optimized predictor based on the benchmark data set, and the performance measures can be reported as well. Furthermore, to maximize user’s convenience, its stand-alone program was also released, which can be downloaded from http://bioinformatics.hitsz.edu.cn/BioSeq-Analysis/download/, and can be directly run on Windows, Linux and UNIX. Applied to three sequence analysis tasks, experimental results showed that the predictors generated by BioSeq-Analysis even outperformed some state-of-the-art methods. It is anticipated that BioSeq-Analysis will become a useful tool for biological sequence analysis.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Although early detection and systemic therapies have improved the diagnosis and clinical cure rate of breast cancer, breast cancer remains the most frequently occurring malignant cancer in women due ...to a lack of sufficiently effective treatments. Thus, to develop potential targeted therapies and thus benefit more patients, it is helpful to understand how cancer cells work. ZIC family members have been shown to play important roles in neural development and carcinogenesis. In our study, we found that ZIC2 is downregulated in breast cancer tissues at both the mRNA and protein levels. Low expression of ZIC2 was correlated with poor outcome in breast cancer patients and serves as an independent prognostic marker. Furthermore, overexpression of ZIC2 repressed, whereas knockdown of ZIC2 promoted, cell proliferation and colony formation ability in vitro and tumor growth in vivo. Using ChIP‐seq and RNA‐seq analysis, we screened and identified STAT3 as a potential target for ZIC2. ZIC2 bound to the STAT3 promoter and repressed the promoter activities of STAT3. ZIC2 knockdown induced the expression of STAT3, increasing the level of phosphorylated STAT3. These results suggest that ZIC2 regulates the transcription of STAT3 by directly binding to the STAT3 promoter. Additionally, interfering STAT3 with siRNAs or inhibitors abrogated the oncogenic effects induced by decreased ZIC2. Taken together, our results indicate that ZIC2 serves as a useful prognostic marker in breast cancer and acts as a tumor suppressor by regulating STAT3, implying that STAT3 inhibitors might provide an alternative treatment option for breast cancer patients with ZIC2 downregulation.
What's new?
ZIC family members regulate neural development but have also been implicated in the development of various tumors. Here the authors report downregulation of ZIC2 in breast cancer cells. Low expression of ZIC2 correlated with poor outcome in breast cancer patients and served as an independent prognostic marker. The transcription factor STAT3 was identified as a potential target for ZIC2, and inhibition of STAT3 abrogated the oncogenic effects induced by decreased ZIC2 expression. STAT3 inhibitors might provide an alternative option for women with breast cancer showing ZIC2 downregulation.
The concept of aggregation‐induced emission (AIE) has opened new opportunities in many research fields. Motivated by the unique feature of AIE fluorogens (AIEgens), during the past decade, many AIE ...molecular probes and AIE nanoparticle (NP) probes have been developed for sensing, imaging and theranostic applications with excellent performance outperforming conventional fluorescent probes. This Review summarizes the latest advancement of AIE molecular probes and AIE NP probes and their emerging biomedical applications. Special focus is to reveal how the AIE probes are evolved with the development of new multifunctional AIEgens, and how new strategies have been developed to overcome the limitations of traditional AIE probes for more translational applications via fluorescence imaging, photoacoustic imaging and image‐guided photodynamic/photothermal therapy. The outlook discusses the challenges and future opportunities for AIEgens to advance the biomedical field.
Fluorogens with aggregation‐induced emission (AIEgens) have stimulated the development of AIE molecular probes and AIE nanoparticle probes for various biomedical applications. This Review reveals how the AIE probes have evolved with the development of new multifunctional AIEgens, and how new strategies have been developed to overcome the limitations of traditional AIE probes for more translational applications.
Conjugated polymers have recently been under active investigation as promising alternatives to traditional inorganic semiconductors for photocatalysis. This is due to their unique advantages of low ...cost, high chemical stability, and molecularly tunable optoelectronic properties. This critical review summarizes the recent advancements in π-conjugated polymers for visible-light-driven photocatalytic applications including water splitting, CO
2
reduction, organic transformation and degradation of organic dyes. Special emphasis is placed on how the changes in the polymer structure could influence their physicochemical properties and photocatalytic activities. This structure-activity relationship analysis should guide rational molecular design of conjugated polymers for improved photocatalytic activity.
This review summarizes the recent advancements in π-conjugated polymers for various photocatalytic applications under visible light.
The near‐infrared window between 1000 and 1700 nm, commonly termed the “second near‐infrared (NIR‐II) window,” has quickly emerged as a highly attractive optical region for biological imaging. In ...contrast to conventional imaging in the visible region between 400 and 700 nm, as well as in the first NIR (NIR‐I) window between 700 and 900 nm, NIR‐II biological imaging offers numerous merits, including higher spatial resolution, deeper penetration depth, and lower optical absorption and scattering from biological substrates with minimal tissue autofluorescence. Noninvasive imaging techniques, specifically NIR‐II fluorescence and photoacoustic (PA) imaging, have embodied the attractiveness of NIR‐II optical imaging, with several NIR‐II contrast agents demonstrating superior performance to the clinically approved NIR‐I agents. Consequently, NIR‐II biological imaging has been increasingly explored due to its tremendous potential for preclinical studies and clinical utility. Herein, the progress of optical imaging in the NIR‐II window is reported. Starting with highlighting the importance of biological imaging in the NIR‐II spectral region, the emergence and latest development of various NIR‐II fluorescence and PA imaging probes and their applications are then discussed. Perspectives on the promises and challenges facing this nascent yet exciting field are then given.
The importance of the second near‐infrared (NIR‐II) spectral region (1000–1700 nm) for biological imaging is highlighted, as well as recent development of inorganic and organic exogenous contrast agents for NIR‐II fluorescence and photoacoustic imaging.
Conspectus Theranostic nanolights refer to luminescent nanoparticles possessing both imaging and therapeutic functions. Their shape, size, surface functions, and optical properties can be precisely ...manipulated through integrated efforts of chemistry, materials, and nanotechnology for customized applications. When localized photons are used to activate both imaging and therapeutic functions such as photodynamic or photothermal therapy, these theranostic nanolights increase treatment efficacy with minimized damage to surrounding healthy tissues, which represents a promising noninvasive nanomedicine as compared to conventional theranostic approaches. As one of the most promising theranostic nanolights, organic dots with aggregation-induced emission (AIE dots) are biocompatible nanoparticles with a dense core of AIE fluorogens (AIEgens) and protective shells, whose sizes are in the range of a few to tens of nanometers. Different from conventional fluorophores that suffer from aggregation-caused quenching (ACQ) due to π–π stacking interaction in the aggregate state, AIEgens emit strongly as nanoaggregates due to the restriction of intramolecular motions. Through precise molecular engineering, AIEgens could also be designed to show efficient photosensitizing or photothermal abilities in the aggregate state. Different from ACQ dyes, AIEgens allow high loading in nanoparticles without compromised performance, which makes them the ideal cores for theranostic nanolights to offer high brightness for imaging and strong photoactivities for theranostic applications. In this Account, we summarize the recent advance of AIE dots and highlight their great potential as theranostic nanolights in biomedical applications. Starting from the design of AIEgens, the fabrication of AIE dots and their bioimaging applications are discussed. The exceptional advantages of superbrightness, high resistance to photobleaching, lack of emission intermittency, and excellent biocompatibility have made them reliable cross platform contrast agents for different imaging techniques such as confocal microscopy, multiphoton fluorescence microscopy, super-resolution nanoscopy, and light-sheet ultramicroscopy, which have been successfully applied for cell tracking, vascular disease diagnosis, and image-guided surgery. The integration of therapeutic functions with customized AIEgens has further empowered AIE dots as an excellent theranostic platform for image-guided phototherapy. Of particular interest is AIE photosensitizer dots, which simultaneously show bright fluorescence and high photosensitization, yielding superior performance to commercial photosensitizer nanoparticles in image-guided therapy. Further development in multiphoton excited photodynamic therapy has offered precise treatment with up to 5 μm resolution at 200 μm depth, while chemiexcited photodynamic therapy has completely eliminated the limitation of penetration depth to realize power-free imaging and therapy. With this Account, we hope to stimulate more collaborative research interests from different fields of chemistry, materials, biology, and medicine to promote translational research of AIE dots as the theranostic nanolights.
Polymer encapsulated organic nanoparticles have recently attracted increasing attention in the biomedical field because of their unique optical properties, easy fabrication and outstanding ...performance as imaging and therapeutic agents. Of particular importance is the polymer encapsulated nanoparticles containing conjugated polymers (CP) or fluorogens with aggregation induced emission (AIE) characteristics as the core, which have shown significant advantages in terms of tunable brightness, superb photo- and physical stability, good biocompatibility, potential biodegradability and facile surface functionalization. In this review, we summarize the latest advances in the development of polymer encapsulated CP and AIE fluorogen nanoparticles, including preparation methods, material design and matrix selection, nanoparticle fabrication and surface functionalization for fluorescence and photoacoustic imaging. We also discuss their specific applications in cell labeling, targeted
in vitro
and
in vivo
imaging, blood vessel imaging, cell tracing, inflammation monitoring and molecular imaging. We specially focus on strategies to fine-tune the nanoparticle property (
e.g.
size and fluorescence quantum yield) through precise engineering of the organic cores and careful selection of polymer matrices. The review also highlights the merits and limitations of these nanoparticles as well as strategies used to overcome the limitations. The challenges and perspectives for the future development of polymer encapsulated organic nanoparticles are also discussed.
In this Critical Review, we summarize the latest advances in the development of polymer encapsulated nanoparticles based on conjugated polymers and fluorogens with aggregation induced emission (AIE) characteristics, elucidate the importance of matrix selection and structure-property relationship of these nanoparticles and discuss their applications in fluorescence and photoacoustic imaging.
Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships. In ...this study, 785 single‐copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato, an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events. The nuclear phylogeny recovered the monophyly of Malus s.l. (including Docynia); however, the genus was supported to be biphyletic in the plastid phylogeny. An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance. Our conflict analysis demonstrated that ILS, hybridization, and allopolyploidy could explain the widespread nuclear gene tree discordance. One deep hybridization event (Malus doumeri) and one recent event (Malus coronaria) were detected in Malus s.l. Furthermore, our historical biogeographic analysis integrating living and fossil data supported a widespread East Asian‐western North American origin of Malus s.l. in the Eocene, followed by several extinction and dispersal events in the Northern Hemisphere. We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.
Phylogenomic conflict analyses in the apple genus Malus s.l. reveal widespread hybridization and allopolyploidy driving diversification, provide insights into the complex biogeographic history in the Northern Hemisphere, and inspire a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming datasets.
This note studies stability problem of solutions for stochastic impulsive systems. By employing Lyapunov-like function method and It's formula, comparison principles of existence and uniqueness and ...stability of solutions for stochastic impulsive systems are established. Based on these comparison principles, the stability properties of stochastic impulsive systems are derived by the corresponding stability properties of a deterministic impulsive system. As the application, the stability results are used to design impulsive control for the stabilization of unstable stochastic systems. Finally, one example is given to illustrate the obtained results.
The establishment of either forest or grassland on degraded cropland has been proposed as an effective method for climate change mitigation because these land use types can increase soil carbon (C) ...stocks. This paper synthesized 135 recent publications (844 observations at 181 sites) focused on the conversion from cropland to grassland, shrubland or forest in China, better known as the ‘Grain‐for‐Green’ Program to determine which factors were driving changes to soil organic carbon (SOC). The results strongly indicate a positive impact of cropland conversion on soil C stocks. The temporal pattern for soil C stock changes in the 0–100 cm soil layer showed an initial decrease in soil C during the early stage (<5 years), and then an increase to net C gains (>5 years) coincident with vegetation restoration. The rates of soil C change were higher in the surface profile (0–20 cm) than in deeper soil (20–100 cm). Cropland converted to forest (arbor) had the additional benefit of a slower but more persistent C sequestration capacity than shrubland or grassland. Tree species played a significant role in determining the rate of change in soil C stocks (conifer < broadleaf, evergreen < deciduous forests). Restoration age was the main factor, not temperature and precipitation, affecting soil C stock change after cropland conversion with higher initial soil C stock sites having a negative effect on soil C accumulation. Soil C sequestration significantly increased with restoration age over the long‐term, and therefore, the large scale of land‐use change under the ‘Grain‐for‐Green’ Program will significantly increase China's C stocks.
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