CancerProteome: a resource to functionally decipher the proteome landscape in cancer.

Advancements in mass spectrometry (MS)-based proteomics have greatly facilitated the large-scale quantification of proteins and microproteins, thereby revealing altered signalling pathways across many different cancer types. However, specialized and comprehensive resources are lacking for cancer proteomics. Here, we describe CancerProteome (http://bio-bigdata.hrbmu.edu.cn/CancerProteome), which functionally deciphers and visualizes the proteome landscape in cancer. We manually curated and re-analyzed publicly available MS-based quantification and post-translational modification (PTM) proteomes, including 7406 samples from 21 different cancer types, and also examined protein abundances and PTM levels in 31 120 proteins and 4111 microproteins. Six major analytical modules were developed with a view to describe protein contributions to carcinogenesis using proteome analysis, including conventional analyses of quantitative and the PTM proteome, functional enrichment, protein-protein associations by integrating known interactions with co-expression signatures, drug sensitivity and clinical relevance analyses. Moreover, protein abundances, which correlated with corresponding transcript or PTM levels, were evaluated. CancerProteome is convenient as it allows users to access specific proteins/microproteins of interest using quick searches or query options to generate multiple visualization results. In summary, CancerProteome is an important resource, which functionally deciphers the cancer proteome landscape and provides a novel insight for the identification of tumor protein markers in cancer.

IEAtlas: an atlas of HLA-presented immune epitopes derived from non-coding regions.

Cancer-related epitopes can engage the immune system against tumor cells, thus exploring epitopes derived from non-coding regions is emerging as a fascinating field in cancer immunotherapies. Here, we described a database, IEAtlas (http://bio-bigdata.hrbmu.edu.cn/IEAtlas), which aims to provide and visualize the comprehensive atlas of human leukocyte antigen (HLA)-presented immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed publicly available mass spectrometry-based HLA immunopeptidome datasets against our integrated benchmarked non-canonical open reading frame information. The current IEAtlas identified 245 870 non-canonical epitopes binding to HLA-I/II allotypes across 15 cancer types and 30 non-cancerous tissues, greatly expanding the cancer immunopeptidome. IEAtlas further evaluates the immunogenicity via several commonly used immunogenic features, including HLA binding affinity, stability and T-cell receptor recognition. In addition, IEAtlas provides the biochemical properties of epitopes as well as the clinical relevance of corresponding genes across major cancer types and normal tissues. Several flexible tools were also developed to aid retrieval and to analyze the epitopes derived from non-coding regions. Overall, IEAtlas will serve as a valuable resource for investigating the immunogenic capacity of non-canonical epitopes and the potential as therapeutic cancer vaccines.

EEF1D stabilized by SRSF9 promotes colorectal cancer via enhancing the proliferation and metastasis.

Colorectal cancer (CRC) is the third most common cancer and causes high mortality worldwide. Although CRC has been studied widely, the molecular mechanism is not completely known. Eukaryotic translation elongation factor 1 delta (EEF1D) participates in the progression of various tumors, however, the effect of EEF1D on CRC remains unclear. Here, we aimed to identify the potential mechanism of EEF1D in CRC. The expression levels of EEF1D were assessed in CRC samples. Functional analysis of EEF1D in CRC was detected in vitro and in vivo. The regulatory mechanism of EEF1D was identified with RNA immunoprecipitation, RNA pull-down assay, and proteomics analysis. Our findings confirmed that EEF1D was upregulated in human CRC tissues. Functionally, EEF1D overexpression accelerated cell proliferation and metastasis, whereas EEF1D knockdown inhibited cell proliferation and metastasis both in vitro and in vivo CRC models. Furthermore, we showed that EEF1D was upregulated by SRSF9 via binding to 3'UTR of EEF1D mRNA. EEF1D knockdown reversed the malignant phenotype induced by SRSF9 overexpression. These findings demonstrated that EEF1D promotes CRC progression, and EEF1D may be a molecular target against CRC.

Source-oriented risk assessment of heavy metal(loid)s in agricultural soils around a multimetal smelting area near the Yellow River, China.

Heavy metal(loid) (HM) contamination in agricultural soils, particularly in areas severely impacted by smelting industries, has attracted worldwide attention. In this study, agricultural soils were collected in a flourishing multimetal smelting area near the Yellow River in central China. By an integrated approach encompassing the positive matrix factorization model, ordinary kriging interpolation and hierarchical clustering analysis (PMF-OK-HC), a total of four major sources and their mass contributions were identified, namely, soil parent material (56.6%), industrial waste and Mo smelting (24.0%), metal smelting and traffic emissions (12.8%), and coal combustion (6.7%). On this basis, the health risk of HMs was evaluated by Monte Carlo simulations and showed that a higher risk, with a higher proportion of exceeding-thresholds risk, was observed for children than for adults in terms of both noncarcinogenic and carcinogenic risks. Exposure pathways of oral ingestion in children could result in a higher attributed risk than other pathways. Furthermore, source-oriented risk assessment (SORA) revealed that the sources of coal combustion, industrial waste and Mo smelting had the highest contributions to noncarcinogenic and carcinogenic risks. Overall, for effective environmental management in agricultural soil, the framework of SORA was verified as an effective tool in the identification of the priority control of HMs and their sources.

Electrochemical filtration for drinking water purification: A review on membrane materials, mechanisms and roles.

Electrochemical filtration can not only enrich low concentrations of pollutants but also produce reactive oxygen species to interact with toxic pollutants with the assistance of a power supply, making it an effective strategy for drinking water purification. In addition, the application of electrochemical filtration facilitates the reduction of pretreatment procedures and the use of chemicals, which has outstanding potential for maximizing process simplicity and reducing operating costs, enabling the production of safe drinking water in smaller installations. In recent years, the research on electrochemical filtration has gradually increased, but there has been a lack of attention on its application in the removal of low concentrations of pollutants from low conductivity water. In this review, membrane substrates and electrocatalysts used to improve the performance of electrochemical membranes are briefly summarized. Meanwhile, the application prospects of emerging single-atom catalysts in electrochemical filtration are also presented. Thereafter, several electrochemical advanced oxidation processes coupled with membrane filtration are described, and the related working mechanisms and their advantages and shortcomings used in drinking water purification are illustrated. Finally, the roles of electrochemical filtration in drinking water purification are presented, and the main problems and future perspectives of electrochemical filtration in the removal of low concentration pollutants are discussed.

Method To Diversify Cyanine Chromophore Functionality Enables Improved Biomolecule Tracking and Intracellular Imaging.

Heptamethine indocyanines are invaluable probes for near-infrared (NIR) imaging. Despite broad use, there are only a few synthetic methods to assemble these molecules, and each has significant limitations. Here, we report the use of pyridinium benzoxazole (PyBox) salts as heptamethine indocyanine precursors. This method is high yielding, simple to implement, and provides access to previously unknown chromophore functionality. We applied this method to create molecules to address two outstanding objectives in NIR fluorescence imaging. First, we used an iterative approach to develop molecules for protein-targeted tumor imaging. When compared to common NIR fluorophores, the optimized probe increases the tumor specificity of monoclonal antibody (mAb) and nanobody conjugates. Second, we developed cyclizing heptamethine indocyanines with the goal of improving cellular uptake and fluorogenic properties. By modifying both the electrophilic and nucleophilic components, we demonstrate that the solvent sensitivity of the ring-open/ring-closed equilibrium can be modified over a wide range. We then show that a chloroalkane derivative of a compound with tuned cyclization properties undergoes particularly efficient no-wash live cell imaging using organelle-targeted HaloTag self-labeling proteins. Overall, the chemistry reported here broadens the scope of accessible chromophore functionality, and, in turn, enables the discovery of NIR probes with promising properties for advanced imaging applications.

Palladium responsive liposomes for triggered release of aqueous contents.

Palladium (Pd) is a promising metal catalyst for novel bioorthogonal chemistry and prodrug activation. This report describes the first example of palladium responsive liposomes. The key molecule is a new caged phospholipid called Alloc-PE that forms stable liposomes (large unilamellar vesicles, ∼220 nm diameter). Liposome treatment with PdCl2 removes the chemical cage, liberates membrane destabilizing dioleoylphosphoethanolamine (DOPE), and triggers liposome leakage of encapsulated aqueous contents. The results indicate a path towards liposomal drug delivery technologies that exploit transition metal triggered leakage.

Nonlinear Stiffness and Nonlinear Damping in Atomically Thin MoS2 Nanomechanical Resonators.

We report on experimental measurements and quantitative analyses of nonlinear dynamic characteristics in ultimately thin nanomechanical resonators built upon single-layer, bilayer, and trilayer (1L, 2L, and 3L) molybdenum disulfide (MoS2) vibrating drumhead membranes. This synergistic study with calibrated measurements and analytical modeling on observed nonlinear responses has led to the determination of nonlinear damping and stiffness coefficients at cubic and quintic orders for these two-dimensional (2D) resonators operating in the very high frequency (VHF) band (up to ∼90 MHz). We find that the quintic force can be ∼20% of the Duffing force at larger amplitudes, and thus, it generally cannot be ignored in a nonlinear dynamics analysis. This study provides the first quantification of nonlinear damping and frequency detuning characteristics in 2D semiconductor nanomechanical resonators and elucidates their origins and dependency on engineerable parameters, setting a foundation for future exploration and utilization of the rich nonlinear dynamics in 2D nanomechanical systems.

Mitigating greenhouse gas emissions by replacing inorganic fertilizer with organic fertilizer in wheat-maize rotation systems in China.

Combining organic and inorganic fertilizer applications can help reduce inorganic fertilizer use and increase soil fertility. However, the most suitable proportion of organic fertilizer is unknown, and the effect of combining organic and inorganic fertilizers on greenhouse gas (GHG) emissions is inconclusive. This study aimed to identify the optimum ratio of inorganic fertilizer to organic fertilizer in a winter wheat-summer maize cropping system in northern China to achieve high grain yields and low GHG intensities. The study compared six fertilizer treatments: no fertilization (CK), conventional inorganic fertilization (NP), and constant total nitrogen input with 25% (25%OF), 50% (50%OF), 75% (75%OF), or 100% (100%OF) organic fertilizer. The results showed that the 75%OF treatment increased the winter wheat and summer maize yields the most, by 7.2-25.1% and 15.3-16.7%, respectively, compared to NP. The 75%OF and 100%OF treatments had the lowest nitrous oxide (N2O) emissions, 187.3% and 200.2% lower than the NP treatment, while all fertilizer treatments decreased methane (CH4) absorption (by 33.1-82.0%) compared to CK. Carbon dioxide flux increased in the summer maize growing season (by 7.7-30.5%) compared to CK but did not significantly differ between fertilizer treatments. The average global warming potential (GWP) rankings across two wheat-maize rotations were NP > 50%OF > 25%OF > 100%OF > 75%OF > CK, and greenhouse gas intensity (GHGI) rankings were NP > 25%OF > 50%OF > 100%OF > 75%OF > CK. We recommend using 75% organic fertilizer/25% inorganic fertilizer to reduce GHG emissions and ensure high crop yields in wheat-maize rotation systems in northern China.

Doubly Strapped Zwitterionic NIR-I and NIR-II Heptamethine Cyanine Dyes for Bioconjugation and Fluorescence Imaging.

Heptamethine cyanine dyes enable deep tissue fluorescence imaging in the near infrared (NIR) window. Small molecule conjugates of the benchmark dye ZW800-1 have been tested in humans. However, long-term imaging protocols using ZW800-1 conjugates are limited by their instability, primarily because the chemically labile C4'-O-aryl linker is susceptible to cleavage by biological nucleophiles. Here, we report a modular synthetic method that produces novel doubly strapped zwitterionic heptamethine cyanine dyes, including a structural analogue of ZW800-1, with greatly enhanced dye stability. NIR-I and NIR-II versions of these doubly strapped dyes can be conjugated to proteins, including monoclonal antibodies, without causing undesired fluorophore degradation or dye stacking on the protein surface. The fluorescent antibody conjugates show excellent tumor-targeting specificity in a xenograft mouse tumor model. The enhanced stability provided by doubly strapped molecular design will enable new classes of in vivo NIR fluorescence imaging experiments with possible translation to humans.

Circular Nonuniform Electric Field Gel Electrophoresis for the Separation and Concentration of Nanoparticles.

A circular nonuniform electric field strategy coupled with gel electrophoresis was proposed to control the precise separation and efficient concentration of nano- and microparticles. The circular nonuniform electric field has the feature of exponential increase in the electric field intensity along the radius, working with three functional zones of migration, acceleration, and concentration. The distribution form of electric field lines is regulated in functional zones to control the migration behaviors of particles for separation and concentration by altering the relative position of the ring electrode (outside) and rodlike electrode (inner). The circular nonuniform electric field promotes the target-type and high-precision separation of nanoparticles based on the difference in charge-to-size ratio. The concentration multiple of nanoparticles is also controlled randomly with the alternation of radius, taking advantage of vertical extrusion and concentric converging of the migration path. This work provides a brand new insight into the simultaneous separation and concentration of particles and is promising for developing a versatile tool for the separation and preparation of various samples instead of conventional methods.

High-Resolution Micro-object Separation by Rotating Magnetic Chromatography.

The development of new technologies for the separation, selection, and isolation of microparticles such as rare target cells, circulating tumor cells, cancer stem cells, and immune cells has become increasingly important in the last few years. Microparticle separation technologies are usually applied to the analysis of disease-associated cells, but these procedures often face a cell separation problem that is often insufficient for single specific cell analyses. To overcome these limitations, a highly accurate size-based microparticle separation technique, herein called "rotating magnetic chromatography", is proposed in this work. Magnetic nanoparticles, placed in a microfluidic separation channel, are forced to move in well-defined trajectories by an external magnetic field, colliding with microparticles that are in this way separated on the basis of their dimensions with high accuracy and reproducibility. The method was optimized by using fluorescein isothiocyanate-modified polystyrene particles (chosen as a reference standard) and then applied to the analysis of cancer cells like Hep-3B and SK-Hep-1, allowing their fast and high-resolution chromatographic separation as a function of their dimensions. Due to its unmatched sub-micrometer cell separation capabilities, RMC can be considered a break-through technique that can unlock new perspectives in different scientific fields, that is, in medical oncology.

Supramolecular Mitigation of the Cyanine Limit Problem.

Currently, there is a substantial research effort to develop near-infrared fluorescent polymethine cyanine dyes for biological imaging and sensing. In water, cyanine dyes with extended conjugation are known to cross over the "cyanine limit" and undergo a symmetry breaking Peierls transition that favors an unsymmetric distribution of π-electron density and produces a broad absorption profile and low fluorescence brightness. This study shows how supramolecular encapsulation of a newly designed series of cationic, cyanine dyes by cucurbit[7]uril (CB7) can be used to alter the π-electron distribution within the cyanine chromophore. For two sets of dyes, supramolecular location of the surrounding CB7 over the center of the dye favors a nonpolar ground state, with a symmetric π-electron distribution that produces a sharpened absorption band with enhanced fluorescence brightness. The opposite supramolecular effect (i.e., broadened absorption and partially quenched fluorescence) is observed with a third set of dyes because the surrounding CB7 is located at one end of the encapsulated cyanine chromophore. From the perspective of enhanced near-infrared bioimaging and sensing in water, the results show how that the principles of host/guest chemistry can be employed to mitigate the "cyanine limit" problem.

Sterically Shielded Hydrophilic Analogs of Indocyanine Green.

A modular synthetic process enables two or four shielding arms to be appended strategically over the fluorochromes of near-infrared cyanine heptamethine dyes to create hydrophilic analogs of clinically approved indocyanine green. A key synthetic step is the facile substitution of a heptamethine 4'-Cl atom by a phenol bearing two triethylene glycol chains. The lead compound is a heptamethine dye with four shielding arms, and a series of comparative spectroscopy studies showed that the shielding arms (a) increased dye photostability and chemical stability and (b) inhibited dye self-aggregation and association with albumin protein. In mice, the dye cleared from the blood primarily through the renal pathway rather than the biliary pathway for ICG. This change in biodistribution reflects the much smaller hydrodynamic diameter of the shielded hydrophilic ICG analog compared to the 67 kDa size of the ICG/albumin complex. An attractive feature of versatile synthetic chemistry is the capability to systematically alter the dye's hydrodynamic diameter. The sterically shielded hydrophilic ICG dye platform is well-suited for immediate incorporation into dynamic contrast-enhanced (DCE) spectroscopy or imaging protocols using the same cameras and detectors that have been optimized for ICG.

On the use of a 2D-carbon microfiber fractionation system to improve flow-injection QTOF-HRMS analysis in complex matrices: the case of Abelmoschus manihot flower extracts.

A two-dimensional microscale carbon fiber/active carbon fiber system combined with a quadrupole time of flight high-resolution mass spectrometry (2DµCFs-QTOF-HRMS) system is proposed for the rapid putative identification of polar, medium-polar and weakly polar constituents in complex matrices while strongly mitigating ionic suppression effects. The capabilities of 2DµCFs-QTOF-HRMS have been proven by analysing the composition of Abelmoschus manihot flower extracts, allowing, in a single run, the detection of 41 known substances and the presence of 6 compounds never revealed before in these samples. 2DµCFs-QTOF-HRMS has been compared with traditional HPLC-MS, showing higher versatility and a significant reduction of both analysis time (70 min to 5 min) and solvent consumption (35 mL to 1.5 mL). A comparison with the results obtained by direct flow-injection MS analyses demonstrated that 2DµCFs-QTOF-HRMS leads to a more comprehensive analysis and to improved detection sensitivity. The proposed method can be considered suitable for the rapid and comprehensive analysis of food, environmental and pharmaceutical complex samples. 2DµCFs-QTOF-HRMS can thus be considered a rapid, versatile, reliable, high-throughput and economical technique that allows for the collection of information on polar, semipolar, and weakly polar components in complex matrices.

Conformational Effects on the Threading Kinetics of Dumbbell-Shaped Guests into the Cavity of Oxatub[4]arene.

Unprecedented threading kinetics were revealed between viologen-based guests and conformationally adaptive oxatub[4]arene. Three representative conformations of oxatub[4]arene are involved in the kinetic and thermodynamic products which follow the opposite orders in their rankings. Consequently, error correction was involved and a complex kinetic process was observed in a simple two-component system. Moreover, it was found that some viologen-based guests have much faster threading kinetics than those of DABCO-based with the same stoppers. This was enabled by an unprecedented threading mechanism in which a tilted conformation of the guests is adopted by involving one linear alkyl group on the 3,5-dialkoxybenzyl stoppers, the viologen core, and the methylene spacers in the transition states. This new mechanism even allows the viologen-based guests with the 3,5-dicetyloxybenzyl stoppers to form a pseudorotaxane with oxatub[4]arene.

High-Performance Near-Infrared Fluorescent Secondary Antibodies for Immunofluorescence.

A broad array of imaging and diagnostic technologies employs fluorophore-labeled antibodies for biomarker visualization, an experimental technique known as immunofluorescence. Significant performance advantages, such as higher signal-to-noise ratio, are gained if the appended fluorophore emits near-infrared (NIR) light with a wavelength >700 nm. However, the currently available NIR fluorophore antibody conjugates are known to exhibit significant limitations, including low chemical stability and photostability, weakened target specificity, and low fluorescence brightness. These fluorophore limitations are resolved by employing a NIR heptamethine cyanine dye named s775z whose chemical structure is very stable, charge-balanced, and sterically shielded. Using indirect immunofluorescence for imaging and visualization, a secondary IgG antibody labeled with s775z outperformed IgG analogues labeled with the commercially available NIR fluorophores, IRDye 800CW and DyLight800. Comparison experiments include three common techniques: immunocytochemistry, immunohistochemistry, and western blotting. Specifically, the secondary IgG labeled with s775z was 3-8 times brighter, 3-6 times more photostable, and still retained excellent target specificity when the degree of antibody labeling was high. The results demonstrate that antibodies labeled with s775z can emit total photon counts that are 1-2 orders of magnitude higher than those currently possible, and thus enable unsurpassed performance for NIR fluorescence imaging and diagnostics. They are especially well suited for analytical applications that require sensitive NIR fluorescence detection or use modern photon-intense methods that require high photostability.

Nanoconfined Liquid Phase Nanoextraction Based on Carbon Nanofibers.

An innovative and versatile microextraction technique based on nanoconfined solvent on carbon nanofibers has been conceived, realized, optimized, and presented here. The extraction capabilities of this technique toward polar, medium polar, and/or nonpolar substances can be easily modulated based on the nanoconfined solvent used. The so-called nanoconfined liquid phase nanoextraction showed excellent characteristics in terms of extraction recoveries, extraction time (≤1 min), reliability, and versatility. A needle-tip device has been realized on the base of this extraction process to allow direct extraction procedures and minimally invasive testing: this device guarantees a safe insertion in aqueous or soft samples, and it allows a fast and minimally invasive analyte extraction. Due to its versatility, chemical stability, and mechanical flexibility, nanoconfined liquid phase nanoextraction can be considered a powerful candidate for high-throughput analyses of biological samples.

Light-Driven Polarity Switching of the Chromatographic Stationary Phase with Photoreversibility.

Regrettably, conventional chromatographic columns have immutable polarity, resulting in requirements of at least two columns with polarity difference and sophisticated mechanical switching valves, which hinders the development of "micro-smart" multidimensional tandem chromatography. In this work, light-driven polarity switching was realized in a single capillary column based on the reversible trans-cis isomerization of 4-[3-(triethoxysilyl)propoxy]azobenzene as the stationary phase under light irradiation, with the change in dipole moment. As a result, the stationary phase offers precise and dynamic control of polarity based on the cis-trans azobenzene ratio, which depends on irradiation wavelength and time. Thus, the continuous adjustment of polarity enables diversified chromatographic separation modes, for example, step-polarity gradient and polarity-conversion separation modes, taking advantage of the superior freedom of polarity switching in time and spatial dimensions. The photosensitive column also shows good reproducibility of polarity photoreversibility and high separation efficiency. The present study might offer brand new insight into developing miniaturization and intellectualization of multidimensional chromatography via designing smart responsive switching valves or stationary phases, besides mechanical means.

Low-loss silicon nitride strip-slot mode converter based on MMI.

Slot waveguide has attracted a lot of attention due to its ability to confine light in the low refractive index region, while strip waveguide acts as the basic component of guiding light due to its relatively low optical loss. In the multifunctional photonic integrated chips, it is critical to achieve the low loss transition between the strip waveguide and the slot waveguide. In this work, a silicon nitride strip-slot mode converter with high efficiency, large bandwidth, and large fabrication tolerance are proposed and demonstrated through the numerical investigation and experiments. The coupling efficiency of the mode converter is up to - 0.1 dB (97.7%), which enables the extremely low transition loss between the strip waveguide and the slot waveguide. Moreover, the fabrication process of silicon nitride photonic devices with high performance is introduced, which is fully compatible with the CMOS technology. Photonic devices based on silicon nitride with the characteristics of the low optical loss and the temperature insensitivity represent a new paradigm in realizing silicon-based photonic multifunctional chips.