Gastrodin alleviates the deterioration of depressive-like behavior and glucolipid metabolism promoted by chronic stress in type 2 diabetic mice.

The growing burden of psychological stress among diabetes patients has contributed to a rising incidence of depression within this population. It is of significant importance to conduct research on the impact of stress on diabetes patients and to explore potential pharmacological interventions to counteract the stress-induced exacerbation of their condition. Gastrodin is a low molecular weight bioactive compound extracted from the rhizome of Gastrodiae elata Blume, and it may be a preventive strategy for diabetes and a novel treatment for depression symptoms.

Peptide- and Protein-Level Combined Strategy for Analyzing Newly Synthesized Proteins by Integrating Tandem Orthogonal Proteolysis with Cleavable Bioorthogonal Tagging.

A newly synthesized proteome reflects perturbations sensitively and maintains homeostasis in cells. To investigate the low abundant newly synthesized proteins (NSPs) from a complex background proteome, an enrichment process with high selectivity and reliability is essential. Here, we have developed a strategy to realize comprehensive analysis of NSPs by integrating tandem orthogonal proteolysis (TOP) with cleavable bioorthogonal tagging (CBOT) called TOP-CBOT.

Enhancing Comprehensive Analysis of Newly Synthesized Proteins Based on Cleavable Bioorthogonal Tagging.

Protein synthesis and degradation responding to environmental cues is critical for understanding the mechanisms involved. Chemical proteomics introducing bioorthogonal tagging into proteins and isolation by biotin affinity purification is applicable for enrichment of newly synthesized proteins (NSPs). Current enrichment methods based on biotin-streptavidin interaction lack efficiency to release enriched NSPs under mild conditions.

Specific Analysis of α-2,3-Sialylated N-Glycan Linkage Isomers by Microchip Capillary Electrophoresis-Mass Spectrometry.

Sialylated N-glycan isomers with α-2,3 and α-2,6 linkages play crucial and distinctive roles in diverse physiological and pathological processes. Changes of α-2,3-linked sialic acids in sialylated N-glycans are especially important in monitoring the initiation and progression of diseases. However, the specific analysis of α-2,3-sialylated N-glycan linkage isomers remains challenging due to their extremely low abundance and technical limitations in separation and detection.

Comparative analysis of intact glycopeptides from mannose receptor among different breast cancer subtypes using mass spectrometry.

Breast cancer is a highly heterogeneous disease, encompassing a number of biologically distinct entities with specific pathologic features and biological behaviors. In the preliminary experiments, we identified several glycosylation sites of mannose receptors in different breast cancer subtypes and showed that the mannose receptors could be a potential marker for breast cancer. However, the glycan composition on each site is still unknown because the glycan was removed by PNGase F in previous work.

FluoroTRAQ: Quantitative Analysis of Protein S-Nitrosylation through Fluorous Solid-Phase Extraction Combining with iTRAQ by Mass Spectrometry.

S-Nitrosylation is an important post-translational modification that occurs on cysteine amino acid and regulates signal transduction in diverse cell processes. Dysregulation of protein nitrosylation has shown close association with cardiovascular and neurological diseases, thus demanding further precise and in-depth understanding. Mass spectrometry-based proteomics has been the method of choice for analyzing S-nitrosylated (SNO-) proteins.

Rapid and Easy Enrichment Strategy for Naturally Acetylated N Termini Based on LysN Digestion and Amine-Reactive Resin Capture.

Protein N-terminal acetylation (N-acetylation) is one of the most common modifications in both eukaryotes and prokaryotes. Although studies have shown that N-acetylation plays important roles in protein assembly, stability, and location, the physiological role has not been fully elucidated. Therefore, a robust and large-scale analytical method is important for a better understanding of N-acetylation.

Stable Isotope Sequential Derivatization for Linkage-Specific Analysis of Sialylated N-Glycan Isomers by MS.

Sialylated N-glycans play pivotal role in several important biological and pathological processes. Their sialyl-linkage isomers, mostly α-2,3- and α-2,6-linked, act differently during the cellular events and several diseases. While mass spectrometry (MS) technology is a powerful tool in N-glycome analysis, it still suffers from an inability to distinguish linkage isomers of native N-glycans.

In-Depth Analysis of C Terminomes Based on LysC Digestion and Site-Selective Dimethylation.

Analysis of protein C termini is very important for functional annotations of proteomes, while proteome-wide C termini analysis still poses substantial challenges. Here we described a simple and robust strategy for specific isolation of protein C termini based on LysC digestion and site-selective dimethylation to deplete N-terminal and internal peptides by scavenger materials. The performance of LysC digestion and conditions of site-selective dimethylation and resin coupling were discussed in detail.

Combining near infrared spectroscopy with predictive model and expertise to monitor herb extraction processes.

Albeit extensively utilized, herb extraction process (HEP) is hard to be monitored because of its batch nature and the fluctuating quality of raw materials. Process analytical tools like near infrared spectroscopy (NIRS) can offer nondestructive examinations and collect abundant data of the process, which in principle contain the information about the quality of both the product and the process itself. However, extra effort is often required for the data mining of such process measurements, and extracting knowledge of the quality of process can be even harder.

Site-Specific Quantification of Protein Ubiquitination on MS2 Fragment Ion Level via Isobaric Peptide Labeling.

Proteome-wide quantitative analysis of protein ubiquitination is important to gain insight into its various cellular functions. However, it is still challenging to monitor how ubiquitination at each individual lysine residue is independently regulated, especially the whereabouts of peptides containing more than one ubiquitination site. In recent years, isobaric peptide termini labeling has been considered a promising strategy in quantitative proteomics, benefiting from its high accuracy by quantifying with a series of b, y fragment ion pairs.

Highly Selective and Large Scale Mass Spectrometric Analysis of 4-Hydroxynonenal Modification via Fluorous Derivatization and Fluorous Solid-Phase Extraction.

Modification of proteins with 4-hydroxynonenal (HNE) is known to alter the function of proteins and regulate the associated biological processes in eukaryotic cells. The development of mass spectrometry (MS) makes high-throughput analysis of HNE modification accessible. However, the identification of HNE modification is still hampered by the low frequency of this modification.

Far infrared-assisted encapsulation of filter paper strips in poly(methyl methacrylate) for proteolysis.

Filter paper strips were enclosed between two poly(methyl methacrylate) plates to fabricate paper-packed channel microchips under pressure in the presence of far infrared irradiation. After the enclosed paper strip was oxidized by periodate, trypsin was covalently immobilized in them to fabricate microfluidic proteolysis bioreactor. The feasibility and performance of the unique bioreactor were demonstrated by digesting BSA and lysozyme.

Immobilization of trypsin on miniature incandescent bulbs for infrared-assisted proteolysis.

A novel efficient proteolysis approach was developed based on trypsin-immobilized miniature incandescent bulbs and infrared (IR) radiation. Trypsin was covalently immobilized in the chitosan coating on the outer surface of miniature incandescent bulbs with the aid of glutaraldehyde. When an illuminated enzyme-immobilized bulb was immersed in protein solution, the emitted IR radiation could trigger and accelerate heterogeneous protein digestion.

Low temperature preparation of a graphene-cobalt microsphere hybrid by borohydride-initiated reduction for enriching proteins and peptides.

A graphene-cobalt microsphere hybrid was prepared by the chemical reduction of a mixture containing graphene oxide and cobalt chloride. It was found that a little amount of potassium borohydride or sodium borohydride could initiate the hydrazine-reduction of the mixture at a low temperature of 80 °C. The structure of the material was investigated by scanning electron microscopy, transmission electron microscopy, energy dispersive spectroscopy, vibrating sample magnetometery, Fourier transform infrared spectroscopy, Raman spectroscopy, and Brunauer-Emmett-Teller (BET) techniques.

Immobilization of trypsin via graphene oxide-silica composite for efficient microchip proteolysis.

In this report, trypsin was covalently immobilized in the graphene oxide (GO)-silica composite coating on the channel wall of poly(methyl methacrylate) (PMMA) microchips to fabricate microfluidic bioreactors for highly efficient proteolysis. A mixture solution containing GO nanosheets and silica gel was injected into the channels to form coating. 1-Ethyl-3-(3-dimethylaminopropyl)carbodiimide and N-hydroxysuccinimide were used as carboxyl activating agents to crosslink the primary amino groups of trypsin to the carboxyl groups of the entrapped GO sheets in the composite to realize covalent immobilization.

Nuclear proteome profile of C57BL/6J mouse liver.

The liver proteome can serve as a reference to better understand both disease mechanisms and possible therapeutics, since the liver is an important organ in the body that performs a large number of tasks. Here we identify the organelle proteome of C57BL/6J mouse liver nuclei as a promising strategy to enrich low abundance proteins, in the sense that analysis of whole liver cells is rather complex for current techniques and may not be suitable for proteins with low abundance. Evaluation of nucleus integrity and purity was performed to demonstrate the effectiveness of the optimized isolation procedure.

14-3-3ε mediates the cell fate decision-making pathways in response of hepatocellular carcinoma to Bleomycin-induced DNA damage.

Background: Lack of understanding of the response of hepatocellular carcinoma (HCC) to anticancer drugs causes the high mortality of HCC patients. Bleomycin (BLM) that induces DNA damage is clinically used for cancer therapy, while the mechanism underlying BLM-induced DNA damage response (DDR) in HCC cells remains ambiguous. Given that 14-3-3 proteins are broadly involved in regulation of diverse biological processes (BPs)/pathways, we investigate how a 14-3-3 isoform coordinates particular BPs/pathways in BLM-induced DDR in HCC.

Efficient proteolysis strategies based on microchip bioreactors.

In proteome research, proteolysis is an important procedure prior to the mass spectrometric identification of proteins. The typical time of conventional in-solution proteolysis is as long as several hours to half a day. To enhance proteolysis efficiency, a variety of microchip bioreactors have been developed for the rapid digestion and identification of proteins in the past decade.

Far-infrared-assisted preparation of a graphene-nickel nanoparticle hybrid for the enrichment of proteins and peptides.

A new approach based on far infrared-assisted in situ reduction was developed for the facile one-step preparation of graphene-nickel nanoparticle hybrid by refluxing a mixture solution containing graphene oxide, nickel(II) sulfate, and hydrazine over an far-infrared heater. The reduction time was as short as 20 min. The structure of the material was investigated by transmission electron microscopy, scanning electron microscopy, X-ray diffraction, energy dispersive spectroscopy, vibrating sample magnetometery, and Fourier transform infrared spectroscopy.

Immobilization of trypsin in the layer-by-layer coating of graphene oxide and chitosan on in-channel glass fiber for microfluidic proteolysis.

In this report, trypsin was immobilized in the layer-by-layer (LBL) coating of graphene oxide (GO) and chitosan on a piece of glass fiber to fabricate microchip bioreactor for efficient proteolysis. LBL deposition driven by electrostatic forces easily took place on the surface of the glass fiber, providing mild environmental conditions so that the denaturation and autolysis of the immobilized trypsin was minimized. Prior to use, a piece of the prepared trypsin-immobilized glass fiber was inserted into the channel of a microchip to form a core-changeable bioreactor.

Immobilization of trypsin on poly(urea-formaldehyde)-coated fiberglass cores in microchip for highly efficient proteolysis.

Trypsin was covalently immobilized on poly(urea-formaldehyde)-coated fiberglass cores based on the condensation reaction between poly(urea-formaldehyde) and trypsin for efficient microfluidic proteolysis in this work. Prior to use, a piece of the trypsin-immobilized fiber was inserted into the main channel of a microchip under a magnifier to form a core-changeable bioreactor. Because trypsin was not permanently immobilized on the channel wall, the novel bioreactor was regenerable.

Inflation bulb-driven microfluidic reactor for infrared-assisted proteolysis.

In this report, an inflation bulb-driven microfluidic reactor was developed for IR-accelerated proteolysis. This novel proteolysis system mainly consisted of an inflation bulb-driving system, a simple cross-PMMA microchip, and a temperature-controllable IR radiation system. The gas pressure generated from an inflation bulb was employed to drive protein and trypsin solutions to flow into the main channel of the microchip via two capillaries and the injection channel.