Biobased Tannic Acid-Chitosan Composite Membranes as Reusable Adsorbents for Effective Enrichment of Phosphopeptides.

High-performance reusable materials from renewable resources are rare and urgently required in bioseparation. Herein, a series of tannic acid-chitosan composite membranes for the enrichment of phosphopeptides were fabricated by the freeze casting method. First, a tannic acid-chitosan composite membrane was acquired via the multiple hydrogen bonds between tannic acid and chitosan, which had a long-range aligned three-dimensional microstructure. Second, a covalent-hydrogen bond hybrid composite was also fabricated, with stable and aligned honeycomb-like microstructures that formed by the synergy of covalence and hydrogen bonding. Besides, a ternary composite membrane was "one-pot" synthesized by the copolymerization of tannic acid, chitosan, and Ti4+ ions, indicating the feasibility of involving metal ions in the composition of the polymer skeleton in place of additional modification steps. The as-prepared chitosan composite membranes exhibited excellent performance in the enrichment of phosphopeptides from ß-casein tryptic digest and human serum. Benefitting from the long-range aligned honeycomb-like structure coordinated by hydrogen bonds and covalent bonds, and a large number of pyrogallol functional groups provided by tannic acid, the covalent-hydrogen bond hybrid membrane showed excellent reusability and could be reused up to 16 times in phosphopeptide enrichment, as far as we know, which is the best reported result to date.

DKI can distinguish high-grade gliomas from IDH1-mutant low-grade gliomas and correlate with their different nuclear-to-cytoplasm ratio: a localized biopsy-based study.

OBJECTIVES: To explore whether differences in diffusional kurtosis imaging (DKI) between therapy-naïve high-grade gliomas (HGGs) and low-grade gliomas (LGGs) are related to the cellularity and/or the nuclear-to-cytoplasmic (N/C) ratio. METHODS: We analyzed 44 and 40 diffuse glioma samples that were pathologically confirmed as HGGs and IDH1-mutant LGGs, respectively. The DKI parameters included kurtosis metrics (mean kurtosis [MK], axial kurtosis [K//], and radial kurtosis [K⊥]), and the diffusional metrics (fractional anisotropy [FA], mean diffusion [MD], axial diffusion [λ//], and radial diffusion [λ⊥]). The cellularity and the N/C ratio were compared within LGGs and HGGs using the Mann-Whitney U test (significant level, p < 0.007 [0.05/7]); Bonferroni correction). Spearman's correlation analysis was used to calculate the correlation coefficients among DKI metrics, cellularity, and the N/C ratio at a significant level of p = 0.05. RESULTS: Excluding FA, all DKI metrics showed significant differences between HGGs and LGGs (all p ≤ 0.001). The N/C ratio of HGGs was significantly higher than that of LGGs; however, differences in cellularity were not significant between the two glioma groups (p = 0.525). Similarly, excluding FA, all DKI metrics were significantly correlated with the N/C ratio in LGGs, with correlation coefficients of - 0.365 (MD), - 0.313 (λ//), - 0.376 (λ⊥), 0.859 (MK), 0.772 (K//), and 0.842 (K//). There was a non-significant correlation between any DKI parameters and the cellularity in LGGs. Additionally, the cellularity and N/C ratios in HGGs did not correlate with any DKI metrics. CONCLUSIONS: DKI differentiate LGGs from HGGs associated with their different N/C ratios. CLINICAL RELEVANCE STATEMENT: This study shows that DKI differentiates LGGs from HGGs may correlated with their different N/C ratios, this could provide a possible histopathological mechanism about why DKI can DKI differentiate LGGs from HGGs. KEY POINTS: • Excluding FA, all DKI metrics showed a significant difference between high-grade gliomas and IDH1-mutant low-grade gliomas. • The nuclear-to-cytoplasm ratios in high-grade gliomas were significantly more extensive than that in IDH1-mutant low-grade gliomas, but not the cellularity. • Significant associations were seen between DKI measures and the N/C ratio; a non-significant correlation was noted between any DKI metric and cellularity in glioma specimens.

The Synergistic Anti-inflammatory Activity and Interaction Mechanism of Ellagic Acid and a Bioactive Tripeptide (Phe-Pro-Leu) from Walnut Meal.

The anti-inflammatory effect of the interaction between ellagic acid (EA) and a bioactive tripeptide (FPL) from walnut meal was investigated in this study. We found that lipopolysaccharide (LPS) -induced expression of nitric oxide, tumor necrosis factor-α, interleukin-6, and interleukin-1ß were significantly inhibited by the interaction of EA and FPL in RAW264.7 macrophage cells. Cell viability assays and CompuSyn simulations predicted the highest synergistic effect of the combination at doses of EA-25 µM and FPL-100 µM, with the lowest combination index (CI) values reaching 0.56. Fluorescence spectra revealed the intrinsic fluorescence of phenylalanine in FPL was quenched by interaction with EA. Fourier transform infrared spectroscopy indicated FPL had electrostatic and hydrophobic interactions with EA through N-H, C = O, C-N bonds and the secondary structure of FPL had effectively changed, with a decrease in α-helix when interacting with EA. Our results demonstrated that the synergistic anti-inflammatory effect of EA and FPL as potential inflammatory inhibitors in food industry.

Nanoscaled and Atomic Ruthenium Electrocatalysts Confined Inside Super-Hydrophilic Carbon Nanofibers for Efficient Hydrogen Evolution Reaction.

A series of Ru-based catalysts have been developed for the hydrogen evolution reaction (HER) by the facile impregnation of copious and eco-friendly bacterial cellulose (BC) with Ru(bpy)3 Cl2 (bpy = 2,2'-bipyridine) followed by pyrolysis. After the oxidation and molecular recomposition processes that occur within the BC precursors during pyrolysis, sub-2 nm Ru nanoparticles (NPs) and atomic Ru species confined within surface-oxidized N-doped carbon nanofibers (CNFs) can be observed in the derived catalysts. The surface oxidation of CNFs leads the derived catalysts with super hydrophilicity and water-absorbing capacity, and also provides dimensional confinement for the nanoscaled and atomic Ru species. With these added structural advantages and the component synergy, the derived catalysts show superior HER activities, for which the overpotentials are as low as 19.6 mV (1 m KOH) and 55.0 mV (0.5 m H2 SO4 ) for the most active case at the current density of 10 mA cm-2 . Moreover, superior HER activity can be also achieved for the catalysts derived with a wide range of Ru loadings. Finally, the influence of Ru NP size on HER activity is investigated by density functional theory simulations. This method provides a reliable protocol for preparing highly active HER catalysts for scale-up applications.

Fabrication of hydrophilic zwitterionic microspheres via inverse suspension polymerization for the enrichment of N-glycopeptides.

A kind of zwitterionic microsphere was prepared via one-step inverse suspension polymerization employing 3-[N,N-dimethyl-[2-(2-methylpropyl-2-enyloxy) ethyl] ammonium] propane-1-sulfonate (MSA) and N,N-methylene bisacrylamide (BIS) as the precursors. The preparation conditions were carefully investigated and optimized by regulating the content of total monomers, ratio of MSA to BIS, ratio of water to oil, and content of stabilizer. The properties of microspheres were characterized by helium ion microscopy (HIM), Fourier transform infrared spectroscopy (FT-IR), X-ray photoelectron spectroscopy (XPS), N2 adsorption/desorption measurement, and water contact angle measurement. The particle size of resulting polydisperse microspheres ranged from 15-25 µm, exhibiting high specific surface area of 138 m2 g-1. Owing to great hydrophilicity, the resulting zwitterionic microspheres could be directly used as hydrophilic interaction chromatography (HILIC) sorbent to enrich glycopeptides from biosamples without any chemical modification. A total of 19 N-glycopeptides was enriched from 10 µg of IgG digest. Besides, up to 383 N-glycopeptides and 224 N-glycosylation sites were unambiguously identified from 2 µL of human serum digest by cLC-MS/MS after enrichment with zwitterionic microspheres, indicating their great enrichment performance to N-glycopeptides. The approach of preparing hydrophilic zwitterionic microspheres contains only one synthesis reaction and is suitable for large-scale preparation.

Novel Two-Dimensional MoS2-Ti4+ Nanomaterial for Efficient Enrichment of Phosphopeptides and Large-Scale Identification of Histidine Phosphorylation by Mass Spectrometry.

Due to its key roles in regulating the occurrence and development of cancer, protein histidine phosphorylation has been increasingly recognized as an important form of post-translational modification in recent years. However, large-scale analysis of histidine phosphorylation is much more challenging than that of serine/threonine or tyrosine phosphorylation, mainly because of its acid lability. In this study, MoS2-Ti4+ nanomaterials were synthesized using a solvothermal method and taking advantage of the electrostatic adsorption between MoS2 nanosheets and Ti4+. The MoS2-Ti4+ nanomaterials have the advantage of the combined affinity of Ti4+ and Mo toward phosphorylation under medium acidic conditions (pH = 3), which is crucial for preventing hydrolysis and loss of histidine phosphorylation during enrichment. The feasibility of using the MoS2-Ti4+ nanomaterial for phosphopeptide enrichment was demonstrated using mixtures of ß-casein and bovine serum albumin (BSA). Further evaluation revealed that the MoS2-Ti4+ nanomaterial is capable of enriching synthetic histidine phosphopeptides from 1000 times excess tryptic-digested HeLa cell lysate. Application of the MoS2-Ti4+ nanomaterials for large-scale phosphopeptide enrichment results in the identification of 10 345 serine, threonine, and tyrosine phosphosites and the successful mapping of 159 histidine phosphosites in HeLa cell lysates, therefore indicating great potential for deciphering the vital biological roles of protein (histidine) phosphorylation.

ARHGAP4 regulates the cell migration and invasion of pancreatic cancer by the HDAC2/ß-catenin signaling pathway.

ß-catenin is a subunit of the cadherin protein complex and acts as an intracellular signal transducer in the Wnt signaling pathway that mediates multiple cellular processes, such as cell migration and invasion. HDAC2 (histone deacetylase 2), a deacetylase that maintains histone H3 in a deacetylated state in the promoter region of Wnt-targeted genes where ß-catenin is bound, negatively regulating ß-catenin activation. However, the regulation of HDAC2/ß-catenin pathway remains unclear. Here, we report ARHGAP4 as a new regulator of the ß-catenin pathway that regulates cell invasion and migration of pancreatic cancer as well as the downstream effector MMP2 and MMP9 expression in vitro. Mechanistically, ARHGAP4 interacts with and ubiquitinates HDAC2, which in turn inhibits ß-catenin activation. Furthermore, treatment of CAY10683, an HDAC2 inhibitor, and XAV939, a Wnt/ß-catenin pathway inhibitor, attenuated the effects of ARHGAP4 silencing on pancreatic cancer cells. Overall, our findings establish ARHGAP4 as a novel regulator of HDAC2/ß-catenin pathway with a critical role in tumorigenesis.

Fluorescence lifetime-based pH sensing by platinum nanoclusters.

In this work, we report for the first time the application of ultrasmall Pt nanoclusters (Pt NCs) as a fluorescence-lifetime-based pH sensor. The fluorescence properties of our prepared Pt NCs show strong pH dependence, due to the change of the surface states of Pt NCs under alkaline/acidic conditions. Interestingly, both the fluorescence intensity and the fluorescence lifetime of Pt NCs exhibit a good linear relationship in the physiologically relevant pH range of 6.02-7.54. Our Pt NC-based pH sensor possesses many important features as an attractive sensor, including high anti-jamming capability, excellent stability and good reversibility. Moreover, the use of fluorescence lifetime as the optical readout signal rather than the intensity makes the present pH sensor more reliable in practical applications because the fluorescence lifetime is invariant to the probe concentration or changes in excitation conditions. Application of the Pt NC-based system for pH detection in real water samples and simulated intracellular environment samples has also been successfully demonstrated.

Fast fabrication of a hybrid monolithic column containing cyclic and aliphatic hydrophobic ligands via photo-initiated thiol-ene polymerization.

Three monomers, octakis (3-mercaptopropyl) octasilsesquioxane, 1,2,4-trivinylcyclohexane and isophytol were employed to synthesize a novel monolithic stationary phase via photo-initiated thiol-ene click polymerization for reversed-phase liquid chromatography. Several factors such as porogenic system, reaction time and the molar ratio of functional groups were investigated in detail. The resulting poly(POSS-co-TVCH-co-isophytol) monolithic column exhibited suitable permeability for fast separation and outstanding thermal stability. Five alkylbenzenes were employed to evaluate the ability of chromatographic separation of the resulting monolithic columns at different flow rates, and showed the highest column efficiencies of 90,200-93,100 N/m (corresponding to 10.4-10.6 µm of plate height) at a velocity of 0.41 mm/s. The baseline separations of five anilines and eight phenols further proved the applicability of poly(POSS-co-TVCH-co-isophytol) monolithic column in the separation of small molecules.

Two-Dimensional MoS2-Based Zwitterionic Hydrophilic Interaction Liquid Chromatography Material for the Specific Enrichment of Glycopeptides.

Mass spectrometry (MS)-based glycoproteomics research requires highly efficient sample preparation to eliminate interference from non-glycopeptides and to improve the efficiency of glycopeptide detection. In this work, a novel MoS2/Au-NP (gold nanoparticle)-L-cysteine nanocomposite was prepared for glycopeptide enrichment. The two-dimensional (2D) structured MoS2 nanosheets served as a matrix that could provide a large surface area for immobilizing hydrophilic groups (such as L-cysteine) with low steric hindrance between the materials and the glycopeptides. As a result, the novel nanomaterial possessed an excellent ability to capture glycopeptides. Compared to commercial zwitterionic hydrophilic interaction liquid chromatography (ZIC-HILIC) materials, the novel nanomaterials exhibited excellent enrichment performance with ultrahigh selectivity and sensitivity (approximately 10 fmol), high binding capacity (120 mg g-1), high enrichment recovery (more than 93%), satisfying batch-to-batch reproducibility, and good universality for glycopeptide enrichment. In addition, its outstanding specificity and efficiency for glycopeptide enrichment was confirmed by the detection of glycopeptides from an human serum immunoglobulin G (IgG) tryptic digest in quantities as low as a 1:1250 molar ratio of IgG tryptic digest to bovine serum albumin tryptic digest. The novel nanocomposites were further used for the analysis of complex samples, and 1920 glycopeptide backbones from 775 glycoproteins were identified in three replicate analyses of 50 µg of proteins extracted from HeLa cell exosomes. The resulting highly informative mass spectra indicated that this multifunctional nanomaterial-based enrichment method could be used as a promising tool for the in-depth and comprehensive characterization of glycoproteomes in MS-based glycoproteomics.

Neural correlates of the popular music phenomenon: evidence from functional MRI and PET imaging.

PURPOSE: Music can induce different emotions. However, its neural mechanism remains unknown. The aim of this study was to use functional magnetic resonance imaging (fMRI) and position emission tomography (PET) imaging for mapping of neural changes under the most popular music in healthy volunteers. METHODS: Blood-oxygen-level-dependent (BOLD) fMRI and monoamine receptor PET imaging with 11C-N-methylspiperone (11C-NMSP) were conducted under the popular music Gangnam Style and light music A Comme Amour in healthy subjects. PET and fMRI images were analyzed by using the Statistical Parametric Mapping software (SPM). RESULTS: Significantly increased fMRI BOLD signals were found in the bilateral superior temporal cortices, left cerebellum, left putamen and right thalamus cortex. Monoamine receptor availability was increased significantly in the left superior temporal gyrus and left putamen, but decreased in the bilateral superior occipital cortices under the Gangnam Style compared with the light music condition. Significant positive correlation was found between 11C-NMSP binding and fMRI BOLD signals in the left temporal cortex. Furthermore, increased 11C-NMSP binding in the left putamen was positively correlated with the mood arousal level score under the Gangnam Style condition. CONCLUSION: Popular music Gangnam Style can arouse pleasure experience and strong emotional response. The left putamen is positively correlated with the mood arousal level score under the Gangnam Style condition. Our results revealed characteristic patterns of brain activity associated with Gangnam Style, and may also provide more general insights into the music-induced emotional processing.

Radiofrequency ablation for hepatic oligometastatic pancreatic cancer: An analysis of safety and efficacy.

OBJECTIVES: This study was to evaluate the value of radiofrequency ablation (RFA) in the treatment of pancreatic cancer with synchronous liver oligometastasis. METHODS: 102 patients diagnosed with pancreatic cancer with synchronous liver oligometastasis undergoing RFA were recruited in this retrospective study between January 2012 and December 2015. Clinical efficacy was evaluated by computed tomography or magnetic resonance imaging 1 month later. All patients were treated with RFA and systemic chemotherapy based on NCCN guideline. RESULTS: The median follow-up was 21 months (range, 4.0-43.8 months). Of all patients, the 1-year survival rate was 47.1% and the median overall survival time was 11.40 months. Complete tumor ablation was achieved in 137 of 145 RFA sessions (94.5%), and in 244 of 254 tumors (96.1%). The incidence of common complications was 9.8%, and no severe complications were reported in any patient. Multivariate Cox regression analysis revealed that primary tumor in the head of the pancreas (HR = 1.868, 95% CI: 1.023-3.409; P = 0.042), maximum diameter of liver metastasis 3-5 cm (HR = 1.801, 95% CI: 1.081-3.001, P = 0.024) and neutrophil/lymphocyte ratio (NLR) ≥2.5 (HR = 1.716, 95% CI: 1.047-2.811; P = 0.032) were independent predictors of poorer survival. CONCLUSION: RFA provides a minimally invasive and safe treatment for patients with pancreatic cancer with liver oligometastases. The clinical efficiency of RFA for hepatic oligometastatic pancreatic cancer was easily affected by the following factors: primary tumor location, maximum diameter of liver metastasis and NLR. These factors could be helpful for treatment decision and clinical trial design.

Covalent organic framework-coated magnetic graphene as a novel support for trypsin immobilization.

Deep and efficient proteolysis is the critical premise in mass spectrometry-based bottom-up proteomics. It is difficult for traditional in-solution digestion to meet the requirement unless prolonged digestion time and enhanced enzyme dosage are employed, which makes the whole workflow time-consuming and costly. The abovementioned problems could be effectively ameliorated by anchoring many proteases on solid supports. In this work, covalent organic framework-coated magnetic graphene (MG@TpPa-1) was designed and prepared as a novel enzyme carrier for the covalent immobilization of trypsin with a high degree of loading (up to 268 µg mg-1). Profiting from the advantages of magnetic graphene and covalent organic frameworks, the novel trypsin bioreactor was successfully applied for the enzymatic digestion of a model protein with dramatically improved digestion efficiency, stability, and reusability. Complete digestion could be achieved in a time period as short as 2 min. For the digestion of proteins extracted from Amygdalus pedunculata, a total of 2833 protein groups were identified, which was slightly more than those obtained by 12 h of in-solution digestion (2739 protein groups). All of the results demonstrate that MG@TpPa-1-trypsin is an excellent candidate for sample preparation in a high-throughput proteomics analysis. Graphical abstract Covalent organic frameworks-coated magnetic graphene was prepared as novel carrier for highly efficient tryptic immobilization.

A novel systemic inflammation response index (SIRI) for predicting the survival of patients with pancreatic cancer after chemotherapy.

BACKGROUND: Predicting survival is uniquely difficult in patients with pancreatic cancer who receive chemotherapy. The authors developed a systemic inflammation response index (SIRI) based on peripheral neutrophil, monocyte, and lymphocyte counts and evaluated the ability of the SIRI to predict the survival of patients with pancreatic cancer who received chemotherapy. METHODS: The SIRI was developed in a training set of 177 patients who had advanced pancreatic cancer and received palliative chemotherapy. The ability of the SIRI to predict a patient's survival after chemotherapy was validated in 2 independent cohorts (n = 397). RESULTS: Compared with patients who had an SIRI <1.8, patients in the training cohort who had an SIRI ≥1.8 had a shorter time to progression (TTP) (hazard ratio [HR], 2.348; 95% confidence interval, 1.559-3.535; P = .003) and shorter overall survival (OS) (HR, 2.789; 95% confidence interval, 1.897-4.121; P < .001). Comparable TTP and OS findings were observed in 2 independent validation cohorts. Multivariate analysis confirmed that the SIRI was an independent prognostic factor for both TTP and OS. In addition, compared with no change, an increase in the SIRI at week 8 was associated with poor TTP and OS, whereas a decrease in the SIRI was associated with improved outcomes. In addition, high SIRI scores were correlated with higher serum levels of interleukin 10, C-C motif chemokine ligand 17 (CCL17), CCL18, and CCL22 and with a shortened TTP. CONCLUSIONS: The SIRI can be used to predict the survival of patients with pancreatic adenocarcinomas who receive chemotherapy, potentially allowing clinicians to improve treatment outcomes by identifying candidates for aggressive therapy. Cancer 2016;122:2158-67. © 2016 American Cancer Society.

Novel Fluorescein-Based Fluorescent Probe for Detecting H2S and Its Real Applications in Blood Plasma and Biological Imaging.

A broad-spectrum fluorescent probe, which can be applied to monitoring H2S in various biological systems, has been rationally designed and synthesized. This specific probe was applied to localize the endogenous H2S in living Raw264.7 macrophage cells, HepG2 cells, and H9C2 cells. At the same time, the probe has successfully visualized CBS- and CSE-induced endogenous H2S production and monitored CBS and CSE activity in H9C2 cells. This probe could serve as a powerful molecular imaging tool to further explore the physiological function and the molecular mechanisms of endogenous H2S in living animal systems.

Randomized, placebo-controlled trial of K1 acupoint acustimulation to prevent cisplatin-induced or oxaliplatin-induced nausea.

BACKGROUND: Greater than 70% of patients with cancer experience chemotherapy-induced nausea and vomiting. In the current study, the authors examined the effects of electrostimulation of the K1 acupoint located on the sole of the foot because it is believed to have the potential to control chemotherapy-induced nausea and vomiting. METHODS: In this trial, 103 patients diagnosed with primary or metastatic liver cancer were recruited before transcatheter arterial infusion (TAI) of cisplatin or oxaliplatin and randomized to either group A (51 patients who were treated with the antiemetic tropisetron and acustimulation at the K1 acupoint for 20 minutes approximately 1 to 2 hours before TAI on the first day and then daily for the subsequent 5 days) or group B (52 patients who were treated with tropisetron and electrostimulation at a placebo point on the heel). The rate, intensity, and duration of nausea and vomiting were collected at baseline and then daily for 5 days after TAI. Quality of life was assessed daily using the MD Anderson Symptom Inventory and the EuroQoL scale. RESULTS: No differences were found between groups A and B with regard to the incidence and degree of nausea or vomiting on day 1 or the following 5 days. Patients in group A had better EuroQoL scores compared with patients in group B (72.83 in group A vs 65.94 in group B; P =.04) on day 4 but not on the other days. No group differences were noted at any time point for MD Anderson Symptom Inventory scores. CONCLUSIONS: Electrostimulation of K1 combined with antiemetics did not result in initial prevention of cisplatin-induced or oxaliplatin-induced nausea or vomiting.

Identifying microRNA-mRNA regulatory network in gemcitabine-resistant cells derived from human pancreatic cancer cells.

Pancreatic cancer is unresectable in over 80 % of patients owing to difficulty in early diagnosis. Chemotherapy is the most frequently adopted therapy for advanced pancreatic cancer. The development of drug resistance to gemcitabine (GEM), which is always used in standard chemotherapy, often results in therapeutic failure. However, the molecular mechanisms underlying the gemcitabine resistance remain unclear. Therefore, we sought to explore the microRNA-mRNA network that is associated with the development of gemcitabine resistance and to identify molecular targets for overcoming the gemcitabine resistance. By exposing SW1990 pancreatic cancer cells to long-term gemcitabine with increasing concentrations, we established a gemcitabine-resistant cell line (SW1990/GEM) with a high IC50 (the concentration needed for 50 % growth inhibition, 847.23 µM). The mRNA and microRNA expression profiles of SW1990 cells and SW1990/GEM cells were determined using RNA-seq analysis. By comparing the results in control SW1990 cells, 507 upregulated genes and 550 downregulated genes in SW1990/GEM cells were identified as differentially expressed genes correlated with gemcitabine sensitivity. Gene ontology (GO) analysis showed that the differentially expressed genes were related to diverse biological processes. The upregulated genes were mainly associated with drug response and apoptosis, and the downregulated genes were correlated with cell cycle progression and RNA splicing. Concurrently, the differentially expressed microRNAs, which are the important player in drug resistance development, were also examined in SW1990/GEM cells, and 56 differential microRNAs were identified. Additionally, the expression profiles of selected genes and microRNAs were confirmed by using Q-PCR assays. Furthermore, combining the differentially expressed microRNAs and mRNAs as well as the predicted targets for these microRNAs, a core microRNA-mRNA regulatory network was constructed, which included hub microRNAs, such as hsa-miR-643, hsa-miR-4644, hsa-miR-4650-5p, hsa-miR-4455, hsa-miR-1261, and hsa-miR-3676. The predicted targets of these hub microRNAs in the microRNA-mRNA network were also observed in the identified differential genes. As a result, a differential gene and microRNA expression pattern was constructed in gemcitabine-resistant pancreatic cancer cells. Therefore, these data may be useful for the detection and treatment of drug resistance in pancreatic cancer patients, and the microRNA-mRNA network-based analysis is expected to be more effective and provides deep insights into the molecular mechanism of drug resistance.

An in silico scheme for optimizing the enzymatic acquisition of natural biologically active peptides based on machine learning and virtual digestion.

BACKGROUND: As a potential natural active substance, natural biologically active peptides (NBAPs) are recently attracting increasing attention. The traditional proteolysis methods of obtaining effective NBAPs are considerably vexing, especially since multiple proteases can be used, which blocks the exploration of available NBAPs. Although the development of virtual digesting brings some degree of convenience, the activity of the obtained peptides remains unclear, which would still not allow efficient access to the NBAPs. It is necessary to develop an efficient and accurate strategy for acquiring NBAPs. RESULTS: A new in silico scheme named SSA-LSTM-VD, which combines a sparrow search algorithm-long short-term memory (SSA-LSTM) deep learning and virtually digested, was presented to optimize the proteolysis acquisition of NBAPs. Therein, SSA-LSTM reached the highest Efficiency value reached 98.00 % compared to traditional machine learning algorithms, and basic LSTM algorithm. SSA-LSTM was trained to predict the activity of peptides in the proteins virtually digested results, obtain the percentage of target active peptide, and select the appropriate protease for the actual experiment. As an application, SSA-LSTM was employed to predict the percentage of neuroprotective peptides in the virtual digested result of walnut protein, and trypsin was ultimately found to possess the highest value (85.29 %). The walnut protein was digested by trypsin (WPTrH) and the peptide sequence obtained was analyzed closely matches the theoretical neuroprotective peptide. More importantly, the neuroprotective effects of WPTrH had been demonstrated in nerve damage mouse models. SIGNIFICANCE: The proposed SSA-LSTM-VD in this paper makes the acquisition of NBAPs efficient and accurate. The approach combines deep learning and virtually digested skillfully. Utilizing the SSA-LSTM-VD based strategy holds promise for discovering and developing peptides with neuroprotective properties or other desired biological activities.