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Abstract Quantitative analysis of the biologically-active metabolites of vitamin D (VitD), which are crucial in regulating various physiological and pathological processes, is important for clinical investigations. Liquid chromatography-tandem mass spectrometry (LC-MS) has been widely used for this purpose but existing LC-MS methods face challenges in achieving highly sensitive and accurate quantification of low-abundance VitD metabolites while maintaining high throughput and robustness. Here we developed a novel pipeline that combines a trapping-micro-LC-(T-µLC) with narrow-window-isolation selected-reaction monitoring MS(NWI-SRM) for ultra-sensitive, robust and high-throughput quantification of VitD metabolites in serum samples after derivatization. The selective-trapping and delivery approach efficiently removes matrix components, enabling high-capacity sample loading and enhancing sensitivity, throughput, and robustness. The NWI-SRM further improves the sensitivity by providing high selectivity. The lower limits of quantification (LOQs) achieved were markedly lower than any existing LC-MS methods: 1.0 pg/mL for 1,25(OH)2D3, 5.0 pg/mL for 24,25(OH)2D3, 30 pg/mL for both 25(OH)D2 and 25(OH)D3, all within a 9-min cycle. The method is applied to quantify VitD metabolites from 218 patients with multiple sclerosis. This study revealed negative correlations(r=− 0.44 to − 0.51) between the levels of 25(OH)D2 and all the three D3 metabolites in multiple sclerosis patients.

During the operation of the drill string, it displays a degree of flexibility. Simultaneously, its dynamic properties, influenced by complex stress conditions, manifest nonlinearity and uncertainty. A comprehensive investigation into the dynamics of flexible drill strings is imperative for deep well drilling. This paper presents a model that simulates random interactions between a flexible drill string and the borehole wall, simplifying the actual drill string model using analogous principles. Dynamic simulation software is utilized for analysis, and an indoor experimental setup has been established. The results reveal that with a constant weight on bit (WOB), higher drill string rotational speeds correlate with increased susceptibility to buckling deformation. Additionally, the critical time for deformation onset exhibits a nearly linear relationship with rotational speed. Maintaining a constant rotational speed, an increase in WOB enhances the likelihood of buckling deformation. The experimental findings suggest a correlation between the drill string’s rotation frequency and the WOB.

Abstract Few studies have been designed to investigate the effect of serum choline on the risk of incident cancer. This study aims to explore the association between serum choline and the risk of new-onset cancer. We conducted a case–control study, including 199 patients with incident cancer and 199 matched controls during a median of 3.9 years of follow-up, nested within the China Stroke Primary Prevention Trial. Cubic spline regression (RCS) and conditional logistic regression analysis was used to assess the association of serum choline and incident cancer risk. We observed a positive dose–response association between serum choline levels and the risk of overall (p for overall = 0.046) and digestive system cancer (p for overall = 0.039). Compared with patients with the lowest choline levels (Q1 group), patients in the highest levels of choline (Q4) had a 3.69-fold and 6.01-fold increased risk of overall (OR = 3.69, 95% CI 1.17–11.63) and digestive system cancer (OR = 6.01, 95% CI 1.14–31.67). Elevated choline levels (per SD, 11.49 μg/mL) were associated with a higher risk of overall cancer among participants who were older, male, and smokers in the subgroup analyses. We found a positive association between elevated levels of serum choline with increased risk of incident cancer. Our findings have critical clinical implications for cancer prevention and diagnosis. Trial registration CSPPT, NCT00794885. Registered: November 20, 2008. https://www.clinicaltrials.gov/ct2/show/study/NCT00794885 https://www.clinicaltrials.gov/ct2/show/study/NCT00794885.

The serrated pathway to colorectal cancers (CRCs) is a significant pathway encompassing five distinct types of lesions, namely hyperplastic polyps (HPs), sessile serrated lesions (SSLs), sessile serrated lesions with dysplasia (SSL-Ds), traditional serrated adenomas (TSAs), and serrated adenoma unclassified. In contrast to the conventional adenoma–carcinoma pathway, the serrated pathway primarily involves two mechanisms: BRAF/KRAS mutations and CpG island methylator phenotype (CIMP). HPs are the most prevalent non-malignant lesions, while SSLs play a crucial role as precursors to CRCs, On the other hand, traditional serrated adenomas (TSAs) are the least frequently encountered subtype, also serving as precursors to CRCs. It is crucial to differentiate these lesions based on their unique morphological characteristics observed in histology and colonoscopy, as the identification and management of these serrated lesions significantly impact colorectal cancer screening programs. The management of these lesions necessitates the crucial steps of removing premalignant lesions and implementing regular surveillance. This article provides a comprehensive summary of the epidemiology, histologic features, molecular features, and detection methods for various serrated polyps, along with recommendations for their management and surveillance.

Continuous wave mud pulse transmission is the most widely used information transmission technology in measurement while drilling (MWD). The increase in transmission distance will cause the signal attenuation and deformation during transmission, the affecting exploration efficiency. The waveform change law of continuous mud pulse wave in the process of downhole transmission, this paper establishes a mathematical analysis model, focuses on the modulation form of continuous wave signal, physical mud characteristics, and drill pipe characteristics, and discusses the transmission rules of various characteristics on continuous pressure wave. A simulation system of drill pipe transmission pressure wave is constructed. The transmission characteristics of continuous wave signals under different modulation forms are discussed. The positive correlation between the amplitude attenuation and waveform distortion of pulse signals caused by increased gas holdup in the mud under bubbly flow patterns is analyzed. The numerical calculation and simulation analysis results show that the viscosity frequency characteristic of mud is the main factor affecting the attenuation of continuous wave signal. The surface roughness, size and other physical characteristics of drill pipe can affect the transmission speed and attenuation of signals in long-distance transmission. The signal is prone to distortion at the position of modulation phase change.

Approximately half of the lubricants sold globally find their way into the environment. The need for Environmentally Acceptable Lubricants (EALs) is gaining increased recognition. A lubricant is composed of a base oil and multiple functional additives. The literature has been focused on EAL base oils, with much less attention given to eco-friendly additives. This study presents the tribological performance and aquatic toxicity of four short-chain phosphonium-phosphate and ammonium-phosphate ionic liquids (ILs) as candidate anti-wear and friction-reducing additives for EALs. The results are benchmarked against those of four commercial bio-derived additives. The four ILs, at a mere 0.5 wt% concentration in a synthetic ester, demonstrated a 30–40% friction reduction and >99% wear reduction, superior to the commercial baselines. More impressively, all four ILs showed significantly lower toxicity than the bio-derived products. In an EPA-standard chronic aquatic toxicity test, the sensitive model organism, Ceriodaphnia dubia, had 90–100% survival when exposed to the ILs but 0% survival in exposure to the bio-derived products at the same concentration. This study offers scientific insights for the future development of eco-friendly ILs as lubricant additives.

We propose a novel Schell model source for generating twisted partially coherent beams with an initial radius of curvature, which is called a twisted flat-topped cosine Gaussian Schell-model (TFCGSM) source. The TFCGSM beam comprises a wavefront phase and a flat-top structure, with the source degree of coherence determined by two cosine functions. Based on the Huygens–Fresnel principle, the general analytical expression of the cross-spectral density function of the TFCGSM beam propagating through the paraxial ABCD optical system is derived, and then its propagation properties are studied. The results show that the conversion of the array of the beam and the non-uniform structure can be realized by adjusting the parameters in the source plane. As the propagation distance of the TFCGSM beam increases, it rotates around the axis and increases the intensity of the array distribution. Surprisingly, the initial radius of curvature can cause the beam to rotate. The unique shape and properties of the TFCGSM beam create new possibilities for optical communication and enhanced optical functions.

Objectives Colorectal cancer (CRC) encompasses a spectrum of pathological types, each exhibiting distinct biological behaviours that challenge the conventional T-staging system’s predictive efficiency. Thus, this study aims to explore the prognostic significance of the T stage across various CRC pathological types, seeking to unravel insights that could enhance prognostic assessment in this complex disease.Study design We performed a retrospective analysis using the Surveillance, Epidemiology, and End Results (SEER) database for primary CRC cases from 2010 to 2017.Setting The SEER database, comprising data from various US regional and state cancer registries, identified 39 321 patients with CRC. Our analysis focused on the three most common CRC pathological types: adenocarcinoma (AC), mucinous adenocarcinoma (MC) and signet ring cell carcinoma (SR).Primary outcome measures The study used Cox regression models to evaluate how different pathological characteristics impact mortality risk in patients with CRC. Time-dependent receiver operating characteristic curves were also applied to assess the prognostic accuracy of various tumour node metastasis (TNM)/non-mucinous (NM) stages.Results We observed significant associations between T stage and mortality risk for patients with AC and MC. Notably, in comparison to those at T1 stage, patients with AC in the T4 stage demonstrated a 2.01-fold increase in mortality risk (HR=2.01, 95% CI: 1.89 to 2.15), while patients with MC at T4 stage showed a 1.42-fold increase (HR=1.42, 95% CI: 1.03 to 1.97). However, within the SR group, T stages did not independently impact survival, showing no significant distinction (HR=1.07, 95% CI: 0.59 to 1.95). Intriguingly, the traditional TNM staging systems demonstrated limited discriminatory power in predicting prognosis for patients with SR when compared with the more innovative NM staging systems.Conclusions This study uncovers important insights about the prognostic significance of the T stage in different types of CRC, highlighting the need for personalised assessments based on specific histological subtypes.

Polyomavirus (PyV) Large T-antigen (LT) is the major viral regulatory protein that targets numerous cellular pathways for cellular transformation and viral replication. LT directly recruits the cellular replication factors involved in initiation of viral DNA replication through mutual interactions between LT, DNA polymerase alpha-primase (Polprim), and single-stranded DNA binding complex, (RPA). Activities and interactions of these complexes are known to be modulated by post-translational modifications; however, high-sensitivity proteomic analyses of the PTMs and proteins associated have been lacking. High-resolution liquid chromatography tandem mass spectrometry (LC–MS/MS) of the immunoprecipitated factors (IPMS) identified 479 novel phosphorylated amino acid residues (PAARs) on the three factors; the function of one has been validated. IPMS revealed 374, 453, and 183 novel proteins associated with the three, respectively. A significant transcription-related process network identified by Gene Ontology (GO) enrichment analysis was unique to LT. Although unidentified by IPMS, the ETS protooncogene 1, transcription factor (ETS1) was significantly overconnected to our dataset indicating its involvement in PyV processes. This result was validated by demonstrating that ETS1 coimmunoprecipitates with LT. Identification of a novel PAAR that regulates PyV replication and LT’s association with the protooncogenic Ets1 transcription factor demonstrates the value of these results for studies in PyV biology.

Choline, a quintessential quaternary ammonium compound, plays a cardinal role in several pivotal biological mechanisms, chiefly in safeguarding cell membrane integrity, orchestrating methylation reactions, and synthesizing vital neurotransmitters. This systematic review meticulously dissects the complex interplay between choline metabolism and its profound implications in oncology. The exposition is stratified into three salient dimensions: Initially, we delve into the intricacies of choline metabolism, accentuating its indispensability in cellular physiology, the enzymatic labyrinth governing its flux, and the pivotal cellular import mechanisms. Subsequently, we elucidate the contemporary comprehension of choline metabolism in the cancer paradigm, traversing its influence from inception to the intricate metamorphosis during oncogenic progression, further compounded by dysregulated enzyme activities and aberrant signaling cascades. Conclusively, we illuminate the burgeoning potential of choline-centric metabolic imaging modalities, notably magnetic resonance spectroscopy (MRS) and positron emission tomography (PET), as avant-garde tools for cancer diagnostics and therapeutic trajectory monitoring. Synoptically, the nuanced perturbations in choline metabolism in neoplastic entities unfurl critical insights, potentially heralding paradigm shifts in diagnostic and therapeutic oncological stratagems. A deeper foray into this realm is anticipated to fortify our molecular understanding and refine intervention modalities in cancer theranostics.

Accurate protein mapping on whole-tissue levels provides critical insights into diseases/therapies. Here, the authors described a novel spatial proteomics method, based on tissue compartmentalization using a 3D-printed micro-scaffold, generated thousands of protein maps across a whole-tissue slice.

Abstract Serum uric acid (SUA) may play an important role in the occurrence of colorectal cancer (CRC). This study aims to explore the association of SUA with the risk of CRC incidence by drawing data from the Kailuan Study. We prospectively examined the association between SUA and risk of CRC incidence among 93,356 Chinese. Eligible participants were divided into three groups based on their tertiles of SUA. Cox proportional hazards regression was used to calculate the hazard ratios (HRs) and 95% confidence intervals (95% CIs) of CRC. During a median follow-up of 13.02 years, 583 new-onset CRC cases were identified. After adjustments were made for confounders, participants in the highest tertiles of SUA exhibited a 1.55-fold increased risk of CRC compared with patients with the lowest SUA levels (HRT3 vs. T1 = 1.55, 95% CI: 1.09–2.30). The associations of SUA with the risk of CRC were slightly reduced but remained substantial in the competing risk analyses when treating CRC unrelated death as the competing risk event. This study found a positive association of SUA with CRC incidence. Specific prevention efforts could be focused on the population with higher levels of SUA.

Abstract Objective To estimate the effect of catheter ablation combined with left appendage occlusion in the treatment of non-valvular atrial fibrillation (NVAF) by a method of meta-analysis. Methods Pubmed, Embase, and Cochrane Library were searched for the studies about catheter ablation combined with left appendage occlusion in treating NVAF. The data analysis was performed using R 4.0.5 software. The retrieval time was from inception to May 12, 2021. Results A total of 18 published studies were identified in the meta-analysis, including 1385 participants. During the perioperative period of catheter ablation combined with left appendage occlusion in treating NVAF, the pooled incidences of pericardial effusion, major or minor bleeding events, and residual flow documented were 0.5%(95%CI 0.0002–0.0099), 1.42%(95% CI 0.00–0.04), 7.24%(95% CI 0.0447–0.0975), respectively. During the follow-up, the incidences of all-cause mortality, embolism events, and bleeding events were 0.32%(95%CI 0.0000–0.0071), 1.29%(95%CI 0.0037–0.0222), 2.07%(95% CI 0.0075–0.0339), respectively. In the follow-up period of the transesophageal echocardiography, the most complication was residual flow event with an incident rate of 10.80%(95% CI 0.054–0.1620). The maximum occurrence probability of residual flow events was 17.92% (95% CI 0.1133–0.2452). Moreover, the incident rate of NVAF recurrence was 29.23% (95% CI 0.2222–0.3623). Conclusion The meta-analysis suggests that the “one-stop” procedure is effective for those patients undergoing NVAF. However, Patients with more residual blood flow have a higher incidence of bleeding complications. More studies are warranted to verify the safety and efficacy of catheter ablation combined with left appendage occlusion in terms of the “one-stop” procedure.

Weathered crust elution-deposited rare earth ores are key strategic resources and the main source of medium and heavy rare earths. This paper summarizes the development of leaching technology of rare earth ores, compares the advantages and disadvantages of the three generations of leaching technology, and introduces the improved heap leaching technology and the new technology of the leaching–extraction integration and enhanced leaching, focusing on the leaching of weathered crust elution-deposited rare earth ores. In this paper, the development of the leaching agents is expounded, and the research status and the development trend of the composite ammonium salt leaching agent, impurity inhibition leaching agent, swelling inhibition leaching agent, and seepage-promotion leaching agent are also introduced. And this paper summarizes the leaching mechanism and the development direction of leaching agents. Moreover, the future key research direction of weathered crust elution-deposited rare earth ores is proposed, which is green, efficient, safe development and utilization.

Abstract Male breast cancer (MBC) is rare. Due to limited information, MBC has always been understudied. We conducted a retrospective population-based cohort study using data from the National Cancer Institute’s Surveillance, Epidemiology, and End Results (SEER) program. The clinical and biological features of female breast cancer (FBC) patients were compared with MBC patients. Cox regression models and competing risks analyses were used to identify risk factors associated with cancer-related survival in MBC and FBC groups. Results showed that MBC patients suffered from higher TNM stages, tumor grades, and a higher percentage of hormone receptor-positive tumors, compared with FBC patients (all p 0.05). Tumor location was an independent prognostic factor for both gender groups.

During the operation of Tokamak power system, a large number of low frequency harmonic currents with complex spectrum will be generated. Low-frequency resonance suppressor is an effective solution to suppress this low-frequency harmonic currents. The low-frequency harmonic suppression theory of low-frequency resonance suppressor is analyzed in this paper. Meanwhile, the state space equation of three-phase four-wire neutral-point-clamped rectifier is established in the LFRS. According to the mathematical model, the double closed-loop and zero sequence current control strategies are proposed to improve power factor operation on AC side and neutral point potential balance control on DC side of three-phase four-wire converter. The results show the correctness of the theoretical analysis and provide a technical reference for suppression of low-frequency harmonics of other Tokamak devices.

Changes in intracellular GTP levels are not considered as a regulatory event in RAC1 activation in live cells since total GTP levels are substantially higher than the RAC1 GTP dissociation constant determined in vitro. Here, the authors demonstrate that the availability of free GTP in live cells controls the activity of RAC1 and cell invasion.

Implementing power quality analysis of the Experimental Advanced Superconducting Tokamak (EAST) power supply is great significance to the stable operation of the power system and the future development of nuclear fusion power stations. Due to the limited channels and fixed resolution of the existing monitoring equipment in the industry, it is difficult to cover the whole requirements of EAST power quality monitoring. And customized highly personalized equipment will be very expensive. Until now, the EAST power system lacks a multi-functional, high-precision power quality monitoring system. So that it cannot solve the impact fault caused by harmonics and inter-harmonics. Thus, a set of high-precision, multi-channel and real-time harmonic monitoring system with automatic trigger storage is established in this paper. Based on the tri-spectrum line interpolation method and the optional frequency-spectrum function, the spectral resolution can be improved to 1.25Hz. Meanwhile, the horizontal comparison of the data can more accurately locate and measure the characteristics of harmonics and inter-harmonics. Finally, the measurement data of the monitoring system is compared and verified by standard sources.

BackgroundThe close association of abdominal obesity rather than general obesity with colorectal cancer (CRC) risk might be mediated by IR and inflammation, which has never been systematically explored in large-scale prospective studies.MethodsWe prospectively examined the mediation effects of the fasting triglyceride-glucose (TyG) index and C-reactive protein (CRP) on the associations of obesity (general and abdominal) with CRC risk among 93,659 participants. We used the Cox proportional hazards regression models and subgroup analyses to evaluate the hazard ratios (HRs) and 95% confidence intervals (95% CIs) of CRC. The CAUSALMED procedure was used to perform the mediation analyses.ResultsDuring 13.02 years of follow-up, a total of 586 CRC cases were verified. Male participants with general obesity and abdominal obesity had a 1.29-fold and a 1.28-fold increased risk of CRC. However, a significant association was only observed among female individuals with abdominal obesity. Both TyG index and CRP were associated with an elevated risk of CRC, and A significant interaction between the TyG index and CRP was found for the risk of CRC (P for interaction

As the exploration of ultra-deep layers and the development of geothermal resources continue, obtaining more accurate downhole parameters becomes increasingly important. Flow measurement, in particular, is a complex parameter that presents significant challenges. In order to enhance the accuracy of the turbine flow logging tool, this research focuses on optimizing the turbine flow metering structure through a range of methods. A calculation model related to the measurement process is established, and the flow field characteristics in the flowmeter are analyzed using CFD software. The sensitivity of various geometric parameters to the meter coefficient is also analyzed, and the significance of 11 influencing factors is classified and optimized using the Plackett–Burman climbing test design. The Box–Behnken design method is then used to conduct an experimental design for the significant influencing factors, and the results show that the regression model fits the actual situation well. The response surface method is used to optimize the structural parameters, and an orthogonal experimental design is carried out for the selected non-significant influencing parameters to obtain the optimal structure combination. After optimization based on the response surface method, the stability of turbine flow measurement accuracy is improved by 34.5%.

Abstract The presence of missing values (MVs) in label-free quantitative proteomics greatly reduces the completeness of data. Imputation has been widely utilized to handle MVs, and selection of the proper method is critical for the accuracy and reliability of imputation. Here we present a comparative study that evaluates the performance of seven popular imputation methods with a large-scale benchmark dataset and an immune cell dataset. Simulated MVs were incorporated into the complete part of each dataset with different combinations of MV rates and missing not at random (MNAR) rates. Normalized root mean square error (NRMSE) was applied to evaluate the accuracy of protein abundances and intergroup protein ratios after imputation. Detection of true positives (TPs) and false altered-protein discovery rate (FADR) between groups were also compared using the benchmark dataset. Furthermore, the accuracy of handling real MVs was assessed by comparing enriched pathways and signature genes of cell activation after imputing the immune cell dataset. We observed that the accuracy of imputation is primarily affected by the MNAR rate rather than the MV rate, and downstream analysis can be largely impacted by the selection of imputation methods. A random forest-based imputation method consistently outperformed other popular methods by achieving the lowest NRMSE, high amount of TPs with the average FADR

Abstract Tuberculosis is caused by the pathogenic bacterium Mycobacterium tuberculosis (Mtb) and remains the leading cause of death by infection world-wide. The Mtb genome encodes a disproportionate number of twenty cytochrome P450 enzymes, of which the essential enzyme cytochrome P450 121A1 (CYP121A1) remains a target of drug design efforts. CYP121A1 mediates a phenol coupling reaction of the tyrosine dipeptide cyclo-L-Tyr-L-Tyr (cYY). In this work, a structure and function investigation of dimerization was performed as an overlooked feature of CYP121A1 function. This investigation showed that CYP121A1 dimers form via intermolecular contacts on the distal surface and are mediated by a network of solvent-exposed hydrophobic residues. Disruption of CYP121A1 dimers by site-directed mutagenesis leads to a partial loss of specificity for cYY, resulting in an approximate 75% decrease in catalysis. 19F labeling and nuclear magnetic resonance of the enzyme FG-loop was also combined with protein docking to develop a working model of a functional CYP121A1 dimer. The results obtained suggest that participation of a homodimer interface in substrate selectivity represents a novel paradigm of substrate binding in CYPs, while also providing important mechanistic insight regarding a relevant drug target in the development of novel anti-tuberculosis agents.

Abstract Background Competing risk method has not been used in a large-scale prospective study to investigate whether increased levels of high-sensitivity C-reactive protein (hs-CRP) elevate the risk of primary liver cancer (PLC). Our study aims to prospectively investigate the relationship between hs-CRP and new-onset PLC. Methods and results Ninety-five thousand seven hundred fifty-nine participants without the diagnosis of PLC, and who had their demographic characteristics and biochemical parameters recorded, were analyzed from the Kailuan Cohort study. Cox proportional hazards regression models and competing risk regression models were used to evaluate the hazard ratios (HRs) and 95% confidence intervals (95% CIs) of PLC. During a median follow-up of 11.07 years, 357 incidental PLC cases were identified over a total of 1,035,039 person-years. The multivariable HRs (95%CI) for the association of hs-CRP of 1–3 mg/L group and hs-CRP>3 mg/L with PLC were 1.07(0.82 ~ 1.38), 1.51(1.15 ~ 1.98) in a Cox proportional hazard regression analysis adjusted for other potential confounders. In the cause-specific hazard model, the multivariable HRs (95%CI) for the association of hs-CRP of 1–3 mg/L group and hs-CRP>3 mg/L with PLC were 1.06(0.81 ~ 1.40), 1.50(1.14 ~ 1.99). Similar results were also observed in the sub-distribution hazard function model with corresponding multivariate HRs (95%CI) of 1.05(0.80 ~ 1.40), 1.49(1.13 ~ 1.98) in hs-CRP of 1–3 mg/L group and hs-CRP>3 mg/L group, respectively. Conclusions This prospective study found a significant association of higher levels of hs-CRP with new-onset PLC. The main clinical implications would be an increased awareness of hs-CRP and its correlation to the risk of PLC. This study should be a steppingstone to further research on chronic inflammation and PLC. Trial registration Registration number: ChiCTR–TNRC–11001489 .

Abstract Background For most patients, pancreatic adenocarcinoma responds poorly to treatment, and novel therapeutic approaches are needed. Standard-of-care paclitaxel (PTX), combined with birinapant (BRP), a bivalent mimetic of the apoptosis antagonist SMAC (second mitochondria-derived activator of caspases), exerts synergistic killing of PANC-1 human pancreatic adenocarcinoma cells. Methods To investigate potential mechanisms underlying this synergistic pharmacodynamic interaction, data capturing PANC-1 cell growth, apoptosis kinetics, and cell cycle distribution were integrated with high-quality IonStar-generated proteomic data capturing changes in the relative abundance of more than 3300 proteins as the cells responded to the two drugs, alone and combined. Results PTX alone (15 nM) elicited dose-dependent G2/M-phase arrest and cellular polyploidy. Combined BRP/PTX (150/15 nM) reduced G2/M by 35% and polyploid cells by 45%, and increased apoptosis by 20%. Whereas BRP or PTX alone produced no change in the pro-apoptotic protein pJNK, and a slight increase in the anti-apoptotic protein Bcl2, the drug combination increased pJNK and decreased Bcl2 significantly compared to the vehicle control. A multi-scale, mechanism-based mathematical model was developed to investigate integrated birinapant/paclitaxel effects on temporal profiles of key proteins involved in kinetics of cell growth, death, and cell cycle distribution. Conclusions The model, consistent with the observed reduction in the Bcl2/BAX ratio, suggests that BRP-induced apoptosis of mitotically-arrested cells is a major contributor to the synergy between BRP and PTX. Coupling proteomic and cellular response profiles with multi-scale pharmacodynamic modeling provides a quantitative mechanistic framework for evaluating pharmacodynamically-based drug-drug interactions in combination chemotherapy, and could potentially guide the development of promising drug regimens.

The past few years have witnessed enormous progresses in the development of antibody-drug conjugates (ADCs). Consequently, comprehensive analysis of ADCs in biological systems is critical in supporting discovery, development and evaluation of these agents. Liquid chromatography-mass spectrometry (LC-MS) has emerged as a promising and versatile tool for ADC analysis across a wide range of scenarios, owing to its multiplexing ability, rapid method development, as well as the capability of analyzing a variety of targets ranging from small-molecule payloads to the intact protein with a high, molecular resolution. However, despite this tremendous potential, challenges persist due to the high complexity in both the ADC molecules and the related biological systems. This review summarizes the up-to-date LC-MS-based strategies in ADC analysis and discusses the challenges and opportunities in this rapidly-evolving field.

A Crumbler® rotary shear system was recently developed to process fuel-grade woodchips into feedstocks having more uniform particle sizes for improved flowability and higher thermochemical output yield than a traditional hammer mill. It represents a significant innovation in the state of the art of biomass comminution equipment. However, the milling unit has experienced significant abrasive wear of the feeding teeth and cutters when processing hard and dusty feedstocks, such as logging residue and corn stover. Here, we present initial simulation results from a finite-element stress analysis of the rotary shear, which is used to investigate the dynamics of interaction between the cutters and woodchips. This is the first step for optimizing the cutter design to improve the system lifetime and processing efficiency, thus reducing downtime and improving overall productivity.

In order to explore the capture of two types of particles with different refractive-indexes with focused partially coherent Lommel-Gaussian beam (PCLGB), we numerically derived the expressions of the intensity, and its distribution is also simulated. We found that the focused PCLGB is able to capture two high refractive-index particles at different positions on the focal plane and a low refractive-index particle at the focus, respectively. when the orbital angular momentum (OAM)quantum number, lens focal length, asymmetry parameter decreased, and the spatial correlation length and beam waist increased, the transverse gradient force of the focused PCLGB increased; when the OAM quantum number, lens focal length, asymmetry parameter, spatial correlation length decreased and the beam waist increased, the axial gradient force and scattering force of the focused PCLGB increased. We can choose the optimum optical and lens parameters, a large range and stable trapping can be achieved. The obtained results have certain reference value for the focused PCLGB applied in micromanipulation technology and biotechnology.

Age-related macular degeneration (AMD) is the leading cause of blindness in elderly people, with limited treatment options available for most patients. AMD involves the death of retinal pigment epithelium (RPE) and photoreceptor cells, with mitochondria dysfunction being a critical early event. In the current study, we utilized our unique resource of human donor RPE graded for AMD presence and severity to investigate proteome-wide dysregulation involved in early AMD. Organelle-enriched fractions of RPE were isolated from donors with early AMD (n = 45) and healthy age-matched controls (n = 32) and were analyzed by UHR-IonStar, an integrated proteomics platform enabling reliable and in-depth proteomic quantification in large cohorts. A total of 5941 proteins were quantified with excellent analytical reproducibility, and with further informatics analysis, many biological functions and pathways were found to be significantly dysregulated in donor RPE samples with early AMD. Several of these directly pinpointed changes in mitochondrial functions, e.g., translation, ATP metabolic process, lipid homeostasis, and oxidative stress. These novel findings highlighted the value of our proteomics investigation by allowing a better understanding of the molecular mechanisms underlying early AMD onset and facilitating both treatment development and biomarker discovery.

Proteomics analysis of circulating exosomes derived from cancer cells represents a promising approach to the elucidation of cell–cell communication and the discovery of putative biomarker candidates for cancer diagnosis and treatment. Nonetheless, the proteome of exosomes derived from cell lines with different metastatic capabilities still warrants further investigation. Here, we present a comprehensive quantitative proteomics investigation of exosomes isolated from immortalized mammary epithelial cells and matched tumor lines with different metastatic potentials in an attempt to discover exosome markers specific to breast cancer (BC) metastasis. A total of 2135 unique proteins were quantified with a high confidence level from 20 isolated exosome samples, including 94 of the TOP 100 exosome markers archived by ExoCarta. Moreover, 348 altered proteins were observed, among which several metastasis-specific markers, including cathepsin W (CATW), magnesium transporter MRS2 (MRS2), syntenin-2 (SDCB2), reticulon-4 (RTN), and UV excision repair protein RAD23 homolog (RAD23B), were also identified. Notably, the abundance of these metastasis-specific markers corresponds well with the overall survival of BC patients in clinical settings. Together, these data provide a valuable dataset for BC exosome proteomics investigation and prominently facilitate the elucidation of the molecular mechanisms underlying primary tumor development and progression.

Optical fiber sensors are used for partial discharge detection in many applications due their advantage of strong anti-electromagnetic interference capability. Multi-point distributed partial discharge detection and location are important for electrical equipment. In this paper, a distributed partial discharge location and detection scheme based on optical fiber Rayleigh backscattering light interference is experimentally demonstrated. At the same time, the location and extraction algorithm is used to demodulate the partial discharge signal; furthermore, the high-pass filter is used to reduce the system low-frequency noise and environment noise. It is clear that the proposed system can detect a partial discharge signal generated by metal needle sensitivity, and the detectable frequency range is 0–2.5 kHz. We carried out 10 locating tests for two sensing units, the experimental results show that the maximum location error is 1.0 m, and the maximum standard deviation is 0.3795. At same time, the signal-to-noise ratio (SNR) of sensing unit 1 and sensing unit 2 are greatly improved after demodulation, which are 39.7 and 38.8, respectively. This provides a new method for a multipoint-distributed optical fiber sensor used for detecting and locating a long-distance electrical equipment partial discharge signal.

Boron-containing compounds are one of the lubricant additive options due to their suitable properties for additives and have been used as commercial lubricant additives. In the present study, the impact of a boron-containing lubricant oil additive, AR9100 (BR), on Pd/Rh-based three-way catalyst (TWC) performance is investigated, and the results are compared with the baseline no-additive (NA) case and the industry standard zinc dialkyl-dithiophosphate (ZDDP) results. Accelerated engine aging is performed using a genset to expose the catalysts to lubricant additives at high temperatures. All aged TWC samples are investigated for reactivity in a bench-flow reactor and characterized using a variety of analytical techniques. Compared with the no-additive case, the temperatures of 90% conversion (T90) of NO, CO, C3H6, and C3H8 for the ZDDP-aged TWC sample increased by 34, 30, 37, and 48 °C. However, the T90 of all gas species for the BR-aged TWC sample are similar to the NA-aged TWC sample. Additionally, a significant decrease in water–gas shift reactivity and oxygen storage capacity is observed in the ZDDP-aged sample, but not in the BR-aged sample. Inductively coupled plasma-optical emission spectrometry (ICP-OES) analysis and electron probe microanalysis (EPMA) maps of accelerated engine aging samples show the presence of phosphorus and boron in ZDDP- and BR-aged TWC samples, respectively. However, no boron-related peaks are observed in the X-ray diffraction (XRD) pattern of the BR-aged TWC sample, which may exist in the form of an amorphous phase.

A novel type of superimposed Hermite-Gaussian correlated Schell-model (SHGCSM) laser beam is first represented in terms of theory and then produced experimentally. Similar to a Hermite-Gaussian correlated Schell-model (HGCSM) beam, the SHGCSM beam demonstrates self-splitting features when it propagates in free space, over time the primary single beam spot that is initially seen gradually develops into four or two beam spots when it is in the far-field. The SHGCSM beam splits itself faster than the HGCSM beam when the other beam parameters are fixed, which has lower intensity at the center of beam at an intermediate distance. The four or two spots are more independent with each other, which can be used in attacking multiple targets. Compared with the propagation M2-factor of the HGCSM [Opt. Express 23, 10 (2015)], it has a lower propagation M2-factor in the non-Kolmogorov turbulence. The SHGCSM beam is unaltered to a lesser extent by turbulence compared with a HGCSM beam, which is beneficial for studies on atmospheric optical communications.

The mitochondria-associated endoplasmic reticulum (ER) membrane (MAM) is the physical contact site between the ER and the mitochondria and plays a vital role in the regulation of calcium signaling, bioenergetics, and inflammation. Disturbances in these processes and dysregulation of the ER and mitochondrial homeostasis contribute to the pathogenesis of diabetic retinopathy (DR). However, few studies have examined the impact of diabetes on the retinal MAM and its implication in DR pathogenesis. In the present study, we investigated the proteomic changes in retinal MAM from Long Evans rats with streptozotocin-induced long-term Type 1 diabetes. Furthermore, we performed in-depth bioinformatic analysis to identify key MAM proteins and pathways that are potentially implicated in retinal inflammation, angiogenesis, and neurodegeneration. A total of 2664 unique proteins were quantified using IonStar proteomics-pipeline in rat retinal MAM, among which 179 proteins showed significant changes in diabetes. Functional annotation revealed that the 179 proteins are involved in important biological processes such as cell survival, inflammatory response, and cellular maintenance, as well as multiple disease-relevant signaling pathways, e.g., integrin signaling, leukocyte extravasation, PPAR, PTEN, and RhoGDI signaling. Our study provides comprehensive information on MAM protein changes in diabetic retinas, which is helpful for understanding the mechanisms of metabolic dysfunction and retinal cell injury in DR.

Recently, the devices commonly used for interaction with a virtual reality (VR) environment include game controllers, data gloves, and motion tracking systems. However, these devices may limit the immersive experience or cause inconvenience, especially for patients with limb paralysis. This paper proposes a new nonmanual human-computer interface (HCI) based on a single-channel electrooculogram (EOG) signal and enables real-time interactions with the VR environment. The graphical user interface of the EOG-based HCI in VR includes several buttons flashing in a random order. The user needs to blink in synchrony with the corresponding button's flashes to issue a command, while the algorithm detects the eye blinks from the EOG signal and determines the users' target button. Furthermore, with the EOG-based HCI, we developed a music-on-demand system in the VR environment. By blinking, users can search and select target songs in the music library, play the selected songs, switch to the next song, and delete songs from the list. Ten healthy subjects and five patients with spinal cord injuries (SCIs) participated in online experiments. The experimental results demonstrated the effectiveness of the EOG-based HCI as a new method for interacting with the VR environment. Furthermore, the music-on-demand system can be used for entertainment not only by healthy people but also by SCI patients with limb paralysis.

Background & Aims: Most targeted therapies against cancer are designed to block growth factor–stimulated oncogenic growth. However, response rates are low, and resistance to therapy is high. One mechanism might relate to the ability of tumor cells to induce growth factor–independent proliferation (GFIP). This project aims to understand how (1) cancer cells preferentially derive a major growth advantage by using critical metabolic products of glucose, such as phosphoenolpyruvate (PEP), to drive proliferation and (2) esophageal squamous cell carcinoma (ESCC) cells, but not esophageal adenocarcinoma cells, can induce GFIP by using glycolysis to activate phosphohistidine (poHis)-mediated signaling through focal adhesion kinase (FAK). Methods: The hypothesis to be tested is that ESCC GFIP induced by glucose is facilitated by PEP-mediated histidine phosphorylation (poHis) of FAK, leading to the possibility that ESCC progression can be targeted by blocking poHis signaling. Biochemical, molecular biological, and in vivo experiments including bromodeoxyuridine/5-ethynyl-2′-deoxyuridine labeling, radioisotope tracing, CRISPR gene editing, and analysis of signaling gene sets in human cancer tissues and xenograft models were performed to define the mechanisms underlying ESCC GFIP. Results: Glucose promotes growth factor–independent DNA replication and accumulation of PEP in ESCC cells. PEP is the direct phospho-donor to poHis58-FAK within a known “HG” motif for histidine phosphorylation. Glucose-induced poHis58 promotes growth factor–independent FAK-mediated proliferation. Furthermore, glucose activates phosphatidylinositol-3′-kinase/AKT via poHis58-FAK signaling. Non-phosphorylatable His58A-FAK reduces xenograft growth. Conclusions: Glucose induces ESCC, but not esophageal adenocarcinoma GFIP via PEP-His58-FAK-AKT signaling. ESCC progression is controlled by actionable growth factor–independent, glucose-induced pathways that regulate proliferation through novel histidine phosphorylation of FAK. Keywords: Esophageal Cancer, Glucose Metabolism, Growth Factors, Cell Adhesion Molecules, Cell Signaling

Coordinated migration of B cells within and between secondary lymphoid tissues is required for robust antibody responses to infection or vaccination. Secondary lymphoid tissues normally expose B cells to a low O2 (hypoxic) environment. Recently, we have shown that human B cell migration is modulated by an O2-dependent molecular switch, centrally controlled by the hypoxia-induced (transcription) factor-1α (HIF1A), which can be disrupted by the immunosuppressive calcineurin inhibitor, cyclosporine A (CyA). However, the mechanisms by which low O2 environments attenuate B cell migration remain poorly defined. Proteomics analysis has linked CXCR4 chemokine receptor signaling to cytoskeletal rearrangement. We now hypothesize that the pathways linking the O2 sensing molecular switch to chemokine receptor signaling and cytoskeletal rearrangement would likely contain phosphorylation events, which are typically missed in traditional transcriptomic and/or proteomic analyses. Hence, we have performed a comprehensive phosphoproteomics analysis of human B cells treated with CyA after engagement of the chemokine receptor CXCR4 with CXCL12. Statistical analysis of the separate and synergistic effects of CyA and CXCL12 revealed 116 proteins whose abundance is driven by a synergistic interaction between CyA and CXCL12. Further, we used our previously described algorithm BONITA to reveal a critical role for Lymphocyte Specific Protein 1 (LSP1) in cytoskeletal rearrangement. LSP1 is known to modulate neutrophil migration. Validating these modeling results, we show experimentally that LSP1 levels in B cells increase with low O2 exposure, and CyA treatment results in decreased LSP1 protein levels. This correlates with the increased chemotactic activity observed after CyA treatment. Lastly, we directly link LSP1 levels to chemotactic capacity, as shRNA knock-down of LSP1 results in significantly increased B cell chemotaxis at low O2 levels. These results directly link CyA to LSP1-dependent cytoskeletal regulation, demonstrating a previously unrecognized mechanism by which CyA modulates human B cell migration. Data are available via ProteomeXchange with identifier PXD036167.

Age-related macular degeneration (AMD), the leading cause of blindness in the elderly, is characterized by the death of retinal pigment epithelium (RPE) and photoreceptors. One of the risk factors associated with developing AMD is the single nucleotide polymorphism (SNP) found within the gene encoding complement factor H (CFH). Part of the innate immune system, CFH inhibits alternative complement pathway activation. Multi-protein complexes called inflammasomes also play a role in the innate immune response. Previous studies reported that inflammasome activation may contribute to AMD pathology. In this study, we used primary human adult RPE cell cultures from multiple donors, with and without AMD, that were genotyped for the Y402H CFH risk allele. We found complement and inflammasome-related genes and proteins at basal levels in RPE tissue and cell cultures. Additionally, treatment with rotenone, bafilomycin A, and ATP led to inflammasome activation. Overall, the response to priming and activation was similar, irrespective of disease state or CFH genotype. While these data show that the inflammasome is present and active in RPE, our results suggest that inflammasome activation may not contribute to early AMD pathology.

A global, quantitative proteomics/systems-biology analysis of the selective pharmacological inhibition of phosphodiesterase-4D (PDE4D) revealed the differential regulation of pathways associated with neuroplasticity in memory-associated brain regions. Subtype selective inhibitors of PDE4D bind in an allosteric site that differs between mice and humans in a single amino acid (tyrosine vs. phenylalanine, respectively). Therefore to study selective inhibition of PDE4D by BPN14770, a subtype selective allosteric inhibitor of PDE4D, we utilized a line of mice in which the PDE4D gene had been humanized by mutating the critical tyrosine to phenylalanine. Relatively low doses of BPN14770 were effective at reversing scopolamine-induced memory and cognitive deficits in humanized PDE4D mice. Inhibition of PDE4D alters the expression of protein kinase A (PKA), Sirt1, Akt, and Bcl-2/Bax which are components of signaling pathways for regulating endocrine response, stress resistance, neuronal autophagy, and apoptosis. Treatment with a series of antagonists, such as H89, sirtinol, and MK-2206, reversed the effect of BPN14770 as shown by behavioral tests and immunoblot analysis. These findings suggest that inhibition of PDE4D enhances signaling through the cAMP-PKA-SIRT1-Akt -Bcl-2/Bax pathway and thereby may provide therapeutic benefit in neurocognitive disorders.

Bronchoalveolar lavage of the epithelial lining fluid (BALF) can sample the profound changes in the airway lumen milieu prevalent in chronic obstructive pulmonary disease (COPD). We compared the BALF proteome of ex-smokers with moderate COPD who are not in exacerbation status to non-smoking healthy control subjects and applied proteome-scale translational bioinformatics approaches to identify potential therapeutic protein targets and drugs that modulate these proteins for the treatment of COPD. Proteomic profiles of BALF were obtained from (1) never-smoker control subjects with normal lung function (n = 10) or (2) individuals with stable moderate (GOLD stage 2, FEV1 50–80% predicted, FEV1/FVC < 0.70) COPD who were ex-smokers for at least 1 year (n = 10). After identifying potential crucial hub proteins, drug–proteome interaction signatures were ranked by the computational analysis of novel drug opportunities (CANDO) platform for multiscale therapeutic discovery to identify potentially repurposable drugs. Subsequently, a literature-based knowledge graph was utilized to rank combinations of drugs that most likely ameliorate inflammatory processes. Proteomic network analysis demonstrated that 233 of the >1800 proteins identified in the BALF were significantly differentially expressed in COPD versus control. Functional annotation of the differentially expressed proteins was used to detail canonical pathways containing the differential expressed proteins. Topological network analysis demonstrated that four putative proteins act as central node proteins in COPD. The drugs with the most similar interaction signatures to approved COPD drugs were extracted with the CANDO platform. The drugs identified using CANDO were subsequently analyzed using a knowledge-based technique to determine an optimal two-drug combination that had the most appropriate effect on the central node proteins. Network analysis of the BALF proteome identified critical targets that have critical roles in modulating COPD pathogenesis, for which we identified several drugs that could be repurposed to treat COPD using a multiscale shotgun drug discovery approach.

Objectives Gallstone disease (GSD) can be caused by various health and clinical factors such as obesity, dyslipidaemia and an unhealthy diet, all of which are associated with higher high-sensitivity C reactive protein (hs-CRP) concentrations. Whether hs-CRP represents an independent risk factor for GSD is still unclear. We prospectively investigated hs-CRP in relation to the occurrence of GSD based on the Kailuan study.Study design Prospective cohort study.Setting The Kailuan cohort study was conducted in Tangshan City in northern China.Participants 95 319 participants who were free from GSD were recruited in this study. Epidemiological data, anthropometric parameters and biochemical data of participants were collected.Primary and secondary outcome measures Cox proportional hazards regression models were used to evaluate the association between hs-CRP concentrations and the risk of GSD after adjustments for potential confounders.Results During the mean 7.58 years of follow-up among 95 319 participants, 4205 participants were identified as newly diagnosed with GSD or having undergone cholecystectomy for cholelithiasis. Compared with the hs-CRP3 mg/L group, respectively. The multivariate model which included hs-CRP not only had a better line of fitness but also had better predictive values to help identify new cases of GSD during follow-up.Conclusion Elevated hs-CRP concentration is an independent risk factor for new-onset GSD among the Chinese population.Trial registration number ChiCTR-TNC-11001489.

Age-related macular degeneration (AMD) is the leading cause of blindness among the elderly. Currently, there are no treatments for dry AMD, which is characterized by the death of retinal pigment epithelium (RPE) and photoreceptors. Reports from human donors with AMD suggest that RPE mitochondrial defects are a key event in AMD pathology. Thus, the most effective strategy for treating dry AMD is to identify compounds that enhance mitochondrial function and subsequently, preserve the RPE. In this study, primary cultures of RPE from human donors with (n = 20) or without (n = 8) AMD were used to evaluate compounds that are designed to protect mitochondria from oxidative damage (N-acetyl-l-cysteine; NAC), remove damaged mitochondria (Rapamycin), increase mitochondrial biogenesis (Pyrroloquinoline quinone; PQQ), and improve oxidative phosphorylation (Nicotinamide mononucleotide, NMN). Mitochondrial function measured after drug treatments showed an AMD-dependent response; only RPE from donors with AMD showed improvements. All four drugs caused a significant increase in maximal respiration (p

Gemcitabine combined with birinapant, an inhibitor of apoptosis protein antagonist, acts synergistically to reduce pancreatic cancer cell proliferation. A large‐scale proteomics dataset provided rich time‐series data on proteome‐level changes that reflect the underlying biological system and mechanisms of action of these drugs. A multiscale network model was developed to link the signaling pathways of cell cycle regulation, DNA damage response, DNA repair, apoptosis, nuclear factor‐kappa β (NF‐κβ), and mitogen‐activated protein kinase (MAPK)‐p38 to cell cycle progression, proliferation, and death. After validating the network model under different conditions, the Sobol Sensitivity Analysis was applied to identify promising targets to enhance gemcitabine efficacy. The effects of p53 silencing and combining curcumin with gemcitabine were also tested with the developed model. Merging proteomics analysis with systems modeling facilitates the characterization of quantitative relations among relevant signaling pathways in drug action and resistance, and such multiscale network models could be applied for prediction of combination efficacy and target selection.

In the present study, two industry primary and secondary zinc dialkyldithiophosphate standards, ZDDP1 and ZDDP2, respectively, are evaluated for their impact on the performance of Pd-based three-way catalyst and bench-marked against two mixed lubricant additives formed from either ZDDP1 or ZDDP2 with a second-generation oil-miscible phosphoric-containing ionic liquid (IL). The three-way catalysts (TWCs) are exposed to the lubricant additives in an engine bench under four different scenarios: a base case with no additive (NA), ZDDP1, IL+ZDDP1, ZDDP2, and IL+ZDDP2. The engine-aged TWC samples are characterized through a variety of analytical techniques, including evaluation of catalyst reactivity in a bench-flow reactor. With respect to the water–gas shift reaction and the oxygen storage capacity, the ZDDP2- and IL+ZDDP2-aged TWC samples are more degraded than the ZDDP1- and IL+ZDDP1-aged TWC samples. X-ray diffraction (XRD) patterns indicate that phosphorus in the form of CePO4 was found to be present in the washcoat of all TWC samples, with the highest amount found in the ZDDP2-aged TWC sample. The results obtained from XRD are further confirmed by those from inductively coupled plasma-optical emission spectroscopy (ICP-OES), which show that more phosphorus is detected in the washcoat of ZDDP2- and IL+ZDDP2-aged TWC samples than in the ZDDP1- and IL+ZDDP1-aged TWC samples.

Abstract Ionic liquids (ILs) have recently been developed as a novel class of lubricant anti-wear (AW) additives, but the formation mechanism of their wear protective tribofilms is not yet well understood. Unlike the conventional metal-containing AW additives that self-react to grow a tribofilm, the metal-free ILs require a supplier of metal cations in the tribofilm growth. The two apparent sources of metal cations are the contact surface and the wear debris, and the latter contains important ‘historical’ interface information but often is overlooked. We correlated the morphological and compositional characteristics of tribofilms and wear debris from an IL-lubricated steel–steel contact. A complete multi-step formation mechanism is proposed for the tribofilm of metal-free AW additives, including direct tribochemical reactions between the metallic contact surface with oxygen to form an oxide interlayer, wear debris generation and breakdown, tribofilm growth via mechanical deposition, chemical deposition, and oxygen diffusion.

Abstract The mitochondria-associated ER membrane (MAM) plays a critical role in cellular energetics and calcium homeostasis; however, how MAM is affected under diabetic condition remains elusive. This study presented a comprehensive proteome profiling of isolated brain MAM from long-term type 2 diabetic mice vs. non-diabetic controls. MAM protein was extracted efficiently by a surfactant-aided precipitation/on-pellet digestion (SOD) method, and MAM proteome was quantified by an ion-current-based MS1 method combined with nanoLC-MS/MS. A total of 1,313 non-redundant proteins of MAM were identified, among which 144 proteins were found significantly altered by diabetes. In-depth IPA analysis identified multiple disease-relevant signaling pathways associated with the MAM proteome changes in diabetes, most significantly the unfolded protein response (UPR), p53, hypoxia-related transcription factors, and methyl CpG binding protein 2. Using immunofluorescence labeling we confirmed the activation of three UPR branches and increased ERp29 and calreticulin in diabetic retinas. Moreover, we found GRP75, a key MAM tethering protein, was drastically reduced by long-term diabetes. In vitro, acute high glucose treatment reduces ER-mitochondrial contact in retinal endothelial cells. This study provides first insight into the significant alterations in MAM proteome associated with activation of the UPR in diabetes, which may serve as novel benchmarks for the future studies of diabetic complications.

Summary: In a porcine model of brief ischemia leading to reversible stunning in the absence of tissue necrosis, we demonstrated delayed release of cardiac troponin I (cTnI) that exceeded the 99th percentile for normal animals 60 min after reperfusion and rose to readily detectable levels 24 h later. Although tissue analysis at 60 min showed no evidence of infarction, TUNEL staining demonstrated isolated myocytes undergoing apoptosis, which was absent after 24 h. These results demonstrate that cTnI elevations occur after ischemia of a duration that is insufficient to produce myocyte necrosis and reflect myocyte injury associated with apoptosis in the absence of pathological evidence of infarction. Key Words: cardiac troponin I, cardiomyocyte apoptosis, myocardial ischemia, myocardial stunning

Regulators of G-protein Signaling are a conserved family of proteins required in various biological processes including cell differentiation. We previously demonstrated that Rgs12 is essential for osteoclast differentiation and its deletion in vivo protected mice against pathological bone loss. To characterize its mechanism in osteoclastogenesis, we selectively deleted Rgs12 in C57BL/6J mice targeting osteoclast precursors using LyzM-driven Cre mice or overexpressed Rgs12 in RAW264.7 cells. Rgs12 deletion in vivo led to an osteopetrotic phenotype evidenced by increased trabecular bone, decreased osteoclast number and activity but no change in osteoblast number and bone formation. Rgs12 overexpression increased osteoclast number and size, and bone resorption activity. Proteomics analysis of Rgs12-depleted osteoclasts identified an upregulation of antioxidant enzymes under the transcriptional regulation of Nrf2, the master regulator of oxidative stress. We confirmed an increase of Nrf2 activity and impaired reactive oxygen species production in Rgs12-deficient cells. Conversely, Rgs12 overexpression suppressed Nrf2 through a mechanism dependent on the 26S proteasome, and promoted RANKL-induced phosphorylation of ERK1/2 and NFκB, which was abrogated by antioxidant treatment. Our study therefore identified a novel role of Rgs12 in regulating Nrf2, thereby controlling cellular redox state and osteoclast differentiation.

ABSTRACT In Trypanosoma brucei and related kinetoplastid parasites, transcription of protein coding genes is largely unregulated. Rather, mRNA binding proteins, which impact processes such as transcript stability and translation efficiency, are the predominant regulators of gene expression. Arginine methylation is a posttranslational modification that preferentially targets RNA binding proteins and is, therefore, likely to have a substantial impact on T. brucei biology. The data presented here demonstrate that cells depleted of T. brucei PRMT1 (TbPRMT1), a major type I protein arginine methyltransferase, exhibit decreased virulence in an animal model. To understand the basis of this phenotype, quantitative global proteomics was employed to measure protein steady-state levels in cells lacking TbPRMT1. The approach revealed striking changes in proteins involved in energy metabolism. Most prominent were a decrease in glycolytic enzyme abundance and an increase in proline degradation pathway components, changes that resemble the metabolic remodeling that occurs during T. brucei life cycle progression. The work describes several RNA binding proteins whose association with mRNA was altered in TbPRMT1-depleted cells, and a large number of TbPRMT1-interacting proteins, thereby highlighting potential TbPRMT1 substrates. Many proteins involved in the T. brucei starvation stress response were found to interact with TbPRMT1, prompting analysis of the response of TbPRMT1-depleted cells to nutrient deprivation. Indeed, depletion of TbPRMT1 strongly hinders the ability of T. brucei to form cytoplasmic mRNA granules under starvation conditions. Finally, this work shows that TbPRMT1 itself binds nucleic acids in vitro and in vivo, a feature completely novel to protein arginine methyltransferases. IMPORTANCE Trypanosoma brucei infection causes human African trypanosomiasis, also known as sleeping sickness, a disease with a nearly 100% fatality rate when untreated. Current drugs are expensive, toxic, and highly impractical to administer, prompting the community to explore various unique aspects of T. brucei biology in search of better treatments. In this study, we identified the protein arginine methyltransferase (PRMT), TbPRMT1, as a factor that modulates numerous aspects of T. brucei biology. These include glycolysis and life cycle progression signaling, both of which are being intensely researched toward identification of potential drug targets. Our data will aid research in those fields. Furthermore, we demonstrate for the first time a direct association of a PRMT with nucleic acids, a finding we believe could translate to other organisms, including humans, thereby impacting research in fields as distant as human cancer biology and immune response modulation.