DeKinomics pulse-chases kinase functions in living cells.

Cellular context is crucial for understanding the complex and dynamic kinase functions in health and disease. Systematic dissection of kinase-mediated cellular processes requires rapid and precise stimulation ('pulse') of a kinase of interest, as well as global and in-depth characterization ('chase') of the perturbed proteome under living conditions. Here we developed an optogenetic 'pulse-chase' strategy, termed decaging kinase coupled proteomics (DeKinomics), for proteome-wide profiling of kinase-driven phosphorylation at second-timescale in living cells. We took advantage of the 'gain-of-function' feature of DeKinomics to identify direct kinase substrates and further portrayed the global phosphorylation of understudied receptor tyrosine kinases under native cellular settings. DeKinomics offered a general activation-based strategy to study kinase functions with high specificity and temporal resolution under living conditions.

Spatial Proteomic Profiling of Colorectal Cancer Revealed Its Tumor Microenvironment Heterogeneity.

Colorectal cancer is a predominant malignancy with a second mortality worldwide. Despite its prevalence, therapeutic options remain constrained and surgical operation is still the most useful therapy. In this regard, a comprehensive spatially resolved quantitative proteome atlas was constructed to explore the functional proteomic landscape of colorectal cancer. This strategy integrates histopathological analysis, laser capture microdissection, and proteomics. Spatial proteome profiling of 200 tissue section samples facilitated by the fully integrated sample preparation technology SISPROT enabled the identification of more than 4000 proteins on the Orbitrap Exploris 240 from 2 mm2 × 10 µm tissue sections. Compared with normal adjacent tissues, we identified a spectrum of cancer-associated proteins and dysregulated pathways across various regions of colorectal cancer including ascending colon, transverse colon, descending colon, sigmoid colon, and rectum. Additionally, we conducted proteomic analysis on tumoral epithelial cells and paracancerous epithelium from early to advanced stages in hallmark rectum cancer and sigmoid colon cancer. Bioinformatics analysis revealed functional proteins and cell-type signatures associated with different regions of colorectal tumors, suggesting potential clinical implications. Overall, this study provides a comprehensive spatially resolved functional proteome landscape of colorectal cancer, serving as a valuable resource for exploring potential biomarkers and therapeutic targets.

Desloratadine alleviates ALS-like pathology in hSOD1G93A mice via targeting 5HTR2A on activated spinal astrocytes.

Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with progressive loss of motor neurons in the spinal cord, cerebral cortex and brain stem. ALS is characterized by gradual muscle atrophy and dyskinesia. The limited knowledge on the pathology of ALS has impeded the development of therapeutics for the disease. Previous studies have shown that autophagy and astrocyte-mediated neuroinflammation are involved in the pathogenesis of ALS, while 5HTR2A participates in the early stage of astrocyte activation, and 5HTR2A antagonism may suppress astrocyte activation. In this study, we evaluated the therapeutic effects of desloratadine (DLT), a selective 5HTR2A antagonist, in human SOD1G93A (hSOD1G93A) ALS model mice, and elucidated the underlying mechanisms. HSOD1G93A mice were administered DLT (20 mg·kg-1·d-1, i.g.) from the age of 8 weeks for 10 weeks or until death. ALS onset time and lifespan were determined using rotarod and righting reflex tests, respectively. We found that astrocyte activation accompanying with serotonin receptor 2 A (5HTR2A) upregulation in the spinal cord was tightly associated with ALS-like pathology, which was effectively attenuated by DLT administration. We showed that DLT administration significantly delayed ALS symptom onset time, prolonged lifespan and ameliorated movement disorders, gastrocnemius injury and spinal motor neuronal loss in hSOD1G93A mice. Spinal cord-specific knockdown of 5HTR2A by intrathecal injection of adeno-associated virus9 (AAV9)-si-5Htr2a also ameliorated ALS pathology in hSOD1G93A mice, and occluded the therapeutic effects of DLT administration. Furthermore, we demonstrated that DLT administration promoted autophagy to reduce mutant hSOD1 levels through 5HTR2A/cAMP/AMPK pathway, suppressed oxidative stress through 5HTR2A/cAMP/AMPK/Nrf2-HO-1/NQO-1 pathway, and inhibited astrocyte neuroinflammation through 5HTR2A/cAMP/AMPK/NF-κB/NLRP3 pathway in the spinal cord of hSOD1G93A mice. In summary, 5HTR2A antagonism shows promise as a therapeutic strategy for ALS, highlighting the potential of DLT in the treatment of the disease. DLT as a 5HTR2A antagonist effectively promoted autophagy to reduce mutant hSOD1 level through 5HTR2A/cAMP/AMPK pathway, suppressed oxidative stress through 5HTR2A/cAMP/AMPK/Nrf2-HO-1/NQO-1 pathway, and inhibited astrocytic neuroinflammation through 5HTR2A/cAMP/AMPK/NF-κB/NLRP3 pathway in the spinal cord of hSOD1G93A mice.

Value of fractional-order calculus (FROC) model diffusion-weighted imaging combined with simultaneous multi-slice (SMS) acceleration technology for evaluating benign and malignant breast lesions.

BACKGROUND: This study explores the diagnostic value of combining fractional-order calculus (FROC) diffusion-weighted model with simultaneous multi-slice (SMS) acceleration technology in distinguishing benign and malignant breast lesions. METHODS: 178 lesions (73 benign, 105 malignant) underwent magnetic resonance imaging with diffusion-weighted imaging using multiple b-values (14 b-values, highest 3000 s/mm2). Independent samples t-test or Mann-Whitney U test compared image quality scores, FROC model parameters (D,, ), and ADC values between two groups. Multivariate logistic regression analysis identified independent variables and constructed nomograms. Model discrimination ability was assessed with receiver operating characteristic (ROC) curve and calibration chart. Spearman correlation analysis and Bland-Altman plot evaluated parameter correlation and consistency. RESULTS: Malignant lesions exhibited lower D, and ADC values than benign lesions (P < 0.05), with higher values (P < 0.05). In SSEPI-DWI and SMS-SSEPI-DWI sequences, the AUC and diagnostic accuracy of D value are maximal, with D value demonstrating the highest diagnostic sensitivity, while value exhibits the highest specificity. The D and combined model had the highest AUC and accuracy. D and ADC values showed high correlation between sequences, and moderate. Bland-Altman plot demonstrated unbiased parameter values. CONCLUSION: SMS-SSEPI-DWI FROC model provides good image quality and lesion characteristic values within an acceptable time. It shows consistent diagnostic performance compared to SSEPI-DWI, particularly in D and values, and significantly reduces scanning time.

Pachymic acid activates TP53INP2/TRAF6/caspase-8 pathway to promote apoptosis in renal cell carcinoma cells.

While pachymic acid (PA), a key component of Poria cocos (Schw.), has demonstrated anti-tumor effects in lung, breast, and pancreatic cancers, its impact on renal cell carcinoma (RCC) is unclear. This study evaluated the effect of PA on proliferation, migration, and apoptosis in human renal cancer A498 and ACHN cells as well as in cancer xenograft mice using wound scratch test, Western blotting, and co-immunoprecipitation assays. In a dose- and time-dependent manner, PA exhibited significant inhibition of RCC cell proliferation, migration, and invasion, accompanied by the induction of apoptosis. Additionally, PA upregulated the expression of tumor protein p53-inducible nuclear protein 2 (TP53INP2) and tumor necrosis factor receptor-associated factor 6 (TRAF6), which were downregulated in renal papillary and chromophobe carcinoma, resulting in inhibited tumor growth in mice. PA treatment elevated cleaved-caspase 3 and 8, and PARP levels, and facilitated TP53INP2 and TRAF6 binding to caspase 8, promoting its ubiquitination. Molecular docking revealed interactions between PA and TP53INP2, TRAF6. In summary, PA inhibits RCC development by upregulating TP53INP2 and promoting TRAF6-induced caspase 8 ubiquitination, activating apoptotic pathways.

Combination of automated sample preparation and micro-flow LC-MS for high-throughput plasma proteomics.

BACKGROUND: Non-invasive detection of blood-based markers is a critical clinical need. Plasma has become the main sample type for clinical proteomics research because it is easy to obtain and contains measurable protein biomarkers that can reveal disease-related physiological and pathological changes. Many efforts have been made to improve the depth of its identification, while there is an increasing need to improve the throughput and reproducibility of plasma proteomics analysis in order to adapt to the clinical large-scale sample analysis. METHODS: We have developed and optimized a robust plasma analysis workflow that combines an automated sample preparation platform with a micro-flow LC-MS-based detection method. The stability and reproducibility of the workflow were systematically evaluated and the workflow was applied to a proof-of-concept plasma proteome study of 30 colon cancer patients from three age groups. RESULTS: This workflow can analyze dozens of samples simultaneously with high reproducibility. Without protein depletion and prefractionation, more than 300 protein groups can be identified in a single analysis with micro-flow LC-MS system on a Orbitrap Exploris 240 mass spectrometer, including quantification of 35 FDA approved disease markers. The quantitative precision of the entire workflow was acceptable with median CV of 9%. The preliminary proteomic analysis of colon cancer plasma from different age groups could be well separated with identification of potential colon cancer-related biomarkers. CONCLUSIONS: This workflow is suitable for the analysis of large-scale clinical plasma samples with its simple and time-saving operation, and the results demonstrate the feasibility of discovering significantly changed plasma proteins and distinguishing different patient groups.

Hypoglycaemia aggravates impaired endothelial-dependent vasodilation in diabetes by suppressing endothelial nitric oxide synthase activity and stimulating inducible nitric oxide synthase expression.

BACKGROUND: Diabetes exacerbates vascular injury by triggering endothelial dysfunction. Endothelial nitric oxide synthase (eNOS) and inducible nitric oxide synthase (iNOS) both play major roles in endothelial dysfunction. However, effects of hypoglycaemia, the main complication of the insulin therapy to the glycemic control in diabetes, on eNOS activity and iNOS expression, and underlying mechanisms in diabetes remain unknown. Hence, we aimed to determine the effects of hypoglycaemia on eNOS activity and iNOS expression in different arterial beds of diabetic rats. METHODS: Sprague-Dawley rats were subjected to Streptozotocin (STZ) combined with high fat diet (HFD) to induce diabetes and then received insulin injection to attain acute and recurrent hypoglycaemia. Immunoblotting was used to analyse the phosphorylation and O-glycosylation status of eNOS and iNOS level from thoracic aorta and mesenteric artery tissue. Indicators of oxidative stress from plasm were determined, and endothelial-dependent vasodilation was detected via wire myograph system. RESULTS: Hypoglycaemia was associated with a marked increase in eNOS O-GlcNAcylation and decrease in Serine (Ser)-1177 phosphorylation from thoracic aortas and mesenteric arteries. Moreover, hypoglycaemia resulted in elevated phosphorylation of eNOS at Threonine (Thr)-495 site in mesenteric arteries. Besides, changes in these post-translational modifications were associated with increased O-GlcNAc transferase (OGT), decreased phosphorylation of Akt at Ser-473, and increased protein kinase C α subunit (PKCα). iNOS expression was induced in hypoglycaemia. Furthermore, endothelial-dependent vasodilation was impaired under insulin-induced hypoglycaemia, and further in recurrent hypoglycaemia. CONCLUSIONS: Conclusively, these findings strongly indicate that hypoglycaemia-dependent vascular dysfunction in diabetes is mediated through altered eNOS activity and iNOS expression. Therefore, this implies that therapeutic modulation of eNOS activity and iNOS expression in diabetics under intensive glucose control may prevent and treat adverse cardiovascular events.

Long-term evaluation of the seroprevalence of SARS-CoV-2 IgG and IgM antibodies in recovered patients: a meta-analysis.

Estimating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -specific immunoglobulin G (IgG) immunoglobulin M (IgM) antibodies are increasingly important for tracking the spread of infection and defining herd immunity barrier and individual immunization levels in the ongoing coronavirus disease 2019 (COVID-19) pandemic. Therefore, we conducted the present systematic review and meta-analysis to evaluate the seroprevalence of SARS-CoV-2 IgM and IgG antibodies of recovered COVID-19 patients in long-term follow-up studies. A systematic search of the MEDLINE, Embase, COVID-19 Primer, PubMed, CNKI, and the Public Health England library databases was conducted. Twenty-fourth eligible studies were included. Meta-analysis showed that 27% (95%CI: 0.04-0.49) and 66% (95%CI:0.47-0.85) were seropositive for SARS-CoV-2 IgM and IgG, respectively, while in long-term 12 months following up studies, the seroprevalences of IgM antibody (17%) decreased and IgG antibody (75%) was higher than 6 months follow-up patients. However, due to the limited number of relevant studies, the high level of heterogeneity, and the large gap in studies conducted, the findings of our study may not accurately reflect the true seroprevalence status of SARS-CoV-2 infection. Nevertheless, sequential vaccination or booster immunization is considered to be a necessary long-term strategy to sustain the fight against the pandemic.

Comparison of Efficacy of ERCP+LC and LC+LCBDE on Cholecysto-Choledocholithiasis and Analysis of Risk Factors for Recurrence of Choledocholithiasis.

Objective: Laparoscopic cholecystectomy (LC) combined with laparoscopic common bile duct exploration (LCBDE) and endoscopic retrograde cholangiopancreatography (ERCP) or endoscopic sphincterotomy (EST) combined with LC are the two primary treatment modalities for common bile duct stones (CCL) at present. The aim of this study is to compare the efficacy and safety of the two surgical approaches in treating CCL and analyze the risk factors for the recurrence of common bile duct stones. Methods: The clinical data of 148 CCL patients treated in the hospital from March 2014 to March 2016 were retrospectively analyzed. ERCP+LC was performed for 74 patients (ERCP+LC group), while the remaining 74 patients underwent LC+LCBDE (LC+LCBDE group). The success rate of lithotomy, operation time, total hospital stay time, postoperative hospital stay time, clinical symptoms, incidence rate of complications, and hospitalization expenses were compared between the two groups. The patients were followed up, the recurrence of choledocholithiasis was recorded, and the risk factors for recurrence were analyzed. Results: The success rate of lithotomy was 97.3% in the LC+LCBDE group and 94.6% in the ERCP+LC group. In the ERCP+LC group and LC+LCBDE group, the average operation time was (125.7±20.3) min and (106.5±25.4) min, the postoperative anal ventilation time was (20.8±3.5) d and (18.7±3.7) d, and the postoperative hospital stay time was (9.3±3.1) d and (7.7±3.3) d, respectively. It can be seen that the above three indexes were all significantly shorter in the LC+LCBDE group than those in ERCP+LC group (P < .001, P < .001, P = .003). The hospitalization expenses in the LC+LCBDE group [(19±1) thousand yuan] were obviously lower than those in the ERCP+LC group [(26±2) thousand yuan] (P < .001). The postoperative symptoms included fever, vomiting, abdominal pain and abdominal distension. The incidence rate of abdominal pain in the LC+LCBDE group was far higher than that in the ERCP+LC group (P = .025), and that of the remaining symptoms had no statistically significant difference between the two groups (P > .05). The postoperative complications mainly included incision infection, bile duct bleeding, biliary fistula, abdominal infection, bile duct pneumatosis, cholangitis and acute pancreatitis. Hyperamylasemia occurred in 8 cases after operation in the ERCP+LC group, greatly more than that in the LC+LCBDE group (1 case) (P = .016), while the incidence of other complications had no statistically significant difference between the two groups (P > .05). The patients were followed up for 3-5 years, and it was found that the recurrence rate of choledocholithiasis was 17.6% and 13.5%, and the mean postoperative recurrence time was 13.7 months and 13.9 months, respectively, in ERCP+LC group and LC+LCBDE group. The results of multivariable logistic regression analysis revealed that the level of cholesterol >572 mm/L (OR=5.108, 95%CI: 1.263-11.472, P = .038), choledochectasia (OR=2.165, 95%CI: 1.019-8.418, P = .034) and parapapillary diverticulum (OR=6.761, 95%CI: 1.334-15.613, P = .039) were independent risk factors for postoperative recurrence of choledocholithiasis. Conclusions: In our study, we found that ERCP+LC and LC+LCBDE have definite efficacy in the treatment of CCL. Patients treated with LC+LCBDE need short hospital stay time and low treatment expenses and have relatively few long-term complications.

A refined toxicokinetic model for quantifying the interaction between Cd and Cu in zebrafish larvae.

The interaction between metals is ubiquitous, but there is still a lack of quantitative models considering the interaction between metals, which leads to the deviations in predicting the joint toxicity of metals. The present study estimated the uptake rate constants (kin) and elimination rate constants (kout) and elucidated how the presence of one metal (Cu or Cd) affects the absorption and excretion of another metal (Cd or Cu) in zebrafish larvae. The results showed that Cd and Cu inhibited each other in the process of absorption and excretion by comparing separately kin and kout of Cd or Cu with the other metal Cu or Cd mixed concentrations increased, thereby affecting the Cd and Cu bioaccumulation in the zebrafish larvae. Then the interactions between Cd and Cu in the uptake and elimination processes were quantified to obtain a refined toxicokinetic model. Verification with independent experiment data showed that the refined toxicokinetic model could significantly improve the prediction of the Cd or Cu bioaccumulation in the zebrafish larvae. This study contributes to understand the toxicokinetic process of the Cd-Cu mixture in the zebrafish larvae, and the developed model could be used to predict the toxicity of the metal mixtures.

ECG criteria to distinguish hypertrophic cardiomyopathy featured with "Pseudo-STEMI" from acute ST-elevation myocardial infarction.

BACKGROUD: The ECG profile of Hypertrophic Cardiomyopathy (HCM) includes ST-segment elevation (STE) that may lead to misdiagnosis of acute ST-segment elevation myocardial infarction (STEMI). This pseudo-STEMI may bring non-essential treatment. We aimed to confirm the ECG differences between HCM featured with pseudo-STEMI and acute STEMI. MATERIAL AND METHODS: We retrospectively enrolled 59 HCM cases (Group A) and 56 acute STEMI cases (Group B). Based on the locations of STE, all the patients were divided into four subgroups, including HCM with STE in anterior leads (Group A1), anterior STEMI (Group B1), HCM with STE in inferior leads (Group A2) and inferior STEMI (Group B2). Several ECG parameters were compared between these subgroups. RESULTS: ECG parameters significantly differed between these groups, especially the number of leads with TWI. We evaluated the diagnostic value of ECG profiles for those groups. ROC analysis showed that for Group A vs. Group B, number of leads with TWI showed the highest AUC value of 0.805 and its cutoff of 2.5, with 76.3% sensitivity and 76.8% specificity. For Group A1 vs. Group B1, it showed the highest AUC value of 0.801 and its cut-off point was 2.5, with 77.1% sensitivity and 79.1% specificity. For Group A2 vs. Group B2, it showed the highest AUC value of 0.822 and the cut-off value was 4.5, with 54.5% sensitivity and 92.3% specificity. CONCLUSION: ECG plays a valid tool to distinguish "Pseudo-STEMI" HCM from acute STEMI, especially number of leads with TWI.

Dynamic Phosphotyrosine-Dependent Signaling Profiling in Living Cells by Two-Dimensional Proximity Proteomics.

Tyrosine phosphorylation (pTyr)-dependent signaling pathways play a vital role in various biological processes, which are spatiotemporally assembled and dynamically regulated on a minute scale by pTyr in living cells. Studying these pTyr-mediated signaling complexes is therefore challenging due to the highly dynamic nature of the protein complexes and the low abundance of pTyr. In this study, we adopted minute-resolution APEX2-based proximity labeling (PL) in living cells and Src SH2 superbinder-based pTyr peptide enrichment for simultaneously profiling these protein complexes and associated pTyr sites from the same affinity-purified sample. Upon different time courses of EGF stimulation of the living cells stably expressing APEX2-FLAG-GRB2, we constructed two-dimensional time-course curves for both interactome and tyrosine phosphoproteome. Well-annotated pTyr signaling complexes in EGFR signaling and located at the endosome were quantified with tightly correlated time-course curves for both interacting proteins and pTyr sites. Importantly, the correlated time-course curves for EGFR and endosomal HGS were well validated by targeted-parallel reaction monitoring (PRM)-MS analysis. Taking advantage of the high sensitivity of the PRM assay, the low-abundant pTyr peptide EGFR pY1110, which cannot be identified in the data-dependent acquisition (DDA) analysis, could be well quantified. Collectively, this two-dimensional proximity proteomic strategy is promising for comprehensively characterizing pTyr-mediated protein complexes with high sensitivity in living cells.

Renal inflamm-aging provokes intra-graft inflammation following experimental kidney transplantation.

Donor age is a major risk factor for allograft outcome in kidney transplantation. The underlying cellular mechanisms and the recipient's immune response within an aged allograft have yet not been analyzed. A comprehensive immunophenotyping of naïve and transplanted young versus aged kidneys revealed that naïve aged murine kidneys harbor significantly higher frequencies of effector/memory T cells, whereas regulatory T cells were reduced. Aged kidney-derived CD8+ T cells produced more IFNγ than their young counterparts. Senescent renal CD8+ T and NK cells upregulated the cytotoxicity receptor NKG2D and the enrichment of memory-like CD49a+ CXCR6+ NK cells was documented in aged naïve kidneys. In the C57BL/6 to BALB/c kidney transplantation model, recipient-derived T cells infiltrating an aged graft produced significantly more IFNγ, granzyme B and perforin on day 7 post-transplantation, indicating an enhanced inflammatory, cytotoxic response towards the graft. Pre-treatment of aged kidney donors with the senolytic drug ABT-263 changed the recipient-derived effector molecule profile to significantly reduced levels of IFNγ and IL-10 compared to controls. Graft function after ABT-263 pre-treatment was significantly improved 28 days post kidney transplantation. In conclusion, renal senescence also occurs at the immunological level (inflamm-aging) and aged organs provoke an altered recipient-dominated immune response in the graft.

Novel Method for Extracting the Spectrum of a Supramolecular Complex via a Comprehensive Approach Involving Two-Dimensional Correlation Spectroscopy, Genetic Algorithm, and Grid Searching.

A supramolecular complex may be formed by two solutes via a weak intermolecular interaction in a solution. The spectrum of the complex is often inundated by the spectra of the solutes that are not involved in the intermolecular interaction. Herein, a novel spectral analysis approach is proposed to retrieve the spectrum of the supramolecular complex. First, a two-dimensional (2D) asynchronous spectrum is constructed. Then, a genetic algorithm is used to obtain a heuristic spectrum of the supramolecular complex. The heuristic spectrum is a linear combination of the spectrum of the complex and the spectrum of a solute. The coefficients of the linear combination are then obtained, according to which the equilibrium constants are invariant among the sample solutions used to construct the 2D asynchronous spectrum. We have applied the approach to a supramolecular system formed by benzene and I2. In the analysis, several binding models are evaluated, and a benzene molecule interacting with two iodine molecules via halogen bonding turns out to be the only possible model. Hence, the characteristic band of the benzene/I2 supramolecular complex around 1819 cm-1 in the Fourier transform infrared (FTIR) spectrum and the corresponding equilibrium constant are obtained. The above results indicate that the novel approach provides a chance to get new insight into various intermolecular interactions studied by spectroscopy.

Honokiol improves endothelial function in type 2 diabetic rats via alleviating oxidative stress and insulin resistance.

We aimed to examine the effect of Honokiol (HKL) on endothelial dysfunction in type 2 diabetic rats and its possible mechanism. A high-fat diet and streptozotocin (STZ) were used to establish the type 2 diabetic model in rats. Part of these rats were intraperitoneally injected with HKL 10 mg/kg daily. Then the expression of Ser1177 phosphorylation of endothelial nitric oxide synthase (p-eNOS), eNOS, and CD31, vasodilation function, insulin signaling, indicators of oxidative stress and relative signaling pathway were measured. Human umbilical vein endothelial cells (HUVECs) were used to explore the underlying mechanism of the effect of HKL on high glucose-related endothelial injury in vitro. The data showed that HKL could reverse the decline of the expression of p-eNOS and CD31, endothelium-related vasodilation dysfunction, insulin resistance and activation of oxidative stress induced by type 2 diabetes in vivo. The similar results were obtained in vitro. In summary, our study demonstrates that HKL improves endothelial function and diminishes insulin resistance and oxidative stress, suggesting that HKL could be used as a treatment option for diabetes in the future.

Simulation of X-ray Hartmann wavefront sensing with the Synchrotron Radiation Workshop.

X-ray wavefront measurement is an important beam diagnostic tool, especially for the diffraction-limited X-ray beam. These in situ diagnostics give a better understanding of beam imperfections, and they enable feedback for possible corrections and/or optical alignment improvements. Hartmann wavefront sensing is one of the promising techniques to perform in situ X-ray wavefront measurements. In this work, a simulation tool of the X-ray Hartmann Wavefront Sensor (HWS) is developed under the Synchrotron Radiation Workshop (SRW) framework. Using this new simulation capability, one can take advantage of the full SRW package to simulate Hartmann wavefront sensing with the beam traveling from the X-ray source to the sample through different X-ray optical components. This SRW HWS simulation tool can help to optimize the wavefront sensor parameters for a specific X-ray energy range. It can also simulate an in situ wavefront measurement experiment with a particular beamline optical layout and predict the expected results of the wavefront measurement under different beamline configurations.

A fully integrated sample preparation strategy for highly sensitive intact glycoproteomics.

A fully integrated sample preparation technology, termed Intact GlycoSISPROT, was developed for the highly sensitive analysis of site-specific glycopeptides. Through integrating all glycoproteomic sample preparation steps into a single spintip, Intact GlycoSISPROT provided a tool for site-specific glycosylation analysis with low micrograms to even nanograms of protein sample.

Identification of gut microbiome and transcriptome changes in ulcerative colitis and pouchitis.

BACKGROUND: Pouchitis is the common postoperative complication of ulcerative colitis (UC) and is also considered as inflammatory bowel disease. The aim was to investigate the microbiological and transcriptional differences between the two illnesses. METHODS: Eighty-five participants were enrolled (37 UC, 15 healthy UC pouches, 15 pouchitis and 18 healthy volunteers) and stool samples were collected. Microbial populations were analyzed by pyrosequencing of 16S ribosomal DNA. Furthermore, transcriptome data of 119 UC and 28 pouch patients were obtained from two data sets for bioinformatics analysis. RESULTS: The results of gut microbiota community analysis showed that with aggravation of UC, intestinal microorganisms were characterized by a gradual decreased in diversity and numbers of butyrate-producing bacteria and Bacteroides. Besides, in addition to the decrease of probiotics, the proliferation of Escherichia-Shigella and Ruminococcus gnavus was observed in pouchitis which is related to multiple infection pathways. The function enrichment of differential expression genes and hub genes, as well as the immunological condition was shown to be distinct using transcriptome bioinformatics analysis between UC and pouchitis. A stronger immune response occurs in UC and may be associated with high expression of tumor necrosis factor and interleukin, while multiple hub genes such as CDK1 in pouchitis are associated with cell cycle regulation. CONCLUSIONS: The characteristics of gut microbiota disturbance and transcriptome alteration in UC and pouchitis are different. Our findings suggested that pouchitis may have a unique pathogenesis which was separated from UC.

SARS-CoV2 mRNA Vaccine-Specific B-, T- and Humoral Responses in Adolescents After Kidney Transplantation.

Protection of adult kidney transplant recipients against SARS-CoV2 was shown to be strongly impaired owing to low reactogenicity of available vaccines. So far, data on vaccination outcomes in adolescents are scarce due to later vaccination approval for this age group. We therefore comprehensively analyzed vaccination-specific humoral-, T- and B-cell responses in kidney transplanted adolescents aged 12-18 years in comparison to healthy controls 6 weeks after standard two-dose BNT162b2 ("Comirnaty"; Pfizer/BioNTech) vaccination. Importantly, 90% (18/20) of transplanted adolescents showed IgG seroconversion with 75% (15/20) developing neutralizing titers. Still, both features were significantly diminished in magnitude compared to controls. Correspondingly, spike-specific B cells were quantitatively reduced and enriched for non-isotype-class-switched IgD+27+ memory cells in patients. Whereas spike specific CD4+ T cell frequencies were similar in both groups, cytokine production and memory differentiation were significantly impaired in transplant recipients. Although our data identify limitations in all arms of vaccine-specific immunity, the majority of our adolescent patients showed robust humoral responses despite antimetabolite-based treatment being associated with poor vaccination outcomes in adults.

Stable and EGF-Induced Temporal Interactome Profiling of CBL and CBLB Highlights Their Signaling Complex Diversity.

The epidermal growth factor receptor (EGFR) signal modulates cell proliferation, migration, and survival. Aberrant activation of EGFR constitutes the major cause of various cancers. Receptor ubiquitination and degradation mediated by CBL proteins play negative regulatory roles and control the intensity and duration of the signaling. With the construction of stable cell lines inducibly expressing FLAG-tagged CBL or CBLB, we identified 102 and 82 stable interacting proteins of CBL and CBLB, respectively, through the affinity purification followed by mass spectrometry (AP-MS) approach. Time-resolved profiling at six different time points combined with functional annotations of the temporal interactomes provides insights into the dynamic assembly of signal proteins upon EGFR signaling activation. Comparison between the interactomes of CBL and CBLB indicates their redundant but also complementary functions. Importantly, we validated the stable association of EPS15L1 and ITSN2 and temporal association of TNK2 to both CBL and CBLB through biochemical assays. Collectively, these results offer a useful resource for CBL and CBLB interactomes and highlight their prominent and diverse roles in the EGFR signaling network.