The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and ...accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with
N/
C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.
Aims
This study aimed to characterize the chromosome and plasmid sequences, and determine the transferability of plasmids in carbapenem‐resistance Acinetobacter baumannii DD520 and Klebsiella ...pneumoniae DD521 isolates from the same patient who was co‐infected in a hospital in China.
Methods and Results
Both isolates DD520 and DD521 exhibited multidrug resistance phenotype, especially the former isolate which was resistant to nine classes of antimicrobials including carbapenems, quinolones, penicillins, cephalosporins, tetracyclines, phenicols, fosfomycins, sulfanilamides and aminoglycosides. Carbapenem resistance genes of blaOXA‐23 and blaOXA‐66 were identified on the chromosome of A. baumannii DD520, and blaKPC‐2 was found in the plasmid pDD521.2 from K. pneumoniae DD521. Phylogenetic analysis revealed that A. baumannii DD520 belonged to the ST540 clone, and K. pneumoniae DD521 belonged to the ST2237 clone. Plasmid analysis suggested that blaKPC‐2 was embedded into plasmid pDD521.2, which might be resulted from IS26‐ and Tn1721‐mediated transposition. Plasmid pDD521.2 carrying blaKPC‐2 successfully transferred from K. pneumoniae DD521 into Escherichia coli C600, and carbapenems resistance also transferred in the conjugation.
Conclusions
To our knowledge, it was the first report of A. baumannii ST540 and K. pneumoniae ST2237 in the same patient in China. Both these two isolates exhibited resistance to carbapenem, which was likely to have resulted from carbapenem‐resistance genes blaOXA‐23‐blaOXA‐66 on the chromosome of A. baumannii ST540, and blaKPC‐2 in the plasmid of K. pneumoniae ST2237.
Significance and Impact of the Study
Our study highlighted that effective measures were urgent to prevent and control the co‐infection caused by two or more carbapenem‐resistance pathogens in the same patient.
Background:
The rerupture or need for revision after anterior cruciate ligament reconstruction (ACLR) is a serious complication. Preventive strategies that target the early identification of risk ...factors are important to reduce the incidence of additional surgery.
Purpose:
To perform a systematic review and meta-analysis to investigate risk factors for revision or rerupture after ACLR.
Study Design:
Systematic review and meta-analysis; Level of evidence, 4.
Methods:
Literature searches were performed in PubMed, Embase, and Web of Science from database inception to November 2021 and updated in January 2022. Quantitative, original studies reporting potential adjusted risk factors were included. Odds ratios (ORs) were calculated for potential risk factors.
Results:
A total of 71 studies across 13 countries with a total sample size of 629,120 met the inclusion criteria. Fifteen factors were associated with an increase in the risk of revision or rerupture after ACLR: male sex (OR, 1.27; 95% CI, 1.14-1.41), younger age (OR, 1.07; 95% CI, 1.05-1.08), lower body mass index (BMI) (OR, 1.03; 95% CI, 1.00-1.06), family history (OR, 2.47; 95% CI, 1.50-4.08), White race (OR, 1.32; 95% CI, 1.08-1.60), higher posterolateral tibial slope (OR, 1.15; 95% CI, 1.05-1.26), preoperative high-grade anterior knee laxity (OR, 2.30; 95% CI, 1.46-3.64), higher baseline Marx activity level (OR, 1.07; 95% CI, 1.02-1.13), return to a high activity level/sport (OR, 2.03; 95% CI, 1.15-3.57), an ACLR within less than a year after injury (OR, 2.05; 95% CI, 1.81-2.32), a concomitant medial collateral ligament (MCL) injury (OR, 1.62; 95% CI, 1.31-2.00), an anteromedial portal or transportal technique (OR, 1.36; 95% CI, 1.22-1.51), hamstring tendon (HT) autografts (vs bone–patellar tendon–bone BPTB autografts) (OR, 1.60; 95% CI, 1.40-1.82), allografts (OR, 2.63; 95% CI, 1.65-4.19), and smaller graft diameter (OR, 1.21; 95% CI, 1.05-1.38). The other factors failed to show an association with an increased risk of revision or rerupture after ACLR.
Conclusion:
Male sex, younger age, lower BMI, family history, White race, higher posterolateral tibial slope, preoperative high-grade anterior knee laxity, higher baseline Marx activity level, return to a high activity level/sport, an ACLR within less than a year from injury, a concomitant MCL injury, an anteromedial portal or transportal technique, HT autografts (vs BPTB autografts), allografts, and smaller graft diameter may increase the risk of revision or rerupture after ACLR. Raising awareness and implementing effective preventions/interventions for risk factors are priorities for clinical practitioners to reduce the incidence of revision or rerupture after ACLR.
Oroxindin is a flavonoid isolated from the traditional Chinese medicine Huang-Qin, which has shown various pharmacological activities including anti-inflammatory, antitumor, antioxidant, etc. Thus ...far, the effect of oroxindin on colonic inflammation and the underlying mechanism remain unknown. In this study, we investigated the tissue distribution of oroxindin and its therapeutic effects on ulcerative colitis (UC) as well as the underlying mechanisms. UC model was established in mice by administrating dextran sulfate sodium (DSS) in drinking water for 7 d. We first showed that oroxindin was largely absorbed by the colon as an active ingredient after normal mice received Huang-Qin-Tang, a traditional Chinese medicine decoction. UC mice were then treated with oroxindin (12.5, 25, 50 mg ·kg
·d
, i.g.) for 10 d. We found that oroxindin treatment greatly suppressed massive macrophages infiltration and attenuated pathological changes in colonic tissue. Furthermore, oroxindin treatment significantly inhibited the generation of IL-1β and IL-18 in the colon via inhibiting the nucleotide-binding oligomerization domain-like receptor 3 (NLRP3) inflammasome formation and activation. In cultured macrophages, LPS induced NLRP3 inflammasome formation and caspase-1 activation, which were suppressed by oroxindin (12.5-50 μM). In LPS-treated macrophages, oroxindin dose-dependently restored the expression of TXNIP protein, leading to suppressing TXNIP-dependent NF-κB activation. In conclusion, these results demonstrate that oroxindin could be absorbed by the colon and attenuate inflammatory responses via inhibiting NLRP3 inflammasome formation and activation, which is related to the inhibitory effect on TXNIP-dependent NF-κB-signaling pathway. Hence, oroxindin has the potential of becoming an effective drug for treating UC.
Ulcerative colitis (UC) is a chronic inflammatory disease of the gastrointestinal tract, which is closely related to gut barrier dysfunction. Emerging evidence shows that interleukin-22 (IL-22) ...derived from group 3 innate lymphoid cells (ILC3s) confers benefits on intestinal barrier, and IL-22 expression is controlled by aryl hydrocarbon receptor (AhR). Previous studies show that baicalein protects the colon from inflammatory damage. In this study we elucidated the molecular mechanisms underlying the protective effect of baicalein on intestinal barrier function in colitis mice. Mice were administered baicalein (10, 20, 40 mg·kg
·d
, i.g.) for 10 days; the mice freely drank 3% dextran sulfate sodium (DSS) on D1-D7 to induce colitis. We showed that baicalein administration simultaneously ameliorated gut inflammation, decreased intestinal permeability, restored tight junctions of colons possibly via promoting AhR/IL-22 pathway. Co-administration of AhR antagonist CH223191 (10 mg/kg, i.p.) partially blocked the therapeutic effects of baicalein in colitis mice, whereas AhR agonist FICZ (1 μg, i.p.) ameliorated symptoms and gut barrier function in colitis mice. In a murine lymphocyte line MNK-3, baicalein (5-20 μM) dose-dependently increased the expression of AhR downstream target protein CYP1A1, and enhanced IL-22 production through facilitating AhR nuclear translocation, these effects were greatly diminished in shAhR-MNK3 cells, suggesting that baicalein induced IL-22 production in AhR-dependent manner. To further clarify that, we constructed an in vitro system consisting of MNK-3 and Caco-2 cells, in which MNK-3 cell supernatant treated with baicalein could decrease FITC-dextran permeability and promoted the expression of tight junction proteins ZO-1 and occluding in Caco-2 cells. In conclusion, this study demonstrates that baicalein ameliorates colitis by improving intestinal epithelial barrier via AhR/IL-22 pathway in ILC3s, thus providing a potential therapy for UC.
Ankylosing spondylitis (AS) is a common inflammatory rheumatic disease that affects the axial skeleton. In this study, we systematically reviewed Chinese AS epidemiological studies from the past ...15 years to elucidate its prevalence and provide scientific data for China’s health care system. AS epidemiological research in China was summarized by conducting a literature review. A review and statistical analysis of the literature on the epidemiology of AS in mainland China published from May 2005 to May 2019 were performed via a meta-analysis. We calculated the prevalence of AS and analysed differences by sex, region, and population source using STATA12.0 software. Eleven papers including 122,558 subjects from mainland China were included. Over the past 15 years, the total prevalence of AS in mainland China was 0.29% (95% CI 0.22–0.35%), ranging from 0.42% (95% CI 0.31–0.52%) in males to 0.15% (95% CI 0.13–0.18%) in females; the difference in the prevalence of AS by sex was statistically significant (
P
< 0.001). The prevalence of AS in both southern and northern China was 0.31% (95% CI 0.21–0.42% and 0.21–0.40%, respectively), with no significant difference noted (
P
= 0.816 > 0.005). The prevalence of AS in Chinese military populations was 0.27% (95% CI 0.09–0.45%), and in community populations, it was 0.29% (95% CI 0.23–0.35%). There was no statistically significant difference in the prevalence of AS by sampling resource (
P
= 0.115 > 0.005). The prevalence of AS in China was 0.29% and continues to increase. Sex differences in its prevalence were identified; the prevalence rate was 2.8 times higher in males than in females. Epidemiologists in China should formulate precise scientific investigations to provide additional authoritative epidemiological data for the prevention and treatment of AS.
Ulcerative colitis (UC) is one of non-specific inflammatory bowel disease that mainly affects the colon. Recently, UC has become a significant social and economic problem worldwide. Baitouweng ...decoction (BD), a traditional Chinese medicine described in the “Treatise on Febrile Diseases”, has been used for centuries to treat intestinal diseases. However, its underlying mechanism remains largely unexplored.
In this study, we aimed to investigate the effect of BD on autophagy for repairing the colonic barrier in DSS-induced colitis mice and explored its role in regulating the autophagic signaling pathway AMPK/mTOR.
Mice with colitis were treated with 3% dextran sulfate sodium (DSS) for 7 days. The effectiveness of BD in treating DSS-induced colitis was evaluated through body weight, disease activity index (DAI), colon length, pathological changes, organ index, and proportion of blood cells. Moreover, intestinal epithelial permeability was analyzed by examining FITC-dextran leakage, the bacterial load of mesenteric lymph nodes (MLNs), and bacterial infiltration of colon tissues. Barrier function was evaluated by assessing the number and proportion of colonic goblet cells and the expression of tight junction proteins, including ZO-1, claudin-1, and occludin. Furthermore, the levels of autophagy were assessed by examining the number of autophagosomes and the expression of the autophagy-related proteins LC3, Beclin1, and P62. Additionally, network pharmacology research was conducted to analyze the potential mechanisms underlying the medicinal effects, as indicated by the role of AMPK/mTOR in regulating the autophagic signaling pathway.
BD improved colitis symptoms in mice by restoring body weight and colon length and reducing inflammatory cell infiltration. Additionally, BD decreased the diffusion of FITC-dextran and bacterial translocation in MLNs, as well as bacterial infiltration of the colonic mucosa. The number and proportion of colonic goblet cells, the expression of ZO-1, Claudin-1, and Occludin, and the levels of autophagy were also increased by BD. Network pharmacology analysis suggested that BD might affect intestinal autophagy through the AMPK signaling pathway, which was confirmed by the activation of AMPK phosphorylation and the downregulation of mTOR expression following BD treatment.
Our study demonstrated that BD repaired the intestinal epithelial barrier in DSS-induced colitis mice by activating AMPK phosphorylation and inhibiting mTOR expression to promote autophagy.
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•The therapeutic effect of Baitouweng decoction in DSS-induced UC mice.•Baitouweng decoction repaired the damaged intestinal barrier in DSS-induced UC mice.•Baitouweng decoction enhanced autophagy in DSS-induced colitis mice.•Baitouweng decoction repaired the damaged intestinal barrier in DSS-induced UC mice in an are autophagy-dependent manner.•Baitouweng decoction plays a therapeutic role in repairing the intestinal epithelial barrier by promoting autophagy through regulating the AMPK/mTOR signaling pathway.
Confident characterization of the microheterogeneity of protein glycosylation through identification of intact glycopeptides remains one of the toughest analytical challenges for glycoproteomics. ...Recently proposed mass spectrometry (MS)-based methods still have some defects such as lack of the false discovery rate (FDR) analysis for the glycan identification and lack of sufficient fragmentation information for the peptide identification. Here we proposed pGlyco, a novel pipeline for the identification of intact glycopeptides by using complementary MS techniques: 1) HCD-MS/MS followed by product-dependent CID-MS/MS was used to provide complementary fragments to identify the glycans, and a novel target-decoy method was developed to estimate the false discovery rate of the glycan identification; 2) data-dependent acquisition of MS3 for some most intense peaks of HCD-MS/MS was used to provide fragments to identify the peptide backbones. By integrating HCD-MS/MS, CID-MS/MS and MS3, intact glycopeptides could be confidently identified. With pGlyco, a standard glycoprotein mixture was analyzed in the Orbitrap Fusion, and 309 non-redundant intact glycopeptides were identified with detailed spectral information of both glycans and peptides.
ObjectiveCementless total hip arthroplasty (THA) is associated with reliable clinical results and high patient satisfaction. Short-stem prostheses (SS) were designed to achieve superior preservation ...of proximal bone stock and stability compared with those of conventional-stem prostheses (CS). This meta-analysis was conducted to determine the proximal bone remodelling, revision rate, Harris Hip Score, radiolucent line and maximum total point motion values of both SS and CS for primary THA.MethodRelevant randomised controlled trials (RCTs) involving SS and CS in primary THA were identified from electronic databases, such as EMBASE, PubMed and the Cochrane Library.ResultUltimately, 12 RCTs involving 1130 patients (1387 hips) were included. The results showed that compared with CS, SS resulted in less bone mineral density (BMD) changes in Gruen zone 7 at 1 year and 2 years postoperatively (mean difference (MD)=5.11; 95% CI, 1.61, 8.61; P=0.30; and MD=4.90; 95% CI, 1.01, 8.79; P=0.17, respectively). No difference in BMD changes was found for Gruen zone 1 (MD=2.66; 95% CI, −3.31, 8.64; P<0.00001), and no differences were observed for the revision rate (relative risk (RR)=1.52; 95% CI, 0.71, 3.26; P=0.94), Harris Hip Score (MD=−0.38; 95% CI, −1.02, 0.26; P=0.89) or stem migration (MD=0.02; 95% CI, −0.07, 0.11; P=0.04).ConclusionOur results suggest that compared with CS, SS may provide superior bone remodelling and similar survival rates and clinical outcomes. However, the short-term follow-up of the included studies was inadequate to determine the long-term performance of SS.
The primary aim was to evaluate risk factors for surgical site infections after anterior cruciate ligament reconstruction (ACLR). The secondary aim was to investigate the surgical site infection ...incidence rate and the mean time to postoperative surgical site infection symptoms.
Systematic review and meta-analysis.
PubMed, Embase and Web of Science were searched from database inception to September 2021 and updated in April 2022.
Quantitative, original studies reporting potential risk factors for surgical site infections after ACLR were included.
Twenty-three studies with 3871 infection events from 469 441 ACLRs met the inclusion criteria. Male sex (OR 1.78, p< 0.00001), obesity (OR 1.82, p=0.0005), tobacco use (OR 1.37, p=0.01), diabetes mellitus (OR 3.40, p=0.002), steroid use history (OR 4.80, p<0.00001), previous knee surgery history (OR 3.63, p=0.02), professional athlete (OR 4.56, p=0.02), revision surgery (OR 2.05, p=0.04), hamstring autografts (OR 2.83, p<0.00001), concomitant lateral extra-articular tenodesis (OR 3.92, p=0.0001) and a long operating time (weighted mean difference 8.12, p=0.005) were identified as factors that increased the risk of surgical site infections (superficial and deep) after ACLR. Age, outpatient or inpatient surgery, bone-patellar tendon-bone autografts or allografts and a concomitant meniscus suture did not increase the risk of surgical site infections. The incidence of surgical site infections after ACLR was approximately 1% (95% CI 0.7% to 1.2%). The mean time from surgery to the onset of surgical site infection symptoms was approximately 17.1 days (95% CI 13.2 to 21.0 days).
Male sex, obesity, tobacco use, diabetes mellitus, steroid use history, previous knee surgery history, professional athletes, revision surgery, hamstring autografts, concomitant lateral extra-articular tenodesis and a long operation time may increase the risk of surgical site infections after ACLR. Although the risk of surgical site infections after ACLR is low, raising awareness and implementing effective preventions for risk factors are priorities for clinicians to reduce the incidence of surgical site infections due to its seriousness.
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