The First Case of Ischemia-Free Kidney Transplantation in Humans

Background: Ischemia-reperfusion injury (IRI) has been considered an inevitable event in organ transplantation since the first successful kidney transplant was performed in 1954. To avoid IRI, we have established a novel procedure called ischemia-free organ transplantation. Here, we describe the first case of ischemia-free kidney transplantation (IFKT). Materials and Methods: The kidney graft was donated by a 19-year-old brain-dead donor. The recipient was a 47-year-old man with end-stage diabetic nephropathy. The graft was procured, preserved, and implanted without cessation of blood supply using normothermic machine perfusion. Results: The graft appearance, perfusion flow, and urine production suggested that the kidney was functioning well-during the whole procedure. The creatinine dropped rapidly to normal range within 3 days post-transplantation. The levels of serum renal injury markers were low post-transplantation. No rejection or vascular or infectious complications occurred. The patient had an uneventful recovery. Conclusion: This paper marks the first case of IFKT in humans. This innovation may offer a unique solution to optimizing transplant outcomes in kidney transplantation.

Hydrogen-Deuterium Exchange and Hydroxyl Radical Footprinting for Mapping Hydrophobic Interactions of Human Bromodomain with a Small Molecule Inhibitor

Mass spectrometry (MS)-based protein footprinting, a valuable structural tool in mapping protein-ligand interaction, has been extensively applied to protein-protein complexes, showing success in mapping large interfaces. Here, we utilized an integrated footprinting strategy incorporating both hydrogen-deuterium exchange (HDX) and hydroxyl radical footprinting (i.e., fast photochemical oxidation of proteins (FPOP)) for molecular-level characterization of the interaction of human bromodomain-containing protein 4 (BRD4) with a hydrophobic benzodiazepine inhibitor. HDX does not provide strong evidence for the location of the binding interface, possibly because the shielding of solvent by the small molecule is not large. Instead, HDX suggests that BRD4 appears to be stabilized by showing a modest decrease in dynamics caused by binding. In contrast, FPOP points to a critical binding region in the hydrophobic cavity, also identified by crystallography, and, therefore, exhibits higher sensitivity than HDX in mapping the interaction of BRD4 with compound 1. In the absence or under low concentrations of the radical scavenger, FPOP modifications on Met residues show significant differences that reflect the minor change in protein conformation. This problem can be avoided by using a sufficient amount of proper scavenger, as suggested by the FPOP kinetics directed by a dosimeter of the hydroxyl radical.

Identification of Shaker K+ channel family members in Rosaceae and a functional exploration of PbrKAT1

PbrKAT1, which is inhibited by external Na⁺ in Xenopus laevis oocytes, is characterized as encoding a typical inward rectifying channel that is mainly expressed in guard cells. Potassium (K⁺) is the most abundant cation in plant cells necessary for plant growth and development. The uptake and transport of K⁺ are mainly completed through transporters and channels, and the Shaker family genes are the most studied K⁺ channels in plants. However, there is far less information about this family in Rosaceae species. We performed a genome-wide analysis and identified Shaker K⁺ channel gene family members in Rosaceae. We cloned and characterized a Shaker K⁺ channel KAT1 from pear (Pyrus × bretschneideri). In total, 36 Shaker K⁺ channel genes were identified from Rosaceae species and were classified into five subgroups based on structural characteristics and a phylogenetic analysis. Whole-genome and dispersed duplications were the primary forces underlying Shaker K⁺ channel gene family expansion in Rosaceae, and purifying selection played a key role in the evolution of Shaker K⁺ channel genes. β-Glucuronidase and qRT-PCR assays revealed that PbrKAT1 was mainly expressed in leaves, especially in guard cells. PbrKAT1 displayed a typical inward-rectifying current when expressed in Xenopus laevis oocytes. The activity of PbrKAT1 was inhibited by external sodium ions, possibly playing an important role in the regulation of salt tolerance in pear. These results provide valuable information on evolution, expression and functions of the Shaker K⁺ channel gene family in plants.

An Integrated Approach for Determining a Protein-Protein Binding Interface in Solution and an Evaluation of Hydrogen-Deuterium Exchange Kinetics for Adjudicating Candidate Docking Models

We describe an integrated approach of using hydrogen-deuterium exchange mass spectrometry (HDX-MS), chemical cross-linking mass spectrometry (XL-MS), and molecular docking to characterize the binding interface and to predict the three-dimensional quaternary structure of a protein-protein complex in solution. Interleukin 7 (IL-7) and its α-receptor, IL-7Rα, serving as essential mediators in the immune system, are the model system. HDX kinetics reports widespread protection on IL-7Rα but shows no differential evidence of binding-induced protection or remote conformational change. Cross-linking with reagents that differ in spacer lengths and targeting residues increases the spatial resolution. Using five cross-links as distance restraints for protein-protein docking, we generated a high-confidence model of the IL-7/IL-7Rα complex. Both the predicted binding interface and regions with direct contacts agree well with those in the solid-state structure, as confirmed by previous X-ray crystallography. An additional binding region was revealed to be the C-terminus of helix B of IL-7, highlighting the value of solution-based characterization. To generalize the integrated approach, protein-protein docking was executed with a different number of cross-links. Combining cluster analysis and HDX kinetics adjudication, we found that two intermolecular cross-link-derived restraints are sufficient to generate a high-confidence model with root-mean-square distance (rmsd) value of all alpha carbons below 2.0 Å relative to the crystal structure. The remarkable results of binding-interface determination and quaternary structure prediction highlight the effectiveness and capability of the integrated approach, which will allow more efficient and comprehensive analysis of interprotein interactions with broad applications in the multiple stages of design, implementation, and evaluation for protein therapeutics.

Identification, Quantification, and Stereoselective Degradation of Triazole Fungicide Cyproconazole in Two Matrixes through Chiral Liquid Chromatography-Tandem Mass Spectrometry

Systematic investigation of cyproconazole, including absolute stereochemistry, fungicidal activity, quantification in two matrixes, and stereoselective degradation in cucumber, are conducted in this study. By virtue of vibrational circular dichroism (VCD) spectroscopy, absolute configurations of four stereoisomers were identified to be (2R,3R)-(+)-, (2R,3S)-(+)-, (2S,3S)-(-)-, and (2S,3R)-(-)-cyproconazoles. Then four stereoisomers exhibited stereoselective fungicidal activities against Fusarium graminearum Schw and Magnaporthe oryzae, and the order of fungicidal activity was (2S,3S)-(-)-stereoisomer > the stereoisomer mixture > (2S,3R)-(-)-stereoisomer > (2R,3R)-(+)-stereoisomer > (2R,3S)-(+)-stereoisomer. Moreover, chiral liquid chromatography-tandem mass spectrometry was used to identify and quantify cyproconazole stereoisomers in soil and cucumber matrixes. Good linearity (R² ≥ 0.99) and recoveries (86.79-92.47%, RSD ≤ 3.94%) for them were achieved, individually. Furthermore, stereoselective degradation of four cyproconazole stereoisomers was observed in cucumber and the order of degradation rate was (2R,3R)-(+)-cyproconazole > (2S,3S)-(-)-cyproconazole > (2R,3S)-(+)-cyproconazole > (2S,3R)-(-)-cyproconazole. We envision that such systematic assessments of chiral fungicides at an enantiomeric level would provide valuable information in future studies involving enantioselective physiological, metabolic, and toxicological activities.

Salidroside pretreatment protects against myocardial injury induced by heat stroke in mice

Objective

To explore the protective effects and mechanisms of salidroside on myocardial injury induced by heat stroke (HS) in mice.

Methods

We pretreated mice with salidroside for 1 week and then established an HS model by exposure to 41.2°C for 1 hour. We then examined the effects of salidroside on survival. We also assessed the severity of cardiac injury by pathology, and analyzed changes in levels of myocardial injury markers, inflammatory cytokines, and oxidative stress.

Results

Salidroside pretreatment significantly reduced HS-induced mortality and improved thermoregulatory function. Salidroside also provided significant protection against HS-induced myocardial damage, and decreased the expression levels of cardiac troponin I, creatine kinase-MB, and lactate dehydrogenase. Moreover, salidroside attenuated HS-induced changes in the inflammation markers tumor necrosis factor-α, interleukin (IL)-6, and IL-10, and down-regulated the oxidative stress response indicated by thiobarbituric acid reactant substances, malondialdehyde, reduced glutathione, and superoxide dismutase.

Conclusions

Salidroside pretreatment protected against HS-induced myocardial damage, potentially via a mechanism involving anti-inflammatory and anti-oxidative effects.

The Status of Epstein-Barr Virus Infection in Intestinal Mucosa of Chinese Patients with Inflammatory Bowel Disease

AIMS

This cross-sectional study is to investigate the presence of Epstein-Barr virus (EBV) in colonic mucosa of inflammatory bowel disease (IBD) patients and its correlation with the clinical disease activities and therapeutic regimens.

METHODS

Subjects undergoing colonoscopy for screening of polyps were recruited as control. EBV DNA load was analyzed by means of quantitative real-time polymerase chain reaction and EBV-encoded RNAs were tested by in situ hybridization in intestinal mucosa of IBD patients. EBV infection was defined as positive with either method. Clinical disease activity was assessed using the Mayo Clinic Score for ulcerative colitis and Crohn's disease activity index for CD.

RESULTS

EBV was detectable in 33 out of 99 IBD patients (33.3%). In controls, EBV prevalence was 7.5% (3/40). We found a significant correlation between EBV prevalence and clinical disease activities (mild [10.71%, 3/28] versus moderate [32.73%, 18/55], severe [75.00%, n = 12/16], p < 0.001). However, no significant difference was found in EBV prevalence between patients who received immunosuppressive therapy and those who did not.

CONCLUSIONS

EBV infection is common in colonic mucosa of IBD patients. There is a significant correlation between EBV infection and clinical disease activities of IBD. However, prospective studies are still needed to explore the exact role of EBV in IBD.

Effects of serratus anterior plane block for postoperative analgesia after thoracoscopic surgery compared with local anesthetic infiltration: a randomized clinical trial

Background

Serratus anterior plane (SAP) block is a relatively novel technique that can block the lateral cutaneous branches of the intercostal nerves as well as the long thoracic nerve.

Purpose

Our study aimed to evaluate the effects of SAP block on postoperative pain after thoracoscopic surgery compared with local anesthetic (LA) infiltration.

Patients and methods

Forty adult patients undergoing video-assisted thoracic surgery were randomized to receive either SAP block (n=20) or LA infiltration of incision (n=20). The primary outcome was postoperative visual analog scale (VAS) score at the 2nd, 8th, 16th, 24th, and 48th hour after surgery. The secondary outcomes were the consumption of sufentanil at 8th, 16th, 24th hours postoperative. In addition, rescue analgesia, drug-related adverse effects after surgery was also analyzed.

Results

The SAP group showed lower VAS scores at the 2nd hour (at rest: SAP group 11 [8-13] vs LA group 28 [26-32], P=0.01; on coughing: 15 [13-18] vs 33 [26-38], P=0.01) and the 8th hour (at rest: 13 [12-18] vs 36 [32-46], P=0.01; on coughing: 19 [16-23] vs 42 [36-53], P=0.01) after surgery. Postoperative sufentanil consumption in the SAP group during 0-8 hrs was significantly lower compared with the LA group (P<0.01). The use of rescue analgesia was also significantly lower in the SAP group (P=0.02) during 0-12 hrs.

Conclusion

Compared to LA infiltration, ultrasound-guided SAP block may provide better pain relief as well as reduce opioid consumption after thoracoscopic surgery.

[Relationship between expression of high-mobility group box-1 and inflammatory cytokines in patients with bone cancer pain]

Objective: To investigate the change and relationship between serum high-mobility group box-1(HMGB1) and related inflammatory cytokines level in patients suffer with bone metastatic pain. Methods: Collection of the bone cancer pain patients who received analgesic therapy the department of pain in The First Affiliated Hospital of Jiaxing University from November 2016 to August 2016. Serum concentration of HMGB1, the Receptor of Advanced Glycation Endproducts (RAGE), monocyte chemotactic protein-1(MCP-1), tumor necrosis factor -α (TNF-α), interleukin-1β (IL-1β), interleukin-10 (IL-10), interleukin-13 (IL-13), and transforming growth factor-β (TGF-β) levels were determined in 15 healthy individuals as healthy donor and 15 patients with bone metastatic pain by enzyme-linked immunosorbent (ELISA) . The healthy individuals and patients with bone metastatic pain were collected before treatment and on 7 d after the treatment. Results: The serum concentration of HMGB1 and RAGE were significantly increased in tumorous group compared with healthy group[(8.8±2.3) vs (1.9±1.1) μg/L,(231±16) vs (46±20) ng/L); t=7.10,12.44, both P<0.05], then decreased after analgesic therapy [(4.77±1.36) μg/L, (129.80±29.32) ng/L, t=7.10, 12.44, both P<0.05]. The serum concentration of proinflammatory cytokines such as MCP-1, TNF-α, and IL-1β were significantly increased in tumorous group when compared with healthy group, and decreased after analgesic therapy (all P<0.05). The expression of anti-inflammatory cytokines such as IL-10, IL-13, and TGF-β were significantly increased in tumorous group when compared with healthy group, and decreased after analgesic therapy (all P<0.05).Compared with healthy group, the levels of MCP-1/IL-10, MCP-1/IL-13, MCP-1/TGF-β, TNF-α/IL-10, TNF-α/IL-13, TNF-α/TGF-β, IL-1β/IL-10, IL-1β/IL-13, IL-1β/TGF-β were significantly increased in tumorous group (all P<0.05). Conclusion: HMGB1 may adjust the proinflammatory-anti-inflammatory system homeostasis to participate in the development of bone metastatic pain.

Interlaboratory Comparison of Hydrogen-Deuterium Exchange Mass Spectrometry Measurements of the Fab Fragment of NISTmAb

Hydrogen-deuterium exchange mass spectrometry (HDX-MS) is an established, powerful tool for investigating protein-ligand interactions, protein folding, and protein dynamics. However, HDX-MS is still an emergent tool for quality control of biopharmaceuticals and for establishing dynamic similarity between a biosimilar and an innovator therapeutic. Because industry will conduct quality control and similarity measurements over a product lifetime and in multiple locations, an understanding of HDX-MS reproducibility is critical. To determine the reproducibility of continuous-labeling, bottom-up HDX-MS measurements, the present interlaboratory comparison project evaluated deuterium uptake data from the Fab fragment of NISTmAb reference material (PDB: 5K8A ) from 15 laboratories. Laboratories reported ∼89 800 centroid measurements for 430 proteolytic peptide sequences of the Fab fragment (∼78 900 centroids), giving ∼100% coverage, and ∼10 900 centroid measurements for 77 peptide sequences of the Fc fragment. Nearly half of peptide sequences are unique to the reporting laboratory, and only two sequences are reported by all laboratories. The majority of the laboratories (87%) exhibited centroid mass laboratory repeatability precisions of ⟨ s^Lab⟩ ≤ (0.15 ± 0.01) Da (1σ_x̅). All laboratories achieved ⟨s^Lab⟩ ≤ 0.4 Da. For immersions of protein at T_HDX = (3.6 to 25) °C and for D₂O exchange times of t_HDX = (30 s to 4 h) the reproducibility of back-exchange corrected, deuterium uptake measurements for the 15 laboratories is σ_{reproducibility}^{15 Laboratories}( t_HDX) = (9.0 ± 0.9) % (1σ). A nine laboratory cohort that immersed samples at T_HDX = 25 °C exhibited reproducibility of σ_{reproducibility}^25C cohort( t_HDX) = (6.5 ± 0.6) % for back-exchange corrected, deuterium uptake measurements.

Characterization of Dof family in Pyrus bretschneideri and role of PbDof9.2 in flowering time regulation

DNA binding with One Finger (Dof) proteins are plant-specific transcription factors with highly conserved Dof domain, including C2-C2 type zinc finger motifs. In this study, we identified 45 PbDofs in pear (Pyrusbretschneideri). PbDofs were classified into eight subfamilies by phylogenetic analysis. Conserved motifs of PbDof proteins were analyzed by MEME. PbDofs in subfamily D₁ werehomologous to CDFs in Arabidopsis. In this study, we showed that PbDof9.2 was regulated by both the circadian clock and photoperiod. PbDof9.2-GFP proteinwas localized in the nucleus. Overexpression of PbDof9.2 in Arabidopsis caused delayed flowering time. PbDof9.2 suppressed the flowering time regulator FT and could repress flowering time by promoting activity of PbTFL1a and PbTFL1b promoter. These results suggest that Doftranscription factors have conserved functions in plant development.

PbrSLAH3 is a nitrate-selective anion channel which is modulated by calcium-dependent protein kinase 32 in pear

BACKGROUND

The functional characteristics of SLAC/SLAH family members isolated from Arabidopsis thaliana, poplar, barley and rice have been comprehensively investigated. However, there are no reports regarding SLAC/SLAH family genes from Rosaceae plants.

RESULTS

In this study, the function of PbrSLAH3, which is predominately expressed in pear (Pyrus bretschneideri) root, was investigated. PbrSLAH3 can rescue the ammonium toxicity phenomenon of slah3 mutant plants under high-ammonium/low-nitrate conditions. In addition, yeast two-hybrid and bimolecular fluorescence complementation assays confirmed that PbrSLAH3 interacts with PbrCPK32. Moreover, when PbrSLAH3 was co-expressed with either the Arabidopsis calcium-dependent protein kinase (CPK) 21 or PbrCPK32 in Xenopus oocytes, yellow fluorescence was emitted from the oocytes and typical anion currents were recorded in the presence of extracellular NO3-. However, when PbrSLAH3 alone was injected, no yellow fluorescence or anion currents were recorded, suggesting that anion channel PbrSLAH3 activity was controlled through phosphorylation. Finally, electrophysiological and transgene results showed that PbrSLAH3 was more permeable to NO3- than Cl-.

CONCLUSION

We suggest that PbrSLAH3 crossing-talk with PbrCPK32 probably participate in transporting of nitrate nutrition in pear root.

Hydrogen-Deuterium Exchange Mass Spectrometry (HDX-MS) Centroid Data Measured between 3.6 °C and 25.4 °C for the Fab Fragment of NISTmAb

The spreadsheet file reported herein provides centroid data, descriptive of deuterium uptake, for the FabFragment of NISTmAb (PDB: 5K8A) reference material, as measured by the bottom-up hydrogen-deuterium exchange mass spectrometry (HDX-MS) method. The protein sample was incubated in deuterium-rich solutions under uniform pH and salt concentrations between 3.6 oC and 25.4 oC for seven intervals ranging over (0 to 14,400) s plus a ∞pseudo s control. The deuterium content of peptic peptide fragments were measured by mass spectrometry. These data were reported by fifteen laboratories, which conducted the measurements using orbitrap and Q-TOF mass spectrometers. The cohort reported ≈ 78,900 centroids for 430 proteolytic peptide sequences of the heavy and light chains of NISTmAb, providing nearly 100 % coverage. In addition, some groups reported ≈ 10,900 centroid measurements for 77 peptide sequences of the Fc fragment. The instrumentation and physical and chemical conditions under which these data were acquired are documented.

[Expression and significance of c-FLIP protein in sepsis mice with acute kidney injury]

OBJECTIVE

To observe the expression of cellular Fas-associated death domain-like interleukin-1β converting enzyme inhibit protein (c-FLIP) in sepsis mice with acute kidney injury (SAKI) and explore its significance.

METHODS

Thirty male ICR mice were divided into the normal control group (Normal group), sham operation group (Sham group) and SAKI group by random number table method, with 10 mice in each group. The SAKI model of mice was established by cecal ligation and puncture (CLP); the Sham group was not ligated and the cecum was not punctured, and other surgical procedures were the same as the SAKI group; the Normal group did not experience any treatment. The serum and renal tissues of mice in each group were harvested 24 hours after CLP model establishment. The levels of serum creatinine (SCr) and blood urea nitrogen (BUN) were detected by enzyme linked immunosorbent assay (ELISA). The renal tissues were stained with hematoxylin-eosin (HE), and the pathological changes of renal tissues were observed under light microscope and the severity of injury was determined. The expression of c-FLIP in renal tissues was detected by immunohistochemistry. The expression of c-FLIP, Bax and caspase-3 protein in renal tissue was detected by Western Blot. The correlation between c-FLIP expression and Bax, caspase-3 protein expressions in renal tissues were analyzed by Pearson test.

RESULTS

In the Normal group and the Sham group, the renal tubular epithelial cells were regular and intact, and no interstitial inflammatory cell infiltration was observed; the renal injury score was both 1.30±0.48; immunohistochemistry showed a large amount of c-FLIP positive expression in renal tubular epithelial cells (IA: 120.20±3.87, 116.70±3.46); Western Blot showed high expression of c-FLIP in renal tissues (c-FLIP/GAPDH: 0.99±0.01, 0.98±0.02), and low expressions of Bax and caspase-3 (Bax/GAPDH: 0.16±0.04, 0.19±0.03, caspase-3/GAPDH: 0.24±0.04, 0.23±0.05). Compared with the Sham group, in the SAKI group, renal tubular epithelial cells were degenerated and necrosis, and a large number of interstitial inflammatory cells infiltrated, the renal injury score was significantly increased (4.60±0.52 vs. 1.30±0.48, P < 0.01); the levels of SCr and BUN were significantly increased [SCr (μmol/L): 193.90±13.54 vs. 24.50±3.78, BUN (mmol/L): 81.60±7.26 vs. 5.20±0.92, both P < 0.01]; the c-FLIP positive cells in renal tissues was significantly reduced (IA: 17.11±0.82 vs. 116.70±3.46, P < 0.01); the expression of c-FLIP protein in renal tissues was significantly decreased (c-FLIP/GAPDH: 0.29±0.03 vs. 0.98±0.02, P < 0.01), while the expressions of Bax and caspase-3 protein were significantly increased (Bax/GAPDH: 0.87±0.06 vs. 0.19±0.03, caspase-3/GAPDH: 0.88±0.07 vs. 0.23±0.05, both P < 0.01]. The correlation analysis showed that the c-FLIP protein was significantly negatively correlated with Bax (r = -0.468, P = 0.029) and caspase-3 protein expressions (r = -0.663, P = 0.004).

CONCLUSIONS

The expression level of c-FLIP protein was significantly down-regulated in renal tissue of SAKI, and its down-regulation mechanism was associated with increased apoptosis of renal tubular epithelial cells, which could be an effective target for the treatment of SAKI.

[Survey on the use of glucocorticoids in severe community-acquired pneumonia in intensive care unit of forty-five hospitals in Zhejiang Province]

OBJECTIVE

To investigate the use of glucocorticoids in patients with severe community-acquired pneumonia (SCAP) in the intensive care unit (ICU) of Hospitals in Zhejiang Province and to provide a reference for guiding clinical use of SCAP patients.

METHODS

To draw up a questionnaire with reference to the Chinese and international guidelines, and to investigate the knowledge of community-acquired pneumonia (CAP) related guidelines and the use of glucocorticoids in patients with SCAP by doctors in hospitals above secondary level in Zhejiang Province by Email. Then the valid questionnaire was analyzed.

RESULTS

In June 2016, 340 questionnaires were distributed, and all were returned after 2 months, with 333 of valid; 333 doctors from 45 ICUs in Zhejiang Province participated in the survey. (1) The knowledge of CAP-related guidelines in ICU doctors: 79.58% (265/333) of the doctors had read the CAP guidelines, and those who work over 10 years had a higher reading rate than those with 1-5 years and 6-10 years [93.07% (94/101) vs. 74.00% (111/150), 73.17% (60/82), both P < 0.05]. Post-graduates and above had higher reading rates than undergraduates [85.35% (134/157) vs. 74.43% (131/176), P < 0.05]. Senior doctors had higher reading rates than the junior and intermediate doctors [93.07% (94/101) vs. 71.43% (80/112), 75.83% (91/120), both P < 0.05]. The rate of understanding the clinical application of glucocorticoids was 13.81% (46/333). The doctors who work over 10 years and the seniorshad a relatively high awareness rate, 23.76% (24/101) and 20.79% (21/101) respectively. However, there was no significant difference in the awareness rate between doctors with different degrees and different levels of hospitals. (2) For the use of glucocorticoids in different causes of pneumonia, 44.74% (149/333) of doctors routinely used glucocorticoids in severe viral pneumonia. The proportion of glucocorticoids used in severe bacterial pneumonia, severe fungal pneumonia, severe pneumocystis pneumonia, chronic obstructive pulmonary disease (COPD) and severe pneumonia were 22.82% (76/333), 9.31% (31/333), 22.52% (75/333) and 18.32% (61/333), respectively. (3) The way of glucocorticoid usage: 79.58% (265/333) of doctors chose methylprednisolone, 4.20% (14/333) chose hydrocortisone, 1.20% (4/333) chose dexamethasone, and 15.02% (50/333) had not use glucocorticoids. The proportion of physicians who chose to use glucocorticoids within 24 hours of admission and 1-7 days after admission were 52.65% (149/283) and 47.35% (134/283), respectively. Glucocorticoids were used more in doctors with lower academic qualifications and hospitals within 24 hours. The undergraduate degree was 61.39% (97/158), and the second-grade class hospital was 67.50% (27/40). Among the doctors who chose methylprednisolone, 60.75% (161/265) prescribe the dose ≤ 80 mg/d; 79.15% (224/283) chose the course of ≤ 7 days. The number of years of work, education, professional title and hospital grade had no significant effect on the choice of methylprednisolone and the course of treatment.

CONCLUSIONS

ICU doctors of 45 hospitals in Zhejiang Province have a high degree of heterogeneity in the understanding of the use and guidelines of glucocorticoids in SCAP. It is necessary to strengthen the ICU doctor's study of clinical guidelines at home and abroad and to develop a glucocorticoid use plan according to the specific conditions of patients, so that SCAP patients can benefit more.

Induction therapy with thymoglobulin or interleukin-2 receptor antagonist for Chinese recipients of living donor renal transplantation: a retrospective study

Background

Recipients of living donor renal transplantation are typically considered to have a relatively lower immunological risk. This retrospective study aimed to compare the therapeutic efficacy and safety between rabbit antithymocyte globulin (rATG) or interleukin-2 receptor antagonist (IL2-RA) induction therapies in Chinese population.

Methods

A total of 188 patients receiving living donor renal transplantation between February 2004 and December 2013 were included and divided into the rATG group and based on their induction therapy. The primary outcome was clinically-suspected rejection. The incidences of de novo donor-specific antigen (dn-DSA), graft survival, and infection were also compared between groups. A multivariate Cox regression analysis was performed to investigate the influential factors associated with clinically-suspected acute rejection and graft survival.

Results

The rATG group had a higher panel reactive antibody (PRA) score and more complete HLA mismatches than the IL2-RA group (both P < 0.001). The incidences of clinically-suspected acute rejection (9.8% vs. 8.8%; P = 0.832) and dn-DSA formation (4.9% vs. 5.4%, P = 0.44) were not significantly different between groups. Kaplan-Meier curve analysis demonstrated that the graft survivals of two groups were comparable (P = 0.857). After adjusting for patients’ age, sex, PRA, HLA mismatch confounders, and the use of corticoids, the multivariate Cox regression analysis showed that methods of induction therapy were not associated with clinically-suspected acute rejection and graft survival (both P > 0.05). The incidences of complications (infections, pneumonia, liver injury and myelosuppression) were all comparable between groups (all P > 0.05).

Conclusions

These results suggested that rATG could be a safe and efficient immunosuppressant when used in a Chinese recipient population with a higher immunological risk in living donor renal transplantation.

[Protective effects of Klotho protein on acute kidney injury in septic mice and its mechanism]

OBJECTIVE

To investigate the protective effects of Klotho protein, a kind of single-pass transmembrane protein, on acute kidney injury (AKI) in septic mice and its mechanism.

METHODS

Sixty SPF healthy male C57BL/6 mice (6-8 weeks) were randomly divided into sham operation group (Sham group), sepsis model group (CLP group) and Klotho protein injection group (CLP+KL group), with 20 in each group. The septic AKI mice model was established by cecal ligation and puncture (CLP); Sham group had the same procedure except that the cecal was not ligated. The CLP+KL group was received Klotho protein (0.02 mg/kg) by intraperitoneal consecutive injection for 4 days after operation; Sham group and CLP group were injected with the same amount of saline. Blood samples were obtained at 24 hours after operation, the levels of serum creatinine (SCr) and urea nitrogen (BUN) were measured by sarcosine oxidase and urease method. The mice were sacrificed under anesthesia at 5 days after operation to harvest renal tissues, and the pathological damage of the kidney was evaluated by hematoxylin-eosin (HE) staining. The ultrastructure of mitochondria in mouse renal tubular epithelial cells was observed under transmission electron microscope. The levels of reduced glutathione hormone (GSH), malondialdehyde (MDA) and nitric oxide synthase (NOS) in mitochondrion were determined by micro-enzyme method, thiobarbituric acid method, colorimetry method, respectively. The protein expressions of Klotho, Bcl-2 and cytochrome C (Cyt C) were detected by Western Blot.

RESULTS

The pathological structure of the kidneys in the Sham group was clear and intact. Compared with the Sham group, the renal tissue edema of the mice in the CLP group was significant, and the transparent tube type was observed in the small lumen, and the interstitial inflammatory cells infiltrated; the levels of SCr and BUN were significantly increased [SCr (μmol/L): 182.60±6.97 vs. 47.20±5.37, BUN (mmol/L): 53.70±5.12 vs. 18.70±2.62, both P < 0.01]; the mitochondria were swollen and deformed, the sputum structure was destroyed, the matrix density was decreased, the outer membrane was lost, and the levels of MDA, GSH and NOS were significantly increased [MDA (μmol/g): 1.172±0.046 vs. 0.746±0.094, GSH (μmol/g): 5.765±0.059 vs. 4.223±0.072, NOS (kU/g): 0.91±0.05 vs. 0.68±0.03, all P < 0.01]; the protein expressions of Klotho and Bcl-2 in renal tissue were decreased, and the protein expression of Cyt C was increased (Klotho/β-actin: 0.188±0.020 vs. 0.538±0.024, Bcl-2/β-actin: 0.311±0.010 vs. 0.391±0.015, Cyt C/β-actin: 0.226±0.010 vs. 0.135±0.006, all P < 0.01). Comparing with the CLP group, the glomerular and tubular tissue epithelial edema and the small lumen in the CLP+KL group were reduced; the levels of SCr and BUN were significantly decreased [SCr (μmol/L): 85.70±7.23 vs. 182.60±6.97, BUN (mmol/L): 35.30±3.50 vs. 53.70±5.12, both P < 0.01]; the mitochondrial structure was relatively intact; the levels of MDA, GSH and NOS were significantly decreased [MDA (μmol/g): 0.958±0.072 vs. 1.172±0.046, GSH (μmol/g): 4.756±0.107 vs. 5.765±0.059, NOS (kU/g): 0.79±0.02 vs. 0.91±0.05, all P < 0.01]; the protein expressions of Klotho, Bcl-2 were significantly increased, but the protein expression of Cyt C was significantly decreased (Klotho/β-actin: 0.336±0.011 vs. 0.188±0.020, Bcl-2/β-actin: 0.474±0.017 vs. 0.311±0.010, Cyt C/β-actin: 0.168±0.006 vs. 0.226±0.010, all P < 0.01).

CONCLUSIONS

Klotho protein has significant protective effects on AKI in septic mice, and its mechanism is related to maintaining mitochondrial structural integrity and oxidative stress response.

Biosynthesis of clinically used antibiotic fusidic acid and identification of two short-chain dehydrogenase/reductases with converse stereoselectivity

Fusidic acid is the only fusidane-type antibiotic that has been clinically used. However, biosynthesis of this important molecule in fungi is poorly understood. We have recently elucidated the biosynthesis of fusidane-type antibiotic helvolic acid, which provides us with clues to identify a possible gene cluster for fusidic acid (fus cluster). This gene cluster consists of eight genes, among which six are conserved in the helvolic acid gene cluster except fusC1 and fusB1. Introduction of the two genes into the Aspergillus oryzae NSAR1 expressing the conserved six genes led to the production of fusidic acid. A stepwise introduction of fusC1 and fusB1 revealed that the two genes worked independently without a strict reaction order. Notably, we identified two short-chain dehydrogenase/reductase genes fusC1 and fusC2 in the fus cluster, which showed converse stereoselectivity in 3-ketoreduction. This is the first report on the biosynthesis and heterologous expression of fusidic acid.

Computational prediction and analysis of species-specific fungi phosphorylation via feature optimization strategy

Protein phosphorylation is a reversible and ubiquitous post-translational modification that primarily occurs at serine, threonine and tyrosine residues and regulates a variety of biological processes. In this paper, we first briefly summarized the current progresses in computational prediction of eukaryotic protein phosphorylation sites, which mainly focused on animals and plants, especially on human, with a less extent on fungi. Since the number of identified fungi phosphorylation sites has greatly increased in a wide variety of organisms and their roles in pathological physiology still remain largely unknown, more attention has been paid on the identification of fungi-specific phosphorylation. Here, experimental fungi phosphorylation sites data were collected and most of the sites were classified into different types to be encoded with various features and trained via a two-step feature optimization method. A novel method for prediction of species-specific fungi phosphorylation-PreSSFP was developed, which can identify fungi phosphorylation in seven species for specific serine, threonine and tyrosine residues (http://computbiol.ncu.edu.cn/PreSSFP). Meanwhile, we critically evaluated the performance of PreSSFP and compared it with other existing tools. The satisfying results showed that PreSSFP is a robust predictor. Feature analyses exhibited that there have some significant differences among seven species. The species-specific prediction via two-step feature optimization method to mine important features for training could considerably improve the prediction performance. We anticipate that our study provides a new lead for future computational analysis of fungi phosphorylation.

PredGly: predicting lysine glycation sites for Homo sapiens based on XGboost feature optimization

Motivation

Protein glycation is a familiar post-translational modification (PTM) which is a two-step non-enzymatic reaction. Glycation not only impairs the function but also changes the characteristics of the proteins so that it is related to many human diseases. It is still much more difficult to systematically detect glycation sites due to the glycated residues without crucial patterns. Computational approaches, which can filter supposed sites prior to experimental verification, can extremely increase the efficiency of experiment work. However, the previous lysine glycation prediction method uses a small number of training datasets. Hence, the model is not generalized or pervasive.

Results

By searching from a new database, we collected a large dataset in Homo sapiens. PredGly, a novel software, can predict lysine glycation sites for H.sapiens, which was developed by combining multiple features. In addition, XGboost was adopted to optimize feature vectors and to improve the model performance. Through comparing various classifiers, support vector machine achieved an optimal performance. On the basis of a new independent test set, PredGly outperformed other glycation tools. It suggests that PredGly can provide more instructive guidance for further experimental research of lysine glycation.

Availability and implementation

https://github.com/yujialinncu/PredGly

Supplementary information

Supplementary data are available at Bioinformatics online.

Dynamic transcriptome analysis of root nitrate starvation and re-supply provides insights into nitrogen metabolism in pear (Pyrus bretschneideri)

Pear (Pyrus bretschneideri) is a popular fruit worldwide, but the irrational utilization of nitrogen as a fertilizer not only greatly affects the fruit' quality, but also wastes resources and results in serious environmental pollution. To better understand the molecular mechanism in pear responsible for the regulation of nitrate transport and assimilation, RNA-seq was performed on samples collected in response to nitrate treatments. Here, 10,273 differentially expressed genes were obtained and annotated into 49 GO terms, 45 clusters having co-expression trends that involved 18 KEGG-defined significantly overrepresented pathways. The KEGG pathways revealed that 15 unigenes, including one NRT gene, two NR genes, one NiR gene, two GDH genes, six GS genes and three GOGAT genes, were related to nitrogen metabolism and significantly differentially expressed in response to nitrate starvation and a nitrate re-supply treatment. Furthermore, 449 transcription factors belonging to 35 different families were identified during the nitrate treatments. The expression patterns of 14 randomly selected differentially expressed genes were validated by qRT-PCR. This study provides valuable resources for investigating the genetics of the nitrogen metabolic pathways and improving nitrogen utilization efficiency in pear.

Identification and comparative analysis of the MCU gene family in pear and its functions during fruit ripening

Mitochondrial calcium uniporter (MCU) plays an important role in cell senescence and aging in mammals. However, the function of MCU homologs during the ripening and senescence of postharvest fruit had not been characterized until recently. In this study, a comprehensive study was conducted on the characteristics of the MCU family genes in the pear genome. In total, seven PbrMCU genes were identified and classified into two subgroups. Whole-genome duplication (WGD)/segmental duplication is the main driving force behind their expansion. The genes contained various conserved motifs and cis-acting elements, and the correspondent proteins possessed a serial of conserved motifs. A total of six PbrMCUs with diverse expression patterns were detected as the pear fruit ripened. Following the results of the impact of postharvest treatments (ethrel and 1-methylcyclopropene) and transient overexpression of 1-aminocyclopropane-1-carboxylate oxidase 1 gene (PbrACO1), the candidate genes PbrMCU3, PbrMCU4, and PbrMCU7 were determined to be involved in pear ripening. Moreover, the response of mitochondrial calcium uptake 1 (PbrMICU1) transcription to the postharvest treatments was similar to that of PbrMCU4.