COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas.

A dysfunctional immune response in coronavirus disease 2019 (COVID-19) patients is a recurrent theme impacting symptoms and mortality, yet a detailed understanding of pertinent immune cells is not complete. We applied single-cell RNA sequencing to 284 samples from 196 COVID-19 patients and controls and created a comprehensive immune landscape with 1.46 million cells. The large dataset enabled us to identify that different peripheral immune subtype changes are associated with distinct clinical features, including age, sex, severity, and disease stages of COVID-19. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA was found in diverse epithelial and immune cell types, accompanied by dramatic transcriptomic changes within virus-positive cells. Systemic upregulation of S100A8/A9, mainly by megakaryocytes and monocytes in the peripheral blood, may contribute to the cytokine storms frequently observed in severe patients. Our data provide a rich resource for understanding the pathogenesis of and developing effective therapeutic strategies for COVID-19.

Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Although host responses to the ancestral SARS-CoV-2 strain are well described, those to the new Omicron variants are less resolved. We profiled the clinical phenomes, transcriptomes, proteomes, metabolomes, and immune repertoires of >1,000 blood cell or plasma specimens from SARS-CoV-2 Omicron patients. Using in-depth integrated multi-omics, we dissected the host response dynamics during multiple disease phases to reveal the molecular and cellular landscapes in the blood. Specifically, we detected enhanced interferon-mediated antiviral signatures of platelets in Omicron-infected patients, and platelets preferentially formed widespread aggregates with leukocytes to modulate immune cell functions. In addition, patients who were re-tested positive for viral RNA showed marked reductions in B cell receptor clones, antibody generation, and neutralizing capacity against Omicron. Finally, we developed a machine learning model that accurately predicted the probability of re-positivity in Omicron patients. Our study may inspire a paradigm shift in studying systemic diseases and emerging public health concerns.

Association and mediation between educational attainment and respiratory diseases: a Mendelian randomization study.

BACKGROUND: Respiratory diseases are a major health burden, and educational inequalities may influence disease prevalence. We aim to evaluate the causal link between educational attainment and respiratory disease, and to determine the mediating influence of several known modifiable risk factors. METHODS: We conducted a two-step, two-sample Mendelian randomization (MR) analysis using summary statistics from genome-wide association studies (GWAS) and single nucleotide polymorphisms (SNPs) as instrumental variables for educational attainment and respiratory diseases. Additionally, we performed a multivariable MR analysis to estimate the direct causal effect of each exposure variable included in the analysis on the outcome, conditional on the other exposure variables included in the model. The mediating roles of body mass index (BMI), physical activity, and smoking were also assessed. FINDINGS: MR analyses provide evidence of genetically predicted educational attainment on the risk of FEV1 (ß = 0.10, 95% CI 0.06, 0.14), FVC (ß = 0.12, 95% CI 0.07, 0.16), FEV1/FVC (ß = - 0.005, 95% CI - 0.05, 0.04), lung cancer (OR = 0.54, 95% CI 0.45, 0.65) and asthma (OR = 0.86, 95% CI 0.78, 0.94). Multivariable MR dicated the effect of educational attainment on FEV1 (ß = 0.10, 95% CI 0.04, 0.16), FVC (ß = 0.07, 95% CI 0.01, 0.12), FEV1/FVC (ß = 0.07, 95% CI 0.01, 0.01), lung cancer (OR = 0.55, 95% CI 0.42, 0.71) and asthma (OR = 0.88, 95% CI 0.78, 0.99) persisted after adjusting BMI and cigarettes per day. Of the 23 potential risk factors, BMI, smoking may partially mediate the relationship between education and lung disease. CONCLUSION: High levels of educational attainment have a potential causal protective effect on respiratory diseases. Reducing smoking and adiposity may be a target for the prevention of respiratory diseases attributable to low educational attainment.

Integrated oral microgel system ameliorates renal fibrosis by hitchhiking co-delivery and targeted gut flora modulation.

BACKGROUND: Renal fibrosis is a progressive process associated with chronic kidney disease (CKD), contributing to impaired kidney function. Active constituents in traditional Chinese herbs, such as emodin (EMO) and asiatic acid (AA), exhibit potent anti-fibrotic properties. However, the oral administration of EMO and AA results in low bioavailability and limited kidney accumulation. Additionally, while oral probiotics have been accepted for CKD treatment through gut microbiota modulation, a significant challenge lies in ensuring their viability upon administration. Therefore, our study aims to address both renal fibrosis and gut microbiota imbalance through innovative co-delivery strategies. RESULTS: In this study, we developed yeast cell wall particles (YCWPs) encapsulating EMO and AA self-assembled nanoparticles (NPYs) and embedded them, along with Lactobacillus casei Zhang, in chitosan/sodium alginate (CS/SA) microgels. The developed microgels showed significant controlled release properties for the loaded NPYs and prolonged the retention time of Lactobacillus casei Zhang (L. casei Zhang) in the intestine. Furthermore, in vivo biodistribution showed that the microgel-carried NPYs significantly accumulated in the obstructed kidneys of rats, thereby substantially increasing the accumulation of EMO and AA in the impaired kidneys. More importantly, through hitchhiking delivery based on yeast cell wall and positive modulation of gut microbiota, our microgels with this synergistic strategy of therapeutic and modulatory interactions could regulate the TGF-ß/Smad signaling pathway and thus effectively ameliorate renal fibrosis in unilateral ureteral obstruction (UUO) rats. CONCLUSION: In conclusion, our work provides a new strategy for the treatment of renal fibrosis based on hitchhiking co-delivery of nanodrugs and probiotics to achieve synergistic effects of disease treatment and targeted gut flora modulation.

Association between plasma metal exposure and health span in very elderly adults: a prospective cohort study with mixture statistical approach.

BACKGROUND: Metals have been linked to a diverse spectrum of age-related diseases; however, the effects of metal exposure on health span remains largely unknown. This cohort study aims to determine the association between plasma metal and health span in elder adults aged ≥ 90 years. METHODS: The plasma concentrations of seven metals were measured at baseline in 300 elder adults. The end of the health span (EHS) was identified as the occurrence of one of eight major morbidities or mortality events. We used Cox regression to assess hazard ratios (HR). The combined effects of multiple metal mixtures were estimated using grouped-weighted quantile sum (GWQS), quantile g-computation (Q-gcomp), and Bayesian kernel machine regression (BKMR) methods. RESULTS: The estimated HR for EHS with an inter-quartile range (IQR) increment for selenium (Se) was 0.826 (95% confidence interval [CI]: 0.737-0.926); magnesium (Mg), 0.806 (95% CI: 0.691-0.941); iron (Fe), 0.756 (95% CI: 0.623-0.917), and copper (Cu), 0.856 (95% CI: 0.750-0.976). The P for trend of Se, Mg, and Fe were all < 0.05. In the mixture analyses, Q-gcomp showed a negative correlation with EHS (P = 0.904), with the sum of the negative coefficients being -0.211. CONCLUSION: Higher plasma Se, Mg, and Fe reduced the risk of premature end of health span, suggesting that essential metal elements played a role in health maintenance in elder adults.

Bone marrow mesenchymal stem cell-derived exosomal lncRNA KLF3-AS1 stabilizes Sirt1 protein to improve cerebral ischemia/reperfusion injury via miR-206/USP22 axis.

BACKGROUND: Cerebral ischemia/reperfusion (I/R) is a pathological process that occurs in ischemic stroke. Bone marrow mesenchymal stem cell-derived exosomes (BMSC-Exos) have been verified to relieve cerebral I/R-induced inflammatory injury. Hence, we intended to clarify the function of BMSC-Exos-delivered lncRNA KLF3-AS1 (BMSC-Exos KLF3-AS1) in neuroprotection and investigated its potential mechanism. METHODS: To mimic cerebral I/R injury in vivo and in vitro, middle cerebral artery occlusion (MCAO) mice model and oxygen-glucose deprivation (OGD) BV-2 cell model were established. BMSC-Exos KLF3-AS1 were administered in MCAO mice or OGD-exposed cells. The modified neurological severity score (mNSS), shuttle box test, and cresyl violet staining were performed to measure the neuroprotective functions, while cell injury was evaluated with MTT, TUNEL and reactive oxygen species (ROS) assays. Targeted genes and proteins were detected using western blot, qRT-PCR, and immunohistochemistry. The molecular interactions were assessed using RNA immunoprecipitation, co-immunoprecipitation and luciferase assays. RESULTS: BMSC-Exos KLF3-AS1 reduced cerebral infarction and improved neurological function in MCAO mice. Similarly, it also promoted cell viability, suppressed apoptosis, inflammatory injury and ROS production in cells exposed to OGD. BMSC-Exos KLF3-AS1 upregulated the decreased Sirt1 induced by cerebral I/R. Mechanistically, KLF3-AS1 inhibited the ubiquitination of Sirt1 protein through inducing USP22. Additionally, KLF3-AS1 sponged miR-206 to upregulate USP22 expression. Overexpression of miR-206 or silencing of Sirt1 abolished KLF3-AS1-mediated protective effects. CONCLUSION: BMSC-Exos KLF3-AS1 promoted the Sirt1 deubiquitinating to ameliorate cerebral I/R-induced inflammatory injury via KLF3-AS1/miR-206/USP22 network.

Radiation-induced bystander effects impair transplanted human hematopoietic stem cells via oxidative DNA damage.

Total body irradiation (TBI) is commonly used in host conditioning regimens for human hematopoietic stem cell (HSC) transplantation to treat various hematological disorders. Exposure to TBI not only induces acute myelosuppression and immunosuppression, but also injures the various components of the HSC niche in recipients. Our previous study demonstrated that radiation-induced bystander effects (RIBE) of irradiated recipients decreased the long-term repopulating ability of transplanted mouse HSCs. However, RIBE on transplanted human HSCs have not been studied. Here, we report that RIBE impaired the long-term hematopoietic reconstitution of human HSCs as well as the colony-forming ability of human hematopoietic progenitor cells (HPCs). Our further analyses revealed that the RIBE-affected human hematopoietic cells showed enhanced DNA damage responses, cell-cycle arrest, and p53-dependent apoptosis, mainly because of oxidative stress. Moreover, multiple antioxidants could mitigate these bystander effects, though at different efficacies in vitro and in vivo. Taken together, these findings suggest that RIBE impair human HSCs and HPCs by oxidative DNA damage. This study provides definitive evidence for RIBE on transplanted human HSCs and further justifies the necessity of conducting clinical trials to evaluate different antioxidants to improve the efficacy of HSC transplantation for the patients with hematological or nonhematological disorders.

Association of ambient PM10 and PM2.5 with coronary stenosis measured using selective coronary angiography.

BACKGROUND: Long-term ambient particulate matter (PM) exposure exerts detrimental effects on cardiovascular health. Evidence on the relation of chronically exposed ambient PM10 and PM2.5 with coronary stenosis remains lacking. Our aim was to investigate the association of PM10 and PM2.5 with coronary stenosis in patients undergoing coronary angiography. METHODS: We performed a retrospective cohort study consisting of 7513 individuals who underwent coronary angiography in Fujian Province, China, from January 2019 to December 2021. We calculated a modified Gensini score (GS) to represent the degree of stenosis in coronary arteries by selective coronary angiography. We fitted linear regressions and logistic models to assess the association of PM10 and PM2.5 with coronary stenosis. We employed restricted cubic splines to describe the exposure-response curves. We performed mediation analyses to assess the potential mediators. RESULTS: Long-term ambient PM10 and PM2.5 (prior three years average) exposure was significantly associated with the GS, with a breakpoint concentration of 47.5 µg/m3 and 25.8 µg/m3 for PM10 and PM2.5, respectively, above which we found a linear positive exposure-response relationship of ambient PM with GS. Each 10 µg /m3 increase in PM10 exposure (ß: 4.81, 95 % CI: 0.44-9.19) and PM2.5 exposure [ß: 10.50, 95 % CI: 3.14-17.86] were positively related to the GS. The adjusted odds ratio (OR) for each 10 µg/m3 increment in PM10 exposure on severe coronary stenosis was 1.33 (95 % CI: 1.04-1.76). Correspondingly, the adjusted OR for PM2.5 was 1.87 (95 % CI: 1.24-2.99). The mediation analysis indicated that the effect of PM10 on coronary stenosis may be partially mediated through total cholesterol, low-density lipoprotein cholesterol, apolipoprotein B, serum creatinine and blood urea nitrogen, and the effect of PM2.5 may be mediated in part by hemoglobin A1c. CONCLUSION: Our study provides the first evidence that chronic ambient PM10 and PM2.5 exposure was associated with coronary stenosis assessed by GS in patients with suspected coronary artery disease and reveals its potential mediators.

Synthetic bone grafting with preserved cartilage flap via a medial malleolus osteotomy approach to treat osteochondral lesion of the talus: technical note and preliminary clinical results.

PURPOSE: Although various surgical procedures are available for osteochondral lesion of the talus (OLT), there is still no consensus on its best treatment. The purposes of this study were to describe a new surgical technique to treat OLT and to analyze its preliminary clinical results. METHODS: Eight patients were enrolled in this retrospective study between March 2019 and May 2022 in the Second Affiliated Hospital of Chongqing Medical University. All patients were treated by synthetic bone grafting with preserved cartilage flap via a medial malleolus osteotomy approach. The patients' characteristics, operative time, and estimated blood loss were evaluated. Intraoperative photos, preoperative and postoperative X-ray and MRI imaging were recorded. The American Orthopaedic Foot and Ankle Society (AOFAS) ankle-hindfoot score and visual analog scale (VAS) score were also recorded before surgery and at each follow-up. RESULTS: At six months after the operation, all patients showed bone ingrowth and remodeling according to X-ray and MRI. No obvious defects or ladder was found on the cartilage surface of all patients according to MRI. The AOFAS score improved from 61.63 ± 8.85 (range, 49-74) to 91.13 ± 4.49 (range, 83-97) (p < 0.001) and VAS score improved from 5.50 ± 1.60 (range, 4-8) before surgery to 1.88 ± 0.83 (range, 1-3) (p < 0.001) at latest follow-up. In all eight patients, no wound infection, skin necrosis, or delayed healing of osteotomy was found. CONCLUSION: We proposed a simple and effective technique that restored the shape of the cartilage surface by preserving the cartilage flap and restoring the natural congruency of the subchondral bone by synthetic bone grafting. We found satisfying clinical outcomes in short-term follow-up. Our new technique might be a new surgical option for the treatment of OLT and its effectiveness should be further evaluated.

Prevalence, correlates, and trajectory of screen viewing among Chinese children in Changsha: a birth cohort study.

BACKGROUND: High screen viewing time has detrimental effects on children's health, development, and behavior developing. Children are being exposed to more and more media devices at an earlier age. This study was aimed to determine the amount of daily screen time and its variation and to assess potential factors of screen time by identifying the trajectory of screen time among children aged 1 to 5 years. METHOD: This study was based on a representative sample of Changsha young children from a cohort study during 2015-2020. The demographic information and children's screen viewing time were collected by parents or caregivers through face-to-face interviews. The Latent growth model was used to test the effects of outdoor play on screen viewing time at eight time points, meanwhile, unconditional and conditional models were examined sequentially. RESULT: After excluding respondents with missing key variables, we included 953 children in the final analysis. Children's outdoor play was slightly increased at 18 months and subsequently declined at 24-60 months, with a maximum duration of 2.96 h per day. Children's average screen time was increased at 18-36 months, and decreased at 42-54 months, with a slight increase at 60 months. The duration of media exposure peaked at 1.4 h/d at age of 36 months and 60 months. Standardized coefficients of the outdoor play at age of 12 months showed negative effects on the screen time in children, but with positive influence at age of 24, 36, and 42 months (P <  0.01). CONCLUSION: High proportions of young Chinese children in Changsha had more screen time than the AAP recommended according to our analysis. Significant predictors of screen time included pregnancy computer use, paternal educational level, and outdoor play in this study, however, further understanding of risk factors is needed to promote great public health efforts to reduce children's screen exposure.

Data-Driven Prediction of Formation Mechanisms of Lithium Ethylene Monocarbonate with an Automated Reaction Network.

Interfacial reactions are notoriously difficult to characterize, and robust prediction of the chemical evolution and associated functionality of the resulting surface film is one of the grand challenges of materials chemistry. The solid-electrolyte interphase (SEI), critical to Li-ion batteries (LIBs), exemplifies such a surface film, and despite decades of work, considerable controversy remains regarding the major components of the SEI as well as their formation mechanisms. Here we use a reaction network to investigate whether lithium ethylene monocarbonate (LEMC) or lithium ethylene dicarbonate (LEDC) is the major organic component of the LIB SEI. Our data-driven, automated methodology is based on a systematic generation of relevant species using a general fragmentation/recombination procedure which provides the basis for a vast thermodynamic reaction landscape, calculated with density functional theory. The shortest pathfinding algorithms are employed to explore the reaction landscape and obtain previously proposed formation mechanisms of LEMC as well as several new reaction pathways and intermediates. For example, we identify two novel LEMC formation mechanisms: one which involves LiH generation and another that involves breaking the (CH2)O-C(═O)OLi bond in LEDC. Most importantly, we find that all identified paths, which are also kinetically favorable under the explored conditions, require water as a reactant. This condition severely limits the amount of LEMC that can form, as compared with LEDC, a conclusion that has direct impact on the SEI formation in Li-ion energy storage systems. Finally, the data-driven framework presented here is generally applicable to any electrochemical system and expected to improve our understanding of surface passivation.

GPA peptide enhances Nur77 expression in intestinal epithelial cells to exert a protective effect against DSS-induced colitis.

Ulcerative colitis (UC) is a widespread inflammatory bowel disease that causes long-lasting inflammation and ulcers in the colon and rectum. In the inflamed tissue of patients with UC, the tight junctions are disrupted and large amounts of pro-inflammatory cytokines are produced, resulting in immune dysregulation. The expression of Nur77 is significantly reduced in the colon of inflammatory bowel disease, while Nur77 deficiency increases the susceptibility to DSS-induced colitis. Here, we report that Gly-Pro-Ala (GPA) peptide isolated from fish skin gelatin hydrolysate can significantly alleviate intestinal inflammation and damage caused by DSS-induced mice colitis. Besides maintaining the intestinal epithelial barrier, GPA alleviates intestinal inflammation and oxidative stress by inhibiting NF-κB activation. Interestingly, GPA binds to the ligand-binding domain of Nur77 and stimulates its autotranscriptional activity to enhance its expression in intestinal epithelial cells. Furthermore, GPA activates the promoter of IκBα to increase its expression, resulting in the abolishment of the NF-κB pathway. In contrast, the inhibitory effects of GPA on colitis are abolished in Nur77-/- mice. Our results suggest that as a Nur77 modulator, GPA may be applied to the prevention of intestinal inflammation.

pH-sensitive dual drug loaded janus nanoparticles by oral delivery for multimodal analgesia.

BACKGROUND: Based on the concept of "multimodal analgesia", a novel dual drug delivery system was designed to achieve synergistic analgesia between najanajaatra venom protein (αCT) and resveratrol (Res). In order to meet the joint loading of two drugs with different physicochemical properties without affecting each other, an oral Janus nanoparticle (JNP) with a unique cavity structure and synergistic drug delivery was constructed using an improved double emulsion solvent evaporation method, and combined with low-molecular-weight chitosan/sodium alginate and PLGA to achieve its pH-responsive. RESULTS: The synthesized αCT/Res-JNPs are homogeneous in shape, with a two-compartment structure, approximately 230 nm in size, and zeta potential of 23.6 mV. Drug release assayed in vitro show that JNP was stable in simulated gastric juice (pH = 1.2) but was released in phosphate buffer saline (pH = 7.4). After intragastric administration in rats, PK evaluation showed that αCT/Res-JNPs could significantly improve the oral bioavailability, and the simultaneous encapsulation of the two drugs had no significant interaction on PK parameters. An obvious synergistic analgesic effects of αCT/Res-JNPs was confirmed in a spinal cord injury and acute pain model. Confocal laser scanning microscopy and single-pass intestinal perfusion model provided strong evidence that αCT/Res-JNPs could pass through intestinal epithelial cells, and the endocytosis pathway was mainly involved in the mediation and pinocytosis of reticulin. The concentrations of αCT and Res from αCT/Res-JNP in lymphatic transport were only about 8.72% and 6.08% of their blood concentrations at 1 h, respectively, which indicated that lymphatic transport in the form of JNP has limited advantages in improving the oral bioavailability of Res and αCT. Cellular uptake efficiency at 4 h was about 10-15% in Caco-2 cell lines for αCT/Res-JNP, but was reduced to 7% in Caco-2/HT29-MTX co-culture models due to the hindrance by the mucus layers. Approximately 12-17% of αCT/Res-JNP were transported across Caco-2/HT29-MTX/Raji monolayers. The cumulative absorption of JNP in three cell models was higher than that of free drug. CONCLUSIONS: This study investigated the contribution of Janus nanoparticles in oral absorption, and provide a new perspective for oral administration and analgesic treatment of dual drug delivery system containing peptide drugs.

Zfp217 mediates m6A mRNA methylation to orchestrate transcriptional and post-transcriptional regulation to promote adipogenic differentiation.

A complex and highly orchestrated gene expression program chiefly establishes the properties that define the adipocyte phenotype, in which the vast majority of factors are involved in transcriptional regulation. However, the mechanisms by post-transcriptional modulation are poorly understood. Here, we showed that zinc finger protein (Zfp217) couples gene transcription to m6A mRNA modification to facilitate adipogenesis. Zfp217 modulates m6A mRNA methylation by activating the transcription of m6A demethylase FTO. Consistently, depletion of Zfp217 compromises adipogenic differentiation of 3T3L1 cells and results in a global increase of m6A modification. Moreover, the interaction of Zfp217 with YTHDF2 is critical for allowing FTO to maintain its interaction with m6A sites on various mRNAs, as loss of Zfp217 leads to FTO decrease and augmented m6A levels. These findings highlight a role for Zfp217-dependent m6A modification to coordinate transcriptional and post-transcriptional regulation and thus promote adipogenic differentiation.

Changes of lipid profiles in human umbilical vein endothelial cells exposed to zirconia nanoparticles with or without the presence of free fatty acids.

Zirconia nanoparticles (NPs) have been widely used in biomedicine, which will likely lead to their interactions with endothelial cells (ECs). However, the toxicity of zirconia NPs to ECs is less investigated and the toxicological data are not consistent. Furthermore, no previous study, to the best of our knowledge, investigated the influence of zirconia NPs on lipid metabolism. This study investigated lipid profiles in human umbilical vein ECs (HUVECs) exposed to zirconia NPs with or without the presence of free fatty acids (FFAs). Incubation with FFA changed the hydrodynamic size, zeta potential, and surface profiles of zirconia NPs, indicating the surface coating effects. Exposure of HUVECs to various concentrations of zirconia NPs with or without the presence of FFA did not significantly decrease cellular viability, but FFA decreased zirconium elemental levels in NP-exposed cells. Oil Red O staining showed that FFA or zirconia NPs and FFA, but not zirconia NPs alone, significantly increased lipid accumulation in HUVECs. Consistently, lipidomic data suggested that exposure to FFA or zirconia NPs and FFA up-regulated most lipid classes in HUVECs. As the mechanisms for increased lipid accumulation, exposure to FFA or zirconia NPs and FFA up-regulated endoplasmic reticulum (ER) stress axis IRE1α-XBP-1, leading to increased FASN and ACSL3, proteins involved in lipid metabolism. Combined, our results demonstrated that zirconia NPs were noncytotoxic and showed minimal impact on ER stress-mediated lipid metabolism in HUVECs under both normal and FFA-challenged conditions, which indicated the relatively high biocompatibility of zirconia NPs to ECs.

Dynamic changes in human HLA-DRA gene expression and Th cell subsets in sepsis: Indications of immunosuppression and associated outcomes.

BACKGROUND: Sepsis is a life-threatening disease that is an immune disorder response that causes multiple organ dysfunction. In this study, we investigated the dynamic changes in mRNA expression of HLA-DRA gene and the specific transcription factor of helper T cell subsets to explore long-term immunophenotyping and its relationship with prognosis. METHODS: Seventy-eight sepsis patients and twelve healthy controls were recruited in this study. Blood samples were collected at eight-time points during their septic course and were assayed for the gene expression of HLA-DRA and T helper cell subset-specific transcription factors (T-bet: Th1, GATA3: Th2, Foxp3: Treg, RORC: Th17). RESULTS: The levels of HLA-DRA in survivors gradually increased but were maintained at lower levels in non-survivors. The specific transcription factor of Th1 and Th2 cells, T-bet and GATA-3 were significantly lower in sepsis patients than in normal controls, and the non-survivors showed significantly lower levels than the survivors (P < .05). RORC and FOXP3, the specific transcription factor of Treg and Th17 were significantly higher in survivors than in non-survivors and normal controls (P < .05). T-bet and GATA-3 had a linear correlation with HLA-DRA expression (P < .01). CONCLUSIONS: The dynamic changes in HLA-DRA expression in peripheral blood could accurately reflect the immune status of sepsis patients, and the reduction in HLA-DRA may be an important reason for abnormal T cell differentiation. The sustained low levels of the Th cell subsets (Th1 and Th2) suggest the suppression of adaptive immunity, and this persistent immunosuppression may be the leading cause of death in septic patients.

Identification of differentially expressed proteins in the injured lung from zinc chloride smoke inhalation based on proteomics analysis.

BACKGROUND: Lung injury due to zinc chloride smoke inhalation is very common in military personnel and leads to a high incidence of pulmonary complications and mortality. The aim of this study was to uncover the underlying mechanisms of lung injury due to zinc chloride smoke inhalation using a rat model. METHODS: Histopathology analysis of rat lungs after zinc chloride smoke inhalation was performed by using haematoxylin and eosin (H&E) and Mallory staining. A lung injury rat model of zinc chloride smoke inhalation (smoke inhalation for 1, 2, 7 and 14 days) was developed. First, isobaric tags for relative and absolute quantization (iTRAQ) and weighted gene co-expression network analysis (WGCNA) were used to identify important differentially expressed proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to study the biological functions of differentially expressed proteins. Then, analysis of lung injury repair-related differentially expressed proteins in the early (day 1 and day 2) and middle-late stages (day 7 and day 14) of lung injury after smoke inhalation was performed, followed by the protein-protein interaction (PPI) analysis of these differentially expressed proteins. Finally, the injury repair-related proteins PARK7 and FABP5 were validated by immunohistochemistry and western blot analysis. RESULTS: Morphological changes were observed in the lung tissues after zinc chloride smoke inhalation. A total of 27 common differentially expressed proteins were obtained on days 1, 2, 7 and 14 after smoke inhalation. WGCNA showed that the turquoise module (which involved 909 proteins) was most associated with smoke inhalation time. Myl3, Ckm, Adrm1 and Igfbp7 were identified in the early stages of lung injury repair. Gapdh, Acly, Tnni2, Acta1, Actn3, Pygm, Eno3 and Tpi1 (hub proteins in the PPI network) were identified in the middle-late stages of lung injury repair. Eno3 and Tpi1 were both involved in the glycolysis/gluconeogenesis signalling pathway. The expression of PARK7 and FABP5 was validated and was consistent with the proteomics analysis. CONCLUSION: The identified hub proteins and their related signalling pathways may play crucial roles in lung injury repair due to zinc chloride smoke inhalation.

pgRNAFinder: a web-based tool to design distance independent paired-gRNA.

SUMMARY: The CRISPR/Cas System has been shown to be an efficient and accurate genome-editing technique. There exist a number of tools to design the guide RNA sequences and predict potential off-target sites. However, most of the existing computational tools on gRNA design are restricted to small deletions. To address this issue, we present pgRNAFinder, with an easy-to-use web interface, which enables researchers to design single or distance-free paired-gRNA sequences. The web interface of pgRNAFinder contains both gRNA search and scoring system. After users input query sequences, it searches gRNA by 3' protospacer-adjacent motif (PAM), and possible off-targets, and scores the conservation of the deleted sequences rapidly. Filters can be applied to identify high-quality CRISPR sites. PgRNAFinder offers gRNA design functionality for 8 vertebrate genomes. Furthermore, to keep pgRNAFinder open, extensible to any organism, we provide the source package for local use. AVAILABILITY AND IMPLEMENTATION: The pgRNAFinder is freely available at http://songyanglab.sysu.edu.cn/wangwebs/pgRNAFinder/, and the source code and user manual can be obtained from https://github.com/xiexiaowei/pgRNAFinder. CONTACT: songyang@bcm.edu or daizhim@mail.sysu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Maternal Soluble Fiber Diet during Pregnancy Changes the Intestinal Microbiota, Improves Growth Performance, and Reduces Intestinal Permeability in Piglets.

Increasing evidence suggests that maternal diet during pregnancy modifies an offspring's microbiota composition and intestinal development in a long-term manner. However, the effects of maternal soluble fiber diet during pregnancy on growth traits and the developing intestine are still underexplored. Sows were allocated to either a control or 2.0% pregelatinized waxy maize starch plus guar gum (SF) dietary treatment during gestation. Growth performance, diarrhea incidence, gut microbiota composition and metabolism, and gut permeability and inflammation status of 14-day-old suckling piglets were analyzed. The maternal SF diet improved the growth rate and decreased the incidence of diarrhea in the piglets. Next-generation sequencing analysis revealed that the intestinal microbiota composition was altered by a maternal SF diet. The fecal and plasma levels of acetate and butyrate were also increased. Furthermore, a maternal SF diet reduced the levels of plasma zonulin and fecal lipocalin-2 but increased the plasma concentrations of interleukin 10 (IL-10) and transforming growth factor ß (TGF-ß). Additionally, the increased relative abundances of Lactobacillus spp. in SF piglets were positively correlated with growth rate, while the decreased abundances of Bilophila spp. were positively correlated with fecal lipocalin-2 levels. Our data reveal that a maternal SF diet during pregnancy has remarkable effects on an offspring's growth traits and intestinal permeability and inflammation, perhaps by modulating the composition and metabolism of gut microbiota.IMPORTANCE Although the direct effects of dietary soluble fiber on gut microbiota have been extensively studied, the more indirect effects of maternal nutrition solely during pregnancy on the development of the offspring's intestine are until now largely unexplored. Our data show that a maternal soluble fiber diet during pregnancy is independently associated with changes in the intestinal microbiota composition and metabolism of suckling piglets. These findings have direct implications for refining dietary recommendations in pregnancy. Moreover, a maternal soluble fiber diet reduces intestinal permeability and prevents intestinal inflammation and an excessive systemic immune response of suckling piglets. Therefore, the suckling piglets' resistance to disease was enhanced, diarrhea was reduced, and weight gain was raised. Additionally, the changes in gut microbiota in response to a maternal soluble fiber diet may also be directly correlated with the offspring's growth and gut development.