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BACKGROUND: Autophagy is a lysosome-dependent degradation pathway that regulates macrophage activation, differentiation, and polarization. Autophagy related 5 (Atg5) is a key protein involved in phagocytic membrane elongation in autophagic vesicles that forms a complex with Atg12 and Atg16L1. Alterations in Atg5 are related to both acute and chronic kidney diseases in experimental models. However, the role of macrophage-expressed Atg5 in acute kidney injury remains unclear. METHODS: Using a myeloid cell-specific Atg5 knockout (MΦ atg5-/-) mouse, we established renal ischemia/reperfusion and unilateral ureteral obstruction models to evaluate the role of macrophage Atg5 in renal macrophage migration and fibrosis. RESULTS: Based on changes in the serum urea nitrogen and creatinine levels, Atg5 deletion had a minimal effect on renal function in the early stages after mild injury; however, MΦ atg5-/- mice had reduced renal fibrosis and reduced macrophage recruitment after 4 weeks of ischemia/reperfusion injury and 2 weeks of unilateral ureteral obstruction injury. Atg5 deficiency impaired the CCL20-CCR6 axis after severe ischemic kidneys. Chemotactic responses of bone marrow-derived monocytes (BMDMs) from MΦ atg5-/- mice to CCL20 were significantly attenuated compared with those of wild-type BMDMs, and this might be caused by the inhibition of PI3K, AKT, and ERK1/2 activation. CONCLUSIONS: Our data indicate that Atg5 deficiency decreased macrophage migration by impairing the CCL20-CCR6 axis and inhibited M2 polarization, thereby improving kidney fibrosis.
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Obstrucción Ureteral , Animales , Ratones , Proteína 5 Relacionada con la Autofagia/metabolismo , Fibrosis , Isquemia/metabolismo , Riñón/metabolismo , Macrófagos/metabolismo , Ratones Endogámicos C57BL , Receptores CCR6/metabolismo , Obstrucción Ureteral/complicaciones , Obstrucción Ureteral/metabolismo , Obstrucción Ureteral/patologíaRESUMEN
RESEARCH QUESTION: Can microbes vertically transmit from semen and follicular fluid to embryo culture media during assisted reproductive technology (ART) treatment? DESIGN: Spent embryo culture media (SECM), seminal fluid and follicular fluid samples were collected from 61 couples with infertility undergoing ART treatment at the Prince of Wales Hospital, Hong Kong SAR, China. Metagenomic analysis was conducted using 16s rRNA sequencing to identify the source of microbes in SECM, correlation between the semen microbiome and male infertility, and correlation between the follicular fluid microbiome and female infertility. RESULTS: Microbial vertical transmission into SECM was reported in 82.5% of cases, and semen was the main source of contamination in conventional IVF cases. The increased abundances of Staphylococcus spp. and Streptococcus anginosus in semen had negative impacts on total motility and sperm count, respectively (P < 0.001). Significant increases in abundance of the genera Prophyromonas, Neisseria and Facklamia were observed in follicular fluid in women with anovulation, uterine factor infertility and unexplained infertility, respectively (P < 0.01). No significant correlation was found between the bacteria identified in all sample types and ART outcomes, including fertilization rate, embryo development, number of available embryos, and clinical pregnancy rate. CONCLUSION: Embryo culture media can be contaminated during ART treatment, not only by seminal microbes but also by follicular fluid and other sources of microbes. Strong correlations were found between specific microbial taxa in semen and sperm quality, and between the follicular fluid microbiome and the aetiology of female infertility. However, no significant association was found between the microbiomes of SECM, semen and follicular fluid and ART outcomes.
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Medios de Cultivo , Líquido Folicular , Microbiota , Técnicas Reproductivas Asistidas , Semen , Humanos , Femenino , Masculino , Adulto , Embarazo , Líquido Folicular/microbiología , Semen/microbiología , Técnicas de Cultivo de Embriones , Fertilización In Vitro , Infertilidad Femenina/microbiología , Infertilidad Femenina/terapiaRESUMEN
BACKGROUND AND AIMS: Chimeric antigen receptor engineered T cells (CARTs) for HCC and other solid tumors are not as effective as they are for blood cancers. CARTs may lose function inside tumors due to persistent antigen engagement. The aims of this study are to develop low-affinity monoclonal antibodies (mAbs) and low-avidity CARTs for HCC and to test the hypothesis that low-avidity CARTs can resist exhaustion and maintain functions in solid tumors, generating durable antitumor effects. METHODS AND RESULTS: New human glypican-3 (hGPC3) mAbs were developed from immunized mice. We obtained three hGPC3-specific mAbs that stained HCC tumors, but not the adjacent normal liver tissues. One of them, 8F8, bound an epitope close to that of GC33, the frequently used high-affinity mAb, but with approximately 17-fold lower affinity. We then compared the 8F8 CARTs to GC33 CARTs for their in vitro function and in vivo antitumor effects. In vitro, low-avidity 8F8 CARTs killed both hGPC3high and hGPC3low HCC tumor cells to the same extent as high-avidity GC33 CARTs. 8F8 CARTs expanded and persisted to a greater extent than GC33 CARTs, resulting in durable responses against HCC xenografts. Importantly, compared with GC33 CARTs, there were 5-fold more of 8F8-BBz CARTs in the tumor mass for a longer period of time. Remarkably, the tumor-infiltrating 8F8 CARTs were less exhausted and apoptotic, and more functional than GC33 CARTs. CONCLUSION: The low-avidity 8F8-BBz CART resists exhaustion and apoptosis inside tumor lesions, demonstrating a greater therapeutic potential than high-avidity CARTs.
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Carcinoma Hepatocelular , Neoplasias Hepáticas , Animales , Anticuerpos Monoclonales/farmacología , Anticuerpos Monoclonales/uso terapéutico , Carcinoma Hepatocelular/tratamiento farmacológico , Glipicanos , Humanos , Neoplasias Hepáticas/patología , Ratones , Ensayos Antitumor por Modelo de XenoinjertoRESUMEN
Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.
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Antibacterianos , Genes Bacterianos , Animales , Humanos , Antibacterianos/farmacología , ARN Ribosómico 16S/genética , Farmacorresistencia Microbiana/genética , Metagenómica/métodosRESUMEN
BACKGROUND: Immediate action is needed to stabilise the climate. Dietitians require knowledge of how the therapeutic diets they prescribe may contribute to climate change. No previous research has quantified the climate footprint of therapeutic diets. This study sought to quantify and compare the climate footprint of two types of therapeutic diets for people with chronic kidney disease (CKD) with two reference diets. METHODS: A usual diet for an individual with CKD and a novel plant-based diet for CKD were compared with the current Australian diet and the Australian-adapted EAT Lancet Planetary Health Diet (PHD). The climate footprint of these diets was measured using the Global Warming Potential (GWP*) metric for a reference 71-year-old male. RESULTS: No diets analysed were climate neutral, and therefore, all contribute to climate change. The novel plant-based diet for CKD (1.20 kg carbon dioxide equivalents [CO2 e] per day) produced 35% less CO2 e than the usual renal diet for an individual with CKD (1.83 kg CO2 e per day) and 50% less than the current Australian diet (2.38 kg CO2 e per day). The Australian-adapted EAT Lancet PHD (1.04 kg CO2 e per day) produced the least amount of CO2 e and 56% less than the current Australian diet. The largest contributors to the climate footprint of all four diets were foods from the meats and alternatives, dairy and alternatives and discretionary food groups. CONCLUSIONS: Dietetic advice to reduce the climate footprint of therapeutic diets for CKD should focus on discretionary foods and some animal-based products. Future research is needed on other therapeutic diets.
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Dióxido de Carbono , Insuficiencia Renal Crónica , Animales , Humanos , Anciano , Australia , Dieta , Insuficiencia Renal Crónica/terapia , AlimentosRESUMEN
The ongoing global pandemic of coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and significantly impacts the world economy and daily life. Symptoms of COVID-19 range from asymptomatic to fever, dyspnoea, acute respiratory distress and multiple organ failure. Critical cases often occur in the elderly and patients with pre-existing conditions. By binding to the angiotensin-converting enzyme 2 receptor, SARS-CoV-2 can enter and replicate in the host cell, exerting a cytotoxic effect and causing local and systemic inflammation. Currently, there is no specific treatment for COVID-19, and immunotherapy has consistently attracted attention because of its essential role in boosting host immunity to the virus and reducing overwhelming inflammation. In this review, we summarise the immunopathogenic features of COVID-19 and highlight recent advances in immunotherapy to illuminate ideas for the development of new potential therapies.
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COVID-19 , Anciano , Humanos , Factores Inmunológicos , Inmunoterapia , Pandemias , SARS-CoV-2RESUMEN
Although several molecular-based studies have demonstrated the involvement of ammonia-oxidizing archaea (AOA) in ammonia oxidation in wastewater treatment plants (WWTPs), factors affecting the persistence and growth of AOA in these engineered systems have not been resolved. Here, we show a seasonal prevalence of AOA in a full-scale WWTP (Shatin, Hong Kong SAR) over a 6-year period of observation, even outnumbering ammonia-oxidizing bacteria in the seasonal peaks in 3 years, which may be due to the high bioavailable copper concentrations. Comparative analysis of three metagenome-assembled genomes of group I.1a AOA obtained from the activated sludge and 16S rRNA gene sequences recovered from marine sediments suggested that the seawater used for toilet flushing was the primary source of the WWTP AOA. A rare AOA population in the estuarine source water became transiently abundant in the WWTP with a metagenome-based relative abundance of up to 1.3% over three seasons of observation. Correlation-based network analysis revealed a robust co-occurrence relationship between these AOA and organisms potentially active in nitrite oxidation. Moreover, a strong correlation between the dominant AOA and an abundant proteobacterial organism suggested that capacity for extracellular polymeric substance production by the proteobacterium could provide a niche for AOA within bioaggregates. Together, the study highlights the importance of long-term observation in identifying biotic and abiotic factors governing population dynamics in open systems such as full-scale WWTPs.
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Archaea , Purificación del Agua , Amoníaco , Archaea/genética , Bacterias/genética , Matriz Extracelular de Sustancias Poliméricas , Hong Kong , Oxidación-Reducción , Filogenia , Prevalencia , ARN Ribosómico 16S/genética , Estaciones del Año , Aguas ResidualesRESUMEN
Increasing evidence indicates that TP53 mutation impacts the patients' prognosis by regulating the gastric cancer (GC) immunophenotype. An immune prognostic signature (IPS) was constructed based on TP53 status. The effects of the IPS on the immune microenvironment of GC were analyzed. We also constructed a nomogram integrating the IPS and other clinical factors. An IPS was constructed in the TCGA cohort and validated in the meta-GEO cohort. TP53 mutation resulted in the downregulation of the immune response in GC. Concretely, high-risk patients were characterized by increased monocyte, macrophage M0 and T cell follicular helper infiltration; increased stromal score, ESTIMATE score and immune score; higher TIM3 and BTLA expression; and decreased dendritic cell and T cell CD4 memory-activated infiltration and tumor purity. The nomogram also showed good predictive performance. These results suggest that the IPS is an effective prognostic indicator for GC patients, which might provide a theoretical foundation for immunotherapy.
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Adenocarcinoma/inmunología , Inmunofenotipificación , Neoplasias Gástricas/inmunología , Proteína p53 Supresora de Tumor/genética , Adenocarcinoma/genética , Humanos , Mutación , Pronóstico , Neoplasias Gástricas/genéticaRESUMEN
AIM: Hepatocellular carcinoma (HCC) is a common malignancy associated with a poor prognosis due to difficulties in reliably estimating overall survival (OS). MicroRNAs (miRNAs) play critical roles in HCC initiation, progression, and metastasis and are highly correlated with patient prognosis. Thus, miRNA-based risk signatures and nomograms are urgently required for predicting OS in patients with HCC. METHODS: We constructed a 13-miRNA-based signature and prognostic nomogram using 408 HCC samples and 58 normal tissues with miRNA sequencing data and clinical data from 323 patients downloaded from The Cancer Genome Atlas. A total of 195 patients were assigned as the internal validation cohort for verification and testing. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis was applied to investigate pathway enrichment for the signature. RESULTS: We identified and validated a 13-miRNA risk signature highly associating with the OS of HCC patients. The signature showed good performances by calculating C-index, area under the curve, and calibration curves. After verification and testing using an internal validation cohort, the results yielded a miRNA-based signature and a prognostic nomogram with reliable predictive accuracy. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis indicated that various genes and multiple pathways were closely related to the mechanisms of HCC proliferation and metastasis. CONCLUSION: We successfully identified a 13-miRNA-based signature and prognostic nomogram that are capable of predicting OS in patients with HCC.
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Motivation: Much global attention has been paid to antibiotic resistance in monitoring its emergence, accumulation and dissemination. For rapid characterization and quantification of antibiotic resistance genes (ARGs) in metagenomic datasets, an online analysis pipeline, ARGs-OAP has been developed consisting of a database termed Structured Antibiotic Resistance Genes (the SARG) with a hierarchical structure (ARGs type-subtype-reference sequence). Results: The new release of the database, termed SARG version 2.0, contains sequences not only from CARD and ARDB databases, but also carefully selected and curated sequences from the latest protein collection of the NCBI-NR database, to keep up to date with the increasing number of ARG deposited sequences. SARG v2.0 has tripled the sequences of the first version and demonstrated improved coverage of ARGs detection in metagenomes from various environmental samples. In addition to annotation of high-throughput raw reads using a similarity search strategy, ARGs-OAP v2.0 now provides model-based identification of assembled sequences using SARGfam, a high-quality profile Hidden Markov Model (HMM), containing profiles of ARG subtypes. Additionally, ARGs-OAP v2.0 improves cell number quantification by using the average coverage of essential single copy marker genes, as an option in addition to the previous method based on the 16S rRNA gene. Availability and implementation: ARGs-OAP can be accessed through http://smile.hku.hk/SARGs. The database could be downloaded from the same site. Source codes for this study can be downloaded from https://github.com/xiaole99/ARGs-OAP-v2.0. Supplementary information: Supplementary data are available at Bioinformatics online.
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Bases de Datos Factuales , Farmacorresistencia Microbiana/genética , Metagenoma , Programas Informáticos , Archaea/genética , Archaea/fisiología , Bacterias/genética , Fenómenos Fisiológicos Bacterianos , Genoma Arqueal , Genoma Bacteriano , Metagenómica/métodos , Análisis de Secuencia de ADN/métodosRESUMEN
Hepatocellular carcinoma (HCC) is the major form of liver cancer for which there is no effective therapy. Genetic modification with T-cell receptors (TCRs) specific for HCC-associated antigens, such as α-fetoprotein (AFP), can potentially redirect human T cells to specifically recognize and kill HCC tumor cells to achieve antitumor effects. In this study, using lentivector and peptide immunization, we identified a population of cluster of differentiation 8 (CD8) T cells in human leukocyte antigen (HLA)-A2 transgenic AAD mice that recognized AFP158 epitope on human HCC cells. Adoptive transfer of the AFP158 -specific mouse CD8 T cells eradicated HepG2 tumor xenografts as large as 2 cm in diameter in immunocompromised nonobese diabetic severe combined immunodeficient gamma knockout (NSG) mice. We then established T-cell hybridoma clones from the AFP158 -specific mouse CD8 T cells and identified three sets of paired TCR genes out of five hybridomas. Expression of the murine TCR genes redirected primary human T cells to bind HLA-A2/AFP158 tetramer. TCR gene-engineered human T (TCR-T) cells also specifically recognized HLA-A2+ AFP+ HepG2 HCC tumor cells and produced effector cytokines. Importantly, the TCR-T cells could specifically kill HLA-A2+ AFP+ HepG2 tumor cells without significant toxicity to normal primary hepatocytes in vitro. Adoptive transfer of the AFP-specific TCR-T cells could eradicate HepG2 tumors in NSG mice. CONCLUSION: We have identified AFP-specific murine TCR genes that can redirect human T cells to specifically recognize and kill HCC tumor cells, and those AFP158 -specific TCRs have a great potential to engineer a patient's autologous T cells to treat HCC tumors. (Hepatology 2018).
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Linfocitos T CD8-positivos/inmunología , Carcinoma Hepatocelular/inmunología , Inmunoterapia/métodos , Neoplasias Hepáticas/inmunología , alfa-Fetoproteínas/inmunología , Animales , Linfocitos T CD8-positivos/metabolismo , Línea Celular Tumoral , Ensayo de Inmunoadsorción Enzimática , Femenino , Antígeno HLA-A2/inmunología , Células Hep G2 , Humanos , Ratones , Ratones Transgénicos , Receptores de Antígenos de Linfocitos T/inmunologíaRESUMEN
BACKGROUND AND AIM: This study aims to systematically analyze the effect of long-term therapy with proton pump inhibitors (PPIs) on the risk of gastric cancer. METHODS: PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure (CNKI), and China biomedical literature database (CBM) were searched for studies before February 2019. We evaluated the quality of the included articles through the Newcastle-Ottawa Scale and gathered relevant data to calculate the pooled odds ratio (OR) through Stata14.0. RESULTS: Seven relevant articles conformed to the inclusion criteria; 943 070 patients were included. The pooled OR was 2.50; 95% CI (1.74, 3.85); the subgroup analysis results showed that patients who had used PPIs for more than 36 months were most likely to develop gastric cancer, and an increased risk was observed among patients after Helicobacter pylori eradication. Noncardia gastric cancer was more likely to develop. CONCLUSIONS: Long-term use of PPIs can possibly increase the risk of gastric cancer even among patients after H. pylori eradication; in particular, for noncardia gastric cancer, the risk increases with longer durations of PPI use. Due to the limited number of studies, more high-quality studies are required to be designed.
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Inhibidores de la Bomba de Protones/administración & dosificación , Inhibidores de la Bomba de Protones/efectos adversos , Neoplasias Gástricas/inducido químicamente , Bases de Datos Bibliográficas , Humanos , Riesgo , Factores de TiempoRESUMEN
The human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). A metagenomic approach and network analysis were used to establish a comprehensive antibiotic resistome catalog and to obtain co-occurrence patterns between ARGs and microbial taxa in fecal samples from 180 healthy individuals from 11 different countries. In total, 507 ARG subtypes belonging to 20 ARG types were detected with abundances ranging from 7.12 × 10-7 to 2.72 × 10-1 copy of ARG/copy of 16S-rRNA gene. Tetracycline, multidrug, macrolide-lincosamide-streptogramin, bacitracin, vancomycin, beta-lactam and aminoglycoside resistance genes were the top seven most abundant ARG types. The multidrug ABC transporter, aadE, bacA, acrB, tetM, tetW, vanR and vanS were shared by all 180 individuals, suggesting their common occurrence in the human gut. Compared to populations from the other 10 countries, the Chinese population harboured the most abundant ARGs. Moreover, LEfSe analysis suggested that the MLS resistance type and its subtype 'ermF' were representative ARGs of the Chinese population. Antibiotic inactivation, antibiotic target alteration and antibiotic efflux were the dominant resistance mechanism categories in all populations. Procrustes analysis revealed that microbial phylogeny structured the antibiotic resistome. Co-occurrence patterns obtained via network analysis implied that 12 species might be potential hosts of 58 ARG subtypes.
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Antibacterianos/farmacología , Farmacorresistencia Microbiana , Microbioma Gastrointestinal/efectos de los fármacos , Adulto , Anciano , Heces/microbiología , Femenino , Genes Bacterianos , Humanos , Masculino , Metagenómica , Persona de Mediana Edad , Filogenia , ARN Ribosómico 16S , Adulto JovenRESUMEN
Wastewater treatment plants (WWTPs) are considered reservoirs of viruses, but the diversity and dynamic changes of viruses are not well understood. In this study, we recovered 8478 metagenomic viral contigs (mVCs; >5 kb) from two WWTPs (Shatin, 2806; Shek Wu Hui, 5672) in Hong Kong. Approximately 60% of the mVCs were poorly covered (<35% of genes in identified mVCs) by the current NCBI and IMG/VR viral databases. The temporal profile of the newly identified mVCs among 98 Shatin AS samples collected monthly (for approximately 9 years) revealed the presence of periodic dynamics at an interval of approximately one year (341 days). The spatial distribution pattern of the virome in the wastewater treatment systems showed that shared viral clusters (viral populations categorized based on shared gene content and network analysis) can be globally found among similar samples of wastewater treatment systems, indicating the presence of core viral communities among geographically isolated wastewater treatment systems. These results not only supplemented the current virome database of engineered systems but also, to some extent, expanded the understanding of long-term cyclical development and spatial distributions of viral communities in wastewater treatment systems.
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Virus , Aguas Residuales , Hong Kong , MetagenómicaRESUMEN
Temporal microbial community studies have broadened our knowledge of the dynamics and correlations among microbes in both natural and artificial engineering systems. Using activated sludge as a model system, we utilized the intensive longitudinal sampling method to identify overlooked diversity and the hidden dynamics of microbes, detect cross-associations among microbes after detrending, and reveal the central microbial dynamics during sludge bulking and foaming. We discovered that the accumulative alpha diversity in activated sludge sampled daily over 392 days could be as high as 14â¯000 OTUs, and that the bacterial community dynamics followed a gradual succession, drifting away from the initial observed day and displaying a significant time-dependent trend. Cross-associations among bacteria were modulated after removing potential spurious correlations based on autocorrelation in microbial time series. Moreover, clusters of bacteria displaying rapid turnover were discovered during the beginning, ongoing, and fading of sludge bulking and foaming, and their physicochemical parameters are resolved. These identified groups of bacteria and their related environmental factors could potentially supply clues to form hypotheses for treating operational problems, such as sludge bulking and foaming.
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Bacterias , Aguas del AlcantarilladoRESUMEN
Bacterial community in activated sludge (AS) is diverse and highly dynamic. Little is known about the mechanism shaping bacterial community composition and dynamics of AS and no study had quantitatively compared the contribution of abiotic environmental factors and biotic associations to the temporal dynamics of AS microbial communities with significantly different diversity. In this study, two full-scale sewage treatment plants (STPs) with distinct operational parameters and influent composition were sampled biweekly over 1 year to reveal the correlating factors to whole and sub-groups of AS bacterial community diversity and dynamics. The results show that the bacterial communities of the two STPs were entirely different and correlated with the influent composition and operating configurations. Bacterial associations represented by cohesion metrics and the environmental factor temperature were the primary correlated factors to the temporal bacterial community dynamics within each STP. The STP with high diversity and evenness could treat influent with higher suspended solid and a shorter sludge retention time, and was less correlated with environmental factors, implying the importance of diversity for AS system.
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Bacterias/genética , Reactores Biológicos/microbiología , Aguas del Alcantarillado/microbiología , Biodiversidad , Ambiente , TemperaturaRESUMEN
MOTIVATION: Environmental dissemination of antibiotic resistance genes (ARGs) has become an increasing concern for public health. Metagenomics approaches can effectively detect broad profiles of ARGs in environmental samples; however, the detection and subsequent classification of ARG-like sequences are time consuming and have been severe obstacles in employing metagenomic methods. We sought to accelerate quantification of ARGs in metagenomic data from environmental samples. RESULTS: A Structured ARG reference database (SARG) was constructed by integrating ARDB and CARD, the two most commonly used databases. SARG was curated to remove redundant sequences and optimized to facilitate query sequence identification by similarity. A database with a hierarchical structure (type-subtype-reference sequence) was then constructed to facilitate classification (assigning ARG-like sequence to type, subtype and reference sequence) of sequences identified through similarity search. Utilizing SARG and a previously proposed hybrid functional gene annotation pipeline, we developed an online pipeline called ARGs-OAP for fast annotation and classification of ARG-like sequences from metagenomic data. We also evaluated and proposed a set of criteria important for efficiently conducting metagenomic analysis of ARGs using ARGs-OAP. AVAILABILITY AND IMPLEMENTATION: Perl script for ARGs-OAP can be downloaded from https://github.com/biofuture/Ublastx_stageone ARGs-OAP can be accessed through http://smile.hku.hk/SARGs CONTACT: zhangt@hku.hk or tiedjej@msu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Antibacterianos , Farmacorresistencia Microbiana , Genes Bacterianos , Metagenómica , Bases de Datos Genéticas , Humanos , Anotación de Secuencia MolecularRESUMEN
During the past years, antibiotic-resistant bacteria (ARB) leading for the spreading of antibiotic resistance genes (ARGs) became a global problem, especially multidrug-resistant (MDR) bacteria are considered the prime culprit of antibiotic resistance. However, the correlation between the antibiotic-resistant phenotype and the ARG profiles remains poorly understood. In the present study, metagenomic functional screening and metagenomic analysis of coliforms were combined to explore the phenotype and genotype of the ARBs from municipal sewage. Our results showed that the ARG co-occurrence was widespread in the municipal sewage. The present study also highlighted the high abundance of ARGs from antibiotic resistance coliforms especially the MDR coliforms with ARG level of 33.8 ± 4.2 copies per cell. The ARG profiles and the antibiotic resistance phenotypes of the isolated antibiotic resistant coliforms were also correlated and indicated that the resistance to the related antibiotic (ampicillin, kanamycin, erythromycin, chloramphenicol, and tetracycline) was mostly contributed by the ARGs belonging to the subtypes of ß-lactamase, aminoglycoside 3-phosphotransferase, phosphotransferase type 2, chloramphenicol acetyltransferase, tetA, etc.
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Bacterias/genética , Farmacorresistencia Microbiana/genética , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Metagenómica/métodos , Aguas del Alcantarillado/microbiología , Animales , Antibacterianos/farmacología , Bacterias/efectos de los fármacos , Bacterias/crecimiento & desarrollo , Ciudades , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/metabolismo , Genes Bacterianos , Humanos , ARN Ribosómico 16S/genética , Tetraciclina/farmacología , beta-Lactamasas/genéticaRESUMEN
Secondary hemophagocytic lymphohistiocytosis (sHLH) is a hyperinflammatory syndrome characterized by immune disorders. It is imperative to elucidate the immunophenotypic panorama and the interactions among these cells in patients. Human peripheral blood mononuclear cells were collected from healthy donors and sHLH patients and tested using multicolor flow cytometry. We used FlowSOM to explore and visualize the immunophenotypic characteristics of sHLH. By demonstrating the phenotypes of immune cells, we discovered that sHLH patients had significantly higher levels of CD56+ monocytes, higher levels of myeloid-derived suppressor cells, low-density neutrophil-to-T cell ratio, and higher heterogeneous T cell activation than healthy donors. However, natural killer cell cytotoxicity and function were impaired. We then assessed the correlations among 30 immune cell types and evaluated metabolic analysis. Our findings demonstrated polymorphonuclear myeloid-derived suppressor cells, CD56+ monocytes, and neutrophil-to-T cell ratio were elevated abnormally in sHLH patients, which may indicate an association with immune overactivation and inflammatory response. We are expected to confirm that they are involved in the occurrence of the disease through further in-depth research.
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BACKGROUND: Hepatitis B core antibody (anti-HBc) is commonly present in patients with chronic hepatitis B virus (HBV) infection and serves as a marker of humoral immunity. Herein, we aim to investigate the correlation between anti-HBc and antiviral immune response and its putative role in HBV control. METHODS: Quantitative anti-HBc and levels of anti-HBc subtypes were measured in chronic hepatitis B (CHB) patients. The effects of anti-HBc on immune cells and HBV replication were evaluated using the HBV mouse models and human hepatoma cell lines. RESULTS: Baseline levels of IgG1 and IgG3 anti-HBc were elevated in CHB patients with favorable treatment response, and correlated with the virological response observed at week 52. Additionally, increased levels of IgM and IgG1 anti-HBc were observed exclusively in CHB patients with liver inflammation. Notably, significant correlations were identified between quantitative levels of anti-HBc and the frequencies of HBcAg-specific CD8+ T cells. Intriguingly, HBcAg efficiently activates T cells aided by B cells in vitro experiments. Moreover, anti-HBc inhibits HBV replication either by a direct effect or through complement-mediated cytotoxicity in HBV-producing cell lines. CONCLUSIONS: Anti-HBc reflects the activation of an HBV-specific CD8+ T cell immune response and may have anti-HBV activity.