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No study on the relationship between hepatic steatosis and sex hormone levels in male patients with chronic hepatitis B (CHB) infection has been conducted.We aimed to investigate the association between serum sex hormones and hepatic steatosis among a cohort of males with CHB.In this cross-sectional study, 268 male patients with CHB were enrolled. All participants underwent anthropometric measurement, blood testing, and FibroScan test. Multiple logistic regression analysis was used to investigate the association of serum sex hormones with hepatic steatosis.We included 137 males with and 131 without hepatic steatosis in this study. Subjects with serum testosterone (T) levels in the highest tertile had an odds ratio (OR) (95% confidence interval [CI]) of 0.35 (0.18-0.70) (P for trend=0.003); those with serum prolactin (PRL) levels in the highest tertile had an OR (95%CI) of 0.21 (0.10-0.45) (P for trend0.001); and those with serum estradiol/testosterone (E2/T) in the highest tertile had an OR (95%CI) of 4.02 (1.97-8.20) (P for trend0.001) for hepatic steatosis.Lower serum total T and PRL levels and higher total E2/T are independently associated with presence of hepatic steatosis in male patients with CHB.

Background The cause and underlying molecular mechanisms of head and neck squamous cell carcinoma (HNSCC) are unclear. Our study aims to identify the key genes associated with HNSCC and reveal potential biomarkers. Methods In this study, the expression profile dataset GSE83519 of the Gene Expression Omnibus database and the RNA sequencing dataset of HNSCC of The Cancer Genome Atlas were included for analysis. Sixteen differentially expressed genes were screened from these two datasets using R software. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) was then adopted for survival analysis, and finally, three key genes related to the overall survival of HNSCC patients were identified. Furthermore, we verified these three genes using the Oncomine database and from real-time PCR and immunohistochemistry results from HNSCC tissues. Results The expression data of 44 samples from GSE83519 and 545 samples from TCGA-HNSC were collected. Using bioinformatics, the two databases were integrated, and 16 DEGs were screened out. Gene Ontology (GO) enrichment analysis showed that the biological functions of DEGs focused primarily on the apical plasma membrane and regulation of anoikis. Kyoto Encyclopedia of Genes and Genomes (KEGG) signalling pathway analysis showed that these DEGs were mainly involved in drug metabolism-cytochrome P450 and serotonergic synapses. Survival analysis identified three key genes, CEACAM5, CEACAM6 and CLCA4, that were closely related to HNSCC prognosis. The Oncomine database, qRT–PCR and IHC verified that all 3 key genes were downregulated in most HNSCC tissues compared to adjacent normal tissues. Conclusions This study indicates that integrated bioinformatics analyses play an important role in screening for differentially expressed genes and pathways in HNSCC, helping us better understand the biomarkers and molecular mechanism of HNSCC.

There are unmet clinical needs for novel therapeutic targets and drugs for bladder cancer. Majority of previous work relied on limited bladder cancer cell lines, which could not well represent the tumor heterogeneity and pathology of this disease. Recently, it has been shown that cancer organoids can recapitulate pathological and molecular properties of bladder cancer. Here, we report, by our knowledge, the first bladder cancer organoid-based small molecule screening for epigenetic drugs. We found that SRT1720, a Sirtuin 1 (SIRT1) activator, significantly inhibits the growth of both mouse and human bladder cancer organoids. And it also restrains the development of mouse in situ bladder cancer and human PDX bladder cancer. Mutation of Sirt1 promotes the growth of cancer organoids and decreases their sensitivity to SRT1720, which validate Sirt1 as the target of SRT1720 in bladder cancer. Mechanistically, SRT1720 treatment represses the hypoxia pathway through deacetylating HIF1α by activating Sirt1. Genetic or pharmaceutic inhibitions of HIF mimic the anti-tumor effect of SRT1720. Furthermore, the SIRT1-repressed gene signature is associated with the hypoxia target gene signature and poor prognosis in human bladder cancers. Thus, our study demonstrates the power of cancer organoid-based drug discovery and, in principle, identifies SRT1720 as a new treatment for bladder cancer.

Introduction Adult immunoglobulin A vasculitis nephritis (IgAVN) was observed to be more severe than the disease in children because it tended to result in a poor prognosis. The present study analyzed the Th17/Treg cell axis in peripheral blood of adult IgAVN patients, aiming to provide new immunological viewpoints for the pathogenesis of adult IgAVN. Material and methods Th17 cell and Treg cell frequencies in peripheral blood of healthy subjects (n = 13) and adult IgAVN patients (n = 12) were analyzed by flow cytometry. Foxp3 mRNA in peripheral blood of healthy subjects and adult IgAVN patients was detected by RT-PCR. Interleukin (IL)-17 and IL-10 in peripheral blood serum of healthy subjects and adult IgAVN patients were examined by ELISA. Results The percentages of CD4+ Th17+ cells in peripheral blood of healthy subjects and adult IgAVN patients were 2.65 ±1.55% and 4.37 ±1.68% respectively. The percentages of Treg cells in peripheral blood of healthy subjects and adult IgAVN patients were 6.44 ±2.90% and 3.91 ±1.94% respectively. The ratio of Th17/Treg in adult IgAVN patients was significantly higher than that of healthy subjects (p = 0.0030). Meanwhile, the Foxp3 mRNA expression of adult IgAVN patients was significantly lower than that of healthy subjects. There was a significant difference in the ratio of IL-17/IL-10 between healthy subjects and adult IgAVN patients (p < 0.0001). A significant correlation between red blood cell distribution width (RDW) and the ratio of Th17/Treg in adult IgAVN patients was observed in Spearman correlation analysis (r = 0.6970, p = 0.0145). Conclusions Imbalanced Th17/Treg contributed to the complex pathogenesis of adult IgAVN.

Yu Lei,&ast; Xiaoyu Liu,&ast; Jingmei Liu, Min Zhang, Yan Zhou, Wei Yan, Dean Tian, Ping Zhang, Ping Han Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, People’s Republic of China&ast;These authors contributed equally to this workCorrespondence: Ping Zhang; Ping HanDepartment of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei Province, People’s Republic of ChinaEmail 845917536@qq.com; hanzhouping@163.comBackground: Isolated terminal ileitis (ITI) is a phenomenon often observed during colonoscopy, but in most cases, the specific etiology of ITI is unclear. Helicobacter pylori (H. pylori) infection has been reported to be associated with a wide variety of diseases, especially gastrointestinal diseases. Here, we conducted a retrospective study to explore a potential correlation between H. pylori infection and unexplained ITI (UITI).Materials and Methods: The retrospective study was conducted at Sino-French New City Branch of Tongji Hospital, Wuhan, China, from April 2017 to October 2020. All subjects underwent total colonoscopy, with the endoscope being inserted more than 10cm into the terminal ileum. Subjects also received a 13C-urea breath test (13C-UBT). Data on the age, gender, endoscopic manifestations, and main clinical symptoms of subjects were collected. The presence of H. pylori infection was defined as a positive 13C-UBT result. Logistic regression models were used to analyze the potential correlation between H. pylori infection and UITI.Results: There were 247 subjects (25.1%) in the H. pylori (+) group and 739 subjects (74.9%) in the H. pylori (-) group. The prevalence of UITI in the H. pylori (+) group was significantly lower than that in the H. pylori (-) group (OR = 0.518; 95% CI 0.281– 0.956; P = 0.035), and there was no difference in other clinical features between groups. Stratification analysis results showed that there was an inverse association between H. pylori infection and UITI in subjects with age < 60 (P = 0.046).Conclusion: These data showed that H. pylori infection was negatively correlated with UITI. Additional studies are needed to validate these findings in a larger cohort as well as to explore the underlying mechanisms.Keywords: Helicobacter pylori infection, unexplained isolated terminal ileitis, colonoscopy, 13C-urea breath test

Haw-Ming Huang,1,2 Ping-Han Wu,3 Po-Chien Chou,4 Wen-Tien Hsiao,5 Hsin-Ta Wang,4 Hsin-Pei Chiang,3 Chi-Ming Lee,6 Shwu-Huey Wang,6 Yu-Cheng Hsiao2,7 1School of Dentistry, College of Oral Medicine, Taipei Medical University, Taipei, Taiwan; 2Graduate Institute of Biomedical Optomechatronics, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan; 3Graduate Institute of Biomedical Materials and Tissue Engineering, College of Biomedical Engineering, Taipei Medical University, Taipei, Taiwan; 4School of Organic and Polymeric, National Taipei University of Technology, Taipei, Taiwan; 5Department of Medical Imaging and Radiological Technology, Yuanpei University of Medical Technology, Hsinchu, Taiwan; 6Core Facility Center, Office of Research and Development, Taipei Medical University, Taipei, Taiwan; 7Cell Physiology and Molecular Image Research Center, Taipei Municipal Wan Fang Hospital, Taipei Medical University, Taipei, TaiwanCorrespondence: Yu-Cheng Hsiao; Ping-Han WuTaipei Medical University, No. 250, Wu-Hsing Street, Taipei, 11031, TaiwanTel +886-291-937-9783Fax +886 2 27362295Email ychsiao@tmu.edu.tw; gahwclbjwph@gmail.comIntroduction: It has been reported that low-molecular-weight hyaluronic acid (LMWHA) exhibits a potentially beneficial effect on cancer therapy through targeting of CD44 receptors on tumor cell surfaces. However, its applicability towards tumor detection is still unclear. In this regard, LMWHA-conjugated iron (Fe3O4) nanoparticles (LMWHA-IONPs) were prepared in order to evaluate its application for enhancing the T2* weighted MRI imaging sensitivity for tumor detection.Methods: LMWHA and Fe3O4 NPs were produced using γ-ray irradiation and chemical co-precipitation methods, respectively. First, LMWHA-conjugated FITC was prepared to confirm the ability of LMWHA to target U87MG cells using fluorescence microscopy. The hydrodynamic size distribution and dispersion of the IONPs and prepared LMWHA-IONPs were analyzed using dynamic light scattering (DLS). In addition, cell viability assays were performed to examine the biocompatibility of LMWHA and LMWHA-IONPs toward U87MG human glioblastoma and NIH3T3 fibroblast cell lines. The ability of LMWHA-IONPs to target tumor cells was confirmed by detecting iron (Fe) ion content using the thiocyanate method. Finally, time-of-flight secondary ion mass spectrometry (TOF-SIMS) imaging and in vitro magnetic resonance imaging (MRI) were performed to confirm the contrast enhancement effect of LMWHA-IONPs.Results: Florescence analysis results showed that LMWHA-FITC successfully targeted the surfaces of both tested cell types. The ability of LMWHA to target U87MG cells was higher than for NIH3T3 cells. Cell viability experiments showed that the fabricated LMWHA-IONPs possessed good biocompatibility for both cell lines. After co-culturing test cells with the LMWHA-IONPs, detected Fe ion content in the U87MG cells was much higher than that of the NIH3T3 cells in both thiocyanate assays and TOF-SIMs images. Finally, the addition of LMWHA-IONPs to the U87MG cells resulted in an obvious improvement in T2* weighted MR image contrast compared to control NIH3T3 cells.Discussion: Overall, the present results suggest that LMWHA-IONPs fabricated in this study provide an effective MRI contrast agent for improving the diagnosis of early stage glioblastoma in MRI examinations.Keywords: hyaluronic acid, Fe3O4 nanoparticles, TOF-SIMS, MRI

The new heterocyclic compound 4-methyl-3-((4-(pyridin-3-yl) pyrimidin-2-yl) amino) benzoic acid (1) designed utilizing methyl 3-amino-4-methylbenzoate (2) as a starting material was successfully fabricated and eventually characterized utilizing single crystal X-ray crystallography, 1H NMR and IR. In biological study, to evaluate the protective effect of compound on acute tracheobronchitis ICR mice model, the ELISA assay was performed to determine the level of inflammatory mediators IL-6 and TNF-α in serum. Then, the western blot was performed to determine the activation of PKA-NF-κB pathway in tissues.

Complete ammonia oxidizers (comammox), which convert ammonia to nitrate through nitrite, are a newly discovered nitrifying group. In recent years, comammox Nitrospira have been discovered in various natural and engineered ecosystems. However, little is known about the distribution dynamics of comammox Nitrospira in estuary tidal flat sediments. Chongming eastern tidal flat, the largest tidal flat in the Yangtze River Estuary, was selected as the research area. Through a combination of molecular biology assays, phylogenetic analysis based on functional gene sequences and statistical correlation with physicochemical properties, we determined the distribution and diversity of comammox Nitrospira in Chongming eastern tidal flat and analyzed the potential influencing environmental factors. The results indicated comammox Nitrospira were widely distributed in Chongming eastern tidal flat, while with lower abundance than the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA). Clade A1 comammox Nitrospira showed adaptation to relatively high salinity, and was more distributed in middle and low tidal flats, while clade A2 and clade A3 were mostly distributed in high tidal flats with low salinity. The abundance and community structure of comammox Nitrospira were mainly affected by salinity, ammonia concentration, and temperature. This study showed the general existence of comammox Nitrospira in Chongming eastern intertidal sediments and indicated that the differences of tidal locations, which lead to a gradient in the physicochemical properties of the sediments, in turn affects the spatial distribution of comammox Nitrospira in estuary tidal flats.

In this study, we presented the first complete mitochondrial genome of the genus Simocephalus determined by next-generation sequencing. The mitogenome of S. sibiricus is 15,818 bp in length, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 tRNAs, and one putative control region, and has the same gene order with Daphnia. ATG and ATT were used as start codons in 11 PCGs, TTG was used in COX1 and GTG in ATP8. Six PCGs used an incomplete stop codon. Phylogenetic analysis based on 13 PCGs showed that, on genus level, Simocephalus was closely related to Daphnia.

Diaphanosoma s.l., with 40+ described species, is the largest genus of the Sididae and the Ctenopoda, similar in many ways to the anomopod genus Daphnia. Here, we offer a c morphological evaluation of 33 species and contrast it with an analysis of the bar coding fragment of the cytochrome c oxidase subunit (COI) gene in order to gain insight into the taxonomy and phylogeny of the group. A search for structure in the genus based on micromorphological characters identified (1) the number of setae on the endopodite of P6 and (2) the relative length of the three apical setae of the exopodite of P6 as consistent markers, recovering two clades, the hexa-clade (with six endital setae) and the hepta-group (with seven setae). A third character is the armament of the posterior zone of the ventral margin of the valves, denticulated in the hexa-group, with fine filaments between the denticles in the hepta-group. Taxonomically, the two clades are assigned the rank of genera. Valid names for both are available in the published literature (Diaphanosoma Fischer s.s. and Neodiaphanosoma Paggi and Da Rocha, amended). A COI-based phylogenetic estimate leads to the same conclusion as morphology, but reveals cryptic speciation as well. COI reveals relatively small genetic distances within and between temperate climate species (e.g., in the D. birgei group) and large differences that form a cline from Australia (the terra typica) across southeast Asia in the tropical Neodiaphanosoma species D. excisum. African populations need more study, but probably represent a separate species. The entire group shows (macro)morphological stasis in the presence of molecular evolution but Neodiaphanosoma is evolving at a much faster rate than Diaphanosoma s.s. that is either a younger group. This hypothesis needs more testing, however. A biogeographic map recovers Neodiaphanosoma (containing slightly over 10 species) as restricted to the tropics, with limited penetration of the subtropics in the southern hemisphere. The more speciose Diaphanosoma group (up to 30 species) lives in the temperate and continental climate zone, with limited extension into subpolar zones, but considerable penetration of the subtropics and tropics. The subtropics, where both groups broadly overlap, is the zone with the highest species richness.

Asgard archaea are widely distributed in anaerobic environments. Previous studies revealed the potential capability of Asgard archaea to utilize various organic substrates including proteins, carbohydrates, fatty acids, amino acids and hydrocarbons, suggesting that Asgard archaea play an important role in sediment carbon cycling. Here, we describe a previously unrecognized archaeal phylum, Hermodarchaeota, affiliated with the Asgard superphylum. The genomes of these archaea were recovered from metagenomes generated from mangrove sediments, and were found to encode alkyl/benzyl-succinate synthases and their activating enzymes that are similar to those identified in alkane-degrading sulfate-reducing bacteria. Hermodarchaeota also encode enzymes potentially involved in alkyl-coenzyme A and benzoyl-coenzyme A oxidation, the Wood–Ljungdahl pathway and nitrate reduction. These results indicate that members of this phylum have the potential to strictly anaerobically degrade alkanes and aromatic compounds, coupling the reduction of nitrate. By screening Sequence Read Archive, additional genes encoding 16S rRNA and alkyl/benzyl-succinate synthases analogous to those in Hermodarchaeota were identified in metagenomic datasets from a wide range of marine and freshwater sediments. These findings suggest that Asgard archaea capable of degrading alkanes and aromatics via formation of alkyl/benzyl-substituted succinates are ubiquitous in sediments.

Graphical abstract, Highlights • Early recognition of chronic pancreatitis (CP) is still lacking. In the setting of CP injury, activated pancreatic stellate cell (PSC) is the central mediator of pancreatic fibrosis. We systematically define highly and uniquely expressed PSC genes and show that these genes are enriched in pancreatic diseases. • Unresolved or recurrent injury causes dysregulation of biological process following AP, which would cause CP. We demonstrated subset genes that may be associated with the progression from AP to CP. Furthermore, SPARC was identified as a candidate marker for the disease progression. • Increased expression of SPARC and canonical PSC genes were verified during AP recovery, especially in recurrent AP mice models., Chronic pancreatitis (CP) is characterized by irreversible fibro-inflammatory changes induced by pancreatic stellate cell (PSC). Unresolved or recurrent injury causes dysregulation of biological process following AP, which would cause CP. Here, we systematically identify genes whose expressions are unique to PSC by comparing transcriptome profiles among total pancreas, pancreatic stellate, acinar, islet and immune cells. We then identified candidate genes and correlated them with the pancreatic disease continuum by performing intersection analysis among total PSC and activated PSC genes, and genes persistently differentially expressed during acute pancreatitis (AP) recovery. Last, we examined the association between candidate genes and AP, and substantiated their potential as biomarkers in experimental AP and recurrent AP (RAP) models. A total of 68 genes were identified as highly and uniquely expressed in PSC. The PSC signatures were highly enriched with extracellular matrix remodeling genes and were significantly enriched in AP pancreas compared to healthy control tissues. Among PSC signature genes that comprised a fibrotic phenotype, 10 were persistently differentially expressed during AP recovery. SPARC was determined as a candidate marker for the pancreatic disease continuum, which was not only persistently differentially expressed even five days after AP injury, but also highly expressed in two clinical datasets of CP. Sparc was also validated as highly elevated in RAP compared to AP mice. This work highlights the unique transcriptional profiles of PSC. These PSC signatures’ expression may help to identify patients with high risk of AP progression to CP.

Hypoxia plays a significant role in tumor progression. This study aimed to develop a hypoxia-related long noncoding RNA (lncRNA) signature for predicting survival outcomes of patients with bladder cancer (BC). The transcriptome and clinicopathologic data were downloaded from The Cancer Genome Atlas (TCGA) database. Univariate Cox regression analysis and Lasso regression analysis were used to screened lncRNAs. Ten lncRNAs were screened out and included into the hypoxia lncRNA signature. The risk score based on hypoxia lncRNA signature could accurately predict the survival outcomes of BC patients. Immune infiltration analysis showed that six types of immune cells had significant different infiltration. Tumor mutation burden (TMB) analysis showed that the risk scores between the wild types and the mutation types of TP53, FGFR3, and RB1 were significantly different. Gene Set Enrichment Analysis (GSEA) showed that cancer-associated pathways belonged to the high risk groups and immune-related signal pathways were enriched into the low risk group. Then, we constructed a predictive model with the risk score, age, and clinical stage, which showed a robust prognostic performance. An lncRNA-mRNA coexpression network was constructed, which contained 62 lncRNA-mRNA links among 10 lncRNAs and 40 related mRNAs. In summary, the hypoxia lncRNA signature could accurately predict prognosis, chemotherapy and immunotherapy response in patients with BC and was relevant to clinicopathologic parameters and immune cell infiltration., Graphical Abstract

Many marine polysaccharides as prebiotics can promote host health by modulating gut microbiota. This study investigated the beneficial effects of purified marine plant-derived Gelidium pacificum Okamura polysaccharide (GPOP-1) and marine animal-derived Cereus sinensis polysaccharide (CSP-1) on normal mice by modulating gut microbiota. The composition and diversity of gut microbiota were evaluated using 16S rRNA high-throughput sequencing. The results showed that GPOP-1 and CSP-1 altered the composition of the gut microbiota and promoted the growth of beneficial bacteria. At the genus level, GPOP-1 increased the relative abundance of Bacteroides, Phascolarctobacterium, and decreased the relative abundance of Ruminococcus, Helicobacter, Allobaculum, Dorea and AF12. While CSP-1 increased the relative abundance of Coprococcus, Adlercreutzia, Roseburia, Phascolarctobacterium, and decreased the relative abundance of Bacteroides, Ruminococcus and Oscillospira. The changes in the gut microbiota may affect the body weight, immune organ index and the production of short-chain fatty acids in normal mice. Compared to the normal control group, GPOP-1 decreased average weight gain while CSP-1 increased average weight gain. Furthermore, both GPOP-1 and CSP-1 significantly increased thymus and spleen indexes and total short chain fatty acids production in mice. In summary, GPOP-1 and CSP-1 exerted prebiotic effects on normal mice.

Vitamin D deficiency is co-prevalent with various liver diseases including cirrhosis, while the underlying mechanism remains elusive. Vitamin D receptor (VDR) is abundantly expressed in the distal region of small intestine, where the Paneth cells are enriched, suggesting that vitamin D signaling may modulates the intestinal Paneth cells and their production of defensins to restrain microbiome growth in the small intestine. In this study we found that in carbon tetrachloride-induced liver injury, hepatic 25-hydroxylation of vitamin D was impaired, leading to down regulated expression of Paneth cell fensins in the small intestine, gut dysbiosis, and endotoxinemia. While intraperitoneal injection of endotoxin (lipopolysaccharides) alone did not elicit liver fibrosis, it exacerbated the carbon tetrachloride initiated liver fibrogenesis. Oral gavage of synthetic Paneth cell alpha-defensin 5 (DEFA5) restored the homeostasis of gut microbiota, reduced endotoxemia, relieved liver inflammation, and ameliorated liver fibrosis. Likewise, Cholestyramine, cationic resin that can sequestrate endotoxin in the intestine, attenuated the liver fibrosis as well. Fecal transplant of the microbes derived from the DEFA5-treated donors improved liver fibrosis in the recipient mice. The intestinal Vdrconditional knockout mice exhibited reduction of Paneth cell defensins and lysozyme production, and worsened liver injury and fibrogenesis. Thus, liver injury impairs synthesis of 25(OH)VD3, which consequently impedes the Paneth cells functions in the small intestine, leading to gut dysbiosis for liver fibrogenesis.

Increasing evidence has revealed that cancer cells undergoing an intermediate state, partial epithelial mesenchymal transition (p‐EMT), tend to metastasize rather than complete EMT. We performed a comprehensive analysis of E‐cadherin and 25 p‐EMT‐related genes in HCC to explore the roles and regulatory mechanisms of them in HCC. We analysed E‐cadherin and 25 p‐EMT‐related genes in HCC and constructed an mRNA‐miRNA‐lncRNA ceRNA subnetwork containing p‐EMT‐related genes by bioinformatic approaches. IHC was used to identify the protein expression of key p‐EMT‐related genes, P4HA2, ITGA5, MMP9, MT1X and SPP1. Complete EMT is not necessary for HCC progression. Overexpression of P4HA2, ITGA5, MMP9, SPP1 and down‐regulation of MT1X were found in HCC tissues, which were significantly associated with poor prognosis of HCC patients. By means of stepwise reverse prediction and validation from mRNA to lncRNA, an mRNA‐miRNA‐lncRNA ceRNA subnetwork correlated with HCC prognosis was identified by expression and survival analysis. This study implied that key p‐EMT‐related genes P4HA2, ITGA5, MMP9, MT1X, SPP1 could be prognostic biomarkers and potential targets of therapy for HCC patients. We constructed an mRNA‐miRNA‐lncRNA subnetwork containing p‐EMT‐related genes successfully, among which each component might be utilized as a prognostic biomarker of HCC.

Diaphanosoma, the “tropical Daphnia”, is common and ubiquitous in South China. Like other ctenopods, Diaphanosoma has a reproductive mode similar to Daphnia’s, but its resting eggs are rarely observed and lack an ephippium. With limited dispersal and reduced buffer effect from resting egg banks, Diaphanosoma is expected to have a population genetic structure different from that of temperate Daphnia. To facilitate genetic comparison, we developed microsatellite markers using next-generation sequencing for the most common species in tropical and subtropical East Asia, Diaphanosoma dubium. Thirty-one polymorphic microsatellite markers were obtained, and 29 of them were efficient for the congeneric species D. excisum, D. orghidani, D. mongolianum and D. chankensis. The markers allowed intra- and interspecific genetic analysis, including population structure, hybridization and introgression. We used 11 selected microsatellite markers to analyze spatial and temporal heterogeneity of genetic diversity in four (sub)tropical D. dubium populations from two large reservoirs and two temporary ponds. In contrast to temperate Cladocera, higher genetic diversity in summer rather than in spring suggested weak contribution from resting eggs in spring. Clustering of DAPC and STRUCTURE analyses indicated a clear-cut genetic structure in the four populations. Variation partitioning revealed that water storage and depth were key factors in genetic differentiation. Within large reservoirs, we detected backward (reversing time) gene flow from resting egg banks. We conclude that resting eggs have an effective contribution to the genetic diversity in large water bodies during growing seasons and that large water bodies can host higher genetic diversity in summer due to environmental heterogeneity and high carrying capacity. Spatial and temporal heterogeneity of genetic diversity detected by our microsatellite markers showed the newly developed markers can be applied for further study of populations of D. dubium and other species of Diaphanosoma at a contemporary scale.

Cyanobacteria are photosynthetic prokaryotes that inhabit diverse aquatic and terrestrial environments. However, the evolutionary mechanisms involved in the cyanobacterial habitat adaptation remain poorly understood. Here, based on phylogenetic and comparative genomic analyses of 650 cyanobacterial genomes, we investigated the genetic basis of cyanobacterial habitat adaptation (marine, freshwater, and terrestrial). We show: (1) the expansion of gene families is a common strategy whereby terrestrial cyanobacteria cope with fluctuating environments, whereas the genomes of many marine strains have undergone contraction to adapt to nutrient-poor conditions. (2) Hundreds of genes are strongly associated with specific habitats. Genes that are differentially abundant in genomes of marine, freshwater, and terrestrial cyanobacteria were found to be involved in light sensing and absorption, chemotaxis, nutrient transporters, responses to osmotic stress, etc., indicating the importance of these genes in the survival and adaptation of organisms in specific habitats. (3) A substantial fraction of genes that facilitate the adaptation of Cyanobacteria to specific habitats are contributed by horizontal gene transfer, and such genetic exchanges are more frequent in terrestrial cyanobacteria. Collectively, our results further our understandings of the adaptations of Cyanobacteria to different environments, highlighting the importance of ecological constraints imposed by the environment in shaping the evolution of Cyanobacteria.

N-acyl-L-homoserine lactones (AHLs) based quorum sensing (QS) phenomenon is recognized as an effective agent for regulating bacterial growth and metabolism. However, diversity and biological role of AHLs in natural environments remain largely unknown. This study focuses on compositions of AHLs and their potential role in nitrogen transformation in intertidal marshes. We investigated the levels of AHLs in rhizosphere (Phragmites australis, Spartina alterniflora and Scirpus mariqueter) and non-rhizosphere soils from Chongming eastern intertidal wetland of the Yangtze Estuary using gas chromatography-mass spectrometry (GC/MS). Molecular techniques were employed to investigate the compositions and structure of bacterial community. Soil-slurry experiments in combination with nitrogen isotope tracing technique were conducted to examine the effects of AHLs on nitrogen transformation processes. AHLs were higher in rhizosphere than non-rhizosphere soils, and correlated significantly with soil organic carbon and pH. C6-, C8-, C10- and C12-HSLs were identified as the probably universal QS signal molecules in intertidal marsh soils. The bacterial biodiversity might be regulated by AHLs, and 12 of the 50 most abundant microorganisms in intertidal marsh soils were related significantly with AHL concentrations. Furthermore, C6-, C8- and C12-HSLs might play an important role in mediating nitrogen transformation processes including nitrification, denitrification and anaerobic ammonium oxidation (anammox). AHLs are favored to accumulate in rhizospheric environments and thus further mediate the bacterial diversity and soil nitrogen cycling. This study highlights the associations of QS signal molecules with the dynamics and activity of nitrogen cycling bacteria in intertidal marshes.

Tolerogenic dendritic cells (tolDCs) have received much attention because of their capacity to restore immune homeostasis. RNA interference techniques have been used in several studies to generate tolDCs by inactivating certain molecules that regulate DC maturation and immunologic function. BAFF is a key B cell survival factor that is not only essential for B cell function but also T cell costimulation, and DCs are the major source of BAFF. In this study, we determined whether BAFF gene silencing in mature DCs could lead to a tolerogenic phenotype as well as the potential therapeutic effect of BAFF-silenced DCs on collagen-induced arthritis (CIA) in mice. Meanwhile, CRISPR/Cas9-mediated BAFF−/− DC2.4 cells were generated to verify the role of BAFF in DC maturation and functionality. BAFF-silenced DCs and BAFF−/− DC2.4 cells exhibited an immature phenotype and functional state. Further, the transplantation of BAFF-silenced DCs significantly alleviated CIA severity in mice, which correlated with a reduction in Th17 populations and increased regulatory T cells. In vitro, BAFF-silenced DCs promoted Foxp3 mRNA and IL-10 expression but inhibited ROR-γt mRNA and IL-17A expression in CD4+ T cells. Together, BAFF-silenced DCs can alleviate CIA, partly by inducing Foxp3+ regulatory T cells and suppressing Th17 subsets. Collectively, BAFF plays an important role in interactions between DCs and T cells, which might be a promising genetic target to generate tolDCs for autoimmune arthritis treatment.

Background Ovarian serous cystadenocarcinoma is one of the most serious gynecological malignancies. Circular RNA (circRNA) is a type of noncoding RNA with a covalently closed continuous loop structure. Abnormal circRNA expression might be associated with tumorigenesis because of its complex biological mechanisms by, for example, functioning as a microRNA (miRNA) sponge. However, the circRNA expression profile in ovarian serous cystadenocarcinoma and their associations with other RNAs have not yet been characterized. The main purpose of this study was to reveal the circRNA expression profile in ovarian serous cystadenocarcinoma. Methods We collected six specimens from three patients with ovarian serous cystadenocarcinoma and adjacent normal tissues. After RNA sequencing, we analyzed the expression of circRNAs with relevant mRNAs and miRNAs to characterize potential function. Results 15,092 unique circRNAs were identified in six specimens. Approximately 46% of these circRNAs were not recorded in public databases. We then reported 353 differentially expressed circRNAs with oncogenes and tumor-suppressor genes. Furthermore, a conjoint analysis with relevant mRNAs revealed consistent changes between circRNAs and their homologous mRNAs. Overall, construction of a circRNA–miRNA network suggested that 4 special circRNAs could be used as potential biomarkers. Conclusions Our study revealed the circRNA expression profile in the tissues of patients with ovarian serous cystadenocarcinoma. The differential expression of circRNAs was thought to be associated with ovarian serous cystadenocarcinoma in the enrichment analysis, and co-expression analysis with relevant mRNAs and miRNAs illustrated the latent regulatory network. We also constructed a complex circRNA–miRNA interaction network and then demonstrated the potential function of certain circRNAs to aid future diagnosis and treatment.

Raphidiopsis raciborskii (previously Cylindrospermopsis raciborskii) can produce cylindrospermopsin (CYN) which is of great concern due to its considerable toxicity to human and animals. Its CYN-producing (toxic) and non-CYN-producing (non-toxic) strains co-exist commonly in natural water bodies, while how their relative dominance is regulated has not been addressed. In this study, we combined field investigation with laboratory experiments to assessed the relationship between toxic and non-toxic R. raciborskii abundances under different nutrient levels. The rpoC1- and cyrJ-based qPCR was applied for quantifying total and toxic R. raciborskii abundances, respectively. The field survey showed that toxic R. raciborskii was detected in 97 of 115 reservoirs where its proportion ranged from 0.3% to 39.7% within the R. raciborskii population. Both total and toxic R. raciborskii abundances increased significantly with trophic level of these reservoirs, consistent with our monoculture and co-culture experiments showing in an increase in R. raciborskii growth with increasing nitrogen (N) or phosphorus (P) concentrations. In the monoculture experiments, growth rates of non-toxic and toxic strains from Australia or China were not significantly different under the same culture conditions. On the other hand, in the co-culture experiments, the toxic strains displayed a significantly faster growth than non-toxic strains under nutrient-replete conditions, resulting in an obvious shift toward the dominance by toxic strains from day 3 to the end of the experiments, regardless of the strain originating from Australia or China. The reverse was found under N- or P-limited conditions. Our results indicated that the toxic strains of R. raciborskii have a competitive advantage relative to the non-toxic strains in a more eutrophic world. In parallel to an increase in dominance, both toxic strains grown in the mixed population significantly increased CYN production under nutrient-replete conditions as compared to nutrient-limited conditions, suggesting that CYN may be of significance for ecological advantage of toxic R. raciborskii. These results highlight the importance of nutrient availability in regulating abundances and strain dominance of two genotypes of R. raciborskii. Our findings demonstrated that elevated nutrients would favor the growth of CYN-producing R. raciborskii and CYN production, leading to more blooms with higher toxicity at global scale.

Non-alcoholic fatty liver diseases (NAFLDs) along with metabolic syndrome and Type-2 diabetes (T2D) are increasingly prevalent worldwide. Without an effective resolution, simple hepatic steatosis may lead to non-alcoholic steatohepatitis (NASH), characterized by hepatocyte damage, chronic inflammation, necrosis, fatty degeneration, and cirrhosis. The gut microbiome is vital for metabolic homeostasis. Conversely, dysbiosis contributes to metabolic diseases including NAFLD. Specifically, diet composition is critical for the enterotype of gut microbiota. We reasoned that green pigment rich in vegetables may modulate the gut microbiome for metabolic homeostasis. In this study, C57BL/6 mice under a high fat diet (HFD) were treated with sodium copper chlorophyllin (CHL), a water-soluble derivative of chlorophyll, in drinking water. After 28 weeks of HFD feeding, liver steatosis was established accompanied by gut microbiota dysbiosis, intestinal impairment, endotoxemia, systemic inflammation, and insulin resistance. Administration of CHL effectively alleviated systemic and intestinal inflammation and maintained tight junction in the intestinal barrier. CHL rebalanced gut microbiota in the mice under high fat feeding and attenuated hepatic steatosis, insulin resistance, dyslipidemia, and reduced body weight. Fecal flora transplants from the CHL-treated mice ameliorated steatosis as well. Thus, dietary green pigment or the administration of CHL may maintain gut eubiosis and intestinal integrity to attenuate systemic inflammation and relieve NASH.

BackgroundVitamin D deficiency (VDD) is overwhelmingly prevalent worldwide in association with metabolic syndrome (MetS), type-2 diabetes (T2D), and non-alcoholic fatty liver diseases (NAFLD). Whether vitamin D supplement or treatment can improve these metabolic diseases is controversial, due in part to absence of large-scale trials. On the other hand, unbalanced gut microbiome, dysbiosis, plays key roles in these metabolic diseases. Moreover, whether sunlight exposure or vitamin D can determine the gut microbiome is elusive. The present study aims to investigate whether intramuscular administration of high dose of vitamin D2 can improve non-alcoholic steatohepatitis (NASH) through balancing of gut microbiome. Methods/designIn a randomized, open-labeled, and parallel-group trial, NASH subjects will be enrolled and randomly allocated to receive ergocalciferol (VD2) treatment or not, n=80 for each group. The NASH patients, diagnosed according to the guideline for NAFLD treatment of China, will be given an initial dose of VD2 at 600,000IU by intramuscular injection followed by additional three administration every other 30 days with total of four injections in 120 days. Anthropometry, liver functions, the metabolic panel will be measured. Fatty liver index will be determined by topological analysis of ultrasound data. Serum 25-hydroxyvitamin D (25(OH)D) and fecal microbiome will be measured. Discussion: This study will determine the efficacy of high dose of VD2 to relieve NASH symptoms and on gut microbiota. Trial registrationChinese Clinical Trial Registry, ChiCTR1800017879, registered on Aguste 20th, 2018.

Inferring an unknown DNA’s ancestry using a set of ancestry-informative single nucleotide polymorphisms (SNPs) in forensic science is useful to provide investigative leads. This is especially true when there is no DNA database match or specified suspect. Thus, a set of SNPs with highly robust and balanced differential power is strongly demanded in forensic science. In addition, it is also necessary to build a genotyping database for estimating the ancestry of an individual or an unknown DNA. For the differentiation of Africans, Europeans, East Asians, Native Americans, and Oceanians, the Global Nano set that includes just 31 SNPs was developed by de la Puente et al. Its ability for differentiation and balance was evaluated using the genotype data of the 1000 Genomes Phase III project and the Stanford University HGDP-CEPH. Just 402 samples were genotyped and analyzed as a reference set based on statistical methods. To validate the differentiating capacity using more samples, we developed a single-tube 28-plex SNP assay in which the SNPs were chosen from the 31 allelic loci of the Global AIMs Nano set. Three tri-allelic SNPs used to differentiate mixed-source DNA contribute little to population differentiation and were excluded here. Then, 998 individuals from 21 populations were typed, and these genotypes were combined with the genotype data obtained from 1000 Genomes Phase III and the Stanford University HGDP-CEPH (3090 total samples,43 populations) to estimate the power of this multiplex assay and build a database for the further inference of an individual or an unknown DNA sample in forensic practice.

Phyllodiaptomus tunguidus (Copepoda: Calanoida) is largely endemic to and widespread in freshwater in southern China, where it inhabits a complex landscape from lowland to highland across an elevation gradient of 2000m. A deep genetic differentiation can be expected between its most distant geographic populations. Here, we sequenced nine mitogenomes from diverse populations. All mitogenomes contained 37 genes, including 13 protein-coding genes (PCG), two rRNA genes, 22 tRNA genes and one control region. Their base composition, genetic distance and tRNA structure indeed revealed a wide differentiation between mitogenomes. Two P. tunguidus from Guangxi near Vietnam differed from the other seven by up to 10.1%. Their tRNA-Arg had a complete clover-leaf structure, whereas that of the others did not contain an entire dihydrouridine arm. The nine mitogenomes also differed in the length of rRNA. NJ, ML, and Bayesian analyses all split them into two clades, viz. the two P. tunguidus from Guangxi (Clade 1), and the other seven (Clade 2). Both the structure and phylogeny of the mitogenomes suggest that P. tunguidus has complex geographic origin, and its populations in Clade 1 have long lived in isolation from those in Clade 2. They currently reach the level of subspecies or cryptic species. An extensive phylogenetic analysis of Copepoda further verified that Diaptomidae is the most recently diverging family in Calanoida and that P. tunguidus is at the evolutionary apex of the family.

ObjectivesTo construct a nomogram model that combines clinical characteristics and radiomics signatures to preoperatively discriminate pancreatic ductal adenocarcinoma (PDAC) in stage I-II and III-IV and predict overall survival.MethodsA total of 135 patients with histopathologically confirmed PDAC who underwent contrast-enhanced CT were included. A total of 384 radiomics features were extracted from arterial phase (AP) or portal venous phase (PVP) images. Four steps were used for feature selection, and multivariable logistic regression analysis were used to build radiomics signatures and combined nomogram model. Performance of the proposed model was assessed by using receiver operating characteristic (ROC) curves, calibration curves and decision curve analysis (DCA). Kaplan-Meier analysis was applied to analyze overall survival in the stage I-II and III-IV PDAC groups.ResultsThe AP+PVP radiomics signature showed the best performance among the three radiomics signatures [training cohort: area under the curve (AUC) = 0.919; validation cohort: AUC = 0.831]. The combined nomogram model integrating AP+PVP radiomics signature with clinical characteristics (tumor location, carcinoembryonic antigen level, and tumor maximum diameter) demonstrated the best discrimination performance (training cohort: AUC = 0.940; validation cohort: AUC = 0.912). Calibration curves and DCA verified the clinical usefulness of the combined nomogram model. Kaplan-Meier analysis showed that overall survival of patients in the predicted stage I-II PDAC group was longer than patients in stage III-IV PDAC group (pConclusionsWe propose a combined model with excellent performance for the preoperative, individualized, noninvasive discrimination of stage I-II and III-IV PDAC and prediction of overall survival.

Although the traditional Folmer and Prosser primers enable successful amplification of COI ‘barcoding’ sequences in freshwater zooplankton species, many freshwater zooplankters including Phyllodiap...

Body size is a functional trait that influences the overall biology and ecology of an organism. Studying the shape of size–frequency distributions and size variability within different scales, approximates the influence of large-scale ecological and evolutionary processes on a species. In this study we examine the patterns of distribution and variability of body size among freshwater Cladocera across different taxonomic levels, geographic distribution and habitat association. Using extensive literature data, we show the global distribution of body size in freshwater Cladocera. Hierarchical models were used to assess the effect of different categorical variables on size variability. Our results show that almost all size–frequency distributions were skewed right in all categories. The hierarchical model showed that taxonomic affiliation contributes the most to size variability in our dataset, suggesting that size might be a conserved trait. Large genera (≥1mm) have larger estimated variability compared to smaller genera. In general, our observations on size–frequency distributions and size variability show a brief insight in the varying advantages of adaptive body size in this group of organisms in both biology (physiology) and ecology (competition and co-existence). Thus, body size is a trait important to the survival and continuing evolution of Cladocera.

In this study, we propose a novel strategy, plasma activated water (PAW) to reduce pesticide residues on agricultural products. To validate its feasibility and effectiveness, we employee high-performance liquid chromatography (HPLC) to detect phoxim on grapes. HPLC results suggest that the reduction of phoxim on grapes achieve 73.60% after treated 10 min by PAW prepared 30 min, and the concentration of phoxim decreased significantly (p 0.05) with the preparation time of PAW. Furthermore, HPLC-MS analysis shows that the reduction effect of phoxim by PAW is dominated by the degradation of phoxim. Combined with analyzing the physicochemical properties of PAW, one possible degradation pathway is proposed under the present experimental conditions, mediated by reactive oxygen and nitrogen species. The acidic environment (pH 3) and high oxidation capacity (ORP 500 mV) are suggested to be a benefit to the reduction of phoxim. Besides, the experimental results regarding color, firmness, sugar, vitamin C, and superoxide dismutase of grapes demonstrate that the PAW treatment will not significantly affect the quality of grapes. In conclusion, phoxim pesticide residues on grapes could be effectively reduced by the PAW strategy and without a significant (p 0.05) effect on grapes quality.

Cylindrospermopsin (CYN) is of great concern to human and animal health due to its potential toxicity. The cyanobacterium Cylindrospermopsis raciborskii is considered the most common cyanobacterial species that produces CYN. The discovery of the cyr gene cluster responsible for CYN biosynthesis allows us to develop molecular methods that detect and quantify potentially CYN-producing C. raciborskii. This paper describes the development of real-time PCR (qPCR) assays capable of quantifying the total and CYN-producing C. raciborskii in subtropical reservoirs of southern China. We designed primers and probes specifically targeting the rpoC1 and cyrJ genes of C. raciborskii, and enabling quantification of its total cell numbers and potentially toxic genotypes, respectively. The qPCR showed strong linearity between 102 and 106 copies per reaction for both genes. This molecular method was validated against microscopic counting and a high correlation was found between them for quantifying C. raciborskii cell numbers in cyanobacterial cultures and water samples. Using qPCR, we detected potentially CYN-producing C. raciborskii in 34 of the 46 subtropical reservoirs of southern China, with the cyrJ/rpoC1 proportion ranging from 0.3 to 34.7%. CYN concentrations significantly correlated with both the copy numbers of cyrJ gene and the proportion of toxic C. raciborskii. Thus, the present real-time PCR method provides a reliable and faster method for estimating the potential toxicity of C. raciborskii blooms in this region. The wide distribution of potential CYN-producing C. raciborskii in the investigated subtropical reservoirs highlights the need for further monitoring.

Collective cell migration plays an important role in embryonic development, wound healing, and cancer metastasis. We aimed to investigate the expression, role, and mechanism of Netrin-1 in collective cell migration using a3D culture model. An immunohistochemical study showed that certain cells invaded surrounding tissue by collective migration and that Netrin-1 expression in these cells was increased, especially at the invasive front. In the 3D culture model, collective cell migration was clearly observed, as leader cells were followed by cells migrating along a canal. N-cadherin-mediated cell junctions were observed in collective cell migration, and Netrin-1 expression was elevated in these cells. Netrin-1 did not affect the expression of N-cadherin in 2D-cultured cells; however, in 3D culture, the overexpression of Netrin-1 increased N-cadherin and promoted the collective migration of Huh7 cells, while the knockdown of Netrin-1 decreased N-cadherin and inhibited collective migration in SK-Hep-1 cells. Interestingly, N-cadherin knockdown in Huh7 cells significantly diminished Netrin-1-promoted collective cell migration, while the overexpression of N-cadherin restored collective migration in Netrin-1-knockdown SK-Hep1 cells. These results suggest that Netrin-1 enhances N-cadherin junctions to promote liver cancer cell collective migration in 3D cell culture and may subsequently increase liver cancer metastasis.

Objectives Microbiota dysbiosis in inflammatory bowel disease (IBD) has been widely reported. The gut microbiota connect diet to the metabolism by producing small molecules via diverse metabolic pathways. In this study we aimed to investigate the dietary preferences of IBD patients, and to explore the interactions among gut microbiota composition, dietary components, and metabolites in relation to IBD. Methods Dietary preferences of IBD patients (including those with ulcerative colitis [UC] and Crohn's disease [CD]) and health controls were investigated, and their gut microbiota were analyzed using 16S rRNA gene sequencing and metagenomic analyses of fecal and biopsy samples. The metabolite profiles of the samples were then analyzed using gas and liquid chromatography-mass spectrometry analyses. Results The daily intake of folic acid, niacin, vitamins C and D, calcium, and selenium differed significantly between patients with IBD and healthy controls. A decrease in long-chain (such as arachidic, and oleic acid) and medium-chain fatty acids (sebacic acid and isocaproic acid) as well as bile acid was observed in patients with IBD. Compared with healthy controls, 22 microbial species (including Sulfolobus acidocaldarius, and Clostridium clostridioforme CAG132) in the UC group and 37 microbial species (such as Bacteroides fragilis and Fusobacterium nucleatum) in the CD group were found to be correlated to diet and metabolites. Bacteroides fragilis was enriched in patients with IBD and associated with multi-nutrients, and 21 metabolites including 25-hydroxyvitamin D3 and taurolithocholic acid. Conclusions This study provides an interaction network to identify key micronutrients, microbiota components and metabolites that contribute to IBD.

Spermatogonial stem cells (SSCs) self-renew and contribute genetic information to the next generation. Pig is wildly used as a model animal for understanding reproduction mechanisms of human being. Inducing directional differentiation of porcine SSCs may be an important strategy in exploring the mechanisms of spermatogenesis and developing better treatment methods for male infertility. Here, we established an in-vitro culture model for porcine small seminiferous tubule segments, to induce SSCs to differentiate into single-tail haploid spermatozoa. The culture model subsequently enabled spermatozoa to express the sperm-specific protein acrosin and oocytes to develop to blastocyst stage after round spermatid injection. The addition of retinoic acid (RA) to the differentiation media promoted the efficiency of haploid differentiation. RT-PCR analysis indicated that RA stimulated the expression of Stra8 but reduced the expression of NANOS2 in spermatogonia. Genes involved in post-meiotic development, transition protein 1 (Tnp1) and protamine 1 (Prm1) were upregulated in the presence of RA. The addition of an RA receptor (RAR) inhibitor, BMS439, showed that RA enhanced the expression of cAMP responsive-element binding protein through RAR and promoted the formation of round spermatids. We established an efficient culture system for in-vitro differentiation of pig SSCs. Our study represents a model for human testis disease and toxicology screening. Molecular regulators of SSC differentiation revealed in this study might provide a therapeutic strategy for male infertility.

The recently discovered complete ammonia-oxidizing (comammox) bacteria occur in various environments, including wastewater treatment plants. To better understand their role in micropollutant biotransformation in comparison with ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA), we investigated the biotransformation capability of Nitrospira inopinata (the only comammox isolate) for 17 micropollutants. Asulam, fenhexamid, mianserin, and ranitidine were biotransformed by N. inopinata, Nitrososphaera gargensis (AOA), and Nitrosomonas nitrosa Nm90 (AOB). More distinctively, carbendazim, a benzimidazole fungicide, was exclusively biotransformed by N. inopinata. The biotransformation of carbendazim only occurred when N. inopinata was supplied with ammonia but not nitrite as the energy source. The exclusive biotransformation of carbendazim by N. inopinata was likely enabled by an enhanced substrate promiscuity of its unique AMO and its much higher substrate (for ammonia) affinity compared with the other two ammonia oxidizers. One major plausible transformation product (TP) of carbendazim is a hydroxylated form at the aromatic ring, which is consistent with the function of AMO. These findings provide fundamental knowledge on the micropollutant degradation potential of a comammox bacterium to better understand the fate of micropollutants in nitrifying environments.

Exotic Spartina alterniflora invasion resulting from anthropogenic activities significantly affects microbial nitrogen (N) transformation and associated nitrous oxide (N2O) emission in coastal wetland soils. However, the responses of soil N2O emission dynamics to plant invasion remain unclear. This study assesses the effects of S. alterniflora invasion on soil N2O potential production and consumption processes. We used natural isotope tracing technique to investigate potential N2O production and consumption rates in S. alterniflora invaded and native saltmarsh zones (Phragmites australis, Scirpus mariqueter and bare mudflat) in the Yangtze Estuary. Soil potential net N2O production rates in summer were lower in S. alterniflora stands than in S. mariqueter and bare mudflat stands, but no significant differences among these saltmarsh habitats occurred during winter. Potential gross N2O production and consumption rates were higher in S. alterniflora and P. australis stands compared to S. mariqueter and bare mudflat stands. The gross consumption proportion in S. alterniflora and P. australis stands was higher, which affected net N2O production. Hydroxylamine (NH2OH) oxidation and nitrifier denitrification contributed 4.52–12.62% and 13.87–21.58% of soil N2O source, respectively, but denitrification was the dominant pathway (69.83–80.09%). S. alterniflora invasion increased the contributions of NH2OH oxidation and nitrifier denitrification to N2O source slightly, but decreased the contribution of denitrification to N2O source. Soil potential N2O production and consumption processes were influenced by water-filled pore space, pH, sulfide, and carbon and N substrates. Exotic S. alterniflora invasion affected soil N2O dynamics by increasing substrates and altering microenvironments, thus mediating N2O emission from coastal saltmarsh soils.

P450c17, a key enzyme in the steroid generation pathway, plays an important role in the production of sex steroid and cortisol. In this study, two cyp17 gene isoforms, Pocyp17-I and Pocyp17-II were isolated from Paralichthys olivaceus gonads. Domain architecture analysis of Pocyp17-I and Pocyp17-II revealed that they had three regions important to enzymatic function. Structural analysis showed that Pocyp17-I and Pocyp17-II had 8 and 9 exons respectively, and the difference was caused by the insertion of an extra intron (intron1) in the latter. Quantitative real-time polymerase chain reaction results indicated that the expression of these two genes showed sexually dimorphism that Pocyp17-I and Pocyp17-II were highest expressed in testis and ovary, respectively. The in situ hybridization analysis of gonads indicated that Pocyp17-I and Pocyp17-II mRNA were both detected in oocytes, spermatocytes and Sertoli cells. After injection of androgen and estrogen (17α-methyltestosterone, 17β-estradiol) of different concentrations, the expression level of Pocyp17-I decreased significantly (P 0.01), whereas estrogen had no influence on Pocyp17-II, but androgen upregulated the expression of Pocyp17-II (P 0.05). Moreover, Pocyp17-I expression level was down-regulated significantly by NR0b1 but up-regulated by NR5a2 (P 0.05), whereas Pocyp17-II expression level was down-regulated significantly by NR0b1 and NR5a2 (P 0.05). All these results demonstrated that there were differences in expression patterns, feedback actions of sex hormones and transcriptional regulations between cyp17-I and cyp17-II, which revealed that cyp17-I and cyp17-II might perform different functions in sex hormones biosynthesis and gonadal differentiation in Japanese flounder.

The original description of Diaptomus vexillifer Brehm, 1933, endemic to Lake Danao (Leyte Island), was elementary and lacking taxonomically satisfactory characters. In this paper, we redescribe the Philippine-endemic genus Filipinodiaptomus Lai, Mamaril Sr. & Fernando, 1979 and the species D. vexillifer collected from its type locality, using light and scanning electron microscopy and an analysis of the mtCOI gene and the ITS of the nuclear 18S operon. We found that D. vexillifer is the second species under this endemic genus. A neotype and paraneotypes are hereby designated. Also a detailed morphological comparison is made between Filipinodiaptomus vexillifer (Brehm, 1933) comb. nov. and Filipinodiaptomus insulanus (Wright, 1928). Their taxonomic characters, interspecies relationship, and biogeography are likewise discussed.

The RNA interference (RNAi) pathway regulates mRNA stability and translation in nearly all human cells. Small double-stranded RNA molecules can efficiently trigger RNAi silencing of specific genes, but their therapeutic use has faced numerous challenges involving safety and potency. However, August 2018 marked a new era for the field, with the US Food and Drug Administration approving patisiran, the first RNAi-based drug. In this Review, we discuss key advances in the design and development of RNAi drugs leading up to this landmark achievement, the state of the current clinical pipeline and prospects for future advances, including novel RNAi pathway agents utilizing mechanisms beyond post-translational RNAi silencing.

The fruits of Xanthium strumarium L., Asteraceae, have been used for various diseases in Chinese folk medicine, including allergic rhinitis, tympanitis, arthritis, ozena etc. The current study was aimed to investigate the therapeutic effects of caffeoylquinic acids from fruits of X. strumarium on allergic rhinitis in animals. The toxicity test indicated that the caffeoylquinic acids have no obvious toxicity. By using HPLC assays combined with reference standards, ten caffeoylquinic acids were identified as the predominant constituents. Anti-allergic activities of the caffeoylquinic acids were evaluated using passive cutaneous anaphylaxis test and Schultz-Dale test; dimethylbenzene induced ear edema test was performed to evaluate its anti-inflammatory effect. Then, the allergic rhinitis model in rats was established to evaluate the therapeutic effects of the caffeoylquinic acids against allergic rhinitis with the following indexes: allergic rhinitis symptom scores, serum levels of pro-inflammatory cytokines, histopathological examination, and histamine release. Our study revealed that the caffeoylquinic acids showed obvious anti-allergic and anti-inflammatory properties, and its treatments were beneficial for ameliorating the nasal symptoms, decreasing pro-inflammatory cytokines, and inhibiting the releases of histamine. Collectively, the caffeoylquinic acids might be utilized as effective and safe disease therapeutic agents for allergic rhinitis. Keywords: Fructus Xanthii, Allergic rhinitis, Caffeoylquinic acids, Histopathology, Histamine

Currently known rapid determination of fungicides usually relies on antibody-based immunoassay. This paper reports a simple antibody-free colorimetric assay for chlorothalonil via the inhibition of an enzyme-triggered reaction. The enzymatic activity of glyceraldehyde-3-phosphate dehydrogenase was significantly inhibited by chlorothalonil, and the color change of NBT-PMS system induced from NADH formation was suppressed, which could be used indirectly to assay chlorothalonil. The limit of detection (LOD) was 0.05 μM with a linear range from 0.5 to 10 μM, and the detection of 1 μM chlorothalonil in solution was achieved with a naked-eye readout. In addition, the colorimetric measurement results of the cucumber samples showed a good recovery rate, although the sensitivity was less effective than the instrumental method. Nevertheless, the results demonstrates that the chlorometric method provides potential opportunities for reliable, cost-effective quantitative detection for chlorothalonil residues in vegetables.

To better understand the fauna of freshwater calanoid copepods of China, including the occurrence of intra- and intergeneric hybridization, we studied five species, distributed across the whole of China or in South China. We sequenced a mitochondrial (COI) and the nuclear ribosome 18S operon (ITS) to reconstruct the phylogenetic trees by using a Bayesian and maximum likelihood (ML) approach with 161 individuals. The phylogeny tree revealed five clades and two geographically separated subclades in both S. ferus and P. tunguidus. We found, for the first time, that the hybrid specimens occurred in Diaptomidae, but low hybridization suggested effective barriers to hybridization and introgression. One hypothesis, that hybridization is recent and was initiated by invasions via canals built between the Yangtze and Pearl rivers c. 2000 years ago, is not supported by K2P genetic distances of the order of 20%. Furthermore, COI analysis of different populations of S. ferus and P. tunguidus revealed two geographical clades in each species, with genetic distances commensurate with cryptic speciation. Both clades occupy subranges maintained without visible barriers to mixis.

The goal of this vision paper is to investigate the possible role that advanced machine learning techniques, especially deep learning (DL), could play in the reintegration of various biological disciplines. To achieve this goal, a series of operational, but admittedly very simplistic, conceptualizations have been introduced: Life has been taken as a multidimensional phenomenon that inhabits three physical dimensions (time, space, and scale) and biological research as establishing connection between different points in the domain of life. Each of these points hence denotes a position in time, space, and scale at which a life phenomenon of interest takes place. Using these conceptualizations, fragmentation of biology can be seen as the result of too few and especially too short-ranged connections. Reintegrating biology could then be accomplished by establishing more, longer ranged connections. DL methods appear to be very well suited for addressing this particular need at this particular time. Notwithstanding the numerous unsubstantiated claims regarding the capabilities of AI, DL networks represent a major advance in the ability to find complex relationships inside large data sets that would have not been accessible with traditional data analytic methods or to a human observer. In addition, ongoing advances in the automation of taking measurements from phenomena on all levels of biological organization continue to increase the number of large quantitative data sets that are available. These increasingly common data sets could serve as anchor points for making long-range connections by virtue of DL. However, connections within the domain of life are likely to be structured in a highly nonuniform fashion and hence it is necessary to develop methods, for example, theoretical, computational, and experimental, to determine linkage of biological data sets most likely to provide useful insights on a biological problem using DL. Finally, specific DL approaches and architectures should be developed to match the needs of reintegrating biology.

Potentially toxic Cylindrospermopsis raciborskii blooms are of emerging concerns, as its scale is spreading from tropical regions to high latitudes, increasing the risk of aquatic biota being exposed to cylindrospermopsin (CYN). So far, CYN-producing C. raciborskii strains have only been reported in tropical waters which are commonly phosphorus (P)-deficient, where they can dominate phytoplankton communities. However, the influence of CYN on phytoplankton communities under different P status remains unclear. In this study, we first analyzed the summer observations of 120 tropical reservoirs in Guangdong Province. The proportion of potential CYN-producers was significantly higher in P-deficient and CYN-present reservoirs than that in P-sufficient or CYN-absent ones. This suggested that in P-deficient condition, the potential CYN producers might gain more advantages by the help of CYN. Then, in laboratory experiments we found that upon P deprivation, CYN did not inhibit the cell growth of other algal cells, but significantly stimulates them to secret more alkaline phosphatase (ALP) than in P-sufficient condition. Through transcriptomics, we further revealed that under such P-deficient condition, CYN remarkably induced intracellular nitrogen allocation and protein export system by activating the PIK3/Akt-cGMP/PKG signaling pathways in Scenedesmus bijugatus, thus enhancing its ALP secretion. Our study implies that CYN-induced ALP secretion is facilitated upon P deficiency, thus supporting the dominance of its producers C. raciborskii.

Cladocera (Crustacea: Branchiopoda) is a key group of invertebrates. Despite a long history of phylogenetic research, relationships within this group remain disputed. We here provide new insights based on 15 new mitochondrial genomes obtained from high-throughput sequencing (HTS) and 40 mitogenomes extracted from published HTS datasets. Together with 25 mitogenomes from GenBank, we generated a matrix of 80 mitogenomes, 44 of them belonging to Cladocera. We also obtained a matrix with 168 nuclear orthologous genes to further assess the phylogenetic result from mitogenomes based on published data and one new HTS data ofLeptodora. Maximum likelihood and Bayesian phylogenetic analyses recovered all Branchiopoda orders as monophyletic and supported a sister-group relationship between Anomopoda and Onychopoda, making the taxon Gymnomera paraphyletic and supporting an independent origin of predatory Haplopoda and Onychopoda. The nuclear phylogeny and topological tests also support Gymnomera as paraphyletic, and the nuclear phylogeny strongly supports a sister-group relationship between Ctenopoda and Haplopoda. We provide a fossil-calibrated time tree, congruent with a Carboniferous origin for Cladocera and a subsequent diversification of the crown group of Anomopoda, Onychopoda, and Ctenopoda, at least in the Triassic. Despite their long evolutionary history, non-Cladoceran Branchiopoda exhibited high mitogenome structural stability. On the other hand, 21 out of 24 gene rearrangements occurred within the relatively younger Cladocera. We found the differential base compositional skewness patterns between Daphnia s.s. and Ctenodaphnia, which might be related to the divergence between these taxa. We also provide evidence to support the recent finding that Spinicaudata possesses mitogenomes with inversed compositional skewness without gene rearrangement. Such a pattern has only been reported in Spinicaudata.

Rotifers are a small-sized but key group of freshwater zooplankters with high species richness, linking primary producers to higher consumers in aquatic food webs. DNA barcoding has been widely used in exploring its biodiversity, cryptic speciation and phylogeny. However, the inefficiency of universal primers to amplify COI of rotifers hinders our understanding of their species richness and genetic diversity. Here, we develop a new pair of primers, 30 F and 885 R, to amplify the COI gene of rotifers. We used 22 species to test their PCR success rate and found that the new pair of primers was more efficient (86%) than two pairs of universal primers, namely, dgLCO and dgHCO (32%), and Folmer primers (59%). The new primers will allow the barcoding of groups that were so far difficult to sequence and will contribute to clarify species diversity and phylogeny of rotifers.

The recent Zika virus (ZIKV) epidemic poses a serious threat to global health due to its association with microcephaly and congenital diseases in newborns and neurological complications and Guillain-Barré syndrome in adults. However, the majority of people infected with ZIKV do not develop symptoms. The platforms aimed to specifically diagnose ZIKV infection are needed for patient care and public health surveillance. In the study, four ZIKV envelope (E) protein-specific monoclonal antibodies (mAbs) (A1, B1, C1, and 9E-1) have been developed by using the conventional mAb technology. The binding epitopes of mAbs A1, B1, C1, and 9E-1 are located at E(238-257), E(410-431), E(258-277), and E(340-356), respectively. mAb 9E-1 performs 1.4- to 47-fold strong affinity to ZIKV E protein compared to another three mAbs. mAbs A1, C1, and 9E-1 do not have cross-reactivity against the recombinant E proteins of dengue virus serotypes 2, 3, and 4. Although these four mAbs do not have ZIKV neutralizing activity, mAbs B1 and 9E-1 have been developed as the lateral flow immunochromatographic assay for specific detection of ZIKV E protein and virions. Key points • The mAbs targeting to the regions of E(238-257), E(410-431), E(258-277), and E(340-356) do not have ZIKV neutralizing activity. • The binding epitope of mAb 9E-1 is highly specific to ZIKV E protein. • mAbs B1 and 9E-1 can bind to ZIKV virions and have been developed as the lateral flow immunochromatographic assay.