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Liver development is a highly complex process that is regulated by the orchestrated interplay of epigenetic regulators, transcription factors, and microRNAs (miRNAs). Owing to the lack of global in vivo targets of all miRNAs during liver development, the mechanisms underlying the dynamic control of hepatocyte differentiation by miRNAs remain elusive. Here, using Argonaute (Ago) high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse liver at different developmental stages, we characterized massive Ago-binding RNAs and obtained a genome-wide map of liver miRNA-mRNA interactions. The dynamic changes of five clusters of miRNAs and their potential targets were identified to be differentially involved at specific stages, a dozen of high abundant miRNAs and their epigenetic regulation by super-enhancer were found during liver development. Remarkably, miR-122, a liver-specific and most abundant miRNA in newborn and adult livers, was found by its targetome and pathway reporter analyses to regulate the Hippo pathway, which is crucial for liver size control and homeostasis. Mechanistically, we further demonstrated that miR-122 negatively regulates the outcomes of the Hippo pathway transcription factor TEAD by directly targeting a number of hippo pathway regulators, including the coactivator TAZ and a key factor of the phosphatase complex PPP1CC, which contributes to the dephosphorylation of YAP, another coactivator downstream of the Hippo pathway. This study identifies for the first time the genome-wide miRNA targetomes during mouse liver development and demonstrates a novel mechanism of terminal differentiation of hepatocytes regulated by the miR-122/Hippo pathway in a coordinated manner. As the Hippo pathway plays important roles in cell proliferation and liver pathological processes like inflammation, fibrosis, and hepatocellular carcinoma (HCC), our study could also provide a new insight into the function of miR-122 in liver pathology.

The Animal QTLdb (https://www.animalgenome.org/QTLdb) and CorrDB (https://www.animalgenome.org/CorrDB) are unique resources for livestock animal genetics and genomics research which have been used extensively by the international livestock genome research community. This is largely due to the active development of the databases over the years to keep up with the rapid advancement of genome sciences. The ongoing development has ensured that these databases provide researchers not only with continually updated data but also with new web tools to disseminate the data. Through our continued efforts, the databases have evolved from the original Pig QTLdb for cross-experiment QTL data comparisons to an Animal QTLdb hosting 220 401 QTL, SNP association and eQTL data linking phenotype to genotype for 2210 traits. In addition, there are 23 552 correlations for 866 traits and 4273 heritability data on 1069 traits in CorrDB. All these data were curated from 3157 publications that cover seven livestock species. Along with the continued data curation, new species, additional genome builds, and new functions and features have been built into the databases as well. Standardized procedures to support data mapping on multiple species/genome builds and the ability to browse data based on linked ontology terms are highlights of the recent developments.

BackgroundRecurrent preimplantation embryo developmental arrest (RPEA) is the most common cause of assisted reproductive technology treatment failure associated with identified genetic abnormalities. Variants in known maternal genes can only account for 20%–30% of these cases. The underlying genetic causes for the other affected individuals remain unknown.MethodsWhole exome sequencing was performed for 100 independent infertile females that experienced RPEA. Functional characterisations of the identified candidate disease-causative variants were validated by Sanger sequencing, bioinformatics and in vitro functional analyses, and single-cell RNA sequencing of zygotes.ResultsBiallelic variants in ZFP36L2 were associated with RPEA and the recurrent variant (p.Ser308_Ser310del) prevented maternal mRNA decay in zygotes and HeLa cells.ConclusionThese findings emphasise the relevance of the relationship between maternal mRNA decay and human preimplantation embryo development and highlight a novel gene potentially responsible for RPEA, which may facilitate genetic diagnoses.

Salmonella is considered one of the leading causes for foodborne diseases in humans. Pork and its products contaminated with Salmonella are increasingly recognized as an important source of human salmonellosis. The aim of this study was to investigate the antimicrobial resistance and prevalence of integrons in Salmonella isolates from pig farms. In total, 92 of 724 (12.7%) samples were Salmonella-positive, including 64 (15.0%) from fecal samples, 27 (12.6%) from floor samples, 1 (4.5%) from water samples, and 0 from feed and air samples. These isolates showed the highest resistance to tetracycline (85.9%), followed by trimethoprim (67.4%), ampicillin (60.9%), and chloramphenicol (51.1%). In addition, 51 isolates carried the complete class 1 integron, most of which (42/51) harbored antibiotic resistance cassettes. A total of six gene cassettes including orfF, est-X, dfrA1+aadA1, aadA1, dfrA12+aadA2, and sat were identified, in which the most prevalent one was orfF (29.4%). Furthermore, all 19 class 1 integron-positive isolates harboring dfr genes showed resistance to trimethoprim (SXT), suggesting that the trimethoprim resistance gene (dfr) may contribute to the emergence of SXT resistance phenotype. Therefore, considering the significance of integrons and related resistance genes for public health, special measures should be taken to control Salmonella spp. on the pig farms and to prevent spread of integrons and associated resistance genes.

Summary Multiple morphological abnormalities of the sperm flagella (MMAF)-induced asthenoteratozoospermia is a common cause of male infertility. Previous studies have identified several MMAF-associated genes, highlighting the condition’s genetic heterogeneity. To further define the genetic causes underlying MMAF, we performed whole-exome sequencing in a cohort of 643 Chinese MMAF-affected men. Bi-allelic DNAH10 variants were identified in five individuals with MMAF from four unrelated families. These variants were either rare or absent in public population genome databases and were predicted to be deleterious by multiple bioinformatics tools. Morphological and ultrastructural analyses of the spermatozoa obtained from men harboring bi-allelic DNAH10 variants revealed striking flagellar defects with the absence of inner dynein arms (IDAs). DNAH10 encodes an axonemal IDA heavy chain component that is predominantly expressed in the testes. Immunostaining analysis indicated that DNAH10 localized to the entire sperm flagellum of control spermatozoa. In contrast, spermatozoa from the men harboring bi-allelic DNAH10 variants exhibited an absence or markedly reduced staining intensity of DNAH10 and other IDA components, including DNAH2 and DNAH6. Furthermore, the phenotypes were recapitulated in mouse models lacking Dnah10 or expressing a disease-associated variant, confirming the involvement of DNAH10 in human MMAF. Altogether, our findings in humans and mice demonstrate that DNAH10 is essential for sperm flagellar assembly and that deleterious bi-allelic DNAH10 variants can cause male infertility with MMAF. These findings will provide guidance for genetic counseling and insights into the diagnosis of MMAF-associated asthenoteratozoospermia.

Objective To investigate the effects of non-Robertsonian translocation with chromosome fusion (N-RBCF) on preimplantation embryos. Design Case series. Setting University-affiliated center. Patient(s) Twelve couples with N-RBCF. Intervention(s) Assisted reproduction with preimplantation genetic testing in chromosomal structural rearrangement (PGT-SR). Main Outcome Measure(s) Normal embryo rate, unbalanced translocation rate. Result(s) PGT was performed in 12 N-RBCF carriers, of whom 4 carried Y-autosome fusions and 8 autosomal fusions. A total of 12 (63.2%) of 19 blastocysts exhibited normal/balanced embryos, and only one (5.3%) embryo exhibited unbalanced translocations among Y-autosome fusion cases. In contrast to these findings, the percentage of normal/balanced blastocysts in 8 autosomal N-RBCF cases was 28.2% (11/39), whereas the unbalanced translocation rate was 53.8%. Furthermore, the percentage of normal/balanced embryos in the Robertsonian translocation group was significantly higher than that of the 8 autosomal N-RBCF (48.7% vs. 28.2%) cases. The rates of abnormality from chromosomal fusion in the 8 autosomal N-RBCF cases were significantly higher than those noted in the Robertsonian translocation (53.8% vs. 31.4%) subjects. The results of the stratified analysis according to the carrier’s sex demonstrated that the rates of unbalanced translocation were significantly higher in the male autosomal N-RBCF subjects than those from the corresponding Robertsonian translocation (55% vs. 19.7%) cases. Conclusion(s) A low number of unbalanced translocations was identified in blastocysts from N-RBCF subjects who carried the Y fusion. The risk of unbalanced translocation in autosomal N-RBCF was higher than that of the Robertsonian translocation, notably in male carriers.

Small cell lung cancer (SCLC) is the most aggressive lung cancer with high heterogeneity. Mouse SCLC cells derived from the Rb1L/L/Trp53L/L (RP) autochthonous mouse model grew as adhesion or suspension in cell culture, and the adhesion cells are defined as non-neuroendocrine (non-NE) SCLC cells. Here, we uncover the heterogenous subpopulations within the non-NE cells and referred to them as mesenchymal-like (Mes) and epithelial-like (Epi) SCLC cells. The Mes cells have increased capability to form colonies in soft agar and harbored stronger metastatic capability in vivo when compared with the Epi cells. Gene Set Enrichment Analysis reveals that the transforming growth factor (TGF)-β signaling is enriched in the Mes cells. Importantly, inhibition of the TGF-β signaling through ectopic expression of dominant-negative Tgfbr2 (Tgfbr2-DN) or treatment with Tgfbr1 inhibitor SD-208 consistently abrogates tumor metastasis in nude mouse allograft assays. Moreover, genetic deletion of Tgfbr2 or Smad4, the key components of the TGF-β signaling pathway, dramatically attenuates SCLC metastasis in the RP autochthonous mouse model. Collectively, our results uncover the high heterogeneity in non-NE SCLC cells and highlight an important role of TGF-β signaling in promoting SCLC metastasis.

Adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) is an annual cultivated leguminous crop commonly grown in Asia and consumed worldwide. However, there has been limited research regarding adzuki bean genetics, which has prevented the efficient application of genes during breeding. In the present study, we constructed a high-density genetic map based on whole genome re-sequencing technology and validated its utility by mining QTLs related to seed size. Moreover, we analyzed the sequences flanking insertions/deletions (InDels) to develop a set of PCR-based markers useful for characterizing adzuki bean genetics. A total of 2904 markers were mapped to 11 linkage groups (LGs). The total length of the map was 1365.0 cM, with an average distance between markers of 0.47 cM. Among the LGs, the number of markers ranged from 208 (LG7) to 397 (LG1) and the total distance ranged from 97.4 cM (LG9) to 155.6 cM (LG1). Twelve QTLs related to seed size were identified using the constructed map. The two major QTLs in LG2 and LG9 explained 22.1 and 18.8% of the total phenotypic variation, respectively. Ten minor QTLs in LG4, LG5 and LG6 explained 3.0–10.4% of the total phenotypic variation. A total of 9718 primer pairs were designed based on the sequences flanking InDels. Among the 200 selected primer pairs, 75 revealed polymorphisms in 24 adzuki bean germplasms. The genetic map constructed in this study will be useful for screening genes related to other traits. Furthermore, the QTL analysis of seed size and the novel markers described herein may be relevant for future molecular investigations of adzuki bean and will be useful for exploiting the mechanisms underlying legume seed development.

Chromobox 4 (CBX4) is a core component of polycomb-repressive complex 1 with important roles in cancer biology and tissue homeostasis. Aberrant expression of CBX4 has been implicated in several human malignancies. However, its role and underlying mechanisms in the tumorigenesis of lung adenocarcinoma (LUAD) have not been defined in vivo. Here, we found that expression of CBX4 was frequently up-regulated in human LUAD samples and correlated with poor patient survival. Importantly, genetic ablation of CBX4 greatly dampened lung tumor formation and improved survival in the KrasG12D/P53L/L (KP) autochthonous mouse model of LUAD. In addition, CBX4 depletion significantly inhibited proliferation and anchorage-independent growth of KP mouse embryonic fibroblasts. Moreover, ectopic CBX4 expression clearly promoted proliferation and anchorage-independent growth in both human and mouse LUAD cells, whereas silencing of CBX4 exerted opposite effects. Mechanistically, CBX4 promoted growth of LUAD cells through activation of the Wnt/β-catenin pathway. Furthermore, expression levels of CBX4 were positively correlated with β-catenin in human LUAD samples. In conclusion, our data suggest that CBX4 plays an oncogenic role via the Wnt/β-catenin pathway and could serve as a potential therapeutic target in LUAD.

Background: The microbiota plays an important role in host health. Although rubidium (Rb) has been used to study for depression and cancers, the interaction between microbial commensals and Rb is still unexplored. To gain the knowledge of the relationship between Rb and microbes, 51 mice receiving RbCl-based treatment and 13 untreated mice were evaluated of their characteristics and bacterial microbiome changes.Results: The 16S ribosomal RNA gene sequencing of feces showed RbCl generally maintained fecal microbial community diversity, while the shifts in fecal microbial composition were apparent after RbCl exposure for the first time. RbCl significantly enhanced the abundances of Rikenellaceae, Alistipes, Clostridium XlVa and sulfate-reducing bacteria including Deltaproteobacteria, Desulfovibrionales, Desulfovibrionaceae and Desulfovibrio. While, RbCl significantly inhibited the abundances of Tenericutes, Mollicutes, Anaeroplasmatales, Anaeroplasmataceae and Anaeroplasma lineages. Besides, with regarding to the composition of archaea, RbCl significantly enhanced the abundances of Crenarchaeota, Thermoprotei, Sulfolobales, Sulfolobaceae and Sulfolobus lineages. Conclusions: These results revealed that enrichments of Clostridium XlVa and Alistipes could affect the levels of serotonin, a critical signaling molecule of brain-gut-microbiota axis. Therefore, anticancer and anti-depressant effects of RbCl might be partly mediated by modifying brain-gut-microbiota axis.

Background: AMP-activated protein kinase (AMPK) activators can improve inflammatory pain and neuropathic pain. Inflammation translocate signal transducers and activators of transcription 3 (STAT3) to the nuclei of activated macrophages, and STAT3 phosphorylation promotes the expression of inducible nitric oxide synthetase (iNOS). In this study, we determined whether AMPK activation alleviate inflammatory pain via STAT3 nuclear translocation and phosphorylation. Methods: Immunoblotting was used to measure the expression of p-AMPK, and iNOS. Immunoblotting and immunofluorescence were used to detect the nuclear translocation of p-STAT3(Ser727) and STAT3 in macrophages of local inflammatory tissues. Flow cytometry was used to measure reactive oxygen species (ROS) accumulation and mitochondrial damage.Results: AMPK activation with AICAR significantly alleviated pain hypersensitivity and inhibited the expression of iNOS in complete Freund's adjust (CFA)-induced inflamed skin tissues. CFA caused nuclear translocation of STAT3 and p-STAT3(Ser727) in macrophages of inflamed skin tissues. AICAR inhibited nuclear translocation of STAT3 and p-STAT3(Ser727) and promoted the phosphorylation of STAT3(Ser727) in the cytoplasm of macrophages. AICAR also inhibited the expression of iNOS and nuclear translocation of STAT3 and p-STAT3(Ser727), and promoted the phosphorylation of STAT3(Ser727) in NR8383 macrophages treated with CFA. AMPK activation also inhibited the ROS generation and the mitochondrial damage of NR8383 macrophages caused by CFA. In addition, transfection of STAT3 S727D decreased ROS and alleviated mitochondrial damage.Conclusions: Activation of AMPK attenuates inflammatory pain and suppresses STAT3 nuclear translocation and phosphorylation of STAT3(Ser727) in macrophages, resulting in reduced iNOS. Activation of AMPK also promotes phosphorylation of STAT3(Ser727) in the cytoplasm of macrophages to alleviate ROS accumulation and mitochondrial damage associated with inflammation.

Skeletal muscle differentiation is a highly coordinated process that involves many cellular signaling pathways and microRNAs (miRNAs). A group of muscle-specific miRNAs has been reported to promote myogenesis by suppressing key signaling pathways for cell growth. However, the functional role and regulatory mechanism of most non-muscle-specific miRNAs with stage-specific changes during differentiation are largely unclear. Here, we describe the functional characterization of miR-101a/b, a pair of non-muscle-specific miRNAs that show the largest change among a group of transiently upregulated miRNAs during myogenesis in C2C12 cells. The overexpression of miR-101a/b inhibits myoblast differentiation by suppressing the p38/MAPK, Interferon Gamma, and Wnt pathways and enhancing the C/EBP pathway. Mef2a, a key protein in the p38/MAPK pathway, was identified as a direct target of miR-101a/b. Interestingly, we found that the long non-coding RNA (lncRNA) Malat1, which promotes muscle differentiation, interacts with miR-101a/b, and this interaction competes with Mef2a mRNA to relieve the inhibition of the p38/MAPK pathway during myogenesis. These results uncovered a “braking” role in differentiation of transiently upregulated miRNAs and provided new insights into the competing endogenous RNA (ceRNA) regulatory mechanism in myoblast differentiation and myogenesis.

Background: PCSK9 (proprotein convertase subtilisin/kexin 9), mainly secreted by the liver and released into the blood, elevates plasma low-density lipoprotein cholesterol by degrading low-density lipoprotein receptor. Pleiotropic effects of PCSK9 beyond lipid metabolism have been shown. However, the direct effects of PCSK9 on platelet activation and thrombosis, and the underlying mechanisms, as well, still remain unclear. Methods: We detected the direct effects of PCSK9 on agonist-induced platelet aggregation, dense granule ATP release, integrin αIIbβ3 activation, α-granule release, spreading, and clot retraction. These studies were complemented by in vivo analysis of FeCl 3 -injured mouse mesenteric arteriole thrombosis. We also investigated the underlying mechanisms. Using the myocardial infarction (MI) model, we explored the effects of PCSK9 on microvascular obstruction and infarct expansion post-MI. Results: PCSK9 directly enhances agonist-induced platelet aggregation, dense granule ATP release, integrin αIIbβ3 activation, P-selectin release from α-granules, spreading, and clot retraction. In line, PCSK9 enhances in vivo thrombosis in a FeCl 3 -injured mesenteric arteriole thrombosis mouse model, whereas PCSK9 inhibitor evolocumab ameliorates its enhancing effects. Mechanism studies revealed that PCSK9 binds to platelet CD36 and thus activates Src kinase and MAPK (mitogen-activated protein kinase)–extracellular signal-regulated kinase 5 and c-Jun N-terminal kinase, increases the generation of reactive oxygen species, and activates the p38MAPK/cytosolic phospholipase A2/cyclooxygenase-1/thromboxane A 2 signaling pathways downstream of CD36 to enhance platelet activation, as well. Using CD36 knockout mice, we showed that the enhancing effects of PCSK9 on platelet activation are CD36 dependent. It is important to note that aspirin consistently abolishes the enhancing effects of PCSK9 on platelet activation and in vivo thrombosis. Last, we showed that PCSK9 activating platelet CD36 aggravates microvascular obstruction and promotes MI expansion post-MI. Conclusions: PCSK9 in plasma directly enhances platelet activation and in vivo thrombosis, and MI expansion post-MI, as well, by binding to platelet CD36 and thus activating the downstream signaling pathways. PCSK9 inhibitors or aspirin abolish the enhancing effects of PCSK9, supporting the use of aspirin in patients with high plasma PCSK9 levels in addition to PCSK9 inhibitors to prevent thrombotic complications.

Salmonella enterica serovar Gallinarum biovar Gallinarum (S. Gallinarum) is a host-specific pathogen causing systemic infection in poultry, which leads to significant economic losses due to high mortality. However, little is known about the dynamic process of systemic infection and pathogenic characteristics of S. Gallinarum in chickens. In the present study, we developed an oral infection model that reproduces the pathology of S. Gallinarum and clarified the host immune response of the infected chickens. Chickens at 20 days of age orally inoculated at a dose of 108 colony forming unit (CFU) showed typical clinical signs of fowl typhoid and died between 6 and 10 days post infection. The inoculated S. Gallinarum rapidly disseminated to multple organs and the bacterial counts increased in the liver and spleen at 3 days post infection. Pathological changes associated wirh inflammation in the liver and spleen became apparent at 4 days post infection, and increased expression of interferon (IFN)-γ and interleuikin (IL)-12 in the liver and spleen did not observed until 3 days post infection. These results indicate that S. Gallinarum rapidly spread to entire body through intestine, and the low-level of inflammatory responses in the liver during the early stage of infection may contribute to rapid, systemic dissemination of the bacteria. Our infection model and findings will contribute to the better understanding of the pathogenic mechanism of S. Gallinarum, and provide new insights into the prevention and control of fowl typhoid.

Staphylococcus aureus produces staphylococcal enterotoxins (SEs) and causes food poisoning. It is known that almost all SE-encoding genes are present on various types of mobile genetic elements and can mobilize among S. aureus populations. Further, plasmids comprise one of SE gene carriers. Previously, we reported novel SEs, SES and SET, harbored by the plasmid pF5 from Fukuoka5. In the present study, we analyzed the distribution of these SEs in various S. aureus isolates in Japan. We used 526 S. aureus strains and found 311 strains positive for at least one SE/SE-like toxin gene, but only two strains (Fukuoka5 and Hiroshima3) were positive for ses and set among the specimens. We analyzed two plasmids (pF5 and pH3) from these strains and found that they were different. Whereas these plasmids partially shared similar sequences involved in the ser/selj/set/ses gene cluster, other sequences were different. A comparison of these plasmids with those deposited in the NCBI database revealed that only one plasmid had the ser/selj/set/ses cluster with a stop mutation in set similar to that in pH3. In addition, the chromosomes of Fukuoka5 and Hiroshima3, positive for ses and set, were classified into different genotypes. Despite the low rate of gene positivity for these SEs, it is suggested that there is diversity in plasmids and strains carrying these two SEs. Consequently, regarding the entire feature of SE prevalence, we improved the multiplex PCR detection method for the SE superfamily to obtain further insight.

Purpose The purpose of this study is to summarize the clinical outcomes of apparently balanced chromosome rearrangement (ABCR) carriers in preimplantation genetic testing (PGT) cycles by next-generation sequencing following microdissecting junction region (MicroSeq) to distinguish non-carrier embryos from balanced carriers. Methods A retrospective study of 762 ABCR carrier couples who requested PGT for structural rearrangements combined with MicroSeq at the Reproductive and Genetic Hospital of CITIC-Xiangya was conducted between October 2014 and October 2019. Results Trophectoderm biopsy was performed in 4122 blastocysts derived from 917 PGT-SR cycles and 3781 blastocysts were detected. Among the 3781 blastocysts diagnosed, 1433 (37.9%, 1433/3781) were balanced, of which 739 blastocysts were carriers (51.57%, 739/1433) and 694 blastocysts were normal (48.43%, 694/1433). Approximately 26.39% of cycles had both carrier and normal embryo transfer, and the average number of biopsied blastocysts was 6.7. In the cumulative 223 biopsied cycles with normal embryo transfer, all couples chose to transfer the normal embryos. In the 225 cycles with only carrier embryos, the couples chose to transfer the carrier embryos in 169/225 (75.11%) cycles. A total of 732 frozen embryo transfer cycles were performed, resulting in 502 clinical pregnancies. Cumulatively, 326 babies were born; all of these babies were healthy and free of any developmental issues. Conclusion Our study provides the first evaluation of the clinical outcomes of a large sample with ABCR carrier couples undergoing the MicroSeq-PGT technique and reveals its powerful ability to distinguish between carrier and non-carrier balanced embryos.

Eukaryotic genomes encode thousands of small and large non-coding RNAs (ncRNAs). However, the expression, functions and evolution of these ncRNAs are still largely unknown. In this study, we have updated deepBase to version 3.0 (deepBase v3.0, http://rna.sysu.edu.cn/deepbase3/index.html), an increasingly popular and openly licensed resource that facilitates integrative and interactive display and analysis of the expression, evolution, and functions of various ncRNAs by deeply mining thousands of high-throughput sequencing data from tissue, tumor and exosome samples. We updated deepBase v3.0 to provide the most comprehensive expression atlas of small RNAs and lncRNAs by integrating ∼67 620 data from 80 normal tissues and ∼50 cancer tissues. The extracellular patterns of various ncRNAs were profiled to explore their applications for discovery of noninvasive biomarkers. Moreover, we constructed survival maps of tRNA-derived RNA Fragments (tRFs), miRNAs, snoRNAs and lncRNAs by analyzing >45 000 cancer sample data and corresponding clinical information. We also developed interactive webs to analyze the differential expression and biological functions of various ncRNAs in ∼50 types of cancers. This update is expected to provide a variety of new modules and graphic visualizations to facilitate analyses and explorations of the functions and mechanisms of various types of ncRNAs.

Kinetoplastid flagellates are known for several unusual features, one of which is their complex mitochondrial genome, known as kinetoplast (k) DNA, composed of mutually catenated maxi- and minicircles. Trypanosoma lewisi is a member of the Stercorarian group of trypanosomes which is, based on human infections and experimental data, now considered a zoonotic pathogen. By assembling a total of 58 minicircle classes, which fall into two distinct categories, we describe a novel type of kDNA organization in T. lewisi. RNA-seq approaches allowed us to map the details of uridine insertion and deletion editing events upon the kDNA transcriptome. Moreover, sequencing of small RNA molecules enabled the identification of 169 unique guide (g) RNA genes, with two differently organized minicircle categories both encoding essential gRNAs. The unprecedented organization of minicircles and gRNAs in T. lewisi broadens our knowledge of the structure and expression of the mitochondrial genomes of these human and animal pathogens. Finally, a scenario describing the evolution of minicircles is presented.

Liver organogenesis begins with hepatic precursors in the foregut endoderm, followed by hepatoblast specification, differentiation, outgrowth, and maturation for the formation of functional hepatocytes. Although several signaling pathways and critical factors that regulate liver specification, differentiation, and proliferation have been identified, little is known about how liver maturation is regulated. Here, we used a screen for mutations affecting liver development in zebrafish and identified a cq96 mutant that exhibits a specific defect in liver maturation. Results from positional cloning revealed that cq96 encodes an RNA-binding protein, Rbm15, which is an evolutionarily conserved Spen family protein and known to play a crucial role in RNA m6A modification, nuclear export, and alternative splicing. However, a function of Rbm15 in embryonic liver development has not been reported. We found that Rbm15 is specifically expressed in the liver after its differentiation. CRISPR/Cas9-mediated loss of rbm15 repressed hepatic maturation, but did not affect hepatoblast specification, differentiation, and hepatocyte proliferation and apoptosis. Additional experiments disclosed that the mTOR complex 1 (mTORC1) pathway is highly activated in rbm15-deficient hepatocytes. Moreover, rapamycin treatment partially restored normal hepatic gene expression as well as the nuclear location of the transcription factor Hnf4a. Taken together, these results reveal an unexpected role of Rbm15 in liver maturation.

In response to far-red light (FR), FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) transports the photoactivated phytochrome A (phyA), the primary FR photoreceptor, into the nucleus, where it initiates FR signaling in plants. Light promotes the 26S proteasome-mediated degradation of FHY1, which desensitizes FR signaling, but the underlying regulatory mechanism remains largely unknown. Here, we show that reversible SUMOylation of FHY1 tightly regulates this process. Lysine K32 (K32) and K103 are major SUMOylation sites of FHY1. We found that FR exposure promotes the SUMOylation of FHY1, which accelerates its degradation. Furthermore, we discovered that ARABIDOPSIS SUMO PROTEASE 1 (ASP1) interacts with FHY1 in the nucleus under FR and facilitates its deSUMOylation. FHY1 was strongly SUMOylated and its protein level was decreased in the asp1-1 loss-of-function mutant compared with that in the wild type under FR. Consistently, asp1-1 seedlings exhibited a decreased sensitivity to FR, suggesting that ASP1 plays an important role in the maintenance of proper FHY1 levels under FR. Genetic analysis further revealed that ASP1 regulates FR signaling through an FHY1- and phyA-dependent pathway. Interestingly, We found that continuous FR inhibits ASP1 accumulation, perhaps contributing to the desensitization of FR signaling. Taken together, these results indicate that FR-induced SUMOylation and ASP1-dependent deSUMOylation of FHY1 represent a key regulatory mechanism that fine-tunes FR signaling.

Inflammatory bowel disease (IBD) involves chronic inflammation, loss of epithelial integrity, and gastrointestinal microbiota dysbiosis. Effective therapies for IBD have not been established. Accordingly, in this study, we evaluated the effects of inorganic nitrate, a potent nitric oxide (NO) donor and microbiota regulator, in a mouse model of dextran sodium sulfate (DSS)-induced colitis. Mice were pretreated with NaNO3 (2 mM) in their drinking water for 5 days, and NaCl was used as a control. Feces were collected for microbiota analyses. The results showed that oral administration of dietary nitrate could maintained colon consistency, improved colon length, maintained body weight, decreased apoptosis in colon epithelial cells, and ameliorated inflammatory cell infiltration in both the colon and peripheral blood. Microbiota profiling revealed that nitrate regulated dysbiosis. Analysis of the top bacteria at the genus level showed that Bacteroidales_S24-7_group_unidentified, Lactobacillus, Bacteroides, and Prevotellaceae_UCG-001 decreased in the DSS group compared with that in the normal group, whereas Lactobacillus, Ruminococcaceae_UCG-014, and Prevotellaceae_UCG-001 were increased in the DSS + NaNO3 group compared with that in the DSS group. The enriched bacteria in the nitrate group included Gordonibacter, Ureaplasama, and Lachnospiraceae_UCG-006. Moreover, microbiota analysis revealed that nitrate could partially decrease the enriched metabolic pathways (p53 signaling pathway and colorectal cancer pathway) compared with that in the DSS and DSS + NaCl groups. Overall, these findings indicated that nitrate could ameliorate DSS-induced colitis by decreasing inflammation, reducing apoptosis, and regulating the microbiota by activation of the NO3−/NO2−/NO pathway. Nitrate might be a potential treatment for colitis patients in the future clinical application.

Charcoal-stripped fetal bovine serum (CS-FBS) is frequently used in studies on hormone-responsive cancers to provide hormone-free cell culture conditions. CS-FBS may influence the growth of cancer cells; however, the underlying mechanisms remain unclear. In this study, we aimed to clarify the effects of CS-FBS on distinct subtypes of breast cancer cells. We found that the crucial oncoprotein c-Myc was significantly inhibited in estrogen receptor alpha (ER-α)-positive breast cancer cells when cultured in CS-FBS-supplemented medium, but it was not suppressed in ER-α-negative cells. The addition of 17β-estradiol (E2) to CS-FBS-supplemented medium rescued the CS-FBS-induced inhibition of c-Myc, while treatment with 5α-dihydrotestosterone (DHT) suppressed c-Myc expression. Our data demonstrated that CS-FBS may impede the growth of ER-α-positive breast cancer cells via c-Myc inhibition, and this was possibly due to the removal of estrogen. These results highlighted that the core drivers of c-Myc expression were subtype-specific depending on the distinct cell context and special caution should be exercised when using CS-FBS in studies of hormone-responsive cancer cells.

This study investigated the variations of the nucleotide sequences and ovarian expression levels of genes related to follicular development and atresia in prolific Jintang black goats and nonprolific Tibetan goats. Eight genes, FSHB, LHB, FSHR, LHCGR, ESR2, B4GANT2, BCL2 and BAX, were examined using reverse transcription‐polymerase chain reaction and quantitative real‐time PCR. The results showed that the nucleotide and deduced amino acid sequences of the LHB and BAX genes were not different, but there was one base change in the FSHR genes between the two breeds. There was one base change in the FSHB gene, which resulted in one amino acid substitution; there were nine base changes in the LHCGR gene, which resulted in five amino acid substitutions; and there were six base changes in the B4GANT2 gene, which resulted in four amino acid substitutions. The expression levels of the FSHR, LHCGR, ESR2, B4GANT2, BCL2 and BAX genes in the ovaries were not different between the two breeds. The plasma concentrations of FSH were not different, but the plasma concentrations of LH, P4 and E2 were lower in prolific Jintang black goats than in nonprolific Tibetan goats (P ˂ 0.05) at 40 hr after removal of the Controlled Internal Drug Release Devices. These results provide some foundations elucidating the endocrine and molecular mechanisms controlling ovulation rate in goats, but these need to be further verified., Plasma concentrations of LH, P4 and E2 were lower in the prolific goat breed. FSH concentration was not different between prolific and non‐prolific goat breeds. Nine base changes in LHR resulted in five amino acid substitutions in prolific breed, and six base changes in B4GANT2 resulted in four amino acid substitutions in prolific breed.

STUDY QUESTION Is the mitochondrial DNA (mtDNA) copy number of cumulus granulosa cells (CGCs) related to the maturation of oocyte cytoplasm? SUMMARY ANSWER Compared with the mtDNA copy number of CGCs from germinal vesicles (GV), CGCs from Metaphase I (MI) oocytes appear to have a lower mtDNA copy number. WHAT IS KNOWN ALREADY The growth and development of CGCs and oocyte are synchronised. The interaction between CGCs and the oocyte provides the appropriate balance of energy, which is necessary for mammalian oocyte development. Moreover, in the oocyte–cumulus complex (OCC), mature oocytes with higher mtDNA copy numbers tend to have corresponding CGCs with higher mtDNA copy numbers. STUDY DESIGN, SIZE, DURATION This is a prospective study of 302 OCCs obtained from 70 women undergoing in vitro fertilisation with intracytoplasmic sperm injection (ICSI) at the Reproductive and Genetic Hospital of CITIC-Xiangya, between 24 February 2018 and 21 December 2019. The CGCs were divided into three groups (GV, MI and MII stages) based on the maturation status of their corresponding oocyte. The sample sizes (n = 302) of CGCs in the three stages were 63 (CGCGV), 70 (CGCMI) and 169 (CGCMII), respectively. Some of the samples (n = 257) was used to quantify the mtDNA copy number, while the rest (n = 45) were used to analyse the expression level of mitochondrial genes. Furthermore, we retrieved 82 immature oocytes from among the 257 OCCs used for mtDNA copy numbers, including 36 GV oocytes and 46 MI oocytes, for analysis of oocyte mtDNA. PARTICIPANTS/MATERIALS, SETTING, METHODS We selected genes with high consistency of real-time PCR results to accurately measure the mtDNA copy number by testing the efficacy and the reproducibility in whole genome amplification (WGA) samples from a human embryonic stem cell line. The CGCs of each oocyte were individually isolated. The mtDNA copy number and gene expression of the CGCs were assessed using real-time PCR techniques. Mitochondrial DNA copy number of the corresponding immature oocytes was also evaluated. MAIN RESULTS AND THE ROLE OF CHANCE MT-ND1, MT-CO1 and β-globin genes were chosen for the assessment of mtDNA content, and mRNA expressions of MT-ND1, MT-CO1, PGC-1α and TFAM were also measured. The genome of 257 CGCs and 82 immature oocytes were amplified according to the multiple displacement amplification (MDA) protocol, and RNA was extracted from 45 CGCs. Compared with CGCGV, CGCMI had a significantly lower mtDNA copy number. In the MT-ND1 assay, the CGCGV: CGCMI was [270 ± 302]: [134 ± 201], P = 0.015. In the MT-CO1 assay, CGCGV: CGCMI was [205 ± 228]: [92 ± 112], P = 0.026. There was no statistical difference in mtDNA between CGCGV and CGCMII. In the MT-ND1 assay, CGCGV: CGCMII was [270 ± 302]: [175 ± 223], P = 0.074. In the MT-CO1 assay, CGCGV: CGCMII was [205 ± 228]: [119 ± 192], P = 0.077. No statistical difference of mtDNA copy number was observed between CGCMI and CGCMII. In the MT-ND1 assay, CGCMI: CGCMII was [134 ± 201]: [175 ± 223], P = 0.422. In the MT-CO1 assay, CGCMI: CGCMII was [92 ± 112]: [119 ± 192], P = 0.478. To verify the reliability of the above results, we further analysed the mtDNA copy number of CGCs of 14 patients with GV, MI and MII oocytes, and the results showed that the mtDNA copy number of CGCMI may be lower. The mtDNA copy number of CGCGV and CGCMI was statistically different in the MT-ND1 assay where CGCGV: CGCMI was [249 ± 173]: [118 ± 113], P = 0.016, but in the MT-CO1 assay, CGCGV: CGCMI was [208 ± 199]: [83 ± 98], P = 0.109. There was no significant difference in mtDNA between CGCGV and CGCMII. In the MT-ND1 assay, CGCGV: CGCMII was [249 ± 173]: [185 ± 200], P = 0.096. In the MT-CO1 assay, CGCGV: CGCMII was [208 ± 199]: [114 ± 139], P = 0.096. There was also no significant difference in mtDNA between CGCMI and CGCMII. In the MT-ND1 assay, CGCMI: CGCMII was [118 ± 113]: [185 ± 200], P = 0.198. In the MT-CO1 assay, CGCMI: CGCMII was [83 ± 98]: [114 ± 139], P = 0.470. Moreover, there were no statistical differences in the expression levels of MT-ND1, MT-CO1, PGC-1α and TFAM between CGCGV, CGCMI and CGCMII (P > 0.05). LARGE SCALE DATA N/A LIMITATIONS, REASONS FOR CAUTION Due to the ethical issues, the study did not quantify the mtDNA content of MII oocytes. Thus, whether the change in mtDNA copy number in CGCs is related to the different developmental stages of oocytes has not been further confirmed. Moreover, the sample size was relatively small. WIDER IMPLICATIONS OF THE FINDINGS The mtDNA copy number of CGCs decreases from the GV phase to the MI phase and stays steady from the MI to MII stage. At different stages of oocyte maturation, the mtDNA of CGCs may undergo self-degradation and replication to meet the energy requirements of the corresponding oocyte and the maturation of the oocyte cytoplasm. STUDY FUNDING/COMPETING INTEREST(S) Funding was provided by the National Key R&D Program of China (Grant 2018YFC1003100, to L.H.), the science and technology major project of the Ministry of Science and Technology of Hunan Province, China (grant 2017SK1030, to G.L.), the National Natural Science Foundation of China (grant 81873478, to L.H.), and Merck Serono China Research Fund for Fertility Experts (to L.H.). There is no conflict of interest.

Alterations of gut microbiota have been implicated in multiple diseases including cancer. However, the gut microbiota spectrum in lung cancer remains largely unknown. Here we profiled the gut microbiota composition in a discovery cohort containing 42 early-stage lung cancer patients and 65 healthy individuals through the 16S ribosomal RNA (rRNA) gene sequencing analysis. We found that lung cancer patients displayed a significant shift of microbiota composition in contrast to the healthy populations. To identify the optimal microbiota signature for noninvasive diagnosis purpose, we took advantage of Support-Vector Machine (SVM) and found that the predictive model with 13 operational taxonomic unit (OTU)-based biomarkers achieved a high accuracy in lung cancer prediction (area under curve, AUC = 97.6%). This signature performed reasonably well in the validation cohort (AUC = 76.4%), which contained 34 lung cancer patients and 40 healthy individuals. To facilitate potential clinical practice, we further constructed a 'patient discrimination index' (PDI), which largely retained the prediction efficiency in both the discovery cohort (AUC = 92.4%) and the validation cohort (AUC = 67.7%). Together, our study uncovered the microbiota spectrum of lung cancer patients and established the specific gut microbial signature for the potential prediction of the early-stage lung cancer.

Clinical observation of the association between cancer aggressiveness and embryonic development stage implies the importance of developmental signals in cancer initiation and therapeutic resistance. However, the dynamic gene expression during organogenesis and the master oncofetal drivers are still unclear, which impeded the efficient elimination of poor prognostic tumors, including human hepatocellular carcinoma (HCC). In this study, human embryonic stem cells were induced to differentiate into adult hepatocytes along hepatic lineages to mimic liver development in vitro. Combining transcriptomic data from liver cancer patients with the hepatocyte differentiation model, the active genes derived from different hepatic developmental stages and the tumor tissues were selected. Bioinformatic analysis followed by experimental assays was used to validate the tumor subtype-specific oncofetal signatures and potential therapeutic values. Hierarchical clustering analysis revealed the existence of two subtypes of liver cancer with different oncofetal properties. The gene signatures and their clinical significance were further validated in an independent clinical cohort and The Cancer Genome Atlas database. Upstream activator analysis and functional screening further identified E2F1 and SMAD3 as master transcriptional regulators. Small-molecule inhibitors specifically targeting the oncofetal drivers extensively down-regulated subtype-specific developmental signaling and inhibited tumorigenicity. Liver cancer cells and primary HCC tumors with different oncofetal properties also showed selective vulnerability to their specific inhibitors. Further precise targeting of the tumor initiating steps and driving events according to subtype-specific biomarkers might eliminate tumor progression and provide novel therapeutic strategy.

Silicon (Si) has been widely employed in agriculture to enhance resistance against pathogens in many crop plants. However, the underlying molecular mechanisms of Si-mediated resistance remain elusive. In this study, the Arabidopsis-powdery mildew pathosystem was employed to investigate possible defense mechanisms of Si-mediated resistance. Because Arabidopsis lacks efficient Si transporters and thus is a low Si-accumulator, two heterologous Si influx transporters (from barley and muskmelon) were individually expressed in wild-type Arabidopsis Col-0 and a panel of mutants defective in different immune signaling pathways. Results from infection tests showed that while very low leaf Si content slightly induced salicylic acid (SA)-dependent resistance, high Si promoted PAD4-dependent but largely EDS1- and SA-independent resistance against the adapted powdery mildew isolate Golovinomyces cichoracearum UCSC1. Intriguingly, our results also showed that high Si could largely reboot non-host resistance in an immune-compromised eds1/pad4/sid2 triple mutant background against a non-adapted powdery mildew isolate G. cichoracearum UMSG1. Taken together, our results suggest that assimilated Si modulates distinct, multi-layered defense mechanisms to enhance plant resistance against adapted and no-adapted powdery mildew pathogens, possibly via synergistic interaction with defense-induced callose.

This study was conducted to evaluate the effects of dietary live yeast (LY) supplementation during late gestation and lactation on reproductive performance, colostrum and milk composition, blood biochemical and immunological parameters of sows. A total of 40 multiparous sows were randomly fed either the control (CON) diet or the CON diet supplemented with LY at 1 g/kg from d 90 of gestation to weaning. Results showed that the number of stillborn piglets and low BW piglets were significantly decreased in the LY-supplemented sows compared with sows in the CON group (P

Melatonin (MT) is a bio-antioxidant that has been widely used to prevent pregnancy complications, such as pre-eclampsia and IUGR during gestation. This experiment evaluated the impacts of dietary MT supplementation during pregnancy on reproductive performance, maternal–placental–fetal redox status, placental inflammatory response, and mitochondrial function, and sought a possible underlying mechanism in the placenta. Sixteen fifth parity sows were divided into two groups and fed each day of the gestation period either a control diet or a diet that was the same but for 36 mg of MT. The results showed that dietary supplementation with MT increased placental weight, while the percentage of piglets born with weight < 900 g decreased. Meanwhile, serum and placental MT levels, maternal–placental–fetal redox status, and placental inflammatory response were increased by MT. In addition, dietary MT markedly increased the mRNA levels of nutrient transporters and antioxidant-related genes involved in the Nrf2/ARE pathway in the placenta. Furthermore, dietary MT significantly increased ATP and NAD+ levels, relative mtDNA content, and the protein expression of Sirt1 in the placenta. These results suggested that MT supplementation during gestation could improve maternal–placental–fetal redox status and reproductive performance by ameliorating placental antioxidant status, inflammatory response, and mitochondrial dysfunction.

Early embryonic arrest and fragmentation (EEAF) is a common phenomenon leading to female infertility, but the genetic determinants remain largely unknown. The Moloney sarcoma oncogene (MOS) encodes a serine/threonine kinase that activates the ERK signaling cascade during oocyte maturation in vertebrates. Here, we identified four rare variants of MOS in three infertile female individuals with EEAF that followed a recessive inheritance pattern. These MOS variants encoded proteins that resulted in decreased phosphorylated ERK1/2 level in cells and oocytes, and displayed attenuated rescuing effects on cortical F‐actin assembly. Using oocyte‐specific Erk1/2 knockout mice, we verified that MOS‐ERK signal pathway inactivation in oocytes caused EEAF as human. The RNA sequencing data revealed that maternal mRNA clearance was disrupted in human mature oocytes either with MOS homozygous variant or with U0126 treatment, especially genes relative to mitochondrial function. Mitochondrial dysfunction was observed in oocytes with ERK1/2 deficiency or inactivation. In conclusion, this study not only uncovers biallelic MOS variants causes EEAF but also demonstrates that MOS‐ERK signaling pathway drives human oocyte cytoplasmic maturation to prevent EEAF., Biallelic variants in MOS gene cause recurrent early embryonic arrest and fragmentation (EEAF) and female infertility. MOS variants impair activation of MOS‐ERK signal cascade, prevent substantial maternal mRNAs decay and hamper embryonic development both in human and mice.

tRNA-derived small RNA (tsRNA), a novel type of regulatory small noncoding RNA, plays an important role in physiological and pathological processes. However, the understanding of the functional mechanism of tsRNAs in cells and their role in the occurrence and development of diseases is limited. Here, we integrated multiomics data such as transcriptome, epitranscriptome, and targetome data, and developed novel computer tools to establish tsRFun, a comprehensive platform to facilitate tsRNA research (http://rna.sysu.edu.cn/tsRFun/ or http://biomed.nscc-gz.cn/DB/tsRFun/). tsRFun evaluated tsRNA expression profiles and the prognostic value of tsRNAs across 32 types of cancers, identified tsRNA target molecules utilizing high-throughput CLASH/CLEAR or CLIP sequencing data, and constructed the interaction networks among tsRNAs, microRNAs, and mRNAs. In addition to its data presentation capabilities, tsRFun offers multiple real-time online tools for tsRNA identification, target prediction, and functional enrichment analysis. In summary, tsRFun provides a valuable data resource and multiple analysis tools for tsRNA investigation.

Hepatocellular carcinoma (HCC) is a type of common cancer, often accompanied by tumor recurrence and metastasis after surgery with poor prognosis. Therefore, searching into potential biomarkers that can effectively predict the prognosis and progression of HCC is crucial. In this study, we identified 1,981 differentially expressed genes (DEGs) using mRNA expression profiles from the TCGA-LIHC dataset. Subsequently, weighted gene co-expression network analysis found that the turquoise module closely associated with the pathological grade and clinical stage of HCC was identified. Then, from the key genes in the turquoise module and protein-protein interaction network analysis, 13 hub genes significantly related to the prognosis of HCC were screened. Through co-expression and functional enrichment analyses, these 13 hub genes were found to play an important role in mitosis. Finally, we evaluated the relationship between these hub genes and overall survival and disease-free survival through survival analysis. The result indicated that HCC patients with high hub gene expression had a poorer prognosis than HCC patients with low expression. Receiver operating characteristic curves showed that each hub gene could predict the prognosis of HCC patients. In summary, a total of 13 hub genes were identified that play an important role in the progression of HCC, which can be used as potential biomarkers for HCC patients.

Background Although oocyte quality is the dominant factor determining embryo quality, few studies have been conducted to evaluate embryo quality based on the metabolites related to the oocyte. With quantification of the follicular fluid (FF) metabolites, in assisted reproductive technology (ART), this study sought to evaluate the embryo or oocyte quality through an informative approach. Results An evaluation model consisting of 17 features was generated to distinguish the embryo quality on day 3 post-fertilization, and phosphatidylcholines (PCs) were the key contributors to the evaluation. The model was extended to the patients under different ages and hyperstimulations, and the features were further enriched to facilitate the evaluation of the embryo quality. The metabolites were clustered through pathway analysis, leading to a hypothesis that accumulation of arachidonic acid induced by PCs might weaken embryo quality on day 3 post-fertilization. Conclusions A discriminating model with metabolic features elicited from follicular fluid was established, which enabled the evaluation of the embryo or oocyte quality even under certain clinical conditions, and the increase of PCs in follicular fluid implies the attenuation of embryo quality on day 3 post-fertilization.

Neutrophils are critical for inflammation and innate immunity, and their adhesion to vascular endothelium is a crucial step in neutrophil recruitment. Mitofusin-2 (MFN2) is required for neutrophil adhesion, but molecular details are unclear. Here, we demonstrated that β2-integrin-mediated slow-rolling and arrest, but not PSGL-1-mediated cell rolling, are defective in MFN2-deficient neutrophil-like HL60 cells. This adhesion defect is associated with reduced expression of fMLP (N-formylmethionyl-leucyl-phenylalanine) receptor FPR1 as well as the inhibited β2 integrin activation, as assessed by conformation-specific monoclonal antibodies. MFN2 deficiency also leads to decreased actin polymerization, which is important for β2 integrin activation. Mn2+-induced cell spreading is also inhibited after MFN2 knockdown. MFN2 deficiency limited the maturation of β2 integrin activation during the neutrophil-directed differentiation of HL60 cells, which is indicated by CD35 and CD87 markers. MFN2 knockdown in β2-integrin activation-matured cells (CD87high population) also inhibits integrin activation, indicating that MFN2 directly affects β2 integrin activation. Our study illustrates the function of MFN2 in leukocyte adhesion and may provide new insights into the development and treatment of MFN2 deficiency-related diseases.

Quantum dots (QDs) have caused large challenges in clinical tests and biomedical applications due to their potential toxicity from nanosize effects and heavy metal components. In this study, the physiological responses of Phanerochaete chrysosporium (P. chrysosporium) to CdSe/ZnS QDs with either an inorganic sulfide NaHS or an organic sulfide cysteine as antidote have been investigated. Scanning electron microscope analysis showed that the hyphal structure and morphology of P. chrysosporium have obviously changed after exposure to 100 nM of COOH CdSe/ZnS 505, NH2 CdSe/ZnS 505, NH2 CdSe/ZnS 565, or NH2 CdSe/ZnS 625. Fourier transform infrared spectroscopy analysis indicated that the existence of hydroxyl, amino, and carboxyl groups on cell surface could possibly conduct the stabilization of QDs in an aqueous medium. However, after NaHS or cysteine treatment, the cell viability of P. chrysosporium exposed to CdSe/ZnS QDs increased as compared to control group, since NaHS and cysteine have assisted P. chrysosporium to alleviate oxidative damage by regulating lipid peroxidation and superoxide production. Meanwhile, NaHS and cysteine have also stimulated P. chrysosporium to produce more antioxidant enzymes (superoxide dismutase and catalase), which played significant roles in the defense system. In addition, NaHS and cysteine were used by P. chrysosporium as sulfide sources to promote the glutathione biosynthesis to relieve CdSe/ZnS QDs-induced oxidative stress. This work revealed that sulfide sources (NaHS and cysteine) exerted a strong positive effect in P. chrysosporium against the toxicity induced by CdSe/ZnS QDs.

Human embryonic stem cells (hESCs) have unlimited proliferation capacity and can differentiate into most types of somatic cells. We previously described that the overexpression of FLI1 as well as the activation of protein kinase C (FLI1-PKC) could rapidly and efficiently differentiate hESCs into endothelial cells (ECs). However, the relationship between vascular endothelial growth factor (VEGF) and PKC in hESC-EC differentiation is debated, and the roles of different PKC isoforms in hESC-EC differentiation remain unknown. In this study, after 2 days of induction, we found that the overexpression of FLI1 and the addition of VEGF-A to hESCs (FLI1-VEGF) could generate 19.6% ± 5.4% ECs. The induction efficiency of ECs was reduced from 72.3% ± 7.6% to 37.9% ± 4.9% following the addition VEGF-A siRNA to the FLI1-PKC system. However, the induction of ECs was nearly completely abrogated following the addition of the pan-PKC inhibitor to the FLI1-VEGF, FLI1-PKC, or other systems. The above results suggested that VEGF can partially replace PKC, but PKC plays a more critical role downstream of VEGF during hESC-EC induction. To further investigate which PKC isoform was mainly involved in converting hESCs to ECs, siRNAs were used to knock down nine PKC isoforms in the FLI1-PKC system. Only the knockdown of PKC-ɛ or PKC-η significantly decreased the induction efficiency of ECs to 51.1% ± 5.8% or 50.3% ± 5.1%, respectively. PKC-ɛ/η siRNA could suppress EC induction in other differentiation systems. Moreover, RNA-seq and quantitative polymerase chain reaction analysis also showed that only the expression of PKC-ɛ and PKC-η was robustly upregulated during hESC-EC induction. In summary, our results suggested that VEGF promoted the differentiation of ECs derived from hESCs, which mainly depended on PKC, specifically the PKC-ɛ and PKC-η pathways.

Background Salmonella is one of the most important foodborne pathogens, causing outbreaks of human salmonellosis worldwide. Owing to large scales of consumption markets, pork and poultry that contaminated by Salmonella could pose a tremendous threat to public health. The aim of this study was to investigate the contamination of Salmonella from chicken, pork and the environment in slaughtering and retail processes in Chongqing, China. Results A total of 115 Salmonella isolates were recovered from 1112 samples collected from pork, chicken and the environment. Compared with the isolation rate of samples from chicken (9.50%) and the environment (6.23%), samples from pork had a significant higher isolation rate (44.00%). The isolation rates in slaughterhouses (10.76%) and in supermarkets (10.07%) showed no statistical difference. Thirty different serotypes were identified among all the isolates. S. Derby (n = 26), S. London (n = 16) and S. Rissen (n = 12) were the dominant serotypes. Antimicrobial susceptibility testing revealed that 73.04% isolates were resistant to tetracycline, followed by 66.96% to ampicillin and 59.13% to doxycycline. More than half (50.43%) of the isolates were multidrug resistant (MDR), and most of the MDR isolates were from supermarkets. Multilocus sequence typing results showed 24 out of 115 isolates were ST40, which was the most prevalent. Furthermore, isolates from supermarkets had 20 different sequence types while isolates from slaughterhouses only had 8 different sequence types. Conclusion Our study highlighted that Salmonella was more frequently isolated in pork production chain than that in chicken. Compared with isolates from slaughterhouses, isolates from supermarkets had more MDR profiles and represented a wider range of serotypes and sequence types, indicating that the retail process had more diverse sources of Salmonella contamination than that of slaughtering process.

Background/aim This study aimed to discuss the effect and possible molecular mechanisms of Aurora-A/NF-ĸB signaling on the radiotherapy resistance of human docetaxel-resistant lung adenocarcinoma cells. Materials and methods The human lung adenocarcinoma SPC-A1 and SPC-A1/DTX cell lines were utilized in the present study. The MTT assay measured the sensitivity of cells to radiotherapy. The tumor-initiating ability of the cells was detected in vitro by cloning assays. Apoptosis was quantified by flow cytometry. Real-time quantitative PCR and western blotting were used to detect the mRNA and protein expression of the Aurora-A/NF-ĸB, respectively. Tumors transplanted subcutaneously into nude mice were used to test the effect of Aurora-A on the in vivo sensitivity of the tumors to radiotherapy. Results The SPC-A1/DTX docetaxel-resistant lung adenocarcinoma cells were radio-resistant compared with the parental SPC-A1 cells. Up-regulated aurora-A was responsible for the in vitro radio-resistance of docetaxel-resistant SPC-A1/DTX cells. Nuclear transcription factor NF-ĸB was identified as a downstream target gene of Aurora-A in SPC-A1/DTX cells, and NF-ĸB also participated in the radio-resistance of SPC-A1/DTX cells regulated by Aurora-A. Conclusion The Aurora-A/NF-ĸB pathway is association with radio-resistance of human lung adenocarcinoma docetaxel-resistant cells.

The skin is the first line of defence against most infections, including those by arthropod-borne viruses (arboviruses). The skin is a compartmentalised organ populated by a variety of immune cells that play a critical role in coordinating immune responses after skin infection. Arboviruses such as Ross River virus (RRV) and Chikungunya virus (CHIKV) cause debilitating musculoskeletal and arthritic disease and are considered significant public health threats of major global concern due to the scale of outbreaks, and the limited treatment options available. To understand the dynamics of arthritogenic arbovirus dissemination following skin infection, we developed a pathogenic model of RRV infection to mimic a mosquito bite. We found that inflammatory monocytes, neutrophils and dermal macrophages dominated the early inflammatory response in the skin. In addition, we found that RRV-infected CD11b+ migratory cells translocate to the skin draining lymph nodes. Importantly, we unveiled a critical role for viral envelope glycosylation in driving viral dissemination kinetics and disease severity. Intradermal infection with RRV derived from mosquito cells resulted in more severe disease compared to RRV derived from mammalian cells. This difference in disease was accompanied by glycosylationspecific transcriptional response in the skin after intradermal infection. Interestingly we also show evidence indicating that viral envelope glycosylation dictates the dissemination of RRV to target tissues in muscle and joint. Using a new model of cutaneous arboviral infection, we show previously unappreciated mechanisms of immune response and viral dissemination that, in future, will help develop novel approaches to limit arboviral dissemination and ameliorate disease outcomes.

Soil ecosystems surrounding chromium slag undergo continuous harsh physicochemical conditions due to multiple heavy metals contamination. Previous studies of soil microbial communities mainly focused on surface soil layer, while little was known about the depth-related distributions of the microbial communities in chromium (Cr)-contaminated soil. In this study, a comprehensive analysis of depth-related distributions of microbial communities in Cr-contaminated soil was carried out by Illumina sequencing of 16s rRNA genes. The results revealed that bacterial diversities at 0 cm depth layer were significantly higher than those below 20 cm depths. And there was a remarkable difference in bacterial compositions along with the sampling depths especially for the dominant phyla of Proteobacteria, Actinobacteria, Chloroflexi and Fimicutes (p 0.05). While the archaea accounted for a relatively low proportion of the microbes and showed stability in the compositions with the predominant phyla of Thaumarchaeota and Euryarchaeota. The linear discriminate analysis (LDA) and effect size (LEfSe) analysis showed that there were thirty-seven kinds of biomarker microbes existing in the five soil layers with LDA threshold of 4.0, and each layer showed distinct microbial divisions, indicating that microbes with different biological functions might survive along with the sampling depths. The environmental variables including total chromium (Cr), Cr(Ⅵ), Mn, Ni, and Zn had considerable influences on microbial community composition in the contaminated soil. A total of 25 Cr(Ⅵ)-reducing strains were further isolated and identified, which were phylogenetically affiliated to Proteobacteria, Actinobacteria and Firmicutes. Among the isolated Cr(Ⅵ)-reducing strains, Bacillus stratosphericus was the first time to be reported with Cr(Ⅵ) reducing capacity.

Background This study aimed to investigate the effects of oral administration of Enterococcus faecium NCIMB 10415 (E. faecium) on intestinal development, immunological parameters and gut microbiota of neonatal piglets challenged with enterotoxigenic Escherichia coli K88 (ETEC). A total of 96 1-day-old sow-reared piglets were randomly assigned to 2 groups, with 48 piglets in each group. The piglets were from 16 litters (6 piglets each litter), and 3 piglets each litter were allocated to the E. faecium-supplemented (PRO) group, while the other 3 piglets were allocated to the control (CON) group. After colostrum intake, piglets in the PRO group were orally administrated with 3 × 109 CFU E. faecium per day for a period of one week. On day 8, one piglet per litter from each group was challenged (CON+ETEC, PRO+ETEC) or not (CON-ETEC, PRO-ETEC) with ETEC in a 2 × 2 factorial arrangement of treatments. On day 10 (2 days after challenge), blood and tissue samples were obtained from piglets. Results Before ETEC challenge, there were no significant differences for the average daily gain (ADG) and fecal score between the two groups of piglets. After ETEC challenge, the challenged piglets had greater fecal score compared to the non-challenged piglets, whereas E. faecium administration was able to decrease the fecal score. Piglets challenged with ETEC had shorter villous height, deeper crypt depth, and reduced number of goblet cells in the jejunum and decreased mRNA abundance of claudin-1 in the ileum, whereas increased the percentage of lymphocytes, concentrations of IL-1β in the plasma and TNF-α in the ileal mucosa, as well as increased the mRNA abundances of innate immunity-related genes in the ileum tissue. These deleterious effects caused by ETEC were partly alleviated by feeding E. faecium. In addition, piglets in PRO-ETEC group had decreased the percentage of CD8+ T cells of the peripheral blood when compared to those in CON-ETEC group. Moreover, E. faecium administration increased Verrucomicrobia at phylum level and decreased Bilophila at genus level. Conclusions These results suggest that oral administration of E. faecium alleviated the intestinal injury and diarrhea severity of neonatal piglets challenged by ETEC, partly through improving the intestinal microbiota and immune response. This offers a potential strategy of dietary intervention against intestinal impairment by ETEC in neonatal piglets. Electronic supplementary material The online version of this article (10.1186/s40104-019-0376-z) contains supplementary material, which is available to authorized users.

Summary: Drug resistance is a significant hindrance to effective cancer treatment. Although resistance mechanisms of epidermal growth factor receptor (EGFR) mutant cancer cells to lethal EGFR tyrosine kinase inhibitors (TKI) treatment have been investigated intensively, how cancer cells orchestrate adaptive response under sublethal drug challenge remains largely unknown. Here, we find that 2-h sublethal TKI treatment elicits a transient drug-tolerant state in EGFR mutant lung cancer cells. Continuous sublethal treatment reinforces this tolerance and eventually establishes long-term TKI resistance. This adaptive process involves H3K9 demethylation-mediated upregulation of branched-chain amino acid aminotransferase 1 (BCAT1) and subsequent metabolic reprogramming, which promotes TKI resistance through attenuating reactive oxygen species (ROS) accumulation. Combination treatment with TKI- and ROS-inducing reagents overcomes this drug resistance in preclinical mouse models. Clinical information analyses support the correlation of BCAT1 expression with the EGFR TKI response. Our findings reveal the importance of BCAT1-engaged metabolism reprogramming in TKI resistance in lung cancer. : How cancer cells, with strong plasticity, orchestrate their adaptive response under sublethal drug exposure remains largely unknown. Wang et al. show that sublethal tyrosine kinase inhibitor (TKI) treatment elicits drug resistance in EGFR-mutant lung cancer cells through H3K9 demethylation-mediated reprogramming of branched-chain amino acid (BCAA) metabolism. Keywords: lung cancer, EGFR tyrosine kinase inhibitors, drug resistance, metabolic reprogramming, branched-chain amino acids, BCAT1

The roles of concealed microproteins encoded by long noncoding RNAs (lncRNAs) are gradually being exposed, but their functions in tumorigenesis are still largely unclear. Here, we identify and characterize a conserved 99-amino acid microprotein named KRASIM that is encoded by the putative lncRNA NCBP2-AS2. KRASIM is differentially expressed in normal hepatocytes and hepatocellular carcinoma (HCC) cells and can suppress HCC cell growth and proliferation. Mechanistically, KRASIM interacts and colocalizes with the KRAS protein in the cytoplasm of human HuH-7 hepatoma cells. More importantly, the overexpression of KRASIM decreases the KRAS protein level, leading to the inhibition of ERK signaling activity in HCC cells. These results demonstrate a novel microprotein repressor of the KRAS pathway for the first time and provide new insights into the regulatory mechanisms of oncogenic signaling and HCC therapy.

Bentonite is a natural and environmentally clay mineral, and bentonite-derived mesoporous materials (BDMMs) were obtained conveniently from the alkali and acid treatment of bentonite. In the present study, BDMMs were explored for immobilization of laccase obtained from Trametes versicolor. As a result, bentonite-derived mesoporous materials-Laccase (BDMMs-Lac) was developed for the removal of tetracycline (TC). The enzyme immobilization process was carried out through physical adsorption contact (ion exchange adsorption, hydrogen bond adsorption, and Van der waals adsorption) between the BDMMs and laccase. The process of immobilization remarkably increased its operating temperature. The BDMMs-Lac exhibited over 60% removal efficiency for TC within 3 h in the presence of 1-hydroxybenzotriazole (HBT). In conclusion, BDMMs-Lac showed more promising potential than free laccase for practical continuous applications.

The density of vertebrate fossils on bedding planes is generally very low in the Upper Jurassic plattenkalks forming the Solnhofen fossil Lagerstatte. There are, however, a few bedding planes where large concentrations of the small fis Leptolepides sprattiformis (BLAINVILLE, 1818) occur. The aim of this paper is to analyse and interpret these f sh concentrations from a taphonomic point of view. For this purpose, the taphonomic features of L. sprattiformis concentrations on three large slabs were semi-quantitatively analysed. The concentrations of individuals on bedding planes are explained as recording local mass mortality events caused by tropical storms that, for short intervals, disrupted the pycnocline which separated hypersaline, oxygen-poor to anoxic bottom waters from normal marine surface waters in the Plattenkalk basins. Mass mortality is supported by tetany features such as gaping jaws, hyperextended branchiostegal rays, and splayed f ns, which occur in the majority of the specimens. The generally excellent preservation of the f sh resulted from lack of postmortem f oatation, rapid burial and/or overgrowth by microbial f lms, and quick re-establishment of the pycnocline with inhospitable conditions on the basin floo. The post-mortem concave-arching of the backbones and various displacements of the vertebral column were most likely caused by varying decay resistance of soft tissues and the pressure of decay gases in the body cavities, respectively. The taphonomic analysis of f sh concentrations can provide very detailed palaeoenvironmental information and serves as an independent line of evidence for palaeoenvironmental reconstructions that complements geochemical and sedimentary data.

The Cr(Ⅵ) removal way and Cr(Ⅵ) reducing site of Oceanobacillus oncorhynchi W4, a novel Cr(Ⅵ) reducing bacterium, were investigated in this study. Results showed that about 74.2% of Cr(Ⅵ) was removed from solution by growing cells within 72 h. Moreover, heating-killed resting cells had little Cr(Ⅵ) removal capacity, which was significantly lower than that of resting cells, which reached nearly 80% removal rate, suggesting that the way of Cr(Ⅵ) removal mainly relied on biological reduction rather than biosorption. And the Cr(Ⅵ) reduction was found to be significantly enhanced by some electron donors, especially glycerin, which further verified enzyme-mediated biological reduction as the way for Cr(Ⅵ) removal. Experiments of Cr(Ⅵ) removal by permeable cells indicated that there was no significant difference in chromium reduction between the impermeable cells and the permeable cells. The cell envelop fraction had a Cr(Ⅵ) removal rate of 82.9%, apparently higher than cytoplasmic fraction (11.1%), indicating that the cell envelop was the main location for Cr(Ⅵ) reduction, which were further demonstrated by Scanning Electron Microscope and Transmission electron microscopy plus EDS analysis. Furthermore, analysis of X-ray photoelectron spectroscopy manifested that C O, C–OH and C–O C groups on the surfaces played major roles in correlation with chromium species.

Sparse labeling of neurons contributes to uncovering their morphology, and rapid expression of a fluorescent protein reduces the experiment range. To achieve the goal of rapid and sparse labeling of neurons in vivo, we established a rapid method for depicting the fine structure of neurons at 24 h post-infection based on a mutant virus-like particle of Semliki Forest virus. Approximately 0.014 fluorescent focus-forming units of the mutant virus-like particle transferred enhanced green fluorescent protein into neurons in vivo, and its affinity for neurons in vivo was stronger than for neurons in vitro and BHK21 (baby hamster kidney) cells. Collectively, the mutant virus-like particle provides a robust and convenient way to reveal the fine structure of neurons and is expected to be a helper virus for combining with other tools to determine their connectivity. Our work adds a new tool to the approaches for rapid and sparse labeling of neurons in vivo. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1007/s12264-019-00362-z) contains supplementary material, which is available to authorized users.