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Anti-tumor immunity through checkpoint inhibitors, specifically anti-programmed death 1 (PD-1)/programmed death ligand 1 (PD-L1) interaction, is a promising approach for cancer therapy. However, as early clinical trials indicate that colorectal cancers (CRCs) do not respond well to immune-checkpoint therapies, new effective immunotherapy approaches to CRC warrant further study. Simvastatin is an inhibitor of 3-hydroxy-3-methylglutaryl-coenzyme A (CoA) reductase (HMGCR), the rate-limiting enzyme of the mevalonate (MVA) pathway for the cholesterol biosynthesis. However, little is known about the functions of simvastatin in the regulation of immune checkpoints or long noncoding RNA (lncRNA)-mediated immunoregulation in cancer. Here, we found that simvastatin inhibited PD-L1 expression and promoted anti-tumor immunity via suppressing the expression of lncRNA SNHG29. Interestingly, SNHG29 interacted with YAP and inhibited phosphorylation and ubiquitination-mediated protein degradation of YAP, thereby facilitating downregulation of PD-L1 transcriptionally. Patient-derived tumor xenograft (PDX) models and the clinicopathological analysis in samples from CRC patients further supported the role of the lncRNA SNHG29-mediated PD-L1 signaling axis in tumor microenvironment reprogramming. Collectively, our study uncovers simvastatin as a potential therapeutic drug for immunotherapy in CRC, which suppresses lncRNA SNHG29-mediated YAP activation and promotes anti-tumor immunity by inhibiting PD-L1 expression.

Two strains of a new mucoralean fungus (M1 and R1) were harvested from the moist walls of Sufu workshop in Liaocheng city, Shandong province, China. Internal transcribed spacer (ITS) and the large subunit (LSU) rDNA region D1/D2 domain-based phylogenetic analysis, along with phenotypic characteristics, revealed that the strains belonged to a new genus in the Mucor category. This new category belongs to Mucor flavus complex. However, unlike M. flavus CBS 234.25 (the type species of the complex), the novel species could grow well at 25 °C and not grow at 28 °C. Moreover, the ITS rDNA sequence similarity of the two species was only 96%. Here, we present the new category Mucor rongii sp. nov. Its holotype is HMAS 248,091, the ex-type culture is M1T (= CICC 41725T), and the other culture examined was R1 (= CICC 41,726).

A Gram-stain-positive, strictly aerobic and rod-shaped bacterium, designated as 3 H-10T, was isolated from a yellow water sample collected from the manufacturing process of strong flavor Chinese baijiu in Yibin region of Sichuan province (PR China). Oval endospores were formed at the subtermini of cells with swollen sporangia. The isolate was able to grow at temperatures of 20–45 °C (optimum growth at 37 °C), at pH 6.0–10.0 (optimum growth at pH 8.0) and in the presence of 0–2 % (w/v) NaCl (optimum growth with 0 % NaCl). Ribose was the major cell-wall sugar, and meso-diaminopimelic acid (meso-DAP) was the diagnostic amino acid. The main polar lipids of 3 H-10T included diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE). MK-7 was predominant menaquinone and iso-C15 : 0 (60.7 %) was the major fatty acid. Comparisons of 16S rRNA gene sequence indicated that 3 H-10T was most closely related to Bacillus mesophilus SA4T (96.30 %), Bacillus ginsengihumi Gsoil 114T (96.27 %) and Bacillus shackletonii LMG 18435T (96.27 %). The average nucleotide identity (ANI) values between strain 3 H-10T and the three type strains mentioned above were 69.56, 70.19 and 70.67 %, respectively. The genomic DNA G+C content was 35.4 mol%. On the basis of its phenotypic, chemotaxonomic and phylogenetic properties, strain 3 H-10T represents a novel species of the genus Bacillus , for which the name Bacillus aquiflavi sp. nov. is proposed. The type strain is Bacillus aquiflavi 3 H-10T (=CICC 24755T=JCM 33703T).

Background YAP activation is crucial for cancer development including colorectal cancer (CRC). Nevertheless, it remains unclear whether N6-Methyladenosine (m6A) modified transcripts of long noncoding RNAs (lncRNAs) can regulate YAP activation in cancer progression. We investigated the functional link between lncRNAs and the m6A modification in YAP signaling and CRC progression. Methods YAP interacting lncRNAs were screened by RIP-sequencing, RNA FISH and immunofluorescence co-staining assays. Interaction between YAP and lncRNA GAS5 was studied by biochemical methods. MeRIP-sequencing combined with lncRNA-sequencing were used to identify the m6A modified targets of YTHDF3 in CRC. Gain-of-function and Loss-of-function analysis were performed to measure the function of GAS5-YAP-YTHDF3 axis in CRC progression in vitro and in vivo. Results GAS5 directly interacts with WW domain of YAP to facilitate translocation of endogenous YAP from the nucleus to the cytoplasm and promotes phosphorylation and subsequently ubiquitin-mediated degradation of YAP to inhibit CRC progression in vitro and in vivo. Notably, we demonstrate the m6A reader YTHDF3 not only a novel target of YAP but also a key player in YAP signaling by facilitating m6A-modified lncRNA GAS5 degradation, which profile a new insight into CRC progression. Clinically, lncRNA GAS5 expressions is negatively correlated with YAP and YTHDF3 protein levels in tumors from CRC patients. Conclusions Our study uncovers a negative functional loop of lncRNA GAS5-YAP-YTHDF3 axis, and identifies a new mechanism for m6A-induced decay of GAS5 on YAP signaling in progression of CRC which may offer a promising approach for CRC treatment.

Virus infections that cause mosaic or mottling in leaves commonly also induce increased levels of reactive oxygen species (ROS). However, how ROS contributes to symptoms is less well documented. Bamboo mosaic virus (BaMV) causes chlorotic mosaic symptoms in both Brachypodium distachyon and Nicotiana benthamiana. The BaMV △CPN35 mutant with an N-terminal deletion of its coat protein gene exhibits asymptomatic infection independently of virus titer. Histochemical staining of ROS in mock-, BaMV-, and BaMV△CPN35-infected leaves revealed that hydrogen peroxide (H2O2) accumulated solely in BaMV-induced chlorotic spots. Moreover, exogenous H2O2 treatment enhanced yellowish chlorosis in BaMV-infected leaves. Both BaMV and BaMV△CPN35 infection could induce the expression of Cu/Zu superoxide dismutase (CSD) antioxidants at messenger RNA and protein level. However, BaMV triggered the abundant accumulation of full-length NbCSD2 preprotein (prNbCSD2, without transit peptide cleavage), whereas BaMV△CPN35 induced a truncated prNbCSD2. Confocal microscopy showed that majority of NbCSD2-green fluorescent protein (GFP) predominantly localized in the cytosol upon BaMV infection, but BaMV△CPN35 infection tended to cause NbCSD2-GFP to remain in chloroplasts. By 5′-RNA ligase-mediated rapid amplification of cDNA ends, we validated CSDs are the targets of miR398 in vivo. Furthermore, BaMV infection increased the level of miR398, while the level of BaMV titer was regulated positively by miR398 but negatively by CSD2. In contrast, overexpression of cytosolic form NbCSD2, impairing the transport into chloroplasts, greatly enhanced BaMV accumulation. Taken together, our results indicate that induction of miR398 by BaMV infection may facilitate viral titer accumulation, and cytosolic prNbCSD2 induction may contribute to H2O2 accumulation, resulting in the development of BaMV chlorotic symptoms in plants.

Taxonomic and functional research of microorganisms has increasingly relied upon genome-based data and methods. As the depository of the Global Catalogue of Microorganisms (GCM) 10K prokaryotic type strain sequencing project, Global Catalogue of Type Strain (gcType) has published 1049 type strain genomes sequenced by the GCM 10K project which are preserved in global culture collections with a valid published status. Additionally, the information provided through gcType includes >12 000 publicly available type strain genome sequences from GenBank incorporated using quality control criteria and standard data annotation pipelines to form a high-quality reference database. This database integrates type strain sequences with their phenotypic information to facilitate phenotypic and genotypic analyses. Multiple formats of cross-genome searches and interactive interfaces have allowed extensive exploration of the database's resources. In this study, we describe web-based data analysis pipelines for genomic analyses and genome-based taxonomy, which could serve as a one-stop platform for the identification of prokaryotic species. The number of type strain genomes that are published will continue to increase as the GCM 10K project increases its collaboration with culture collections worldwide. Data of this project is shared with the International Nucleotide Sequence Database Collaboration. Access to gcType is free at http://gctype.wdcm.org/.

Halomonas alkalicola CICC 11012s can grow at pH 12.5, the highest pH at which the organisms in the genus Halomonas can grow. Genomic analysis reveals that H. alkalicola adapts to alkaline stress using a variety of adaptive strategies; however, the detailed mechanism for its growth at high-alkaline conditions has not been elucidated. Therefore, in this study, the adaptations of H. alkalicola in response to extreme alkaline stress were investigated. A sharp decrease of alkaliphilic tolerance was observed in mutants E. coli ΔEctonB and H. alkalicola ΔHatonB. Expressions of the gene clusters encoding TonB-dependent transport system and iron complex transport system in H. alkalicola grown under extreme alkaline conditions were markedly up-regulated. We then compared the intracellular ionic iron content and iron-chelating ability of mutant strain with those of wild-type strain to understand the influence of TonB-dependent transport system on the alkaline responses. The results indicated that the presence of TonB-dependent transport system increased the alkaline tolerance of H. alkalicola grown at high-alkaline conditions, but had no effects when the strain was grown at neutral pH and low-alkaline conditions. Meanwhile, the presence of this system increased the transport and accumulation of ionic irons to maintain intracellular metabolic homeostasis, which in turn could increase the tolerance of the strain to extreme alkaline conditions. Based on the results, we established a model representing the interactions between TonB-dependent transport system, alkaline tolerance, and intracellular ionic iron that could help deepen the understanding of the alkaline response mechanism of alkaliphilic bacteria.

The early-life microbiota triggers life-long effects on physiological functions and health disorders. Previous studies in adult twins or animal models have revealed associations between host genetics and the harmonious microbiota. However, such associations may be obscured by the fact that each intra-pair of twins will continually encounter various environmental factors as they grow up. Here, we collected the meconium samples from nineteen dizygotic pairs (DZ, n = 38) and nine monozygotic pairs (MZ, n = 18) with cesarean delivery, and 16S rRNA gene sequencing was performed to profile the microbiome at birth. Diversity analysis showed that alpha diversity was not significantly different between two groups, whereas beta diversity of MZ twins was significantly lower than that of either DZ twins or unrelated individuals (i.e., randomly selected individual pairs of non-twinship) (p < 0.05). Two groups had very similar microbial classifications but different relative abundances of certain taxa including more Firmicutes (p = 0.05, Wilcoxon test) at the phylum level and lower abundances of five genera (p < 0.05) in DZ group compared to MZ group, including Rheinheimera, Proteus, SMB53, Sphingobium, and Megamonas. Co-occurrence analysis in each group showed slightly more complicated microbial interactions in DZ than MZ twins, although 22 shared bacterial genera co-existed in two groups, with both Rheinheimera and Megamonas having different centralities in their respective co-occurrence networks. Mean intra-class correlation coefficient (ICC) were also significantly higher for MZ (0.312) compared to DZ twins (0.138) (p < 0.05). The predicted microbial gene functions related to carbohydrate were higher in DZ group, whereas folding, sorting, degradation, cell motility pathways and energy metabolism were markedly over-represented in the microbiota of MZ group. In summary, our study uncovered that microbial diversity and components of the meconium microbiome between DZ and MZ twins were partially consistent with that in singleton neonates by cesarean delivery, but several distinctions related to the heritability supported genetic contributions to intestinal microbiome in early life.

A Gram-stain-negative, rod-shaped, bright-yellow-pigmented bacterium, designated 164T, was isolated from a used sponge for equipment cleaning at a household product plant in China. The 16S rRNA gene sequence comparisons indicated that strain 164T was most closely related to Novosphingobium panipatense DSM 22890T (98.28 % similarity) and shared sequence similarities of 97.73–98.27 % with other members of the genus Novosphingobium . In DNA–DNA hybridization studies the relatedness between strain 164T and its closest phylogenetic neighbours was

Background & Aims Aberrant estrogen receptor-α (ERα) expression and signaling are implicated in the development of hepatocellular carcinoma (HCC), but its regulation in HCC remains enigmatic. Herein, we aimed to identify a new mechanism by which ERα signaling is regulated in HCC, which may lead to a potential new strategy for HCC therapy. Methods Expression levels of Erbin and ERα in human HCC samples were evaluated by immunohistochemistry. In vitro and in vivo experiments were used to assess the effect of Erbin and ERα signaling on HCC cell growth. Crosstalk between Erbin and ERα signaling was analyzed by molecular methods. Animal models of diethylnitrosamine (DEN) or DEN/CCl 4 -induced HCC in wild-type Erbin +/+ and mutant Erbin ΔC/ΔC mice were observed. The regulatory effects of Erbin on tamoxifen treatment of HCC were evaluated in vitro and in vivo . Results Erbin inactivated ERα signaling to drive tumorigenesis of HCC, acting to enhance binding of Chip to ERα via its interaction with ERα and thereby promoting ubiquitination and degradation of ERα. Deletion of the PDZ domain of Erbin in Erbin ΔC/ΔC mice, disrupted the interaction of Chip and ERα, increased the stability of ERα protein, and thus inhibited tumorigenesis of HCC. Silencing of Erbin effectively sensitized the response of HCC after tamoxifen treatment in vitro and in vivo . Conclusions Our data uncovered an important role of Erbin in regulating HCC tumorigenesis through inactivating ERα-mediated tumor-suppressive signaling, suggesting a new strategy for tamoxifen therapy in HCC by targeting Erbin/ERα signaling axis. Lay summary Erbin expression is significantly elevated in human hepatocellular carcinoma (HCC) tissue. This elevated expression of Erbin contributes to tumorigenesis of HCC by negatively regulating ERα signaling. However, restoring ERα signaling by inhibiting Erbin expression enhances the sensitivity of HCC cells to tamoxifen treatment, providing a new approach for tamoxifen treatment in HCC.

Genomic information is essential for taxonomic, phylogenetic and functional studies to comprehensively decipher the characteristics of microorganisms, to explore microbiomes through metagenomics, and to answer fundamental questions of nature and human life. However, large gaps remain in the available genomic sequencing information published for bacterial and archaeal species, and the gaps are even larger for fungal type strains. The Global Catalogue of Microorganisms (GCM) leads an internationally coordinated effort to sequence type strains and close gaps in the genomic maps of microbes. Hence, the GCM aims to promote research by deep-mining genomic data., This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (grant XDA19050301), the Bureau of International Cooperation of the Chinese Academy of Sciences (grants 153211KYSB20160029 and 153211KYSB20150010), the National Key Research Program of China (grants 2017YFC1201202, 2016YFC1201303, and 2016YFC0901702), the 13th Five-year Informatization Plan of the Chinese Academy of Sciences (grant XXH13506), and the National Science Foundation for Young Scientists of China (grant 31701157)., info:eu-repo/semantics/publishedVersion

Four Gram-stain positive bacterial strains, designated as 4R1(T), 4R9, 4L13 and 4L18, isolated from seeds of hybrid maize (Zea mays L., Jingke 968), were investigated using a polyphasic taxonomic approach. The cells were found to be facultatively aerobic, motile, spore-forming and rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolates should be recognised as a species of the genus Paenibacillus, with two close neighbours being Paenibacillus nicotianae YIM h-19(T) (98.41 % similarity) and Paenibacillus hordei RH-N24(T) (98.37 %). The DNA G+C content of strain 4R1(T) was determined to be 51.6 mol %. Its polar lipid profile was found to consist of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid. The predominant respiratory quinone was identified as MK-7 and the major fatty acids were found to be anteiso-C15:0, anteiso-C12:0, anteiso-C13:0 and anteiso-C11:0. Strains 4R1(T), 4R9, 4L13 and 4L18 were clearly distinguished from the reference type strains using phylogenetic analysis, DNA-DNA hybridization and a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains 4R1(T), 4R9, 4L13 and 4L18 represent a novel species of the genus Paenibacillus, for which the name Paenibacillus chinensis sp. nov. is proposed. The type strain is 4R1(T) (=KCTC 33672(T) = CICC 23864(T)).

A Gram-stain-positive bacterial strain, designated as NR2T, isolated from noni (Morinda citrifolia L.) branch was investigated using a polyphasic taxonomic approach. The cells were small coccoid to ovoid, non-spore-forming and motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain was a representative of a member of the genus Brachybacterium, to which the most closely related neighbours were Brachybacterium squillarum M-6-3T (97.90 % similarity), Brachybacterium faecium DSM 4810T (97.50 %), Brachybacterium sacelli LMG 20345T (97.41 %), Brachybacterium phenoliresistens phenol-AT (97.36 %), Brachybacterium nesterenkovii DSM 9573T (97.36 %) and Brachybacterium rhamnosum LMG 19848T (97.32 %). The polar lipid profile of strain NR2T consisted of diphosphatidylglycerol, phosphatidylglycerol, unknown phospholipids and unknown glycolipids. The predominant respiratory quinone was MK-8, with MK-9 and MK-7 as minor components. The major fatty acids were anteiso-C15 : 0 and iso-C15 : 0. Strain NR2T was clearly distinguishable from the type strains of related species on the basis of phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data analysis and a range of physiological and comparison of biochemical characteristics. It is evident from the genotypic and phenotypic data that strain NR2T represents a novel species of the genus Brachybacterium, for which the name Brachybacterium hainanense sp. nov. is proposed. The type strain is NR2T ( = DSM 29535T = CICC 10874T).

Noni (Morinda citrifolia L.) is a plant used by traditional cultures and also in modern health care products. Various chemical substances are derived from the plant and include, but are not limited to anthraquinone flavonol glycosides, iridoid glycosides, lipids glycosides and triterpenoids. Also commonly found on the plant are endophytic bacteria however, there are no reports on endophytic bacterial community of Noni. We collected samples from five sites of Noni plant (roots, branches, leaves, fruits and seeds) and performed 16S rDNA analysis. Results show that these five parts harbor a highly similar bacterial composition with the top four being Sphingomonas, Pseudomonas, Halomonas and Geobacillus. Sphingomonas and Pseudomonas were found to be widely distributed in plant endophytic biotope; while there are little reports on plant-associated Halomonas and Geobacillus, indicating distribution in the plant hosts. Unknown genus also is abundant in five sites of Noni, ranging from 26.70 to 33.66%, implicating necessity to reveal them. This study provides information on endophytic bacteria in the Noni for future analysis based on a metagenome strategy. Key words: Noni, endophytic bacteria, diversity, metagenome.

The epidermal growth factor receptor (EGFR) is implicated in many types of cancer, including colorectal cancer (CRC), and has become one of the most common candidates for targeted therapy. Here, we found that Erbin, a member of the leucine-rich repeat and PDZ domain (LAP) family, plays a key role in EGFR signalling. Erbin inhibited EGFR ubiquitination and stabilized the EGFR protein by interacting with c-Cbl. Moreover, the PDZ domain of Erbin was critical for the interaction between Erbin and c-Cbl and EGFR ubiquitination. Interestingly, Erbin expression was elevated in tumour samples from CRC patients, increased in advanced clinical stage disease and correlated with EGFR expression. In vivo studies using mouse xenograft models of CRC showed that Erbin promotes tumour growth, and that the effects of Erbin on tumour growth are mainly related to the regulatory effects of Erbin on EGFR. The azoxymethane (AOM)-induced colon carcinogenesis model in Erbin(ΔC) (/) (ΔC) mice, with the PDZ domain of Erbin deleted, demonstrated that the PDZ domain of Erbin and its regulation of EGFR signalling are necessary for the tumourigenesis and tumour growth of CRC. We found that Erbin promotes tumourigenesis and tumour growth in CRC by stabilizing EGFR. Our study sheds light on developing Erbin, especially its PDZ domain, as a potential target for CRC treatment.

A Gram-stain-negative, alkaliphilic and moderately halophilic bacterium, designated 56-L4-10aEnT, was isolated from a household product plant in China. Cells of the novel isolate were rod-shaped, non-spore-forming and non-motile. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 56-L4-10aEnT belongs to the genus Halomonas , with the six closest neighbours being Halomonas mongoliensis Z-7009T (97.59 % 16S rRNA gene sequence similarity), Halomonas ventosae Al12T (97.35 %), Halomonas campaniensis 5AGT (97.22 %), Halomonas alimentaria YKJ-16T (97.22 %), Halomonas shengliensis SL014B-85T (97.12 %) and Halomonas fontilapidosi 5CRT (97.09 %). The main polar lipids of strain 56-L4-10aEnT contained diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine. The predominant respiratory quinone was Q-9, with Q-8 as a minor component. The major fatty acids were C18 : 1ω7c/C18 : 1ω6c and C16 : 0. Strain 56-L4-10aEnT was clearly distinguished from the type strains mentioned above through phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data and a range of physiological and biochemical characteristics comparisons. It is evident from the genotypic and phenotypic data that strain 56-L4-10aEnTcould be classified as a representative of a novel species of the genus Halomonas , for which the name Halomonas alkalicola sp. nov. is proposed. The type strain is 56-L4-10aEnT (=CICC 11012sT=DSM 103354T).

The interaction effect of co-existence of toluene and CH4 on community and activity of methanotrophs and toluene-degrading bacteria was characterized in three consortia enriched with CH4 and toluene (MT), toluene (T), and CH4 (M), respectively, in this study. The CH4 oxidation activity in the enrichment culture of MT was significantly lower than that of M at the end of the experiment (P = 0.001). The toluene degradation rate could be enhanced by continuous addition of CH4 and toluene in the initial days, but it was inhibited in the later days. Phylogenetic analysis of 16S rRNA genes showed that Proteobacteria and Bacteroidetes were dominant in the three enriched consortia, but the community of methanotrophs and toluene-degrading bacteria was significantly affected by the co-existence of CH4 and toluene. Both Methylosinus (91.8 %) and Methylocystis (8.2 %) were detected in the enrichment culture of MT, while only Methylocystis species were detected in M. The toluene-degrading bacteria including Burkholderia, Flavobacteria, Microbacterium, and Azoarcus were all detected in the enrichment culture of T. However, only Azoarcus was found in the enrichment culture of MT. Significantly higher contents of extracellular polymeric substances polysaccharose and protein in the enrichment culture of MT than that of T and M suggested that a higher environmental stress occurred in the enrichment culture of MT.

Motivation Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. Results We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. Availability and implementation Accurity is implemented in C++/Rust, available at http://www.yfish.org/software/. Supplementary information Supplementary data are available at Bioinformatics online.

Background The ubiquitin-ligase Fbw7 acts as a tumor suppressor, targeting lots of proto-oncogenes for proteolysis. However, the exact role of Fbw7 in diffuse large B-cell lymphoma (DLBCL) development remains unclear. Methods We evaluated Fbw7 expression in patient samples of DLBCL using immunohistochemical staining. The effect of Fbw7 overexpression on cell viability and apoptosis was investigated using activated B-cell (ABC) like DLBCL cell lines. The mechanism of Fbw7 activity in DLBCL was investigated using immunoprecipitation, ubiquitination, western blot and qualitative analyses. Results The non-germinal center B-cell-like subtype of DLBCL showed reduced Fbw7 expression compared with the germinal center B-cell (GBC) subtype, and low Fbw7 expression was associated with a worse prognosis. Fbw7 overexpression caused decreased cell viability and increased apoptosis rates in the ABC-DLBCL cell lines SU-DHL-2 and OCI-LY-3. Importantly, Stat3 and phospho-Stat3Tyr705 stability were reduced following Fbw7 overexpression in ABC-DLBCL cell lines. In HEK293T and SU-DHL-2 cells, we demonstrated that Fbw7 interacts with Stat3 and pStat3Tyr705 to regulate their ubiquitylation and degradation. Downstream anti-apoptotic target genes of activated Stat3, including Myc, Survivin, Mcl-1, Pim-1, Bcl-2 and Bcl-xl showed decreased mRNA expression following exogenous Fbw7 overexpression. The negative relationship between Fbw7 and pStat3Tyr705 levels was also confirmed in DLBCL patient samples. Conclusion The ubiquitin-ligase Fbw7 mediates apoptosis through targeting Stat3 for ubiquitylation and degradation in ABC-DLBCL. Thus, our study may offer a promising approach for ABC-DLBCL therapy through Stat3 inhibition. Electronic supplementary material The online version of this article (doi:10.1186/s13046-016-0476-y) contains supplementary material, which is available to authorized users.

A Gram-stain-positive, facultatively anaerobic, thermophilic bacterium, designated ZQ18-1T, was isolated from a high temperature daqu sample collected from the sesame-flavour liquor-making process. Oval endospores were formed at the centre of cells with swollen sporangia. The isolate was able to grow at temperatures of 20–60 °C (optimum growth at 50 °C), at pH 4–9 (optimum growth at pH 8) and in the presence of 0–10 % (w/v) NaCl (optimum growth with 2 % NaCl). Glucose and galactose were major cell-wall sugars, and meso-diaminopimelic acid was the diagnostic amino acid. The major polar lipids consisted of phosphatidylglycerol, diphosphatidylglycerol and three glycolipids. The major cellular fatty acids were anteiso-C17 : 0 and iso-C16 : 0, and the predominant menaquinone was MK-7. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain ZQ18-1T was most closely related to Scopulibacillus darangshiensis DLS-06T, Pullulanibacillus pueri YN3T, Tuberibacillus calidus 607T, Pullulanibacillus naganoensis ATCC 53909T, Pullulanibacillus uraniitolerans UG-2T, Sporolactobacillus terrae DSM 11697T and Sporolactobacillus inulinus NRIC 1133T. Strain ZQ18-1T showed low DNA–DNA relatedness (40.7, 23.1, 46.5, 27.2, 45.6, 33.7 and 55.1 %) with the strains mentioned above. Based on morphological characteristics, chemotaxonomic characteristics, DNA–DNA hybridization data and physiological properties, strain ZQ18-1T represents a novel species of the genus Scopulibacillus , for which the name Scopulibacillus daqui sp. nov. is proposed. The type strain is Scopulibacillus daqui ZQ18-1T (=DSM 28236T=CICC 10824T). An emended description of the genus Scopulibacillus is provided.

A total of five strains were isolated from two different hybrid rice seeds samples (Oryza sativa L. Shenliangyou 5814 and Yliangyou 900) in Sanya city, Hainan province, China. Sequence analysis and physiological characteristics indicated that these strains were identical and represented a novel species. Molecular phylogenetic analysis of the D1/D2 domain of the large subunit rRNA gene and the internal transcribed spacer regions revealed that this new species is located in the Microsporomyces clade, with four closely related species, namely, M. magnisporus, M. orientalis, M. bloemfonteinensis, and M. pini. The novel species differed from these four described species in ability to assimilate sorbose, cellobiose, lactose, D-arabinose, and maltose. Based on these results, the following novel yeast species is proposed: Microsporomyces hainanensis sp. nov. with the type strain of Z8(T) (CICC 33066(T) = CBS 14092(T)) belongs to phylum Basidiomycota, subphylum Pucciniomycotina, class Cystobasidiomycetes, family Microsporomycetaceae. The new species were registered in MycoBank under MB 815471.

Escherichia phage CICC 80001 was isolated from the bacteriophage contaminated medium of an Escherichia coli strain HY-05C (CICC 11022S) which could produce L-aspartic acid. The phage had a head diameter of 45-50 nm and a tail of about 10 nm. The one-step growth curve showed a latent period of 10 min and a rise period of about 20 min. The average burst size was about 198 phage particles per infected cell. Tests were conducted on the plaques, multiplicity of infection, and host range. The genome of CICC 80001 was sequenced with a length of 38,810 bp, and annotated. The key proteins leading to host-cell lysis were phylogenetically analyzed. One protein belonged to class II holin, and the other two belonged to the endopeptidase family and N-acetylmuramoyl-L-alanine amidase family, respectively. The genome showed the sequence identity of 82.7% with that of Enterobacteria phage T7, and carried ten unique open reading frames. The bacteriophage resistant E. coli strain designated CICC 11021S was breeding and its L-aspartase activity was 84.4% of that of CICC 11022S.

Two yellow bacterial strains, designated NBD5T and NBD8, isolated from Noni (Morinda citrifolia L.) branch were investigated using a polyphasic taxonomic approach. Cells were Gram-stain-negative, aerobic, non-spore-forming, non-motile and short rod-shaped. Phylogenetic analysis based on 16S rRNA gene sequences suggested that the strains were members of a novel species of the genus Sphingomonas, the seven closest neighbours being Sphingomonas oligoaromativorans SY-6T (96.9 % similarity), Sphingomonas polyaromaticivorans B2-7T (95.8 %), Sphingomonas yantingensis 1007T (94.9 %), Sphingomonas sanguinis IFO 13937T (94.7 %), Sphingomonas ginsenosidimutans Gsoil 1429T (94.6 %), Sphingomonas wittichii RW1T (94.6 %) and Sphingomonas formosensis CC-Nfb-2T (94.5 %). Strains NBD5T and NBD8 had sphingoglycolipid, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylcholine as the major polar lipids, ubiquinone 10 as the predominant respiratory quinone, and sym-homospermidine as the major polyamine. Strains NBD5T and NBD8 were clearly distinguished from reference type strains based on phylogenetic analysis, DNA–DNA hybridization, fatty acid composition data analysis, and comparison of a range of physiological and biochemical characteristics. It is evident from the genotypic and phenotypic data that strains NBD5T and NBD8 represent a novel species of the genus Sphingomonas, for which the name Sphingomonas morindae sp. nov. is proposed. The type strain is NBD5T ( = DSM 29151T = KCTC 42183T = CICC 10879T).

Thermoactinomyces daqus H-18 is a new species of Thermoactinomyces isolated from high-temperature Daqu used in the fermentation of Bandongjing sesame-flavor liquor. Its genome was sequenced and assembled (3.44 Mb). The coding sequences (CDSs) that correlated to high-temperature tolerance were annotated. The metabolic pathways for the compounds responsible for flavor were also found.

A highly selective, convenient, and precise method, first-order derivative spectrophotometry, was applied for the determination of astaxanthin in Haematococcus pluvialis. Ethyl acetate and ethanol (1:1, v/v) were found to be the best extraction solvent tested due to their high efficiency and low toxicity compared with nine other organic solvents. Astaxanthin coexisting with chlorophyll and β-carotene was analyzed by first-order derivative spectrophotometry in order to optimize the conditions for the determination of astaxanthin. The results show that when detected at 432 nm, the interfering substances could be eliminated. The dynamic linear range was 2.0–8.0 μg/mL, with a correlation coefficient of 0.9916. The detection threshold was 0.41 μg/mL. The RSD for the determination of astaxanthin was in the range of 0.01–0.06%; the results of recovery test were 98.1–108.0%. The statistical analysis between first-order derivative spectrophotometry and HPLC by T-testing did not exceed their critical values, revealing no significant differences between these two methods. It was proved that first-order derivative spectrophotometry is a rapid and convenient method for the determination of astaxanthin in H. pluvialis that can eliminate the negative effect resulting from the coexistence of astaxanthin with chlorophyll and β-carotene.

Noni is a plant reported to have nutritional and therapeutic properties. Paenibacillus polymyxa CICC 10580 is a strain that was isolated from the fruit of noni and showed comprehensive antagonistic activity against many pathogens. Its genome was sequenced and assembled (6.10 Mb). The coding sequences (CDSs) correlated with antagonistic activity were annotated.

Luteimonas huabeiensis HB-2 is a novel and newly isolated strain, which shows a superior property of oil displacement. Here, we present a 4.3-Mb assembly of its genome. The key genes for phospholipid and fatty acid metabolism were annotated, which are crucial for crude oil emulsification and recovery.

Daqu is a fermentation starter used in the production of Chinese liquors. A thermophilic bacterium, designated strain H-18T, was isolated from a high-temperature Daqu sample collected from the manufacturing process of a sesame-flavoured liquor in Shandong province, China. It was investigated in a taxonomic study using a polyphasic approach. Strain H-18T formed white aerial mycelium and greyish-yellow substrate mycelium, bearing single endospores on aerial and substrate hyphae or on unbranched short sporophores. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major fatty acids were iso-C15 : 0 and iso-C17 : 0. The predominant menaquinone was MK-7. These chemotaxonomic properties are similar to those of members of the genus Thermoactinomyces . The G+C content of the genomic DNA was 49.1 mol%. 16S rRNA gene sequence comparisons indicated that strain H-18T was most closely related to Thermoactinomyces vulgaris KCTC 9076T (96.42 % similarity), Thermoactinomyces intermedius KCTC 9646T (96.06 %), Laceyella putida KCTC 3666T (96.32 %) and Laceyella sacchari KCTC 9790T (95.55 %). Strain H-18T showed low DNA–DNA relatedness (40.8, 33.4, 20.0 and 14.4 %) with the above strains. Based on morphological and chemotaxonomic characteristics, DNA–DNA hybridization data and physiological properties, strain H-18T represents a novel species of the genus Thermoactinomyces , for which the name Thermoactinomyces daqus sp. nov. is proposed. The type strain is H-18T ( = DSM 45914T = CICC 10681T).

Genes associated with induced pluripotent stem cells (iPS genes) are several pivotal transcriptional factors, which are used to induce pluripotent stem cells from some adult somatic cells. The roles of these iPS genes and especially the signature for these iPS genes in colorectal cancer (CRC) are still unclear. Overexpressed Oct4 and Lin28 but down-regulated Nanog were found in tumor tissues compared with that in their paired normal counterparts of CRC patients. Interestingly, we found that Oct4, Lin28 and Nanog were highly overexpressed in some patients. And the signature for iPS genes was correlated with tumor site (P = 0.012), lymph node status (P = 0.033), Dukes classification (P = 0.033) of CRC patients. Moreover, an independent public expression profiling data showed signature for the four iPS genes could successfully be used to predict the survival of CRC patients with Dukes stages B and C. Immunofluorescent staining of fresh CRC tissues from patients showed that strong co-expressions of Oct4 and Nanog proteins or Sox2 and Lin28 were present in some CRC cells. Then, CRC cell subclone with four iPS genes overexpression were establish by a mixed retroviral system. We found that iPS genes promote sphere-formation, proliferation, colony formation, migration of human CRC cells in vitro and tumor growth in vivo. Our study first shows the clinical significance of iPS signature in CRC patients.

Objective This study investigated the epigenetic role of PRL-3, a key metastasis gene in colorectal cancer (CRC), as a regulator of histone demethylation and the functions of Jumonji domain-containing protein 1B (JMJD1B) and JMJD2B in the progression of CRC. Methods PRL-3-associated proteins were analysed using functional distribution and category enrichment analysis. Western blotting and immunofluorescence were used to detect nuclear PRL-3. The relationship between PRL-3 and JMJD1B or JMJD2B and the roles of JMJD1B, JMJD2B and PRL-3 in histone demethylation were determined after these proteins were knocked down using RNA interference. Case–control studies on JMJD1B and JMJD2B in patients with CRC were performed using immunohistochemical analysis. The in vitro functional effects of JMJD2B and JMJD1B were examined further. Results JMJD1B and JMJD2B, two histone demethylases, were enriched among PRL-3-associated proteins. Nuclear PRL-3 was observed in CRC cells and clinical samples of CRC. The expression of nuclear PRL-3 was increased in patients with CRC at more advanced Dukes9 stages. PRL-3 was involved in the regulation of histone methylation by affecting the activities of JMJD1B and JMJD2B. A low expression of the JMJD1B protein was positively correlated with the lymph node status (p=0.032), Dukes9 classification (p=0.008) and TNM staging (p=0.022) of patients with CRC. A high expression of JMJD2B was positively correlated with the lymph node status (p=0.03), Dukes9 classification (p=0.036) and tumour invasion (p=0.003) of patients with CRC. A loss-of-function analysis confirmed that JMJD2B promoted the proliferation, colony formation and migration of human CRC cells. Conclusion Our data reveal a new role for PRL-3 as a key regulator of histone demethylation. JMJD1B seems to be a candidate tumour suppressor and JMJD2B seems to be a potential oncoprotein in the development and progression of CRC.