Methanooceanicella nereidis gen. nov., sp. nov., the first oceanic Methanocellaceae methanogen, isolated from potential methane hydrate bearing area offshore southwestern Taiwan

A novel mesophilic, hydrogenotrophic methanogen, strain CWC-04T, was obtained from a sediment sample extracted from a gravity core retrieved at station 22 within the KP-9 area off the southwestern coast of Taiwan during the ORIII-1368 cruise in 2009. Cells of strain CWC-04T were rod-shaped, 1.4-2.9 µm long by 0.5-0.6 µm wide, and occurred singly. Strain CWC-04Tutilized formate, H2/CO2, 2-propanol/CO2 or 2-butanol/CO2 as catabolic substrates. The optimal growth conditions were 42 °C, 0.17 M NaCl and pH 5.35. The genomic DNA G+C content calculated from the genome sequence of strain CWC-04T was 46.19 mol%. Phylogenetic analysis of 16S rRNA gene revealed that strain CWC-04T is affiliated with the genus Methanocella. The 16S rRNA gene sequences similarities within strains Methanocella arvoryzae MRE50T, Methanocella paludicola SANAET and Methanocella conradii HZ254T were 93.7, 93.0 and 91.3 %, respectively. In addition, the optical density of CWC-04T culture dropped abruptly upon entering the late-log growth phase, with virus-like particles (150 nm in diameter) being observed on and around the cells. This observation suggests that strain CWC-04T harbours a lytic virus. Based on these phenotypic, phylogenetic and genomic results, we propose that strain CWC-04T represents a novel species of a novel genus in the family Methanocellaceae, for which the name Methanooceanicella nereidis gen. nov., sp. nov. is proposed. The type strain is CWC-04T (=BCRC AR10050T=NBRC 113165T).

Spontaneous Ferromagnetism Induced Topological Transition in EuB_{6}

The interplay between various symmetries and electronic bands topology is one of the core issues for topological quantum materials. Spontaneous magnetism, which leads to the breaking of time-reversal symmetry, has been proven to be a powerful approach to trigger various exotic topological phases. In this Letter, utilizing the combination of angle-resolved photoemission spectroscopy, magneto-optical Kerr effect microscopy, and first-principles calculations, we present the direct evidence on the realization of the long-sought spontaneous ferromagnetism induced topological transition in soft ferromagnetic EuB_{6}. Explicitly, we reveal the topological transition is from Z_{2}=1 topological insulator in paramagnetic state to χ=1 magnetic topological semimetal in low temperature ferromagnetic state. Our results demonstrate that the simple band structure near the Fermi level and rich topological phases make EuB_{6} an ideal platform to study the topological phase physics.

Shifting in the Dominant Bacterial Group Endozoicomonas Is Independent of the Dissociation With Coral Symbiont Algae

The coral-associated Endozoicomonas are dominant bacteria in the coral holobiont. Their relative abundance usually decreases with heat-induced coral bleaching and is proposed to be positively correlated with Symbiodiniaceae abundance. It remains unclear whether this phenomenon of decreased Endozoicomonas abundance is caused by temperature stress or a decreased abundance of Symbiodiniaceae. This study induced bleaching in the coral Euphyllia glabrescens using a dark treatment over 15 weeks. We examined shifts in Endozoicomonas abundance and experimentally reduced Symbiodiniaceae density. 16S rRNA gene amplicon sequencing was used to characterize the changes in bacterial community (incl. Endozoicomonas) over time, and the 16S rRNA gene copy number of Endozoicomonas was quantified by qPCR. We detected a high abundance of Endozoicomonas in E. glabrescens that underwent dark-induced bleaching. The results reveal that changes in the relative abundance of Endozoicomonas are unrelated to Symbiodiniaceae abundance, indicating that Endozoicomonas can be independent of Symbiodiniaceae in the coral holobiont.

Insights into gene regulation of the halovirus His2 infecting Haloarcula hispanica

Gene expression in Haloarcula hispanica cells infected with the gammapleolipovirus His2 was studied using a custom DNA microarray. Total RNA from cells sampled at 0, 1, 2, 3, and 4.5 hr postinfection was reverse‐transcribed into labeled cDNA and hybridized to microarrays, revealing temporal and differential expression in both host and viral genes. His2 gene expression occurred in three main phases (early, middle, and late), and by 4.5 hr p.i. the majority of genes were actively transcribed, including those encoding the major structural proteins. Eighty host genes were differentially regulated ≥twofold postinfection, with most of them predicted to be involved in transport, translation, and metabolism. Differentially expressed host genes could also be grouped into early‐, middle‐, and late‐expressed genes based on the timing of their up‐ and downregulation postinfection. The altered host transcriptional pattern suggests regulation by His2 infection, which may reprogram host metabolism to facilitate its own DNA replication and propagation. This study enhances the characterization of many hypothetical viral genes and provides insights into the interaction between His2 and its host.

A Newly Designed Primer Revealed High Phylogenetic Diversity of Endozoicomonas in Coral Reefs

Endozoicomonas bacteria are commonly regarded as having a potentially symbiotic relationship with their coral hosts. However, their diversity and phylogeny in samples collected from various sources remain unclear. Therefore, we designed an Endozoicomonas-specific primer paired with a bacterial universal primer to detect the 16S ribosomal RNA (rRNA) genes of this taxon and conducted an in-depth investigation of the Endozoicomonas community structure in reef-building corals. The primer had high specificity in the V3-V4 region (95.6%) and its sensitivity was high, particularly when Endozoicomonas was rare in samples (e.g., in seawater, which had a higher alpha diversity of Endozoicomonas than corals). In coral samples, predominant V3-V4 ribotypes had greater divergence than predominant V1-V2 ribotypes, and were grouped into at least 9 novel clades in a phylogenetic tree, indicating Endozoicomonas had high phylogenetic diversity. Divergence within this genus was potentially higher than that among 7 outgroup genera based on the phylogenetic distances of partial 16S rDNA sequences, suggesting that the taxonomy of this genus needs to be revised. In conclusion, dominant Endozoicomonas populations had variable phylogenies; furthermore, the newly designed primers may be useful molecular tools for the reliable detection of the Endozoicomonas community in marine environments.

Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host

The bacterial genus Endozoicomonas was commonly detected in healthy corals in many coral-associated bacteria studies in the past decade. Although, it is likely to be a core member of coral microbiota, little is known about its ecological roles. To decipher potential interactions between bacteria and their coral hosts, we sequenced and investigated the first culturable endozoicomonal bacterium from coral, the E. montiporae CL-33(T). Its genome had potential sign of ongoing genome erosion and gene exchange with its host. Testosterone degradation and type III secretion system are commonly present in Endozoicomonas and may have roles to recognize and deliver effectors to their hosts. Moreover, genes of eukaryotic ephrin ligand B2 are present in its genome; presumably, this bacterium could move into coral cells via endocytosis after binding to coral's Eph receptors. In addition, 7,8-dihydro-8-oxoguanine triphosphatase and isocitrate lyase are possible type III secretion effectors that might help coral to prevent mitochondrial dysfunction and promote gluconeogenesis, especially under stress conditions. Based on all these findings, we inferred that E. montiporae was a facultative endosymbiont that can recognize, translocate, communicate and modulate its coral host.

Complete Genome Sequence of the Extremely Halophilic Archaeon Haloarcula hispanica Strain N601

Haloarcula hispanica has been widely used in haloarchaeal studies, particularly in the isolation of haloviruses. The genome of strain N601, a laboratory derivative of the type strain ATCC 33960, was sequenced. Several potentially significant differences from the published sequence of the type strain (CGMCC 1.2049 = ATCC 33960) were observed.

The expression of CXCR4 and its relationship with matrix metalloproteinase-9/vascular endothelial growth factor in esophageal squamous cell cancer

Esophageal cancer (EC) is a highly aggressive neoplasm with poor prognosis. The main reason for this disappointing outcome is the strong behavior of esophageal cancer cell's invasion and metastasis. CXC chemokine receptor 4 (CXCR4) was found to be expressed in many tumors and significantly correlated with invasion, angiogenesis, metastasis, and prognosis. In the present study, we investigated the expressions of CXCR4, matrix metalloproteinase-9 (MMP-9), and vascular endothelial growth factor (VEGF) in esophageal squamous cell cancer (ESCC) and analyzed the relationship among the three proteins. Sections of paraffin-embedded tissues were obtained from 127 patients with ESCC undergoing esophagectomy at Zhongshan Hospital, Fudan University in 2005. The CXCR4, MMP-9, and VEGF expressions in EC tissues were evaluated according to the immunohistochemical staining area and intensity. The correlations between patients' prognosis and covariates were analyzed by Kaplan--Meier method (univariate analysis) and Cox regression (multivariate analysis). The overall expression rate of CXCR4, MMP-9, and VEGF was 88.2%, 93.7%, and 79.5%, respectively. CXCR4 expression was significantly associated with tumor grade, tumor size, tumor depth, regional lymph node metastasis, and tumor, node, metastasis (TNM) stage (P < 0.05). MMP-9 expression was significantly associated with age and tumor grade (P < 0.05). VEGF expression was significantly associated with tumor grade, tumor depth, and TNM stage (P < 0.05). CXCR4 expression was positively correlated with MMP-9 expression (P < 0.01, r= 0.365) and VEGF expression (P < 0.01, r= 0.380). However, there was no significant correlation between MMP-9 and VEGF expression (P > 0.05). In univariate analysis, CXCR4 expression, tumor size, tumor depth, lymph node metastasis, and TNM stage were correlated with patients' prognosis (P < 0.05); in multivariate analysis, tumor size and lymph node metastasis were the independent factors of poor prognosis. CXCR4 was highly expressed in ESCC and correlated with MMP-9, VEGF, clinicopathological features and prognosis. We speculated CXCR4 play an important role during the progression of this disease and there might be some regulatory mechanism existing between CXCR4 and MMP-9/VEGF in ESCC.

The biotechnological potential of the extreme halophilic archaea Haloterrigena sp. H13 in xenobiotic metabolism using a comparative genomics approach

Extreme halophilic archaea are thriving and dominant populations within hypersaline environments. Because of the extreme properties of the enzymes of halophilic archaea and similar metabolic abilities to their bacterial counterparts, our interests focus on their potential biotechnological applications. In this study, the partial genome of a newly isolated extreme halophilic archaeon, Haloterrigena sp. H13, was investigated. The genome size was estimated to be about 3.9 MB, and a genomic shotgun library was constructed. A total of 1479 clones from the library were sequenced once, and 1186 contigs were obtained. From these contigs, 580 open reading frames (ORFs) were identified, and 394 ORFs were annotated. From the partial genome of strain H13, we identified genes that may be involved in 1,2-dichloroethane degradation, naphthalene/anthracene degradation, gamma-hexachlorocyclohexane degradation, 1-/2-methylnaphthalene degradation and benzoate degradation via CoA ligation. Among the identified ORFs, gene homologs of (S)-2-haloacid dehalogenase (EC 3.8.1.2) and salicylate hydroxylase (EC 1.14.13.1), which might be involved in the degradation of dichloroethane, gamma-hexachlorocyclohexane and naphthalene, were found in the partial genome sequence of strain H13. According to the current genome annotation of peripheral metabolic pathways and the putative xenobiotic-degrading enzymes, the potential of extreme haloarchaea in bioremediation applications is proposed.

Simultaneous identification of Bulbus Fritillariae cirrhosae using PCR-RFLP analysis

Bulbus Fritillariae (BF) is the most commonly used antitussive herb in China. There are nine species of Fritillaria recorded as the drug BF in the Chinese Pharmacopoeia. Bulbus Fritillariae cirrhosae (BF cirrhosae) is a group that includes four species of BF; these four species come from wild sources with higher efficiency and lower toxicity compared to the other five species of BF. Due to reasons of carelessness and reduced costs, the other five species are often sold as BF cirrhosae. Analysis through appearance, microscopic and chemical techniques has limitations. Identifying botanical resources is a primary step in the standardization of herbal medicine. In the present article, the internal transcribed spacer 1 (ITS1) regions of the nuclear ribosomal DNA (nrDNA) of nine species and one variety of Fritillaria genus have been sequenced. A mutation site in the ITS1 region among BF cirrhosae and other species of BF has been found and can be recognized by the restriction endonuclease SmaI. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the nuclear ribosomal ITS1 region was used to differentiate BF cirrhosae from other species of BF and is a successful method in distinguishing the subgroups.

Antibacterial and antifungal activity of Erigeron breviscapus

The antibacterial and antifungal properties of the ethanol extract of Erigeron breviscapus whole plant was evaluated. The extract showed a moderate antibacterial activity and a high antifungal activity.

[Studies on the arbutin biosynthesis by hairy root of Panax ginseng C.A. Mayer]

OBJECTIVE

To study basic conditions for biosynthesis arbutin by the hairy root of Panax ginseng.

METHOD

Based on the content of arbutin and the biotransformation rate of hydroquione, these conditions such as the culture stage, the lasting time and the concentration of hydroquione fitting for biosynthesis were found.

RESULT

After cultured for 22 days, transferred in fresh B5 medium having 2 mmol.L-1 hydroquione, the hairy root biotransformated hydroquione into arbutin in 24 hours, the bioconversion rate was 89.0% and the content of arbutin in dry root was 13.0%.

CONCLUSION

Arbutin, was which never found in the genus of Panax ginseng, can be biosynthesized by the hairy root of Panax ginseng.

[Studies on tissue culture of Dendrobium chrysotoxum Lindl in vitro]

OBJECTIVE

To set up a system for the culture of Dendrobium chrysotoxum in vitro.

METHOD

Tissue culture, fire fly luminescence and phenol-H2SO4 method.

RESULT

The embryo could germinate with or without light, the MS, 1/2MS, B5, N6 mediums are suitable to the growth and the differentiation of sprout with light, 0.5 mg.L-1 NAA and 1 mg.L-1 6-BA, and ATP have regular changes, the content of polysaccharide was 2.833% in plant and 7.254% in sprout.

CONCLUSION

The light has no effects on the embryo germination, but the phytohormone, nitrogen source and organized elements are important to the growth and differentiation of the sprout which should be transferred to the MS, 1/2MS, B5, N6 mediums in time supplemented with NAA [symbol: see text] 6-BA, ATP may be served as the dynamic indication of nourishment demand in the plant. The content of polysaccharide in the sprout is higher and can be utilized.

[Genetic transformation of Panax ginseng C.A. Meyer induced by root inducing plasmid(Ri) of Agrobacterium rhizogenes]

OBJECTIVE

To obtain the hairy root of Panax ginseng (HRPG).

METHOD

HRPG was obtained by infecting the germ-free seedling, cotyledon, leaf the blade, Petiole with Agrobacterium rhizogenes 15,834 harbouring agropine-type Ri plasmid. The transformation was proved by PCR and TLC.

RESULT

HRPG grew rapidly on hormone-free medium and showed typical phenotype of hairy root. The induced rate and time can be improved by adding exogenous hormone and AS(hydroxyacetosyringone). PCR analysis confirmed the integration of TL-DNA, including 564 bp rolC sequence in the HRPG. Opine analysis evidenced the integration and expression of TL-DNA. The total saponin in HRPG (2.486%) was higher the than control(1.403% Panax ginseng).

CONCLUSION

HRPG grows rapidly and proves high in content of ginseng saponin. This culture system of HRPG will be useful for the production of active components in ginseng.

[Experimental morphological study of injection nerve injuries in rabbits]

The sciatic nerve of 16 rabbits were examined with the optical and electron microscope 2, 24, 72 hours and 7 days after injecting penicillin (200,000 U) into nerve or its peripheral in experiment group and control group. The experiment group showed successively nerve fiber tumefaction, myelin sheath lamellar separation and degeneration partly, the construction of axonal change abnormality myelin and axonal obvious degeneration from 2 hours to 7 days. The control group showed perinerve edema, hyperemia, epineurium hyperplasia, the nerve fiber of near epineurium had mild pathologic changes.

Role of glycoconjugates in adherence of Salmonella pullorum to the intestinal epithelium of chicks

1. The distribution of glycoconjugates on the surface of Salmonella pullorum and the ileal epithelium of chicks was demonstrated by lectin cytochemistry. The role of glycoconjugates in adherence of S. pullorum to the ileal epithelium was determined by a sugar inhibition assay using the scanning electron microscope. 2. S. pullorum exhibited binding to Concanavalin A (Con A) and wheat germ agglutinin (WGA) but not to soyabean agglutinin (SBA), Ricinus communis agglutinin (RCA) and Ulex europaeus agglutinin (UEA). 3. The ileal epithelium of chicks bound WGA, Con A and SBA. The binding sites for WGA were on the brush border and cytoplasm of columnar enterocytes as well as on goblet cells. The binding of Con A was confined to the cytoplasm of columnar enterocytes, while SBA bound, in a limited way, to the brush border of columnar enterocytes. 4. After an oral dose of S. pullorum, adherence to the ileal epithelium was inhibited by methyl alpha-D-mannopyranoside.

The inhibitory effect of hydrocortisone on interferon production by rat spleen cells

The effect of hydrocortisone on interferon r(IFN-r) production by rat spleen cells and its mechanism were studied. The results showed that hydrocortisone inhibited IFN-r production at concentrations as low as 5.52 x 10(-10) M, with complete suppression at 5.52 x 10(-8) M, and the total number and survival rate of the cultured spleen cells were not apparently affected by 5.52 x 10(-8) M hydrocortisone. The inhibitory effect was dose-dependent when the concentration was from 5.52 x 10(-10) M to 5.52 x 10(-8) M and could be blocked by RU38486, a competitive antagonist of glucocorticoid. Our results suggested that glucocorticoid may inhibit IFN-r production through a receptor-mediated mechanism.