Publications by authors named "Shih-Yao Lin"

97 Publications

Description of sp. nov., harboring antibiotic- and toxic compound-resistace genes, isolated from poultry manure.

Int J Syst Evol Microbiol 2021 Jul;71(7)

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-negative bacterium, designated strain CC-YST696, harbouring antibiotic- and toxic compound-resistace genes, isolated from poultry manure in Taiwan. Cells of CC-YST696 were short rods, motile with polar flagella, catalase- and oxidase-positive. Optimal growth occurred at 30 °С, pH 9 and with 1 % NaCl. The results of phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by CC-YST696 associated with (97.9 % sequence identity), (97.3 %) and (97.2 %), and with lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 72.8-80.0 % (=17) compared within the type strains of species of of the genus . CC-YST696 contained C, C, Cω7 11-methyl and Cω6/ Cω7 as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, phosphatidylglycerol, two unidentified aminolipids, three unidentified glycolipids, two unidentified phospholipids and three unidentified lipids. The DNA G+C content was 62.2 mol% and the predominant quinone was ubiquinone Q-10. On the basis of its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-YST696 is proposed to represent a novel species of the genus , for which the name sp. nov. (type strain CC-YST696=BCRC 81284=JCM 34167) is proposed.
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http://dx.doi.org/10.1099/ijsem.0.004901DOI Listing
July 2021

Flavobacterium difficile sp. nov., isolated from a freshwater waterfall.

Arch Microbiol 2021 Sep 16;203(7):4449-4459. Epub 2021 Jun 16.

Department of Marine Biotechnology, National Kaohsiung University of Science and Technology, No. 142, Hai-Chuan Rd. Nan-Tzu, Kaohsiung City, 811, Taiwan.

A bacterial strain designated KDG-16 is isolated from a freshwater waterfall in Taiwan and characterized to determine its taxonomic affiliation. Cells of strain KDG-16 are Gram-stain-negative, strictly aerobic, motile by gliding, rod-shaped and form light yellow colonies. Optimal growth occurs at 20-25 °C, pH 6-7, and with 0% NaCl. Phylogenetic analyses based on 16S rRNA gene sequences and an up-to-date bacterial core gene set reveal that strain KDG-16 is affiliated with species in the genus Flavobacterium. Analysis of 16S rRNA gene sequences shows that strain KDG-16 shares the highest similarity with Flavobacterium terrigena DSM 17934 (97.7%). The average nucleotide identity, average amino acid identity and digital DNA-DNA hybridization values between strain KDG-16 and the closely related Flavobacterium species are below the cut-off values of 95-96, 90 and 70%, respectively, used for species demarcation. Strain KDG-16 contains iso-C, iso-C G and iso-C 3-OH as the predominant fatty acids. The polar lipid profile consists of phosphatidylethanolamine, one uncharacterized aminophospholipid, one uncharacterized phospholipid, two uncharacterized aminolipids and two uncharacterized lipids. The major polyamine is homospermidine. The major isoprenoid quinone is MK-6. Genomic DNA G + C content of strain KDG-16 is 31.6%. Based on the polyphasic taxonomic data obtained, strain KDG-16 is considered to represent a novel species in the genus Flavobacterium, for which the name Flavobacterium difficile sp. nov. is proposed. The type strain is KDG-16 (= BCRC 81194 = LMG 31332).
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http://dx.doi.org/10.1007/s00203-021-02440-1DOI Listing
September 2021

Analytical validation of human epidermal growth factor receptor 2 immunohistochemistry by the use of the A0485 antibody versus the 4B5 antibody and breast versus gastric scoring guidelines in ovarian clear cell carcinoma.

Histopathology 2021 May 26. Epub 2021 May 26.

Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.

Aims: The aim of this study was to evaluate human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) in ovarian clear cell carcinoma (OCCC) by using two antibodies and two scoring guidelines in correlation with HER2 amplification and clinicopathological features.

Methods And Results: A tissue microarray was constructed by use of a total of 71 OCCC cases for IHC (the A0485 antibody and the 4B5 antibody) and dual-colour silver in-situ hybridisation (DISH). Two pathologists independently scored the IHC according to the 2018 American Society of Clinical Oncology (ASCO)/College of American Pathologists (CAP) breast cancer guidelines (breast guidelines) and the 2016 ASCO/CAP gastro-oesophageal adenocarcinoma guidelines (gastric guidelines). IHC concordances between A0485 and 4B5 were 87.3-93.0%. Three to 16 (4.2-22.5%) cases had an IHC score of 2+/3+ with frequent basolateral/lateral membranous staining. The 4B5 antibody yielded fewer IHC 2+ cases than the A0485 antibody (n = 2-6 versus n = 5-12). Five (7.0%) cases had HER2 amplification as determined with DISH. Cases with papillary-predominant growth patterns were significantly more likely to have HER2 amplification (P = 0.0051). In predicting DISH results, IHC scored according to the gastric guidelines yielded 100%/100% sensitivity and 83.3-95.5%/98.2-100% specificity, and IHC scored according to the breast guidelines yielded 60-80%/33.3-66.7% sensitivity and 95.5-100%/100% specificity (including/excluding IHC 2+ cases). One case had intratumoral heterogeneity, with discordant results between primary and metastatic tumour specimens.

Conclusion: We demonstrated HER2 amplification in 7% of OCCC cases, and the molecular change is significantly associated with papillary-predominant growth patterns. In predicting HER2 amplification, a combination of 4B5 IHC and gastric guidelines provides the best sensitivity and fewer equivocal (IHC 2+) cases. Given the intratumoral heterogeneity, assessment of HER2 status on whole tissue sections and on both primary and metastatic tumour specimens is recommended.
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http://dx.doi.org/10.1111/his.14419DOI Listing
May 2021

Corrigendum: gen. nov., sp. nov., a novel bacterium of the family isolated from an agricultural soil, and emended description of the genus .

Int J Syst Evol Microbiol 2021 05;71(5)

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taiwan, ROC.

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http://dx.doi.org/10.1099/ijsem.0.004802DOI Listing
May 2021

sp. nov., isolated from a maize field.

Int J Syst Evol Microbiol 2021 Feb;71(2)

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT486, isolated from soil sampled in a maize field in Taiwan. Cells of strain CC-CFT486 were short rods, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT486 associated with (97.0 % sequence identity), (97.0 %), (96.8 %) and (96.8 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) values were 70.6-77.8 % (=11) compared within the type strains of the genus . Strain CC-CFT486 contained C, C, C 8c and C 9c as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, two unidentified aminophospholipids and three unknown phospholipids. The cell wall peptidoglycan of strains CC-CFT486 contained ll-diaminopimelic acid (ll-DAP) and the major polyamine was spermidine. The DNA G+C content was 70.6 mol% and the predominant quinone was menaquinone 9 (MK-9). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence and ANI analyses, strain CC-CFT486 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-CFT486=BCRC 81217=JCM 33499).
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http://dx.doi.org/10.1099/ijsem.0.004616DOI Listing
February 2021

sp. nov., isolated from maize field, and emended description of Nakamura 2004.

Int J Syst Evol Microbiol 2020 Nov;70(11):5725-5733

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a Gram-stain-positive bacterium, designated strain CC-CFT480, isolated from soil sampled in a maize field in Taiwan, ROC. Cells of strain CC-CFT480 were rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 8 and 3 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-CFT480 associated with (97.2 % sequence identity), (95.7 %), (95.4 %) and (95.2 %), and lower sequence similarity values to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-CFT480 and were 74.2 and 20.1 %, respectively. Strain CC-CFT480 contained iso-C, C c alcohol and iso-C 10 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, two unknown aminophospholipids, one uncharacterized aminophospholipid and two unknown phospholipids. The major polyamine was spermidine. The DNA G+C content was 34.8 mol% and the predominant quinone was menaquinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-CFT480 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-CFT480=BCRC 81216=JCM 33498).
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http://dx.doi.org/10.1099/ijsem.0.004470DOI Listing
November 2020

Diffuse Intratumoral Stromal Inflammation in Ovarian Clear Cell Carcinoma is Associated With Loss of Mismatch Repair Protein and High PD-L1 Expression.

Int J Gynecol Pathol 2021 Mar;40(2):148-155

Ovarian clear cell carcinoma (OCCC) is an aggressive chemotherapy-resistant cancer with limited treatment options, and some OCCCs have mismatch repair (MMR) deficiency (MMRD). Emerging evidence has revealed that various cancers with MMRD are susceptible to anti-programmed death-1/programmed death ligand-1 (anti-PD-1/PD-L1) immunotherapy, and certain histologic features are associated with MMRD. However, few studies have addressed this in OCCC. We reviewed 76 OCCCs for tumor-associated inflammation (intratumoral stromal inflammation and peritumoral lymphocytes) and performed immunohistochemistry for 4 MMR proteins and PD-L1. MMR-deficient OCCCs were analyzed for microsatellite instability (MSI), and those with MLH1 loss were tested for MLH1 promoter methylation. No patients fulfilled the Amsterdam II criteria for the diagnosis of Lynch syndrome. Four (5.3%) tumors showed diffuse intratumoral stromal inflammation obliterating the tumor-stroma interfaces, and none had peritumoral lymphoid aggregates. MMRD was found in 2 (2.6%) tumors; one had MLH1/PMS2 loss (MSI-high and MLH1 promoter methylation was detected) and the other had MSH2/MSH6 loss (MSI-low). Twenty (26.3%) tumors showed tumoral PD-L1 expression ≥1%. Both MMR-deficient tumors showed diffuse intratumoral stromal inflammation and tumoral PD-L1 expression ≥50%. Three of the 4 (75%) tumors with diffuse intratumoral stromal inflammation also showed tumoral PD-L1 expression ≥50%. None of the tumors without diffuse intratumoral stromal inflammation showed MMRD (P=0.021) or tumoral PD-L1 expression ≥50% (P=0.0001). We identified a strong correlation among diffuse intratumoral stromal inflammation, MMRD, and high tumoral PD-L1 expression in a small but significant subset of OCCCs. Histologic evaluation can facilitate patient selection for subsequent anti-PD-1/PD-L1 immunotherapy.
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http://dx.doi.org/10.1097/PGP.0000000000000682DOI Listing
March 2021

Ultralow Threshold Cavity-Free Laser Induced by Total Internal Reflection.

ACS Omega 2020 Aug 21;5(30):18551-18556. Epub 2020 Jul 21.

Department of Physics, National Taiwan University, Taipei 10617, Taiwan.

Total internal reflection is one of the most important phenomena when a propagated wave strikes a medium boundary, which possesses a wide range of applications spanning from optical communication to a fluorescence microscope. It has also been widely used to demonstrate conventional laser actions with resonant cavities. Recently, cavity-free stimulated emission of radiation has attracted great attention in disordered media because of several exciting physical phenomena, ranging from Anderson localization of light to speckle-free imaging. However, unlike conventional laser systems, the total internal reflection has never been implemented in the study of laser actions derived from randomly distributed media. Herein, we demonstrate an ultra-low threshold cavity-free laser system using air bubbles as scattering centers in which the total internal reflection from the surface of air bubbles can greatly reduce the leakage of the scattered beam energy and then enhance light amplification within a coherent closed loop. Our approach provides an excellent alternative for the manipulation of optical energy flow to achieve ultra-low threshold cavity-free laser systems, which should be very useful for the development of high performance optoelectronic devices.
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http://dx.doi.org/10.1021/acsomega.9b04094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7407540PMC
August 2020

Characterization of Driver Mutations in Anaplastic Thyroid Carcinoma Identifies and Mutations as Negative Survival Predictors.

Cancers (Basel) 2020 Jul 20;12(7). Epub 2020 Jul 20.

Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei 112, Taiwan.

Anaplastic thyroid carcinoma (ATC) is rare but highly aggressive. We investigated the association of selected driver mutations, including , , promoter, , , and mismatch repair deficiency (MMR-D) with the clinicopathological features of ATC to identify prognostic and predictive biomarkers. Thirty-nine retrospective cases from pathology archives were enrolled for clinicopathology analysis and immunohistochemistry, and 27 cases had sufficient specimens for further molecular testing using targeted next-generation sequencing and mass spectrometry. and mutations were identified in 25.9% and 40.7% of ATC, respectively. mutation was significantly associated with coexisting papillary thyroid carcinoma ( = 0.009) and mutations with female gender ( = 0.012). In univariant analysis, the non- tumors were significantly associated with the presence of a sarcomatoid pattern ( = 0.045). , promoter, and mutations were identified in 14.8%, 81.5%, and 70.4% of cases, respectively. No MMR-D or mutations were detected. In survival analyses, and mutations were significantly associated with inferior outcomes ( = 0.03 and = 0.006, respectively). In conclusion, driver mutations in ATC are associated with distinct clinicopathological features. and mutations were negative predictors for patient survival. Emerging therapeutic agents targeting BRAF, RAS, and PI3 kinase may benefit a substantial proportion of ATC patients.
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http://dx.doi.org/10.3390/cancers12071973DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7409295PMC
July 2020

sp. nov., isolated from an abandoned construction timber.

Int J Syst Evol Microbiol 2020 Jun;70(6):3731-3739

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A bacterial strain CC-CTC003 was isolated from a synthetic wooden board. Cells of strain CC-CTC003 were Gram-stain-negative, rod-shaped, motile by gliding and formed yellow colonies. Optimal growth occurred at 25 °C, pH 7 and in the presence of 1 % NaCl. The phylogenetic analyses based on 16S rRNA genes revealed that strain CC-CTC003 belonged to the genus and was most closely related to (95.3 % sequence identity), (94.9 % sequence identity), (94.8 %) and (94.7 %) and had less than 94.7 % sequence similarity to other members of the genus. Average nucleotide identity (ANI) values between strain CC-CTC003 and the type strains of other closely related species were 70.1-74.1 %. The digital DNA-DNA hybridization (dDDH) with was 19.4 %. Strain CC-CTC003 contained C, -C, -C 3-OH, -C 3-OH, summed feature 3 (C 6c / C 7c) and summed feature 9 (C 10-methyl / -C 9c) as the predominant fatty acids. The polar lipid profile consisted of phosphatidylethanolamine, four uncharacterized aminophospholipids, two aminolipids and one unidentified glycolipid. The major polyamine was -homospermidine and contained MK-6 as major isoprenoid quinone. The DNA G+C content of the genomic DNA was 39.2 mol%. On the basis of the phylogenetic inference and phenotypic data, strain CC-CTC003 should be classified as a novel species, for which the name sp. nov. is proposed. The type strain is CC-CTC003 (=BCRC 81146=JCM 32838).
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http://dx.doi.org/10.1099/ijsem.0.004227DOI Listing
June 2020

Description of Azoarcus nasutitermitis sp. nov. and Azoarcus rhizosphaerae sp. nov., two nitrogen-fixing species isolated from termite nest and rhizosphere of Ficus religiosa.

Antonie Van Leeuwenhoek 2020 Jul 28;113(7):933-946. Epub 2020 Mar 28.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan.

A polyphasic taxonomic approach was used to characterise two presumably novel bacteria, designated strains CC-YHH838 and CC-YHH848 isolated from termite nest and rhizosphere of Ficus religiosa, respectively. These two nitrogen-fixing strains were observed to be Gram-staining-negative, aerobic rod, and colonies were yellowish in color. Growth of strains was observed at 20-37 °C, pH 7-8, and in the presence of 1-2% NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-YHH838 and CC-YHH848 associated with Thauera hydrothermalis (97.1% sequence identity), and formed a separate branch with Azoarcus indigens (95.4%), Aromatoleum aromaticum (96.2%), and lower sequence similarity to other species. The calculation of OrthoANI values pointed out strains CC-YHH838 and CC-YHH848 gave 78.9% and 79.8% compared to Thauera hydrothermalis, respectively. The major fatty acids (> 5%) were C, C cyclo, C 3-OH, Cω7c/Cω6c and Cω7c/Cω6c. The polar lipid profile comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol and unidentified aminophospholipid and phospholipids; the predominant polyamines were putrescine and spermidine. The predominant respiratory system was ubiquinone (Q-8) and the DNA G + C contents were 61.4 ± 0.1 mol% and 60.2 ± 1.3 mol%, respectively. Based on the phylogenetic and polyphasic comparisons, strains CC-YHH838 and CC-YHH848 are proposed to represent two novel species within the genus Azoarcus in the family Rhodocyclaceae, for which the name Azoarcus nasutitermitis sp. nov. (type strain CC-YHH838 = BCRC 81059 = JCM 32001) and Azoarcus rhizosphaerae sp. nov. (type strain CC-YHH848 = BCRC 81060 = JCM 32002) were proposed.
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http://dx.doi.org/10.1007/s10482-020-01401-wDOI Listing
July 2020

sp. nov., isolated from a fermentation process.

Int J Syst Evol Microbiol 2020 Apr 11;70(4):2602-2610. Epub 2020 Mar 11.

Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung, Taiwan, ROC.

A novel Gram-stain-positive, aerobic, motile with peritrichous flagella, rod-shaped bacterium, designated CC-MHH1044, was isolated from a preserved vegetable sample. A polyphasic taxonomic approach was applied to the isolates in order to clarify its taxonomic position. Growth of the strain CC-MHH1044 occurred at 15-50 °C (optimum, 30 °C), pH 6.0-8.0 (optimum, pH 7.0) and with 0-2.0 % (w/v) NaCl (optimum, 1 %, w/v). The genome of strain CC-MHH1044 consisted of 8.5 Mb and the genomic DNA G+C content was 58.5 mol%. Comparison of the 16S rRNA gene sequences showed that CC-MHH1044 belonged to the genus and showed a close relationship with the type strains of (96.2 %) and (95.9 %), and lower sequence similarity to other species. Average nucleotide identity values calculated from whole-genome sequencing data proved that CC-MHH1044 represents a distinct species. The dominant cellular fatty acids (>5 %) included iso-C(7.4 %), iso-C (6.4 %), anteiso-C(40.3 %), C (6.6 %) and iso-C (27.0 %). The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, four unidentified aminophospholipids, one unidentified phospholipid and glycolipid. The major polyamine was spermidine. The predominant isoprenoid quinone was menaqinone 7 (MK-7). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits, together with results of comparative 16S rRNA gene sequence, average nucleotide identity and digital DNA-DNA hybridization analyses, we conclude that strain CC-MHH1044 represents a novel member of the genus , for which the name sp. nov. is proposed. The type strain is CC-MHH1044 (=BCRC 81147=JCM 32834).
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http://dx.doi.org/10.1099/ijsem.0.004080DOI Listing
April 2020

Differential visible spectral influence on carbon metabolism in heterotrophic marine flavobacteria.

FEMS Microbiol Ecol 2020 03;96(3)

Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Road, Taichung 40227, Taiwan.

The visible spectrum of solar radiation is known to stimulate photoheterotrophic bacterial carbon metabolism. However, its impact on 'strictly' heterotrophic bacteria remains less explored. Here, we show that heterotrophic flavobacteria exhibit enhanced uptake and mineralization of dissolved organic carbon with increasing wavelengths of visible light, without employing any 'known' light-harvesting mechanisms. RNA sequencing identified blue light as a major constraint in the extracellular enzymatic hydrolysis of polymeric carbohydrates and acquisition of sugars, despite acting as a stimulus for inorganic carbon sequestration. In contrast, green-red and continuous full-spectrum lights activated diverse hydrolytic enzymes and sugar transporters, but obstructed inorganic carbon fixation. This 'metabolic switching' was apparent through limited nutrient uptake, suppressed light-sensitivity, oxidative stress response and promotion of inorganic carbon sequestration pathways under blue light. The visible light impact on metabolism may be of significant ecological relevance as it appears to promote cell-mediated mineralization of organic carbon in 'green-colored' chlorophyll-rich copiotrophic coastal seawater and inorganic carbon sequestration in 'blue-colored' oligotrophic open ocean. Thus, a novel regulatory role played by light on heterotrophic metabolism and a hidden potential of flavobacteria to sense and respond differentially to monochromatic lights influencing marine carbon cycling were unraveled.
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http://dx.doi.org/10.1093/femsec/fiaa011DOI Listing
March 2020

Description of Gemmobacter aestuarii sp. nov., isolated from estuarine surface water and reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013.

Arch Microbiol 2020 Jul 16;202(5):1035-1042. Epub 2020 Jan 16.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, 402, Taiwan.

A Gram-stain-negative, tyrosine-metabolizing, non-motile, strictly aerobic, non-spore-forming, rod-shaped marine bacterium, designated strain CC-PW-75, was isolated from the estuarine water off Pintung, Taiwan. Strain CC-PW-75 formed a distinct phyletic lineage associated with Gemmobacter species, sharing the highest 16S rRNA gene sequence similarity with G. megaterium CF17 and G. straminiformis CAM-8 (96.0% each) followed by G. aquatilis IFAM 1031 and G. nectariphilus AST4 (95.8% each). Analysis of the draft genome (3.76 Mbp) revealed the presence of genes encoding light-harvesting complexes, photosynthetic reaction centers and proteins involved in the metabolism of CO, CO, HCO and HS. However, bacteriochlorophyll a was not detected. Average nucleotide identity values between the genome sequence of CC-PW-75 and the related Gemmobacter species (n = 6) were estimated to be 72.8-76.3%. Polar lipid analysis revealed the presence of phosphatidylglycerol, phosphatidylethanolamine and an unidentified lipid in major amounts, and phosphatidylmonomethylethanolamine, phosphatidylcholine, an unidentified aminolipid and an unidentified lipid in minor amounts. Cω7c and/or Cω6c, C and Cω7c 11-methyl were identified to be major fatty acids. The DNA G + C content was 66.2 mol% (draft genome sequence). Ubiquinone-10 (Q-10) was the sole respiratory quinone. Based on the polyphasic taxonomic evidence, CC-PW-75 is most likely a novel species of the genus Gemmobacter, affiliated to the family Rhodobacteraceae, for which the name Gemmobacter aestuarii sp. nov. is proposed. The type strain is CC-PW-75 (= JCM 19754 = BCRC 80759). Also, we propose the reclassification of Cereibacter changlensis as Gemmobacter changlensis Chen et al. 2013 using the polyphasic data presented in this study.
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http://dx.doi.org/10.1007/s00203-020-01809-yDOI Listing
July 2020

Draft genome sequence reveals co-occurrence of multiple antimicrobial resistance and plant probiotic traits in rice root endophytic strain Burkholderia sp. LS-044 affiliated to Burkholderia cepacia complex.

J Glob Antimicrob Resist 2020 03 3;20:28-30. Epub 2019 Dec 3.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, XingDa Rd., Taichung, 40227, Taiwan; Innovation and Development Center of Sustainable Agriculture, National Chung Hsing University, Taichung 402, Taiwan. Electronic address:

Objectives: Members of the Burkholderia cepacia complex (Bcc) have been isolated from various environmental and clinical samples and reportedly pose a threat to human health. Here we examine the draft genome sequence of Burkholderia sp. LS-044, an antibiotic-resistant endophytic strain affiliated to the Bcc (ST895) inhabiting rice (Oryza sativa ssp. japonica cv. Tainung 71) root.

Methods: Antimicrobial susceptibility of LS-044 was evaluated comparatively with other Burkholderia sp. (CC-Al74 and CC-3XP9) using commercial ATB PSE 5 test strips. The genome of LS-044 was sequenced using an Illumina MiSeq platform. Plant probiotic and antimicrobial resistance genes were screened by Rapid Annotation using Subsystem Technology (RAST), CARD 2017, NCBI and/or UniProt.

Results: Plant-associated members of Bcc (LS-044 and CC-Al74) exhibited greater resistance to the majority of antibiotics tested. The draft genome sequence of LS-044 contained 8.78 Mbp in 62 contigs having a G + C content of 66.5%, 8868 coding sequences and 75 RNAs. The genome harboured genes coding for LysR-type β-lactamase transcription regulator, classes A, C and D β-lactamases, several metal-dependent β-lactamases, antibiotic efflux proteins, and proteins conferring resistance to colistin, streptothricin, colicin and fluoroquinolones. Similarly, it also possessed genes for copper homeostasis, copper-cobalt-zinc-cadmium-chromium resistance and reduction of mercury. Genes involved in flagellar motility, hydrolysis of murein and chitin, production of siderophore and auxin, and metabolism of aromatic compounds were also found.

Conclusion: Genome sequence data revealed an interlinked occurrence of plant probiotic traits and antimicrobial resistance in the rice root endophyte LS-044.
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http://dx.doi.org/10.1016/j.jgar.2019.11.017DOI Listing
March 2020

sp. nov., isolated from paddy soil, and reclassification of (Zhao . 2017) as comb. nov.

Int J Syst Evol Microbiol 2020 Jan;70(1):397-405

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a nitrogen-fixing bacterium, designated strain CC-HIH110, isolated from paddy soil in Taiwan. Cells of strain CC-HIH110 were Gram-stain-negative, rod-shaped, motile with polar flagella, catalase-positive and oxidase-positive. Optimal growth occurred at 30 °С, pH 7 and 1 % NaCl. Phylogenetic analyses based on 16S rRNA genes revealed a distinct taxonomic position attained by strain CC-HIH110 associated with (98.4 % sequence identity), (97.8 %), (97.7 %) and (96.0 %), and lower sequence similarity to other species. Average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain CC-HIH110 and the type strains of other closely related species were 71.5-88.6 % and 19.6-35.5 %, respectively. Strain CC-HIH110 contained C 3-OH, C 3-OH/iso C I and C 7/C 6 as the predominant fatty acids. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, phosphatidyldimethylethanolamine, phosphatidylcholine, three unknown aminophospholipids, two unknown phospholipids and an unknown lipid. The major polyamine was homospermidine. The DNA G+C content was 55.0 mol% and the predominant quinone was ubiquinone (Q-10). Based on its distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence, ANI and dDDH analyses, strain CC-HIH110 is proposed to represent a novel species, for which the name sp. nov. (type strain CC-HIH110=BCRC 80932=JCM 31228). In addition, is reclassified as (type strain N19=ACCC 19962=KCTC 52413) comb. nov.
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http://dx.doi.org/10.1099/ijsem.0.003770DOI Listing
January 2020

Self-Healing Nanophotonics: Robust and Soft Random Lasers.

ACS Nano 2019 08 12;13(8):8977-8985. Epub 2019 Aug 12.

Department of Physics , National Taiwan University , Taipei 10617 , Taiwan.

Self-healing technology promises a generation of innovation in cross-cutting subjects ranging from electronic skins, to wearable electronics, to point-of-care biomedical sensing modules. Recently, scientists have successfully pulled off significant advances in self-healing components including sensors, energy devices, transistors, and even integrated circuits. Lasers, one of the most important light sources, integrated with autonomous self-healability should be endowed with more functionalities and opportunities; however, the study of self-healing lasers is absent in all published reports. Here, the soft and self-healable random laser (SSRL) is presented. The SSRL can not only endure extreme external strain but also withstand several cutting/healing test cycles. Particularly, the damaged SSRL enables its functionality to be restored within just few minutes without the need of additional energy, chemical/electrical agents, or other healing stimuli, truly exhibiting a supple yet robust laser prototype. It is believed that SSRL can serve as a vital building block for next-generation laser technology as well as follow-on self-healing optoelectronics.
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http://dx.doi.org/10.1021/acsnano.9b02858DOI Listing
August 2019

Mesorhizobium composti sp. nov., isolated from compost.

Antonie Van Leeuwenhoek 2019 Sep 4;112(9):1387-1398. Epub 2019 May 4.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, 145, Xingda Rd, Taichung, 40227, Taiwan.

A polyphasic taxonomic approach was used to characterize a presumptively novel diazotrophic bacterium, designated strain CC-YTH430, isolated from a compost sample in Taiwan. Cells of strain CC-YTH430 were found to be Gram-stain negative, facultative anaerobic rods that formed yellow-colored colonies on nutrient agar. Cell growth occurred at 15-40 °C, pH 5.0-9.0 and in the presence of 0-2% NaCl. Strain CC-YTH430 resembled Mesorhizobium species while sharing high pair-wise 16S rRNA gene sequence similarities with Mesorhizobium silamurunense, Mesorhizobium thiogangeticum, Mesorhizobium plurifarium, Mesorhizobium tamadayense, Mesorhizobium amorphae (96.9% each), Mesorhizobium sediminum (96.8%), and Mesorhizobium soli (96.5%) and < 96.5% similarity to other species. Strain CC-YTH430 showed 78.8-79.7% average nucleotide identity compared to the type strains of M. amorphae, M. plurifarium, M. soli, M. tamadayense and M. wenxiniae. The N-fixing activity of strain CC-YTH430 was 0.2 nmol ethylene h at 30 °C. The respiratory system was ubiquinone 10 (Q-10) and the DNA G+C content was 62.0 ± 0.2 mol%. The major fatty acids (> 5%) were C, C cyclo, C cyclo ω8c, C 3OH/C iso I and Cω7c/Cω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylmonomethylethanolamine and an unidentified aminolipid in major amounts. In addition, phosphatidylethanolamine, an unidentified lipid and several unidentified polar lipids were also found in moderate-to-trace amounts. Based on the phylogenetic, phenotypic and chemotaxonomic features, strain CC-YTH430 is proposed to represent a novel Mesorhizobium species, for which the name Mesorhizobium composti sp. nov. (type strain CC-YTH430 = BCRC 81024 = JCM 31762) is proposed.
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http://dx.doi.org/10.1007/s10482-019-01270-yDOI Listing
September 2019

Transient and Flexible Hyperbolic Metamaterials on Freeform Surfaces.

Sci Rep 2018 Jun 21;8(1):9469. Epub 2018 Jun 21.

Graduate Institute of Applied Physics, National Taiwan University, Taipei, 106, Taiwan.

Transient technology is deemed as a paramount breakthrough for its particular functionality that can be implemented at a specific time and then totally dissolved. Hyperbolic metamaterials (HMMs) with high wave-vector modes for negative refraction or with high photonic density of states to robustly enhance the quantum transformation efficiency represent one of the emerging key elements for generating not-yet realized optoelectronics devices. However, HMMs has not been explored for implementing in transient technology. Here we show the first attempt to integrate transient technology with HMMs, i.e., transient HMMs, composed of multilayers of water-soluble and bio-compatible polymer and metal. We demonstrate that our newly designed transient HMMs can also possess high-k modes and high photonic density of states, which enables to dramatically enhance the light emitter covered on top of HMMs. We show that these transient HMMs devices loss their functionalities after immersing into deionized water within 5 min. Moreover, when the transient HMMs are integrated with a flexible substrate, the device exhibits an excellent mechanical stability for more than 3000 bending cycles. We anticipate that the transient HMMs developed here can serve as a versatile platform to advance transient technology for a wide range of application, including solid state lighting, optical communication, and wearable optoelectronic devices, etc.
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http://dx.doi.org/10.1038/s41598-018-27812-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6013475PMC
June 2018

Ultrahigh Sensitive and Flexible Magnetoelectronics with Magnetic Nanocomposites: Toward an Additional Perception of Artificial Intelligence.

ACS Appl Mater Interfaces 2018 May 9;10(20):17393-17400. Epub 2018 May 9.

Department of Physics , National Taiwan University , Taipei 10617 , Taiwan.

In recent years, flexible magnetoelectronics has attracted a great attention for its intriguing functionalities and potential applications, such as healthcare, memory, soft robots, navigation, and touchless human-machine interaction systems. Here, we provide the first attempt to demonstrate a new type of magneto-piezoresistance device, which possesses an ultrahigh sensitivity with several orders of resistance change under an external magnetic field (100 mT). In our device, Fe-Ni alloy powders are embedded in the silver nanowire-coated micropyramid polydimethylsiloxane films. Our devices can not only serve as an on/off switch but also act as a sensor that can detect different magnetic fields because of its ultrahigh sensitivity, which is very useful for the application in analog signal communication. Moreover, our devices contain several key features, including large-area and easy fabrication processes, fast response time, low working voltage, low power consumption, excellent flexibility, and admirable compatibility onto a freeform surface, which are the critical criteria for the future development of touchless human-machine interaction systems. On the basis of all of these unique characteristics, we have demonstrated a nontouch piano keyboard, instantaneous magnetic field visualization, and autonomous power system, making our new devices be integrable with magnetic field and enable to be implemented into our daily life applications with unfamiliar human senses. Our approach therefore paves a useful route for the development of wearable electronics and intelligent systems.
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http://dx.doi.org/10.1021/acsami.8b04950DOI Listing
May 2018

A White Random Laser.

Sci Rep 2018 02 9;8(1):2720. Epub 2018 Feb 9.

Department of Physics, National Taiwan University, Taipei, 10617, Taiwan.

Random laser with intrinsically uncomplicated fabrication processes, high spectral radiance, angle-free emission, and conformal onto freeform surfaces is in principle ideal for a variety of applications, ranging from lighting to identification systems. In this work, a white random laser (White-RL) with high-purity and high-stability is designed, fabricated, and demonstrated via the cost-effective materials (e.g., organic laser dyes) and simple methods (e.g., all-solution process and self-assembled structures). Notably, the wavelength, linewidth, and intensity of White-RL are nearly isotropic, nevertheless hard to be achieved in any conventional laser systems. Dynamically fine-tuning colour over a broad visible range is also feasible by on-chip integration of three free-standing monochromatic laser films with selective pumping scheme and appropriate colour balance. With these schematics, White-RL shows great potential and high application values in high-brightness illumination, full-field imaging, full-colour displays, visible-colour communications, and medical biosensing.
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http://dx.doi.org/10.1038/s41598-018-21228-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5807428PMC
February 2018

Complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1, a flavobacterium isolated from coastal surface seawater.

Mar Genomics 2018 Feb 29;37:21-25. Epub 2017 Nov 29.

Department of Soil & Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung 402, Taiwan; Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan. Electronic address:

Here we present the complete genome sequence of Siansivirga zeaxanthinifaciens CC-SAMT-1, a flavobacterium isolated from coastal surface seawater. A 3.3Mb genome revealed remarkable specialization of this bacterium particularly in the degradation of sulfated polysaccharides available as detritus or in dissolved phase. Besides utilizing high molecular weight organic biopolymers, this strain appears to accomplish assimilatory sulfate reduction, sulfide oxidation, and acquisition and inter-conversion of inorganic carbon. Genes encoding zeaxanthin and three different kinds of DNA photolyase/cryptochrome (senses blue light) were present, while genes that code for blue light sensing BLUF domain proteins and red/far-red light sensing phytochromes were absent. Furthermore, CC-SAMT-1 lacked the rhodopsin photosystem and all other genes that confer any other known forms of phototrophy. The genomic data revealed that CC-SAMT-1 is highly adapted to sulfur-rich coastal environments, where it most likely contributes to marine carbon and sulfur cycles by metabolizing sulfated polysaccharides as well as inorganic sulfur.
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http://dx.doi.org/10.1016/j.margen.2017.09.003DOI Listing
February 2018

Primary effusion lymphoma in Taiwan shows two distinctive clinicopathological subtypes with rare human immunodeficiency virus association.

Histopathology 2018 May 14;72(6):930-944. Epub 2018 Feb 14.

Department of Pathology, Chi-Mei Medical Center, Tainan, Taiwan.

Aims: To investigate the clinicopathological and molecular features of primary effusion lymphoma (PEL) in Taiwan and the association with human immunodeficiency virus (HIV), human herpesvirus 8 (HHV8) and Epstein-Barr virus (EBV).

Methods And Results: We investigated retrospectively 26 cases with a median age of 76.5. Only one (4%) patient was infected with HIV. Cytologically, all lymphoma cells revealed typical immunoblastic to plasmablastic morphology. Immunohistochemically, HHV8 was positive in eight (32%) tumours and negative in 17 (68%) cases. All 23 tested cases examined were of the non-germinal-centre B cell phenotype. MYC proto-oncogene (MYC) and Epstein-Barr encoding mRNA (EBER) were positive in 43% (nine of 21) and 17% (four of 23) cases, respectively. Immunoglobulin heavy chain (IGH), B cell lymphoma (BCL)2, BCL6 and MYC were rearranged in 71%, 11%, 12% and 18% cases, respectively. By univariate analysis, the overall survival (OS) was associated statistically with MYC expression (P = 0.012) and BCL2 rearrangement (P = 0.035), but not with the others. By multivariate analysis, no factor was statistically significant. Compared to the HHV8-negative cases, the HHV8-positive cases were mainly of the plasmablastic immunophenotype expressing CD30 and CD138, and with a less frequent expression of pan-B cell markers.

Conclusions: Apart from the phenotypical difference, our HHV8-positive neoplasms were not distinct from the HHV8-negative group. Literature review of 256 cases, including our cases, revealed that HHV8-positive cases were associated more frequently with HIV and EBV infection, with rare MYC rearrangement, and a poorer prognosis than HHV8-negative cases. We propose to name the HHV8-positive cases as 'classical' or 'type I PEL' and the HHV8-negative cases as 'type II PEL', stressing the similarities and the distinctive features between these two groups.
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http://dx.doi.org/10.1111/his.13449DOI Listing
May 2018

Targeting the 15-keto-PGE2-PTGR2 axis modulates systemic inflammation and survival in experimental sepsis.

Free Radic Biol Med 2018 02 22;115:113-126. Epub 2017 Nov 22.

Institute of Molecular Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan; Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan; Department of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan. Electronic address:

Sepsis is a systemic inflammation accompanied by multi-organ dysfunction due to microbial infection. Prostaglandins and their metabolites have long been studied for their importance in regulating the innate immune response. 15-keto-PGE2 (15k-PGE) is a prostaglandin E2 (PGE) metabolite, whose further processing is catalyzed by prostaglandin reductase 2 (PTGR2). We showed disruption of the Ptgr2 gene in mice improves the survival rate under both LPS- and cecum ligation/puncture (CLP)-induced experimental sepsis. Knockdown of PTGR2 showed significant accumulation of intracellular 15k-PGE in activated macrophages. Both PTGR2 knockdown and exogenous treatment with 15k-PGE resulted in reduced pro-inflammatory cytokines production in LPS-stimulated RAW264.7 cells or bone marrow-derived macrophages (BMDM). The same treatment in RAW264.7 and BMDM also led to increased levels of the anti-oxidative transcription factor, Nuclear factor (erythroid-2) related factor-2 (NRF2), augmented anti-oxidant response element (ARE)-mediated reporter activity and upregulated expression of the corresponding anti-oxidant genes. 15k-PGE further demonstrated modification to Kelch-like ECH-associated protein 1 (Keap1), a negative regulator of Nrf2, at cysteine 288 (Cys288) site post-translationally. Finally, 15k-PGE-treated mice were found to be more resistant to experimental sepsis. Taken together, our study affirms the significance of PTGR2 and 15k-PGE in mitigating inflammatory responses and suggests a novel anti-oxidative and anti-inflammatory therapy for sepsis through targeting PTGR2 and administering15k-PGE.
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http://dx.doi.org/10.1016/j.freeradbiomed.2017.11.016DOI Listing
February 2018

Sphingomonas colocasiae sp. nov., isolated from taro (Colocasia esculanta).

Int J Syst Evol Microbiol 2018 Jan 8;68(1):133-140. Epub 2017 Nov 8.

Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic approach was used to characterize an aerobic, Gram-stain-negative, rod-shaped bacterium (designed as strain CC-MHH0539) isolated from the chopped tuber of taro (Colocasia esculanta) in Taiwan. Strain CC-MHH0539 was able to grow at 15-30 °C (optimum, 25 °C), at pH 6.0-9.0 (optimum, 7.0) and with 0-1 % (w/v) NaCl. Strain CC-MHH0539 showed highest 16S rRNA gene sequence similarity to Sphingomonas laterariae LNB2 (96.8 %), Sphingobium boeckii 469 (96.5 %), Sphingomonas faucium E62-3 (96.4 %) and Sphingosinicella vermicomposti YC7378 (96.2 %) and <96.1 % similarity to other sphingomonads. Strain CC-MHH0539 was found to cluster mainly with the clade that accommodated members of the genus Sphingomonas. The dominant cellular fatty acids were C16 : 0, C16 : 1ω5c, C14 : 0 2-OH, C16 : 1ω7c/C16 : 1ω6c and C18 : 1ω7c/C18 : 1ω6c. Diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, two sphingoglycolipids and two unidentified phospholipids were detected in strain CC-MHH0539. The DNA G+C content was 69.5 mol%. The respiratory quinone system and predominant polyamine was ubiquinone 10 (Q-10) and sym-homospermidine, respectively, which is in line with Sphingomonas representatives. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, strain CC-MHH0539 is considered to represent a novel species of the genus Sphingomonas, for which the name Sphingomonas colocasiae sp. nov. is proposed. The type strain is CC-MHH0539 (=BCRC 80933=JCM 31229).
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http://dx.doi.org/10.1099/ijsem.0.002471DOI Listing
January 2018

Castellaniella fermenti sp. nov., isolated from a fermented meal.

Int J Syst Evol Microbiol 2018 Jan 8;68(1):52-57. Epub 2017 Nov 8.

Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic taxonomic approach was used to characterize a presumably novel bacterium, designated strain CC-YTH191, isolated from a fermented meal in Taiwan. Cells of strain CC-YTH191 were Gram-stain-negative aerobic rods, which grew at 15-40 °C (optimal 25-30 °C), pH 6.0-9.0 (optimal 7.0) and 1-2 % (w/v) NaCl (optimal 1 %). On the basis of 16S rRNA gene sequence analysis, strain CC-YTH191 appeared to belong to the genus Castellaniella, and was closely related to Castellaniella hirudinis (96.7 % similarity), Castellaniella ginsengisoli (96.7 %) and Castellaniella caeni (96.0 %), while with other related species it shared <96.0 % similarity. The major cellular fatty acids of the isolate were C16 : 0, C17 : 0cyclo, C14 : 0 3OH/C16 : 1iso I and C18 : 1ω7c/C18 : 1ω6c. The polar lipid profile contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylserine, three unidentified phospholipids, an unidentified aminolipid and an unidentified aminophospholpid. Putrescine was the predominant polyamine followed by spermidine. The DNA G+C content was 62.2 mol% and the predominant quinone system was ubiquinone 8 (Q-8). All these features confirmed the placement of the strain CC-YTH191 as a novel species within the genus Castellaniella, for which the name Castellaniella fermenti sp. nov. is proposed. The type strain is CC-YTH191 (=BCRC 81023=JCM 31755).
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http://dx.doi.org/10.1099/ijsem.0.002436DOI Listing
January 2018

Hydrogenophaga aquatica sp. nov., isolated from a hot spring.

Int J Syst Evol Microbiol 2017 Oct 13;67(10):3716-3721. Epub 2017 Sep 13.

Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic approach was used to characterize an aerobic, Gram-negative, rod-shaped bacterium (designated strain CC-KL-3) isolated from a hot spring. Phylogenetic analyses based on 16S rRNA genes indicated that strain CC-KL-3 showed highest sequence similarity to Hydrogenophaga bisanensis (97.7 %) and Hydrogenophaga atypica (97.6 %) and lower sequence similarity to other species (less than 97.6 %). The levels of DNA-DNA relatedness between strain CC-KL-3, H. bisanensis and H. atypica were estimated to be 13.0 and 8.7 % (the reciprocal value was 14.7 and 6.3 %). Strain CC-KL-3 was non-motile, without apparent flagella and able to grow between 15-42 °C (optimal 30 °С), pH 6.0-8.0 (optimal 7.0) and 0-2 % (w/v) NaCl (optimal 0 %). The DNA G+C content was 61.4 mol% and the major quinone system was ubiquinone (Q-8). The polyamine profile revealed the predominance of 2-hydroxyputrescine and putrescine and the dominant cellular fatty acids were C16 : 0 (28.9 %), C16 : 1ω7c/C16 : 1ω6c (41.4 %) and C18 : 1ω7c/C18 : 1ω6c (11.9 %). These data corroborated the affiliation of strain CC-KL-3 to the genus Hydrogenophaga. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits, and the results of comparative 16S rRNA gene sequence analysis, strain CC-KL-3 is considered to represent a novel species of the genus Hydrogenophaga, affiliated to the family Comamonadaceae, for which the name Hydrogenophaga aquatica sp. nov. is proposed. The type strain is CC-KL-3 (=BCRC 80937=JCM 31216).
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http://dx.doi.org/10.1099/ijsem.0.002146DOI Listing
October 2017

Filimonas aquilariae sp. nov., isolated from agarwood chips.

Int J Syst Evol Microbiol 2017 Sep 22;67(9):3219-3225. Epub 2017 Aug 22.

Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan, ROC.

A polyphasic approach was used to characterize a Gram-staining negative bacterium (designated strain CC-YHH650T) isolated from agarwood chips. Strain CC-YHH650T was aerobic and rod-shaped, able to grow at 15-37 °C (optimal 30 °С), pH 6.0-8.0 (optimal 7.0) and 0-1 % (w/v) NaCl (optimal 0 %). Phylogenetic analysis based on 16S rRNA genes revealed that strain CC-YHH650T shared highest sequence similarities with Filimonas lacunae (97.5 %), F. zeae (97.4 %), F. endophytica (97.3 %) and F. aurantiibacter (93.0 %), and lower sequence similarity with other genera (less than 93.0 %). The levels of DNA-DNA relatedness between strain CC-YTH209T, F. lacunae, F. endophytica and F. zeae were estimated to be 18.3, 6.1, 24.7 % (the reciprocal values were 9.8, 8.8, 18.3 %). The major fatty acids were iso-C15 : 0, iso-C15 : 1 G, C16 : 0 3-OH, iso-C17 : 0 3-OH and C16 : 1ω7c/C16 : 1ω6c. The polar lipid profile contained phosphatidylethanolamine, an unidentified phospholipid, two unidentified aminophospholipids, three unidentified aminolipids and three unidentified lipids. The DNA G+C content was 46.6 mol% and the predominant quinone was menaquinone-7 (MK-7). The major polyamine was sym-homospermidine. Based on the distinct phylogenetic, phenotypic and chemotaxonomic traits together with results of comparative 16S rRNA gene sequence analysis, strain CC-YHH650T is considered to represent a novel species of the genus Filimonas, for which the name Filimonas aquilariae sp. nov. is proposed. The type strain is CC-YHH650T (=BCRC 80935T=JCM 31197T).
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http://dx.doi.org/10.1099/ijsem.0.002087DOI Listing
September 2017

Human papillomavirus-related carcinoma with adenoid cystic-like features: a series of five cases expanding the pathological spectrum.

Histopathology 2017 Dec 15;71(6):887-896. Epub 2017 Sep 15.

Department of Pathology and Laboratory Medicine, Taipei Veterans General Hospital, Taipei, Taiwan.

Aims: Human papillomavirus (HPV)-related carcinoma with adenoid cystic-like features is a newly described entity of the sinonasal tract. In this study, we evaluated histomorphology, immunophenotype and molecular testing to identify potentially helpful features in distinguishing it from classic adenoid cystic carcinoma (AdCC).

Methods And Results: We retrospectively collected five HPV-related carcinomas with adenoid cystic-like features and 14 AdCCs of the sinonasal tract. All histological slides were retrieved for morphological evaluation. As comparing with AdCC, HPV-related carcinomas with adenoid cystic-like features were associated with squamous dysplasia of surface epithelium (80% versus 0%, P < 0.01) and the presence of a solid growth pattern (100% versus 29%, P = 0.01), but less densely hyalinized tumour stroma (20% versus 86%, P = 0.02). Squamous differentiation in the invasive tumour was seen in three HPV-related carcinomas with adenoid cystic-like features, two of them showing abrupt keratinization and one with scattered non-keratinizing squamous nests. Diffuse p16 staining in ≥75% of tumour cells was noted in all HPV-related carcinomas with adenoid cystic-like features but in only one AdCC (100% versus 7%, P < 0.01). High-risk HPV testing gave positive results in all HPV-related carcinomas with adenoid cystic-like features (four associated with type 33 and one associated with type 16) but not in AdCCs. MYB rearrangement was tested in four HPV-related carcinomas with adenoid cystic-like features, and all were negative.

Conclusions: This study has further clarified the histological spectrum of this tumour type, and reports the first HPV type 16-related case. Diffuse p16 staining followed by HPV molecular testing is useful in distinguishing HPV-related carcinomas with adenoid cystic features from classic AdCCs.
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http://dx.doi.org/10.1111/his.13301DOI Listing
December 2017

Dissolvable and Recyclable Random Lasers.

ACS Nano 2017 08 28;11(8):7600-7607. Epub 2017 Jun 28.

Department of Physics, National Taiwan University , Taipei 10617, Taiwan.

An integrated random laser based on green materials with dissolubility and recyclability is created and demonstrated. The dissolvable and recyclable random laser (DRRL) can be dissolved in water, accompanying the decay of emission intensity and the increment in lasing threshold. Furthermore, the DRRL can be reused after the process of deionized treatment, exhibiting excellent reproducibility with several recycling processes.
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http://dx.doi.org/10.1021/acsnano.7b00201DOI Listing
August 2017
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