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Complete genome sequence of hyperthermophilic archaeon Thermococcus sp. ES1
Jung, J.H.,Kim, Y.T.,Jeon, E.J.,Seo, D.H.,Hensley, S.A.,Holden, J.F.,Lee, J.H.,Park, C.S. Elsevier Science Publishers 2014 Journal of biotechnology Vol.174 No.-
Thermococcus sp. strain ES1 is an anaerobic, hyperthermophilic archaeon from a hydrothermal vent that catabolizes sugars and peptides and produces H<SUB>2</SUB>S from S<SUP>o</SUP>, H<SUB>2</SUB>, acetate and CO<SUB>2</SUB> as its primary metabolites. We present the complete genome sequence of this strain (1,957,742bp) with a focus on its substrate utilization and metabolite production capabilities. The sequence will contribute to the development of heterotrophic archaea for bioenergy production and biogeochemical modeling in hydrothermal environments.
This text is called (an) article: Referring nouns in name-informing quotation
Álvaro Cortés Rodríguez,Holden Härtl,Natascha Raue,Kristina Weissbecker 경희대학교 언어정보연구소 2022 언어연구 Vol.39 No.2
This paper examines quotations involving predicates like call or refer to that inform the addressee about the name of a lexicalized concept. Quotations of this sort often contain names that are accompanied by a determiner, e.g., This phenomenon is called a “sun halo.” We claim that name-informing constructions imply an underspecified copular relation which entails a referring interpretation of the name. Crucially, the determiner is optional in name-informing quotations, cf. This phenomenon is called “sun halo.” Specifically, our studies aim to determine whether the name in name-informing constructions is perceived as referentially more salient when it is accompanied by a determiner. To test this, three experimental studies were conducted, employing forced-choice tasks, acceptability judgment, and self-paced reading paradigms. Those three experimental methods showed non-significant differences indicating an equivalent behavioral treatment of the two alternatives. Therefore, we conclude that names used in name-informing constructions accompanied by a determiner do not differ referentially from uses not involving a determiner. The data thus suggest that the two realizations of name-informing constructions are semantically equivalent and entail identical semantic features.
( Estria F Pramudyawardani ),( Hajrial Aswidinnoor ),( Bambang S Purwoko ),( Willy B Suwarno ),( M R Islam ),( Holden Verdeprado ),( Bertrand Cy Collard ) 한국육종학회 2018 Plant Breeding and Biotechnology Vol.6 No.3
Higher productivity of new varieties is the most common target for breeders. The discovery of new quantitative trait loci (QTLs) for important traits is an effective method to support this goal. The variety Ciherang has been dominant in Indonesia for many decades. The objective of this study was to identify QTLs for agronomic and yield-related traits, especially those derived from elite variety Ciherang-Sub1. The SNP and SSR markers were used to construct a framework map for preliminary QTL analysis. In total, the 104 markers resulted in the identification of 17 QTLs from 149 backcross families. One QTL (qPH1.1) was identified in the same position across seasons. Six QTLs were confirmed by combined analysis, namely: qHd1c, qDTF3.1, qDTF11.1, qGW3.1, qGW11.1, and qY1.1. One QTL (qgy10.1) was identified from combined analysis, while 9 others were identified from one season trial, namely: qDTF1.1, qHD-6, qDTF11.2, qPH6.1, qUFG3.1, qUFG9.1, qGW2.1, qGW3.2, and qY4.1. The PVE were ranged from 4.1% to 59.5%. Five QTLs in this study were novel QTLs, namely: qDTF11.2, qUFG3.1, qUFG9.1, qGW11.1, and qY4.1. QTL alleles were detected from both parents. Interestingly, QTLs for yield were detected from the low yielding parent. These QTLs should be useful for molecular breeding in the future, since they represent elite genetic backgrounds. Importantly, the mapping populations were part of the breeding program and the best lines were advanced within the program. Furthermore, marker assisted selection (MAS) was used to make the mapping population, demonstrating an example of molecular genetics research fully integrated with actual breeding.
Kim, Y.T.,Jung, J.H.,Stewart, L.C.,Kwon, S.W.,Holden, J.F.,Park, C.S. Elsevier Publishing Services 2015 MARINE GENOMICS Vol.24 No.3
Methanocaldococcus bathoardescens JH146<SUP>T</SUP> is a hyperthermophilic and obligate hydrogenotrophic methanogen isolated from low-temperature (26<SUP>o</SUP>C) hydrothermal vent fluid at Axial Seamount in the northeastern Pacific Ocean. It is most closely related to the N<SUB>2</SUB>-fixing methanogen Methanocaldococcus sp. FS406-22; however, they differ in that JH146 cannot fix N<SUB>2</SUB> or reductively assimilate nitrate. In this study, we present the complete genome sequence of strain JH146<SUP>T</SUP> (1,607,556bp) with its 1635 protein coding genes, and 41 RNA genes. Our analysis focuses on its methane production via the acetyl-CoA pathway and its deleted gene clusters related to nitrogen assimilation. This study extends our understanding of methanogenesis at high temperatures and the impact of these organisms on the biogeochemistry of subseafloor hydrothermal environments and the deep sea.
Jeon, E.J.,Jung, J.H.,Seo, D.H.,Jung, D.H.,Holden, J.F.,Park, C.S. IPC Science and Technology Press ; Elsevier Scienc 2014 Enzyme and microbial technology Vol.60 No.-
Maltose-forming α-amylase is a glycoside hydrolase family 57 (GH57) member that is unique because it displays dual hydrolysis activity toward α-1,4- and α-1,6-glycosidic linkages and only recognizes maltose. This enzyme was previously identified only in Pyrococcus sp. ST04 (PSMA); however, we recently found two homologs subgroups in Thermococcus species. One subgroup (subgroup A) showed relatively high amino acid sequence similarity to PSMA (>71%), while the other subgroup (subgroup B) showed lower homology with PSMA (<59%). To characterize the subgroup B maltose-forming α-amylase from Thermococcus species (TCMA), we cloned the CL1_0868 gene from Thermococcus sp. CL1 and then successfully expressed the gene in Escherichia coli. Although TCMA has a different oligomeric state relative to PSMA, TCMA showed similar substrate specificity. However, TCMA was shown to hydrolyze maltooligosaccharides more easily than PSMA. Also, TCMA displayed different optimum conditions depending on the glycosidic linkage of the substrate. TCMA had the highest activity at 85<SUP>o</SUP>C and at pH 5.0 for α-1,4-glycosidic linkage hydrolysis whereas it showed its maximal activity to cleave α-1,6-glycosidic linkages at 98<SUP>o</SUP>C and pH 6.0.