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Fig. 1. Phylogenetic relationship derived from 16S rRNA gene sequences between strains A1T, B1T and H1T in Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs
No full textFig. 1. Phylogenetic relationship derived from 16S rRNA gene sequences between strains A1T, B1T and H1T and other related taxa of the family Comamonadaceae. The tree was reconstructed using the maximum-likelihood method based on 16S rRNA gene sequences. Bootstrap values greater than 80% are shown at branch points. Bar, 0.02 substitutions per nucleotide position.Published as part of Bird, Lina J., Kuenen, J. Gijs, Osburn, Magdalena R., Tomioka, Naotaka, Ishii, Shun'ichi, Barr, Casey, Nealson, Kenneth H. & Suzuki, Shino, 2021, Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs, pp. 1-10 in International Journal of Systematic and Evolutionary Microbiology (004945) 71 (8) on page 3, DOI: 10.1099/ijsem.0.004945, http://zenodo.org/record/622417
Serpentinimonas raichei Bird & Kuenen & Osburn & Tomioka & Ishii & Barr & Nealson & Suzuki 2021, SP. NOV.
No full textDESCRIPTION OF SERPENTINIMONAS RAICHEI SP. NOV. Serpentinimonas raichei (rai′ che.i. N.L. gen. n. raichei, named after R. Raiche, one of the owners of The Cedars nature reserve). In addition to the characteristics given above in the genus description, S. raichei has the characteristics described below. Growth occurs at 18–37 °C and pH 10.0–11.5 with optimal growth at 30°C and pH 11.0. NaCl ranges from 0 to 0.5 g l−1. The DNA base composition of the type strain is 66.6% G+C (determined from the genome). The strain grows autotrophically with hydrogen gas and calcium carbonate and heterotrophically on acetate, butyrate, lactate, pyruvate, ethanol, cyclohexane and fumarate under microaerophilic condition. The strain cannot utilize nitrate, sulphate, iron (III) hydroxide or iron (II/III) oxide as electron acceptors. The strain cannot ferment glucose. Major fatty acids are C 16:1 ω7 c and C 18:1 ω7 c. The respiratory quinone is ubiquinone. The type strain, A1 T, (=NBRC 111848 T =DSM 103917 T), was isolated from a highly alkaline serpentinizing spring (Barnes Spring 1) in The Cedars located in north California, USA.Published as part of Bird, Lina J., Kuenen, J. Gijs, Osburn, Magdalena R., Tomioka, Naotaka, Ishii, Shun'ichi, Barr, Casey, Nealson, Kenneth H. & Suzuki, Shino, 2021, Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs, pp. 1-10 in International Journal of Systematic and Evolutionary Microbiology (004945) (004945) 71 (8) on page 8, DOI: 10.1099/ijsem.0.004945, http://zenodo.org/record/622417
Serpentinimonas maccroryi Bird & Kuenen & Osburn & Tomioka & Ishii & Barr & Nealson & Suzuki 2021, SP. NOV.
No full textDESCRIPTION OF SERPENTINIMONAS MACCRORYI SP. NOV. Serpentinimonas maccroryi (mac.cro′ ry.i. N.L. gen. n. maccroryi, named after D. McCrory, one of the owners of The Cedars nature reserve). In addition to the characteristics given above in the genus description, the type strain has the characteristics described below. Growth occurs at 18–37°C and pH 9.0–12.5 with optimal growth at 30 °C and pH 11.0. The strain tolerates NaCl ranges from 0 to 0.5 g l−1. The DNA G+C composition of the type strain is 66.7mol% (determined from the genome). The strain grows autotrophically on formate and hydrogen gas but not on thiosulfate under microaerophilic conditions. The strain can use nitrate, but not thiosulfate as an electron acceptor. The strain can ferment glucose and grow heterotrophically on acetate, butyrate, lactate, pyruvate, ethanol, glucose and fumarate. Major fatty acids are C 16:0, C 16:1 ω7 c and C 18:1 ω7 c. The respiratory quinone is ubiquinone. The type strain, B1 T (=NBRC 111850 T =DSM 103919 T), was isolated from a highly alkaline serpentinizing spring (Barnes Spring 1) in The Cedars located in north California, USA.Published as part of Bird, Lina J., Kuenen, J. Gijs, Osburn, Magdalena R., Tomioka, Naotaka, Ishii, Shun'ichi, Barr, Casey, Nealson, Kenneth H. & Suzuki, Shino, 2021, Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs, pp. 1-10 in International Journal of Systematic and Evolutionary Microbiology (004945) (004945) 71 (8) on page 9, DOI: 10.1099/ijsem.0.004945, http://zenodo.org/record/622417
Serpentinimonas barnesii Bird & Kuenen & Osburn & Tomioka & Ishii & Barr & Nealson & Suzuki 2021, SP. NOV.
No full textDESCRIPTION OF SERPENTINIMONAS BARNESII SP. NOV. Serpentinimonas barnesii (bar.ne′ si.i. N.L. gen. n. barnesii, named after I. Barnes, geochemist and first describer of The Cedars serpentinization site). In addition to the characteristics given above in the genus description, the type strain has the characteristics described below. Growth occurs at 18–37 °C and pH 9.0–12.0 with optimal growth at 30 °C and pH 11.0. NaCl ranges from 0 to 0.5g l−1. The DNA G+C composition of the type strain is 66.7mol% (determined from the genome). The strain grows autotrophically with hydrogen gas and calcium carbonate and heterotrophically on acetate, butyrate, lactate, pyruvate, ethanol and fumarate under microaerophilic conditions. The strain can ferment glucose. The strain is also able to utilize glucose as an electron donor, and nitrate as an electron acceptor. Major fatty acids are C 16:0 and C 18:1 ω7 c. The respiratory quinone is ubiquinone. The type strain, H1 T (=NBRC 111849 T =DSM 103920 T), was isolated from a highly alkaline serpentinizing spring (Barnes Spring 5) in The Cedars located in north California, USA.Published as part of Bird, Lina J., Kuenen, J. Gijs, Osburn, Magdalena R., Tomioka, Naotaka, Ishii, Shun'ichi, Barr, Casey, Nealson, Kenneth H. & Suzuki, Shino, 2021, Serpentinimonas gen. nov., Serpentinimonas raichei sp. nov., Serpentinimonas barnesii sp. nov. and Serpentinimonas maccroryi sp. nov., hyperalkaliphilic and facultative autotrophic bacteria isolated from terrestrial serpentinizing springs, pp. 1-10 in International Journal of Systematic and Evolutionary Microbiology (004945) (004945) 71 (8) on pages 8-9, DOI: 10.1099/ijsem.0.004945, http://zenodo.org/record/622417
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Defining How a Microbial Cell Senses and Responds to a Redox Active Environment
Full text linkThis grant was for four years, and the work was designed to look at the mechanisms of extracellular electron transfer by the dissimilatory iron reducing bacteria Shewanella oneidensis MR-1, and other closely related Shewanella strains and species. During this work, we defined many of the basic physiological and biochemical properties of the Shewanella group, Much of which was summarized in review articles. We also finished and published the genome sequence of strain MR-1, the first of the shewanellae to have its genome sequenced. Control at the transcriptional and translational level was studied in collaboration with colleagues at PNNL and ANL. We utilized synchrotron X-ray radiation to image both the bacteria and the metal oxide particles via a technique called STXM, synchrotron X-ray absorption (ref. No.9), and X-ray microbeam analysis. We purified several of the cytochromes involved with metal reduction, and improved gene annotation of the MR-1 genome. The conductive appendages (nanowires) of MR-1 were described and characterized. Comparative genomics and biochemistry revealed that the pathway for the utilization of N-acetyl glucosamine in the various strains of Shewanella exhibited great variability, and had a number of previously unknown genes
Genome-Facilitated Analyses of Geomicrobial Processes
Full text linkThis project had the goal(s) of understanding the mechanism(s) of extracellular electron transport (EET) in the microbe Shewanella oneidensis MR-1, and a number of other strains and species in the genus Shewanella. The major accomplishments included sequencing, annotation, and analysis of more than 20 Shewanella genomes. The comparative genomics enabled the beginning of a systems biology approach to this genus. Another major contribution involved the study of gene regulation, primarily in the model organism, MR-1. As part of this work, we took advantage of special facilities at the DOE: e.g., the synchrotron radiation facility at ANL, where we successfully used this system for elemental characterization of single cells in different metabolic states (1). We began work with purified enzymes, and identification of partially purified enzymes, leading to initial characterization of several of the 42 c-type cytochromes from MR-1 (2). As the genome became annotated, we began experiments on transcriptome analysis under different conditions of growth, the first step towards systems biology (3,4). Conductive appendages of Shewanella, called bacterial nanowires were identified and characterized during this work (5, 11, 20,21). For the first time, it was possible to measure the electron transfer rate between single cells and a solid substrate (20), a rate that has been confirmed by several other laboratories. We also showed that MR-1 cells preferentially attach to cells at a given charge, and are not attracted, or even repelled by other charges. The interaction with the charged surfaces begins with a stimulation of motility (called electrokinesis), and eventually leads to attachment and growth. One of the things that genomics allows is the comparative analysis of the various Shewanella strains, which led to several important insights. First, while the genomes predicted that none of the strains looked like they should be able to degrade N-acetyl glucosamine (NAG), the monomer that makes up chitin, virtually all of the strains were in fact capable. This led to the discovery of a great many new genes involved with chitin and NAG metabolism (7). In a similar vein, a detailed study of the sugar utilization pathway revealed a major new insight into the regulation of sugar metabolism in this genus (19). Systems Biology and Comparative Genomics of the shewanellae: Several publications were put together describing the use of comparative genomics for analyses of the group Shewanella, and these were a logical culmination of our genomic-driven research (10,15,18). Eight graduate students received their Ph.D. degrees doing part of the work described here, and four postdoctoral fellows were supported. In addition, approximately 20 undergraduates took part in projects during the grant period
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