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1.  Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring 
Standards in Genomic Sciences  2014;9(3):1105-1117.
Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum ‘Thermotogae’. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.3016383
PMCID: PMC4148951  PMID: 25197486
anaerobic; motile; thermophilic; chemoorganotrophic; solfataric spring; outer sheath-like structure; Thermotogaceae; GEBA
2.  IMG 4 version of the integrated microbial genomes comparative analysis system 
Nucleic Acids Research  2013;42(Database issue):D560-D567.
The Integrated Microbial Genomes (IMG) data warehouse integrates genomes from all three domains of life, as well as plasmids, viruses and genome fragments. IMG provides tools for analyzing and reviewing the structural and functional annotations of genomes in a comparative context. IMG’s data content and analytical capabilities have increased continuously since its first version released in 2005. Since the last report published in the 2012 NAR Database Issue, IMG’s annotation and data integration pipelines have evolved while new tools have been added for recording and analyzing single cell genomes, RNA Seq and biosynthetic cluster data. Different IMG datamarts provide support for the analysis of publicly available genomes (IMG/W: http://img.jgi.doe.gov/w), expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er) and teaching and training in the area of microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu).
doi:10.1093/nar/gkt963
PMCID: PMC3965111  PMID: 24165883
3.  Genome sequence of Frateuria aurantia type strain (Kondô 67T), a xanthomonade isolated from Lilium auratium Lindl. 
Standards in Genomic Sciences  2013;9(1):83-92.
Frateuria aurantia (ex Kondô and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondô 67T was initially (1958) identified as a member of ‘Acetobacter aurantius’, a name that was not considered for the approved list. Kondô 67T was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondô 67T is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.4338002
PMCID: PMC3910546  PMID: 24501647
strictly aerobic; motile; rod-shaped; acetogenic; mesophilic; ‘Acetobacter aurantius’; Xanthomonadaceae; GEBA
4.  Quantitative CT with finite element analysis: towards a predictive tool for bone remodelling around an uncemented tapered stem 
International Orthopaedics  2012;36(7):1363-1369.
Purpose
We used quantitative CT in conjunction with finite element analysis to provide a new tool for assessment of bone quality after total hip arthroplasty in vivo. The hypothesis of this prospective five-year study is that the combination of the two modalities allows 3D patient-specific imaging of cortical and cancellous bone changes and stress shielding.
Method
We tested quantitative CT in conjunction with finite elements on a cohort of 29 patients (31 hips) who have been scanned postoperatively and at one year, two years and five years follow-up. The method uses cubic Hermite finite element interpolation for efficient mesh generation directly from qCT datasets. The element Gauss points that are used for the geometric interpolation functions are also used for interpolation of osteodensitometry data.
Results
The study showed changes of bone density suggestive of proximal femur diaphysis load transfer with osteointegration and moderate metaphyseal stress shielding. Our model revealed that cortical bone initially became porous in the greater trochanter, but this phenomenon progressed to the cortex of the lesser trochanter and the posterior aspect of the metaphysis. The diaphyseal area did not experience major change in bone density for either cortical or cancellous bone.
Conclusion
The combination of quantitative CT with finite element analysis allows visualization of changes to bone density and architecture. It also provides correlation of bone density/architectural changes with stress patterns enabling the study of the effects of stress shielding on bone remodelling in vivo. This technology can be useful in predicting bone remodeling and the quality of implant fixation using prostheses with different design and/or biomaterials.
doi:10.1007/s00264-012-1513-x
PMCID: PMC3385889  PMID: 22527334
5.  Complete Genome Sequence of Desulfurococcus fermentans, a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka, Russia 
Journal of Bacteriology  2012;194(20):5703-5704.
Desulfurococcus fermentans is the first known cellulolytic archaeon. This hyperthermophilic and strictly anaerobic crenarchaeon produces hydrogen from fermentation of various carbohydrates and peptides without inhibition by accumulating hydrogen. The complete genome sequence reported here suggested that D. fermentans employs membrane-bound hydrogenases and novel glycohydrolases for hydrogen production from cellulose.
doi:10.1128/JB.01314-12
PMCID: PMC3458677  PMID: 23012283
6.  Improving Microbial Genome Annotations in an Integrated Database Context 
PLoS ONE  2013;8(2):e54859.
Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG) family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.
doi:10.1371/journal.pone.0054859
PMCID: PMC3570495  PMID: 23424620
7.  The Genome of the Basidiomycetous Yeast and Human Pathogen Cryptococcus neoformans 
Science (New York, N.Y.)  2005;307(5713):1321-1324.
Cryptococcus neoformans is a basidiomycetous yeast ubiquitous in the environment, a model for fungal pathogenesis, and an opportunistic human pathogen of global importance. We have sequenced its ~20-megabase genome, which contains ~6500 intron-rich gene structures and encodes a transcriptome abundant in alternatively spliced and antisense messages. The genome is rich in transposons, many of which cluster at candidate centromeric regions. The presence of these transposons may drive karyotype instability and phenotypic variation. C. neoformans encodes unique genes that may contribute to its unusual virulence properties, and comparison of two phenotypically distinct strains reveals variation in gene content in addition to sequence polymorphisms between the genomes.
doi:10.1126/science.1103773
PMCID: PMC3520129  PMID: 15653466
8.  Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8T) 
Standards in Genomic Sciences  2012;7(2):210-220.
Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8T is of interest for its ability to produce a variety of glycosyl hydrolases. The genome of N. soli strain JS13-8T is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.3117229
PMCID: PMC3569382  PMID: 23408178
aerobic; non-motile; Gram-negative; mesophilic; chemoorganotrophic; glycosyl hydrolases; soil; Chitinophagaceae; GEBA
9.  Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT) 
Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp harbors 3,626 protein-coding and 69 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.2736042
PMCID: PMC3558970  PMID: 23407703
aerobic; motile; Gram-positive; acidophilic; moderately thermophilic; sulfide- and iron-oxidizing; biomining; autotrophic; mixotrophic; soil; insertis sedis; Clostridiales; GEBA
10.  Genomics of Aerobic Cellulose Utilization Systems in Actinobacteria 
PLoS ONE  2012;7(6):e39331.
Cellulose degrading enzymes have important functions in the biotechnology industry, including the production of biofuels from lignocellulosic biomass. Anaerobes including Clostridium species organize cellulases and other glycosyl hydrolases into large complexes known as cellulosomes. In contrast, aerobic actinobacteria utilize systems comprised of independently acting enzymes, often with carbohydrate binding domains. Numerous actinobacterial genomes have become available through the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project. We identified putative cellulose-degrading enzymes belonging to families GH5, GH6, GH8, GH9, GH12, GH48, and GH51 in the genomes of eleven members of the actinobacteria. The eleven organisms were tested in several assays for cellulose degradation, and eight of the organisms showed evidence of cellulase activity. The three with the highest cellulase activity were Actinosynnema mirum, Cellulomonas flavigena, and Xylanimonas cellulosilytica. Cellobiose is known to induce cellulolytic enzymes in the model organism Thermobifida fusca, but only Nocardiopsis dassonvillei showed higher cellulolytic activity in the presence of cellobiose. In T. fusca, cellulases and a putative cellobiose ABC transporter are regulated by the transcriptional regulator CelR. Nine organisms appear to use the CelR site or a closely related binding site to regulate an ABC transporter. In some, CelR also regulates cellulases, while cellulases are controlled by different regulatory sites in three organisms. Mining of genome data for cellulose degradative enzymes followed by experimental verification successfully identified several actinobacteria species which were not previously known to degrade cellulose as cellulolytic organisms.
doi:10.1371/journal.pone.0039331
PMCID: PMC3377646  PMID: 22723998
11.  Complete genome sequence of the thermophilic sulfate-reducing ocean bacterium Thermodesulfatator indicus type strain (CIR29812T) 
Standards in Genomic Sciences  2012;6(2):155-164.
Thermodesulfatator indicus Moussard et al. 2004 is a member of the Thermodesulfobacteriaceae, a family in the phylum Thermodesulfobacteria that is currently poorly characterized at the genome level. Members of this phylum are of interest because they represent a distinct, deep-branching, Gram-negative lineage. T. indicus is an anaerobic, thermophilic, chemolithoautotrophic sulfate reducer isolated from a deep-sea hydrothermal vent. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 2,322,224 bp long chromosome with its 2,233 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.2665915
PMCID: PMC3387792  PMID: 22768359
strictly anaerobic; motile; Gram-negative; thermophilic; sulfate-reducing; chemolithoautotrophic; black smoker; Thermodesulfobacteria; Thermodesulfobacteriaceae; GEBA
12.  Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T) 
Standards in Genomic Sciences  2012;6(2):174-184.
Holophaga foetida Liesack et al. 1995 is a member of the phylum Acidobacteria and is of interest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first to be sequenced for a representative of the class Holophagae. Here we describe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.2746047
PMCID: PMC3387795  PMID: 22768361
anaerobic; motile; Gram-negative; mesophilic; chemoorganotrophic; sulfide-methylation; fresh water mud; Acidobacteria; Holophagaceae; GEBA
13.  Complete genome sequence of Halopiger xanaduensis type strain (SH-6T) 
Standards in Genomic Sciences  2012;6(1):31-42.
Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.
doi:10.4056/sigs.2505605
PMCID: PMC3368405  PMID: 22675596
Archaea; Euryarchaeota; Halobacteriaceae; extreme halophile
14.  SOP for pathway inference in Integrated Microbial Genomes (IMG) 
Standards in Genomic Sciences  2011;5(3):420-423.
One of the most important aspects of genomic analysis is the prediction of which pathways, both metabolic and non-metabolic, are present in an organism. In IMG, this is carried out by the assignment of IMG terms, which are organized into IMG pathways. Based on manual and automatic assignment of IMG terms, the presence or absence of IMG pathways is automatically inferred. The three categories of pathway assertion are asserted (likely present), not asserted (likely absent), and unknown. In the unknown category, at least one term necessary for the pathway is missing, but an ortholog in another organism has the corresponding term assigned to it. Automatic pathway inference is an important initial step in genome analysis.
doi:10.4056/sigs.1193182
PMCID: PMC3368422  PMID: 22675591
15.  IMG: the integrated microbial genomes database and comparative analysis system 
Nucleic Acids Research  2011;40(Database issue):D115-D122.
The Integrated Microbial Genomes (IMG) system serves as a community resource for comparative analysis of publicly available genomes in a comprehensive integrated context. IMG integrates publicly available draft and complete genomes from all three domains of life with a large number of plasmids and viruses. IMG provides tools and viewers for analyzing and reviewing the annotations of genes and genomes in a comparative context. IMG's data content and analytical capabilities have been continuously extended through regular updates since its first release in March 2005. IMG is available at http://img.jgi.doe.gov. Companion IMG systems provide support for expert review of genome annotations (IMG/ER: http://img.jgi.doe.gov/er), teaching courses and training in microbial genome analysis (IMG/EDU: http://img.jgi.doe.gov/edu) and analysis of genomes related to the Human Microbiome Project (IMG/HMP: http://www.hmpdacc-resources.org/img_hmp).
doi:10.1093/nar/gkr1044
PMCID: PMC3245086  PMID: 22194640
16.  IMG/M: the integrated metagenome data management and comparative analysis system 
Nucleic Acids Research  2011;40(Database issue):D123-D129.
The integrated microbial genomes and metagenomes (IMG/M) system provides support for comparative analysis of microbial community aggregate genomes (metagenomes) in a comprehensive integrated context. IMG/M integrates metagenome data sets with isolate microbial genomes from the IMG system. IMG/M's data content and analytical capabilities have been extended through regular updates since its first release in 2007. IMG/M is available at http://img.jgi.doe.gov/m. A companion IMG/M systems provide support for annotation and expert review of unpublished metagenomic data sets (IMG/M ER: http://img.jgi.doe.gov/mer).
doi:10.1093/nar/gkr975
PMCID: PMC3245048  PMID: 22086953
17.  Complete genome sequence of Ferroglobus placidus AEDII12DO 
Standards in Genomic Sciences  2011;5(1):50-60.
Ferroglobus placidus belongs to the order Archaeoglobales within the archaeal phylum Euryarchaeota. Strain AEDII12DO is the type strain of the species and was isolated from a shallow marine hydrothermal system at Vulcano, Italy. It is a hyperthermophilic, anaerobic chemolithoautotroph, but it can also use a variety of aromatic compounds as electron donors. Here we describe the features of this organism together with the complete genome sequence and annotation. The 2,196,266 bp genome with its 2,567 protein-coding and 55 RNA genes was sequenced as part of a DOE Joint Genome Institute Laboratory Sequencing Program (LSP) project.
doi:10.4056/sigs.2225018
PMCID: PMC3236036  PMID: 22180810
Archaea; Euryarchaeota; Archaeoglobales; hydrothermal vent; hyperthermophile; anaerobe
18.  Complete genome sequence of Staphylothermus hellenicus P8T 
Standards in Genomic Sciences  2011;5(1):12-20.
Staphylothermus hellenicus belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. Strain P8T is the type strain of the species and was isolated from a shallow hydrothermal vent system at Palaeochori Bay, Milos, Greece. It is a hyperthermophilic, anaerobic heterotroph. Here we describe the features of this organism together with the complete genome sequence and annotation. The 1,580,347 bp genome with its 1,668 protein-coding and 48 RNA genes was sequenced as part of a DOE Joint Genome Institute (JGI) Laboratory Sequencing Program (LSP) project.
doi:10.4056/sigs.2054696
PMCID: PMC3236042  PMID: 22180806
Archaea; Crenarchaeota; Desulfurococcaceae; hyperthermophile; hydrothermal vent; anaerobe
19.  Complete genome sequence of the hyperthermophilic chemolithoautotroph Pyrolobus fumarii type strain (1AT) 
Standards in Genomic Sciences  2011;4(3):381-392.
Pyrolobus fumarii Blöchl et al. 1997 is the type species of the genus Pyrolobus, which belongs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106°C). This is the first completed genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on September 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.2014648
PMCID: PMC3156397  PMID: 21886865
hyperthermophile; chemolithoautotroph; facultative microaerophilic; non-motile; hydrothermal solfataric vents; black smoker; Pyrodictiaceae; GEBA
20.  Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1T) 
Standards in Genomic Sciences  2011;4(3):322-330.
Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity for nitrate reduction via conversion to N2 through respiration, which is a key compound in plant nutrition. The strain is also of interest because it represents the first mesophilic and facultatively anaerobic member of the Epsilonproteobacteria reported to grow on molecular hydrogen. This is the first completed genome sequence of a member of the genus Nitratifractor and the second sequence from the family Nautiliaceae. The 2,101,285 bp long genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.1844518
PMCID: PMC3156401  PMID: 21886859
anaerobic; microaerobic; non-motile; Gram-negative; mesophilic; strictly chemolithoautotroph; Nautiliaceae; GEBA
21.  Novel Insights into the Diversity of Catabolic Metabolism from Ten Haloarchaeal Genomes 
PLoS ONE  2011;6(5):e20237.
Background
The extremely halophilic archaea are present worldwide in saline environments and have important biotechnological applications. Ten complete genomes of haloarchaea are now available, providing an opportunity for comparative analysis.
Methodology/Principal Findings
We report here the comparative analysis of five newly sequenced haloarchaeal genomes with five previously published ones. Whole genome trees based on protein sequences provide strong support for deep relationships between the ten organisms. Using a soft clustering approach, we identified 887 protein clusters present in all halophiles. Of these core clusters, 112 are not found in any other archaea and therefore constitute the haloarchaeal signature. Four of the halophiles were isolated from water, and four were isolated from soil or sediment. Although there are few habitat-specific clusters, the soil/sediment halophiles tend to have greater capacity for polysaccharide degradation, siderophore synthesis, and cell wall modification. Halorhabdus utahensis and Haloterrigena turkmenica encode over forty glycosyl hydrolases each, and may be capable of breaking down naturally occurring complex carbohydrates. H. utahensis is specialized for growth on carbohydrates and has few amino acid degradation pathways. It uses the non-oxidative pentose phosphate pathway instead of the oxidative pathway, giving it more flexibility in the metabolism of pentoses.
Conclusions
These new genomes expand our understanding of haloarchaeal catabolic pathways, providing a basis for further experimental analysis, especially with regard to carbohydrate metabolism. Halophilic glycosyl hydrolases for use in biofuel production are more likely to be found in halophiles isolated from soil or sediment.
doi:10.1371/journal.pone.0020237
PMCID: PMC3102087  PMID: 21633497
22.  A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea 
Nature  2009;462(7276):1056-1060.
Sequencing of bacterial and archaeal genomes has revolutionized our understanding of the many roles played by microorganisms1. There are now nearly 1,000 completed bacterial and archaeal genomes available2, most of which were chosen for sequencing on the basis of their physiology. As a result, the perspective provided by the currently available genomes is limited by a highly biased phylogenetic distribution3–5. To explore the value added by choosing microbial genomes for sequencing on the basis of their evolutionary relationships, we have sequenced and analysed the genomes of 56 culturable species of Bacteria and Archaea selected to maximize phylogenetic coverage. Analysis of these genomes demonstrated pronounced benefits (compared to an equivalent set of genomes randomly selected from the existing database) in diverse areas including the reconstruction of phylogenetic history, the discovery of new protein families and biological properties, and the prediction of functions for known genes from other organisms. Our results strongly support the need for systematic ‘phylogenomic’ efforts to compile a phylogeny-driven ‘Genomic Encyclopedia of Bacteria and Archaea’ in order to derive maximum knowledge from existing microbial genome data as well as from genome sequences to come.
doi:10.1038/nature08656
PMCID: PMC3073058  PMID: 20033048
23.  Complete genome sequence of Methanothermus fervidus type strain (V24ST) 
Standards in Genomic Sciences  2010;3(3):315-324.
Methanothermus fervidus Stetter 1982 is the type strain of the genus Methanothermus. This hyperthermophilic genus is of a thought to be endemic in Icelandic hot springs. M. fervidus was not only the first characterized organism with a maximal growth temperature (97°C) close to the boiling point of water, but also the first archaeon in which a detailed functional analysis of its histone protein was reported and the first one in which the function of 2,3-cyclodiphosphoglycerate in thermoadaptation was characterized. Strain V24ST is of interest because of its very low substrate ranges, it grows only on H2 + CO2. This is the first completed genome sequence of the family Methanothermaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,243,342 bp long genome with its 1,311 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.1283367
PMCID: PMC3035299  PMID: 21304736
hyperthermophile; strictly anaerobic; motile; Gram-positive; chemolithoautotroph; Methanothermaceae; Euryarchaeota; GEBA
24.  Accuracy of Computer-assisted Navigation for Femoral Head Resurfacing Decreases in Hips with Abnormal Anatomy 
Computer-assisted navigation systems for hip resurfacing arthroplasty are designed to minimize the chance of implant malposition. However, there is little evidence computer navigation is useful in the presence of anatomical deformity. We therefore determined the accuracy of an image-free resurfacing hip arthroplasty navigation system in the presence of a pistol grip deformity of the head and femoral neck junction and of a slipped upper femoral epiphysis deformity. We constructed an artificial phantom leg from machined aluminum with a simulated hip and knee. The frontal and lateral plane implant-shaft angles for the guide wire of the femoral component reamer were calculated with the computer navigation system and with an electronic caliper combined with micro-CT. There was a consistent disagreement between the navigation system and our measurement system in both the frontal plane and lateral plane with the pistol grip deformity. We found close agreement only for the frontal plane angle calculation in the presence of the slipped upper femoral epiphysis deformity, but calculation of femoral head size was inaccurate. The use of image-free navigation for the positioning of the femoral component appears questionable in these settings.
doi:10.1007/s11999-009-0850-6
PMCID: PMC2866914  PMID: 19421830
25.  Complete genome sequence of Thermocrinis albus type strain (HI 11/12T) 
Standards in Genomic Sciences  2010;2(2):194-202.
Thermocrinis albus Eder and Huber 2002 is one of three species in the genus Thermocrinis in the family Aquificaceae. Members of this family have become of significant interest because of their involvement in global biogeochemical cycles in high-temperature ecosystems. This interest had already spurred several genome sequencing projects for members of the family. We here report the first completed genome sequence a member of the genus Thermocrinis and the first type strain genome from a member of the family Aquificaceae. The 1,500,577 bp long genome with its 1,603 protein-coding and 47 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.
doi:10.4056/sigs.761490
PMCID: PMC3035279  PMID: 21304702
microaerophilic; (hyper-)thermophile; chemolithoautotrophic; biogeochemistry; non-sporeforming; Gram-negative; flagellated; non-pathogen; Aquificaceae; GEBA

Results 1-25 (47)