Complete genome sequence of Leptotrichia buccalis type strain (C-1013-b)

Leptotrichia buccalis (Robin 1853) Trevisan 1879 is the type species of the genus, and is of phylogenetic interest because of its isolated location in the sparsely populated and neither taxonomically nor genomically adequately accessed family 'Leptotrichiaceae' within the phylum 'Fusobacteria'. Species of Leptotrichia are large, fusiform, non-motile, non-sporulating rods, which often populate the human oral flora. L. buccalis is anaerobic to aerotolerant, and saccharolytic. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of the order 'Fusobacteriales' and no more than the second sequence from the phylum 'Fusobacteria'. The 2,465,610 bp long single replicon genome with its 2306 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575)

Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.     

Complete genome sequence of Rhodothermus marinus type strain (R-10)

Rhodothermus marinus Alfredsson et al. 1995 is the type species of the genus and is of phylogenetic interest because the Rhodothermaceae represent the deepest lineage in the phylum Bacteroidetes. R. marinus R-10(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from marine hot springs off the coast of Iceland. Strain R-10(T) is strictly aerobic and requires slightly halophilic conditions for growth. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Rhodothermus, and only the second sequence from members of the family Rhodothermaceae. The 3,386,737 bp genome (including a 125 kb plasmid) with its 2914 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.     

The Influence of Soil Inoculum and Nitrogen Availability on Restoration of High-Elevation Steppe Communities Invaded by Bromus tectorum

Cheatgrass ( Bromus tectorum L.) is an exotic annual grass that has invaded approximately 40,000,000 ha of rangelands in the United States, including montane ecosystems that are important habitats for wildlife and livestock. In addition to well-understood mechanisms by which Cheatgrass gains competitive advantage, recent studies have shown that Cheatgrass may also change the associated soil microbial community to impact native perennial plants and promote the persistence of Cheatgrass. Furthermore, reducing plant-available N represents a tool for initiating conditions that accelerate successional change from annual- to perennial-dominated communities. At a montane, mixed shrub–grassland Cheatgrass-dominated site in Colorado, we applied sucrose to reduce available N, and we added soil from a native plant community in order to reestablish the microbial community. This approach tested the idea that intact native soil microbial communities may enhance the beneficial effect of reducing soil N availability in a restoration setting. By the end of the experiment, reduced N availability decreased Cheatgrass by 9.8%, non-native annual/biennial plant cover by 15.0%, and increased relative perennial plant cover by 13.4%; soil inoculation reduced Cheatgrass by 7.6% and increased perennial abundance by 11.3%. Soil inoculum additions and reduced N availability both contributed toward restoring a perennial-dominated community and demonstrates that addition of native soil inoculum may be a useful tool for restoration efforts.     

Mechanisms for reaching the differentiated state: Insights from neural crest-derived melanocytes

Black pigment cells, or melanocytes, are the major contributing cells to pigmentation in vertebrate organisms. Although the function of these cells is distinct depending on the organism, the events involved in their development are remarkably similar. Here, we review the mechanisms involved in the early development of melanocytes from neural crest, many of which are conserved in organisms as diverse as zebrafish, birds and humans. We also discuss recent studies that provide further insight into how melanocyte differentiation is achieved and maintained.     

Tissue-targeted metabonomics: biological considerations and application to doxorubicin-induced hepatic oxidative stress

Tissue-targeted metabonomics, or the use of microdialysis sampling with NMR detection, can be used to monitor the metabolic profiles of specific tissues without the need to take tissue biopsies. This allows for sampling from the same animal over the time course of the experiment, reducing animal-to-animal variability and decreasing the number of animals required, however, this approach to metabonomics studies has not been fully characterized. In this work liver microdialysis sampling was performed on male Sprague–Dawley rats and the effects of diurnal rhythms, animal activity and anesthesia on the liver extracellular fluid composition examined. Diurnal rhythms and animal activity caused little change in liver metabolism, but anesthesia caused dramatic effects attributed to the hyperglycemia induced by xylazine and isoflurane. This approach was then applied to the characterization of the hepatotoxicity of doxorubicin, an anticancer agent known to induce oxidative stress. In these studies, two probes were implanted in the liver and doxorubicin was dosed through one of the probes. Comparisons were made between the metabolic profiles from the two probes to distinguish basal metabolic effects from those induced by doxorubicin. Doxorubicin altered hepatic metabolism by different mechanisms in anesthetized and awake rats. These studies also provided important implications for the design of future tissue-targeted metabonomics experiments.     

Phylogenetic relationships of the Aurantioideae (Rutaceae) based on the nuclear ribosomal DNA ITS region and three noncoding chloroplast DNA regions, atpB-rbcL spacer, rps16, and trnL-trnF

The tribes and subtribes of Aurantioideae, an economically important subfamily of the Rutaceae, have a controversial taxonomic history because a phylogenetic framework has been lacking. In order to construct an evolutionary history and evaluate the most recent classification system [Swingle and Reece 1967. The botany of Citrus and its wild relatives, in: The Citrus Industry, vol. 1, History, World Distribution, Botany, and Varieties. University of California, Berkeley, pp. 190-430], one nuclear and three noncoding chloroplast genes were sequenced and analyzed phylogenetically along with selected non-molecular characters. Taxa representing tribes Citreae and Clauseneae and their six subtribes were sampled. In all analyses Aurantioideae is monophyletic. The majority-rule consensus tree from the combined analysis indicates that the two tribes are not monophyletic. The combined topology is not congruent with the widely used classification of Aurantioideae by Swingle and Reece (1967). The tribes and subtribes are in need of revision.     

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

The HIV-1 epidemic in sub-Saharan Africa is driven largely by heterosexual transmission of non-subtype B viruses, of which subtypes C and A are predominant. Previous studies of subtype B and subtype C transmission pairs have suggested that a single variant from the chronically infected partner can establish infection in their newly infected partner. However, in subtype A infected individuals from a sex worker cohort and subtype B individuals from STD clinics, infection was frequently established by multiple variants. This study examined over 1750 single-genome amplified viral sequences derived from epidemiologically linked subtype C and subtype A transmission pairs very early after infection. In 90% (18/20) of the pairs, HIV-1 infection is initiated by a single viral variant that is derived from the quasispecies of the transmitting partner. In addition, the virus initiating infection in individuals who were infected by someone other than their spouse was characterized to determine if genital infections mitigated the severe genetic bottleneck observed in a majority of epidemiologically linked heterosexual HIV-1 transmission events. In nearly 50% (3/7) of individuals infected by someone other than their spouse, multiple genetic variants from a single individual established infection. A statistically significant association was observed between infection by multiple genetic variants and an inflammatory genital infection in the newly infected individual. Thus, in the vast majority of HIV-1 transmission events in cohabiting heterosexual couples, a single genetic variant establishes infection. Nevertheless, this severe genetic bottleneck can be mitigated by the presence of inflammatory genital infections in the at risk partner, suggesting that this restriction on genetic diversity is imposed in large part by the mucosal barrier.     

Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide

Sirtuin proteins comprise a unique class of NAD+-dependent protein deacetylases. Although several structures of sirtuins have been determined, the mechanism by which NAD+ cleavage occurs has remained unclear. We report the structures of ternary complexes containing NAD+ and acetylated peptide bound to the bacterial sirtuin Sir2Tm and to a catalytic mutant (Sir2Tm(H116Y)). NAD+ in these structures binds in a conformation different from that seen in previous structures, exposing the alpha face of the nicotinamide ribose to the carbonyl oxygen of the acetyl lysine substrate. The NAD+ conformation is identical in both structures, suggesting that proper coenzyme orientation is not dependent on contacts with the catalytic histidine. We also present the structure of Sir2Tm(H116A) bound to deacteylated peptide and 3'-O-acetyl ADP ribose. Taken together, these structures suggest a mechanism for nicotinamide cleavage in which an invariant phenylalanine plays a central role in promoting formation of the O-alkylamidate reaction intermediate and preventing nicotinamide exchange.