Draft genome sequence of Komagataeibacter rhaeticus Strain AF1, a high producer of cellulose, isolated from kombucha tea

Here, we present the draft genome sequence of Komagatabaeicter rhaeticus strain AF1, which was isolated from Kombucha tea and is capable of producing high levels of cellulose.

Draft genome sequence of Salmonella enterica subsp. enterica Serovar gallinarum biovar pullorum strain FCAV198, a Brazilian chicken pathogen

Salmonella enterica subsp. enterica serovar Gallinarum biovar Pullorum is a bird-restricted pathogen which causes pullorum disease. The strain FCAV198 was isolated from a pool of chicken ovaries in Brazil, and its genome may be helpful for studies involving molecular mechanisms related to pathogenesis and other related applications.

Draft genome sequence of shiga toxin-producing Escherichia coli Strain D92/09

Escherichia coli is suspected to be involved with Crohn's disease. Adherence and invasion to epithelial cells are properties commonly observed in these bacteria. Here, we present a draft genome sequence of E. coli D92/09, a multidrug-resistant strain, which besides showing these properties produces Shiga cytotoxin-1 and possibly other toxins.

Metagenomic assembly and draft genome sequence of an Uncharacterized prevotella sp. from Nelore rumen

Prevotella is one of the most abundant genera in bovine rumen, although no genome has yet been assembled by a metagenomics approach applied to Brazilian Nelore. We report the draft genome sequence of Prevotella sp., comprising 2,971,040 bp, obtained using the Illumina sequencing platform. This genome includes 127 contigs and presents a low 48% GC.

Analisys of thermal efficiency of a modified solar collector type evacuated tube

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Draft U.S. Pacific Marine Mammal Stock Assessments: 2009

Under the 1994 amendments to the Marine Mammal Protection Act (MMPA), the National Marine Fisheries Service (NMFS) and the U.S. Fish and Wildlife Service (USFWS) are required to publish Stock Assessment Reports for all stocks of marine mammals within U.S. waters, to review new information every year for strategic stocks and every three years for non-strategic stocks, and to update the stock assessment reports when significant new information becomes available. This report presents stock assessments for 13 Pacific marine mammal stocks under NMFS jurisdiction, including 8 “strategic” stocks and 5 “non-strategic” stocks (see summary table). A new stock assessment for humpback whales in American Samoa waters is included in the Pacific reports for the first time. New or revised abundance estimates are available for 9 stocks, including Eastern North Pacific blue whales, American Samoa humpback whales, five U.S. west coast harbor porpoise stocks, the Hawaiian monk seal, and southern resident killer whales. A change in the abundance estimate of Eastern North Pacific blue whales reflects a recommendation from the Pacific Scientific Review Group to utilize mark-recapture estimates for this population, which provide a better estimate of total population size than the average of recent line-transect and mark-recapture estimates. The ‘Northern Oregon/Washington Coast Stock’ harbor porpoise stock assessment includes a name change (‘Oregon’ is appended to ‘Northern Oregon’) to reflect recent stock boundary changes. Changes in abundance estimates for the two stocks of harbor porpoise that occur in Oregon waters are the result of these boundary changes, and do not reflect biological changes in the populations. Updated information on the three stocks of false killer whales in Hawaiian waters is also included in these reports. Information on the remaining 50 Pacific region stocks will be reprinted without revision in the final 2009 reports and currently appears in the 2008 reports (Carretta et al. 2009). Stock Assessments for Alaskan marine mammals are published by the National Marine Mammal Laboratory (NMML) in a separate report. Pacific region stock assessments include those studied by the Southwest Fisheries Science Center (SWFSC, La Jolla, California), the Pacific Islands Fisheries Science Center (PIFSC, Honolulu, Hawaii), the National Marine Mammal Laboratory (NMML, Seattle, Washington), and the Northwest Fisheries Science Center (NWFSC, Seattle, WA). Northwest Fisheries Science Center staff prepared the report on the Eastern North Pacific Southern Resident killer whale. National Marine Mammal Laboratory staff prepared the Northern Oregon/Washington coast harbor porpoise stock assessment. Pacific Islands Fisheries Science Center staff prepared the report on the Hawaiian monk seal. Southwest Fisheries Science Center staff prepared stock assessments for 9 stocks. The stock assessment for the American Samoa humpback whale was prepared by staff from the Center for Coastal Studies, Hawaiian Islands Humpback National Marine Sanctuary, the Smithsonian Institution, and the Southwest Fisheries Science Center. Draft versions of the stock assessment reports were reviewed by the Pacific Scientific Review Group at the November 2008, Maui meeting. The authors also wish to thank those who provided unpublished data, especially Robin Baird and Joseph Mobley, who provided valuable information on Hawaiian cetaceans. Any omissions or errors are the sole responsibility of the authors. This is a working document and individual stock assessment reports will be updated as new information on marine mammal stocks and fisheries becomes available. Background information and guidelines for preparing stock assessment reports are reviewed in Wade and Angliss (1997). The authors solicit any new information or comments which would improve future stock assessment reports. These Stock Assessment Reports summarize information from a wide range of sources and an extensive bibliography of all sources is given in each report. We strongly urge users of this document to refer to and cite original literature sources rather than citing this report or previous Stock Assessment Reports. If the original sources are not accessible, the citation should follow the format: [Original source], as cited in [this Stock Assessment Report citation].

Evolutionary Diversification of Banded Tube-Dwelling Anemones (Cnidaria; Ceriantharia; Isarachnanthus) in the Atlantic Ocean

The use of molecular data for species delimitation in Anthozoa is still a very delicate issue. This is probably due to the low genetic variation found among the molecular markers (primarily mitochondrial) commonly used for Anthozoa. Ceriantharia is an anthozoan group that has not been tested for genetic divergence at the species level. Recently, all three Atlantic species described for the genus Isarachnanthus of Atlantic Ocean, were deemed synonyms based on morphological simmilarities of only one species: Isarachnanthus maderensis. Here, we aimed to verify whether genetic relationships (using COI, 16S, ITS1 and ITS2 molecular markers) confirmed morphological affinities among members of Isarachnanthus from different regions across the Atlantic Ocean. Results from four DNA markers were completely congruent and revealed that two different species exist in the Atlantic Ocean. The low identification success and substantial overlap between intra and interspecific COI distances render the Anthozoa unsuitable for DNA barcoding, which is not true for Ceriantharia. In addition, genetic divergence within and between Ceriantharia species is more similar to that found in Medusozoa (Hydrozoa and Scyphozoa) than Anthozoa and Porifera that have divergence rates similar to typical metazoans. The two genetic species could also be separated based on micromorphological characteristics of their cnidomes. Using a specimen of Isarachnanthus bandanensis from Pacific Ocean as an outgroup, it was possible to estimate the minimum date of divergence between the clades. The cladogenesis event that formed the species of the Atlantic Ocean is estimated to have occured around 8.5 million years ago (Miocene) and several possible speciation scenarios are discussed.

SIS: a program to generate draft genome sequence scaffolds for prokaryotes

Background: Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results: We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of SIS, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that SIS has overall better performance. Conclusions: SIS is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of SIS in our tests adds evidence that large-scale inversions are widespread in prokaryotic genomes.

Human Fallopian Tube Mesenchymal Stromal Cells Enhance Bone Regeneration in a Xenotransplanted Model

We have recently reported that human fallopian tubes, which are discarded during surgical procedures of women submitted to sterilization or hysterectomies, are a rich source of human fallopian tube mesenchymal stromal cells (htMSCs). It has been previously shown that human mesenchymal stromal cells may be useful in enhancing the speed of bone regeneration. This prompted us to investigate whether htMSCs might be useful for the treatment of osteoporosis or other bone diseases, since they present a pronounced capacity for osteogenic differentiation in vitro. Based on this prior knowledge, our aim was to evaluate, in vivo, the osteogenic capacity of htMSCs to regenerate bone through an already described xenotransplantation model: nonimmunosuppressed (NIS) rats with cranial defects. htMSCs were obtained from five 30-50 years old healthy women and characterized by flow cytometry and for their multipotenciality in vitro capacity (osteogenic, chondrogenic and adipogenic differentiations). Two symmetric full-thickness cranial defects on each parietal region of seven NIS rats were performed. The left side (LS) of six animals was covered with CellCeram (Scaffdex)-a bioabsorbable ceramic composite scaffold that contains 60% hydroxyapatite and 40% beta-tricalciumphosphate-only, and the right side (RS) with the CellCeram and htMSCs (10(6) cells/scaffold). The animals were euthanized at 30, 60 and 90 days postoperatively and cranial tissue samples were taken for histological analysis. After 90 days we observed neobone formation in both sides. However, in animals euthanized 30 and 60 days after the procedure, a mature bone was observed only on the side with htMSCs. PCR and immunofluorescence analysis confirmed the presence of human DNA and thus that human cells were not rejected, which further supports the imunomodulatory property of htMSCs. In conclusion, htMSCs can be used successfully to enhance bone regeneration in vivo, opening a new field for future treatments of osteoporosis and bone reconstruction.

Automated analysis of lidocaine and its metabolite in plasma by in-tube solid-phase microextraction coupled with LC-UV for pharmacokinetic study

A sensitive, selective, and reproducible in-tube solid-phase microextraction and liquid chromatographic (in-tube SPME/LC-UV) method for determination of lidocaine and its metabolite monoethylglycinexylidide (MEGX) in human plasma has been developed, validated, and further applied to pharmacokinetic study in pregnant women with gestational diabetes mellitus (GDM) subjected to epidural anesthesia. Important factors in the optimization of in-tube SPME performance are discussed, including the draw/eject sample volume, draw/eject cycle number, draw/eject flow rate, sample pH, and influence of plasma proteins. The limits of quantification of the in-tube SPME/LC method were 50 ng/mL for both metabolite and lidocaine. The interday and intraday precision had coefficients of variation lower than 8%, and accuracy ranged from 95 to 117%. The response of the in-tube SPME/LC method for analytes was linear over a dynamic range from 50 to 5000 ng/mL, with correlation coefficients higher than 0.9976. The developed in-tube SPME/LC method was successfully used to analyze lidocaine and its metabolite in plasma samples from pregnant women with GDM subjected to epidural anesthesia for pharmacokinetic study.

Variability of physicochemical properties of an epoxy resin sealer taken from different parts of the same tube

Baldi JV, Bernardes RA, Duarte MAH, Ordinola-Zapata R, Cavenago BC, Moraes JCS, de Moraes IG. Variability of physicochemical properties of an epoxy resin sealer taken from different parts of the same tube. International Endodontic Journal,similar to 45, 915920, 2012. Abstract Aim To analyse several physicochemical properties of AH Plus (Dentsply DeTrey, Konstanz, Germany), including setting time, flow, radiopacity and the degree of conversion (DC); and to correlate the results with the source of the material: from the beginning, middle or end of the tubes in which they were supplied. Methodology Three experimental groups were established for each property investigated. Group 1 corresponded to material taken from the beginning of tubes A and B; Group 2 corresponded to material taken from the middle of each tube; and group 3 corresponded to that from the end of each tube. The setting time, flow and radiopacity were studied according to American National Standards Institute/American Dental Association (ANSI/ADA) Specification 57. DC was determined from infrared spectra, which were recorded at 1-h intervals for the first 6 h; then, at 2-h intervals for the next 14 h; then, at 24 and 30 h. Data were analysed statistically by analysis of variance (anova), TukeyKramer, KruskalWallis and Dunn tests, with a significance level of 5%. Results Group 1 had a significantly longer setting time (2303 +/- 1058 min) (P < 0.05). Group 3 had the lowest flowability (30.0 +/- 0.7 mm) and the highest radiopacity (14.85 +/- 1.8 mm Al) (P < 0.05). No differences were found for the DC test (P > 0.05). Conclusion The results suggest that segregation occurs between the organic and inorganic components of AH Plus sealer, thereby changing the setting time, flow and radiopacity.

Two-Phase Frictional Pressure Drop and Flow Boiling Heat Transfer for R245fa in a 2.32-mm Tube

Experimental two-phase frictional pressure drop and flow boiling heat transfer results are presented for a horizontal 2.32-mm ID stainless-steel tube using R245fa as working fluid. The frictional pressure drop data was obtained under adiabatic and diabatic conditions. Experiments were performed for mass velocities ranging from 100 to 700 kg m−2 s−1 , heat flux from 0 to 55 kW m−2 , exit saturation temperatures of 31 and 41◦C, and vapor qualities from 0.10 to 0.99. Pressures drop gradients and heat transfer coefficients ranging from 1 to 70 kPa m−1 and from 1 to 7 kW m−2 K−1 were measured. It was found that the heat transfer coefficient is a strong function of the heat flux, mass velocity, and vapor quality. Five frictional pressure drop predictive methods were compared against the experimental database. The Cioncolini et al. (2009) method was found to work the best. Six flow boiling heat transfer predictive methods were also compared against the present database. Liu and Winterton (1991), Zhang et al. (2004), and Saitoh et al. (2007) were ranked as the best methods. They predicted the experimental flow boiling heat transfer data with an average error around 19%.

A new Fenestrulina (Bryozoa, Cheilostomata) commensal with tube-dwelling anemones (Cnidaria, Ceriantharia) in the tropical southwestern Atlantic

A new species of cheilostome bryozoan, Fenestrulina commensalis n. sp., was collected in December 2008 by scuba at 5–10 meters depth at Guaibura Beach, Guarapari, Espírito Santo state, southeastern Brazil. The specimen was found associated with tubes of the cerianthid Pachycerianthus sp., representing the first commensal association between a bryozoan and a tube-dwelling anemone. Fenestrulina commensalis n. sp. is the third species of the genus found in Brazilian waters; it is distinguished from other Atlantic species of Fenestrulina by its small angular orificial condyles, a single oral spine and basal anchoring rhizoids arising from abfrontal pore chambers. Morphological adaptations to encrust the tubes of cerianthids include anchoring rootlets and weakly contiguous zooids. These morphological features allow the colony the flexibility to grow around the tube and feed relatively undisturbed by silt and detritus, being raised well above the softsediment substratum in which the tube-anemone grows.

Sphingosine kinase 1 is critically involved in nitric oxide-mediated human endothelial cell migration and tube formation

Sphingosine kinases (SKs) convert sphingosine to sphingosine 1-phosphate (S1P), which is a bioactive lipid that regulates a variety of cellular processes including proliferation, differentiation and migration.