Defining Sequence Space and Reaction Products within the Cyanuric Acid Hydrolase (AtzD)/Barbiturase Protein Family

Cyanuric acid hydrolases (AtzD) and barbiturases are homologous, found almost exclusively in bacteria, and comprise a rare protein family with no discernible linkage to other protein families or an X-ray structural class. There has been confusion in the literature and in genome projects regarding the reaction products, the assignment of individual sequences as either cyanuric acid hydrolases or barbiturases, and spurious connection of this family to another protein family. The present study has addressed those issues. First, the published enzyme reaction products of cyanuric acid hydrolase are incorrectly identified as biuret and carbon dioxide. The current study employed (13)C nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry to show that cyanuric acid hydrolase releases carboxybiuret, which spontaneously decarboxylates to biuret. This is significant because it revealed that homologous cyanuric acid hydrolases and barbiturases catalyze completely analogous reactions. Second, enzymes that had been annotated incorrectly in genome projects have been reassigned here by bioinformatics, gene cloning, and protein characterization studies. Third, the AtzD/barbiturase family has previously been suggested to consist of members of the amidohydrolase superfamily, a large class of metallohydrolases. Bioinformatics and the lack of bound metals both argue against a connection to the amidohydrolase superfamily. Lastly, steady-state kinetic measurements and observations of protein stability suggested that the AtzD/barbiturase family might be an undistinguished protein family that has undergone some resurgence with the recent introduction of industrial s-triazine compounds such as atrazine and melamine into the environment.     

Meteorological factors and ambient bacterial levels in a subtropical urban environment

We conducted a study to investigate the characteristics and determinants of ambient bacteria in Taipei, Taiwan from August 2004 to March 2005. We monitored ambient culturable bacteria in Shin-Jhuang City, an urban area in the Taipei metropolitan areas, using duplicate Burkard Portable Air Samplers with R2A agar. The average concentration of total bacteria was 1,986 colony-forming units per cubic meter of air (CFU/m³) (median?=?780 CFU/m³) over the study period, with the highest level in autumn. Most bacterial taxa had similar seasonal variation, with higher concentrations in autumn and winter. During the study period, Gram negative rods and cocci were predominant. Multivariate analyses indicated that wind speed and wind direction significantly influenced ambient bacterial distribution. Temperature and relative humidity were also important environmental factors positively associated with ambient bacterial concentrations. We observed statistically significant relationships between ambient bacteria and air pollutants, including sulfur dioxide (SO₂), ozone, particulate matter (aerodynamic diameter ≤10 μm (PM₁₀)), methane and total hydrocarbons. The concentrations of methane and total hydrocarbons during the previous day were positively associated with total bacteria and Gram negative rods, respectively. Ozone level on the previous day had a negative relationship with Gram negative cocci. SO₂ level with a 3-day lag was positively correlated with concentrations of both total bacteria and Gram negative cocci. In the future, more longitudinal studies are needed to confirm the relationships and possible mechanisms between ambient bacteria and meteorological factors, as well as to evaluate the ecological and health impacts of ambient bacteria.     

The effects of transported Asian dust on the composition and concentration of ambient fungi in Taiwan

This study was conducted to evaluate the effects of transported Asian dust and other environmental parameters on the levels and compositions of ambient fungi in the atmosphere of northern Taiwan. We monitored Asian dust events in Taipei County, Taiwan from January 2003 to June 2004. We used duplicate Burkard portable air samplers to collect ambient fungi before, during, and after dust events. Six transported Asian dust events were monitored during the study period. Elevated concentrations of Aspergillus (A. niger, specifically), Coelomycetes, Rhinocladiella, Sporothrix and Verticillium were noted (p < 0.05) during Asian dust periods. Botryosporium and Trichothecium were only recovered during dust event days. Multiple regression analysis showed that fungal levels were positively associated with temperature, wind speed, rainfall, non-methane hydrocarbons and particulates with aerodynamic diameters ≤10 μm (PM₁₀), and negatively correlated with relative humidity and ozone. Our results demonstrated that Asian dust events affected ambient fungal concentrations and compositions in northern Taiwan. Ambient fungi also had complex dynamics with air pollutants and meteorological factors. Future studies should explore the health impacts of ambient fungi during Asian dust events, adjusting for the synergistic/antagonistic effects of weather and air pollutants.     

Is the poleward expansion by Atlantic cod and haddock threatening native polar cod, <Emphasis Type="Italic">Boreogadus saida</Emphasis>?

During a recent period of increased influx of warm Atlantic water to the western coast of Svalbard, we have observed a northward expansion of boreal Atlantic cod (Gadus morhua) and haddock (Melanogrammus aeglefinus) into areas dominated by the native polar cod (Boreogadus saida). To determine the potential impact of new ecological interactions, we studied the diet of co-occurring juvenile gadoids in fjords, open water, and sea ice around Svalbard. We also reviewed the available literature on polar cod feeding in different habitats across the Arctic to determine whether region, habitat, or fish size may influence diet. Feeding by polar cod in the pelagic zone was size dependent, with small fish primarily consuming Calanus spp. and smaller copepods, with an increasing ration of Themisto spp. at larger sizes. In benthic habitats, diets were more varied and included considerably more unidentified material and sediment. Less than 40% dietary overlap was detected among the three species when they were found together. Stable isotope analyses indicated these patterns were representative of longer-term assimilation. The low interspecific dietary overlap suggests little direct competition. Future increases in abundance and the high predation potential of the boreal taxa, however, may impact the persistence of polar cod on some Arctic shelves.     

Split parturition observed in a captive North American brown bear (Ursus arctos)

Reproductive physiology in North American ursids is characterized by mating from spring to early summer, delayed implantation, and birth during hibernation. During spring 2008, a captive adult female brown bear was mated with two adult males. Pregnancy was determined by elevated progesterone concentrations during late fall before hibernation. Two male cubs were born on December 31, 2008, and a third female cub was born 17 days later on January 16. All were successfully raised and all were confirmed to have identical paternity. When normalized to age, cub growth rates did not differ. To our knowledge, this is the first documented case of markedly different birth dates in a single litter of brown bear cubs.     

The cartilage specific microRNA-140 targets histone deacetylase 4 in mouse cells

MicroRNAs (miRNA) are short RNA molecules regulating the expression of specific mRNAs. We investigated the expression pattern and potential targets of mouse miR-140 and found that miR-140 is specifically expressed in cartilage tissues of mouse embryos during both long and flat bone development. MiR-140 expression was detected in the limbs of E11.5 embryos in the primorida of future bones both in the fore and hindlimb and across autopod, zeugopod and stylopod. All digits of E14.5 fore- and hindlimbs showed accumulation of miR-140, except the first digit of the hindlimb. MiR-140 expression was also detected in the cartilagenous base of E17.5 skulls and in the sternum, the proximal rib heads and the developing vertebral column of E15.5 embryos. A potential target of miR-140, histone deacetylase 4, was validated experimentally and the possible role of miR-140 in long bone development is discussed.     

Resource requirements of four freshwater diatom taxa determined by in situ growth bioassays using natural populations from alpine lakes

We performed a series of in situ batch culture experiments to assess the resource requirements of common diatom taxa in alpine lakes of the central Rocky Mountains of North America. While physiological data are available on the resource requirements of some of these taxa, it is unclear whether intraspecific generalizations can be made across aquatic systems due to the potential development of ecotypes. In these experiments, we used amended lake water for a culture medium and natural diatom populations. Growth kinetics were determined for Asterionella formosa Hassall, Fragilaria crotonensis Kitton, Staurosirella pinnata (Ehr.) Williams and Round and Tetracyclus glans (Ehr.) Mills. Staurosirella pinnata, a historically abundant alpine diatom, had very low N and P requirements. Asterionella formosa and F. crotonensis, generally considered meso- or eutrophic species, exhibited low P requirements if N and Si were in moderate supply. Tetracyclus glans had the highest Si requirement. These experiments reveal that the recent changes in diatom community structure in these alpine lakes may be driven by changes in nutrient supply. We suggest that local diatom taxa and a natural culturing medium should be used to obtain more representative algal physiological data from a particular area.     

Discovery of N-{N-[(3-cyanobenzene) sulfonyl]-4(R)-(3,3-difluoropiperidin-1-yl)-(l)-prolyl}-4-[(3′,5′-dichloro-isonicotinoyl) amino]-(l)-phenylalanine (MK-0617), a highly potent and orally active VLA-4 antagonist

A series of prolyl-N-isonicotinoyl-(L)-4-aminophenylalanine derivatives substituted at the proline 4-position with cyclic amines was evaluated as VLA-4 antagonists. The ring size and presence or absence of fluorine affected potency and receptor occupancy. The analog with 3,3-difluoropiperidine at the proline 4-position (13) was the most potent compound and had very good duration of receptor occupancy in vitro. The ethyl ester prodrug of 13 demonstrated excellent receptor occupancy after oral dosing in rats.