G28.17+0.05: An unusual giant HI cloud in the inner Galaxy

New 21 cm HI observations have revealed a giant HI cloud in the Galactic plane that has unusual properties. It is quite well defined, about 150 pc in diameter at a distance of 5 kpc, and contains as much as 100,000 Solar Masses of atomic hydrogen. The outer parts of the cloud appear in HI emission above the HI background, while the central regions show HI self-absorption. Models which reproduce the observations have a core with a temperature <40 K and an outer envelope as much as an order of magnitude hotter. The cold core is elongated along the Galactic plane, whereas the overall outline of the cloud is approximately spherical. The warm and cold parts of the HI cloud have a similar, and relatively large, line width of approximately 7 km/s. The cloud core is a source of weak, anomalously-excited 1720 MHz OH emission, also with a relatively large line width, which delineates the region of HI self-absorption but is slightly blue-shifted in velocity. The intensity of the 1720 MHz OH emission is correlated with N(H) derived from models of the cold core. There is 12CO emission associated with the cloud core. Most of the cloud mass is in molecules, and the total mass is > 200,000 Solar Masses. In the cold core the HI mass fraction may be 10 percent. The cloud has only a few sites of current star formation. There may be about 100 more objects like this in the inner Galaxy; every line of sight through the Galactic plane within 50 degrees of the Galactic center probably intersects at least one. We suggest that G28.17+0.05 is a cloud being observed as it enters a spiral arm and that it is in the transition from the atomic to the molecular state.Comment: 35 pages, inludes 12 figure

Sequence Conservation and Functional Constraint on Intergenic Spacers in Reduced Genomes of the Obligate Symbiont Buchnera

Analyses of genome reduction in obligate bacterial symbionts typically focus on the removal and retention of protein-coding regions, which are subject to ongoing inactivation and deletion. However, these same forces operate on intergenic spacers (IGSs) and affect their contents, maintenance, and rates of evolution. IGSs comprise both non-coding, non-functional regions, including decaying pseudogenes at varying stages of recognizability, as well as functional elements, such as genes for sRNAs and regulatory control elements. The genomes of Buchnera and other small genome symbionts display biased nucleotide compositions and high rates of sequence evolution and contain few recognizable regulatory elements. However, IGS lengths are highly correlated across divergent Buchnera genomes, suggesting the presence of functional elements. To identify functional regions within the IGSs, we sequenced two Buchnera genomes (from aphid species Uroleucon ambrosiae and Acyrthosiphon kondoi) and applied a phylogenetic footprinting approach to alignments of orthologous IGSs from a total of eight Buchnera genomes corresponding to six aphid species. Inclusion of these new genomes allowed comparative analyses at intermediate levels of divergence, enabling the detection of both conserved elements and previously unrecognized pseudogenes. Analyses of these genomes revealed that 232 of 336 IGS alignments over 50 nucleotides in length displayed substantial sequence conservation. Conserved alignment blocks within these IGSs encompassed 88 Shine-Dalgarno sequences, 55 transcriptional terminators, 5 Sigma-32 binding sites, and 12 novel small RNAs. Although pseudogene formation, and thus IGS formation, are ongoing processes in these genomes, a large proportion of intergenic spacers contain functional sequences

Antibacterial activity of traditional medicinal plants used by Haudenosaunee peoples of New York State

<p>Abstract</p> <p>Background</p> <p>The evolution and spread of antibiotic resistance, as well as the evolution of new strains of disease causing agents, is of great concern to the global health community. Our ability to effectively treat disease is dependent on the development of new pharmaceuticals, and one potential source of novel drugs is traditional medicine. This study explores the antibacterial properties of plants used in Haudenosaunee traditional medicine. We tested the hypothesis that extracts from Haudenosaunee medicinal plants used to treat symptoms often caused by bacterial infection would show antibacterial properties in laboratory assays, and that these extracts would be more effective against moderately virulent bacteria than less virulent bacteria.</p> <p>Methods</p> <p>After identification and harvesting, a total of 57 different aqueous extractions were made from 15 plant species. Nine plant species were used in Haudenosaunee medicines and six plant species, of which three are native to the region and three are introduced, were not used in traditional medicine. Antibacterial activity against mostly avirulent (<it>Escherichia coli, Streptococcus lactis</it>) and moderately virulent (<it>Salmonella typhimurium, Staphylococcus aureus</it>) microbes was inferred through replicate disc diffusion assays; and observed and statistically predicted MIC values were determined through replicate serial dilution assays.</p> <p>Results</p> <p>Although there was not complete concordance between the traditional use of Haudenosaunee medicinal plants and antibacterial activity, our data support the hypothesis that the selection and use of these plants to treat disease was not random. In particular, four plant species exhibited antimicrobial properties as expected (<it>Achillea millefolium, Ipomoea pandurata, Hieracium pilosella</it>, and <it>Solidago canadensis</it>), with particularly strong effectiveness against <it>S. typhimurium</it>. In addition, extractions from two of the introduced species (<it>Hesperis matronalis </it>and <it>Rosa multiflora</it>) were effective against this pathogen.</p> <p>Conclusions</p> <p>Our data suggest that further screening of plants used in traditional Haudenosaunee medicine is warranted, and we put forward several species for further investigation of activity against <it>S. typhimurium </it>(<it>A. millefolium, H. matronalis, I. pandurata, H. pilosella, R. multiflora, S. canadensis</it>).</p

The Eagle Nebula's fingers - pointers to the earliest stages of star formation?

Molecular line, millimetre/submillimetre continuum, and mid-IR observations are reported of the opaque fingers which cross the Eagle Nebula. The fingers are surprisingly warm when viewed in the CO J= 3-2 lines, with kinetic temperatures approaching 60 K, although the lines are relatively narrow. Most of the mass in the fingers is concentrated in cores which lie at the tips of the fingers, and contain from ~ 10 to 60 M⊙, representing 55-80% of the mass of the individual fingers. The integrated mass contained in the three fingers and the nearby extended material is ~ 200 M⊙. The velocity fields of the gas are complex and the material is very clumpy. The best evidence for coherent velocity structure is seen running along the central finger, which has a velocity gradient ~ 1.7 km s-1 pc-1 . The fingers contain several embedded submm continuum cores, with the most intense located at the tips of the fingers. The continuum spectra of these cores shows that they are much cooler, Tdust ~ 20 K, than Tgas ~ 60 K of their respective fingers. A simple thermal and chemical model of a finger was developed to study the physical environment, which takes into account the external UV illumination ( ~ 1700 G0), and the chemical and thermal structure of a finger. The model predictions are consistent with all of the available observations. The fingers appear to have been formed after primordial dense clumps in the original cloud were irradiated by the light of its OB stars. These clumps then shielded material lying behind from the photoevaporative dispersal of the cloud, and facilitated the formation of the finger structures. The cores in the tips of the fingers appear to be at a very early stage of pre-protostellar development: there are no embedded infrared sources or molecular outflows present. The pressure inside the cores is just less than that of the surrounding gas, allowing them to be compressed by the external pressure. The cores are probably just starting the final stages of collapse, which will lead to the formation of a condensed, warm object. It is well known that such characteristics are expected from the earliest stages of objects popularly known as `protostars'. The cores in the tips of the Eagle Nebula's fingers have characteristics similar to those expected to occur in the earliest stages of protostellar formation.</i

A new scheme of radiation transfer in H II regions including transient heating of grains

A new scheme of radiation transfer for understanding infrared spectra of H II regions, has been developed. This scheme considers non-equilibrium processes (e. g. transient heating of the very small grains, VSG; and the polycyclic aromatic hydrocarbon, PAH) also, in addition to the equilibrium thermal emission from normal dust grains (BG). The spherically symmetric interstellar dust cloud is segmented into a large number of "onion skin" shells in order to implement the non-equilibrium processes. The scheme attempts to fit the observed SED originating from the dust component, by exploring the following parameters : (i) geometrical details of the dust cloud, (ii) PAH size and abundance, (iii) composition of normal grains (BG), (iv) radial distribution of all dust (BG, VSG & PAH). The scheme has been applied to a set of five compact H II regions (IRAS 18116- 1646, 18162-2048, 19442+2427, 22308+5812 & 18434-0242) whose spectra are available with adequate spectral resolution. The best fit models and inferences about the parameters for these sources are presented.Comment: 16 pages total including 3 tables and 2 figure

The Metallicity-Luminosity Relation, Effective Yields, and Metal Loss in Spiral and Irregular Galaxies

I present results on the correlation between galaxy mass, luminosity, and metallicity for a sample of spiral and irregular galaxies having well-measured abundance profiles, distances, and rotation speeds. Additional data for low surface brightness galaxies from the literature are also included for comparison. These data are combined to study the metallicity-luminosity and metallicity-rotation speed correlations for spiral and irregular galaxies. The metallicity luminosity correlation shows its familiar form for these galaxies, a roughly uniform change in the average present-day O/H abundance of about a factor 100 over 11 magnitudes in B luminosity. However, the O/H - V(rot) relation shows a change in slope at a rotation speed of about 125 km/sec. At faster V(rot), there appears to be no relation between average metallicity and rotation speed. At lower V(rot), the metallicity correlates with rotation speed. This change in behavior could be the result of increasing loss of metals from the smaller galaxies in supernova-driven winds. This idea is tested by looking at the variation in effective yield, derived from observed abundances and gas fractions assuming closed box chemical evolution. The effective yields derived for spiral and irregular galaxies increase by a factor of 10-20 from V(rot) approximately 5 km/sec to V(rot) approximately 300 km/sec, asympotically increasing to approximately constant y(eff) for V(rot) > 150 km/sec. The trend suggests that galaxies with V(rot) < 100-150 km/sec may lose a large fraction of their SN ejecta, while galaxies above this value tend to retain metals.Comment: 40 pages total, including 7 encapsulated postscript figures. Accepted for publication in 20 Dec 2002 Ap

Discovery of very high energy gamma rays from PKS 1424+240 and multiwavelength constraints on its redshift

We report the first detection of very-high-energy (VHE) gamma-ray emission above 140 GeV from PKS 1424+240, a BL Lac object with an unknown redshift. The photon spectrum above 140 GeV measured by VERITAS is well described by a power law with a photon index of 3.8 +- 0.5_stat +- 0.3_syst and a flux normalization at 200 GeV of (5.1 +- 0.9_stat +- 0.5_syst) x 10^{-11} TeV^-1 cm^-2 s^-1, where stat and syst denote the statistical and systematical uncertainty, respectively. The VHE flux is steady over the observation period between MJD 54881 and 55003 (2009 February 19 to June 21). Flux variability is also not observed in contemporaneous high energy observations with the Fermi Large Area Telescope (LAT). Contemporaneous X-ray and optical data were also obtained from the Swift XRT and MDM observatory, respectively. The broadband spectral energy distribution (SED) is well described by a one-zone synchrotron self-Compton (SSC) model favoring a redshift of less than 0.1. Using the photon index measured with Fermi in combination with recent extragalactic background light (EBL) absorption models it can be concluded from the VERITAS data that the redshift of PKS 1424+240 is less than 0.66.Comment: accepted for publication, Ap

Systematic discovery of unannotated genes in 11 yeast species using a database of orthologous genomic segments

<p>Abstract</p> <p>Background</p> <p>In standard BLAST searches, no information other than the sequences of the query and the database entries is considered. However, in situations where two genes from different species have only borderline similarity in a BLAST search, the discovery that the genes are located within a region of conserved gene order (synteny) can provide additional evidence that they are orthologs. Thus, for interpreting borderline search results, it would be useful to know whether the syntenic context of a database hit is similar to that of the query. This principle has often been used in investigations of particular genes or genomic regions, but to our knowledge it has never been implemented systematically.</p> <p>Results</p> <p>We made use of the synteny information contained in the Yeast Gene Order Browser database for 11 yeast species to carry out a systematic search for protein-coding genes that were overlooked in the original annotations of one or more yeast genomes but which are syntenic with their orthologs. Such genes tend to have been overlooked because they are short, highly divergent, or contain introns. The key features of our software - called SearchDOGS - are that the database entries are classified into sets of genomic segments that are already known to be orthologous, and that very weak BLAST hits are retained for further analysis if their genomic location is similar to that of the query. Using SearchDOGS we identified 595 additional protein-coding genes among the 11 yeast species, including two new genes in <it>Saccharomyces cerevisiae</it>. We found additional genes for the mating pheromone a-factor in six species including <it>Kluyveromyces lactis</it>.</p> <p>Conclusions</p> <p>SearchDOGS has proven highly successful for identifying overlooked genes in the yeast genomes. We anticipate that our approach can be adapted for study of further groups of species, such as bacterial genomes. More generally, the concept of doing sequence similarity searches against databases to which external information has been added may prove useful in other settings.</p

The Cryo-EM Structure of a Complete 30S Translation Initiation Complex from Escherichia coli

Formation of the 30S initiation complex (30S IC) is an important checkpoint in regulation of gene expression. The selection of mRNA, correct start codon, and the initiator fMet-tRNAfMet requires the presence of three initiation factors (IF1, IF2, IF3) of which IF3 and IF1 control the fidelity of the process, while IF2 recruits fMet-tRNAfMet. Here we present a cryo-EM reconstruction of the complete 30S IC, containing mRNA, fMet-tRNAfMet, IF1, IF2, and IF3. In the 30S IC, IF2 contacts IF1, the 30S subunit shoulder, and the CCA end of fMet-tRNAfMet, which occupies a novel P/I position (P/I1). The N-terminal domain of IF3 contacts the tRNA, whereas the C-terminal domain is bound to the platform of the 30S subunit. Binding of initiation factors and fMet-tRNAfMet induces a rotation of the head relative to the body of the 30S subunit, which is likely to prevail through 50S subunit joining until GTP hydrolysis and dissociation of IF2 take place. The structure provides insights into the mechanism of mRNA selection during translation initiation

Structural Diversity in Bacterial Ribosomes: Mycobacterial 70S Ribosome Structure Reveals Novel Features

Here we present analysis of a 3D cryo-EM map of the 70S ribosome from Mycobacterium smegmatis, a saprophytic cousin of the etiological agent of tuberculosis in humans, Mycobacterium tuberculosis. In comparison with the 3D structures of other prokaryotic ribosomes, the density map of the M. smegmatis 70S ribosome reveals unique structural features and their relative orientations in the ribosome. Dramatic changes in the periphery due to additional rRNA segments and extra domains of some of the peripheral ribosomal proteins like S3, S5, S16, L17, L25, are evident. One of the most notable features appears in the large subunit near L1 stalk as a long helical structure next to helix 54 of the 23S rRNA. The sharp upper end of this structure is located in the vicinity of the mRNA exit channel. Although the M. smegmatis 70S ribosome possesses conserved core structure of bacterial ribosome, the new structural features, unveiled in this study, demonstrates diversity in the 3D architecture of bacterial ribosomes. We postulate that the prominent helical structure related to the 23S rRNA actively participates in the mechanisms of translation in mycobacteria