A first genome assembly of the barley fungal pathogen Pyrenophora teres f. teres

Background: Pyrenophora teres f. teres is a necrotrophic fungal pathogen and the cause of one of barley’s most important diseases, net form of net blotch. Here we report the first genome assembly for this species based solely on short Solexa sequencing reads of isolate 0-1. The assembly was validated by comparison to BAC sequences, ESTs, orthologous genes and by PCR, and complemented by cytogenetic karyotyping and the first genome-wide genetic map for P. teres f. teres. Results: The total assembly was 41.95 Mbp and contains 11,799 gene models of 50 amino acids or more. Comparison against two sequenced BACs showed that complex regions with a high GC content assembled effectively. Electrophoretic karyotyping showed distinct chromosomal polymorphisms between isolates 0-1 and 15A, and cytological karyotyping confirmed the presence of at least nine chromosomes. The genetic map spans 2477.7 cM and is composed of 243 markers in 25 linkage groups, and incorporates SSR markers developed from the assembly. Among predicted genes, non-ribosomal peptide synthetases and efflux pumps in particular appear to have undergone a P. teres f. teres-specific expansion of non-orthologous gene families. Conclusions: This study demonstrates that paired-end Solexa sequencing can successfully capture coding regions of a filamentous fungal genome. The assembly contains a plethora of predicted genes that have been implicated in a necrotrophic lifestyle and pathogenicity and presents a significant resource for examining the bases for P. teres f. teres pathogenicity

The Green Bank Ammonia Survey (GAS): First Results of NH3 mapping the Gould Belt

We present an overview of the first data release (DR1) and first-look science from the Green Bank Ammonia Survey (GAS). GAS is a Large Program at the Green Bank Telescope to map all Gould Belt star-forming regions with $A_V \gtrsim 7$ mag visible from the northern hemisphere in emission from NH$_3$ and other key molecular tracers. This first release includes the data for four regions in Gould Belt clouds: B18 in Taurus, NGC 1333 in Perseus, L1688 in Ophiuchus, and Orion A North in Orion. We compare the NH$_3$ emission to dust continuum emission from Herschel, and find that the two tracers correspond closely. NH$_3$ is present in over 60\% of lines-of-sight with $A_V \gtrsim 7$ mag in three of the four DR1 regions, in agreement with expectations from previous observations. The sole exception is B18, where NH$_3$ is detected toward ~ 40\% of lines-of-sight with $A_V \gtrsim 7$ mag. Moreover, we find that the NH$_3$ emission is generally extended beyond the typical 0.1 pc length scales of dense cores. We produce maps of the gas kinematics, temperature, and NH$_3$ column densities through forward modeling of the hyperfine structure of the NH$_3$ (1,1) and (2,2) lines. We show that the NH$_3$ velocity dispersion, ${\sigma}_v$, and gas kinetic temperature, $T_K$, vary systematically between the regions included in this release, with an increase in both the mean value and spread of ${\sigma}_v$ and $T_K$ with increasing star formation activity. The data presented in this paper are publicly available.Comment: 33 pages, 27 figures, accepted to ApJS. Datasets are publicly available: https://dataverse.harvard.edu/dataverse/GAS_DR

Droplets I: Pressure-Dominated Sub-0.1 pc Coherent Structures in L1688 and B18

We present the observation and analysis of newly discovered coherent structures in the L1688 region of Ophiuchus and the B18 region of Taurus. Using data from the Green Bank Ammonia Survey (GAS), we identify regions of high density and near-constant, almost-thermal, velocity dispersion. Eighteen coherent structures are revealed, twelve in L1688 and six in B18, each of which shows a sharp "transition to coherence" in velocity dispersion around its periphery. The identification of these structures provides a chance to study the coherent structures in molecular clouds statistically. The identified coherent structures have a typical radius of 0.04 pc and a typical mass of 0.4 Msun, generally smaller than previously known coherent cores identified by Goodman et al. (1998), Caselli et al. (2002), and Pineda et al. (2010). We call these structures "droplets." We find that unlike previously known coherent cores, these structures are not virially bound by self-gravity and are instead predominantly confined by ambient pressure. The droplets have density profiles shallower than a critical Bonnor-Ebert sphere, and they have a velocity (VLSR) distribution consistent with the dense gas motions traced by NH3 emission. These results point to a potential formation mechanism through pressure compression and turbulent processes in the dense gas. We present a comparison with a magnetohydrodynamic simulation of a star-forming region, and we speculate on the relationship of droplets with larger, gravitationally bound coherent cores, as well as on the role that droplets and other coherent structures play in the star formation process.Comment: Accepted by ApJ in April, 201

Ataluren stimulates ribosomal selection of near-cognate tRNAs to promote nonsense suppression

A premature termination codon (PTC) in the ORF of an mRNA generally leads to production of a truncated polypeptide, accelerated degradation of the mRNA, and depression of overall mRNA expression. Accordingly, nonsense mutations cause some of the most severe forms of inherited disorders. The small-molecule drug ataluren promotes therapeutic nonsense suppression and has been thought to mediate the insertion of near-cognate tRNAs at PTCs. However, direct evidence for this activity has been lacking. Here, we expressed multiple nonsense mutation reporters in human cells and yeast and identified the amino acids inserted when a PTC occupies the ribosomal A site in control, ataluren-treated, and aminoglycoside-treated cells. We find that ataluren\u27s likely target is the ribosome and that it produces full-length protein by promoting insertion of near-cognate tRNAs at the site of the nonsense codon without apparent effects on transcription, mRNA processing, mRNA stability, or protein stability. The resulting readthrough proteins retain function and contain amino acid replacements similar to those derived from endogenous readthrough, namely Gln, Lys, or Tyr at UAA or UAG PTCs and Trp, Arg, or Cys at UGA PTCs. These insertion biases arise primarily from mRNA:tRNA mispairing at codon positions 1 and 3 and reflect, in part, the preferred use of certain nonstandard base pairs, e.g., U-G. Ataluren\u27s retention of similar specificity of near-cognate tRNA insertion as occurs endogenously has important implications for its general use in therapeutic nonsense suppression

The Green Bank Ammonia Survey: A Virial Analysis of Gould Belt Clouds in Data Release 1

We perform a virial analysis of starless dense cores in three nearby star-forming regions : L1688 in Ophiuchus, NGC 1333 in Perseus, and B18 in Taurus. Our analysis takes advantage of comprehensive kinematic information for the dense gas in all of these regions made publicly available through the Green Bank Ammonia Survey Data Release 1, which used to estimate internal support against collapse. We combine this information with ancillary data used to estimate other important properties of the cores, including continuum data from the James Clerk Maxwell Telescope Gould Belt Survey for core identification, core masses, and core sizes. Additionally, we used \textit{Planck} and \textit{Herschel}-based column density maps for external cloud weight pressure, and Five College Radio Astronomy Observatory $^{13}$CO observations for external turbulent pressure. Our self-consistent analysis suggests that many dense cores in all three star-forming regions are not bound by gravity alone, but rather require additional pressure confinement to remain bound. Unlike a recent, similar study in Orion~A, we find that turbulent pressure represents a significant portion of the external pressure budget. Our broad conclusion emphasizing the importance of pressure confinement in dense core evolution, however, agrees with earlier work.Comment: 35 pages, 8 tables, and 14 figures consisting of 16 .pdf files. Accepted for publication in the Astrophysical Journa

Ubiquitous NH3\rm NH_3 supersonic component in L1688 coherent cores

Context : Star formation takes place in cold dense cores in molecular clouds. Earlier observations have found that dense cores exhibit subsonic non-thermal velocity dispersions. In contrast, CO observations show that the ambient large-scale cloud is warmer and has supersonic velocity dispersions. Aims : We aim to study the ammonia ($\rm NH_3$) molecular line profiles with exquisite sensitivity towards the coherent cores in L1688 in order to study their kinematical properties in unprecedented detail. Methods : We used $\rm NH_3$ (1,1) and (2,2) data from the first data release (DR1) in the Green Bank Ammonia Survey (GAS). We first smoothed the data to a larger beam of 1' to obtain substantially more extended maps of velocity dispersion and kinetic temperature, compared to the DR1 maps. We then identified the coherent cores in the cloud and analysed the averaged line profiles towards the cores. Results : For the first time, we detected a faint (mean $\rm NH_3$(1,1) peak brightness $<$0.25 K in $T_{MB}$), supersonic component towards all the coherent cores in L1688. We fitted two components, one broad and one narrow, and derived the kinetic temperature and velocity dispersion of each component. The broad components towards all cores have supersonic linewidths ($\mathcal{M}_S \ge 1$). This component biases the estimate of the narrow dense core component's velocity dispersion by $\approx$28% and the kinetic temperature by $\approx$10%, on average, as compared to the results from single-component fits. Conclusions : Neglecting this ubiquitous presence of a broad component towards all coherent cores causes the typical single-component fit to overestimate the temperature and velocity dispersion. This affects the derived detailed physical structure and stability of the cores estimated from $\rm NH_3$ observations.Comment: Accepted for publication in Astronomy & Astrophysics on 06/07/2020. 15 pages, 16 figures, 1 table. Language edits from previous versio

The James Clerk Maxwell telescope Legacy Survey of the Gould Belt: a molecular line study of the Ophiuchus molecular cloud

CO, 13CO, and C18O J = 3-2 observations are presented of the Ophiuchus molecular cloud. The 13CO and C18O emission is dominated by the Oph A clump, and the Oph B1, B2, C, E, F, and J regions. The optically thin(ner) C18O line is used as a column density tracer, from which the gravitational binding energy is estimated to be 4.5 × 1039 J (2282 M⊙ km2 s-2). The turbulent kinetic energy is 6.3 × 1038 J (320 M⊙ km2 s-2), or seven times less than this, and therefore the Oph cloud as a whole is gravitationally bound. 30 protostars were searched for high-velocity gas, with 8 showing outflows, and 20 more having evidence of high-velocity gas along their lines of sight. The total outflow kinetic energy is 1.3 × 1038 J (67 M⊙ km2 s-2), corresponding to 21 per cent of the cloud's turbulent kinetic energy. Although turbulent injection by outflows is significant, but does not appear to be the dominant source of turbulence in the cloud. 105 dense molecular clumplets were identified, which had radii ˜0.01-0.05 pc, virial masses ˜0.1-12 M⊙, luminosities ˜0.001-0.1 K km s-1 pc-2, and excitation temperatures ˜10-50 K. These are consistent with the standard Giant Molecular Cloud (GMC) based size-linewidth relationships, showing that the scaling laws extend down to size scales of hundredths of a parsec, and to subsolar-mass condensations. There is however no compelling evidence that the majority of clumplets are undergoing free-fall collapse, nor that they are pressure confined

Better than DEET Repellent Compounds Derived from Coconut Oil

Hematophagous arthropods are capable of transmitting human and animal pathogens worldwide. Vector-borne diseases account for 17% of all infectious diseases resulting in 700,000 human deaths annually. Repellents are a primary tool for reducing the impact of biting arthropods on humans and animals. N,N-Diethyl-meta-toluamide (DEET), the most effective and long-lasting repellent currently available commercially, has long been considered the gold standard in insect repellents, but with reported human health issues, particularly for infants and pregnant women. In the present study, we report fatty acids derived from coconut oil which are novel, inexpensive and highly efficacious repellant compounds. These coconut fatty acids are active against a broad array of blood-sucking arthropods including biting flies, ticks, bed bugs and mosquitoes. The medium-chain length fatty acids from C8:0 to C12:0 were found to exhibit the predominant repellent activity. In laboratory bioassays, these fatty acids repelled biting flies and bed bugs for two weeks after application, and ticks for one week. Repellency was stronger and with longer residual activity than that of DEET. In addition, repellency was also found against mosquitoes. An aqueous starch-based formulation containing natural coconut fatty acids was also prepared and shown to protect pastured cattle from biting flies up to 96-hours in the hot summer, which, to our knowledge, is the longest protection provided by a natural repellent product studied to date

Human Rights and the War on Terror: Complete 2005 - 2007 Topical Research Digest

“9/11 changed everything.” Not really. In fact, there has been far more continuity than change over the past six years in both international and domestic politics. Nonetheless, human rights often have been harmed—although not by terrorism but by “the war on terror.