Two Yeast Plasmids that Confer Nourseothricin-Dihydrogen Sulfate and Hygromycin B Resistance in Neurospora crassa and Cryphonectria parasitica

Two plasmids that were previously used with yeast, pRS41N and pRS41H, were found to confer clonNAT and hygromycin B resistance, respectively, in the filamentous fungi Neurospora crassa and Cryphonectria parasitica. These plasmids are suitable for routine cloning and for use in forcing heterokaryons and are available through the FGSC

Exploring root rot pathogens in wheat-pea rotations in Kansas

In 2018, over 277,000 bushels of wheat were produced on 7.7 million acres of land in Kansas alone. Based on the price of wheat by the end of 2018, this accounted for $1.44 million. This wheat is normally rotated with soybeans or fallow, but recent interest has arisen regarding the growth of peas in northern Kansas. As of 2019, there are both research and commercial growing operations underway. Many plant diseases have been especially prevalent during the summer because of the high rainfall and heat. In order to assess the severity of pea disease in Kansas, as well as explore potential interconnectivity between wheat and pea pathogens, a survey was conducted, and efforts were made to isolate and culture fungal pathogens of both wheat and pea

Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics

Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. 
Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.
Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
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The Remarkable Be Star HD110432

HD110432 has gained considerable attention because it is a hard, variable X-ray source similar to gamma Cas. From time-serial echelle data obtained over two weeks during 2005 January and February, we find several remarkable characteristics in the star's optical spectrum. The line profiles show rapid variations on some nights which can be most likely be attributed to irregularly occurring and short-lived migrating subfeatures. Such features have only been observed to date in gamma Cas and AB Dor, two stars for which it is believed magnetic fields force circumstellar clouds to corotate over the stellar surface. The star's optical spectrum also exhibits a number of mainly FeII and HeI emission features with profiles typical of an optically thin disk viewed edge-on. Using spectral synthesis techniques, we find that its temperature is 9800K +/-300K, that its projected area is a remarkably large 100 stellar areas, and its emitting volume resides at a distance of 1 AU from the star. We also find that the star's absorption profiles extend to +/-1000 km/s, a fact which we cannot explain. Otherwise, HD110432 and gamma Cas share similarly peculiar X-ray and optical characteristics such as high X-ray temperature, erratic X-ray variability on timescales of a few hours, optical emission lines, and submigrating features in optical line profiles. Because of these similarities, we suggest that this star is a new member of a select class of "gamma Cas analogs."Comment: 31 pages, 9 figures, accepted by ApJ (3/20/06

Genome Sequence of the Chestnut Blight Fungus Cryphonectria parasitica EP155: A Fundamental Resource for an Archetypical Invasive Plant Pathogen.

Cryphonectria parasitica is the causal agent of chestnut blight, a fungal disease that almost entirely eliminated mature American chestnut from North America over a 50-year period. Here, we formally report the genome of C. parasitica EP155 using a Sanger shotgun sequencing approach. After finishing and integration with simple-sequence repeat markers, the assembly was 43.8 Mb in 26 scaffolds (L50 = 5; N50 = 4.0Mb). Eight chromosomes are predicted: five scaffolds have two telomeres and six scaffolds have one telomere sequence. In total, 11,609 gene models were predicted, of which 85% show similarities to other proteins. This genome resource has already increased the utility of a fundamental plant pathogen experimental system through new understanding of the fungal vegetative incompatibility system, with significant implications for enhancing mycovirus-based biological control

High Resolution Chandra Spectroscopy of Gamma Cassiopeia (B0.5IVe)

gamma Cas has long been famous for its unique hard X-ray characteristics. We report herein on a 53 ks Chandra HETGS observation of this target. An inspection of our spectrum shows that it is quite atypical for a massive star, with abnormally weak Fe XXV, XXVI lines, Ly-alpha lines of H-like species from Fe XVII, XXIII, XXIV, S XVI, Si XIV, Mg XII, Ne X, O VII, VIII, and N VII. Also, line ratios of the rif-triplet of for a few He-like ions XVII are consistent with the dominance of collisional atomic processes. Yet, the presence of Fe and Si fluorescence K features indicates that photoionization also occurs in nearby cold gas. The line profiles indicate a mean velocity at rest and a broadening of 500 km/s. A global fitting analysis of the line and continuum spectrum finds that there are 3-4 plasma emission components. The dominant hot (12 keV) component and has a Fe abundance of 0.22 solar. Some fraction of this component (10-30%) is heavily absorbed. The other 2-3 components, with temperatures 0.1, 0.4, 3 keV, are "warm," have a nearly solar composition, a lower column absorption, and are responsible for most other emission lines. The strength of the fluorescence features and the dual-column absorption model for the hot plasma component suggest the presence near the hot sites of a cold gas structure with a column density of 10^23 cm^-2. Since this value is consistent with theoretical estimates of the vertical disk column of this star, these attributes suggest that the X-rays originate near the star or disk. It is possible that the Fe anomaly in the hot component is related to the First Ionization Potential effect found in coronal structures around active cool stars. This would be yet another indication that the X-rays -rays are produced in the immediate vicinity of the Be star.Comment: 32 pages, 4 figures (Fig. 3 colorized.) To be published in 01/10/04 Astrophysical Journal, Main Journal; included figures and updated formattin

PCR-based markers for genetic mapping in Neurospora crassa.

Eighteen PCR-based markers are described for use in mapping mutations in Oak Ridge background strains of Neurospora crassa. These markers are located on each of the seven linkage groups and in the mitochondrial genome to enable course-scale linkage mapping. Following mapping to a linkage group, additional markers can be developed in the co-segregating region for fine-scale mapping of mutations. As with the N. crassa RFLP map (Metzenberg and Grotelueschen, 1993; Nelson and Perkins, 2000), the addition of PCR-based markers by members of the Neurospora community will enhance this marker set for mapping purposes

Remnant Fermi surface in the presence of an underlying instability in layered 1T-TaS_2

We report high resolution angle-scanned photoemission and Fermi surface (FS) mapping experiments on the layered transition-metal dichalcogenide 1T-TaS_2 in the quasi commensurate (QC) and the commensurate (C) charge-density-wave (CDW) phase. Instead of a nesting induced partially removed FS in the CDW phase we find a pseudogap over large portions of the FS. This remnant FS exhibits the symmetry of the one-particle normal state FS even when passing from the QC-phase to the C-phase. Possibly, this Mott localization induced transition represents the underlying instability responsible for the pseudogapped FS

The Democratic Biopolitics of PrEP

PrEP (Pre-Exposure Prophylaxis) is a relatively new drug-based HIV prevention technique and an important means to lower the HIV risk of gay men who are especially vulnerable to HIV. From the perspective of biopolitics, PrEP inscribes itself in a larger trend of medicalization and the rise of pharmapower. This article reconstructs and evaluates contemporary literature on biopolitical theory as it applies to PrEP, by bringing it in a dialogue with a mapping of the political debate on PrEP. As PrEP changes sexual norms and subjectification, for example condom use and its meaning for gay subjectivity, it is highly contested. The article shows that the debate on PrEP can be best described with the concepts ‘sexual-somatic ethics’ and ‘democratic biopolitics’, which I develop based on the biopolitical approach of Nikolas Rose and Paul Rabinow. In contrast, interpretations of PrEP which are following governmentality studies or Italian Theory amount to either farfetched or trivial positions on PrEP, when seen in light of the political debate. Furthermore, the article is a contribution to the scholarship on gay subjectivity, highlighting how homophobia and homonormativity haunts gay sex even in liberal environments, and how PrEP can serve as an entry point for the destigmatization of gay sexuality and transformation of gay subjectivity. ‘Biopolitical democratization’ entails making explicit how medical technology and health care relates to sexual subjectification and ethics, to strengthen the voice of (potential) PrEP users in health politics, and to renegotiate the profit and power of Big Pharma