Distinct amino acid compositional requirements for formation and maintenance of the [PSI+] prion in yeast

Multiple yeast prions have been identified that result from the structural conversion of proteins into a self-propagating amyloid form. Amyloid-based prion activity in yeast requires a series of discrete steps. First, the prion protein must form an amyloid nucleus that can recruit and structurally convert additional soluble proteins. Subsequently, maintenance of the prion during cell division requires fragmentation of these aggregates to create new heritable propagons. For the Saccharomyces cerevisiae prion protein Sup35, these different activities are encoded by different regions of the Sup35 prion domain. An N-terminal glutamine/asparagine-rich nucleation domain is required for nucleation and fiber growth, while an adjacent oligopeptide repeat domain is largely dispensable for prion nucleation and fiber growth but is required for chaperone-dependent prion maintenance. Although prion activity of glutamine/asparagine-rich proteins is predominantly determined by amino acid composition, the nucleation and oligopeptide repeat domains of Sup35 have distinct compositional requirements. Here, we quantitatively define these compositional requirements in vivo. We show that aromatic residues strongly promote both prion formation and chaperone-dependent prion maintenance. In contrast, nonaromatic hydrophobic residues strongly promote prion formation but inhibit prion propagation. These results provide insight into why some aggregation-prone proteins are unable to propagate as prions

Effects of Ultraviolet Light and Pheromone Release Rate in Trapping Coconut Rhinoceros Beetles, Oryctes rhinoceros (Coleoptera: Scarabaeidae), on Guam

Coconut rhinoceros beetle (CRB), Oryctes rhinoceros L., is a serious pest of coconut and oil palms throughout Southeast Asia and the Pacific. CRB was found on Guam in 2007 and, despite suppression efforts, has subsequently spread across the island. The CRB population on Guam is genetically different from other populations in Asia and the Pacific, and is considered a new invasive biotype (termed CRB-G). CRB-G is apparently resistant to Oryctes rhinoceros nudivirus, the preferred biocontrol agent for this pest. CRB populations are typically controlled with a combination of biocontrol, pheromone traps, and breeding site removal. A field trial was performed at six locations on Guam to test potential improvements to standard CRB pheromone trapping with oryctalure (ethyl 4-methyloctanoate). Two modifications were tested, 1) addition of ultraviolet light emitting diodes (UV LEDs), and 2) reduction of pheromone release rate. Addition of UV LED light sources to pheromone traps significantly increased trap catch by 2.85 times. Reduction in oryctalure release rate by up to an order of magnitude did not significantly change CRB capture rate. Further, when linear regression analyses of CRB trap capture rate as a function of pheromone release rate were conducted for traps with and without UV LEDs separately, only a very weak relationship between trap capture and oryctalure release rate was observed and only when a UV LED was present. Results suggest that addition of UV LED light sources to pheromone traps could improve detection trapping of CRB and that reduction of pheromone release rate could extend service life of lures without changing capture rate

Concert recording 2018-04-08c

[Track 1]. Revolutions. Groove machine [Track 2]. Black / Marc Mellits -- [Track 3]. Adagio and allegro / G.F. Handel -- [Track 4]. Sonata. Allegro / Lawson Lunde -- [Track 5]. American quartet. Allegro ma non troppo / Antonin Dvořák -- [Track 6]. Spain / Chick Corea arranged by Eddie Jennings -- [Track 7]. First suite in E♭. Chaconne Intermezzo March / Gustav Holst

Extraterrestrial Amino Acids in the Almahata Sitta Meteorite

Amino acid analysis of a meteorite fragment of asteroid 2008 TC3 called Almahata Sitta was carried out using reverse-phase liquid chromatography coupled with UV fluorescence detection and time-of-flight mass spectrometry (LC-FD/ToF-MS) as part of a sample analysis consortium. LC-FD/ToF-MS analyses of hot-water extracts from the meteorite revealed a complex distribution of two- to seven-carbon aliphatic amino acids and one- to three-carbon amines with abundances ranging from 0.5 to 149 parts-per-billion (ppb). The enantiomeric ratios of the amino acids alanine, R-amino-n-butyric acid (beta-ABA), 2-amino-2-methylbutanoic acid (isovaline), and 2-aminopentanoic acid (norvaline) in the meteorite were racemic (D/L approximately 1), indicating that these amino acids are indigenous to the meteorite and not terrestrial contaminants. Several other non-protein amino acids were also identified in the meteorite above background levels including alpha-aminoisobutyric acid (alpha-AIB), 4-amino-2- methylbutanoic acid, 4-amino-3-methylbutanoic acid, and 3-, 4-, and 5-aminopentanoic acid. The total abundances of isovaline and alpha-AIB in Almahata Sitta are 1000 times lower than the abundances of these amino acids found in the CM carbonaceous chondrite Murchison. The extremely low abundances and unusual distribution of five carbon amino acids in Almahata Sitta compared to Cl, CM, and CR carbonaceous chondrites may reflect extensive thermal alteration of amino acids on the parent asteroid by partial melting during formation or subsequent impact shock heating. It is also possible that amino acids were synthesized by catalytic reactions on the parent body after asteroid 2008 TC3 cooled to lower temperatures

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

<p>Abstract</p> <p>Background</p> <p>Massive parallel sequencing has the potential to replace microarrays as the method for transcriptome profiling. Currently there are two protocols: full-length RNA sequencing (RNA-SEQ) and 3'-tag digital gene expression (DGE). In this preliminary effort, we evaluated the 3' DGE approach using two reference RNA samples from the MicroArray Quality Control Consortium (MAQC).</p> <p>Results</p> <p>Using Brain RNA sample from multiple runs, we demonstrated that the transcript profiles from 3' DGE were highly reproducible between technical and biological replicates from libraries constructed by the same lab and even by different labs, and between two generations of Illumina's Genome Analyzers. Approximately 65% of all sequence reads mapped to mitochondrial genes, ribosomal RNAs, and canonical transcripts. The expression profiles of brain RNA and universal human reference RNA were compared which demonstrated that DGE was also highly quantitative with excellent correlation of differential expression with quantitative real-time PCR. Furthermore, one lane of 3' DGE sequencing, using the current sequencing chemistry and image processing software, had wider dynamic range for transcriptome profiling and was able to detect lower expressed genes which are normally below the detection threshold of microarrays.</p> <p>Conclusion</p> <p>3' tag DGE profiling with massive parallel sequencing achieved high sensitivity and reproducibility for transcriptome profiling. Although it lacks the ability of detecting alternative splicing events compared to RNA-SEQ, it is much more affordable and clearly out-performed microarrays (Affymetrix) in detecting lower abundant transcripts.</p

Multifactorial Patterns of Gene Expression in Colonic Epithelial Cells Predict Disease Phenotypes in Experimental Colitis

Background— The pathogenesis of inflammatory bowel disease (IBD) is complex and the need to identify molecular biomarkers is critical. Epithelial cells play a central role in maintaining intestinal homeostasis. We previously identified five “signature” biomarkers in colonic epithelial cells (CEC) that are predictive of disease phenotype in Crohn\u27s disease. Here we investigate the ability of CEC biomarkers to define the mechanism and severity of intestinal inflammation. Methods— We analyzed the expression of RelA, A20, pIgR, tumor necrosis factor (TNF), and macrophage inflammatory protein (MIP)-2 in CEC of mice with dextran sodium sulfate (DSS) acute colitis or T-cell-mediated chronic colitis. Factor analysis was used to combine the five biomarkers into two multifactorial principal components (PCs). PC scores for individual mice were correlated with disease severity. Results— For both colitis models, PC1 was strongly weighted toward RelA, A20, and pIgR, and PC2 was strongly weighted toward TNF and MIP-2, while the contributions of other biomarkers varied depending on the etiology of inflammation. Disease severity was correlated with elevated PC2 scores in DSS colitis and reduced PC1 scores in T-cell transfer colitis. Downregulation of pIgR was a common feature observed in both colitis models and was associated with altered cellular localization of pIgR and failure to transport IgA. Conclusions— A multifactorial analysis of epithelial gene expression may be more informative than examining single gene responses in IBD. These results provide insight into the homeostatic and proinflammatory functions of CEC in IBD pathogenesis and suggest that biomarker analysis could be useful for evaluating therapeutic options for IBD patients

Concert recording 2017-04-26

[Track 1]. Fantazia / Orlando Gibbons arranged by Fred Hemke -- [Track 2-3]. Quartette (Allegro de concert) / Caryl Florio -- [Track 4]. O magnum mysterium / Morten Lauridsen arranged by Chase Shumsky -- [Track 5]. Petite symphonie. Scherzo / Charles Gounod arranged by Aaron M. Durst -- [Track 6]. Grainger set. Mock Morris / Percy Aldridge Grainger arranged by Gary Bricault -- [Track 7]. Grainger set. Two British folk settings. I. Mo nighean dubh [Track 8]. II. The hunter in his career / Percy Aldridge Grainger arranged by Chalon Ragsdale -- [Track 9]. Molly on the shore / Percy Aldridge Grainger arranged by Jacques Larocque -- [Track 10]. The great gate of Kiev / Modest Mussorgsky and Maurice Ravel arranged by B.L. Bruske

Airborne methane remote measurements reveal heavy-tail flux distribution in Four Corners region

Methane (CH_4) impacts climate as the second strongest anthropogenic greenhouse gas and air quality by influencing tropospheric ozone levels. Space-based observations have identified the Four Corners region in the Southwest United States as an area of large CH_4 enhancements. We conducted an airborne campaign in Four Corners during April 2015 with the next-generation Airborne Visible/Infrared Imaging Spectrometer (near-infrared) and Hyperspectral Thermal Emission Spectrometer (thermal infrared) imaging spectrometers to better understand the source of methane by measuring methane plumes at 1- to 3-m spatial resolution. Our analysis detected more than 250 individual methane plumes from fossil fuel harvesting, processing, and distributing infrastructures, spanning an emission range from the detection limit ∼2 kg/h to 5 kg/h through ∼5,000 kg/h. Observed sources include gas processing facilities, storage tanks, pipeline leaks, and well pads, as well as a coal mine venting shaft. Overall, plume enhancements and inferred fluxes follow a lognormal distribution, with the top 10% emitters contributing 49 to 66% to the inferred total point source flux of 0.23 Tg/y to 0.39 Tg/y. With the observed confirmation of a lognormal emission distribution, this airborne observing strategy and its ability to locate previously unknown point sources in real time provides an efficient and effective method to identify and mitigate major emissions contributors over a wide geographic area. With improved instrumentation, this capability scales to spaceborne applications [Thompson DR, et al. (2016) Geophys Res Lett 43(12):6571–6578]. Further illustration of this potential is demonstrated with two detected, confirmed, and repaired pipeline leaks during the campaign