Latent protein trees

Unbiased, label-free proteomics is becoming a powerful technique for measuring protein expression in almost any biological sample. The output of these measurements after preprocessing is a collection of features and their associated intensities for each sample. Subsets of features within the data are from the same peptide, subsets of peptides are from the same protein, and subsets of proteins are in the same biological pathways, therefore, there is the potential for very complex and informative correlational structure inherent in these data. Recent attempts to utilize this data often focus on the identification of single features that are associated with a particular phenotype that is relevant to the experiment. However, to date, there have been no published approaches that directly model what we know to be multiple different levels of correlation structure. Here we present a hierarchical Bayesian model which is specifically designed to model such correlation structure in unbiased, label-free proteomics. This model utilizes partial identification information from peptide sequencing and database lookup as well as the observed correlation in the data to appropriately compress features into latent proteins and to estimate their correlation structure. We demonstrate the effectiveness of the model using artificial/benchmark data and in the context of a series of proteomics measurements of blood plasma from a collection of volunteers who were infected with two different strains of viral influenza.Comment: Published in at http://dx.doi.org/10.1214/13-AOAS639 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Differential Uptake of Gold Nanoparticles by 2 Species of Tadpole, the Wood Frog (Lithobates Sylvaticus) and the Bullfrog (Lithobates Catesbeianus)

Engineered nanoparticles are aquatic contaminants of emerging concern that exert ecotoxicological effects on a wide variety of organisms. We exposed cetyltrimethylammonium bromide–capped spherical gold nanoparticles to wood frog and bullfrog tadpoles with conspecifics and in combination with the other species continuously for 21 d, then measured uptake and localization of gold. Wood frog tadpoles alone and in combination with bullfrog tadpoles took up significantly more gold than bullfrogs. Bullfrog tadpoles in combination with wood frogs took up significantly more gold than controls. The rank order of weight-normalized gold uptake was wood frogs in combination \u3e wood frogs alone \u3e bullfrogs in combination \u3e bullfrogs alone \u3e controls. In all gold-exposed groups of tadpoles, gold was concentrated in the anterior region compared with the posterior region of the body. The concentration of gold nanoparticles in the anterior region of wood frogs both alone and in combination with bullfrogs was significantly higher than the corresponding posterior regions. We also measured depuration time of gold in wood frogs. After 21 d in a solution of gold nanoparticles, tadpoles lost \u3e83% of internalized gold when placed in gold-free water for 5 d. After 10 d in gold-free water, tadpoles lost 94% of their gold. After 15 d, gold concentrations were below the level of detection. Our finding of differential uptake between closely related species living in similar habitats with overlapping geographical distributions argues against generalizing toxicological effects of nanoparticles for a large group of organisms based on measurements in only one species

A Polymerase-chain-reaction Assay for the Specific Identification of Transcripts Encoded by Individual Carcinoembryonic Antigen (CEA)-gene-family Members

Carcinoembryonic antigen (CEA) is a tumor marker that belongs to a family of closely related molecules with variable expression patterns. We have developed sets of oligonucleotide primers for the specific amplification of transcripts from individual CEA-family members using the reverse transcriptase/ polymerase chain reaction (RT/PCR). Specific primer sets were designed for CEA, non-specific cross-reacting antigen (NCA), biliary glycoprotein (BGP), carcinoembryonic antigen gene-family members 1, 6 and 7 (CGMI, CGM6 and CGM7), and one set for all pregnancy-specific glycoprotein (PSG) transcripts. Primers were first tested for their specificity against individual cDNA clones and product-hybridization with internal, transcript-specific oligonucleotides. Total RNA from 12 brain and 63 gynecological tumors were then tested for expression of CEA-related transcripts. None were found in tumors located in the brain, including various mesenchymal and neuro-epithelial tumors. CEA and NCA transcripts were, however, present in an adenocarcinoma located in the nasal sinuses. In ovarian mucinous adenocarcinomas, we always found co-expression of CEA and NCA transcripts, and occasionally BGP mRNA. CEA-related transcripts were also found in some serous, endometrioid and clear-cell ovarian carcinomas. CEA, NCA and BGP transcripts were present in endometrial carcinomas of the uterus and cervical carcinomas, whereas uterine leiomyomas were completely negative. No transcripts were found from CGM 1, CGM6, CGM7 or from PSG genes in any of the tumors tested. The PCR data were compared with immunohistochemical investigations of ovarian tumors at the protein level using CEA (26/3/13)-, NCA-50/90 (9A6FR) and NCA-95 (80H3)-specific monoclonal antibodies

Type I interferons act directly on CD8 T cells to allow clonal expansion and memory formation in response to viral infection

T cell expansion and memory formation are generally more effective when elicited by live organisms than by inactivated vaccines. Elucidation of the underlying mechanisms is important for vaccination and therapeutic strategies. We show that the massive expansion of antigen-specific CD8 T cells that occurs in response to viral infection is critically dependent on the direct action of type I interferons (IFN-Is) on CD8 T cells. By examining the response to infection with lymphocytic choriomeningitis virus using IFN-I receptor–deficient (IFN-IR0) and –sufficient CD8 T cells adoptively transferred into normal IFN-IR wild-type hosts, we show that the lack of direct CD8 T cell contact with IFN-I causes >99% reduction in their capacity to expand and generate memory cells. The diminished expansion of IFN-IR0 CD8 T cells was not caused by a defect in proliferation but by poor survival during the antigen-driven proliferation phase. Thus, IFN-IR signaling in CD8 T cells is critical for the generation of effector and memory cells in response to viral infection

Photocatalytic Hydrogen Production at Titania-Supported Pt Nanoclusters that are Derived from Surface-Anchored Molecular Precursors

Degussa P-25 TiO2 bearing surface-anchored Pt(dcbpy)Cl-2 [dcbpy = 4,4\u27-dicarboxylic acid-2,2\u27-bipyridine] prepared with systematically varied surface coverage produced Pt-0 nanoparticles under bandgap illumination in the presence of methanol hole scavengers. Energy-dispersive X-ray spectroscopy confirmed the presence of elemental platinum in the newly formed nanoparticles during scanning transmission electron microscopy (STEM) eleriments. According to the statistical analysis of numerous STEM images, the Pt-0 nanoclusters were distributed in a segregated manner throughout the titania surface, ranging in size from 1 to 3 nm in diameter. The final achieved nanoparticle size and net hydrogen production were determined as a function of the Pt(dcbpy)Cl-2 surface coverage as well as other systematically varied experimental parameters. The hybrid Pt/TiO2 nanomaterials obtained upon complete decomposition of the Pt(dcbpy)Cl-2 precursor displayed higher photocatalytic activity (300 mu mol/h) for hydrogen evolution in aqueous suspensions when compared with platinized TiO2 derived from H2PtCl6 precursors (130 mu mol/h), as ascertained through gas chromatographic analysis of the photoreactor headspace under identical experimental conditions. The conclusion that H-2 was evolved from Pt-0 sites rather than from molecular Pt(dcbpy)Cl-2 entities was independently supported by Hg and CO poisoning experiments. The formation of small Pt nanopartides (1.5 nm in diameter) prevail at low surface coverage of Pt(dcbpy)Cl-2 on TiO2 (0.5 to 2% by mass) that exhibit enhanced turnover frequencies with respect to all other materials investigated, induding those produced from the in situ photochemical reduction of H2PtCl6 center dot Pt-II precursor absorption in the ultraviolet region appeared to be partially responsible for attenuation of the H-2 evolution rate at higher Pt(dcbpy)Cl-2 surface coverage. The nanoparticle size and hydrogen evolution characteristics of the surface-anchored materials generated through photodeposition were directly compared with those derived from chemical reduction using NaBH4. Finally, Degussa P-25 thin films deposited on FTO substrates enabled electrochemically induced (-1.0 V vs Ag/AgCl, pH 7.0, phosphate buffer) electron trapping (TiO2(e(-))) throughout the titania. After removal of the applied bias and the anaerobic introduction of Pt(dcbpy)Cl-2, the accumulated electrons reduce this molecular species to Pt-0 nanoparticles on the titania electrode surface, as confirmed by TEM measurements, with the concomitant production of H-2 gas. The combined experiments illustrate that TiO2(e(-)) generated with bandgap excitation or via electrochemical bias affords the reduction of Pt(dcbpy)Cl-2 to Pt-0 nanoparticles that in turn are responsible for heterogeneous hydrogen gas evolution

The Circumstellar Disk of the Butterfly Star in Taurus

We present a model of the circumstellar environment of the so-called ``Butterfly Star'' in Taurus (IRAS 04302+2247). The appearance of this young stellar object is dominated by a large circumstellar disk seen edge-on and the light scattering lobes above the disk. The model is based on multi-wavelength continuum observations: Millimeter maps and high-resolution near-infrared images obtained with HST/NICMOS. It was found that the disk and envelope parameters are comparable with those of the circumstellar environment of other young stellar objects. A main result is that the dust properties must be different in the circumstellar disk and in the envelope: While a grain size distribution with grain radii up to 100 micron is required to reproduce the millimeter observations of the disk, the envelope is dominated by smaller grains similar to those of the interstellar medium. Preprint with high figure quality available at: http://spider.ipac.caltech.edu/staff/swolf/homepage/public/preprints/i04302.psComment: 32 pages, 9 figure

VVV-WIT-01: highly obscured classical nova or protostellar collision?

© 2020 The Author(s).A search of the first Data Release of the VISTA Variables in the Via Lactea (VVV) Survey discovered the exceptionally red transient VVV-WIT-01 (H-Ks=5.2). It peaked before March 2010, then faded by ~9.5 mag over the following two years. The 1.6-22 µm spectral energy distribution in March 2010 was well fit by a highly obscured black body with T ~ 1000 K and AKs ~ 6.6 mag. The source is projected against the Infrared Dark Cloud (IRDC) SDC G331.062-0.294. The chance projection probability is small for any single event (p ≈ 0.01 to 0.02) which suggests a physical association, e.g. a collision between low mass protostars. However, black body emission at T ~ 1000 K is common in classical novae (especially CO novae) at the infrared peak in the light curve, due to condensation of dust ~30-60 days after the explosion. Radio follow up with the Australia Telescope Compact Array (ATCA) detected a fading continuum source with properties consistent with a classical nova but probably inconsistent with colliding protostars. Considering all VVV transients that could have been projected against a catalogued IRDC raises the probability of a chance association to p=0.13 to 0.24. After weighing several options, it appears likely that VVV-WIT-01 was a classical nova event located behind an IRDC.Peer reviewedFinal Published versio

The Spitzer Gould Belt Survey of Large Nearby Interstellar Clouds: Discovery of A Dense Embedded Cluster in the Serpens-Aquila Rift

We report the discovery of a nearby, embedded cluster of young stellar objects, associated filamentary infrared dark cloud, and 4.5 mu m shock emission knots from outflows detected in Spitzer IRAC mid-infrared imaging of the Serpens-Aquila Rift obtained as part of the Spitzer Gould Belt Legacy Survey. We also present radial velocity measurements of the region from molecular line observations obtained with the Submillimeter Array (SMA) that suggest the cluster is comoving with the Serpens Main embedded cluster to the north. We therefore assign it 3 degrees the same distance, 260 pc. The core of the new cluster, which we call Serpens South, is composed of an unusually large fraction of protostars (77%) at high mean surface density (> 430 pc(-2)) and short median nearest neighbor spacing (3700 AU). We perform basic cluster structure characterization using nearest neighbor surface density mapping of the YSOs and compare our findings to other known clusters with equivalent analyses available in the literature.Astronom

No disks around low-mass stars and brown dwarfs in the young sigma Orionis cluster?

We report on the analysis of 2MASS near-infrared data of a sample of low-mass stars and brown dwarfs in the sigma Orionis cluster. Youth and cluster membership have been spectroscopically confirmed using the Li I spectral line. We find little evidence in the JHKs colour-colour diagram for near-infrared excess emission for these cluster members. By comparison with model expectations, at most 2 out of 34 stars show (H-K) colour consistent with a near-infrared excess. This scarcity of near-infrared signatures of circumstellar disks in the lower-mass and substellar regimes of this cluster contrasts with findings in younger clusters, hinting at an age dependence of the disk frequency. Taking into account the apparent cluster age, our result supports the idea of a relatively fast (few Myr) disk dissipation and extends this conclusion to the substellar regime. We also find some evidence that, in this cluster, the disk frequency as measured by the Ks-band excess may be mass dependent.Comment: 4 pages, 2 eps figures, accepted by Astronomy and Astrophysics Letter

Genomic Organization, Splice Variants and Expression of CGMl, a CD66-related Member of the Carcinoembryonic Antigen Gene Family

The tumor marker carcinoembryonic antigen (CEA) belongs to a family of proteins which are composed of one immunogiobulin variable domain and a varying number of immunoglobulin constant-like domains. Most of the membrane-bound members, which are anchored either by a glycosylphosphatidylinositol moiety or a transmembrane domain, have been shown to convey cell adhesion in vitro. Here we describe two splice variants of CGMI. a transmembrane member of the CEA family without immunoglobulin constant.like domains. CGM1a and CGM1c contain cytopiasmic domains of 71 and 31 amino acids, respectively, The cytoplasmic region of CGM1a is encoded by four exons (Cyt1-Cyt4). Differential splicing of the Cyt1 exon (53 bp)..