THE TAXONOMIC STATUS OF THE WYOMING TOAD, BUFO BAXTERI PORTER

The population of toads in southeastern Wyoming named Bufo hemiophrys baxteri by Porter in 1968 is presumed to be extinct in nature, except perhaps for released, captive-bred specimens. It is sufficiently distinct in several respects, and sufficiently isolated geographically from its nearest rela- tive, B. h. hemiophrys, that it should be regarded as a distinct species, forming a superspecies group with B. hemiophrys

Resolving genetic engineering signatures in yeast on-site with the MinION and iSeq

Generating an assembly that captures all of the genome and plasmid modifications resulting from metabolic engineering is essential for quality control, connecting genotype to phenotype, establishing and protecting intellectual property, and generating “ground truth” for monitoring potential release events. Furthermore, high quality de novo assemblies can be used to accurately determine the presence and function of metabolic engineering signatures in an unknown sample. Here, we use two new inexpensive sequencers, the Oxford Nanopore MinION and the Illumina iSeq, to enable fast acquisition of sequence on-site. We also use new processing algorithms to enable fast transformation of sequence information into a high-quality genome assembly. The resulting pipeline can generate de novo microbial genome assemblies that capture complete chromosomal pathways and episomal plasmids. We further extend the pipeline to resequence six nonconventional yeasts of interest for metabolic engineering. To establish the most accurate workflow, we evaluated four nanopore de novo assemblers and three polishing algorithms at varying genome coverage depths for the lab strain S. cerevisiae CEN.PK113-7D. Our results show that (1) nanopore genome coverage depth must be at least 40X, (2) Flye and Canu are currently the best assemblers due to their combination of structure, completeness, and accuracy, and (3) Illumina data is essential for polishing. Our final pipeline (Figure 1A) generated a better S. cerevisiae CEN.PK113-7D assembly than the publicly available reference genome. Please click Additional Files below to see the full abstract

Review: \u3ci\u3eVeratrum californicum\u3c/i\u3e Alkaloids

Veratrum spp. grow throughout the world and are especially prevalent in high mountain meadows of North America. All parts of Veratrum plants have been used for the treatment of ailments including injuries, hypertension, and rheumatic pain since as far back as the 1600s. Of the 17–45 Veratrum spp., Veratrum californicum alkaloids have been proven to possess favorable medicinal properties associated with inhibition of hedgehog (Hh) pathway signaling. Aberrant Hh signaling leads to proliferation of over 20 cancers, including basal cell carcinoma, prostate and colon among others. Six of the most well-studied V. californicum alkaloids are cyclopamine (1), veratramine (2), isorubijervine (3), muldamine (4), cycloposine (5), and veratrosine (6). Recent inspection of the ethanolic extract from V. californicum root and rhizome via liquid chromatography–mass spectrometry has detected up to five additional alkaloids that are proposed to be verazine (7), etioline (8), tetrahydrojervine (9), dihydrojervine (10), 22-keto-26-aminocholesterol (11). For each alkaloid identified or proposed in V. californicum, this review surveys literature precedents for extraction methods, isolation, identification, characterization and bioactivity to guide natural product drug discovery associated with this medicinal plant

A comparative study of WASP-67b and HAT-P-38b from WFC3 data

Atmospheric temperature and planetary gravity are thought to be the main parameters affecting cloud formation in giant exoplanet atmospheres. Recent attempts to understand cloud formation have explored wide regions of the equilibrium temperature-gravity parameter space. In this study, we instead compare the case of two giant planets with nearly identical equilibrium temperature ($T_\mathrm{eq}$ $\sim 1050 \, \mathrm{K}$) and gravity ($g \sim 10 \, \mathrm{m \, s}^{-1})$. During $HST$ Cycle 23, we collected WFC3/G141 observations of the two planets, WASP-67 b and HAT-P-38 b. HAT-P-38 b, with mass 0.42 M$_\mathrm{J}$ and radius 1.4 $R_\mathrm{J}$, exhibits a relatively clear atmosphere with a clear detection of water. We refine the orbital period of this planet with new observations, obtaining $P = 4.6403294 \pm 0.0000055 \, \mathrm{d}$. WASP-67 b, with mass 0.27 M$_\mathrm{J}$ and radius 0.83 $R_\mathrm{J}$, shows a more muted water absorption feature than that of HAT-P-38 b, indicating either a higher cloud deck in the atmosphere or a more metal-rich composition. The difference in the spectra supports the hypothesis that giant exoplanet atmospheres carry traces of their formation history. Future observations in the visible and mid-infrared are needed to probe the aerosol properties and constrain the evolutionary scenario of these planets.Comment: 16 pages, 17 figures, 8 tables, accepted for publication in The Astronomical Journa

Exclusive Production of Higgs Bosons in Hadron Colliders

We study the exclusive, double--diffractive production of the Standard Model Higgs particle in hadronic collisions at LHC and FNAL (upgraded) energies. Such a mechanism would provide an exceptionally clean signal for experimental detection in which the usual penalty for triggering on the rare decays of the Higgs could be avoided. In addition, because of the color singlet nature of the hard interaction, factorization is expected to be preserved, allowing the cross--section to be related to similar hard--diffractive events at HERA. Starting from a Fock state expansion in perturbative QCD, we obtain an estimate for the cross section in terms of the gluon structure functions squared of the colliding hadrons. Unfortunately, our estimates yield a production rate well below what is likely to be experimentally feasible.Comment: 17 pages, RevTeX file, four uufiled PostScript figures. UMPP #94-177. (Revised version. Some mistakenly missing Feynman diagrams are now added. Results do not change qualitatively. Paper reorganized.

Combinatorics of renormalization as matrix calculus

We give a simple presentation of the combinatorics of renormalization in perturbative quantum field theory in terms of triangular matrices. The prescription, that may be of calculational value, is derived from first principles, to wit, the ``Birkhoff decomposition'' in the Hopf-algebraic description of renormalization by Connes and Kreimer.Comment: 10 pages, revised version, typos corrected, to appear in Phys. Lett.

Instrumentation for Routine Analysis of Acrylamide in French Fries: Assessing Limitations for Adoption

The purpose of this experimental review was to detect acrylamide in French fries using methods most adaptable to the food process industry for quality control assessment of products. French fries were prepared at different cook times using the same fryer oil over a five-day period to assess the influence of oil degradation and monitor trends in acrylamide formation. Acrylamide detection was performed using LC-MS, GC-MS and FT-NIR. The low levels of acrylamide produced during frying, low molecular weight of the analyte, and complexity of the potato matrix make routine acrylamide measurement challenging in a well-outfitted analytical lab with trained personnel. The findings of this study are presented from the perspective of pros and cons of each acrylamide measurement method in enough detail for food processors to appraise the method that may work best for them based on their available instrumentation and extent of personnel training

Two real parton contributions to non-singlet kernels for exclusive QCD DGLAP evolution

Results for the two real parton differential distributions needed for implementing a next-to-leading order (NLO) parton shower Monte Carlo are presented. They are also integrated over the phase space in order to provide solid numerical control of the MC codes and for the discussion of the differences between the standard $\bar{MS}$ factorization and Monte Carlo implementation at the level of inclusive NLO evolution kernels. Presented results cover the class of non-singlet diagrams entering into NLO kernels. The classic work of Curci-Furmanski-Pertonzio was used as a guide in the calculations.Comment: 34 pages, 3 figure

How Anisotropic is our Universe?

Large-scale cosmic microwave background anisotropies in homogeneous, globally anisotropic cosmologies are investigated. We perform a statistical analysis in which the four-year data from the Cosmic Background Explorer satellite is searched for the specific anisotropy patterns predicted by these models and thereby set definitive upper limits on the amount of shear, $(\sigma/H)_0$ and vorticity, $(\omega/H)_0$, which are orders of magnitude stronger than previous constraints. We comment on how these results might impact our understanding of primordial global anisotropy.Comment: 12 pages (1 figure), uses RevTex and psfig, submitted to PR