198 research outputs found
Testing the use of marine protected areas to restore and manage tropical multispecies invertebrate fisheries at the Arnavon Islands, Solomon Islands : termination report
This report aimed to determine if the number and size of commercially important invertebrates (e.g. trochus, sea
cucumbers and giant clams) increases as the result of the declaration of the Arnavon Islands Marine
Conservation Area (MCA) relative to fished areas
A taxonomic and phylogenetic revision of Penicillium section Aspergilloides
AbstractSpecies belonging to Penicillium section Aspergilloides have a world-wide distribution with P. glabrum, P. spinulosum and P. thomii the most well-known species of this section. These species occur commonly and can be isolated from many substrates including soil, food, bark and indoor environments. The taxonomy of these species has been investigated several times using various techniques, but species delimitation remains difficult. In the present study, 349 strains belonging to section Aspergilloides were subjected to multilocus molecular phylogenetic analyses using partial β-tubulin (BenA), calmodulin (CaM) and RNA polymerase II second largest subunit (RPB2) sequences. Section Aspergilloides is subdivided into 12 clades and 51 species. Twenty-five species are described here as new and P. yezoense, a species originally described without a Latin diagnosis, is validated. Species belonging to section Aspergilloides are phenotypically similar and most have monoverticillate conidiophores and grow moderately or quickly on agar media. The most important characters to distinguish these species were colony sizes on agar media, growth at 30 °C, ornamentation and shape of conidia, sclerotium production and stipe roughness
A taxonomic and phylogenetic revision of the Penicillium sclerotiorum complex
The morphological concept of Penicillium sclerotiorum (subgenus Aspergilloides) includes strains with monoverticillate, vesiculate conidiophores, and vivid orange to red colony colours, with colourful sclerotia sometimes produced. Multigene phylogenetic analyses with the nuclear ribosomal internal transcribed spacer (ITS) region, cytochrome c oxidase subunit 1 (cox1), β-tubulin (benA), translation elongation factor 1-α (tef1-α), and calmodulin (cmd), reveal that the P. sclerotiorum morphospecies is a complex of seven phylogenetically distinct species, three of which were recently described, namely P. guanacastense, P. mallochii, and P. viticola. Three previously unidentified species are described here as P. cainii, P. jacksonii, and P. johnkrugii. The phylogenetic species are morphologically similar, but differ in combinations of colony characters, sclerotium production, conidiophore stipe roughening and branching, and conidial shape. Ecological characters and differences in geographical distribution further characterise some of the species, but increased sampling is necessary to confirm these differences. The fungal DNA barcode, the ITS, and the animal DNA barcode, cox1, have lower species resolving ability in our phylogenetic analyses, but still allow identification of all the species. Tef1-α and cmd were superior in providing fully resolved, statistically well-supported phylogenetic trees for this species complex, whereas benA resolved all species but had some issues with paraphyly. Penicillium adametzioides and P. multicolor, considered synonyms of P. sclerotiorum by some previous authors, do not belong to the P. sclerotiorum complex
Measurement of the vector analyzing power in elastic electron-proton scattering as a probe of double photon exchange amplitudes
We report the first measurement of the vector analyzing power in inclusive
transversely polarized elastic electron-proton scattering at Q^2 = 0.1
(GeV/c)^2 and large scattering angles. This quantity should vanish in the
single virtual photon exchange, plane wave impulse approximation for this
reaction, and can therefore provide information on double photon exchange
amplitudes for electromagnetic interactions with hadronic systems. We find a
non-zero value of A=-15.4+/-5.4 ppm. No calculations of this observable for
nuclei other than spin 0 have been carried out in these kinematics, and the
calculation using the spin orbit interaction from a charged point nucleus of
spin 0 cannot describe these data.Comment: 4 pages, 2 figures, submitted to Phys. Rev. Let
Phylogeny and nomenclature of the genus Talaromyces and taxa accommodated in Penicillium subgenus Biverticillium
The taxonomic history of anamorphic species attributed to Penicillium subgenus Biverticillium is reviewed, along with evidence supporting their relationship with teleomorphic species classified in Talaromyces. To supplement previous conclusions based on ITS, SSU and/or LSU sequencing that Talaromyces and subgenus Biverticillium comprise a monophyletic group that is distinct from Penicillium at the generic level, the phylogenetic relationships of these two groups with other genera of Trichocomaceae was further studied by sequencing a part of the RPB1 (RNA polymerase II largest subunit) gene. Talaromyces species and most species of Penicillium subgenus Biverticillium sensu Pitt reside in a monophyletic clade distant from species of other subgenera of Penicillium. For detailed phylogenetic analysis of species relationships, the ITS region (incl. 5.8S nrDNA) was sequenced for the available type strains and/or representative isolates of Talaromyces and related biverticillate anamorphic species. Extrolite profiles were compiled for all type strains and many supplementary cultures. All evidence supports our conclusions that Penicillium subgenus Biverticillium is distinct from other subgenera in Penicillium and should be taxonomically unified with the Talaromyces species that reside in the same clade. Following the concepts of nomenclatural priority and single name nomenclature, we transfer all accepted species of Penicillium subgenus Biverticillium to Talaromyces. A holomorphic generic diagnosis for the expanded concept of Talaromyces, including teleomorph and anamorph characters, is provided. A list of accepted Talaromyces names and newly combined Penicillium names is given. Species of biotechnological and medical importance, such as P. funiculosum and P. marneffei, are now combined in Talaromyces. Excluded species and taxa that need further taxonomic study are discussed. An appendix lists other generic names, usually considered synonyms of Penicillium sensu lato that were considered prior to our adoption of the name Talaromyces
Transverse Beam Spin Asymmetries in Forward-Angle Elastic Electron-Proton Scattering
We have measured the beam-normal single-spin asymmetry in elastic scattering
of transversely-polarized 3 GeV electrons from unpolarized protons at Q^2 =
0.15, 0.25 (GeV/c)^2. The results are inconsistent with calculations solely
using the elastic nucleon intermediate state, and generally agree with
calculations with significant inelastic hadronic intermediate state
contributions. A_n provides a direct probe of the imaginary component of the
2-gamma exchange amplitude, the complete description of which is important in
the interpretation of data from precision electron-scattering experiments.Comment: 5 pages, 3 figures, submitted to Physical Review Letters; shortened
to meet PRL length limit, clarified some text after referee's comment
Strange Quark Contributions to Parity-Violating Asymmetries in the Forward G0 Electron-Proton Scattering Experiment
We have measured parity-violating asymmetries in elastic electron-proton
scattering over the range of momentum transfers 0.12 < Q^2 < 1.0 GeV^2. These
asymmetries, arising from interference of the electromagnetic and neutral weak
interactions, are sensitive to strange quark contributions to the currents of
the proton. The measurements were made at JLab using a toroidal spectrometer to
detect the recoiling protons from a liquid hydrogen target. The results
indicate non-zero, Q^2 dependent, strange quark contributions and provide new
information beyond that obtained in previous experiments.Comment: 5 pages, 2 figure
The G0 Experiment: Apparatus for Parity-Violating Electron Scattering Measurements at Forward and Backward Angles
In the G0 experiment, performed at Jefferson Lab, the parity-violating
elastic scattering of electrons from protons and quasi-elastic scattering from
deuterons is measured in order to determine the neutral weak currents of the
nucleon. Asymmetries as small as 1 part per million in the scattering of a
polarized electron beam are determined using a dedicated apparatus. It consists
of specialized beam-monitoring and control systems, a cryogenic hydrogen (or
deuterium) target, and a superconducting, toroidal magnetic spectrometer
equipped with plastic scintillation and aerogel Cerenkov detectors, as well as
fast readout electronics for the measurement of individual events. The overall
design and performance of this experimental system is discussed.Comment: Submitted to Nuclear Instruments and Method
Comparison of Breast Cancer Molecular Features and Survival by African and European Ancestry in The Cancer Genome Atlas
Importance: African Americans have the highest breast cancer mortality rate. Although racial difference in the distribution of intrinsic subtypes of breast cancer is known, it is unclear if there are other inherent genomic differences that contribute to the survival disparities. Objectives: To investigate racial differences in breast cancer molecular features and survival and to estimate the heritability of breast cancer subtypes. Design, Setting, and Participants: Among a convenience cohort of patients with invasive breast cancer, breast tumor and matched normal tissue sample data (as of September 18, 2015) were obtained from The Cancer Genome Atlas. Main Outcomes and Measures: Breast cancer–free interval, tumor molecular features, and genetic variants. Results: Participants were 930 patients with breast cancer, including 154 black patients of African ancestry (mean [SD] age at diagnosis, 55.66 [13.01] years; 98.1% [n = 151] female) and 776 white patients of European ancestry (mean [SD] age at diagnosis, 59.51 [13.11] years; 99.0% [n = 768] female). Compared with white patients, black patients had a worse breast cancer-free interval (hazard ratio, HR=1.67; 95% CI, 1.02-2.74; P = .043). They had a higher likelihood of basal-like (odds ratio, 3.80; 95% CI, 2.46-5.87; P < .001) and human epidermal growth factor receptor 2 (ERBB2 [formerly HER2])–enriched (odds ratio, 2.22; 95% CI, 1.10-4.47; P = .027) breast cancer subtypes, with the Luminal A subtype as the reference. Blacks had more TP53 mutations and fewer PIK3CA mutations than whites. While most molecular differences were eliminated after adjusting for intrinsic subtype, the study found 16 DNA methylation probes, 4 DNA copy number segments, 1 protein, and 142 genes that were differentially expressed, with the gene-based signature having an excellent capacity for distinguishing breast tumors from black vs white patients (cross-validation C index, 0.878). Using germline genotypes, the heritability of breast cancer subtypes (basal vs nonbasal) was estimated to be 0.436 (P = 1.5 × 10−14). The estrogen receptor–positive polygenic risk score built from 89 known susceptibility variants was higher in blacks than in whites (difference, 0.24; P = 2.3 × 10−5), while the estrogen receptor–negative polygenic risk score was much higher in blacks than in whites (difference, 0.48; P = 2.8 × 10−11). Conclusions and Relevance: On the molecular level, after adjusting for intrinsic subtype frequency differences, this study found a modest number of genomic differences but a significant clinical survival outcome difference between blacks and whites in The Cancer Genome Atlas data set. Moreover, more than 40% of breast cancer subtype frequency differences could be explained by genetic variants. These data could form the basis for the development of molecular targeted therapies to improve clinical outcomes for the specific subtypes of breast cancers that disproportionately affect black women. Findings also indicate that personalized risk assessment and optimal treatment could reduce deaths from aggressive breast cancers for black women
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