The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that ...chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.
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Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The Broadbalk experiment was started in 1843 to investigate the relative importance of different plant nutrients (N, P, K, Na, Mg) on grain yield of winter wheat. Weeds were controlled initially by ...hand hoeing and fallowing, but since 1964, herbicides have been applied to the whole experiment with the exception of the 18 plots on Section 8. Approximately 130 weed species have been recorded on Broadbalk and about 30 of these are currently recorded annually on Section 8. Detailed weed surveys, conducted from 1930 to 1979, provide a unique 50-yr record, but the relatively small number of frequency categories used (six) poses a limitation on the interpretation of these data for ecological studies. Weed surveys were restarted in 1991 on Section 8. The current assessment method records the presence of individual weed species in 25 random 0.1-m2 quadrats per plot, which is more appropriate for detecting long-term trends in weed frequencies and population differences between plots. A principal components analysis of the 1991–2002 survey data for 15 species showed clearly the influence of inorganic N fertilizer levels on the frequency of individual species. The frequency of one species (common chickweed) was greatly favored by increasing amounts of nitrogen fertilizer from 0 to 288 kg N ha−1, others were strongly disadvantaged (e.g., black medic and field horsetail), some were slightly disadvantaged (e.g., common vetch and parsley-piert), and some showed little response to differing N rates (e.g., blackgrass and corn poppy). Other weed investigations include studies on the effects of fallowing on the weed seed bank, seed dormancy and persistence, agroecology, and population dynamics of individual weed species. Recently, molecular approaches have been used to study the genetic diversity of weeds found on Section 8, which is one of the few arable sites in the country where herbicides have never been applied. This site also provides an invaluable reserve for seven nationally rare or uncommon species. Broadbalk continues to act as a valuable resource for weed investigations 160 yr after it was established.
E-cadherin (CDH1) is a putative tumor suppressor gene implicated in breast carcinogenesis. Yet, whether risk factors or survival differ by E-cadherin tumor expression is unclear. We evaluated ...E-cadherin tumor immunohistochemistry expression using tissue microarrays of 5,933 female invasive breast cancers from 12 studies from the Breast Cancer Consortium. H-scores were calculated and case-case odds ratios (OR) and 95% confidence intervals (CIs) were estimated using logistic regression. Survival analyses were performed using Cox regression models. All analyses were stratified by estrogen receptor (ER) status and histologic subtype. E-cadherin low cases (N = 1191, 20%) were more frequently of lobular histology, low grade, >2 cm, and HER2-negative. Loss of E-cadherin expression (score < 100) was associated with menopausal hormone use among ER-positive tumors (ever compared to never users, OR = 1.24, 95% CI = 0.97-1.59), which was stronger when we evaluated complete loss of E-cadherin (i.e. H-score = 0), OR = 1.57, 95% CI = 1.06-2.33. Breast cancer specific mortality was unrelated to E-cadherin expression in multivariable models. E-cadherin low expression is associated with lobular histology, tumor characteristics and menopausal hormone use, with no evidence of an association with breast cancer specific survival. These data support loss of E-cadherin expression as an important marker of tumor subtypes.
Automated methods are needed to facilitate high‐throughput and reproducible scoring of Ki67 and other markers in breast cancer tissue microarrays (TMAs) in large‐scale studies. To address this need, ...we developed an automated protocol for Ki67 scoring and evaluated its performance in studies from the Breast Cancer Association Consortium. We utilized 166 TMAs containing 16,953 tumour cores representing 9,059 breast cancer cases, from 13 studies, with information on other clinical and pathological characteristics. TMAs were stained for Ki67 using standard immunohistochemical procedures, and scanned and digitized using the Ariol system. An automated algorithm was developed for the scoring of Ki67, and scores were compared to computer assisted visual (CAV) scores in a subset of 15 TMAs in a training set. We also assessed the correlation between automated Ki67 scores and other clinical and pathological characteristics. Overall, we observed good discriminatory accuracy (AUC = 85%) and good agreement (kappa = 0.64) between the automated and CAV scoring methods in the training set. The performance of the automated method varied by TMA (kappa range= 0.37–0.87) and study (kappa range = 0.39–0.69). The automated method performed better in satisfactory cores (kappa = 0.68) than suboptimal (kappa = 0.51) cores (p‐value for comparison = 0.005); and among cores with higher total nuclei counted by the machine (4,000–4,500 cells: kappa = 0.78) than those with lower counts (50–500 cells: kappa = 0.41; p‐value = 0.010). Among the 9,059 cases in this study, the correlations between automated Ki67 and clinical and pathological characteristics were found to be in the expected directions. Our findings indicate that automated scoring of Ki67 can be an efficient method to obtain good quality data across large numbers of TMAs from multicentre studies. However, robust algorithm development and rigorous pre‐ and post‐analytical quality control procedures are necessary in order to ensure satisfactory performance.
The supernova remnant (SNR) Puppis A (aka G260.4-3.4) is a middle-aged supernova remnant, which displays increasing X-ray surface brightness from West to East corresponding to an increasing density ...of the ambient interstellar medium at the Eastern and Northern shell. The dense IR photon field and the high ambient density around the remnant make it an ideal case to study in γ-rays. Gamma-ray studies based on three years of observations with the Large Area Telescope (LAT) aboard Fermi have revealed the high energy gamma-ray emission from SNR Puppis A. The γ-ray emission from the remnant is spatially extended, and nicely matches the radio and X-ray morphologies. Its γ-ray spectrum is well described by a simple power law with an index of ~2.1, and it is among the faintest supernova remnants yet detected at GeV energies. To constrain the relativistic electron population, seven years of Wilkinson Microwave Anisotropy Probe (WMAP) data were also analyzed, and enabled to extend the radio spectrum up to 93 GHz. The results obtained in the radio and γ-ray domains are described in detail, as well as the possible origins of the high energy γ-ray emission (Bremsstrahlung, Inverse Compton scattering by electrons or decay of neutral pions produced by proton interactions).
Millisecond pulsars (MSPs) are old neutron stars that spin hundreds of times per second and appear to pulsate as their emission beams cross our line of sight. To date, radio pulsations have been ...detected from all rotation-powered MSPs. In an attempt to discover radio-quiet gamma-ray MSPs, we used the aggregated power from the computers of tens of thousands of volunteers participating in the Einstein@Home distributed computing project to search for pulsations from unidentified gamma-ray sources in Fermi Large Area Telescope data. This survey discovered two isolated MSPs, one of which is the only known rotation-powered MSP to remain undetected in radio observations. These gamma-ray MSPs were discovered in completely blind searches without prior constraints from other observations, raising hopes for detecting MSPs from a predicted Galactic bulge population.
We present newly obtained X-ray and radio observations of Tycho's supernova remnant using Chandra and the Karl G. Jansky Very Large Array in 2015 and 2013/14, respectively. When combined with earlier ...epoch observations by these instruments, we now have time baselines for expansion measurements of the remnant of 12-15 years in the X-rays and 30 years in the radio. The remnant's large angular size allows for proper motion measurements at many locations around the periphery of the blast wave. Consistent with earlier measurements, we find a clear gradient in the expansion velocity of the remnant, despite its round shape. The proper motions on the western and southwestern sides of the remnant are about a factor of two higher than those in the east and northeast. We showed in an earlier work that this is related to an offset of the explosion site from the geometric center of the remnant due to a density gradient in the ISM, and using our refined measurements reported here, we find that this offset is approximately 23″ toward the northeast. An explosion center offset in such a circular remnant has implications for searches for progenitor companions in other remnants.
Recent observations suggest that some high-velocity clouds may be confined by massive dark matter halos. In particular, the proximity and proposed dark matter content of the Smith Cloud make it a ...tempting target for the indirect detection of dark matter annihilation. We argue that the Smith Cloud may be a better target than some Milky Way dwarf spheroidal satellite galaxies and use γ-ray observations from the Fermi Large Area Telescope to search for a dark matter annihilation signal. No significant γ-ray excess is found coincident with the Smith Cloud, and we set strong limits on the dark matter annihilation cross section assuming a spatially extended dark matter profile consistent with dynamical modeling of the Smith Cloud. Notably, these limits exclude the canonical thermal relic cross section (∼ 3 × 10{sup –26} cm{sup 3} s{sup –1}) for dark matter masses ≲ 30 GeV annihilating via the b b-bar or τ{sup +}τ{sup –} channels for certain assumptions of the dark matter density profile; however, uncertainties in the dark matter content of the Smith Cloud may significantly weaken these constraints.
Layered peptide array is a new methodology for multiplex molecular measurements from two-dimensional life science platforms. The technology can be used in several different configurations depending ...on the needs of the investigator. Described here is an indirect layered peptide array (iLPA) that is capable of measuring proteins on a solid surface, such as target antigens on a tissue section. A prototype iLPA system was developed and subsequently examined for reproducibility and specificity and then compared with standard immunohistochemistry. Semiquantitative, multiplex proteomic analysis of histological sections was achieved with up to 20 membranes. The experimental variability was 18%. Overall, the data suggest that iLPA technology will be a relatively simple and inexpensive method for molecular measurements from tissue sections.
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