Molecular evolution of urea amidolyase and urea carboxylase in fungi

Background: Urea amidolyase breaks down urea into ammonia and carbon dioxide in a two-step process, while another enzyme, urease, does this in a one step-process. Urea amidolyase has been found only in some fungal species among eukaryotes. It contains two major domains: the amidase and urea carboxylase domains. A shorter form of urea amidolyase is known as urea carboxylase and has no amidase domain. Eukaryotic urea carboxylase has been found only in several fungal species and green algae. In order to elucidate the evolutionary origin of urea amidolyase and urea carboxylase, we studied the distribution of urea amidolyase, urea carboxylase, as well as other proteins including urease, across kingdoms. Results: Among the 64 fungal species we examined, only those in two Ascomycota classes (Sordariomycetes and Saccharomycetes) had the urea amidolyase sequences. Urea carboxylase was found in many but not all of the species in the phylum Basidiomycota and in the subphylum Pezizomycotina (phylum Ascomycota). It was completely absent from the class Saccharomycetes (phylum Ascomycota; subphylum Saccharomycotina). Four Sordariomycetes species we examined had both the urea carboxylase and the urea amidolyase sequences. Phylogenetic analysis showed that these two enzymes appeared to have gone through independent evolution since their bacterial origin. The amidase domain and the urea carboxylase domain sequences from fungal urea amidolyases clustered strongly together with the amidase and urea carboxylase sequences, respectively, from a small number of beta- and gammaproteobacteria. On the other hand, fungal urea carboxylase proteins clustered together with another copy of urea carboxylases distributed broadly among bacteria. The urease proteins were found in all the fungal species examined except for those of the subphylum Saccharomycotina. Conclusions: We conclude that the urea amidolyase genes currently found only in fungi are the results of a horizontal gene transfer event from beta-, gamma-, or related species of proteobacteria. The event took place before the divergence of the subphyla Pezizomycotina and Saccharomycotina but after the divergence of the subphylum Taphrinomycotina. Urea carboxylase genes currently found in fungi and other limited organisms were also likely derived from another ancestral gene in bacteria. Our study presented another important example showing plastic and opportunistic genome evolution in bacteria and fungi and their evolutionary interplay

The representation of scientific research in the national curriculum and secondary school pupils’ perceptions of research, its function, usefulness and value to their lives

Young people’s views on what research is, how it is conducted and whether it is important, influences the decisions they make about their further studies and career choices. In this paper we report the analysis of questionnaire data with a particular focus on pupil perceptions of research in the sciences and of the scientific method. The questionnaire was a 25-item Likert Scale (1-5) distributed to seven collaborating schools. We received 2634 returns from pupils across key stages 3, 4 and 5. We also asked teachers to complete the questionnaire in order to explore how they thought their pupils would respond. We received 54 teacher responses. Statistically significant differences in the responses were identified through a chi-square test on SPSS. As what is being taught influences secondary pupil views on research we also consider how the term ‘research’ appears in the national curriculum for England and Wales and the three main English exam boards. The main theoretical construct that informs our analysis of the questionnaire data and the national curriculum is Angela Brew’s 4-tier descriptor of perceptions of research (domino, trading, layer, journey). We use this framework in order to map what, when and how research is presented to school pupils in England and Wales. We also use this framework in order to highlight and discuss certain pupil views that emerged from the questionnaire data and which indicate areas where curriculum and pedagogy intervention may be necessary: pupils seem less confident in their understanding of research as involving the identification of a research question; and, they often see research as a means to confirm one’s own opinion. They do however understand research as involving the generation of new knowledge and the collection of new data, such as interviews and questionnaires as well as laboratory work, field trips and library searches and they appear relatively confident in their statements about their ability to do research, their school experiences of research and the importance of research in their future career choice

Terminal digit preference biases polyp size measurements at endoscopy, computed tomographic colonography and histopathology

BACKGROUND AND STUDY AIMS: Terminal digit preference bias for "pleasing" numbers has been described in many areas of medicine. The aim of this study was to determine whether endoscopists, radiologists, and pathologists exhibit such bias when measuring colorectal polyp diameters. METHODS: Colorectal polyp diameters measured at endoscopy, computed tomographic colonography (CTC), and histopathology were collated from a colorectal cancer screening program and two parallel multicenter randomized trials. Smoothing models were fitted to the data to estimate the expected number of polyps at 1-mm increments, assuming no systematic measurement bias. The difference between the expected and observed numbers of polyps was calculated for each terminal digit using statistical modeling. The impact of measurement bias on per-patient detection rates of polyps ≥ 10 mm was estimated for each modality. RESULTS: A total of 92 124 individual polyps were measured by endoscopy (91 670 screening and 454 from trials), 2385 polyps were measured by CTC (1664 screening, 721 trials), and 79 272 were measured by histopathology (78 783 screening, 489 trials). Clustering of polyp diameter measurements at 5-mm intervals was demonstrated for all modalities, both in the screening program and the trials. The statistical models estimated that per-patient detection rates of polyps ≥ 10 mm were over-inflated by 2.4 % for endoscopy, 3.1 % for CTC, and 3.3 % for histopathology in the screening program, with similar trends in the randomized trials. CONCLUSION: Endoscopists, radiologists, and pathologists all exhibit terminal digit preference when measuring colorectal polyps. This will bias trial data, referral rates for further testing, adenoma surveillance regimens, and comparisons between tests

Testing the Resolving Power of 2-D K^+ K^+ Interferometry

Adopting a procedure previously proposed to quantitatively study two-dimensional pion interferometry, an equivalent 2-D chi^2 analysis was performed to test the resolving power of that method when applied to less favorable conditions, i.e., if no significant contribution from long lived resonances is expected, as in kaon interferometry. For that purpose, use is made of the preliminary E859 K^+ K^+ interferometry data from Si+Au collisions at 14.6 AGeV/c. As expected, less sensitivity is achieved in the present case, although it still is possible to distinguish two distinct decoupling geometries. The present analysis seems to favor scenarios with no resonance formation at the AGS energy range, if the preliminary K^+ K^+ data are confirmed. The possible compatibility of data with zero decoupling proper time interval, conjectured by the 3-D experimental analysis, is also investigated and is ruled out when considering more realistic dynamical models with expanding sources. These results, however, clearly evidence the important influence of the time emission interval on the source effective transverse dimensions. Furthermore, they strongly emphasize that the static Gaussian parameterization, commonly used to fit data, cannot be trusted under more realistic conditions, leading to distorted or even wrong interpretation of the source parameters!Comment: 11 pages, RevTeX, 4 Postscript figures include

The energy gap of intermediate-valent SmB6 studied by point-contact spectroscopy

We have investigated the intermediate valence narrow-gap semiconductor SmB6 at low temperatures using both conventional spear-anvil type point contacts as well as mechanically controllable break junctions. The zero-bias conductance varied between less than 0.01 mikrosiemens and up to 1 mS. The position of the spectral anomalies, which are related to the different activation energies and band gaps of SmB6, did not depend on the the contact size. Two different regimes of charge transport could be distinguished: Contacts with large zero - bias conductance are in the diffusive Maxwell regime. They had spectra with only small non-linearities. Contacts with small zero - bias conductance are in the tunnelling regime. They had larger anomalies, but still indicating a finite 45 % residual quasiparticle density of states at the Fermi level at low temperatures of T = 0.1 K. The density of states derived from the tunelling spectra can be decomposed into two energy-dependent parts with Eg = 21 meV and Ed = 4.5 meV wide gaps, respectively.Comment: 9 pages incl. 13 figure

Microbial Community of Saline, Alkaline Lakes in the Nebraska Sandhills Based on 16S rRNA Gene Amplicon Sequence Data

The Nebraska Sandhills region contains over 1,500 geochemically diverse interdunal lakes, some of which are potassium rich, alkaline, and hypersaline. Here, we report 16S rRNA amplicon pyrosequencing data on the water and sediment microbial communities of eight alkaline lakes in the Sandhills of western Nebraska

Local host response following an intramammary challenge with Staphylococcus fleurettii and different strains of Staphylococcus chromogenes in dairy heifers

Coagulase-negative staphylococci (CNS) are a common cause of subclinical mastitis in dairy cattle. The CNS inhabit various ecological habitats, ranging between the environment and the host. In order to obtain a better insight into the host response, an experimental infection was carried out in eight healthy heifers in mid-lactation with three different CNS strains: a Staphylococcus fleurettii strain originating from sawdust bedding, an intramammary Staphylococcus chromogenes strain originating from a persistent intramammary infection (S. chromogenes IM) and a S. chromogenes strain isolated from a heifer's teat apex (S. chromogenes TA). Each heifer was inoculated in the mammary gland with 1.0 x 10(6) colony forming units of each bacterial strain (one strain per udder quarter), whereas the remaining quarter was infused with phosphate-buffered saline. Overall, the CNS evoked a mild local host response. The somatic cell count increased in all S. fleurettii-inoculated quarters, although the strain was eliminated within 12 h. The two S. chromogenes strains were shed in larger numbers for a longer period. Bacterial and somatic cell counts, as well as neutrophil responses, were higher after inoculation with S. chromogenes IM than with S. chromogenes TA. In conclusion, these results suggest that S. chromogenes might be better adapted to the mammary gland than S. fleurettii. Furthermore, not all S. chromogenes strains induce the same local host response

Multidisciplinary engagement for fencing research informs efficacy and rancher-to-researcher knowledge exchange

Across much of the Western United States, recovery of large carnivore populations is creating new challenges for livestock producers. Reducing the risks of sharing the landscape with recovering wildlife populations is critical to private working lands, which play an vital role in securing future energy, water, food, and fiber for an ever-expanding human population. Fencing is an important mitigation practice that many ranchers, land managers, and conservationists implement to reduce carnivore-livestock conflict. While fencing strategies have been reviewed in the literature, research seldom incorporates knowledge from the people who utilize fencing the most (i.e., livestock producers). Incorporating producers and practitioners early in the process of producing scientific knowledge is proving to be a critical endeavor for enhancing knowledge exchange, better evaluation of the practice, and more realistic understanding of the costs and benefits. Here, we describe how our multidisciplinary effort of co-producing knowledge informs understanding of the effectiveness of various fencing designs and more importantly provides a better mechanism for transferring this knowledge between producers, researchers, and land managers. We explain the process underway and demonstrate that incorporating producers and practitioners from the onset allows research priorities and expected outcomes to be set collaboratively, gives transparency to the agricultural community of the research process, provides a critical lens to evaluate efficacy and functionality, and will inform the practicality of fencing as a conflict prevention tool. We discuss opportunities and challenges of this co-production process and how it can be applied to other realms of fencing and conflict prevention strategies

Imaging Sources with Fast and Slow Emission Components

We investigate two-proton correlation functions for reactions in which fast dynamical and slow evaporative proton emission are both present. In such cases, the width of the correlation peak provides the most reliable information about the source size of the fast dynamical component. The maximum of the correlation function is sensitive to the relative yields from the slow and fast emission components. Numerically inverting the correlation function allows one to accurately disentangle fast dynamical from slow evaporative emission and extract details of the shape of the two-proton source.Comment: 13 pages, 4 figure

Differential Form Valued Forms and Distributional Electromagnetic Sources

Properties of a fundamental double-form of bi-degree $(p,p)$ for $p\ge 0$ are reviewed in order to establish a distributional framework for analysing equations of the form $$\Delta \Phi + \lambda^2 \Phi = {\cal S}$$ where $\Delta$ is the Hodge-de Rham operator on $p-$forms $\Phi$ on ${\bf R}^3$. Particular attention is devoted to singular distributional solutions that arise when the source ${\cal S}$ is a singular $p-$form distribution. A constructive approach to Dirac distributions on (moving) submanifolds embedded in ${\bf R}^3$ is developed in terms of (Leray) forms generated by the geometry of the embedding. This framework offers a useful tool in electromagnetic modeling where the possibly time dependent sources of certain physical attributes, such as electric charge, electric current and polarization or magnetization, are concentrated on localized regions in space.Comment: 40 page