Molecular phylogeny of brachiopods and phoronids based on nuclear-encoded small subunit ribosomal RNA gene sequences

Brachiopod and phoronid phylogeny is inferred from SSU rDNA sequences of 28 articulate and nine inarticulate brachiopods, three phoronids, two ectoprocts and various outgroups, using gene trees reconstructed by weighted parsimony, distance and maximum likelihood methods. Of these sequences, 33 from brachiopods, two from phoronids and one each from an ectoproct and a priapulan are newly determined. The brachiopod sequences belong to 31 different genera and thus survey about 10% of extant genus-level diversity. Sequences determined in different laboratories and those from closely related taxa agree well, but evidence is presented suggesting that one published phoronid sequence (GenBank accession UO12648) is a brachiopod-phoronid chimaera, and this sequence is excluded from the analyses. The chiton, Acanthopleura, is identified as the phenetically proximal outgroup; other selected outgroups were chosen to allow comparison with recent, non-molecular analyses of brachiopod phylogeny. The different outgroups and methods of phylogenetic reconstruction lead to similar results, with differences mainly in the resolution of weakly supported ancient and recent nodes, including the divergence of inarticulate brachiopod sub-phyla, the position of the rhynchonellids in relation to long- and short-looped articulate brachiopod clades and the relationships of some articulate brachiopod genera and species. Attention is drawn to the problem presented by nodes that are strongly supported by non-molecular evidence but receive only low bootstrap resampling support. Overall, the gene trees agree with morphology-based brachiopod taxonomy, but novel relationships are tentatively suggested for thecideidine and megathyrid brachiopods. Articulate brachiopods are found to be monophyletic in all reconstructions, but monophyly of inarticulate brachiopods and the possible inclusion of phoronids in the inarticulate brachiopod clade are less strongly established. Phoronids are clearly excluded from a sister-group relationship with articulate brachiopods, this proposed relationship being due to the rejected, chimaeric sequence (GenBank UO12648). Lineage relative rate tests show no heterogeneity of evolutionary rate among articulate brachiopod sequences, but indicate that inarticulate brachiopod plus phoronid sequences evolve somewhat more slowly. Both brachiopods and phoronids evolve slowly by comparison with other invertebrates. A number of palaeontologically dated times of earliest appearance are used to make upper and lower estimates of the global rate of brachiopod SSU rDNA evolution, and these estimates are used to infer the likely divergence times of other nodes in the gene tree. There is reasonable agreement between most inferred molecular and palaeontological ages. The estimated rates of SSU rDNA sequence evolution suggest that the last common ancestor of brachiopods, chitons and other protostome invertebrates (Lophotrochozoa and Ecdysozoa) lived deep in Precambrian time. Results of this first DNA-based, taxonomically representative analysis of brachiopod phylogeny are in broad agreement with current morphology-based classification and systematics and are largely consistent with the hypothesis that brachiopod shell ontogeny and morphology are a good guide to phylogeny

Mapping of health technology assessment in selected countries

Objectives: The aim of this study was to develop and apply an instrument to map the level of health technology assessment (HTA) development at country level in selected countries. We examined middle-income countries (Argentina, Brazil, India, Indonesia, Malaysia, Mexico, and Russia) and countries well-known for their comprehensive HTA programs (Australia, Canada, and United Kingdom). Methods: A review of relevant key documents regarding the HTA process was performed to develop the instrument which was then reviewed by selected HTAi members and revised. We identified and collected relevant information to map the level of HTA in the selected countries. This was supplemented by information from a structured survey among HTA experts in the selected countries (response rate: 65/385). Results: Mapping of HTA in a country can be done by focusing on the level of institutionalization and the HTA process (identification, priority setting, assessment, appraisal, reporting, dissemination, and implementation in policy and practice). Although HTA is most advanced in industrialized countries, there is a growing community in middle-income countries that uses HTA. For example, Brazil is rapidly developing effective HTA programs. India and Russia are at the very beginning of introducing HTA. The other middle-income countries show intermediate levels of HTA development compared with the reference countries. Conclusions: This study presents a set of indicators for documenting the current level and trends in HTA at country level. The findings can be used as a baseline measurement for future monitoring and evaluation. This will allow a variety of stakeholders to assess the development of HTA in their country, help inform strategies, and justify expenditure for HTA

Genome-Wide Patterns of Arabidopsis Gene Expression in Nature

Organisms in the wild are subject to multiple, fluctuating environmental factors, and it is in complex natural environments that genetic regulatory networks actually function and evolve. We assessed genome-wide gene expression patterns in the wild in two natural accessions of the model plant Arabidopsis thaliana and examined the nature of transcriptional variation throughout its life cycle and gene expression correlations with natural environmental fluctuations. We grew plants in a natural field environment and measured genome-wide time-series gene expression from the plant shoot every three days, spanning the seedling to reproductive stages. We find that 15,352 genes were expressed in the A. thaliana shoot in the field, and accession and flowering status (vegetative versus flowering) were strong components of transcriptional variation in this plant. We identified between ∼110 and 190 time-varying gene expression clusters in the field, many of which were significantly overrepresented by genes regulated by abiotic and biotic environmental stresses. The two main principal components of vegetative shoot gene expression (PCveg) correlate to temperature and precipitation occurrence in the field. The largest PCveg axes included thermoregulatory genes while the second major PCveg was associated with precipitation and contained drought-responsive genes. By exposing A. thaliana to natural environments in an open field, we provide a framework for further understanding the genetic networks that are deployed in natural environments, and we connect plant molecular genetics in the laboratory to plant organismal ecology in the wild

Remote mining for in-situ waste containment. Final report

This document presents the findings of a study conducted at West Virginia University to determine the feasibility of using a combination of longwall mining and standard landfill lining technologies to mitigate contamination of groundwater supplies by leachates from hazardous waste sites

Using Comparative Genomics for Inquiry-Based Learning to Dissect Virulence of Escherichia coli O157:H7 and Yersinia pestis

Genomics and bioinformatics are topics of increasing interest in undergraduate biological science curricula. Many existing exercises focus on gene annotation and analysis of a single genome. In this paper, we present two educational modules designed to enable students to learn and apply fundamental concepts in comparative genomics using examples related to bacterial pathogenesis. Students first examine alignments of genomes of Escherichia coli O157:H7 strains isolated from three food-poisoning outbreaks using the multiple-genome alignment tool Mauve. Students investigate conservation of virulence factors using the Mauve viewer and by browsing annotations available at the A Systematic Annotation Package for Community Analysis of Genomes database. In the second module, students use an alignment of five Yersinia pestis genomes to analyze single-nucleotide polymorphisms of three genes to classify strains into biovar groups. Students are then given sequences of bacterial DNA amplified from the teeth of corpses from the first and second pandemics of the bubonic plague and asked to classify these new samples. Learning-assessment results reveal student improvement in self-efficacy and content knowledge, as well as students’ ability to use BLAST to identify genomic islands and conduct analyses of virulence factors from E. coli O157:H7 or Y. pestis. Each of these educational modules offers educators new ready-to-implement resources for integrating comparative genomic topics into their curricula

Turbulence Regimes and Turbulence Intermittency in the Stable Boundary Layer during CASES-99

An investigation of nocturnal intermittent turbulence during the Cooperative Atmosphere Surface Exchange Study in 1999 (CASES-99) revealed three turbulence regimes at each observation height: 1) regime 1, a weak turbulence regime when the wind speed is less than a threshold value; 2) regime 2, a strong turbulence regime when the wind speed exceeds the threshold value; and 3) regime 3, a moderate turbulence regime when top-down turbulence sporadically bursts into the otherwise weak turbulence regime. For regime 1, the strength of small turbulence eddies is correlated with local shear and weakly related to local stratification. For regime 2, the turbulence strength increases systematically with wind speed as a result of turbulence generation by the bulk shear, which scales with the observation height. The threshold wind speed marks the transition above which the boundary layer approaches near-neutral conditions, where the turbulent mixing substantially reduces the stratification and temperature fluctuations. The preference of the turbulence regimes during CASES-99 is closely related to the existence and the strength of low-level jets. Because of the different roles of the bulk and local shear with regard to turbulence generation under different wind conditions, the relationship between turbulence strength and the local gradient Richardson number varies for the different turbulence regimes. Turbulence intermittency at any observation height was categorized in three ways: turbulence magnitude oscillations between regimes 1 and 2 as wind speed varies back and forth across its threshold value, episodic turbulence enhancements within regime 1 as a result of local instability, and downbursts of turbulence in regime 3.Keywords: Atmosphere, Fluxes, Velocity, Vertical variations, Gravity waves, Doppler lidar, Energy, Low level jet, Surface, MotionsKeywords: Atmosphere, Fluxes, Velocity, Vertical variations, Gravity waves, Doppler lidar, Energy, Low level jet, Surface, Motion

Evaluation of Real-time Catch and Effort Reporting in the U.S. Ilex illecebrosus Fishery

The Illex illecebrosus fishery in the northwestern Atlantic Ocean is a trawl-based fishery. Illex illecebrosus normally lives less than one year, thus managing the fishery using a standard stock assessment approach is difficult. Real-time management is an attractive option. The purpose of this study was to investigate the validity and utility of data reported by commercial vessels for application in real-time management in the I. illecebrosus fishery. The assessment includes evaluating the frequency of erroneous reports, identifying the best measure of effort for catch per unit effort (CPUE) analysis, and examining the influence of vessel type and vessel behavior on subsequent analysis of trends in catch and effort. Incomplete reports occurred 24% of the time in the commercial data. Misreported times and positions occurred less than 1% of the time. Searching time was not discriminated consistently. Searching times and distances were recovered from the more accurately-reported data on tow times and tow positions. Tow duration was more accurately estimated from Captains\u27 reports than tow distance. True distances were underestimated by 10-20% using the position of net deployment and retrieval to measure tow distance because tows did not follow a straight-line path. Effort could be estimated based on tow distance or tow duration. Duration was the most accurate effort term. Searches between tows did not improve subsequent catch. Similarly, overnight transits, arguably a type of searching behavior, did not improve the subsequent day\u27s catch. Thus, vessels, on the average, would have improved trip economics by not searching. Because of the apparent absence of a positive effect of searching and the lower accuracy of searching time and searching distance in comparison to tow-based metrics, particularly tow duration, addition of searching time or searching distance to effort did not materially improve the measurement of CPUE. RSW (refrigerated seawater) trawlers search much less often than freezer trawlers. As a consequence of lower catch and longer duration tows, the CPUE for RSW trawlers is distinctly lower than for freezer trawlers. Catch per tow was higher by more than a factor of two for larger vessels. As a consequence of the higher catch and longer tows, CPUE was significantly higher also for the larger vessels. Managing the I. illecebrosus fishery using an industry-based reporting scheme would require information from freezer and RSW trawlers and specified vessel size categories

Energy- and flux-budget (EFB) turbulence closure model for the stably stratified flows. Part I: Steady-state, homogeneous regimes

We propose a new turbulence closure model based on the budget equations for the key second moments: turbulent kinetic and potential energies: TKE and TPE (comprising the turbulent total energy: TTE = TKE + TPE) and vertical turbulent fluxes of momentum and buoyancy (proportional to potential temperature). Besides the concept of TTE, we take into account the non-gradient correction to the traditional buoyancy flux formulation. The proposed model grants the existence of turbulence at any gradient Richardson number, Ri. Instead of its critical value separating - as usually assumed - the turbulent and the laminar regimes, it reveals a transition interval, 0.1< Ri <1, which separates two regimes of essentially different nature but both turbulent: strong turbulence at Ri<<1; and weak turbulence, capable of transporting momentum but much less efficient in transporting heat, at Ri>1. Predictions from this model are consistent with available data from atmospheric and lab experiments, direct numerical simulation (DNS) and large-eddy simulation (LES).Comment: 40 pages, 6 figures, Boundary-layer Meteorology, resubmitted, revised versio

DETERMINATION OF TYPES OF INDIVIDUALS IN APHIDS, ROTIFERS AND CLADOCERA 1

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/72827/1/j.1469-185X.1929.tb00888.x.pd