DNA Sequence Analysis of Freshwater Eustigmatophyceae, a Potential Source of Essential Fatty Acids

Freshwater Eustigmatophyceae are a group of microalgae that are considered rare and of low diversity, with only a few genera and species in a single order. Some Eustigmatophyceae produce fatty acids that are important nutrients for aquaculture, as well as for human food consumption. In addition, some Eustigmatophyceae produce hydrocarbons that may be useful in biofuel production. In our studies of the diversity of coccoid algae from Itasca State Park, Minnesota, we discovered several isolates that we tentatively identified as Eustigmatophyceae. Preliminary molecular characterization indicated that these isolates were highly diverse and probably represented species new to science. In this study, we examined fifteen of the Eustigmatophyceae isolates from Itasca State Park using DNA sequence analysis of the plastid rbcL gene. Phylogenetic analyses of these sequences strongly supported Eustigmatophyceae as a monophyletic group and indicated two distinct lineages among our isolates within Eustigmatophyceae. Our results suggest that many of these isolates represent new genera and species. We can also infer the existence of at least two orders in the Eustigmatophyceae, based on the presence of two distinct lineages in the class. In addition to the taxonomic implications, this study will aid in the selection of isolates for further characterization of fatty acids and hydrocarbons, or as part of a regenerative life support system during extended space missions

Polar-cap accelerator and radio emission from pulsars

Electric currents j flow along the open magnetic field lines from the polar caps of neutron stars. Activity of a polar cap depends on the ratio \alpha=j/c\rho_GJ, where \rho_GJ is the corotation charge density. The customary assumption \alpha\approx 1 is not supported by recent simulations of pulsar magnetospheres and we study polar caps with arbitrary \alpha. We argue that no significant activity is generated on field lines with 0<\alpha<1. Charges are extracted from the star and flow along such field lines with low energies. By contrast, if \alpha>1 or \alpha<0, a high voltage is generated, leading to unsteady e^+- discharge on a scale-height smaller than the size of the polar cap. The discharge can power observed pulsars. Voltage fluctuations in the discharge imply unsteady twisting of the open flux tube and generation of Alfven waves. These waves are ducted along the tube and converted to electromagnetic waves, providing a new mechanism for pulsar radiation.Comment: 11 pages, accepted to ApJ

Speeding up simulations of relativistic systems using an optimal boosted frame

It can be computationally advantageous to perform computer simulations in a Lorentz boosted frame for a certain class of systems. However, even if the computer model relies on a covariant set of equations, it has been pointed out that algorithmic difficulties related to discretization errors may have to be overcome in order to take full advantage of the potential speedup. We summarize the findings, the difficulties and their solutions, and show that the technique enables simulations important to several areas of accelerator physics that are otherwise problematic, including self-consistent modeling in three-dimensions of laser wakefield accelerator stages at energies of 10 GeV and above.Comment: To be published in the proceedings of DPF-2009, Detroit, MI, July 2009, eConf C09072

Vegetation Diversity in Natural and Restored Forested Wetland Sites in Southeast Arkansas

The loss of forested wetlands in the Lower Mississippi River Alluvial Valley in Arkansas has altered regional vegetation communities. Multiple restoration projects have been established in this region to restore wetlands and the services they provide. In order to return these functions to the environment, microtopographic features were constructed in 2001 at Bob White Memorial Wetlands Research and Teaching Station (Bob White). Vegetation diversity was examined at Cut-Off Creek Wildlife Management Area (Cutoff), a naturally forested wetland, and Bob White, an area formally converted to cropland that is now undergoing forest wetland restoration. Vegetation diversity is one way to determine if restoration efforts are effectively restoring ecosystem structure and functions to natural wetland conditions. Vegetation diversity and composition were examined across three topographical features: hummocks/ridges, swales, and flats. Vegetation diversity was examined in the spring, summer, and fall. Indices were used for determining composition similarities between Bob White and Cutoff. Bob White had a species richness of 33 and Cutoff’s species richness was 47. Beta diversity between the two sites was 76 species, this value is high and suggests there is low similarity between the two sites. Sorensen-Dice Similarity Index value was calculated as 0.05, where on a scale of zero to one a low value indicates low similarity in composition. The low similarity between the two sites suggests that vegetation composition at Bob White has not been fully restored to conditions comparable to a natural setting. An explanation for this is the presence of Baccharis halimifolia (Eastern baccharis). B. halimifolia inhibits other species from colonizing. Another factor for the difference between the vegetation at Bob White and Cutoff is that Cutoff is an older forest. Hydrophyte communities in a forested wetland take 50 years after restoration begins for them to resemble a natural forested wetland. The results from this study provide mixed evidence that restoration at Bob White is succeeding; there is a high percentage of wetlands species, while vegetation lacks similarity. This study improves our understanding of the influence that anthropogenic changes have on wetland functions as agricultural lands are restored to their previous land cover. Ecosystem functions should continue to be monitored to determine time frames as these functions are restored to Bob Whit

An Enhanced GINGERSimulation Code with Harmonic Emission and HDF5IO Capabilities

GINGER [1] is an axisymmetric, polychromatic (r-z-t) FEL simulation code originally developed in the mid-1980's to model the performance of single-pass amplifiers. Over the past 15 years GINGER's capabilities have been extended to include more complicated configurations such as undulators with drift spaces, dispersive sections, and vacuum chamber wakefield effects; multi-pass oscillators; and multi-stage harmonic cascades. Its coding base has been tuned to permit running effectively on platforms ranging from desktop PC's to massively parallel processors such as the IBM-SP. Recently, we have made significant changes to GINGER by replacing the original predictor-corrector field solver with a new direct implicit algorithm, adding harmonic emission capability, and switching to the HDF5 IO library [2] for output diagnostics. In this paper, we discuss some details regarding these changes and also present simulation results for LCLS SASE emission at {lambda} = 0.15 nm and higher harmonics

Possible new Arkansas endemic plant revealed by DNA sequence analysis, A

Cardamine angustata var. ouachitana, a wildflower in the mustard family (Brassicaceae), was described by Smith in 1982 to include a form of Cardamine found only in the Ouachita Mountains of Arkansas. This variety is morphologically very similar to typical Cardamine angustata. The major difference noted by Smith for the two varieties was the complete lack of leaf hairs (trichomes) in the new variety, whereas typical Cardamine angustata normally possesses trichomes. However, Al-Shehbaz rejected the variety ouachitana and reduced it to synonymy with the typical C. angustata. The recommendation of Al-Shehbaz has been followed and the taxon Cardamine angustata var. ouachitana is currently not accepted by most plant taxonomists. We performed a preliminary evaluation of the status of Cardamine angustata var. ouachitana by comparing ribosomal internal transcribed spacer region DNA sequences from specimens of Cardamine angustata var. ouachitana with sequences of Cardamine angustata from the main range of the species and other related species of Cardamine. Phylogenetic analyses of these data produced an unexpected result; specimens of C. angustata var. ouachitana were actually closely related to C. concatenata, rather than the expected close relationship with C. angustata. However, C. angustata var. ouachitana is morphologically distinct from C. concatenata. These results suggest that Cardamine angustata var. ouachitana is actually a new species found only in the Ouachita Mountains of Arkansas

In vitro assessment of Clostridium difficile PCR ribotype 002: the most prevalent C. difficile ribotype in the United Kingdom.

Simon Baines, Iye Ameh, Jane Freeman, W.N. Fawley, M.H. Wilcox, ‘In vitro assessment of Clostridium difficile PCR ribotype 002: the most prevalent C. difficile ribotype in the United Kingdom’, poster presented at the 25th European Congress on Clinical Microbiology and Infectious Diseases, Copenhagen, Denmark, 25-28 August, 2015.Background: Clostridium difficile infection (CDI) causes substantial morbidity and healthcare expenditure across Europe. UK prevalence of C. difficile PCR ribotype 027 (NAP1) has declined dramatically recently and other ribotypes have emerged, including ribotype 002 (CD002); now the most prevalent UK ribotype. CD002 is also responsible for CDI in many countries across Europe, including: France, Germany, Ireland, and The Netherlands. We assessed the in vitro phenotypic characteristics of CD002 from across Europe to determine traits that may contribute to its increasing clinical prevalence. Material/methods: Sixty CD002 were studied: UK isolates from 2007-2008 (geographically distinct, N=15), UK isolates from 2011-2013 (19 locations, N=22), and non-UK European isolates from 2012-2014 (N=23, 20 locations). Antimicrobial susceptibilities (13 antimicrobials) were evaluated using an agar incorporation method. Maximum specific growth rates (μmax) were calculated and cytotoxin titres (log10-relative units, RU) determined using Vero cell cytotoxicity assays. Biofilm formation was quantified using 96-well microtitre plate assays and sporulation capacities assessed in liquid culture by quantifying spore-formation over 120 h (CFU/mL). Results: All isolates were susceptible metronidazole, vancomycin, tetracycline and linezolid (MICs ≤2 mg/L). Clindamycin resistance (MIC ≥8 mg/L) was more common in non-UK CD002 (30%) than UK strains (5-13%). Resistance to erythromycin, clarithromycin, nitrofurantoin, chloramphenicol, and moxifloxacin was uncommon (5-7%). MICs for penicillin’s remained below resistance breakpoints, regardless of origin, in all but one isolate (ampicillin MIC 2 mg/L). All CD002 were resistant to trimethoprim (MICs >128 mg/L) and ciprofloxacin (MICs ≥8 mg/L). One MDR strain (UK, 2007) was observed that was macrolide, fluoroquinolone, ampicillin, and nitrofurantoin resistant. Significantly faster μmax was seen in non-UK CD002 (0.92 ±0.058 h-1) than recent/older UK strains (0.76 ±0.063/0.69 ±0.028 h-1 respectively) (P<0.001). Cytotoxin production did not differ significantly (median titres 2-3 RU) between CD002 groups. Recent UK/non-UK CD002 formed significantly greater biofilms by 3 days than asynchronous UK CD002 (P<0.001). Sporulation studies demonstrated that recent UK/non-UK CD002 sporulated more at 24 h than older UK CD002; 18.6-fold/31.2-fold respectively (P<0.05), but by 120 h sporulation did not differ. Conclusions: Recent CD002 from diverse European locations were assessed for traits that may help to explain emergence of CD002 in the UK and compared to asynchronous CD002. Previous studies demonstrated elevated CD002 μmax compared to hypervirulent ribotypes 027/078; and the present study demonstrated that recent non-UK CD002 μmax were significantly further elevated vs. UK isolates. Non-UK CD002 were more clindamycin resistant, but other antimicrobial susceptibilities were similar between CD002 groups. Recent CD002 demonstrated significantly increased sporulation capacities at 24 h and more extensive 3 day biofilm formation compared to asynchronous UK CD002, which could enhance their survival and transmission early in an episode CDI. Further phenotypic and genetic studies are required to evaluate further characteristics of CD002 that may be associated with its emergence in the UK.Peer reviewedFinal Published versio

Use of the Lorentz-Boosted Frame Transformation to Simulate Free-Electron Laser Amplifier Physics

Recently [1]it has been pointed out that numerical simulation of some systems containing charged particles with highly relativistic directed motion can by speeded up by orders of magnitude by choice of the proper Lorentz boosted frame. A particularly good example is that of short wavelength free-electron lasers (FELs) in which a high energy (E0&gt;_ 250 MeV) electron beam interacts with a static magnetic undulator. In the optimal boost frame with Lorentz factor gamma F, the red-shifted FEL radiation and blue shifted undulator have identical wavelengths and the number of required time-steps (presuming the Courant condition applies) decreases by a factor of g2 F for fullyelectromagnetic simulation. We have adapted the WARP code [2]to apply this method to several FEL problems including coherent spontaneous emission (CSE) from pre-bunched e-beams, and strong exponential gain in a single pass amplifier configuration. We discuss our results and compare with those from the&quot;standard&quot; FEL simulation approach which adopts the eikonal approximation for propagation ofthe radiation field