Survival of Escherichia coli on onion during field curing and packout.

The Food and Drug administration has expressed concern that Onions (Allium cepa) irrigated with water contaminated with high rates of Escherichia coli could harbor E. coli on their surface or interior. On the other hand, since onions contain antimicrobial compounds and field conditions may not be conducive to E. coli survival, the E. coli population on the surface of onions might become negligible through the course of field curing. Further, the relationship between the E. coli in the irrigation water to the E. coli on onion bulbs after field curing, harvest, and packout has not been studied. To determine if E. coli should be of concern in onion production, we sought to measure the die-off of E. coli on onions between the last irrigation and harvest and the presence of E. coli on onions after packout. Well water was tested and had no E. coli; ditch water intentionally run across a pasture prior to use had 218 to > 2400 MPN of E. coli/100ml. Onions were sampled from those furrow irrigated (ditch water) and those drip irrigated (well water) starting at lifting 3 September 2013 for four consecutive weeks. At 0 and 28 days after lifting, both interior and exterior of the onions were tested for E. coli. At 7, 14, and 21 days after lifting, only the exterior of the onions was tested. None of the onions contained E. coli internally at 0 or 28 days after lifting. At lifting E. coli was present on the exterior of both the drip and furrow irrigated onions and seemed to be largely unrelated to the irrigation water. The exterior E. coli contamination decreased rapidly after lifting. After harvest and packout on 14 October 2013, no E. coli was detected on the onion bulb exteriors from either irrigation treatment. E. coli introduced into the onion field through furrow irrigation was not present on or in the packed out onion bulbs

Movement of Escherichia coli in soil as applied in irrigation water.

The US Food and Drug Administration (FDA) has proposed that If irrigation water exceeds 235 colony-forming units (CFU) of E. coli /100 ml in any one sample or 126 CFU/100 ml in the average of any five consecutive samples, growers would have to cease using that water in any way that directly contacts the surface of fresh produce (FDA 2013). The FDA has proposed that these E. coli levels are an indication of high risk of bacterial contamination of fresh onion (Allium cepa L.) bulbs regardless of the irrigation system. If onion irrigation exceeds 235 CFU, it is not known whether the contaminated water applied by furrow or drip irrigation actually reaches the onion bulb. Soil could filter E. coli and other bacteria before irrigation water reaches onion bulbs. ?Vaquero? onions were grown on Owyhee silt loam. In our preliminary studies reported here, well water free of E. coli was applied to onions through drip irrigation or through furrow irrigation. A second water source was intentionally enriched with E. coli by being run across a pasture and recaptured prior to use. Furrow and drip irrigation were used to apply this water containing 218 to >2400 MPN/100ml for 11+ hours per irrigation. E. coli was monitored in the soil water at the end of irrigation cycles through direct sampling of the soil. Soil water was also sampled using sterile soil solution capsules (SSSC) to sample E. coli in the soil water that moved into place, to differentiate the movement of soil water from the soil water already in place. Soil water measurements were made adjacent to the water source, half way to the bulbs, and immediately adjacent to the onion bulbs. For furrow irrigation with ditch water the E. coli counts in the soil next to the onion bulbs was only 0% and 21% of the counts in the irrigation water following the first and second irrigations, respectively. During subsequent furrow irrigations, the E. coli counts in the soil water next to the onion bulbs exceeded the counts in the irrigation water. For drip irrigation with ditch water, the E. coli counts in the soil solution next to the onion bulbs remained very low. The soil water sampled by the SSSC adjacent to the onion bulbs drip-irrigated with ditch water also had very low E. coli counts

Gene expression differs in susceptible and resistant amphibians exposed to Batrachochytrium dendrobatidis.

Chytridiomycosis, the disease caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd), has devastated global amphibian biodiversity. Nevertheless, some hosts avoid disease after Bd exposure even as others experience near-complete extirpation. It remains unclear whether the amphibian adaptive immune system plays a role in Bd defence. Here, we describe gene expression in two host species-one susceptible to chytridiomycosis and one resistant-following exposure to two Bd isolates that differ in virulence. Susceptible wood frogs (Rana sylvatica) had high infection loads and mortality when exposed to the more virulent Bd isolate but lower infection loads and no fatal disease when exposed to the less virulent isolate. Resistant American bullfrogs (R. catesbeiana) had high survival across treatments and rapidly cleared Bd infection or avoided infection entirely. We found widespread upregulation of adaptive immune genes and downregulation of important metabolic and cellular maintenance components in wood frogs after Bd exposure, whereas American bullfrogs showed little gene expression change and no evidence of an adaptive immune response. Wood frog responses suggest that adaptive immune defences may be ineffective against virulent Bd isolates that can cause rapid physiological dysfunction. By contrast, American bullfrogs exhibited robust resistance to Bd that is likely attributable, at least in part, to their continued upkeep of metabolic and skin integrity pathways as well as greater antimicrobial peptide expression compared to wood frogs, regardless of exposure. Greater understanding of these defences will ultimately help conservationists manage chytridiomycosis

Simulated filtration pond to remove Escherichia coli from irrigation water.

The United States Food and Drug Administration?s (FDA) proposed water rules to implement the Food Safety Modernization Act (FSMA) could leave some growers, especially those who rely on an irrigation system based on recycled water, unable to irrigate fresh produce with their irrigation water, especially those who rely on an irrigation system based on recycled water. Irrigation water could be treated with chlorine, ozone, or other product to reduce the bacterial load in the water; however, at present not one of these options has been approved by the Environmental Protection Agency for treating irrigation water. In an attempt to reduce the number of bacteria present in irrigation water entering a farm, a simulated filter pond was constructed using gravel, sand, and silt-loam soil. The filter pond sought to utilize in part what occurs naturally with the filtration of water through the soil profile. This natural process provides clean water in wells and aquifers. The simulated pond reduced the Escherichia coli load in water by 95% with a flow rate of 3.9 gal/h/yd2. In order to increase the water productivity of the simulated filter pond, most of the dirt was removed; subsequently the E. coli filtration rate went to 55% and 46%, with flow rates of 12.9 gal/h/yd2 and 17.6 gal/h/yd2, respectively

Insights into the Conformation of Aminofluorene-Deoxyguanine Adduct in a DNA Polymerase Active Site

The active site conformation of the mutagenic fluoroaminofluorene-deoxyguanine adduct (dG-FAF, N-(2′-deoxyguanosin-8-yl)-7-fluoro-2-aminofluorene) has been investigated in the presence of Klenow fragment of Escherichia coli DNA polymerase I (Kfexo−) and DNA polymerase β (pol β) using 19F NMR, insertion assay, and surface plasmon resonance. In a single nucleotide gap, the dG-FAF adduct adopts both a major-groove- oriented and base-displaced stacked conformation, and this heterogeneity is retained upon binding pol β. The addition of a non-hydrolysable 2′-deoxycytosine-5′-[(α,β)-methyleno]triphosphate (dCMPcPP) nucleotide analog to the binary complex results in an increase of the major groove conformation of the adduct at the expense of the stacked conformation. Similar results were obtained with the addition of an incorrect dAMPcPP analog but with formation of the minor groove binding conformer. In contrast, dG-FAF adduct at the replication fork for the Kfexo− complex adopts a mix of the major and minor groove conformers with minimal effect upon the addition of non-hydrolysable nucleotides. For pol β, the insertion of dCTP was preferred opposite the dG-FAF adduct in a single nucleotide gap assay consistent with 19F NMR data. Surface plasmon resonance binding kinetics revealed that pol β binds tightly with DNA in the presence of correct dCTP, but the adduct weakens binding with no nucleotide specificity. These results provide molecular insights into the DNA binding characteristics of FAF in the active site of DNA polymerases and the role of DNA structure and sequence on its coding potential

Universal Holographic Chiral Dynamics in an External Magnetic Field

In this work we further extend the investigation of holographic gauge theories in external magnetic fields, continuing earlier work. We study the phenomenon of magnetic catalysis of mass generation in 1+3 and 1+2 dimensions, using D3/D7- and D3/D5-brane systems, respectively. We obtain the low energy effective actions of the corresponding pseudo Goldstone bosons and study their dispersion relations. The D3/D7 system exhibits the usual Gell-Mann--Oakes--Renner (GMOR) relation and a relativistic dispersion relation, while the D3/D5 system exhibits a quadratic non-relativistic dispersion relation and a modified linear GMOR relation. The low energy effective action of the D3/D5 system is related to that describing magnon excitations in a ferromagnet. We also study properties of general Dp/Dq systems in an external magnetic field and verify the universality of the magnetic catalysis of dynamical symmetry breaking.Comment: 41 pages, 11 figures, references adde

A note on conductivity and charge diffusion in holographic flavour systems

We analyze the charge diffusion and conductivity in a Dp/Dq holographic setup that is dual to a supersymmetric Yang-Mills theory in p+1 dimensions with N_f<< N_c flavour degrees of freedom at finite temperature and nonvanishing U(1) baryon number chemical potential. We provide a new derivation of the results that generalize the membrane paradigm to the present context. We perform a numerical analysis in the particular case of the D3/D7 flavor system. The results obtained support the validity of the Einstein relation at finite chemical potential.Comment: 15 pages, 3 figures, v2 with minor correction

AdS/CFT with Flavour in Electric and Magnetic Kalb-Ramond Fields

We investigate gauge/gravity duals with flavour for which pure-gauge Kalb-Ramond B fields are turned on in the background, into which a D7 brane probe is embedded. First we consider the case of a magnetic field in two of the spatial boundary directions. We show that at finite temperature, i.e. in the AdS-Schwarzschild background, the B field has a stabilizing effect on the mesons and chiral symmetry breaking occurs for a sufficiently large value of the B field. Then we turn to the electric case of a B field in the temporal direction and one spatial boundary direction. In this case, there is a singular region in which it is necessary to turn on a gauge field on the brane in order to ensure reality of the brane action. We find that the brane embeddings are attracted towards this region. Far away from this region, in the weak field case at zero temperature, we investigate the meson spectrum and find a mass shift similar to the Stark effect.Comment: 34 pages, 18 figures, v2: added references and comments on mode decoupling, on thermodynamics and holographic renormalisation, JHEP style, v3: Final published versio

NGN, QCD_2 and chiral phase transition from string theory

We construct a D2-D8-$\bar{D8}$ configuration in string theory, it can be described at low energy by two dimensional field theory. In the weak coupling region, the low energy theory is a nonlocal generalization of Gross-Neveu(GN) model which dynamically breaks the chiral flavor symmetry $U(N_f)_L \times U(N_f)_R$ at large $N_c$ and finite $N_f$. However, in the strong coupling region, we can use the SUGRA/Born-Infeld approximation to describe the low energy dynamics of the system. Also, we analyze the low energy dynamics about the configuration of wrapping the one direction of D2 brane on a circle with anti-periodic boundary condition of fermions. The fermions and scalars on D2 branes get mass and decouple from the low energy theory. The IR dynamics is described by the $QCD_2$ at weak coupling. In the opposite region, the dynamics has a holographic dual description. And we have discussed the phase transition of chiral symmetry breaking at finite temperature. Finally, after performing T-duality, this configuration is related to some other brane configurations.Comment: 30 pages, 3 figures, minor change

Sum rules, plasma frequencies and Hall phenomenology in holographic plasmas

We study the AC optical and hall conductivities of Dp/Dq-branes intersections in the probe approximation and use sum-rules to study various associated transport coefficients. We determine that the presence of massive fundamental matter, as compared to massless fundamental matter described holographically by a theory with no dimensional defects, reduces the plasma frequency. We further show that this is not the case when the brane intersections include defects. We discuss in detail how to implement correctly the regularization of retarded Green's functions so that the dispersion relations are satisfied and the low energy behaviour of the system is physically realistic.Comment: 25 pages, 5 figures. v2.minor changes, published versio