Genomic and experimental evidence for multiple metabolic functions in the RidA/YjgF/YER057c/UK114 (Rid) protein family.

BackgroundIt is now recognized that enzymatic or chemical side-reactions can convert normal metabolites to useless or toxic ones and that a suite of enzymes exists to mitigate such metabolite damage. Examples are the reactive imine/enamine intermediates produced by threonine dehydratase, which damage the pyridoxal 5'-phosphate cofactor of various enzymes causing inactivation. This damage is pre-empted by RidA proteins, which hydrolyze the imines before they do harm. RidA proteins belong to the YjgF/YER057c/UK114 family (here renamed the Rid family). Most other members of this diverse and ubiquitous family lack defined functions.ResultsPhylogenetic analysis divided the Rid family into a widely distributed, apparently archetypal RidA subfamily and seven other subfamilies (Rid1 to Rid7) that are largely confined to bacteria and often co-occur in the same organism with RidA and each other. The Rid1 to Rid3 subfamilies, but not the Rid4 to Rid7 subfamilies, have a conserved arginine residue that, in RidA proteins, is essential for imine-hydrolyzing activity. Analysis of the chromosomal context of bacterial RidA genes revealed clustering with genes for threonine dehydratase and other pyridoxal 5'-phosphate-dependent enzymes, which fits with the known RidA imine hydrolase activity. Clustering was also evident between Rid family genes and genes specifying FAD-dependent amine oxidases or enzymes of carbamoyl phosphate metabolism. Biochemical assays showed that Salmonella enterica RidA and Rid2, but not Rid7, can hydrolyze imines generated by amino acid oxidase. Genetic tests indicated that carbamoyl phosphate overproduction is toxic to S. enterica cells lacking RidA, and metabolomic profiling of Rid knockout strains showed ten-fold accumulation of the carbamoyl phosphate-related metabolite dihydroorotate.ConclusionsLike the archetypal RidA subfamily, the Rid2, and probably the Rid1 and Rid3 subfamilies, have imine-hydrolyzing activity and can pre-empt damage from imines formed by amine oxidases as well as by pyridoxal 5'-phosphate enzymes. The RidA subfamily has an additional damage pre-emption role in carbamoyl phosphate metabolism that has yet to be biochemically defined. Finally, the Rid4 to Rid7 subfamilies appear not to hydrolyze imines and thus remain mysterious

Exfoliated hexagonal BN as gate dielectric for InSb nanowire quantum dots with improved gate hysteresis and charge noise

We characterize InSb quantum dots induced by bottom finger gates within a nanowire that is grown via the vapor-liquid-solid process. The gates are separated from the nanowire by an exfoliated 35\,nm thin hexagonal BN flake. We probe the Coulomb diamonds of the gate induced quantum dot exhibiting charging energies of $\sim 2.5\,\mathrm{meV}$ and orbital excitation energies up to $0.3\,\mathrm{meV}$. The gate hysteresis for sweeps covering 5 Coulomb diamonds reveals an energy hysteresis of only $60\mathrm{\mu eV}$ between upwards and downwards sweeps. Charge noise is studied via long-term measurements at the slope of a Coulomb peak revealing potential fluctuations of $\sim 1\,\mu \mathrm{eV}/\mathrm{\sqrt{Hz}}$ at 1\,Hz. This makes h-BN the dielectric with the currently lowest gate hysteresis and lowest low-frequency potential fluctuations reported for low-gap III-V nanowires. The extracted values are similar to state-of-the art quantum dots within Si/SiGe and Si/SiO${_2}$ systems

Improving Cerebral Cortical Magnetic Resonance Imaging Using a Readily Available Surface Coil

Subtle structural deformities of the cerebral cortex have been shown to be the cause of seizures in patients with refractory epilepsy. Brain imaging using high-resolution focused protocols with standard head coils may not provide sufficient image quality needed for evaluating subtle cortical abnormalities. The authors describe the use of a readily available shoulder coil placed over a specific area of the brain that has been clinically determined to enhance the signal to noise and resolution of the cortical surface. Delineating the cortical surface using a shoulder coil can help to detect subtle areas of cortical thickening, blurring of the gray-white matter junction, or focally abnormal gyral and sulcal patterns.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74666/1/j.1552-6569.2004.tb00243.x.pd

Utilizing Animal Waste Amendments to Impaired Rangeland Soils to Reduce Runoff

Composted biological wastes contain vital plant nutrients that assist in plant growth as well as contain organic matter that promotes good soil conditions; both aid in rangeland restoration. Most importantly, it has the potential to restore water availability through increased infiltration and reduced runoff. In this thesis, local sources of composted dairy manure are utilized for application onto the degraded Fort Hood Western Training Grounds in central Texas in hopes to restore the rangeland for continued military training. Small scale rainfall simulations are applied two and eight months post-application of seven different agronomic rates of composted waste treatment (0, 5, 10, 15, 20, 25, and 30 y^3/acre) in order to determine changes in infiltration rates. July 2004 rainfall simulations, two months post application, indicate that composted wastes have not had sufficient time to incorporate into the soil matrix. Percent organic matter of the parent soil is the only significant variable of impact on maximum infiltration capacity. Composted waste treatments are concluded to have no effect on infiltration rates for any of the application rates in the summer rainfall simulations and are observed to exhibit very high variability in the amount of infiltration by a plot. January 2005 rainfall simulations, eight months post waste application, are observed to continue the trend of high variability across all treatment application rates. This variability is attributed to masking any potential effects from the treatment applications. Overall, this high natural variability disables the detection of potential effects of waste application treatments leading to the conclusion that composted waste applications do not affect infiltration on the Fort Hood Western Training Grounds. Runoff nutrient analysis observed nitrate-N to be well below Texas drinking water standards for all plots and phosphate to be above non-standardized values known to cause problematic algal growth. Natural rainfall events at intensities needed to generate runoff observed in this study are rare; therefore, nutrient pollution concern for local water bodies is low

Studies of a Lacustrine-Volcanic Mars Analog Field Site with Mars-2020-like Instruments

On the upcoming Mars‐2020 rover two remote sensing instruments, Mastcam‐Z and SuperCam, and two microscopic proximity science instruments, SHERLOC and PIXL, will collect compositional (mineralogy, chemistry, and organics) data essential for paleoenvironmental reconstruction. The synergies between and limitations of these instruments were evaluated via study of a Mars analog field site in the Mojave Desert, using instruments approximating the data that will be returned by Mars‐2020. A ground truth dataset was generated for comparison to validate the results. The site consists of a succession of clay‐rich mudstones of lacustrine origin, interbedded tuffs, a carbonate‐silica travertine deposit, and gypsiferous mudstone strata. The major geological units were mapped successfully using simulated Mars‐2020 data. Simulated Mastcam‐Z data identified unit boundaries and Fe‐bearing weathering products. Simulated SuperCam passive shortwave infrared and green Raman data were essential in identifying major mineralogical composition and changes in lacustrine facies at distance; this was possible even with spectrally downsampled passive IR data. LIBS and simulated PIXL data discriminated and mapped major element chemistry. Simulated PIXL revealed mm‐scale zones enriched in zirconium, of interest for age dating. SHERLOC‐like data mapped sulfate and carbonate at sub‐mm scale; silicates were identified with increased laser pulses/spot or by averaging of hundreds of spectra. Fluorescence scans detected and mapped varied classes of organics in all samples, characterized further with follow‐on spatially targeted deep‐UV Raman spectra. Development of dedicated organics spectral libraries is needed to aid interpretation. Given these observations, the important units in the outcrop would be sampled and cached for sample return