Surveying ubiquitin structure by noncovalent attachment of distance constrained bis(crown) ethers

Selective noncovalent adduct protein probing (SNAPP) mass spectrometry was recently developed to study solution-phase conformations of proteins by exploiting the specific affinity between 18-crown-6 ether (18C6) and lysine side chains. To obtain more detailed information about protein tertiary structure, a novel noncovalent cross-linking reagent with two 18C6 molecules bridged by a covalent phenyl linker (called PBC for phenyl bis-crown) was synthesized. PBC introduces a distance constraint into SNAPP experiments where pairs of lysine side chains that are held in proximity by tertiary structure should be the most favored binding sites. Application of this method to ubiquitin reveals that PBC can bind to one lysine in a monodentate fashion or bind to two lysines via a bidentate interaction. Comparison with 18C6 can be used to reveal the mode of binding. For the native state of ubiquitin, bidentate binding of PBC is not observed. The partially denatured A-state, however, contains a single pair of lysines that are both chemically available and spaced by less than approximately 19 A (the maximum distance spanning the crown ether binding sites in PBC). Collision-induced dissociation and site-directed mutagenesis reveal that the bidentate PBC attaches to K29 and K33, which is in agreement with previous structural data on the A-state of ubiquitin. PBC is shown to be an effective probe of protein structure in SNAPP experiments, although assigning the specific residues to which PBC is attached can be experimentally challenging.     

Parallel electrophoretic depletion, fractionation, concentration, and desalting of 96 complex biological samples for mass spectrometry

The preparation of complex biological samples for high-throughput mass spectrometric analyses remains a significant bottleneck, limiting advancement of the capabilities of mass spectrometry (MS) and ultimately limiting development of novel clinical assays. The removal of interfering species (e.g., salts, detergents, and buffers), concentration of dilute analytes, and the reduction of sample complexity are required in order to maximize the quality of resultant MS data. This study describes a novel sample preparation method that makes use of electrophoresis to prepare complex biological samples for high-throughput MS analysis. The method provides for integration of key sample preparation steps, including depletion, fractionation, desalting, and concentration. The prepared samples are captured onto a monolithic reversed-phase capture target that can be analyzed directly by a mass spectrometer. Up to 96 individual samples are simultaneously prepared for MS analysis in under 1 h. For standard proteins added to serum, this method provides femtomole level sensitivity and reproducible label-free detection (coefficient of variation <30%). This study demonstrates that this electrophoretic sample preparation system permits high-throughput sample preparation for mass spectrometric analysis of complex biological samples, such as serum, plasma, and tissue extracts.     

Conversion of 4-Methylanisole Catalyzed by Pt/γ-Al<Subscript>2</Subscript>O<Subscript>3</Subscript> and by Pt/SiO<Subscript>2</Subscript>-Al<Subscript>2</Subscript>O<Subscript>3</Subscript>: Reaction Networks and Evidence of Oxygen Removal

Abstract  

The conversion of 4-methylanisole, a prototypical bio-oil compound, was catalyzed by Pt/Al₂O₃, Pt/SiO₂-Al₂O₃, or HY zeolite at 573 K and atmospheric pressure. More than a dozen products were formed with each catalyst, the most abundant being 4-methylphenol, 2,4-dimethylphenol, and 2,4,6-trimethylphenol; toluene was also a major product when the catalyst was supported platinum with H₂ as a co-reactant. 4-Methylphenol was the only methylphenol isomer formed in significant yields, which indicates that migration of the methyl group on the aromatic ring is not significant under the selected reaction conditions. The data determine approximate reaction networks including reactions forming 4-methylphenol, 2,4-dimethylphenol, and toluene as primary products. The kinetically significant reaction classes were transalkylation, observed with all three catalysts, and hydrogenolysis (including hydrodeoxygenation) and hydrogenation, observed only with the platinum-containing catalysts operating in the presence of H₂. Data such as those reported here provide a starting point for predicting the conversion of whole bio-oils for removal of oxygen and upgrading of fuel properties.     

Light concentration and redistribution in polymer solar cells by plasmonic nanoparticles

We propose an optoelectronic model to investigate polymer solar cells with plasmonic nanoparticles. The optical properties of the plasmonic active layers, approximated by the effective medium theory, are combined with the organic semiconductor model. The simulation suggests the enhancement on short-circuit photocurrent is due to light concentration and redistribution by particle plasmons.     

联合收割机双闭环负荷控制系统的设计

联合收割机是一个高阶时变非线性系统,存在大滞后,工况复杂,简要分析联合收割机数学模型及作业期间可能存在的各种内部、外部扰动。针对收割机负荷控制系统中利用一个控制器综合多个扰动,各参数相互影响,参数调整困难,系统动态性能不够好的问题,提出一种双闭环负荷控制系统,将收割机系统分为行走、作业两部分,分别利用车速闭环和滚筒转速闭环进行控制。车速闭环采用单神经元比例积分微分(Proportion,integration,differentiation,PID)算法,根据车辆行走系统的工况变化不断调整控制参数,尽可能跟踪给定车速。滚筒转速闭环采用直接广义预测控制算法,也可自动适应系统参数和工况的变化,保证滚筒恒定在最佳转速。整个控制算法实时计算量较小,可保证系统具有足够高的实时性。仿真和试验证明双闭环负荷控制系统能获得较高的控制精度和优良的动态特性。     

Effect of sodium citrate plus sodium diacetate or buffered vinegar on quality attributes of enhanced beef top sirloins

As new pathogen intervention products come to market, it is important to ensure that they maintain or improve meat quality. Shelf-life and palatability traits were measured for top sirloins enhanced to 110% with solutions containing 0.5% sodium chloride and 0.4% sodium tripolyphosphate (CNT); CNT with a 1% solution of 80% sodium citrate plus 20% sodium diacetate (SC+D); or CNT with 2% buffered vinegar (VIN) in the final product. Enhancement solution did not influence color over 7days of retail display, except VIN was subjectively more red than CNT and SC+D on d 7 and SC+D had less discoloration than CNT on d 7 (P<0.05). VIN was rated lower (P<0.05) than CNT for trained sensory tenderness and there was no difference in shear force between treatments. SC+D and VIN show promise for use in beef enhancement solutions, however, further sensory studies are warranted.     

Near-real-time combustion monitoring for PCDD/PCDF indicators by GC-REMPI-TOFMS

The boiler exit flue gas of a municipal waste combustor was sampled to evaluate an online monitoring system for chlorobenzene congeners as indicators of polychlorinated dibenzodioxin and dibenzofuran (PCDD/PCDF) concentrations. Continuous measurements of chlorobenzene congeners using gas chromatography coupled to a resonance-enhanced multiphoton ionization - time-of-flight mass spectrometry (GC-REMPI-TOFMS) system were compared over 5-min periods with conventional sampling methods for PCDD/PCDF. Three pairs of values were taken every hour over a period of three days to characterize the combustor's response to transient operating conditions (shutdowns and startups). Isolation of specific chlorobenzene congeners from other same-mass compounds was accomplished by using a GC column separator ahead of the REMPI-TOFMS. The 50-fold variation of PCDD/PCDF concentration was paralleled by similar changes in monitored compounds of 1,4-dichlorobenzene, 1,2,4-trichlorobenzene, 1,2,3-trichlorobenzene, and 1,2,4,5-tetrachlorobenzene. A correlation of R = 0.85 and 0.89 was established between 40 pairs of simultaneous 5-min GC-REMPI-TOFMS measurements of 1,2,4-trichlorobenzene and 5 min conventional sampling and analysis for the TEQ and Total measures of PCDD/PCDF, respectively. The GC-REMPI-TOFMS system can be used to provide frequent measures of correlative PCDD/PCDF concentration thereby allowing for an understanding of measures to minimize PCDD/PCDF formation and develop operational feedback to limit emissions.     

Toluene depletion in produced oil contributes to souring control in a field subjected to nitrate injection

Souring in the Medicine Hat Glauconitic C field, which has a low bottom-hole temperature (30 °C), results from the presence of 0.8 mM sulfate in the injection water. Inclusion of 2 mM nitrate to decrease souring results in zones of nitrate-reduction, sulfate-reduction, and methanogenesis along the injection water flow path. Microbial community analysis by pyrosequencing indicated dominant community members in each of these zones. Nitrate breakthrough was observed in 2-PW, a major water- and sulfide-producing well, after 4 years of injection. Sulfide concentrations at four other production wells (PWs) also reached zero, causing the average sulfide concentration in 14 PWs to decrease significantly. Interestingly, oil produced by 2-PW was depleted of toluene, the preferred electron donor for nitrate reduction. 2-PW and other PWs with zero sulfide produced 95% water and 5% oil. At 2 mM nitrate and 5 mM toluene, respectively, this represents an excess of electron acceptor over electron donor. Hence, continuous nitrate injection can change the composition of produced oil and nitrate breakthrough is expected first in PWs with a low oil to water ratio, because oil from these wells is treated on average with more nitrate than is oil from PWs with a high oil to water ratio.     

Risk of gastrointestinal illness associated with the consumption of rainwater: a systematic review

The collection of rainwater for human consumption is a practice well established in many parts of the world. Much of the research to date regarding this inexpensive and sustainable source has focused on its microbiological or chemical quality and there have been no reviews of epidemiological evidence regarding actual health risks associated with rainwater consumption. Electronic bibliographic databases were searched for epidemiological studies that attempted to quantify the risk of gastrointestinal disease linked to the consumption of harvested rainwater. Online databases were searched from the oldest date up to January 2011. Both observational and experimental studies were included. In addition, reference sections of key articles were searched and authors of previous studies were contacted where appropriate. Studies were assessed for relevance independently and in duplicate. Searches returned a total of 764 articles, 13 met inclusion criteria, 5 of these were outbreak reports, and 9 were studies of other design types. Pooled subgroup analysis suggests that rainwater is associated with reduced risk of illness compared to unimproved supplies (relative risk 0.57 95% CI 0.42, 0.77). There was no significant difference in risk in the pooled analysis of studies that compared rainwater to improved water supplies (relative risk 0.82 95% CI 0.38, 1.73). However, there was heterogeneity with one study showing an excess risk of campylobacteriosis. Classification of outbreak reports determined that 4 reports were "strongly associated with rainwater" while 1 report was "probably associated with rainwater". We conclude that the evidence suggests that rainwater is safer than water from unimproved water supplies. Where feasible rainwater harvesting should be encouraged as a step toward achieving millennium development targets.