The Role of Microenvironment Reagent Solubility on Reaction Kinetics of 4-Nitrophenol Reduction

The Role of Microenvironment Reagent Solubility on Reaction Kinetics of 4-Nitrophenol Reduction Michael Zeevi1 with Andrew Harrison1 and Christina Tang, PhD1 1Department of Chemical and Life Science Engineering, VCU School of Engineering Introduction: Nanoparticles are of increasing interest due to their high surface area to volume ratio, as well as that they enable fine-tuning of the reaction microenvironment. Through flash nanoprecipitation, core-shell polymer nanoreactors were formed by directed self-assembly. Using the reduction of 4-nitrophenol as a model reduction reaction, we investigated the effect of reagent solubility in the nanoreactor microenvironment’s on nanoreactor kinetics. Methods: The standard reaction was conducted at room temperature, with a 1000-fold excess of sodium borohydride in a quartz cuvette for real-time in situ­ UV-Vis analysis. Reagent concentrations were varied to examine the resulting effect on the calculated reaction rate constant. Reagent solubility limits in the nanoreactor microenvironment were estimated from solubility measurements in solvents with similar Hansen solubility parameters. Ethanol was chosen to represent the hydrophilic poly(ethylene) glycol phase and chloroform was chosen to represent the hydrophobic polystyrene phase. The hydrophilic phase had a visual absorbance at nm, and thus UV-Vis spectrometry was used to determine the saturation concentration. 1H NMR analysis with chloroform-D containing an internal standard (v/v TMS 0.03%) was used to measure the reagent solubility in the hydrophobic phase. Results: 4-nitrophenol solubility in ethanol was determined by UV-Vis spectrometry to be . The solubility in chloroform-D was determined by 1H NMR to be . When 4-nitrophenol concentration is varied independently of sodium borohydride, an inverse relationship is observed with respect to the rate constant. However, when 4-nitrophenol and sodium borohydride concentrations are varied concurrently, no change is witnessed in the rate constant above the standard reaction concentration. Conclusions: This experiment demonstrated that the rate of reaction in polystyrene core nanoreactors is not dependent on the reagent concentrations above the standard concentration. Solubility in each phase was measured in an effort to explain this behavior. The differences in solubility observed between the hydrophobic and hydrophilic phases may serve to explain this behavior if the interior, hydrophobic phase is saturated by 4-nitrophenol at the standard concentration. Future work should include study of concentrations at lower values than the standard concentration to determine when a change in the observed rate constant occurs.https://scholarscompass.vcu.edu/uresposters/1287/thumbnail.jp

Affymetrix probes containing runs of contiguous guanines are not gene-specific

High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene's presence. However, we demonstrate by data mining thousands of CEL files from NCBI's GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that 4G-probes should be ignored when calculating gene expression levels. Furthermore, future microarray designs should make no use of 4G-probes

A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia

We have previously discovered that probes containing runs of four or more contiguous guanines are not reliable for measuring gene expression in the Human HG_U133A Affymetrix GeneChip data. These probes are not correlated with other members of their probe set, but they are correlated with each other. We now extend our analysis to different3′GeneChip designs of mouse, rat, and human. We find that, in all these chip designs, the G-stack probes (probes with a run of exactly four consecutive guanines) are correlated highly with each other, indicating that such probes are not reliable measures of gene expression in mammalian studies. Furthermore, there is no specific position of G-stack where the correlation is highest in all the chips. We also find that the latest designs of rat and mouse chips have significantly fewer G-stack probes compared to their predecessors, whereas there has not been a similar reduction in G-stack density across the changes in human chips. Moreover, we find significant changes in RMA values (after removing G-stack probes) as the number of G-stack probes increases.</jats:p

Basal rot of narcissus : understanding pathogenicity in fusarium oxysporum f. sp. narcissi

Fusarium oxysporum is a globally distributed soilborne fungal pathogen causing root rots, bulb rots, crown rots and vascular wilts on a range of horticultural plants. Pathogenic F. oxysporum isolates are highly host specific and are classified as formae speciales. Narcissus is an important ornamental crop and both the quality and yield of flowers and bulbs can be severely affected by a basal rot caused by F. oxysporum f. sp. narcissi (FON); 154 Fusarium isolates were obtained from different locations and Narcissus cultivars in the United Kingdom, representing a valuable resource. A subset of 30 F. oxysporum isolates were all found to be pathogenic and were therefore identified as FON. Molecular characterisation of isolates through sequencing of three housekeeping genes, suggested a monophyletic origin with little divergence. PCR detection of 14 Secreted in Xylem (SIX) genes, previously shown to be associated with pathogenicity in other F. oxysporum f. spp., revealed different complements of SIX7, SIX9, SIX10, SIX12 and SIX13 within FON isolates which may suggest a race structure. SIX gene sequences were unique to FON and SIX10 was present in all isolates, allowing for molecular identification of FON for the first time. The genome of a highly pathogenic isolate was sequenced and lineage specific (LS) regions identified which harboured putative effectors including the SIX genes. Real-time RT-PCR, showed that SIX genes and selected putative effectors were expressed in planta with many significantly upregulated during infection. This is the first study to characterise molecular variation in FON and provide an analysis of the FON genome. Identification of expressed genes potentially associated with virulence provides the basis for future functional studies and new targets for molecular diagnostics

Rapid compensatory evolution promotes the survival of conjugative plasmids

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome

G-spots cause incorrect expression measurement in Affymetrix microarrays

Background: High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene’s probe set will provide a consistent message signifying the gene’s presence. We have tested this expectation by examining the correlations between probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. Results: We have identified probes that are not well-correlated with the other probes in their probeset but nevertheless are highly correlated with probes in other probesets. The common element of these highly correlated probes is that they contain a G-spot (a sequence of four or more guanines). Conclusions: Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes

Nanosecond laser texturing for high friction applications

AbstractA nanosecond pulsed Nd:YAG fibre laser with wavelength of 1064nm was used to texture several different steels, including grade 304 stainless steel, grade 316 stainless steel, Cr–Mo–Al ‘nitriding’ steel and low alloy carbon steel, in order to generate surfaces with a high static friction coefficient. Such surfaces have applications, for example, in large engines to reduce the tightening forces required for a joint or to secure precision fittings easily. For the generation of high friction textures, a hexagonal arrangement of laser pulses was used with various pulse overlaps and pulse energies. Friction testing of the samples suggests that the pulse energy should be high (around 0.8mJ) and the laser pulse overlap should be higher than 50% in order to achieve a static friction coefficient of more than 0.5. It was also noted that laser processing increases the surface hardness of samples which appears to correlate with the increase in friction. Energy-Dispersive X-ray spectroscopy (EDX) measurements indicate that this hardness is caused by the formation of hard metal-oxides at the material surface