Chemoenzymatic synthesis of the pH responsive surfactant octyl β-D-glucopyranoside uronic acid

Methodology was developed to expand the range of benign alkyl glycoside surfactants to include also anionic types. This was demonstrated possible through conversion of the glycoside to its carboxyl derivative. Specifically, octyl β-D-glucopyranoside (OG) was oxidized to the corresponding uronic acid (octyl β-D-glucopyranoside uronic acid, OG-COOH) using the catalyst system T. versicolor laccase/2,2,6,6-tetramethylpiperidinyloxy (TEMPO) and oxygen from air as oxidant. The effects of oxygen supply methodology, concentrations of laccase, TEMPO and OG as well as reaction temperature were evaluated. At 10 mM substrate concentration, the substrate was almost quantitatively converted into product and even at a substrate concentration of 60 mM, 85 % conversion was reached within 24 hours. The surfactant properties of OG-COOH were markedly dependent on pH. Foaming was only observed at low pH, while no foam was formed at pH values above 5.0. Thus, OG-COOH can be an attractive low-foaming surfactant, for example for cleaning applications and emulsification, in a wide pH range (pH 1.5-10.0)

Barefoot vs common footwear:A systematic review of the kinematic, kinetic and muscle activity differences during walking

Habitual footwear use has been reported to influence foot structure with an acute exposure being shown to alter foot position and mechanics. The foot is highly specialised thus these changes in structure/position could influence functionality. This review aims to investigate the effect of footwear on gait, specifically focussing on studies that have assessed kinematics, kinetics and muscle activity between walking barefoot and in common footwear. In line with PRISMA and published guidelines, a literature search was completed across six databases comprising Medline, EMBASE, Scopus, AMED, Cochrane Library and Web of Science. Fifteen of 466 articles met the predetermined inclusion criteria and were included in the review. All articles were assessed for methodological quality using a modified assessment tool based on the STROBE statement for reporting observational studies and the CASP appraisal tool. Walking barefoot enables increased forefoot spreading under load and habitual barefoot walkers have anatomically wider feet. Spatial-temporal differences including, reduced step/stride length and increased cadence, are observed when barefoot. Flatter foot placement, increased knee flexion and a reduced peak vertical ground reaction force at initial contact are also reported. Habitual barefoot walkers exhibit lower peak plantar pressures and pressure impulses, whereas peak plantar pressures are increased in the habitually shod wearer walking barefoot. Footwear particularly affects the kinematics and kinetics of gait acutely and chronically. Little research has been completed in older age populations (50+ years) and thus further research is required to better understand the effect of footwear on walking across the lifespan

Application of Iterative Robust Model-based Optimal Experimental Design for the Calibration of Biocatalytic Models

The aim of model calibration is to estimate unique parameter values from available experimental data, here applied to a biocatalytic process. The traditional approach of first gathering data followed by performing a model calibration is inefficient, since the information gathered during experimentation is not actively used to optimize the experimental design. By applying an iterative robust model-based optimal experimental design, the limited amount of data collected is used to design additional informative experiments. The algorithm is used here to calibrate the initial reaction rate of an ω-transaminase catalyzed reaction in a more accurate way. The parameter confidence region estimated from the Fisher Information Matrix is compared with the likelihood confidence region, which is not only more accurate but also a computationally more expensive method. As a result, an important deviation between both approaches is found, confirming that linearization methods should be applied with care for nonlinear models

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Protection of Biomolecules by Antioxidants - Mechanisms and Applications

Reactive oxygen species (ROS) consisting of various oxygen-based free radicals as well as other reactive non-radical species produced in O2-related metabolism or through other processes are involved in the oxidation of such vital biomolecules as DNA, proteins and lipids. The types of oxidation represented here are known to cause many different diseases and disorders in human beings, such as cancer, Alzheimer's disease and ageing. In addition, oxidation by ROS causes deterioration of food and is sometimes involved in the deactivation of enzymes. A particularly important source of ROS is believed to be the reaction of hydrogen peroxide with transition metal ions, mostly iron and copper, resulting in the formation of the highly deleterious hydroxyl radical, which is able to basically oxidize any organic molecule present. Several antioxidative defence mechanisms have evolved, serving to keep the biomolecules intact and prevent them from being damaged by ROS. The action of small-molecule antioxidants having the function of reacting with free radicals so as to prevent more vital molecules from being oxidized are an important part of this defence. The thesis is based on papers dealing with research on naturally occurring small-molecule antioxidants and the oxidation of DNA and proteins. In the case of DNA, a study was performed of the mechanisms involved, in which reaction intermediates and the formation of adducts were examined, using the iron-mediated Fenton reaction to induce oxidation of the nucleoside dG. Several oxidation products were identified and quantified by use of various reaction conditions. It was found that 8-oxodG, frequently used as a marker for oxidative DNA-damage, was highly susceptible to secondary oxidation. The measured level of this adduct being highly dependent upon both the reaction time and Fenton reagent concentrations involved. Two antioxidants, the iron-chelating antioxidant catechin and the strong radical-scavenger ascorbic acid, were evaluated by use of the same reaction system. It was concluded that catechin was more effective. Again, problems regarding 8-oxodG were observed, its being clearly shown that more reliable results could be obtained when a marker of more than one type was used to evaluate the effects of the antioxidants. In another study the effects of antioxidants were evaluated using a cellular test developed based on the Ames-tester strain Salmonella typhimurium TA102. Oxidation was induced by use of either hydrogen peroxide or the organic peroxide tert-butyl hydroperoxide (tBHP). Similar to the study just referred to, chelating antioxidants, in this case phenolic quercetin and caffeic acid, were the antioxidants found to be most effective. In the protein oxidation study carried out, use was made of the commercially interesting enzyme chloroperoxidase (CPO) from Caldariomyces fumago. This enzyme is able to catalyze various stereoselective oxygen-insertion reactions useful in the synthesis of drugs, for example, a clean source of hydrogen peroxide being used as the external oxidant. The main limitation of CPO is its poor stability, caused by its oxidative inactivation by hydrogen peroxide during the catalytic cycle. It was found that the inactivation was correlated with the oxidation of a key amino acid, a cysteine residue acting as the axial ligand to the prosthetic heme group of the enzyme, along with the disappearance of the heme. Furthermore, the addition of antioxidants significantly improved its operational stability, leading in the best case to 10 times as many turnovers of CPO being observed prior to its inactivation. Again it was found that a chelating antioxidant, caffeic acid in this case, was the antioxidant inhibiting unwanted oxidation the most. One thing these rather differing oxidation studies had in common was that the chelating antioxidants were clearly superior to the antioxidants that only possessed a radical scavenging mechanism. The results indicate two things in particular, first that the Fenton reaction is highly relevant in vivo and is thus a good way of producing radicals in in vitro assays, and secondly that the chelating mechanism is an important antioxidative mechanism, one which involves the action of small-molecule antioxidants both in vitro and in vivo

Evaluation of multiple oxidation products for monitoring effects of antioxidants in Fenton oxidation of 2 '-deoxyguanosine

The objective of this study was to investigate the influence of the two antioxidants, ascorbic acid and (+)catechin, on the oxidation of 2'-deoxyguanosine (dG), using an iron-mediated Fenton reaction. The oxidation products 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8,5'-cyclo-2'-deoxyguanosine, together with the secondary oxidation products guanidinohydantoin and dehydroguanidinohydantoin, were identified and quantified through the use of an LC-MS/MS system. The results obtained showed that catechin inhibited the oxidation better than ascorbic acid did, indicating that the chelating ability of catechin rather than the radical scavenging mechanism alone is vital for the observed antioxidative efficiency. The correlation between the different oxidation products was found to be quite low, primarily because of the instability of 8-oxodG, making it prone to further oxidation. This led to apparent anti- and pro-oxidative results being obtained, emphasizing the potential problems in evaluating oxidative stress, by use of a single marker

Time and concentration dependence of Fenton-induced oxidation of dG

The influence of incubation time and Fenton reagent concentrations was investigated on the oxidation of 2'-deoxyguanosine. The compounds identified and quantified, through use of an LC-MS/MS system, were 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) and 8,5'- cyclo-2'-deoxyguanosine (8,5'cyclodG) and the secondary oxidation products guanidinohydantoin and dehydro-guanidinohydantoin. 8-oxodG and 8,5'cyclodG formed very quickly, reaching a maximum rapidly, but with 8-oxodC a rapid decline occurred thereafter due to its further oxidation into the secondary products, which formed more slowly. Due to the better stability, 8,5'cyclodG correlated better with the general level of oxidation than 8-oxodG. The results emphasize the advantages of measuring other oxidation adducts than 8-oxodG atone

Ability of antioxidants to prevent oxidative mutations in Salmonella typhimurium TA102,

An assay for the ability of antioxidants to prevent mutations induced by various oxidants in Salmonella typhimurium TA102 cells was developed. Protection against hydrogen-peroxide-induced mutagenicity was observed for quercetin, caffeic acid, ascorbic acid and dimethyl sulfoxide (used as a solvent for water-insoluble antioxidants). No protective effect was observed for green tea extract (weakly pro-oxidative), catechin, rutin, sinigrin, ferulic acid and -tocopherol. Mutagenicity caused by tert-butyl hydroperoxide (tBOOH) was prevented most effectively by quercetin and ascorbic acid, whereas weaker effects were observed for green tea extract and for rutin, and no effect being observed for the other antioxidants tested. The results for hydrogen peroxide indicate iron chelation to be the most important protective mechanism. Radical scavenging appeared to be effective only with dimethyl sulfoxide and ascorbic acid, which are effective scavengers of hydroxyl radicals and were used here in high concentrations. It is proposed that the hydrogen-peroxide-induced mutations in the Salmonella cells are caused by hydroxyl radicals generated by iron ions closely associated with DNA. Protection against mutagenicity caused by tert-butyl hydroperoxide appears to occur mainly through the scavenging of alkoxyl and possibly of alkyl radicals