STAR : Predicting recombination sites from amino acid sequence

Background Designing novel proteins with site-directed recombination has enormous prospects. By locating effective recombination sites for swapping sequence parts, the probability that hybrid sequences have the desired properties is increased dramatically. The prohibitive requirements for applying current tools led us to investigate machine learning to assist in finding useful recombination sites from amino acid sequence alone. Results We present STAR, Site Targeted Amino acid Recombination predictor, which produces a score indicating the structural disruption caused by recombination, for each position in an amino acid sequence. Example predictions contrasted with those of alternative tools, illustrate STAR'S utility to assist in determining useful recombination sites. Overall, the correlation coefficient between the output of the experimentally validated protein design algorithm SCHEMA and the prediction of STAR is very high (0.89). Conclusion STAR allows the user to explore useful recombination sites in amino acid sequences with unknown structure and unknown evolutionary origin. The predictor service is available from http://pprowler.itee.uq.edu.au/star.

Weight-related differences in glucose metabolism and free fatty acid production in two South African population groups

OBJECTIVE The effects of free fatty acids (FFA), leptin, tumour necrosis factor (TNF) alpha and body fat distribution on in vivo oxidation of a glucose load were studied in two South African ethnic groups. DESIGN AND MEASUREMENTS Anthropometric and various metabolic indices were measured at fasting and during a 7h oral glucose tolerance test (OGTT). Body composition was measured using bioelectrical impedance analysis and subcutaneous and visceral fat mass was assessed using a five- and two-level CT-scan respectively. Glucose oxidation was evaluated by measuring the ratio of (13)CO(2) to (12)CO(2) in breath following ingestion of 1-(13)C-labelled glucose. SUBJECTS Ten lean black women (LBW), ten obese black women (OBW), nine lean white women (LWW) and nine obese white women (OWW) were investigated after an overnight fast. RESULTS Visceral fat levels were significantly higher (P < 0.01) in obese white than black women, despite similar body mass indexes (BMIs). There were no ethnic differences in glucose oxidation however; in the lean subjects of both ethnic groups the area under the curve (AUC) was higher than in obese subjects (P < 0.05 for both) and was found to correlate negatively with weight (r = -0.69, P < 0.01) after correcting for age. Basal TNF alpha concentrations were similar in all groups. Percentage suppression of FFAs at 30 min of the OCTT was 24 +/- 12% in OWW and - 38 +/- 23% (P < 0.05) in OBW, ie the 30 min FFA level was higher than the fasting level in the latter group. AUC for FFAs during the late postprandial period (120 - 420 min) was significantly higher in OWW than OBW (P < 0.01) and LWW (P < 0.01) and correlated positively with visceral fat mass independent of age (r = 0.78, P < 0.05) in the OWW only. Leptin levels were higher (P < 0.01) both at fasting and during the course of the OCTT in obese women from both ethnic groups compared to the lean women. CONCLUSIONS Glucose oxidation is reduced in obese subjects of both ethnic groups; inter- and intra-ethnic differences were observed in visceral fat mass and FFA production and it is possible that such differences may play a role in the differing prevalences of obesity-related disorders that have been reported in these two populations.

Electrocatalytic oxidation of ascorbic acid using a single layer of gold nanoparticles immobilized on 1,6-hexanedithiol modified gold electrode

This paper describes the electrocatalytic oxidation of ascorbic acid (AA) in phosphate buffer solution by the immobilized citrate capped gold nanoparticles (AuNPs) on 1,6-hexanedithiol (HDT) modified Au electrode. X-ray photoelectron spectrum (XPS) of HDT suggests that it forms a monolayer on Au surface through one of the two single bondSH groups and the other single bondSH group is pointing away from the electrode surface. The free single bondSH groups of HDT were used to covalently attach colloidal AuNPs. The covalent attachment of AuNPs on HDT monolayer was confirmed from the observed characteristic carboxylate ion stretching modes of citrate attached with AuNPs in the infra-red reflection absorption spectrum (IRRAS) in addition to a higher reductive desorption charges obtained for AuNPs immobilized on HDT modified Au (Au/HDT/AuNPs) electrode in 0.1 M KOH when compared to HDT modified Au (Au/HDT) electrode. The electron transfer reaction of [Fe(CN)6]4−/3− was markedly hindered at the HDT modified Au (Au/HDT) electrode while it was restored with a peak separation of 74 mV after the immobilization of AuNPs on Au/HDT (Au/HDT/AuNPs) electrode indicating a good electronic communication between the immobilized AuNPs and the underlying bulk Au electrode through a HDT monolayer. The Cottrell slope obtained from the potential-step chronoamperometric measurements for the reduction of ferricyanide at Au/HDT/AuNPs was higher than that of bare Au electrode indicating the increased effective surface area of AuNPs modified electrode. The Au/HDT/AuNPs electrode exhibits excellent electrocatalytic activity towards the oxidation of ascorbic acid (AA) by enhancing the oxidation peak current to more than two times with a 210 mV negative shift in the oxidation potential when compared to a bare Au electrode. The standard heterogeneous electron transfer rate constant (ks) calculated for AA oxidation at Au/HDT/AuNPs electrode was 5.4 × 10−3 cm s−1. The oxidation peak of AA at Au/HDT/AuNPs electrode was highly stable upon repeated potential cycling. Linear calibration plot was obtained for AA over the concentration range of 1–110 μM with a correlation coefficient of 0.9950. The detection limit of AA was found to be 1 μM. The common physiological interferents such as glucose, oxalate ions and urea do not show any interference within the detection limit of AA. The selectivity of the AuNPs modified electrode was illustrated by the determination of AA in the presence of uric acid.

The effects of geochemical conditions on the establishment and growth of mangrove seedlings in acid sulfate soil environments

Acid sulfate soils (ASS) is a stress factor that is responsible for the failure of some mangrove restoration projects, including abandoned aquaculture ponds converted from mangrove ecosystems. Through experimental and field studies, this research provides a better understanding of the biogeochemistry of ASS disturbance and the response of mangrove seedlings (Rhizophoraceae) under high metal levels and acidic conditions. This study found that mangrove restorations under ASS disturbance can work but with lower numbers of survived seedlings. To prevent toxicity under high levels of metal, seedlings retained metals in their roots and sparingly distributed them into aerial parts with low mobility. The presence of high levels of potential acidity parameters would allow pyrite to oxidise, thus increasing metal levels and acidity, which in turn affected the survival and growth of the seedlings.

Inhibition of form-deprivation myopia by a GABAAOr receptor antagonist, (1,2,5,6-tetrahydropyridin-4-yl) methylphosphinic acid (TPMPA), in guinea pigs

Purpose To investigate the effects of the relatively selective GABAAOr receptor antagonist (1,2,5,6-tetrahydropyridin-4-yl) methylphosphinic acid (TPMPA) on form-deprivation myopia (FDM) in guinea pigs. Methods A diffuser was applied monocularly to 30 guinea pigs from day 10 to 21. The animals were randomized to one of five treatment groups. The deprived eye received daily sub-conjunctival injections of 100 μl TPMPA at a concentration of (i) 0.03 %, ( ii) 0.3 %, or (iii) 1 %, a fourth group (iv) received saline injections, and another (v) no injections. The fellow eye was left untreated. An additional group received no treatment to either eye. Prior to and at the end of the treatment period, refraction and ocular biometry were performed. Results Visual deprivation produced relative myopia in all groups (treated versus untreated eyes, P < 0.05). The amount of myopia was significantly affected by the drug treatment (one-way ANOVA, P < 0.0001); myopia was less in deprived eyes receiving either 0.3 % or 1 % TPMPA (saline = −4.38 ± 0.57D, 0.3 % TPMPA = −3.00 ± 0.48D, P < 0.01; 1 % TPMPA = −0.88 ± 0.51D, P < 0.001). The degree of axial elongation was correspondingly less (saline = 0.13 ± 0.02 mm, 0.3 % TPMPA = 0.09 ± 0.01 mm, P < 0.01, 1 % TPMPA = 0.02 ± 0.01 mm, P < 0.001) as was the VC elongation (saline = 0.08 ± 0.01 mm, 0.3 % TPMPA = 0.05 ± 0.01 mm, P < 0.01, 1 % TPMPA = 0.01 ± 0.01 mm; P < 0.001). ACD and LT were not affected (one-way ANOVA, P > 0.05). One percent TPMPA was more effective at inhibiting myopia than 0.3 % (P < 0.01), and 0.03 % did not appreciably inhibit the myopia (0.03 % TPMPA versus saline, P > 0.05). Conclusions Sub-conjunctival injections of TPMPA inhibit FDM in guinea pig models in a dose-dependent manner.

The fatty acid synthase inhibitor triclosan : repurposing an anti-microbial agent for targeting prostate cancer

Inhibition of FASN has emerged as a promising therapeutic target in cancer, and numerous inhibitors have been investigated. However, severe pharmacological limitations have challenged their clinical testing. The synthetic FASN inhibitor triclosan, which was initially developed as a topical antibacterial agent, is merely affected by these pharmacological limitations. Yet, little is known about its mechanism in inhibiting the growth of cancer cells. Here we compared the cellular and molecular effects of triclosan in a panel of eight malignant and non-malignant prostate cell lines to the well-known FASN inhibitors C75 and orlistat, which target different partial catalytic activities of FASN. Triclosan displayed a superior cytotoxic profile with a several-fold lower IC50 than C75 or orlistat. Structure-function analysis revealed that alcohol functionality of the parent phenol is critical for inhibitory action. Rescue experiments confirmed that end product starvation was a major cause of cytotoxicity. Importantly, triclosan, C75 and orlistat induced distinct changes to morphology, cell cycle, lipid content and the expression of key enzymes of lipid metabolism, demonstrating that inhibition of different partial catalytic activities of FASN activates different metabolic pathways. These finding combined with its well-documented pharmacological safety profile make triclosan a promising drug candidate for the treatment of prostate cancer.

Nursing Management : Fluid, Electrolyte, and Acid-Base Imbalances

Lewis’s Medical-Surgical Nursing: Assessment and Management of Clinical Problems, 4th Edition is the most comprehensive go-to reference for essential information about all aspects of professional nursing care of patients. Using the nursing process as a framework for practice, the fourth edition has been extensively revised to reflect the rapid changing nature of nursing practice and the increasing focus on key nursing care priorities. Building on the strengths of the third Australian and New Zealand edition and incorporating relevant global nursing research and practice from the prominent US title Medical-Surgical Nursing, 9Th Edition, Lewis’s Medical-Surgical Nursing, 4th Edition is an essential resource for students seeking to understand the role of the professional nurse in the contemporary health environment.

Interaction of erythrocyte eicosapentaenoic acid and physical activity predicts reduced risk of mild cognitive impairment

Objectives To evaluate relationships between self-reported physical activity, proportions of long-chain omega-3 polyunsaturated fatty acids (LCn3) in erythrocyte content (percentage of total fatty acids) and risk of mild cognitive impairment (MCI) in older adults. Method A cross-sectional study was conducted. Community-dwelling male and female (n = 84) participants over the age of 65 years with and without MCI were tested for erythrocyte proportions of the LCn3s eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA). Physical activity was measured using a validated questionnaire. Results The interaction between erythrocyte EPA, but not DHA, and increased physical activity was associated with increased odds of a non-MCI classification. Conclusion An interaction between physical activity and erythrocyte EPA content (percentage of fatty acids) significantly predicted MCI status in older adults. Randomised control trials are needed to examine the potential for supplementation with EPA in combination with increased physical activity to mitigate the risk of MCI in ageing adults.

Preparation and characterization of poly(lactic-co-glycolic acid) microparticles containing DNA molecules encoding a malaria vaccine candidate

Background A novel ultrasonic atomization approach for the formulation of biodegradable poly(lactic-co-glycolic acid) (PLGA) microparticles of a malaria DNA vaccine is presented. A 40 kHz ultrasonic atomization device was used to create the microparticles from a feedstock containing 5 volumes of 0.5% w/v PLGA in acetone and 1 volume of condensed DNA which was fed at a flow rate of 18ml h-1. The plasmid DNA vectors encoding a malaria protein were condensed with a cationic polymer before atomization. Results High levels of gene expression in vitro were observed in COS-7 cells transfected with condensed DNA at a nitrogen to phosphate (N/P) ratio of 10. At this N/P ratio, the condensed DNA exhibited a monodispersed nanoparticle size (Z-average diameter of 60.8 nm) and a highly positive zeta potential of 38.8mV. The microparticle formulations of malaria DNA vaccine were quality assessed and it was shown that themicroparticles displayed high encapsulation efficiencies between 82-96% and a narrow size distribution in the range of 0.8-1.9 μm. In vitro release profile revealed that approximately 82% of the DNA was released within 30 days via a predominantly diffusion controlledmass transfer system. Conclusions This ultrasonic atomization technique showed excellent particle size reproducibility and displayed potential as an industrially viable approach for the formulation of controlled release particles.

Degradation of hydroxycinnamic acid mixtures in aqueous sucrose solutions by the Fenton process

The degradation efficiencies and behaviors of caffeic acid (CaA), p-coumaric acid (pCoA) and ferulic acid (FeA) in aqueous sucrose solutions containing the mixture of these hydroxycinnamic acids (HCAs) mixtures were studied by the Fenton oxidation process. Central composite design and multi-response surface methodology were used to evaluate and optimize the interactive effects of process parameters. Four quadratic polynomial models were developed for the degradation of each individual acid in the mixture and the total HCAs degraded. Sucrose was the most influential parameter that significantly affected the total amount of HCA degraded. Under the conditions studied there was < 0.01% loss of sucrose in all reactions. The optimal values of the process parameters for a 200 mg/L HCA mixture in water (pH 4.73, 25.15 °C) and sucrose solution (13 mass%, pH 5.39, 35.98 °C) were 77% and 57% respectively. Regression analysis showed goodness of fit between the experimental results and the predicted values. The degradation behavior of CaA differed from those of pCoA and FeA, where further CaA degradation is observed at increasing sucrose and decreasing solution pH. The differences (established using UV/Vis and ATR-FTIR spectroscopy) were because, unlike the other acids, CaA formed a complex with Fe(III) or with Fe(III) hydrogen-bonded to sucrose, and coprecipitated with lepidocrocite, an iron oxyhydroxide.

Exploration of the fundamental equilibrium behaviour of calcium exchange with weak acid cation resins

This study evaluated the complexity of calcium ion exchange with sodium exchanged weak acid cation resin (DOW MAC-3). Exchange equilibria recorded for a range of different solution normalities revealed profiles which were represented by conventional “L” or “H” type isotherms at low values of equilibrium concentration (Ce) of calcium ions, plus a superimposed region of increasing calcium uptake was observed at high Ce values. The loading of calcium ions was determined to be ca. 53.5 to 58.7 g/kg of resin when modelling only the sorption curve created at low Ce values,which exhibited a well-defined plateau. The calculated calcium ion loading capacity for DOWMAC-3 resin appeared to correlate with the manufacturer's recommendation. The phenomenon of super equivalent ion exchange (SEIX) was observed when the “driving force” for the exchange process was increased in excess of 2.25 mmol calcium ions per gram of resin in the starting solution. This latter event was explained in terms of displacement of sodium ions from sodium hydroxide solution which remained in the resin bead following the initial conversion of the as supplied “H+” exchanged resin sites to the “Na+” version required for softening studies. Evidence for hydrolysis of a small fraction of the sites on the sodium exchanged resin surface was noted. The importance of carefully choosing experimental parameters was discussed especially in relation to application of the Langmuir–Vageler expression. This latter model which compared the ratio of the initial calcium ion concentration in solution to resin mass, versus final equilibrium loading of the calcium ions on the resin; was discovered to be an excellent means of identifying the progress of the calcium–sodium ion exchange process. Moreover, the Langmuir–Vageler model facilitated standardization of various calcium–sodium ion exchange experiments which allowed systematic experimental design.

Equilibrium and column studies of iron exchange with strong acid cation resin

The exchange of iron species from iron (III) chloride solutions with a strong acid cation resin has been investigated in relation to a variety of water and wastewater applications. A detailed equilibrium isotherm analysis was conducted wherein models such as Langmuir Vageler, Competitive Langmuir, Freundlich, Temkin, Dubinin Astakhov, Sips and Brouers-Sotolongo were applied to the experimental data. An important conclusion was that both the bottle-point method and solution normality used to generate the ion exchange equilibrium information influenced which sorption model fitted the isotherm profiles optimally. Invariably, the calculated value for the maximum loading of iron on strong acid cation resin was substantially higher than the value of 47.1 g/kg of resin which would occur if one Fe3+ ion exchanged for three “H+” sites on the resin surface. Consequently, it was suggested that above pH 1, various iron complexes sorbed to the resin in a manner which required less than 3 sites per iron moiety. Column trials suggested that the iron loading was 86.6 g/kg of resin when 1342 mg/L Fe (III) ions in water were flowed at 31.7 bed volumes per hour. Regeneration with 5 to 10 % HCl solutions reclaimed approximately 90 % of exchange sites.

An examination of isotherm generation : impact of bottle-point method upon potassium ion exchange with strong acid cation resin

This paper relates to the importance of impact of the chosen bottle-point method when conducting ion exchange equilibria experiments. As an illustration, potassium ion exchange with strong acid cation resin was investigated due to its relevance to the treatment of various industrial effluents and groundwater. The “constant mass” bottle-point method was shown to be problematic in that depending upon the resin mass used the equilibrium isotherm profiles were different. Indeed, application of common equilibrium isotherm models revealed that the optimal fit could be with either the Freundlich or Temkin equations, depending upon the conditions employed. It could be inferred that the resin surface was heterogeneous in character, but precise conclusions regarding the variation in the heat of sorption were not possible. Estimation of the maximum potassium loading was also inconsistent when employing the “constant mass” method. The “constant concentration” bottle-point method illustrated that the Freundlich model was a good representation of the exchange process. The isotherms recorded were relatively consistent when compared to the “constant mass” approach. Unification of all the equilibrium isotherm data acquired was achieved by use of the Langmuir Vageler expression. The maximum loading of potassium ions was predicted to be at least 116.5 g/kg resin.

Weak acid extractable metals in Bramble Bay, Queensland, Australia : temporal behaviour, enrichment and source apportionment

Sediment samples were taken from six sampling sites in Bramble Bay, Queensland, Australia between February and November in 2012. They were analysed for a range of heavy metals including Al, Fe, Mn, Ti, Ce, Th, U, V, Cr, Co, Ni, Cu, Zn, As, Cd, Sb, Te, Hg, Tl and Pb. Fraction analysis, enrichment factors and Principal Component Analysis –Absolute Principal Component Scores (PCA-APCS) were carried out in order to assess metal pollution, potential bioavailability and source apportionment. Cr and Ni exceeded the Australian Interim Sediment Quality Guidelines at some sampling sites, while Hg was found to be the most enriched metal. Fraction analysis identified increased weak acid soluble Hg and Cd during the sampling period. Source apportionment via PCA-APCS found four sources of metals pollution, namely, marine sediments, shipping, antifouling coatings and a mixed source. These sources need to be considered in any metal pollution control measure within Bramble Bay.

A novel population balance model for the dilute acid hydrolysis of hemicellulose

Acid hydrolysis is a popular pretreatment for removing hemicellulose from lignocelluloses in order to produce a digestible substrate for enzymatic saccharification. In this work, a novel model for the dilute acid hydrolysis of hemicellulose within sugarcane bagasse is presented and calibrated against experimental oligomer profiles. The efficacy of mathematical models as hydrolysis yield predictors and as vehicles for investigating the mechanisms of acid hydrolysis is also examined. Experimental xylose, oligomer (degree of polymerisation 2 to 6) and furfural yield profiles were obtained for bagasse under dilute acid hydrolysis conditions at temperatures ranging from 110C to 170C. Population balance kinetics, diffusion and porosity evolution were incorporated into a mathematical model of the acid hydrolysis of sugarcane bagasse. This model was able to produce a good fit to experimental xylose yield data with only three unknown kinetic parameters ka, kb and kd. However, fitting this same model to an expanded data set of oligomeric and furfural yield profiles did not successfully reproduce the experimental results. It was found that a ``hard-to-hydrolyse'' parameter, $\alpha$, was required in the model to ensure reproducibility of the experimental oligomer profiles at 110C, 125C and 140C. The parameters obtained through the fitting exercises at lower temperatures were able to be used to predict the oligomer profiles at 155C and 170C with promising results. The interpretation of kinetic parameters obtained by fitting a model to only a single set of data may be ambiguous. Although these parameters may correctly reproduce the data, they may not be indicative of the actual rate parameters, unless some care has been taken to ensure that the model describes the true mechanisms of acid hydrolysis. It is possible to challenge the robustness of the model by expanding the experimental data set and hence limiting the parameter space for the fitting parameters. The novel combination of ``hard-to-hydrolyse'' and population balance dynamics in the model presented here appears to stand up to such rigorous fitting constraints.