A proteomic investigation into the bacteriostatic mechanism of glycocin F, secreted by Lactiplantibacillus plantarum KW30 : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry at Massey University, Manawatū, New Zealand

Figures are re-used with the respective publishers' permission.Antimicrobial resistance to clinical antibiotics has increased significantly over the past decade and continues to pose a serious public health concern worldwide. Due to this rise in antimicrobial resistance, clinical health professionals and scientific researchers alike have been eager to explore alternative options in place of traditional treatments (e.g. antibiotics). Bacteriocins are antimicrobial polypeptides secreted by bacteria. The therapeutic potential of these diverse natural products is largely unexplored and, as such, they constitute a novel source of potentially viable treatment options in the fight against resistant strains of pathogenic bacteria. At the most basic level, bacteriocins can be divided into two groups, those that are modified and those that are not. Glycocins fall into the former group as they are post-translationally modified by one or more monosaccharide moieties. These monosaccharides can be O-linked to the hydroxyl group of serine or threonine residues, or S-linked to the sidechain thiol group of cysteine residues. Glycocin F (GccF) is a doubly glycosylated bacteriocin secreted by the lactic acid bacterium Lactiplantibacillus plantarum (Lb. plantarum) KW30 that inhibits the growth of its bacterial targets. Although it is known that GccF is bacteriostatic, the exact mechanism by which it inhibits cell growth within two minutes, at nanomolar (nM) concentrations, remains unknown. Previous bacterial genomics, nuclear magnetic resonance (NMR) spectroscopy, total chemical synthesis and analysis of synthetic peptides, and transcriptomic studies have provided the framework for this present research. Collectively, these studies led to the proposal that GccF binds to the transmembrane domain of a specific N-acetylglucosamine (GlcNAc) phosphotransferase system (PTS) transporter on the surface of targeted bacterial cells, causing the amplification of a signal that results in the rapid onset of bacteriostasis. This project used proteomic methods to investigate changes that occurred in the proteome of susceptible cells when treated with GccF. Cultures were sampled immediately before, and then at specific timepoints after the addition of GccF. Sampled cells were separated into membrane and cytosol fractions, then analysed for changes in their proteomes. Changes in the abundances of specific target cell proteins were linked to biochemical pathways that may be affected by treatment with GccF, providing clues to its mechanism of action. The results showed clear changes in the abundance of proteins involved in cell wall metabolism and protein translation in GccF-treated Lb. plantarum ATCC 8014 cells

A vibrational circular dichroism implementation within a Slater-type-orbital based density functional framework and its application to hexa- and hepta-helicenes

We describe the implementation of the rotational strengths for vibrational circular dichroism (VCD) in the Slater-type orbital based Amsterdam Density Functional (ADF) package. We show that our implementation, which makes use of analytical derivative techniques and London atomic orbitals, yields origin independent rotational strengths. The basis set dependence in the particular case of Slater-type basis functions is also discussed. It turns out that the triple zeta STO basis sets with one set of polarization functions (TZP) are adequate for VCD calculations. The origin- dependence of the atomic axial tensors is checked by a distributed origin gauge implementation. The distributed and common origin gauge implementations yield virtually identical atomic axial tensors with the Slater-type basis sets employed here, proving that our implementation yields origin independent rotational strengths. We verify the implementation for a set of benchmark molecules, for which the dependence of the VCD spectra on the particular choice of the exchange–correlation functional is studied. The pure functionals BP86 and OLYP show a particularly good performance. Then, we apply this approach to study the VCD spectra of hexa- and hepta- helicenes. In particular we focus on relationships between the sign of the rotational strengths of the two helicenes

Transmission Spectra of Transiting Planet Atmospheres: Model Validation and Simulations of the Hot Neptune GJ 436b for JWST

We explore the transmission spectrum of the Neptune-class exoplanet GJ 436b, including the possibility that its atmospheric opacity is dominated by a variety of non- equilibrium chemical products. We also validate our transmission code by demonstrating close agreement with analytic models that use only Rayleigh scattering or water vapor opacity. We find broad disagreement with radius variations predicted by another published model. For GJ 436b, the relative coolness of the planet's atmosphere, along with its implied high metallicity, may make it dissimilar in character compared to "hot Jupiters." Some recent observational and modeling efforts suggest low relative abundances of H2O and CH4 present in GJ 436b's atmosphere, compared to calculations from equilibrium chemistry. We include these characteristics in our models and examine the effects of absorption from methane-derived higher order hydrocarbons. Significant absorption from HCN and C2H2 are found throughout the infrared, while C2H4 and C2H6 are less easily seen. We perform detailed simulations of JWST observations, including all likely noise sources, and find that we will be able to constrain chemical abundance regimes from this planet's transmission spectrum. For instance, the width of the features at 1.5, 3.3, and 7 microns indicates the amount of HCN versus C2H2 present. The NIRSpec prism mode will be useful due to its large spectral range and the relatively large number of photo-electrons recorded per spectral resolution element. However, extremely bright host stars like GJ 436 may be better observed with a higher spectroscopic resolution mode in order to avoid detector saturation. We find that observations with the MIRI low resolution spectrograph should also have high signal-to-noise in the 5 - 10 micron range due to the brightness of the star and the relatively low spectral resolution (R ~ 100) of this mode.Comment: 33 pages, 12 figures, Accepted to Ap

Predictive use of the Maximum Entropy Production principle for Past and Present Climates

In this paper, we show how the MEP hypothesis may be used to build simple climate models without representing explicitly the energy transport by the atmosphere. The purpose is twofold. First, we assess the performance of the MEP hypothesis by comparing a simple model with minimal input data to a complex, state-of-the-art General Circulation Model. Next, we show how to improve the realism of MEP climate models by including climate feedbacks, focusing on the case of the water-vapour feedback. We also discuss the dependence of the entropy production rate and predicted surface temperature on the resolution of the model

SCAMP:standardised, concentrated, additional macronutrients, parenteral nutrition in very preterm infants: a phase IV randomised, controlled exploratory study of macronutrient intake, growth and other aspects of neonatal care

<p>Abstract</p> <p>Background</p> <p>Infants born <29 weeks gestation are at high risk of neurocognitive disability. Early postnatal growth failure, particularly head growth, is an important and potentially reversible risk factor for impaired neurodevelopmental outcome. Inadequate nutrition is a major factor in this postnatal growth failure, optimal protein and calorie (macronutrient) intakes are rarely achieved, especially in the first week. Infants <29 weeks are dependent on parenteral nutrition for the bulk of their nutrient needs for the first 2-3 weeks of life to allow gut adaptation to milk digestion. The prescription, formulation and administration of neonatal parenteral nutrition is critical to achieving optimal protein and calorie intake but has received little scientific evaluation. Current neonatal parenteral nutrition regimens often rely on individualised prescription to manage the labile, unpredictable biochemical and metabolic control characteristic of the early neonatal period. Individualised prescription frequently fails to translate into optimal macronutrient delivery. We have previously shown that a standardised, concentrated neonatal parenteral nutrition regimen can optimise macronutrient intake.</p> <p>Methods</p> <p>We propose a single centre, randomised controlled exploratory trial of two standardised, concentrated neonatal parenteral nutrition regimens comparing a standard macronutrient content (maximum protein 2.8 g/kg/day; lipid 2.8 g/kg/day, dextrose 10%) with a higher macronutrient content (maximum protein 3.8 g/kg/day; lipid 3.8 g/kg/day, dextrose 12%) over the first 28 days of life. 150 infants 24-28 completed weeks gestation and birthweight <1200 g will be recruited. The primary outcome will be head growth velocity in the first 28 days of life. Secondary outcomes will include a) auxological data between birth and 36 weeks corrected gestational age b) actual macronutrient intake in first 28 days c) biomarkers of biochemical and metabolic tolerance d) infection biomarkers and other intravascular line complications e) incidence of major complications of prematurity including mortality f) neurodevelopmental outcome at 2 years corrected gestational age</p> <p>Trial registration</p> <p>Current controlled trials: <a href="http://www.controlled-trials.com/ISRCTN76597892">ISRCTN76597892</a>; EudraCT Number: 2008-008899-14</p

Cysteinyl-tRNA Deacylation Can Be Uncoupled from Protein Synthesis

Aminoacyl-tRNA synthetases (ARSs) are critical components of protein translation, providing ribosomes with aminoacyl-tRNAs. In return, ribosomes release uncharged tRNAs as ARS substrates. Here, we show that tRNA deacylation can be uncoupled from protein synthesis in an amino acid specific manner. While tRNAs coupled to radiolabeled Met, Leu Lys, or Ser are stable in cells following translation inhibition with arsenite, radiolabeled Cys is released from tRNA at a high rate. We discuss possible translation independent functions for tRNACys

Deletion of the GABAA α2-subunit does not alter self dministration of cocaine or reinstatement of cocaine seeking

Rationale GABAA receptors containing α2-subunits are highly represented in brain areas that are involved in motivation and reward, and have been associated with addiction to several drugs, including cocaine. We have shown previously that a deletion of the α2-subunit results in an absence of sensitisation to cocaine. Objective We investigated the reinforcing properties of cocaine in GABAA α2-subunit knockout (KO) mice using an intravenous self-administration procedure. Methods α2-subunit wildtype (WT), heterozygous (HT) and KO mice were trained to lever press for a 30 % condensed milk solution. After implantation with a jugular catheter, mice were trained to lever press for cocaine (0.5 mg/kg/infusion) during ten daily sessions. Responding was extinguished and the mice tested for cue- and cocaine-primed reinstatement. Separate groups of mice were trained to respond for decreasing doses of cocaine (0.25, 0.125, 0.06 and 0.03 mg/kg). Results No differences were found in acquisition of lever pressing for milk. All genotypes acquired self-administration of cocaine and did not differ in rates of self-administration, dose dependency or reinstatement. However, whilst WT and HT mice showed a dose-dependent increase in lever pressing during the cue presentation, KO mice did not. Conclusions Despite a reported absence of sensitisation, motivation to obtain cocaine remains unchanged in KO and HT mice. Reinstatement of cocaine seeking by cocaine and cocaine-paired cues is also unaffected. We postulate that whilst not directly involved in reward perception, the α2-subunit may be involved in modulating the “energising” aspect of cocaine’s effects on reward-seeking

Sex-biased parental care and sexual size dimorphism in a provisioning arthropod

The diverse selection pressures driving the evolution of sexual size dimorphism (SSD) have long been debated. While the balance between fecundity selection and sexual selection has received much attention, explanations based on sex-specific ecology have proven harder to test. In ectotherms, females are typically larger than males, and this is frequently thought to be because size constrains female fecundity more than it constrains male mating success. However, SSD could additionally reflect maternal care strategies. Under this hypothesis, females are relatively larger where reproduction requires greater maximum maternal effort – for example where mothers transport heavy provisions to nests. To test this hypothesis we focussed on digger wasps (Hymenoptera: Ammophilini), a relatively homogeneous group in which only females provision offspring. In some species, a single large prey item, up to 10 times the mother’s weight, must be carried to each burrow on foot; other species provide many small prey, each flown individually to the nest. We found more pronounced female-biased SSD in species where females carry single, heavy prey. More generally, SSD was negatively correlated with numbers of prey provided per offspring. Females provisioning multiple small items had longer wings and thoraxes, probably because smaller prey are carried in flight. Despite much theorising, few empirical studies have tested how sex-biased parental care can affect SSD. Our study reveals that such costs can be associated with the evolution of dimorphism, and this should be investigated in other clades where parental care costs differ between sexes and species

Superconductivity above 30 K in alkali-metal-doped hydrocarbon

The recent discovery of superconductivity with a transition temperature (Tc) at 18 K in Kxpicene has extended the possibility of high-Tc superconductors in organic materials. Previous experience based on similar hydrocarbons, like alkali-metal doped phenanthrene, suggested that even higher transition temperatures might be achieved in alkali-metals or alkali-earth-metals doped such polycyclic-aromatic-hydrocarbons (PAHs), a large family of molecules composed of fused benzene rings. Here we report the discovery of high-Tc superconductivity at 33 K in K-doped 1,2:8,9-dibenzopentacene (C30H18). To our best knowledge, it is higher than any Tc reported previously for an organic superconductor under ambient pressure. This finding provides an indication that superconductivity at much higher temperature may be possible in such PAHs system and is worthy of further exploration