Quantitative proteomics for epigenetics

Mass spectrometry has made many contributions to the chromatin field through the mapping of histone modifications and the identification of protein complexes involved in gene regulation. MS-based proteomics has now evolved from the identification of single protein spots in gels to the identification and quantification of thousands of proteins in complex mixtures. Quantitative approaches also allow comparative and time-resolved analysis of post-translational modifications. An important emerging field is the unbiased interaction analysis of proteins with other proteins, defined protein modifications, specific DNA and RNA sequences, and small molecules. Quantitative proteomics can also accurately monitor whole proteome changes in response to perturbation of the gene expression machinery. We provide an up-to-date review of modern quantitative proteomic technology and its applications in the field of epigenetics.     

Novel amorphous precursor densification to transparent Nd:Y2O3 Ceramics

A novel approach of neodymium ion doped yttrium oxide (Nd:Y₂O₃) amorphous precursor compaction and sintering is being reported for the first time. Precursor of 2 at.% Nd³⁺ doped Y₂O₃ was synthesized by gelation of sol of yttrium and neodymium nitrates with l-alanine at 80 °C for 16 h followed by gel combustion in microwave. A part of microwave precursor was heat treated at 700 °C for 5 h to give the partially crystalline Nd:Y₂O₃ amorphous precursor. Thermogravimetric analysis (TGA) of partially crystalline amorphous precursor of Nd:Y₂O₃ gave 8.5% total weight loss indicating removal of maximum organics. X-Ray diffraction (XRD) showed broad peaks indicating incomplete crystallization of cubic Nd:Y₂O₃. Morphology was found to be close to spherical with particles in size range 17–19 nm by TEM. Another part of microwave precursor on calcination at 1000 °C for 3 h led to formation of fully crystalline Nd:Y₂O₃ with particles in size range of 35–85 nm. Both partially crystalline amorphous precursor and fully crystalline Nd:Y₂O₃ were compacted at 400 MPa by cold isostatic press and sintered at 1750 °C for 10 h under vacuum (10^?5 mbar). The partially crystalline Nd:Y₂O₃ amorphous precursor densified to 99% with 65% transmission at 2500 nm (0.5 mm thickness) compared to 96% densification with 34% transmission for fully crystalline Nd:Y₂O₃ without any sintering aids. Retention of cubic phase purity of Y₂O₃ was observed in both the ceramic pellets post sintering by XRD. Good grain fusion with grain growth to ≤2 μm was observed by scanning electron microscope (SEM) for partially crystalline Nd:Y₂O₃ amorphous precursor. Thus partially crystalline Nd:Y₂O₃ amorphous precursor nanopowders, with homogeneous close to spherical fine particles and high reactivity due to ionic mobility of amorphous phase, led to better densification.     

Homoserine Lactones,Methyl Oligohydroxybutyrates,and Other Extracellular Metabolites of Macroalgae‐Associated Bacteria of the Roseobacter Clade: Identification and Functions

Twenty‐four strains of marine Roseobacter clade bacteria were isolated from macroalgae and investigated for the production of quorum‐sensing autoinducers, N‐acylhomoserine lactones (AHLs). GC/MS analysis of the extracellular metabolites allowed us to evaluate the release of other small molecules as well. Nineteen strains produced AHLs, ranging from 3‐OH‐C10:0‐HSL (homoserine lactone) to (2E,11Z)‐C18:2‐HSL, but no specific phylogenetic or ecological pattern of individual AHL occurrence was observed when cluster analysis was performed. Other identified compounds included indole, tropone, methyl esters of oligomers of 3‐hydroxybutyric acid, and various amides, such as N‐9‐hexadecenoylalanine methyl ester (9‐C16:1‐NAME), a structural analogue of AHLs. Several compounds were tested for their antibacterial and antialgal activity on marine isolates likely to occur in the habitat of the macroalgae. Both AHLs and 9‐C16:1‐NAME showed high antialgal activity against Skeletonema costatum, whereas their antibacterial activity was low.     

Structure and Substrate Recognition of the Bottromycin Maturation Enzyme BotP

The bottromycins are a family of highly modified peptide natural products, which display potent antimicrobial activity against Gram‐positive bacteria, including methicillin‐resistant Staphylococcus aureus. Bottromycins have recently been shown to be ribosomally synthesized and post‐translationally modified peptides (RiPPs). Unique amongst RiPPs, the precursor peptide BotA contains a C‐terminal “follower” sequence, rather than the canonical N‐terminal “leader” sequence. We report herein the structural and biochemical characterization of BotP, a leucyl‐aminopeptidase‐like enzyme from the bottromycin pathway. We demonstrate that BotP is responsible for the removal of the N‐terminal methionine from the precursor peptide. Determining the crystal structures of both apo BotP and BotP in complex with Mn²⁺ allowed us to model a BotP/substrate complex and to rationalize substrate recognition. Our data represent the first step towards targeted compound modification to unlock the full antibiotic potential of bottro‐ mycin.     

Cavitation Erosion Characteristics of Nitrocarburized and HPDL-Treated Martensitic Stainless Steels

This article deals with plasma ion-nitrocarburising and high power diode laser (HPDL) surface treatment of 13Cr4Ni and X10CrNiMoV1222 martensitic stainless steels to enhance their cavitation erosion resistance. These steels are commonly used in hydro turbines and boiler feed pumps. These treated steels have been evaluated for cavitation erosion resistance and it has been observed that the plasma ion-nitrocarburising process has significantly enhanced the cavitation erosion resistance as compared to untreated steel whereas HPDL-treated steels have shown marginal improvement. This is due to formation of high hardness nitrides during nitrocarburising and formation of moderate hardness martensitic phase due to rapid heating and cooling rates involved in HPDL treatment. The cavitation erosion and micro-hardness data of plasma ion-nitrocarburized as well as HPDL-treated steel samples and their comparison with hard deposits such as stellite and HVOF coating form the main part of the article.     

Comparison of Seal Oil to Tuna Oil on Plasma Lipid Levels and Blood Pressure in Hypertriglyceridaemic Subjects

As meat is a rich source of the omega-3 fatty acid docosapentaenoic acid (DPA) and Australians consume six times more meat than fish, investigation of the potential health benefit of DPA is warranted. The aims were to compare the effects of seal oil supplementation with fish oil, on measures of plasma lipids and blood pressure in hypertriglyceridaemic subjects. Forty-eight volunteers were recruited from the Wollongong community and were randomly allocated to one of three groups either receiving 1 g/day of long-chain omega-3 polyunsaturated fatty acids (LC n-3 PUFA) using one of three oils: seal oil capsules (340 mg eicosapentaenoic acid (EPA), 230 mg DPA, 450 mg DHA), fish oil capsules (210 mg EPA, 30 mg DPA, 810 mg DHA) or placebo capsules (containing sunola oil) for 6 weeks. Plasma triglycerides remained unchanged in the placebo group, whilst reductions of 7 and 14% (P < 0.05) were seen in the fish oil and seal oil groups respectively. Systolic blood pressure improved by 8 and 5 mmHg with seal oil and fish oil respectively (P < 0.05). The mean arterial pressure was significantly lower after seal oil supplementation (P < 0.005) compared with the placebo group. These results indicate that seal oil is as effective as fish oil in lowering plasma triglycerides and blood pressure.     

Synthesis of Carbonated Vernonia Oil

The research objective was to determine whether naturally occurring epoxy functional vernonia oil would result in lower viscosity compounds after converting the virgin oil into the cyclic carbonate using supercritical carbon dioxide as the reactant. The cyclic carbonate was produced using relatively mild conditions as described in the paper. Carbonated vernonia oil retains the characteristic low viscosity of vernonia oil, and offers potential as a valuable, biobased intermediate for synthesizing low viscosity resins.     

Maternal Exposure to Dibutyl Phthalate (DBP) or Diethylstilbestrol (DES) Leads to Long-Term Changes in Hypothalamic Gene Expression and Sexual Behavior

Xenobiotic exposure during pregnancy and lactation has been linked to perinatal changes in male reproductive outcomes and other endocrine parameters. This pilot study wished to assess whether brief maternal exposure of rats to xenobiotics dibutyl phthalate (DBP) or diethylstilbestrol (DES) might also cause long-term changes in hypothalamic gene expression or in reproductive behavior of the resulting offspring. Time-mated female Sprague Dawley rats were given either DBP (500 mg/kg body weight, every second day from GD14.5 to PND6), DES (125 µg/kg body weight at GD14.5 and GD16.5 only), or vehicle (n = 8–12 per group) and mild endocrine disruption was confirmed by monitoring postnatal anogenital distance. Hypothalamic RNA from male and female offspring at PND10, PND24 and PND90 was analyzed by qRT-PCR for expression of aromatase, oxytocin, vasopressin, ER-alpha, ER-beta, kisspeptin, and GnRH genes. Reproductive behavior was monitored in male and female offspring from PND60 to PND90. Particularly, DES treatment led to significant changes in hypothalamic gene expression, which for the oxytocin gene was still evident at PND90, as well as in sexual behavior. In conclusion, maternal xenobiotic exposure may not only alter endocrine systems in offspring but, by impacting on brain development at a critical time, can have long-term effects on male or female sexual behavior.     

Risk Perceptions and Terror Management Theory: Assessing Public Responses to Urban Flooding in Toronto,Canada

Terror Management Theory (TMT) suggests that mortality salience (MS), or death reminders, should impact environmental behaviour and decision-making by increasing consumption and resource usage, shifting aesthetic preferences toward cultivated landscapes, and affecting adherence to environmental norms. We examined MS effects on residential flood risk perceptions in Toronto, Canada, following the major urban flood in July 2013. Survey responses were analyzed to assess risk perceptions across nine categories; analyses through the Wilcoxon-Mann–Whitney test show statistically insignificant differences between MS and control groups for all subcategories. Coupled with the TMT literature, the results indicate that existential anxiety is more likely to affect flood risk perceptions through worldview defense when the social dimension of flooding is made clear. Toronto residents’ societal beliefs about flooding play a major role in guiding flood management strategies. Our results provide scholarly and practical direction for flood risk communication strategies to promote the adoption of private flood-prevention measures, suggesting that anthropocentric framing of flooding issues will not induce negative environmental behaviour and may increase concern for flooding issues.     

Nutrition, metabolism, and fertility in dairy cows: 1. Dietary energy source and ovarian function

In previous studies, high plasma insulin was associated with earlier resumption of postpartum estrous cycles in dairy cows. The objective of this experiment was to quantify hormonal and ovarian responses to dietary starch and fat contents. Thirty cows were fed on a standard diet from calving until 40 d in milk (DIM) and then 6 cows were allocated to each of 5 isoenergetic diets containing 231, 183, 159, 135, and 87 g of starch and 39, 42, 43, 45, and 48 g of fat/kg of dry matter (DM) for diets 1 to 5, respectively, until 70 DIM. Estrus was synchronized at 60 DIM. Between 60 and 70 DIM, energy intake, milk yield, and energy balance were similar among diet groups. Plasma insulin-to-glucagon ratio increased with increasing dietary starch and decreasing dietary fat concentrations, reaching a break point at 159 g of starch, 43 g of fat/kg of DM (diets 1 to 5: mean 3.86, 3.78, 3.59, 2.98, 2.06 ± standard error 0.22). Growth hormone, insulin-like growth factor-I, and leptin did not vary among diets. The greatest dietary starch concentration was associated with elevated plasma urea-N (diets 1 to 5: mean 3.69, 3.01, 2.94, 2.95, 2.75, ± standard error 0.13 mmol/L, respectively) and delayed postovulatory progesterone increase (progesterone at 3 to 5 d postovulation for diets 1 to 5: mean 2.7, 5.9, 4.2, 5.6, 4.3 ± standard error 0.9 ng/mL, respectively). The number of small (<5 mm) ovarian follicles was positively related to starch intake (r = 0.381) and plasma insulin concentration (r = 0.402). It is concluded that to maintain adequate insulin-to-glucagon ratio in cows at the start of the breeding period, dietary starch concentration should be above 160 g/kg of DM and dietary fat below 44 g/kg of DM, and this should have a positive effect on ovarian function.