Identification of protein remains in archaeological potsherds by proteomics

We demonstrate here the possibility of identifying proteins trapped in few milligrams of the clay matrix of a 1200-1400 AD I?upiat potsherd fragment from Point Barrow, Alaska, by a dedicated proteomics approach. The four main steps of a proteomics analysis, (i) protein extraction from biological samples, (ii) protein hydrolysis using a hydrolase enzyme, (iii) nanoLC, nanoESI MS, and MS/MS analysis of the generated peptides, and (iv) protein identification using protein databank proceeded from genomic data, have been optimized for archeological remains. Briefly our procedure starts by grinding the potsherds, extraction with 1% trifluoroacetic acid, digestion with excess of trypsin, nanoLC, nanoESI FT-ICR analysis, and data mining by homology search. The developed conditions were evaluated on protein extracts from remains obtained by heated muscle tissues and blubbers of different seal and whale species, these samples representing the main diet sources of the Eskimo population. Most of the proteins were identified by sequence homology to other species due to the lack of cetacean and pinniped proteins in the databanks. More interestingly, two proteins, myoglobin and hemoglobin, respectively, identified in muscle tissue samples and blubber samples highlight several specific peptides of cetacean and pinniped species; these peptides are significant to prove the presence of these marine species in the analyzed samples. Based on the developed methodology and on protein identification results obtained from the heated seal/whale muscle tissues and blubbers, the analysis of the clay matrix of a 1200-1400 AD I?upiat potsherd fragment from Point Barrow was investigated. The described method succeeds in identifying four peptides corresponding to the harbor seal myoglobin (species Phoca vitulina) with a measured mass accuracy better than 1 ppm (MS and MS/MS experiments) including one specific peptide of the cetacean and pinniped species and one specific peptide of the seal species. These results highlight, for the first time, a methodology able to identify proteins from a few milligrams of archeological potsherd buried for years; the obtained results confirm the presence of a seal muscle tissue protein in this Punuk potsherd.     

Conversion of a plasma enhanced chemical vapor deposited silicon-carbon-nitride thin film at ultra-low temperature by oxygen plasma

In this work we present an ultra-low temperature method for the oxidation of an amorphous silicon-carbide-nitride (SiCN) material. The SiCN is deposited on silicon substrates by plasma enhanced chemical vapor deposition using CH₄, SiH₄, and N₂ chemistry. The physical and chemical properties are characterized for the as-deposited SiCN and post-oxidized films are discussed. The SiCN film is exposed to oxygen plasma, where it undergoes a chemical transformation into a binary SiO₂ material system. A 1.7 nm/min oxidation rate is typical for this process and compares favorably to oxidation methods utilizing much higher temperatures. The substrate temperature remains extremely low throughout the oxidation process, T_s < 200 °C. Changes in film stress, optical constants, film thickness, surface roughness, and film density are measured. Chemical analysis by X-ray photoelectron spectroscopy is reported for both the as-deposited and oxidized film and confirms the resultant film to be the chemical equivalent of thermally grown SiO₂. We discuss applications specifically targeted to the conversion of SiCN to SiO₂.     

Comparison of drinking water treatment process streams for optimal bacteriological water quality

Four pilot-scale treatment process streams (Stream 1 - Conventional treatment (coagulation/flocculation/dual media filtration); Stream 2 - Magnetic ion exchange (MIEX)/Conventional treatment; Stream 3 - MIEX/Conventional treatment/granular activated carbon (GAC) filtration; Stream 4 - Microfiltration/nanofiltration) were commissioned to compare their effectiveness in producing high quality potable water prior to disinfection. Despite receiving highly variable source water quality throughout the investigation, each stream consistently reduced colour and turbidity to below Australian Drinking Water Guideline levels, with the exception of Stream 1 which was difficult to manage due to the reactive nature of coagulation control. Of particular interest was the bacteriological quality of the treated waters where flow cytometry was shown to be the superior monitoring tool in comparison to the traditional heterotrophic plate count method. Based on removal of total and active bacteria, the treatment process streams were ranked in the order: Stream 4 (average log removal of 2.7) > Stream 2 (average log removal of 2.3) > Stream 3 (average log removal of 1.5) > Stream 1 (average log removal of 1.0). The lower removals in Stream 3 were attributed to bacteria detaching from the GAC filter. Bacterial community analysis revealed that the treatments affected the bacteria present, with the communities in streams incorporating conventional treatment clustering with each other, while the community composition of Stream 4 was very different to those of Streams 1, 2 and 3. MIEX treatment was shown to enhance removal of bacteria due to more efficient flocculation which was validated through the novel application of the photometric dispersion analyser.     

Reduced progesterone concentration during growth of the first follicular wave affects embryo quality but has no effect on embryo survival post transfer in lactating dairy cows

Fertility of lactating dairy cows is associated with reduced progesterone (P(4)) concentration compared with nonlactating animals. The objective of the current study was to determine whether P(4) during growth of the first follicular wave (FFW) affects embryo quality. Lactating Holstein cows at 33±3 days post partum were allocated to one of three treatments. Cows in the FFW and FFW with P(4) (FFWP) treatments started the superstimulation protocol on day 1 of the estrous cycle and second follicular wave (SFW) cows started the superstimulation protocol on estrous cycle day 7. Cows were superstimulated with 400 mg of NIH-FSH-P1 (FSH) given twice daily for 5 days, two prostaglandin F(2α) (PGF(2α)) injections given with the ninth and tenth injections of FSH, GNRH given 48 h after the first PGF(2α) injection, and timed insemination 12 and 24 h after the GNRH injection. Cows in the FFWP treatment received two intravaginal P(4) inserts during the superstimulation. Embryos were recovered 6.5 days after artificial insemination and excellent/good and fair embryos were frozen and transferred. Blood was sampled daily from estrous cycle day 0 until insemination from donor cows. During the superstimulation protocol, P(4) was (P<0.01) greatest for SFW cows followed by FFWP and FFW cows respectively. The percentage of embryos-oocytes from SFW and FFWP cows classified as excellent/good and fair embryos was (P=0.02) greater than those of FFW cows. Pregnancy per embryo transfer was not (P≥0.73) affected by embryo donor treatment. Reduced embryo quality of cows induced to ovulate the follicles from the first follicular wave is a consequence of reduced P(4) during follicle growth.     

Formation of Soy Protein Isolate Cold-set Gels: Protein and Salt Effects

ABSTRACT: The influence of protein and calcium concentration on soy protein cold-set gel formation and rheology has been investigated. Cold-set gels can be formed at soy protein concentrations from 6% to 9% and calcium concentrations from 10 to 20 mM. Gel properties can be modulated by changing the protein and/or CaCl₂ concentrations. An increase in CaCl₂ concentration from 10 to 20 mM increased gel opacity while an increase in protein concentration from 6% to 9% decreased opacity. Water-holding capacity improved with increasing protein concentration and decreasing CaCl₂ concentration. The elastic modulus (G') increased with protein and calcium chloride concentrations. Microscopy revealed an increase in the diameters of aggregates and pores as CaCl₂ concentration increased and as protein concentration decreased. Cold-set gels with a broad range of characteristics can be obtained from soy protein.     

Interactive Effects of Simulated Nitrogen Deposition and Altered Precipitation Patterns on Plant Allelochemical Concentrations

Global environmental change alters the supply of multiple limiting resources that regulate plant primary and secondary metabolism. Through modifications in resource availability, acquisition, and allocation, global change is likely to influence plant chemical defenses, and consequently species interactions that are mediated by these compounds. While many studies focus on individual global change factors, simultaneous changes in abiotic factors may interact to influence plant allelochemicals. In this study, we examined the individual and interactive effects of nitrogen enrichment and altered precipitation patterns on chemical defense compounds (iridoid glycosides) of an invasive plant, Linaria dalmatica. Plants were grown from seed in native mixed-grass prairie for 2 years. Nitrogen and water treatments were applied in each growing season over this period. Results indicate that soil water and nitrogen availability interact to shape plant chemical defense concentrations in L. dalmatica. Nitrogen addition decreased iridoid glycoside concentrations by approximately 25 % under reduced water availability, increased concentrations by 37 % in ambient water plots, and had no effect on these chemical defenses for plants growing under augmented water supply. Thus, results show differing patterns of allelochemical response to nitrogen enrichment, with respect to both the magnitude and direction of change, depending on water availability. Our study demonstrates the importance of examining multiple environmental factors in order to predict potential changes in plant chemical defenses with climate change.     

Interactive effects of abiotic,hydrological and anthropogenic factors on fish abundance and distribution in natural run‐of‐the‐river shallow lakes

Ecological processes in lowland rivers are mostly dominated by hydrology and its interactions with other environmental factors. Fish–habitat relationships in rivers are also influenced by human impacts. In this study, we describe patterns of abundance and distribution of fish species in a group of natural lowland river lakes along spatial anthropogenic and abiotic gradients when four hydrologically different summers are compared. We also describe the proportion of the total variances in fish species abundances that can be accounted for by selected abiotic (water conductivity), hydrological (water residence time) and human activity‐derived (total phosphorus (TP) concentration and NO₃:NH₄) variables. Consequently, our main purpose is to explore how abiotic and anthropogenic factors interact to affect fish abundance and distribution together with consistent results across different hydrological conditions. We conclude with a briefly discussion of some management implications. The anthropogenic impacts on water quality, the extreme hydrological variability and the fluctuating abiotic environment affected fish abundance and distribution. Pampa inland silverside Odontesthes bonariensis was benefited from a less human disturbed environment with higher water residence time and total salinity, whereas species as Cyphocharax voga, Parapimelodus valenciennis and Cyprinus carpio found these conditions largely disadvantageous. On the other hand, while most species showed stronger—either negative or positive—response to anthropogenic, hydrological or abiotic factors Oligosarcus jenynsii was only slightly affected. This paper identified the ecological function of a lowland river under its natural flow regime. There are not many opportunities to study unmodified rivers worldwide. Therefore, our findings may help in assessment programmes of fish communities in flow altered and human disturbed aquatic ecosystems. Copyright © 2008 John Wiley & Sons, Ltd.     

Laser cladding of SiC/Si composite coating on Si-SiC ceramic substrates

Pieces of silicon infiltrated silicon carbide (Si-SiC) were coated with a SiC particles reinforced Si matrix composite (SiC/Si) obtained from mixtures of SiC + SiO₂ and SiC + Si by laser cladding. A Nd:YAG pulsed laser delivering an average power of 920 W was used to apply such coatings using the powder blowing technique. The results demonstrate that the use of the SiC + SiO₂ powder mixture produces a severe damage on the base material, whereas the use of the SiC + Si mixture leads to the formation of sound coatings without substrate damage. XRD and nanoindentation measurements corroborate the production of silicon carbides surrounded by a metallic silicon matrix. This method could be used for repairing surface defects of silicon infiltrated silicon carbide ceramics (Si-SiC).