The use of FT-IR as a screening technique for organic residue analysis of archaeological samples

A range of archaeological samples have been examined using FT-IR spectroscopy. These include suspected coprolite samples from the Neolithic site of Catalhoyuk in Turkey, pottery samples from the Roman site of Silchester, UK and the Bronze Age site of Gatas, Spain and unidentified black residues on pottery sherds from the Roman sites of Springhead and Cambourne, UK. For coprolite samples the aim of FT-IR analysis is identification. Identification of coprolites in the field is based on their distinct orange colour; however, such visual identifications can often be misleading due to their similarity with deposits such as ochre and clay. For pottery the aim is to screen those samples that might contain high levels of organic residues which would be suitable for GC-MS analysis. The experiments have shown coprolites to have distinctive spectra, containing strong peaks from calcite, phosphate and quartz; the presence of phosphorus may be confirmed by SEM-EDX analysis. Pottery containing organic residues of plant and animal origin has also been shown to generally display strong phosphate peaks. FT-IR has distinguished between organic resin and non-organic compositions for the black residues, with differences also being seen between organic samples that have the same physical appearance. Further analysis by CC-MS has confirmed the identification of the coprolites through the presence of coprostanol and bile acids, and shows that the majority of organic pottery residues are either fatty acids or mono- or di-acylglycerols from foodstuffs, or triterpenoid resin compounds exposed to high temperatures. One suspected resin sample was shown to contain no organic residues. and it is seen that resin samples with similar physical appearances have different chemical compositions. FT-IR is proposed as a quick and cheap method of screening archaeological samples before subjecting them to the more expensive and time-consuming method of GC-MS. This will eliminate inorganic samples such as clays and ochre from CC-MS analysis, and will screen those samples which are most likely to have a high concentration of preserved organic residues. (C) 2008 Elsevier B.V. All rights reserved.

Consumer attitudes towards and willingness to pay for pesticide residue limit compliant 'safe' vegetables in Northeast Thailand

Pesticide residue in vegetables is a major food safety issue in Thailand. A range of vegetable products (organic/pesticide-free/ hydroponic) has emerged in Thai markets that guarantee compliance with maximum residue limits. The Government of Thailand is eager to extend the benefits of this suite of alternative vegetables to the entire population, particularly the semi-urban/rural segments that are often bypassed by such speciality products. However, little information is available to guide such an effort, particularly with regard to up-country consumer attitudes, shopping and consumption habits and willingness to pay premiums for such produce. This research aims to fill this gap in knowledge. It reports the results of a survey of vegetable consumption and shopping habits and attitudes of 608 consumers in northeast Thailand. Willingness to pay premiums for pesticide residue limit compliant vegetables is also assessed by using a contingent valuation method, and determinants of willingness to pay are examined using an ordered probit empirical model. Results indicate that, given adequate awareness of relative risks, even up-country consumers are willing to pay market premium levels for these products, and that inadequate availability, rather than lack of demand is the constraining factor. Willingness to pay is found to increase with income, age and supermarket sourcing of vegetables. We also discuss the challenge of improving availability at mainstream outlets.

The effect of wheat straw residue on the emergence and early growth of sugar beet (Beta vulgaris) and oilseed rape (Brassica napus)

The management of straw residue can be a concern in non-inversion tillage systems where straw tends to be incorporated at shallow depths or left on the soil surface. This can lead to poor crop establishment because straw residue can impede or hinder crop emergence and growth. Small container-based experiments were undertaken using varying amounts of wheat straw residue either incorporated or placed oil the soil surface. The effects on (lays to seedling emergence, percentage emergence, seedling dry-weight and soil temperature using sugar beet and oilseed rape were investigated because these crops often follow wheat in a cropping sequence. The position of the straw residue was found to be the primary factor in reducing crop emergence and growth. Increasing the amount of straw residue (from 3.3 t ha(-1) to 6.7 t ha(-1)) did not show any consistent trends in reducing crop emergence or growth. However, in some instances, results indicated that an interaction between the position and the amount of straw residue Occurred particularly when the straw and seed was placed on the soil surface. Straw placed on the soil surface significantly reduced mean day-time soil temperature by approximately 2.5 degrees C compared to no residue. When the seed and straw was placed on the soil Surface a lack of seed-to-soil contact caused a reduction in emergence by approximately 30% because of the restriction in available moisture that limited the ability for seed imbibition. This trend was reversed when the seed was placed in the soil, but with straw residue still on the soil surface, because the surface straw was likely to reduce moisture evaporation and improved seed-to-soil contact that led to rapid emergence. In general, when straw was mixed in or placed on the soil surface along with the seed, sugar beet and oilseed rape emergence and early growth biomass was significantly restricted by approximately 50% compared to no residue. The consequences of placing seed with or near to straw residue have been shown to cause a restriction in crop establishment. In both oilseed tape and sugar beet, this could lead to a reduction in final crop densities, poor, uneven growth and potentially lower yields that could lower financial margins. Therefore, if farmers are planning to use non-inversion tillage methods for crop establishment, the management and removal of straw residue from near or above the seed is considered important for successful crop establishment. (C) 2008 Elsevier B.V. All rights reserved.

Supramolecular parallel beta-sheet and amyloid-like fibril forming peptides using delta-aminovaleric acid residue

Four terminally blocked tripeptides containing delta-aminovaleric acid residue self-assemble to form supramolecular beta-sheet structures as are revealed from their FT-IR data. Single crystal X-ray diffraction studies of two representative peptides also show that they form parallel beta-sheet structures. Self-aggregation of these beta-sheet forming peptides leads to the formation of fibrillar structures, as is evident from scanning electron microscopic (SEM) and transmission electron microscopic (TEM) images. These peptide fibrils bind to a physiological dye, Congo red and exhibit a typical green-gold birefringence under polarized light, showing close resemblance to neurodegenerative disease causing amyloid fibrils. (c) 2005 Elsevier Ltd. All rights reserved.

alpha-Aminoisobutyric acid modified protected analogues of beta-amyloid residue 17-20: a change from sheet to helix

The strong intermolecular interactions mediated by short hydrophobic sequences (e.g., 17-20, -L-Leu-L-Val-L-Phe-L-Phe-) in the middle of A beta are known to play a crucial role in the neuropathology of Alzheimer's disease. FTIR, TEM and Congo red binding studies indicated that a series of L-Ala substituted terminally protected peptides related to the sequence 17-20 of the beta-amyloid peptide, adopted D-sheet conformations. However, the Aib-modified analogues disrupt the D-sheet structure and switch over to a 310 helix with increasing number of Aib residues. X-ray crystallography shed some light on the change from sheet to helix at atomic resolution. (c) 2006 Elsevier Ltd. All rights reserved.

Supramolecular beta-sheet and nanofibril formation by self-assembling tripeptides containing an N-terminally located gamma-aminobutyric acid residue

Three terminally protected tripeptides Boc-gamma-Abu-Val-Leu-OMe 1, Boc-gamma-Abu-Leu-Phe-OMe 2 and Boc-gamma-Abu-Val-Tyr-OMe 3 (gamma-Abu = gamma-aminobutyric acid) each containing an N-terminally positioned gamma-aminobutyric acid residue have been synthesized, purified and studied. FT-IR studies of all these peptides revealed that these peptides form intermolecularly hydrogen bonded supramolecular beta-sheet structures. Peptides 1, 2 and 3 adopt extended backbone beta-strand molecular structures in crystals. Crystal packing of all these peptides demonstrates that these beta-strand structures self-assemble to form intermolecularly H-bonded parallel beta-sheet structures. Peptide 3 uses a side chain tyrosyl -OH group as an additional hydrogen bonding functionality in addition to the backbone CONH groups to pack in crystals. Transmission electron microscopic studies of all peptides indicate that they self-assemble to form nanofibrillar structures of an average diameter of 65 nm. These peptide fibrils exhibit amyloid-like behavior as they bind to a physiological dye Congo red and show a characteristic green-gold birefringence under polarizing microscope.

Nanozipper formation in the solid state from a self-assembling tripeptide with a single tryptophan residue

The self-assembly of a terminally protected tripeptide Boc-gamma-Abu(1)-Ala(2)-Trp(3)-OMe (gamma-Abu = gamma-aminobutyric acid) I results in the formation of a nanostructured supramolecular zipper through various non-covalent interactions in the crystal in which the indole side-chain of the Trp(3) residue plays a key role via N-H...pi interactions. (c) 2006 Published by Elsevier Ltd.

Stubs versus swabs? A comparison of gunshot residue collection techniques

The collection efficiency of two widely used gunshot residue (GSR) collection techniques—carbon-coated adhesive stubs and alcohol swabs—has been compared by counting the number of characteristic GSR particles collected from the firing hand of a shooter after firing one round. Samples were analyzed with both scanning electron microscopy and energy dispersive X-rays by an experienced GSR analyst, and the number of particles on each sample containing Pb, Ba, and Sb counted. The adhesive stubs showed a greater collection efficiency as all 24 samples gave positive results for GSR particles whereas the swabs gave only positive results for half of the 24 samples. Results showed a statistically significant collection efficiency for the stub collection method and likely reasons for this are considered.

FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions

The estimation of prediction quality is important because without quality measures, it is difficult to determine the usefulness of a prediction. Currently, methods for ligand binding site residue predictions are assessed in the function prediction category of the biennial Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment, utilizing the Matthews Correlation Coefficient (MCC) and Binding-site Distance Test (BDT) metrics. However, the assessment of ligand binding site predictions using such metrics requires the availability of solved structures with bound ligands. Thus, we have developed a ligand binding site quality assessment tool, FunFOLDQA, which utilizes protein feature analysis to predict ligand binding site quality prior to the experimental solution of the protein structures and their ligand interactions. The FunFOLDQA feature scores were combined using: simple linear combinations, multiple linear regression and a neural network. The neural network produced significantly better results for correlations to both the MCC and BDT scores, according to Kendall’s τ, Spearman’s ρ and Pearson’s r correlation coefficients, when tested on both the CASP8 and CASP9 datasets. The neural network also produced the largest Area Under the Curve score (AUC) when Receiver Operator Characteristic (ROC) analysis was undertaken for the CASP8 dataset. Furthermore, the FunFOLDQA algorithm incorporating the neural network, is shown to add value to FunFOLD, when both methods are employed in combination. This results in a statistically significant improvement over all of the best server methods, the FunFOLD method (6.43%), and one of the top manual groups (FN293) tested on the CASP8 dataset. The FunFOLDQA method was also found to be competitive with the top server methods when tested on the CASP9 dataset. To the best of our knowledge, FunFOLDQA is the first attempt to develop a method that can be used to assess ligand binding site prediction quality, in the absence of experimental data.

Local orientational disorder in peptide fibrils probed by a combination of residue-specific 13C-18O labelling, polarised infrared spectroscopy and molecular combing

A novel combination of site-specific isotope labelling, polarised infrared spectroscopy and molecular combing reveal local orientational ordering in the fibril-forming peptide YTIAALLSPYSGGRADS. Use of 13C-18O labelled alanine residues demonstrates that the Nterminal end of the peptide is incorporated into the cross-beta structure, while the C-terminal end shows orientational disorder

Peptide based hydrogels for cancer drug release: modulation of stiffness, drug release and proteolytic stability of hydrogels by incorporating D-amino acid residue(s)

Synthetic tripeptide based noncytotoxic hydrogelators have been discovered for releasing an anticancer drug at physiological pH and temparature. Interestingly, gel stiffness, drug release capacity and proteolytic stability of these hydrogels have been successfully modulated by incorporating D-amino acid residues, indicating their potential use for drug delivery in the future.

Matrix effects observed during pesticides residue analysis in fruits by GC

The influence of the sample matrix in the CC-electron-capture detection analysis of the pesticides dimethoate, diazinon, chlorothalonil.. parathion methyl and fenitrothion in fruits samples has been studied. Experiments have been carried out where the pesticide responses in standard solutions prepared in selected solvent were compared with their response when present in apple, mango, papaya, banana, pineapple and melon extracts. The presence of matrix effects (MEs) and their extent were shown to be simultaneously influenced by several factors (matrix concentration, matrix type, pesticide concentration, analytical range). Pronounced MEs were observed particularly for dimethoate and diazinon in all matrices tested; in lower concentrations, all pesticides presented significant ME. The other pesticides presented variable ME. Higher ME enhancement was detected at lower pesticide concentration levels of and/or at higher matrix concentration solutions. The ME detected for fenitrothion, in the analytical range evaluated, were dependent on matrix type. For each pesticide, solvent and matrix-matched calibrations were compared for all fruit samples, and it could be concluded that quantitation based on standard solutions prepared in blank matrix extract (matrix-matched calibration) should be used to compensate the MEs and to obtain more accurate results for the pesticides studied.

Soil water evaporation under densities of coverage with vegetable residue

O presente estudo foi realizado no Instituto Agronômico do Paraná (IAPAR), em Londrina, Estado do Paraná (latitude de 23º18'S, longitude de 51º09'W e altitude média de 585 m). O clima local, segundo a classificação do Köppen, é do tipo Cfa, ou seja, subtropical úmido, com chuvas em todas as estações, podendo ocorrer secas no período de inverno. Determinou-se a evaporação (E) da água do solo sob diferentes densidades de cobertura com resíduo da cultura de trigo. Os tratamentos foram instalados em lisímetros de pesagem de 2,66 m² e 1,3 m de profundidade, que permitem determinar E por diferença de massa com precisão equivalente a 0,1 mm em intervalos de uma hora. Os tratamentos consistiram em 0; 2,5; 5 e 10 t ha-1 de resíduos da cultura do trigo, colocadas de forma homogênea em cada lisímetro. No primeiro ciclo (22/09 a 20/10/2008), a redução de E em relação ao solo descoberto foi de 4; 15 e 24%, enquanto no segundo ciclo (01/12 a 30/12/2008), a redução foi de 15; 22 e 25%, respectivamente, para os tratamentos 2,5; 5 e 10 t ha-1.

Optimization of acid hydrolysis from the hemicellulosic fraction of Eucalyptus grandis residue using response surface methodology

Biotechnological conversion of biomass into fuels and chemicals requires hydrolysis of the polysaccharide fraction into monomeric sugars. Hydrolysis can be performed enzymatically and with dilute or concentrate mineral acids. The present study used dilute sulfuric acid as a catalyst for hydrolysis of Eucalyptus grandis residue. The purpose of this paper was to optimize the hydrolysis process in a 1.41 pilot-scale reactor and investigate the effects of the acid concentration, temperature and residue/acid solution ratio on the hemicellulose removal and consequently on the production of sugars (xylose, glucose and arabinose) as well as on the formation of by-products (furfural, 5-hydroxymethylfurfural and acetic acid). This study was based on a model composition corresponding to a 2 3 orthogonal factorial design and employed the response surface methodology (RSM) to optimize the hydrolysis conditions, aiming to attain maximum xylose extraction from hemicellulose of residue. The considered optimum conditions were: H2SO4 concentration of 0.65%, temperature of 157 degrees C and residue/acid solution ratio of 1/8.6 with a reaction time of 20 min. Under these conditions, 79.6% of the total xylose was removed and the hydrolysate contained 1.65 g/l glucose, 13.65 g/l xylose, 1.55 g/l arabinose, 3.10 g/l acetic acid, 1.23 g/l furfural and 0.20 g/l 5-hydroxymethylfurfural. (c) 2006 Published by Elsevier Ltd.

Composite materials obtained from textile fiber residue

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