Comparative surface accessibility of a pore-lining threonine residue (T6') in the glycine and GABA(A) receptors

The substituted cysteine accessibility method was used to probe the surface exposure of a pore-lining threonine residue (T6’) common to both the glycine receptor (GlyR) and GABAA receptor (GABAAR) chloride channels. This residue lies close to the channel activation gate, the ionic selectivity filter and the main pore blocker binding site. Recent studies have suggested that the GlyRs and GABAARs have divergent open state pore structures at the 6’ position. When both the human a1T6’C homomeric GlyR and the rat a1T6’Cb1T6’C heteromeric GABAAR were expressed in HEK293 cells, their 6’ residue surface accessibilities differed significantly in the closed state. However, when a soluble cysteine-modifying compound was applied in the presence of saturating agonist concentrations, both receptors were locked into the open state. This action was not induced by oxidising agents in either receptor. These results provide evidence for a conserved pore opening mechanism in anion-selective members of the ligand-gated ion channel family. The results also indicate that the GABAAR pore structure at the 6’ level may vary between different expression systems.

Tyrosine residue 271 of the norepinephrine transporter is an important determinant of its pharmacology

The aim was to examine the functional importance in the norepinephrine transporter (NET) of (i) the phenylalanine residue at position 531 in transmembrane domain (TMD) 11 by mutating it to tyrosine in the rat (rF531Y) and human (hF531Y) NETs and (ii) the highly conserved tyrosine residues at positions 249 in TMD 4 of human NET (hNET) (mutated to alanine: hY249A) and 271 in TMD 5, by mutating to alanine (hY271A), phenylalanine (hY271F) and histidine (hY271H). The effects of the mutations on NET function were for uptake of the substrates, examined by expressing the mutant and wildtype NETs in COS-7 cells and measuring the K-m and V-max for uptake of the substrates, [H-3]norepinephrine, [H-3]MPP+ and [H-3]dopamine, the K-D and B-max for [H-3]nisoxetine binding and the K-i of the inhibitors, nisoxetine, desipramine and cocaine, for inhibition of [H-3]norepinephrine uptake. The K-m values of the substrates were lower for the mutants at amino acid 271 than hNET and unaffected for the other mutants, and each mutant had a significantly lower than NET for substrate uptake. The mutations at position 271 caused an increase in the K-i or K-D values of nisoxetine, desipramine and cocaine, but there were no effects for the other mutations. Hence, the 271 tyrosine residue in TMD 5 is an important determinant of NET function, with the mutants showing an increase in the apparent affinities of substrates and a decrease in the apparent affinities of inhibitors, but the 249 tyrosine and 531 phenylalanine residues do not have a major role in determining NET function. (C) 2001 Elsevier Science B.V. All rights reserved.

A single beta subunit M2 domain residue controls the picrotoxin sensitivity of alpha beta heteromeric glycine receptor chloride channels

This study investigated the residues responsible for the reduced picrotoxin sensitivity of the alpha beta heteromeric glycine receptor relative to the alpha homomeric receptor. By analogy with structurally related receptors, the beta subunit M2 domain residues P278 and F282 were considered the most likely candidates for mediating this effect. These residues align with G254 and T258 of the alpha subunit. The T258A, T258C and T258F mutations dramatically reduced the picrotoxin sensitivity of the alpha homomeric receptor. Furthermore, the converse F282T mutation in the beta subunit increased the picrotoxin sensitivity of the alpha beta heteromeric receptor. The P278G mutation in the beta subunit did not affect the picrotoxin sensitivity of the alpha beta heteromer. Thus, a ring of five threonines at the M2 domain depth corresponding to alpha subunit T258 is specifically required for picrotoxin sensitivity. Mutations to alpha subunit T258 also profoundly influenced the apparent glycine affinity. A substituted cysteine accessibility analysis revealed that the T258C sidechain increases its pore exposure in the channel open state. This provides further evidence for an allosteric mechanism of picrotoxin inhibition, but renders it unlikely that picrotoxin las an allosterically acting 'competitive' antagonist) binds to this residue.

A cassette ligation strategy with thioether replacement of three Gly-Gly peptide bonds: Total chemical synthesis of the 101 residue protein early pregnancy factor [psi(CH2S)(28-29,56-57,76-77)]

The 101 residue protein early pregnancy factor (EPF), also known as human chaperonin 10, was synthesized from four functionalized, but unprotected, peptide segments by a sequential thioether ligation strategy. The approach exploits the differential reactivity of a peptide-NHCH2CH2SH thiolate with XCH2CO-peptides, where X = Cl or I/Br. Initial model studies with short functionalized (but unprotected) peptides showed a significantly faster reaction of a peptide-NHCH2CH2SH thiolate with a BrCH2CO-peptide than with a CICH2CO-peptide, where thiolate displacement of the halide leads to chemoselective formation of a thioether surrogate for the Gly-Gly peptide bond. This rate difference was used as the basis of a novel sequential ligation approach to the synthesis of large polypeptide chains. Thus, ligation of a model bifunctional N-alpha-chloroacetyl, C-terminal thiolated peptide with a second N-alpha-bromoacetyl peptide demonstrated chemoselective bromide displacement by the thiol group. Further investigations showed that the relatively unreactive N-alpha-chloroacetyl peptides could be activated by halide exchange using saturated KI solutions to yield the highly reactive No-iodoacetyl peptides. These findings were used to formulate a sequential thioether ligation strategy for the synthesis of EPF, a 101 amino acid protein containing three Gly-Gly sites approximately equidistantly spaced within the peptide chain. Four peptide segments or cassettes comprising the EPF protein sequence (BrAc-[EPF 78-101] 12, ClAc-[EPF 58-75]-[NHCH2CH2SH] 13, ClAc-[EPF 30-55]-[NHCH2CH2SH] 14, and Ac-[EPF 1-27]-[NHCH2CH2SH] 15) of EPF were synthesized in high yield and purity using Boc SPPS chemistry. In the stepwise sequential ligation strategy, reaction of peptides 12 and 13 was followed by conversion of the N-terminal chloroacetyl functional group to an iodoacetyl, thus activating the product peptide for further ligation with peptide 14. The process of ligation followed by iodoacetyl activation was repeated to yield an analogue of EPF (EPF psi(CH2S)(28-29,56-57,76-77)) 19 in 19% overall yield.

Fate of N-15-labelled nitrate in a wet summer under different residue management regimes in young hoop pine plantations

A field study was conducted to investigate the fate of N-15-labelled nitrate applied at 20 kg N ha(-1) in a wet summer to microplots installed in areas under different residue management regimes in second-rotation hoop pine (Araucaria cunninghamii) plantations aged 1-3 years in south-east Queensland, Australia. PVC microplots of 235 mm diameter and 300 mm long were driven into 250 mm soil. There were three replications of each of eight treatments. These were areas just under and between 1-year-old windrows (ca. 2-3 m in width) of harvesting residues spaced 15 m apart, and with and without incorporated foliage residues (20 t DM ha(-1)); the areas just under and between 2- or 3-year-old windrows spaced 10 m apart. Only 7-29% of the added N-15 was recovered from the top 750 mm of the soil profile with the leaching loss estimated to be 70-86% over the 34-day period. The N-15 loss via denitrification was 3.7-6.3% by directly measuring the N-15 gases emitted. The microplots with the incorporated residues at the 1-year-old site had the highest N-15 loss (6.3%) as compared with the other treatments. The N-15 mass balance method together with the use of bromide (Br) tracer applied at 100 kg Br ha(-1) failed to obtain a reliable estimate of the denitrification loss. The microplots at the 1-year-old site had higher N-15 immobilisation rate (7.5-24.7%) compared with those at 2- and 3-year-old sites (2.1-3.6%). Incorporating the residues resulted in an increase in N-15 immobilisation rate (24.5-24.7%) compared with the control without the incorporated residues (8.4-14.3%). These findings suggest that climatic conditions played important roles in controlling the N-15 transformations in the wet summer season and that the residue management regimes could also significantly influence the N-15 transformations. Most of the N-15 loss occurred through leaching, but a considerable amount of the N-15 was lost through denitrification. Bromide proved to be an unsuitable tracer for monitoring the N-15 leaching and movement under the wet summer conditions. (C) 2002 Elsevier Science B.V. All rights reserved.

Solution Structures of the cis- and trans-Pro30 Isomers of a Novel 38-Residue Toxin from the Venom of Hadronyche Infensa sp. that Contains a Cystine-Knot Motif within Its Four Disulfide Bonds

The primary sequence and three-dimensional structure of a novel peptide toxin isolated from the Australian funnel-web spider Hadronyche infensa sp. is reported. ACTX-HI:OB4219 contains 38 amino acids, including eight-cysteine residues that form four disulfide bonds. The connectivities of these disulfide bonds were previously unknown but have been unambiguously determined in this study. Three of these disulfide bonds are arranged in an inhibitor cystine-knot (ICK) motif, which is observed in a range of other disulfide-rich peptide toxins. The motif incorporates an embedded ring in the structure formed by two of the disulfides and their connecting backbone segments penetrated by a third disulfide bond. Using NMR spectroscopy, we determined that despite the isolation of a single native homologous product by RP-HPLC, ACTX-HI:OB4219 possesses two equally populated conformers in solution. These two conformers were determined to arise from cis/trans isomerization of the bond preceding Pro30. Full assignment of the NMR spectra for both conformers allowed for the calculation of their structures, revealing, the presence of a triple-stranded antiparallel sheet consistent with the inhibitor cystine-knot (ICK) motif.

Functional significance of a highly conserved glutamate residue of the human noradrenaline transportere

The aim of the study was to investigate the role of glutamate residue 113 in transmembrane domain 2 of the human noradrenaline transporter in determining cell surface expression and functional activity. This residue is absolutely conserved in all members of the Na+- and Cl--dependent transporter family. Mutations to alanine (hE113A), aspartate (hE113D) and glutamine (hE113Q) were achieved by site-directed mutagenesis and the mutants were expressed in transfected COS-7 or HEK-293 cells. Cell surface expression of IIE113A and hE113D, but not hE113Q, was markedly reduced compared with wild type, and functional noradrenaline uptake was detected only for the hE113Q mutant. The pharmacological properties of the hE113Q mutant showed very little change compared with wild type, except for a decrease in V-max values for noradrenaline and dopamine uptake of 2-3-fold. However, the hE113D mutant showed very marked changes in its properties, compared with wild type, with 82-260-fold decreases in the affinities of the substrates, noradrenaline, dopamine and MPP+, and increased Na+ affinity for stimulation of nisoxetine binding. The results of the study show that the size and not the charge of the 113 glutamate residue of the noradrenaline transporter seems to be the most critical factor for maintenance of transporter function and surface expression.

Molecular and functional analyses of Kunjin virus infectious cDNA clones demonstrate the essential roles for NS2A in virus assembly and for a nonconservative residue in NS3 in RNA replication

A number of full-length cDNA clones of Kunjin virus (KUN) were previously prepared; it was shown that two of them, pAKUN and FLSDX, differed in specific infectivities of corresponding in vitro transcribed RNAs by similar to100,000-fold (A. A. Khromykh et al., J. Virol. 72:7270-7279, 1998). In this study, we analyzed a possible genetic determinant(s) of the observed differences in infectivity initially by sequencing the entire cDNAs of both clones and comparing them with the published sequence of the parental KUN strain MRM61C. We found six common amino acid residues in both cDNA clones that were different from those in the published MRM61C sequence but were similar to those in the published sequences of other flaviviruses from the same subgroup. pAKUN clone had four additional codon changes, i.e., Ile59 to Asn and Arg175 to Lys in NS2A and Tyr518 to His and Ser557 to Pro in NS3. Three of these substitutions except the previously shown marker mutation, Arg175 to Lys in NS2A, reverted to the wild-type sequence in the virus eventually recovered from pAKUN RNA-transfected BHK cells, demonstrating the functional importance of these residues in viral replication and/or viral assembly. Exchange of corresponding DNA fragments between pAKUN and FLSDX clones and site-directed mutagenesis revealed that the Tyr518-to-His mutation in NS3 was responsible for an similar to5-fold decrease in specific infectivity of transcribed RNA, while the Ile59-to-Asn mutation in NS2A completely blocked virus production. Correction of the Asn59 in pAKUN NS2A to the wild-type lie residue resulted in complete restoration of RNA infectivity. Replication of KUN replicon RNA with an Ile59-to-Asn substitution in NS2A and with a Ser557-to-Pro substitution in NS3 was not affected, while the Tyr518-to-His substitution in NS3 led to severe inhibition of RNA replication. The impaired function of the mutated NS2A in production of infectious virus was complemented in trans by the helper wild-type NS2A produced from the KUN replicon RNA. However, replicon RNA with mutated NS2A could not be packaged in trans by the KUN structural proteins. The data demonstrated essential roles for the KUN nonstructural protein NS2A in virus assembly and for NS3 in RNA replication and identified specific single-amino-acid residues involved in these functions.

Composition and quality of harvest residues and soil organic matter under windrow residue management in young hoop pine plantations as revealed by solid-state C-13 NMR spectroscopy

Solid-state C-13 nuclear magnetic resonance (NMR) with cross-polarisation (CP) and magic-angle-spinning (MAS) was used to: (a) examine the changes in carbon (C) composition of windrowed harvest residues during the first 3 years of hoop pine plantations in subtropical Australia; (b) assess the impacts of windrowed harvest residues on soil organic matter (SOM) composition and quality in the 0-10 cm soil layer. Harvest residues were collected from 0-, 1-, 2- and 3-year-old windrows of ca. 2.5 m width (15 m apart for 0-, 1- and 2-year-old sites and 10 m apart for 3-year-old site). Soils from the 0 to 10 cm soil layer were collected from the 1-, 2- and 3-year-old sites. The 13C NMR spectra of the harvest residues indicated the presence of lignin in the hoop pine wood, foliage and newly incorporated organic matter (NIOM). Condensed tannin structures were found in the decay-resistant bark, small wood and foliage, but were absent in other residue components and SOM. The NMR spectra of small wood samples contained condensed tannin structures because the outer layer of bark was not removed. NIOM showed a shift from foliage-like structures (celluloses) to lignin-type structures, indicating an incorporation of woody residues from the decomposing harvest residues. Suberins were also present in the small wood, foliage and bark. The 13C CP NMR spectra of SOM indicated that in areas where windrows were present, SOM did not show compositional changes. However, an increase in SOM quality under the windrows in the second year after their formation as characterised by the alkyl C/O-alkyl C (A/O-A) ratio was mainly due to inputs from the decomposition of the labile, readily available components of the windrowed harvest residues. (C) 2002 Published by Elsevier Science B.V.

Valorization of pumpkin residue by supercritical extraction of added-value compounds

Dissertação para a obtenção do Grau de Mestre em Engenharia Química e Bioquímica

Lipid composition of fingermark residue and donor classification using GC/MS

Lipids available in fingermark residue represent important targets for enhancement and dating techniques. While it is well known that lipid composition varies among fingermarks of the same donor (intra-variability) and between fingermarks of different donors (inter-variability), the extent of this variability remains uncharacterised. Thus, this worked aimed at studying qualitatively and quantitatively the initial lipid composition of fingermark residue of 25 different donors. Among the 104 detected lipids, 43 were reported for the first time in the literature. Furthermore, palmitic acid, squalene, cholesterol, myristyl myristate and myristyl myristoleate were quantified and their correlation within fingermark residue was highlighted. Ten compounds were then selected and further studied as potential targets for dating or enhancement techniques. It was shown that their relative standard deviation was significantly lower for the intra-variability than for the inter-variability. Moreover, the use of data pretreatments could significantly reduce this variability. Based on these observations, an objective donor classification model was proposed. Hierarchical cluster analysis was conducted on the pre-treated data and the fingermarks of the 25 donors were classified into two main groups, corresponding to "poor" and "rich" lipid donors. The robustness of this classification was tested using fingermark replicates of selected donors. 86% of these replicates were correctly classified, showing the potential of such a donor classification model for research purposes in order to select representative donors based on compounds of interest.

Composition of fingermark residue: a qualitative and quantitative review

This article describes the composition of fingermark residue as being a complex system with numerous compounds coming from different sources and evolving over time from the initial composition (corresponding to the composition right after deposition) to the aged composition (corresponding to the evolution of the initial composition over time). This complex system will additionally vary due to effects of numerous influence factors grouped in five different classes: the donor characteristics, the deposition conditions, the substrate nature, the environmental conditions and the applied enhancement techniques. The initial and aged compositions as well as the influence factors are thus considered in this article to provide a qualitative and quantitative review of all compounds identified in fingermark residue up to now. The analytical techniques used to obtain these data are also enumerated. This review highlights the fact that despite the numerous analytical processes that have already been proposed and tested to elucidate fingermark composition, advanced knowledge is still missing. Thus, there is a real need to conduct future research on the composition of fingermark residue, focusing particularly on quantitative measurements, aging kinetics and effects of influence factors. The results of future research are particularly important for advances in fingermark enhancement and dating technique developments.

Composition of fingermark residue: a qualitative and quantitative review

This article describes the composition of fingermark residue as being a complex system with numerous compounds coming from different sources and evolving over time from the initial composition (corresponding to the composition right after deposition) to the aged composition (corresponding to the evolution of the initial composition over time). This complex system will additionally vary due to effects of numerous influence factors grouped in five different classes: the donor characteristics, the deposition conditions, the substrate nature, the environmental conditions and the applied enhancement techniques. The initial and aged compositions as well as the influence factors are thus considered in this article to provide a qualitative and quantitative review of all compounds identified in fingermark residue up to now. The analytical techniques used to obtain these data are also enumerated. This review highlights the fact that despite the numerous analytical processes that have already been proposed and tested to elucidate fingermark composition, advanced knowledge is still missing. Thus, there is a real need to conduct future research on the composition of fingermark residue, focusing particularly on quantitative measurements, aging kinetics and effects of influence factors. The results of future research are particularly important for advances in fingermark enhancement and dating technique developments.

Probabilistic evidential assessment of gunshot residue particle evidence (Part II) : Bayesian parameter estimation for experimental count data.

Part I of this series of articles focused on the construction of graphical probabilistic inference procedures, at various levels of detail, for assessing the evidential value of gunshot residue (GSR) particle evidence. The proposed models - in the form of Bayesian networks - address the issues of background presence of GSR particles, analytical performance (i.e., the efficiency of evidence searching and analysis procedures) and contamination. The use and practical implementation of Bayesian networks for case pre-assessment is also discussed. This paper, Part II, concentrates on Bayesian parameter estimation. This topic complements Part I in that it offers means for producing estimates useable for the numerical specification of the proposed probabilistic graphical models. Bayesian estimation procedures are given a primary focus of attention because they allow the scientist to combine (his/her) prior knowledge about the problem of interest with newly acquired experimental data. The present paper also considers further topics such as the sensitivity of the likelihood ratio due to uncertainty in parameters and the study of likelihood ratio values obtained for members of particular populations (e.g., individuals with or without exposure to GSR).