Phylogenetic analysis of the pPT23A plasmid family of Pseudomonas syringae

The pPT23A plasmid family of Pseudomonas syringae contains members that contribute to the ecological and pathogenic fitness of their P. syringae hosts. In an effort to understand the evolution of these plasmids and their hosts, we undertook a comparative analysis of the phylogeny of plasmid genes and that of conserved chromosomal genes from P. syringae. In total, comparative sequence and phylogenetic analyses were done utilizing 47 pPT23A family plasmids (PFPs) from 16 pathovars belonging to six genomospecies. Our results showed that the plasmid replication gene (repA), the only gene currently known to be distributed among all the PFPs, had a phylogeny that was distinct from that of the P. syringae hosts of these plasmids and from those of other individual genes on PFPs. The phylogenies of two housekeeping chromosomal genes, those for DNA gyrase B subunit (gyrB) and primary sigma factor (rpoD), however, were strongly associated with genomospecies of P. syringae. Based on the results from this study, we conclude that the pPT23A plasmid family represents a dynamic genome that is mobile among P. syringae pathovars.

Analysis of the antigen combining site: Correlations between length and sequence composition of the hypervariable loops and the nature of the antigen

It has long been suggested that the overall shape of the antigen combining site (ACS) of antibodies is correlated with the nature of the antigen. For example, deep pockets are characteristic of antibodies that bind haptens, grooves indicate peptide binders, while antibodies that bind to proteins have relatively flat combining sites. In. 1996, MacCallum, Martin and Thornton used a fractal shape descriptor and showed a strong correlation of the shape of the binding region with the general nature of the antigen. However, the shape of the ACS is determined primarily by the lengths of the six complementarity-determining regions (CDRs). Here, we make a direct correlation between the lengths of the CDRs and the nature of the antigen. In addition, we show significant differences in the residue composition of the CDRs of antibodies that bind to different antigen classes. As well as helping us to understand the process of antigen recognition, autoimmune disease and cross-reactivity these results are of direct application in the design of antibody phage libraries and modification of affinity. (C) 2003 Elsevier Science Ltd. All rights reserved.

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

The poliovirus cis-acting replication element (CRE) templates the uridylylation of VPg, the protein primer for genome replication. The CRE is a highly conserved structural RNA element in the enteroviruses and located within the polyprotein-coding region of the genome. We have determined the native structure of the CRE, defined the regions of the structure critical for activity, and investigated the influence of genomic location on function. Our results demonstrate that a 14-nucleotide unpaired terminal loop, presented on a suitably stable stem, is all that is required for function. These conclusions complement the recent analysis of the 14-nucleotide terminal loop in the CRE of human rhinovirus type 14. The CRE can be translocated to the 5' noncoding region of the genome, at least 3.7-kb distant from the native location, without adversely influencing activity, and CRE duplications do not adversely influence replication. We do not have evidence for a specific interaction between the CRE and the RNA-binding 3CD(pro) complex, an essential component of the uridylylation reaction, and the mechanism by which the CRE is coordinated and orientated during the reaction remains unclear. These studies provide a detailed overview of the structural determinants required for CRE function, and will facilitate a better understanding of the requirements for picornavirus replication.

Analysis of the sulfate-reducing bacterial and methanogenic archaeal populations in contrasting Antarctic sediments

The distribution and activity of communities of sulfate-reducing bacteria (SRB) and methanogenic archaea in two contrasting Antarctic sediments were investigated. Methanogenesis dominated in freshwater Lake Heywood, while sulfate reduction dominated in marine Shallow Bay. Slurry experiments indicated that 90% of the methanogenesis in Lake Heywood was acetoclastic. This finding was supported by the limited diversity of clones detected in a Lake Heywood archaeal clone library, in which most clones were closely related to the obligate acetate-utilizing Methanosaeta concilii. The Shallow Bay archaeal clone library contained clones related to the C-1-utilizing Methanolobus and Methanococcoides and the H-2-utilizing Methanogenium. Oligonucleotide probing of RNA extracted directly from sediment indicated that archaea represented 34% of the total prokaryotic signal in Lake Heywood and that Methanosaeta was a major component (13.2%) of this signal. Archaea represented only 0.2% of the total prokaryotic signal in RNA extracted from Shallow Bay sediments. In the Shallow Bay bacterial clone library, 10.3% of the clones were SRB-like, related to Desulfotalea/Desulforhopalus, Desulfofaba, Desulfosarcina, and Desulfobacter as well as to the sulfur and metal oxidizers comprising the Desulfuromonas cluster. Oligonucleotide probes for specific SRB clusters indicated that SRB represented 14.7% of the total prokaryotic signal, with Desulfotalea/Desulforhopalus being the dominant SRB group (10.7% of the total prokaryotic signal) in the Shallow Bay sediments; these results support previous results obtained for Arctic sediments. Methanosaeta and Desulfotalea/Desulforhopalus appear to be important in Lake Heywood and Shallow Bay, respectively, and may be globally important in permanently low-temperature sediments.

Analysis of the SDS-lysozyme binding isotherm

A scheme to describe SDS-lysozyme complex formation has been proposed on the basis of isothermal titration calorimetry (ITC) and FTIR spectroscopy data. ITC isotherms are convoluted and reveal a marked effect of both SDS and lysozyme concentration on the stoichiometry of the SDS-lysozyme complex. The binding isotherms have been described with the aid of FTIR spectroscopy in terms of changes in the lysozyme structure and the nature of the SDS binding. At low SDS concentrations, ITC isotherms feature an exothermic region that corresponds to specific electrostatic binding of SDS to positively charged amino acid residues on the lysozyme surface. This leads to charge neutralization of the complex and precipitation. The number of SDS molecules that bind specifically to lysozyme is approximately 8, as determined from our ITC isotherms, and is independent of lysozyme solution concentration. At high SDS concentrations, hydrophobic cooperative association dominates the binding process. Saturated binding stoichiometries as a molar ratio of SDS per molecule of lysozyme range from 220: 1 to 80: 1, depending on the lysozyme solution concentration. A limiting value of 78: 1 has been calculated for lysozyme solution concentrations above 0.25 mM.

Hygiene assessment system (HAS) scores: an analysis of the available data from English slaughterhouses

As control systems have developed and the implications of poor hygienic practices have become better known, the evaluation of the hygienic status of premises has become more critical. The assessment of the overall status of premises hygiene call provide useful management data indicating whether the premises are improving or whether, whilst still meeting legal requirements, they might be failing to maintain previously high standards. Since the creation, for the United Kingdom, of the meat hygiene service (MHS), one of the aims of the service was to monitor hygiene on different premises to provide a means of comparing standards and to identify and encourage improvements. This desire led to the implementation of a scoring system known as the hygiene assessment system (HAS). This paper analyses English slaughterhouses HAS scores between 1998 and 2005 outlining the main incidents throughout this period, Although rising initially, the later results displayed a clear decrease in the general hygiene scores. These revealing results coincide with the start of a new meat inspection system where, after several years of discussion, risk based inspection is finally coming to a reality within Europe. The paper considers the implications of these changes in the way hygiene standards will be monitored in the future.

Analysis of the headspace aroma compounds of walnuts (Juglans regia L.)

The aroma volatiles of walnuts from three different geographical locations were studied. Over 110 compounds were identified in the headspace volatiles, many for the first time as walnut components. Walnuts from China and the Ukraine contained high levels of lipid-derived volatiles, in particular hexanal, pentanal, 1-hexanol and 1-pentanol from linoleic acid breakdown, and 1-penten-3-ol from alpha-linolenic acid breakdown. Chilean walnuts, however, contained high levels of alkylbenzenes of molecular weight 120, with the lipid-derived aldehydes and alcohols present at much lower levels than in the other two walnut samples. The relationship between the fatty acid composition of the walnuts and their volatile composition is discussed. Copyright (C) 2005 John Wiley & Sons, Ltd.

Proteomic analysis of the site specificity of glycation and carboxymethylation of ribonuclease

Proteomic analysis using electrospray liquid chromatography-mass spectrometry (ESI-LC-MS) has been used to compare the sites of glycation (Amadori adduct formation) and carboxymethylation of RNase and to assess the role of the Amadori adduct in the formation of the advanced glycation end-product (AGE), N-is an element of-(carboxymethyl)lysine (CIVIL). RNase (13.7 mg/mL, 1 mM) was incubated with glucose (0.4 M) at 37 degreesC for 14 days in phosphate buffer (0.2 M, pH 7.4) under air. On the basis of ESI-LC-MS of tryptic peptides, the major sites of glycation of RNase were, in order, K41, K7, K1, and K37. Three of these, in order, K41, K7, and K37 were also the major sites of CIVIL formation. In other experiments, RNase was incubated under anaerobic conditions (1 mM DTPA, N-2 purged) to form Amadori-modified protein, which was then incubated under aerobic conditions to allow AGE formation. Again, the major sites of glycation were, in order, K41, K7, K1, and K37 and the major sites of carboxymethylation were K41, K7, and K37. RNase was also incubated with 1-5 mM glyoxal, substantially more than is formed by autoxidation of glucose under experimental conditions, but there was only trace modification of lysine residues, primarily at K41. We conclude the following: (1) that the primary route to formation of CIVIL is by autoxidation of Amadori adducts on protein, rather than by glyoxal generated on autoxidation of glucose; and (2) that carboxymethylation, like glycation, is a site-specific modification of protein affected by neighboring amino acids and bound ligands, such as phosphate or phosphorylated compounds. Even when the overall extent of protein modification is low, localization of a high proportion of the modifications at a few reactive sites might have important implications for understanding losses in protein functionality in aging and diabetes and also for the design of AGE inhibitors.

A situation analysis of the food control systems in Arab Gulf Cooperation Council (GCC) countries

Increased concerns over food safety have led to the adoption of international guidance on the key elements for national food control systems. This guidance had been used to conduct an initial assessment of the status of the food control systems in the countries belonging to the Gulf Cooperation Council. Our research has identified how the countries have been attempting to enhance their food control systems. Although the countries have different approaches to food control management, cooperation is leading to increased harmonization of legislation and food control practices. Progress is being made but there is evidence of some weakness where additional efforts may be needed. (c) 2009 Elsevier Ltd. All rights reserved.

Intensive case management for severe psychotic illness: is there a general benefit for patients with complex needs? A secondary analysis of the UK700 trial data

The UK700 trial failed to demonstrate an overall benefit of intensive case management (ICM) in patients with severe psychotic illness. This does not discount a benefit for particular subgroups, and evidence of a benefit of ICM for patients of borderline intelligence has been presented. The aim of this study is to investigate whether this effect is part of a general benefit for patients with severe psychosis complicated by additional needs. In the UK700 trial patients with severe psychosis were randomly allocated to ICM or standard case management. For each patient group with complex needs the effect of ICM is compared with that in the rest of the study cohort. Outcome measures are days spent in psychiatric hospital and the admission and discharge rates. ICM may be of benefit to patients with severe psychosis complicated by borderline intelligence or depression, but may cause patients using illicit drugs to spend more time in hospital. There was no convincing evidence of an effect of ICM in a further seven patient groups. ICM is not of general benefit to patients with severe psychosis complicated by additional needs. The benefit of ICM for patients with borderline intelligence is an isolated effect which should be interpreted cautiously until further data are available.

From dichotic listening to the irrelevant sound effect: a behavioural and neuroimaging analysis of the processing of unattended speech

The assumption that ignoring irrelevant sound in a serial recall situation is identical to ignoring a non-target channel in dichotic listening is challenged. Dichotic listening is open to moderating effects of working memory capacity (Conway et al., 2001) whereas irrelevant sound effects (ISE) are not (Beaman, 2004). A right ear processing bias is apparent in dichotic listening, whereas the bias is to the left ear in the ISE (Hadlington et al., 2004). Positron emission tomography (PET) imaging data (Scott et al., 2004, submitted) show bilateral activation of the superior temporal gyrus (STG) in the presence of intelligible, but ignored, background speech and right hemisphere activation of the STG in the presence of unintelligible background speech. It is suggested that the right STG may be involved in the ISE and a particularly strong left ear effect might occur because of the contralateral connections in audition. It is further suggested that left STG activity is associated with dichotic listening effects and may be influenced by working memory span capacity. The relationship of this functional and neuroanatomical model to known neural correlates of working memory is considered.

Analysis of the Fugl-Meyer outcome measures assessing the effectiveness of robot-mediated stroke therapy

Robot-mediated therapies offer a new approach to neurorehabilitation. This paper analyses the Fugl-Meyer data from the Gentle/S project and finds that the two intervention phases (sling suspension and robot mediated therapy) have approximately equal value to the further recovery of chronic stroke subjects (on average 27 months post stroke). Both sling suspension and robot mediated interventions show a recovery over baseline and further work is needed to establish the common factors in treatment, and to establish intervention protocols for each that will give individual subjects a maximum level of recovery.