Transvaginal ultrasound (TVUS)-guided biopsy is safe and effective in diagnosing peritoneal carcinomatosis and recurrent pelvic malignancy.

AIM: To assess safety and accuracy of transvaginal ultrasound (TVUS)-guided biopsy in achieving a diagnosis of peritoneal carcinomatosis (PC). MATERIALS AND METHODS: This was a retrospective study comprising a cohort of 54 consecutive women aged 18-85 years referred from the gynaecological oncology multidisciplinary team meeting (MDTM) who attended for TVUS-guided biopsy procedures in a tertiary oncology centre over a 4-year period (2010-2014). Clinicopathological validation was assessed using online patient records and radiological information systems. An independent oncologist assessed patient outcomes. RESULTS: The procedure was successful in all 19 patients with suspected recurrent malignancy with diagnosis validated against previous histology. Successful histological confirmation was achieved in 31 of 35 patients with suspected PC, which was thereafter validated by histology from subsequent surgery and favourable response to site-specific therapies (n=22). In three patients with suspected PC, the procedure did not result in biopsy as a suitable target could not be identified. Another woman had two false-negative biopsies. Thus overall a site-specific and subtype cancer diagnosis was obtained for 50 women giving an overall patient success rate of 93% (50/54). There were no procedure-related complications. CONCLUSION: TVUS core biopsy is a safe, effective, well-tolerated, and valuable technique in modern oncological management of PC when other diagnostic options are unavailable.

Influence of dietary protein level on body composition and energy expenditure in calorically restricted overweight cats.

High-protein (HP) diets help prevent loss of lean mass in calorie-restricted (CR) cats. However, it is not entirely known whether these diets also induce changes of energy expenditure during periods of CR. To investigate this issue, sixteen overweight cats were fed either a high-protein [(HP), 54.2% of metabolizable energy (ME)] or a moderate-protein [(MP), 31.5% of ME] diet at 70% of their maintenance energy intakes for 8 weeks, and energy expenditure, energy intake, body weight and composition, and serum metabolites and hormones were measured. While both groups of cats lost weight at a similar rate, only cats eating the HP diet maintained lean mass during weight loss. Indirect respiration calorimetry measurements revealed that both total and resting energy expenditure (kcal/d) significantly decreased during weight loss for both treatment groups. However, only cats eating the MP diet exhibited significant decreases of total and resting energy expenditures after energy expenditure was normalized for body weight or lean mass. Results from this study suggest that in addition to sparing the loss of lean mass, feeding HP diets to overweight cats in restricted amounts may be beneficial for preventing or minimizing decreases of mass-adjusted energy expenditure during weight loss.

Loss of coupling between calcium influx, energy consumption and insulin secretion associated with development of hyperglycaemia in the UCD-T2DM rat model of type 2 diabetes.

AIMS/HYPOTHESIS: Previous studies on isolated islets have demonstrated tight coupling between calcium (Ca(2+)) influx and oxygen consumption rate (OCR) that is correlated with insulin secretion rate (ISR). To explain these observations, we have proposed a mechanism whereby the activation of a highly energetic process (Ca(2+)/metabolic coupling process [CMCP]) by Ca(2+) mediates the stimulation of ISR. The aim of the study was to test whether impairment of the CMCP could play a role in the development of type 2 diabetes. METHODS: Glucose- and Ca(2+)-mediated changes in OCR and ISR in isolated islets were compared with the time course of changes of plasma insulin concentrations observed during the progression to hyperglycaemia in a rat model of type-2 diabetes (the University of California at Davis type 2 diabetes mellitus [UCD-T2DM] rat). Islets were isolated from UCD-T2DM rats before, 1 week, and 3 weeks after the onset of hyperglycaemia. RESULTS: Glucose stimulation of cytosolic Ca(2+) and OCR was similar for islets harvested before and 1 week after the onset of hyperglycaemia. In contrast, a loss of decrement in islet OCR and ISR in response to Ca(2+) channel blockade coincided with decreased fasting plasma insulin concentrations observed in rats 3 weeks after the onset of hyperglycaemia. CONCLUSIONS/INTERPRETATION: These results suggest that phenotypic impairment of diabetic islets in the UCD-T2DM rat is downstream of Ca(2+) influx and involves unregulated stimulation of the CMCP. The continuously elevated levels of CMCP induced by chronic hyperglycaemia in these islets may mediate the loss of islet function.

Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

Identification of protein binding surfaces using surface triplet propensities.

MOTIVATION: The ability to reliably predict protein-protein and protein-ligand interactions is important for identifying druggable binding sites and for understanding how proteins communicate. Most currently available algorithms identify cavities on the protein surface as potential ligand recognition sites. The method described here does not explicitly look for cavities but uses small surface patches consisting of triplets of adjacent surface atomic groups that can be touched simultaneously by a probe sphere representing a solvent molecule. A total of 455 different types of triplets can be identified. A training set of 309 protein-ligand protein X-ray structures has been used to generate interface propensities for the triplets, which can be used to predict their involvement in ligand-binding interactions. RESULTS: The success rate for locating protein-ligand binding sites on protein surfaces using this new surface triplet propensities (STP) algorithm is 88% which compares well with currently available grid-based and energy-based approaches. Q-SiteFinder's dataset (Laurie and Jackson, 2005. Bioinformatics, 21, 1908-1916) was used to show the favorable performance of STP. An analysis of the different triplet types showed that higher ligand binding propensity is related to more polarizable surfaces. The interaction statistics between triplet atoms on the protein surface and ligand atoms have been used to estimate statistical free energies of interaction. The ΔG(stat) for halogen atoms interacting with hydrophobic triplets is -0.6 kcal/mol and an estimate of the maximal ΔG(stat) for a ligand atom interacting with a triplet in a binding pocket is -1.45 kcal/mol. AVAILABILITY: Freely available online at http://opus.bch.ed.ac.uk/stp. Website implemented in Php, with all major browsers supported. CONTACT: m.walkinshaw@ed.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

An automated framework for understanding structural variations in the binding grooves of MHC class II molecules.

BACKGROUND: MHC/HLA class II molecules are important components of the immune system and play a critical role in processes such as phagocytosis. Understanding peptide recognition properties of the hundreds of MHC class II alleles is essential to appreciate determinants of antigenicity and ultimately to predict epitopes. While there are several methods for epitope prediction, each differing in their success rates, there are no reports so far in the literature to systematically characterize the binding sites at the structural level and infer recognition profiles from them. RESULTS: Here we report a new approach to compare the binding sites of MHC class II molecules using their three dimensional structures. We use a specifically tuned version of our recent algorithm, PocketMatch. We show that our methodology is useful for classification of MHC class II molecules based on similarities or differences among their binding sites. A new module has been used to define binding sites in MHC molecules. Comparison of binding sites of 103 MHC molecules, both at the whole groove and individual sub-pocket levels has been carried out, and their clustering patterns analyzed. While clusters largely agree with serotypic classification, deviations from it and several new insights are obtained from our study. We also present how differences in sub-pockets of molecules associated with a pair of autoimmune diseases, narcolepsy and rheumatoid arthritis, were captured by PocketMatch13. CONCLUSION: The systematic framework for understanding structural variations in MHC class II molecules enables large scale comparison of binding grooves and sub-pockets, which is likely to have direct implications towards predicting epitopes and understanding peptide binding preferences.

Predicting functional upstream open reading frames in Saccharomyces cerevisiae.

BACKGROUND: Some upstream open reading frames (uORFs) regulate gene expression (i.e., they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not yet fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of experimentally verified functional uORFs are needed. Unfortunately, wet-experiments to verify that uORFs are functional are expensive. RESULTS: In this paper, a new computational approach to predicting functional uORFs in the yeast Saccharomyces cerevisiae is presented. Our approach is based on inductive logic programming and makes use of a novel combination of knowledge about biological conservation, Gene Ontology annotations and genes' responses to different conditions. Our method results in a set of simple and informative hypotheses with an estimated sensitivity of 76%. The hypotheses predict 301 further genes to have 398 novel functional uORFs. Three (RPC11, TPK1, and FOL1) of these 301 genes have been hypothesised, following wet-experiments, by a related study to have functional uORFs. A comparison with another related study suggests that eleven of the predicted functional uORFs from genes LDB17, HEM3, CIN8, BCK2, PMC1, FAS1, APP1, ACC1, CKA2, SUR1, and ATH1 are strong candidates for wet-lab experimental studies. CONCLUSIONS: Learning based prediction of functional uORFs can be done with a high sensitivity. The predictions made in this study can serve as a list of candidates for subsequent wet-lab verification and might help to elucidate the regulatory roles of uORFs.

PROPHECY--a yeast phenome database, update 2006.

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics--the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale--connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization. Our yeast phenomics database PROPHECY is available at http://prophecy.lundberg.gu.se. Via phenotyping of 984 heterozygous diploids for all essential genes the genotypes analysed and presented in PROPHECY have been extended and now include all genes in the yeast genome. Further, phenotypic data from gene overexpression of 574 membrane spanning proteins has recently been included. To facilitate the interpretation of quantitative phenotypic data we have developed a new phenotype display option, the Comparative Growth Curve Display, where growth curve differences for a large number of mutants compared with the wild type are easily revealed. In addition, PROPHECY now offers a more informative and intuitive first-sight display of its phenotypic data via its new summary page. We have also extended the arsenal of data analysis tools to include dynamic visualization of phenotypes along individual chromosomes. PROPHECY is an initiative to enhance the growing field of phenome bioinformatics.

Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation.

BACKGROUND: The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational reinitiation at the main start codon. uORFs also occur by chance in the genome, in which case they do not have a regulatory role. Since the sequence determinants for functional uORFs are not understood, it is difficult to discriminate functional from spurious uORFs by sequence analysis. RESULTS: We have used comparative genomics to identify novel uORFs in yeast with a high likelihood of having a translational regulatory role. We examined uORFs, previously shown to play a role in regulation of translation in Saccharomyces cerevisiae, for evolutionary conservation within seven Saccharomyces species. Inspection of the set of conserved uORFs yielded the following three characteristics useful for discrimination of functional from spurious uORFs: a length between 4 and 6 codons, a distance from the start of the main ORF between 50 and 150 nucleotides, and finally a lack of overlap with, and clear separation from, neighbouring uORFs. These derived rules are inherently associated with uORFs with properties similar to the GCN4 locus, and may not detect most uORFs of other types. uORFs with high scores based on these rules showed a much higher evolutionary conservation than randomly selected uORFs. In a genome-wide scan in S. cerevisiae, we found 34 conserved uORFs from 32 genes that we predict to be functional; subsequent analysis showed the majority of these to be located within transcripts. A total of 252 genes were found containing conserved uORFs with properties indicative of a functional role; all but 7 are novel. Functional content analysis of this set identified an overrepresentation of genes involved in transcriptional control and development. CONCLUSION: Evolutionary conservation of uORFs in yeasts can be traced up to 100 million years of separation. The conserved uORFs have certain characteristics with respect to length, distance from each other and from the main start codon, and folding energy of the sequence. These newly found characteristics can be used to facilitate detection of other conserved uORFs.

PROPHECY--a database for high-resolution phenomics.

The rapid recent evolution of the field phenomics--the genome-wide study of gene dispensability by quantitative analysis of phenotypes--has resulted in an increasing demand for new data analysis and visualization tools. Following the introduction of a novel approach for precise, genome-wide quantification of gene dispensability in Saccharomyces cerevisiae we here announce a public resource for mining, filtering and visualizing phenotypic data--the PROPHECY database. PROPHECY is designed to allow easy and flexible access to physiologically relevant quantitative data for the growth behaviour of mutant strains in the yeast deletion collection during conditions of environmental challenges. PROPHECY is publicly accessible at http://prophecy.lundberg.gu.se.

River flow and associated transport of sediments and solutes through a highly urbanised catchment, Bradford, West Yorkshire.

The hydrological characteristics of catchments become drastically modified in response to urbanisation. The total contributions and dynamics of runoff, suspended sediment and solutes may change significantly and have important implications downstream where they may affect flooding, instream ecological habitat, water quality and siltation of river channels and lakes. Although an appreciation of the likely hydrological changes is crucial for effective catchment management they are still poorly understood. In this paper we present data from a network of river monitoring stations throughout the heavily urbanised Bradford catchment, West Yorkshire. Sites are upstream, within and downstream of the highly urbanised central part of the catchment. Flow, turbidity (calibrated to suspended sediment concentration) and specific conductance (surrogate for solute concentration), logged at 15-min intervals, are presented for a 12-month period (June 2000 to June 2001). The total amounts and dynamics of flow, solute and suspended sediment transport were investigated. Estimated total flow and suspended sediment transport for the monitoring period were found to be high in response to the high total rainfall. Flow and sediment transport regimes were extremely 'flashy' throughout the catchment and became increasingly flashy in a downstream direction. Suspended sediment discharged from the Bradford subcatchment makes an important contribution to downstream sediment transport on the river Aire at Beal. Data suggest that the urbanised part of the Bradford catchment is extremely important in contributing solutes to the Beck (river). Although flow and sediment are also contributed to the Bradford Beck in the urbanised part of the catchment the data suggest that significant amounts may enter the combined sewer system and bypass the river. Understanding the spatial and temporal variations of flow and the transport of suspended sediment and solutes in rivers in urbanized subcatchments is crucial to their effective management and monitoring. Furthermore, this knowledge may be extremely important to the management and monitoring of downstream rivers in large scale mixed catchments.

Conformation of the exopolysaccharide of Burkholderia cepacia predicted with molecular mechanics (MM3) using genetic algorithm search.

We present a computational conformational analysis of the exopolysaccharide of Burkholderia cepacia, which is believed to play a role in colonization and persistence of B. cepacia in the lungs of cystic fibrosis patients. The repeating unit of the exopolysaccharide is a heptasaccharide with three branches, which cause significant steric restraints. Conformational searches using glygal, an in-house developed software using genetic algorithm search methods, were performed on fragments as well as on the complete repeating unit with wrap-over residues. The force field used for the calculations was MM3(96). The search showed four favored conformations for an isolated repeating unit. However, for a sequence of several repeating units, the calculations indicate a single, well-defined linear conformation.

The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides.

We have implemented a system called glygal that can perform conformational searches on oligosaccharides using several different genetic algorithm (GA) search methods. The searches are performed in the torsion angle conformational space, considering both the primary glycosidic linkages as well as the pendant groups (C-5-C-6 and hydroxyl groups) where energy calculations are performed using the MM3(96) force field. The system includes a graphical user interface for setting calculation parameters and incorporates a 3D molecular viewer. The system was tested using dozens of structures and we present two case studies for two previously investigated O-specific oligosaccharides of the Shigella dysenteriae type 2 and 4. The results obtained using glygal show a significant reduction in the number of structures that need to be sampled in order to find the best conformation, as compared to filtered systematic search.

Analysis of fish IL-1beta and derived peptide sequences indicates conserved structures with species-specific IL-1 receptor binding: implications for pharmacological design.

A large number of IL-1 protein sequences have become available recently from a range of vertebrate species and especially from bony fish. However, 3D structures are still only known for mammalian IL-1. In this review, we use a multiple sequence alignment of all published non-mammalian vertebrate IL-1beta proteins to locate the structurally important residues critical for maintaining the beta-trefoil fold and we investigate the degree to which functionally important residues involved in receptor binding are conserved across vertebrate species. We find that although there is a high level of variability of positions involved in receptor binding, the mode of binding and overall shape of the ligand-receptor complex is probably maintained. This implies that each species has evolved its own unique interleukin-1 signalling system through ligand-receptor co-evolution. Nonetheless, the IL-1beta processing mechanism in non-mammalian vertebrates remains unclear because, with the exception of three bony fish, all non-mammalian IL-1beta sequences discovered so far lack an ICE (Interleukin Converting Enzyme) cut site. The IL-1 system has become an important drug target because of its significance in inflammatory diseases. Research on peptides derived from IL-1beta has identified peptides that possess agonist activity in humans and in trout, and peptides with antagonist activity. The agonist peptides map to two distinct loop regions of IL-1beta that are known to interact with the flexible domain III of the corresponding receptor. Further analysis of the IL-1 system may prove useful in engineering IL-1 with improved features and in suggesting new avenues for therapeutic intervention.

The vital dye Evans blue mimics limbic seizures induced by kainate or pilocarpine.

Evans blue dye, given i.c.v. in rats in a dose of 208 nmol, causes electrical and behavioural seizures which resemble those induced by the glutamate analogue, kainate, or by electrical kindling of the amygdala. Chicago sky blue, 201 nmol i.c.v., produces similar seizures. The principal elements of the seizures are wet-rat-shakes, facial and forelimb clonus, rearing and spike-and-waves in the EEG. A non-NMDA receptor antagonist, GYKI 52466 and a benzodiazepine, diazepam, significantly delay the onset to the occurrence of the first forelimb clonus. The cholinergic antagonist, scopolamine, significantly reduces the delay to onset of first facial clonus. The competitive NMDA receptor antagonist, D-CPPene, the non-specific dopamine antagonist, haloperidol, and the purinergic agonist, 2-chloroadenosine, have no effect on the measured parameters. During the induction of seizures by Evans blue, the average extracellular glutamate concentration in hippocampus or cortex does not increase statistically significantly in comparison to pre-seizure values. Histological examination of limbic areas indicates that the moderate to severe Evans blue-induced cell damage is similar to that seen after limbic seizures induced by pilocarpine and in the hippocampus is partially preventable by D-CPPene but not by diazepam or GYKI 52466. It is proposed that Evans blue-induced seizures may be useful as a new model for studying the mechanisms of intractable epilepsy of the complex partial seizure type.

Receptor--ion channel interactions in Torpedo electric organ: influence of thiol group modification.

The influence of sulfhydryl and disulfide reagents on nicotinic cholinergic receptors and ion channels and their interactions was investigated using specific probes for receptor and channel binding sites in electric organs from Torpedo californica. N-ethylmaleimide, a sulfhydryl alkylating agent, did not alter receptor or ion channel binding, or receptor-mediated ion channel binding activation or desensitization. Alteration of receptor--ion channel coupling produced by treatment with an organic sulfhydryl, dithiothreitol, could be accounted for on the basis of decreases in receptor affinity for agonists. These changes were reversed by exposure to an oxidizing agent. Following reduction by dithiothreitol, N-ethylmaleimide treatment produced large decreases in the extent and affinity of both receptor and channel binding. No evidence for a direct role of thiol groups in ion channel function was obtained.

Anticonvulsant activity of the NMDA antagonists, D(-)4-(3-phosphonopropyl) piperazine-2-carboxylic acid (D-CPP) and D(-)(E)-4-(3-phosphonoprop-2-enyl) piperazine-2-carboxylic acid (D-CPPene) in a rodent and a primate model of reflex epilepsy.

D-(-)4-(3-phosphonopropyl)piperazine-2-carboxylic acid (D-CPP) and its unsaturated analogue (D(-)(E)-4-(3-phosphonoprop-2-enyl) piperazine-2-carboxylic acid (D-CPPene) have been administered to DBA/2 mice (intracerebroventricularly, i.c.v., intraperitoneally, i.p., and orally, p.o.) and to photosensitive baboons, Papio papio (intravenously, i.v., and orally), and their effects on reflexly induced epileptic responses assessed. In DBA/2 mice the clonic phase of the seizure response to sound is suppressed by D-CPP with an ED50 of 5.5 micrograms/mouse, i.c.v.; 0.69 mg (2.75 mumol)/kg i.p. and 16.6 mg (65.8 mumol)/kg p.o. compared with, for D-CPPene, 2.2 micrograms/mouse i.c.v., 0.41 mg (1.54 mumol)/kg i.p. and 10.8 mg (40.2 mumol)/kg, p.o. In Papio papio myoclonic responses to stroboscopic stimulation are suppressed 24 and 48 h after D-CPP 32 mg (127 mumol)/kg p.o. Administration of D-CPPene 8-16 mg (30-60 mumol)/kg i.v. produces protection against myoclonic responses after 1-2 h, lasting for 48 h. Oral administration of D-CPPene 32-64 mg (119-239 mumol)/kg produces protection beginning after 4 h and sustained for 48 h. Measurements of plasma D-CPPene concentration show rapid clearance after i.v. injection and a low plasma concentration 1.5-5 h after oral administration. The prolonged anticonvulsant action of D-CPP and D-CPPene following oral administration suggests that these compounds merit evaluation as antiepileptic therapy in man.

Fingerprinting suspended sediment sources in a large urban river system.

Very few studies have attempted to quantify the sources of suspended sediment transported in urban river systems. In this study, statistically verified composite fingerprints and a multivariate mixing model have been used to identify the main sources of the suspended sediment transported by the River Aire and its main tributary, the River Calder. Because of the polluted nature of the Aire/Calder catchment and its effect on fingerprint property concentrations, source tracing was undertaken separately for the upper and lower reaches. The mean contributions from individual source types (i.e. surface materials from woodland, uncultivated and cultivated areas, channel bank material, road dust and solids from sewage treatment works) varied between the upper and lower reaches of the rivers, reflecting the change in land use from primarily pasture and moorland in the upper reaches to mainly urban areas (with some cultivated land) in the lower reaches. The suspended sediment in the upper reaches of the River Aire originates largely from channel bank sources (43-84%) and from uncultivated topsoil (16-57%). In the lower reaches of the Aire/Calder system, local sources of cultivated topsoil contribute 20-45% of the suspended sediment load and there is a significant contribution from urban sources, such as road dust (19-22%) and solids from sewage treatment works (14-18%). In the upper reaches, the proportion of sediment derived from each of the two main geological areas corresponds broadly to the proportion of the catchment occupied by each geological area. The relative contribution from the Rivers Aire and Calder to the suspended sediment load transported below the confluence demonstrates that most of the sediment is derived from the River Calder.

Land-ocean interaction: processes, functioning and environmental management from a UK perspective: an introduction.

This paper provides a foreword to a special edition of Science of the Total Environment concerned with land-ocean interaction from a UK perspective as linked to processes, functioning and environmental management. The volume structure is presented together with an outline of the nature of the individual papers. The areas covered are: (1) freshwater chemistry, (2) riverine sedimentology, (3) tidal river, estuarine and coastal chemistry, (4) estuarine and coastal sediments and (5) shelf-sea-ocean linkages. The foreword provides as an introductory link to the broader perspectives of contemporary UK research in this area, which comes in a conclusions paper at the end of the volume.