bluuebunny/crossref_metadata_2025 huggingface dataset:
Less is more: towards an optimal universal description of protein folds
Authors: Szustakowski Joseph D. , Kasif Simon , Weng Zhiping
Published: October 2005

Motivation: Identification and characterization of protein structure regularities can reveal the mechanisms governing protein structure, function and evolution. Here we focus on an intermediate level of regularity. We have developed automated methods to systematically construct a dictionary of supersecondary structures that can be used as ‘protein parts’ to describe fold-sized structures.

Results: The dictionary was constructed by aligning representative structures of all known folds, clustering similar substructures and selecting the most descriptive substructures in a minimum description length fashion. We show that the dictionary is compact and descriptive, capable of describing a substantial fraction of all known protein folds. We performed simulations using independent sets of training and testing folds. Dictionaries generated using the training set had high coverage over the folds in the testing set, suggesting that dictionary entries reflect general features of protein structures and should be capable of describing novel protein folds.

Contact:  zhiping@bu.edu
Genome-wide decoding of hierarchical modular structure of transcriptional regulation by cis-element and expression clustering
Authors: Leyfer Dmitriy , Weng Zhiping
Published: October 2005

Motivation: A holistic approach to the study of cellular processes is identifying both gene-expression changes and regulatory elements promoting such changes. Cellular regulatory processes can be viewed as transcriptional modules (TMs), groups of coexpressed genes regulated by groups of transcription factors (TFs). We set out to devise a method that would identify TMs while avoiding arbitrary thresholds on TM sizes and number.

Method: Assuming that gene expression is determined by TFs that bind to the gene's promoter, clustering of genes based on TF binding sites (cis-elements) should create gene groups similar to those obtained by gene expression clustering. Intersections between the expression and cis-element-based gene clusters reveal TMs. Statistical significance assigned to each TM allows identification of regulatory units of any size.

Results: Our method correctly identifies the number and sizes of TMs on simulated datasets. We demonstrate that yeast experimental TMs are biologically relevant by comparing them with MIPS and GO categories. Our modules are in statistically significant agreement with TMs from other research groups. This work suggests that there is no preferential division of biological processes into regulatory units; each degree of partitioning exhibits a slice of biological network revealing hierarchical modular organization of transcriptionalregulation.

Contact:  dleyfer@gnsbiotech.com
Decomposing protein networks into domain–domain interactions
Authors: Albrecht Mario , Huthmacher Carola , Tosatto Silvio C. E. , Lengauer Thomas
Published: October 2005

Summary: The application of novel experimental techniques has generated large networks of protein–protein interactions. Frequently, important information on the structure and cellular function of protein–protein interactions can be gained from the domains of interacting proteins. We have designed a Cytoscape plugin that decomposes interacting proteins into their respective domains and computes a putative network of corresponding domain–domain interactions. To this end, the network graph of proteins has been extended by additional node and edge types for domain interactions, including different node and edge shapes and coloring schemes used for visualization. An additional plugin provides supplementary web links to Internet resources on domain function and structure.

Availability: Both Cytoscape plugins can be downloaded from http://www.cytoscape.org

Contact:  mario.albrecht@mpi-inf.mpg.de
Horizontal gene transfer depends on gene content of the host
Authors: Pál Csaba , Papp Balázs , Lercher Martin J.
Published: October 2005

Horizontal gene transfer is a major contributor to the evolution of bacterial genomes. We examine this process through a combination of comparative genomics and in silico analysis of the Escherichia coli metabolic network. We validate our horizontal transfer estimates by confirming the predicted gradual amelioration of GC content over time. We find that the chance of acquiring a gene by horizontal transfer is up to six times higher if an enzyme that catalyses a coupled metabolite flux is already encoded in the host genome.

Contact:  Lercher@embl.de
Functional stoichiometric analysis of metabolic networks
Authors: Urbanczik R. , Wagner C.
Published: September 2005

Motivation: An important tool in Systems Biology is the stoichiometric modeling of metabolic networks, where the stationary states of the network are described by a high-dimensional polyhedral cone, the so-called flux cone. Exhaustive descriptions of the metabolism can be obtained by computing the elementary vectors of this cone but, owing to a combinatorial explosion of the number of elementary vectors, this approach becomes computationally intractable for genome scale networks.

Result: Hence, we propose to instead focus on the conversion cone, a projection of the flux cone, which describes the interaction of the metabolism with its external chemical environment. We present a direct method for calculating the elementary vectors of this cone and, by studying the metabolism of Saccharomyces cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.

Contact:  robert.urbanczik@pki.unibe.ch
Bioinformatics analyses of circular dichroism protein reference databases
Authors: Janes Robert W.
Published: September 2005

Motivation: Circular dichroism (CD) spectroscopy has become established as a key method for determining the secondary structure contents of proteins which has had a significant impact on molecular biology. Many excellent mathematical protocols have been developed for this purpose and their quality is above question. However, reference database sets of proteins, with CD spectra matched to secondary structure components derived from X-ray structures, provide the key resource for this task. These databases were created many years ago, before most CD spectrophotometers became standardized and before it was commonplace to validate X-ray structures prior to publication. The analyses presented here were undertaken to investigate the overall quality of these reference databases in light of their extensive usage in determining protein secondary structure content from CD spectra.

Results: The analyses show that there are a number of significant problems associated with the CD reference database sets in current use. There are disparities between CD spectra for the same protein collected by different groups. These include differences in magnitudes, peak positions or both. However, many current reference sets are now amalgamations of spectra from these groups, introducing inconsistencies that can lead to inaccuracies in the determination of secondary structure components from the CD spectra. A number of the X-ray structures used fall short on the validation criteria now employed as standard for structure determination. Many have substantial percentages of residues in the disallowed regions of the Ramachandran plot. Hence their calculated secondary structure components, used as a foundation for the reference databases, are likely to be in error. Additionally, the coverage of secondary structure space in the reference datasets is poorly correlated to the secondary structure components found in the Protein Data Bank. A conclusion is that a new reference CD database with cross-correlated, machine-independent CD spectra and validated X-ray structures that cover more secondary structure components, including diverse protein folds, is now needed. However, that reasonably accurate values for the secondary structure content of proteins can be determined from spectra is a testament to CD spectroscopy being a very powerful technique.

Contact:  r.w.janes@qmul.ac.uk
MACiE: a database of enzyme reaction mechanisms
Authors: Holliday Gemma L. , Bartlett Gail J. , Almonacid Daniel E. , O'Boyle Noel M. , Murray-Rust Peter , Thornton Janet M. , Mitchell John B. O.
Published: September 2005

Summary: MACiE (mechanism, annotation and classification in enzymes) is a publicly available web-based database, held in CMLReact (an XML application), that aims to help our understanding of the evolution of enzyme catalytic mechanisms and also to create a classification system which reflects the actual chemical mechanism (catalytic steps) of an enzyme reaction, not only the overall reaction.

Availability:  

Contact:  jbom1@cam.ac.uk
Mapping PDB chains to UniProtKB entries
Authors: Martin Andrew C. R.
Published: September 2005

Motivation: UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly updated mapping between UniProtKB entries and PDB entries at the chain or residue level is not straightforward. In particular, there is no regularly updated resource which allows a UniProtKB/SwissProt entry to be identified for a given residue of a PDB file.

Results: We have created a completely automatically maintained database which maps PDB residues to residues in UniProtKB/SwissProt and UniProtKB/trEMBL entries. The protocol uses links from PDB to UniProtKB, from UniProtKB to PDB and a brute-force sequence scan to resolve PDB chains for which no annotated link is available. Finally the sequences from PDB and UniProtKB are aligned to obtain a residue-level mapping.

Availability: The resource may be queried interactively or downloaded from

Contact:  andrew@bioinf.org.uk
Medusa: a simple tool for interaction graph analysis
Authors: Hooper Sean D. , Bork Peer
Published: September 2005

Summary: Medusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING database. It features an intuitive user interface developed with the help of biologists. Medusa is optimized for accessing protein interaction data from STRING, but can be used for any type of graph from any scientific field.

Availability: Medusa, along with sample datasets and instructions, can be downloaded from

Contact:  hooper@embl.de
Poor Intraoperative Blood Glucose Control Is Associated with a Worsened Hospital Outcome after Cardiac Surgery in Diabetic Patients
Authors: Ouattara Alexandre , Lecomte Patrick , Le Manach Yannick , Landi Marc , Jacqueminet Sophie , Platonov Igor , Bonnet Nicolas , Riou Bruno , Coriat Pierre
Published: September 2005

Background

Tight perioperative control of blood glucose improves the outcome of diabetic patients undergoing cardiac surgery. Because stress response and cardiopulmonary bypass can induce profound hyperglycemia, intraoperative glycemic control may become difficult. The authors undertook a prospective cohort study to determine whether poor intraoperative glycemic control is associated with increased intrahospital morbidity.

Methods

Two hundred consecutive diabetic patients undergoing on-pump heart surgery were enrolled. A standard insulin protocol based on subcutaneous intermediary insulin was given the morning of the surgery. Intravenous insulin therapy was initiated intraoperatively from blood glucose concentrations of 180 mg/dl or greater and titrated according to a predefined protocol. Poor intraoperative glycemic control was defined as four consecutive blood glucose concentrations greater than 200 mg/dl without any decrease in despite insulin therapy. Postoperative blood glucose concentrations were maintained below 140 mg/dl by using aggressive insulin therapy. The main endpoints were severe cardiovascular, respiratory, infectious, neurologic, and renal in-hospital morbidity.

Results

Insulin therapy was required intraoperatively in 36% of patients, and poor intraoperative glycemic control was observed in 18% of patients. Poor intraoperative glycemic control was significantly more frequent in patients with severe postoperative morbidity (37% vs. 10%; P < 0.001). The adjusted odds ratio for severe postoperative morbidity among patients with a poor intraoperative glycemic control as compared with patients without was 7.2 (95% confidence interval, 2.7-19.0).

Conclusion

Poor intraoperative control of blood glucose concentrations in diabetic patients undergoing cardiac surgery is associated with a worsened hospital outcome after surgery.
Arterial and Venous Pharmacokinetics of Ropivacaine with and without Epinephrine after Thoracic Paravertebral Block
Authors: Karmakar Manoj K. , Ho Anthony M.-H. , Law Bonita K. , Wong April S. Y. , Shafer Steven L. , Gin Tony
Published: September 2005

Background

Animal and volunteer studies indicate that ropivacaine is associated with less neurologic and cardiac toxicity than bupivacaine. Ropivacaine may offer advantages when used for thoracic paravertebral block. This study was designed to describe the pharmacokinetics of ropivacaine after thoracic paravertebral block.

Methods

Twenty female patients undergoing elective unilateral breast surgery were randomly assigned to receive a single bolus thoracic paravertebral injection of 2 mg/kg ropivacaine, with or without 5 mug/ml epinephrine. Simultaneous arterial and venous blood samples were obtained for plasma ropivacaine assay. Data were analyzed with NONMEM, using two possible absorption models: conventional first-order absorption and absorption following the inverse gaussian density function.

Results

Epinephrine reduced the peak plasma concentrations and delayed the time of peak concentration of ropivacaine in both the arterial and venous blood. The time course of drug input into the systemic circulation was best described by two inverse gaussian density functions. The median bioavailability of the rapid component was approximately 20% higher when epinephrine was not used. The mean absorption times were 7.8 min for the rapid absorption phase and 697 min for the slow absorption phase, with wide dispersion of the absorption function for the acute phase. The half-time of arterial-venous equilibration was 1.5 min.

Conclusion

The absorption of ropivacaine after thoracic paravertebral block is described by rapid and slow absorption phases. The rapid phase approximates the speed of intravenous administration and accounts for nearly half of ropivacaine absorption. The addition of 5 mug/ml epinephrine to ropivacaine significantly delays its systemic absorption and reduces the peak plasma concentration.
Synthetic Colloids Attenuate Leukocyte-Endothelial Interactions by Inhibition of Integrin Function
Authors: Nohé Boris , Johannes Tanja , Reutershan Jörg , Rothmund Albert , Haeberle Helene A. , Ploppa Annette , Schroeder Torsten H. , Dieterich Hans-Juergen
Published: September 2005

Background

It has been suspected that synthetic colloids may interfere with leukocyte adhesion by down-regulation of endothelial cell adhesion molecules. Although inhibition of endothelial inflammation might reduce leukocyte-related tissue injury, the same mechanism may be detrimental for host defense during severe infection. Regarding the widespread use of colloids, the authors performed a laboratory investigation to determine the mechanisms by which synthetic colloids interfere with leukocyte-endothelial interactions.

Methods

Adhesion molecule expression on native and cytokine-activated endothelium from umbilical veins was measured after pretreatment with gelatin and various preparations of dextran or hydroxyethyl starch. Inhibition of neutrophil adhesion to activated endothelium was examined in a flow chamber by perfusion of untreated and colloid-treated neutrophils over colloid-pretreated endothelium at 2 dyn/cm. Comparisons were made between untreated controls, colloid-pretreated endothelium, and colloid-cotreated neutrophils.

Results

Intercellular adhesion molecule 1, vascular cell adhesion molecule 1, E-selectin, and P-selectin were not attenuated by any colloid. Accordingly, colloid pretreatment of endothelium alone did not reduce neutrophil adhesion. In contrast, when neutrophils were cotreated by addition of colloids to the perfusate immediately before perfusion, adhesion decreased by 31-51% (P < 0.05) regardless of the colloid type. As indicated by the twofold increased rolling fractions, this reduction was due to an inhibition of neutrophil integrins.

Conclusions

This study shows that synthetic colloids inhibit neutrophil adhesion by a neutrophil-dependent mechanism rather than interfering with endothelial cell activation. This suggests that inhibition of leukocyte sequestration by volume support is a common and transient phenomenon depending on the colloid concentration in plasma.
Volatile Anesthetics Bind Rat Synaptic Snare Proteins
Authors: Nagele Peter , Mendel J Brett , Placzek William J. , Scott Barbara A. , d'Avignon D André , Crowder C Michael
Published: September 2005

Background

Volatile general anesthetics (VAs) have a number of synaptic actions, one of which is to inhibit excitatory neurotransmitter release; however, no presynaptic VA binding proteins have been identified. Genetic data in Caenorhabditis elegans have led to the hypothesis that a protein that interacts with the presynaptic protein syntaxin 1A is a VA target. Motivated by this hypothesis, the authors measured the ability of syntaxin 1A and proteins that interact with syntaxin to bind to halothane and isoflurane.

Methods

Recombinant rat syntaxin 1A, SNAP-25B, VAMP2, and the ternary SNARE complex that they form were tested. Binding of VAs to these proteins was detected by F-nuclear magnetic resonance relaxation measurements. Structural alterations in the proteins were examined by circular dichroism and ability to form complexes.

Results

Volatile anesthetics did not bind to VAMP2. At concentrations in the clinical range, VAs did bind to SNAP-25B; however, binding was detected only in preparations containing SNAP-25B homomultimers. VAs also bound at clinical concentrations to both syntaxin and the SNARE complex. Addition of an N-terminal His6 tag to syntaxin abolished its ability to bind VAs despite normal secondary structure and ability to form SNARE complexes; thrombin cleavage of the tag restored VA binding. Thus, the VA binding site(s) has structural requirements and is not simply any alpha-helical bundle. VAs at supraclinical concentrations produced an increase in helicity of the SNARE complex; otherwise, VA binding produced no gross alteration in the stability or secondary structure of the SNARE complex.

Conclusion

SNARE proteins are potential synaptic targets of volatile anesthetics.
Morphine Inhibits Acetylcholine Release in Rat Prefrontal Cortex When Delivered Systemically or by Microdialysis to Basal Forebrain
Authors: Osman Nadir I. , Baghdoyan Helen A. , Lydic Ralph
Published: September 2005

Background

Cortical acetylcholine originates in the basal forebrain and is essential for maintaining normal cognition and arousal. Morphine impairs these cholinergically mediated cortical functions. The current study tested the hypothesis that morphine decreases prefrontal cortical acetylcholine release by acting at the level of the basal forebrain.

Methods

Adult male Sprague-Dawley rats (n = 18) were anesthetized with isoflurane. One microdialysis probe was placed in the substantia innominata region of the basal forebrain and perfused with Ringer's solution (control) followed by one concentration of morphine (1, 10, 100, or 1,000 microm) or morphine (1,000 microm) plus naloxone (100 microm). A second microdialysis probe was placed in the prefrontal cortex for measuring acetylcholine. In a second series of experiments, rats (n = 6) were implanted with electrodes for recording states of arousal, a guide cannula positioned above the prefrontal cortex for inserting a microdialysis probe, and an indwelling jugular vein catheter. The effects of administering intravenous morphine (30 mg/kg) versus normal saline (0.9%) on prefrontal cortical acetylcholine release, cortical electroencephalographic power, and behavior were quantified.

Results

Dialysis delivery of morphine to the substantia innominata caused a concentration-dependent, naloxone-sensitive decrease in acetylcholine release within the prefrontal cortex. The maximal decrease in acetylcholine was 36.3 +/- 11.5%. Intravenous morphine administration significantly decreased cortical acetylcholine release, increased electroencephalographic power in the 0.5- to 5-Hz range, and eliminated normal wakefulness.

Conclusion

Morphine causes obtundation of arousal and may cause cognitive impairment by acting at the level of the substantia innominata to disrupt cortical cholinergic neurotransmission.
Inhibition of Kv4.3/KChIP2.2 Channels by Bupivacaine and Its Modulation by the Pore Mutation Kv4.3V401I
Authors: Solth Anna , Siebrands Cornelia C. , Friederich Patrick
Published: September 2005

Background

The transient outward current Ito is an important repolarizing K current in human ventricular myocardium mediated by Kv4.3 and KChIP2.2 subunits. Inhibition of Ito by amino-amide local anesthetics may be involved in severe cardiotoxic side effects. This study elucidates the molecular mechanisms of bupivacaine interaction with complexes formed by Kv4.3 and KChIP2.2 as well as the modulatory effect of KChIP2.2. For this purpose, the pharmacologic effects of bupivacaine on Kv4.3wt/KChIP2.2 channels and on the pore mutant Kv4.3V401I were investigated.

Methods

Kv4.3/KChIP2.2 cDNA was transiently expressed in Chinese hamster ovary cells. Site-directed mutagenesis and patch clamp experiments were performed to analyze the effects of bupivacaine on wild-type and mutant channels.

Results

Inhibition of Kv4.3wt/KChIP2.2 channels by bupivacaine was concentration-dependent and reversible. The IC50s for inhibition of the charge conducted by Kv4.3wt/KChIP2.2 channels by bupivacaine and levobupivacaine were 55 +/- 8 and 50 +/- 5 microm, respectively. The local anesthetic accelerated macroscopic current decline of Kv4.3wt/KChIP2.2 and slowed recovery from inactivation without altering steady state inactivation. KChIP2.2 altered the response of Kv4.3wt channels to bupivacaine and bupivacaine modulated KChIP2.2 effects on Kv4.3wt channels. The pore mutation V401I slowed macroscopic current decline of Kv4.3 channels and recovery from inactivation, and it diminished modulation of gating by KChIP2.2. Bupivacaine inhibition of Kv4.3V401I resembled Kv4.3wt and was not changed by coexpression of KChIP2.2.

Conclusions

These results indicate that bupivacaine blocks Kv4.3/KChIP2.2 channels from the open state. They furthermore give structural evidence that amino-amide local anesthetics interfere with the effects of KChIP2.2 on Kv4.3 by an indirect mechanism.
Estimation of Errors in Determining Intrathoracic Blood Volume Using the Single Transpulmonary Thermal Dilution Technique in Hypovolemic Shock
Authors: Nirmalan Mahesh , Willard Terrance M. , Edwards Dennis J. , Little Rod A. , Dark Paul M.
Published: September 2005

Background

The transpulmonary thermal dilution technique has been widely adopted for monitoring cardiac preload and extravascular lung water in critically ill patients. This method assumes intrathoracic blood volume (ITBV) to be a fixed proportion of global end-diastolic volume (GEDV). This study determines the relation between GEDV and ITBV under normovolemic and hypovolemic conditions and quantifies the errors in estimating ITBV.

Methods

Nineteen pigs allocated to control (n = 9) and shock (n = 10) groups were studied. Shock was maintained for 60 min followed by volume resuscitation. The dual dye-thermal dilution technique was used to measure GEDV and ITBV (ITBVm) at baseline (time 0), shock phase (30 and 90 min), and after resuscitation (150 min). The regression equations estimated from paired GEDV and ITBVm measurements under normovolemic and hypovolemic conditions were used to estimate ITBV from the corresponding GEDV, and the estimation errors were quantified. A more simplified equation, used in a commercially available clinical monitor (ITBV = 1.25 x GEDV), was then used to estimate ITBV.

Results

The regression equation in the control group was ITBVm = 1.21 x GEDV + 99 (r = 0.89, P < 0.0001) and in the shock group at 30 and 90 min was ITBVm = 1.45 x GEDV + 0.6 (r = 0.95, P < 0.0001). The 95% confidence interval for the y-intercept was relatively wide, ranging from 31 to 168 and -47 to 49, respectively, for the two equations. The equation estimated in the control group led to overestimation of ITBV and a significant (P < 0.05) increase in errors in the shock group at 30 and 90 min. Errors in estimating ITBV using the simplified commercial algorithm were less than 15% under normovolemic and hypovolemic conditions.

Conclusions

The linear relation between GEDV and ITBV is maintained in hypovolemic shock. Even though the relation between GEDV and ITBV is influenced by circulatory volume and cardiac output, the mean errors in predicting ITBV were small and within clinically tolerable limits.
Short Hairpin RNA–mediated Selective Knockdown of NaV1.8 Tetrodotoxin-resistant Voltage-gated Sodium Channel in Dorsal Root Ganglion Neurons
Authors: Mikami Maya , Yang Jay
Published: September 2005

Background

Voltage-gated sodium channels comprise a family of closely related proteins, each subserving different physiologic and pathologic functions. NaV1.8 is an isoform of voltage-gated sodium channel implicated in the pathogenesis of inflammatory and neuropathic pain, but currently, there is no isoform-specific inhibitor of any voltage-gated sodium channels. The authors explored the possibility of short hairpin RNA-mediated selective knockdown of NaV1.8 expression.

Methods

DNA constructs designed to transcribe short hairpin RNA targeting NaV1.8 were created and incorporated into recombinant lentiviruses. The virus-induced selective knockdown of NaV1.8 was examined at the protein, messenger RNA, and functional levels using Western blot, immunohistochemistry, reverse-transcription polymerase chain reaction, and patch clamp electrophysiology.

Results

Transduction of HEK293 cells stably expressing NaV1.8 or primary dorsal root ganglion neurons with lentivirus expressing short hairpin RNA resulted in the knockdown of NaV1.8 protein and messenger RNA concentrations. Whole cell patch clamp recordings confirmed decrease in the NaV1.8-mediated current density without changes in other biophysical properties.

Conclusions

A selective knockdown of NaV1.8 expression in dorsal root ganglion neurons can be attained by short hairpin RNA delivered with lentivirus. This method may provide a new gene therapy approach to controlling neuronal hyperexcitability and pathologic pain.
Role for Cyclooxygenase 2 in the Development and Maintenance of Neuropathic Pain and Spinal Glial Activation
Authors: Takeda Kenji , Sawamura Shigehito , Tamai Hisayoshi , Sekiyama Hiroshi , Hanaoka Kazuo
Published: September 2005

Background

Lines of evidence have indicated that cyclooxygenase 2 plays a role in the pathophysiology of neuropathic pain. However, the site and mechanism of its action are still unclear. Spinal glia has also been reported to mediate pathologic pain states. The authors evaluated the effect of continuous intrathecal or systemic cyclooxygenase-2 inhibitor on the development and maintenance of neuropathic pain and glial activation in a spinal nerve ligation model of rats.

Methods

Continuous intrathecal infusion of meloxicam (32 or 320 mug . kg . day) or saline was started immediately after L5-L6 spinal nerve ligation. Mechanical allodynia and thermal hyperalgesia were evaluated on days 4 and 7 postoperatively. Spinal astrocytic activation was evaluated with glial fibrially acidic protein immunoreactivity on day 7. In other groups of rats, continuous intrathecal meloxicam was started 7 days after spinal nerve ligation, and effects on established neuropathic pain and glial activation were evaluated. Last, effects of continuous systemic meloxicam (16 mg . kg . day) on existing neuropathic pain and glial activation were examined.

Results

Intrathecal meloxicam prevented the development of mechanical allodynia and thermal hyperalgesia induced by spinal nerve ligation. It also inhibited spinal glial activation responses. In contrast, when started 7 days after the nerve ligation, intrathecal meloxicam did not reverse established neuropathic pain and glial activation. Systemic meloxicam started 7 days after ligation partially reversed neuropathic behaviors but not glial activation.

Conclusions

Spinal cyclooxygenase 2 mediates the development but not the maintenance of neuropathic pain and glial activation in rats. Peripheral cyclooxygenase 2 plays a part in the maintenance of neuropathic pain.
Nitrous Oxide Revisited
Authors: Richebé Philippe , Rivat Cyril , Creton Cyril , Laulin Jean-Paul , Maurette Pierre , Lemaire Marc , Simonnet Guy
Published: September 2005

Background

Although opioids are unsurpassed analgesics for surgery, they also induce an N-methyl-D-aspartate-dependent enhancement of postoperative hyperalgesia. Because nitrous oxide (N2O) has anti-N-methyl-D-aspartate properties, the purpose of this study was to evaluate nitrous oxide ability to prevent such an opioid-induced hyperalgesia in rats.

Methods

First, preventive effects of 50/50% N2O-O2 on the development of delayed hyperalgesia observed after inflammatory pain (hind paw carrageenan injection on D0) were examined for several days. Second, the ability of nitrous oxide (10-40%) to limit opioid-induced hyperalgesia induced by fentanyl was evaluated in nonsuffering rats. Third, antihyperalgesic effects of various nitrous oxide concentrations (20-50%) were assessed in both inflammatory and incisional pain models in fentanyl-treated rats (4 x 100 microg/kg subcutaneously). Finally, the analgesic effect of a single dose of morphine was evaluated 24 h after fentanyl administration and nitrous oxide (D0) to assess its preventive effect on acute morphine tolerance in both nonsuffering and hind paw-incised rats.

Results

When applied on D0, nitrous oxide reduced delayed hyperalgesia induced by inflammation. Exposure to nitrous oxide on D0 also reduced opioid-induced hyperalgesia in nonsuffering rats in a dose-dependent manner. In fentanyl-treated rats with inflammatory or incisional pain, nitrous oxide strongly limited both magnitude and duration of hyperalgesia. Moreover, nitrous oxide exposure on D0 opposed development of acute tolerance to analgesic effects of morphine administered on D1 in both nonsuffering and incised fentanyl-treated rats.

Conclusions

Nitrous oxide, an N-methyl-D-aspartate receptor antagonist, prevented the enhancement of pain sensitivity induced by both nociceptive inputs and fentanyl and opposed acute morphine tolerance. Results suggest that perioperative nitrous oxide use reduces exaggerated postoperative pain and morphine consumption.
Propofol
Authors: Baker Max T. , Naguib Mohamed , Warltier David C.
Published: September 2005

Propofol is a potent lipophilic anesthetic that was initially formulated in Cremophor El for human use. Because of the occurrence of Cremophor EL anaphylaxis and improvements in the quality of lipid emulsions, it was ultimately brought to market as 1% propofol formulated in 10% soybean oil emulsion. Emulsions represent complex formulation compositions whose suitability for intravenous administration is dependent on a number of factors. Despite the success of propofol emulsions, drawbacks to such formulations include inherent emulsion instability, injection pain, a need for antimicrobial agents to prevent sepsis, and a concern of hyperlipidemia-related side effects. Efforts to overcome such drawbacks have involved the development of propofol emulsions with altered propofol and lipid contents, the addition of different excipients to emulsions for antimicrobial activity, and study of nonemulsion formulations including propofol-cyclodextrin and propofol-polymeric micelle formulations. In addition, a number of propofol prodrugs have been made and evaluated.
Prevention of Succinylcholine-induced Fasciculation and Myalgia
Authors: Schreiber Jan-Uwe , Lysakowski Christopher , Fuchs-Buder Thomas , Tramèr Martin R.
Published: September 2005

Fifty-two randomized trials (5,318 patients) were included in this meta-analysis. In controls, the incidence of fasciculation was 95%, and the incidence of myalgia at 24 h was 50%. Nondepolarizing muscle relaxants, lidocaine, or magnesium prevented fasciculation (number needed to treat, 1.2-2.5). Best prevention of myalgia was with nonsteroidal antiinflammatory drugs (number needed to treat, 2.5) and with rocuronium or lidocaine (number needed to treat, 3). There was a dose-dependent risk of blurred vision, diplopia, voice disorders, and difficulty in breathing and swallowing (number needed to harm, < 3.5) with muscle relaxants. There was evidence of less myalgia with 1.5 mg/kg succinylcholine (compared with 1 mg/kg). Opioids had no impact. Succinylcholine-induced fasciculation may best be prevented with muscle relaxants, lidocaine, or magnesium. Myalgia may best be prevented with muscle relaxants, lidocaine, or nonsteroidal antiinflammatory drugs. The risk of potentially serious adverse events with muscle relaxants is not negligible. Data that allow for a risk-benefit assessment are lacking for other drugs.
Importance of Providencia species as a major cause of travellers’ diarrhoea
Authors: Yoh Myonsun , Matsuyama Junko , Ohnishi Motoki , Takagi Kazuhiro , Miyagi Hirozane , Mori Kazuhiro , Park Kwon-Sam , Ono Takahiro , Honda Takeshi
Published: September 2005

In this study the importance of Providencia species as a cause of travellers’ diarrhoea was examined using a selective medium developed by the authors. Providencia species could easily be distinguished from other enteric pathogens by the colour of the colonies obtained. Nine strains of Providencia alcalifaciens, nine of Providencia rettgeri and five of Providencia stuartii were isolated from 130 specimens, representing a surprisingly high incidence of infection compared with other pathogens isolated on SS agar and TCBS agar. Patients infected with P. rettgeri complained of abdominal pain, as for other Providencia species, but also of vomiting, which is rather characteristic of P. rettgeri infection. To analyse the pathogenicity of these isolates, their invasiveness was examined using Caco-2 cells. Most of the P. rettgeri strains invaded Caco-2 cells. Random amplified polymorphic DNA (RAPD) fingerprinting showed the same profile for two P. rettgeri isolates from individuals travelling in the same tour group. The results show that Providencia species, especially P. rettgeri, might cause diarrhoea, and that these species are important pathogens.
Penicillin-binding proteins of Bacteroides fragilis and their role in the resistance to imipenem of clinical isolates
Authors: Ayala Juan , Quesada Alberto , Vadillo Santiago , Criado Jerónimo , Píriz Segundo
Published: September 2005

In this study penicillin-binding proteins (PBPs) of Bacteroides fragilis and the resistance mechanisms of this micro-organism to 11 β-lactam antibiotics were analysed. The study focused on the role of PBP2Bfr and metallo-β-lactamase in the mechanism of resistance to imipenem. The mechanism of β-lactam resistance in B. fragilis was strain dependent. The gene encoding the orthologue of Escherichia coli PBP3 gene (pbpBBfr, which encodes the protein PBP2Bfr) was sequenced in five of the eight strains studied, along with the ccrA (cfiA) gene in strain 119, and their implications for resistance were examined. Differences were found in the amino-acid sequence of PBP2Bfr in strains AK-2 and 119, and the production of β-lactamases indicated that these differences may be involved in the mechanism of resistance to imipenem. In vitro binding competition assays with membrane extracts using imipenem indicated that the PBP that bound imipenem with the highest affinity was PBP2Bfr, and that increased affinity in strain 7160 may be responsible for the moderate susceptibility of this strain to imipenem. In the same way, the importance of the chromosomal class A β-lactamase CepA in the resistance mechanism of the B. fragilis strains NCTC 9344, 7160, 2013E, AK-4, 0423 and R-212 was studied. In these strains this is the principal resistance mechanism to antimicrobial agents studied other than imipenem.
Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism
Authors: Hayashi Hidenori , Takahashi Rei , Nishi Takahiro , Sakamoto Mitsuo , Benno Yoshimi
Published: September 2005

Microbiota in gut contents of jejunum, ileum, caecum and recto-sigmoid colon obtained from three elderly individuals at autopsy were compared using 16S rRNA gene libraries and terminal restriction fragment length polymorphism (T-RFLP). Random clones of 16S rRNA gene sequences were isolated after PCR amplification with universal primer sets of total genomic DNA extracted from each sample of gut contents. An average of 90 randomly selected clones were partially sequenced (about 500 bp). T-RFLP analysis was performed using the 16S rRNA gene amplified from each sample. The lengths of the terminal restriction fragments were analysed after digestion with HhaI and MspI. The jejunal and ileal microbiota consisted of simple microbial communities of streptococci, lactobacilli, ‘Gammaproteobacteria', the Enterococcus group and the Bacteroides group. Most of the species were facultative anaerobes or aerobes. The Clostridium coccoides group and the Clostridium leptum subgroup, which are the most predominant groups in human faeces, were not detected in samples from the upper gastrointestinal tract. The caecal microbiota was more complex than the jejunal and ileal microbiota. The C. coccoides group, the C. leptum subgroup and the Bacteroides group were detected in the caecum. The recto-sigmoidal colonic microbiota consisted of complex microbial communities, with numerous species that belonged to the C. coccoides group, the C. leptum subgroup, the Bacteroides group, ‘Gammaproteobacteria', the Bifidobacterium group, streptococci and lactobacilli, and included more than 26 operational taxonomic units. The results showed marked individual differences in the composition of microbiota in each region.
Three cases of vertebral osteomyelitis caused by Streptococcus dysgalactiae subsp. equisimilis
Authors: Kumar Aravind , Sandoe Jonathan , Kumar Naresh
Published: September 2005

Three cases of vertebral osteomyelitis caused byStreptococcus dysgalactiaesubsp.equisimilis(Strep. equisimilis) are presented here. All three cases presented with fever, back pain, general malaise and weight loss for at least 4 weeks. Diagnosis was established by culture of a spinal biopsy and/or positive blood cultures together with radiological findings. In all three cases, 6–12 weeks of antibiotics were curative without recourse to surgery. The ability ofStrep. equisimilisto cause vertebral osteomyelitis is highlighted. The need is emphasized for biopsy and microbiological investigation in patients presenting with back pain, fever, weight loss and evidence of a spinal lesion on imaging, even if neoplastic disease is suspected. Prolonged antibiotic therapy (at least 6 weeks) seems to be indicated.
Identification and antimicrobial susceptibility of micro-organisms recovered from cutaneous lesions of human American tegumentary leishmaniasis in Minas Gerais, Brazil
Authors: Fontes Claúdia O , Carvalho Maria Auxiliadora R , Nicoli Jacques R , Hamdan Junia S , Mayrink Wilson , Genaro Odair , Carmo Luiz S , Farias Luiz M
Published: September 2005

An evaluation of the microbiota present in cutaneous ulcers from 31 patients with a clinical and parasitological diagnosis of American tegumentary leishmaniasis (ATL) was carried out by the standard filter paper disc technique, including antimicrobial susceptibility of the bacterial isolates. Microbial examination indicated that 21 patients (67.7 %) were contaminated with one to four bacteria and some of them also with yeast. A total of 142 micro-organisms were isolated.Staphylococcus aureuswas the most frequently recovered bacterium (95.2 % of positive patients) and was found to produce type B (70 % of the staphylococcal isolates) and type C (50 %) enterotoxins as well as toxic shock syndrome toxin (60 %).Proteus mirabilis(33.3 % of the positive patients),Streptococcus pyogenes(19.0 %), H2S-negativeProteusspecies (19.0 %),Klebsiella oxytoca(14.3 %),Enterobacterspecies (9.5 %),Peptostreptococcusspecies (9.5 %),Pseudomonasspecies (4.8 %),Prevotella bivia(4.8 %),Escherichia coli(4.8 %),Streptococcus agalactiae(4.8 %),Bacteroides fragilis(4.8 %),Candida albicans(9.5 %) andCandida tropicalis(4.8 %) were also isolated. Surprisingly,Staph. aureusisolates were susceptible to almost all tested drugs, although some of them were resistant to penicillin (69 %) and ampicillin + sulbactam (68 %). Concerning obligate anaerobes, all the Gram-negative isolates (25 % of the total) were resistant to metronidazole. The results of the present study show that microbial secondary contaminants, particularlyStaph. aureus, should be considered in the diagnosis and treatment of ATL lesions.
Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection of Mycoplasma pneumoniae
Authors: Saito Ryoichi , Misawa Yoshiki , Moriya Kyoji , Koike Kazuhiko , Ubukata Kimiko , Okamura Noboru
Published: September 2005

A loop-mediated isothermal amplification (LAMP) assay for the rapid detection ofMycoplasma pneumoniaewas developed and evaluated. The assay specifically amplified onlyM. pneumoniaesequences, and no cross-reactivity was observed for otherMycoplasmaspecies or respiratory bacterial species. The detection limit for this assay was found to be 2 × 102copies, corresponding to 2–20 colour changing units ofM. pneumoniaein 1 h, as observed in a real-time turbidimeter and electrophoretic analysis. The accuracy of the LAMP reaction was confirmed by restriction endonuclease analysis as well as direct sequencing of the amplified product. The assay was applied to 95 nasopharyngeal swab samples collected from patients or from healthy individuals, and compared to a real-time PCR assay in-house. A concordance of 100 % was observed between the two assays. The LAMP assay is easy to perform, shows a rapid reaction and is inexpensive. It may therefore be applied in the routine diagnosis ofM. pneumoniaeinfection in the clinical laboratory.
Disseminated Nocardia farcinica infection in a uraemia patient with idiopathic thrombocytopenia purpura receiving steroid therapy
Authors: Lai Chih-Cheng , Lee Li-Na , Teng Lee-Jene , Wu Ming Shiou , Tsai Jui-Chang , Hsueh Po-Ren
Published: September 2005

Nocardia farcinica has been reported as an increasingly frequent cause of localized and disseminated infections in immunocompromised patients in recent years, but N. farcinica bacteraemia remains a rare finding. Here, the case is described of a 68-year-old man with end-stage renal disease and idiopathic thrombocytopenia purpura treated with steroid therapy who developed disseminated infection (bacteraemia, multilobar pneumonia and brain abscesses) due to N. farcinica. The isolate was confirmed by partial sequencing analysis of the 16S rRNA gene. The patient recovered after prolonged trimethoprim-sulfamethoxazole therapy with no recurrence in over 1 year.
Rhodococcus equi can survive a phagolysosomal environment in macrophages by suppressing acidification of the phagolysosome
Authors: Toyooka Kiminori , Takai Shinji , Kirikae Teruo
Published: September 2005

Rhodococcus equiis one of the most important causes of pneumonia in foals and has emerged as a significant opportunistic pathogen of immunosuppressed hosts such as human immunodeficiency virus-infected patients. VirulentR. equiharbouring an 85 kb plasmid, but not the avirulent form lacking the plasmid, has the ability to survive in macrophages. However, the survival mechanism is not known. In the present study, morphological interactions were observed between virulent or plasmid-cured avirulentR. equiand phagolysosomes in murine macrophage-like J774.1 cells by immunocytological methods. The J774.1 cells phagocytosed virulent and avirulent bacteria to a similar extent, and both bacteria replicated in single membrane vacuoles at similar rates up to 6 h after infection. Thereafter, the virulent bacteria continued to grow, whereas the avirulent bacteria stopped growing. When the infected cells were stained with phagosomal and lysosomal markers and observed with a confocal fluorescence microscope, the majority of phagosomes containing these bacteria were fused with lysosomes. NeitherR. equiorganism has the ability to hinder phagosome-lysosome fusion. The acidity in phagolysosomes containingR. equiwas examined by staining with LysoTracker Red DND-99, an acidotropic probe. The phagolysosomes containing virulent organisms were not acidic as compared with avirulent organisms. Over 90 % of the phagolysosomes containing avirulentR. equiwere stained with LysoTracker 6 h after infection, whereas less than 50 % of those containing virulentR. equiwere stained. Furthermore, when the supernatant obtained from a virulentR. equiculture was added to the cell cultures, the acidity of acidic compartments in macrophages was reduced. The authors conclude that some substance(s) produced by virulentR. equisuppress acidification in phagolysosomes, and helpR. equisurvival and replication in the bactericidal environment.
Molecular identification of Helicobacter DNA present in human colorectal adenocarcinomas by 16S rDNA PCR amplification and pyrosequencing analysis
Authors: Grahn Niclas , Hmani-Aifa Mounira , Fransén Karin , Söderkvist Peter , Monstein Hans-Jürg
Published: September 2005

Seroepidemiological studies have indicated thatHelicobacter pyloriinfection might be a possible risk factor for colorectal adenocarcinoma (CRC) development. However, limited information is available as to whether or notHelicobacterspecies are present in CRC tissues. In this study the presence ofHelicobacterDNA in 77 CRC biopsies was investigated by means of aHelicobacterspecies-specific 16S rDNA PCR assay and real-time DNA pyrosequencing of the 16S rDNA variable V3 region. Pyrosequencing revealed the presence ofHelicobacterDNA sequences in 21 of 77 biopsy specimens (27 %). 16S rDNA sequences corresponding toH. pylori26695 andH. pyloriJ99 were most commonly found. Intriguingly, one sequence belonged toHelicobacter mustelae, previously identified in ferrets. No significant correlations were found in the prevalence ofHelicobacterDNA between colon and rectum tumour biopsies (P= 0.815), nor between Dukes’ classes A/B and C/D (P= 0.262). 16S rDNA PCR amplification combined with pyrosequencing analysis of 16S rDNA variable V3 regions provides a powerful molecular tool to identifyHelicobacterspecies in human biopsy specimens.