Influenza C virus and bovine coronavirus esterase reveal a similar catalytic mechanism: new insights for drug discovery

Both, the influenza C (INF-C) virus haemagglutinin esterase fusion and bovine coronavirus (BCoV) haemagglutinin esterase surface glycoproteins exhibit a lectin binding capability and a receptor-destroying 9-O-acetyl esterase activity that recognise 9-O-acetyl-N-acetylneuraminic acid (Neu5,9Ac(2))-containing glycans. Here we report nuclear magnetic resonance and molecular modelling studies on the 9-O-acetyl esterase showing that the alpha-configured Neu5,9Ac(2) is strictly preferred by the INF-C and BCoV esterases. Interestingly, we have discovered that the INF-C esterase function releases acetate independently of the chemical nature of the aglycon moiety, whereas subtle differences in substrate recognition were found for BCoV esterase. Analysis of the apo and complexed X-ray crystal structure of INF-C esterase revealed that binding of 9-O-acetylated N-acetylneuraminic acids is a dynamic process that involves conformational rearrangement of serine-57 in the esterase active site. This study provides valuable insights towards the design of drugs to combat INF-C virus and coronavirus infections causing outbreaks of upper respiratory infections and severe diarrhea in calves, respectively.

In vitro activity of moxifloxacin and piperacillin/sulbactam against pathogens of acute cholangitis

AIM: To analyze the in vitro activity of moxifloxacin and piperacillin/sulbactam against pathogens isolated from patients with acute cholangitis.

METHODS: In this prospective study a total of 65 patients with acute cholangitis due to biliary stone obstruction (n = 7), benign biliary stricture (n = 16), and malignant biliary stricture (n = 42) were investigated with regard to spectrum of bacterial infection and antibiotic resistance. Pathogens were isolated from bile cultures in all study patients. In 22 febrile patients, blood cultures were also obtained. In vitro activity of moxifloxacin and piperacillin/sulbactam was determined by agar diffusion.

RESULTS: Thirty-one out of 65 patients had positive bile and/or blood cultures. In 31 patients, 63 isolates with 17 different species were identified. The predominant strains were Enterococcus species (26/63), E.coli (13/63) and Klebsiella species (8/63). A comparable in vitro activity of moxifloxacin and piperacillin/sulbactam was observed for E.coli and Klebsiella species. In contrast, Enterococcus species had higher resistances towards moxifloxacin. Overall bacteria showed antibiotic resistances in vitro of 34.9% for piperacillin/sulbactam and 36.5% for moxifloxacin.

CONCLUSION: Enterococcus species, E.coli and Klebsiella species were the most common bacteria isolated from bile and/or blood from patients with acute cholangitis. Overall, a mixed infection with several species was observed, and bacteria showed a comparable in vitro activity for piperacillin/sulbactam and moxifloxacin.

Coverage and error models of protein-protein interaction data by directed graph analysis

Using a directed graph model for bait to prey systems and a multinomial error model, we assessed the error statistics in all published large-scale datasets for Saccharomyces cerevisiae and characterized them by three traits: the set of tested interactions, artifacts that lead to false-positive or false-negative observations, and estimates of the stochastic error rates that affect the data. These traits provide a prerequisite for the estimation of the protein interactome and its modules.

Making the most of high-throughput protein-interaction data

We review the estimation of coverage and error rate in high-throughput protein-protein interaction datasets and argue that reports of the low quality of such data are to a substantial extent based on misinterpretations. Probabilistic statistical models and methods can be used to estimate properties of interest and to make the best use of the available data.

A rare reason for the end of a career in competitive tennis

Stress fractures are reported in adolescents taking part in high standard sports and they are associated with specific sites for stress fractures. The first rib is also affected in rowers and ball throwing sports. This report describes the complications of such a case in a competitive tennis player at international level practicing 5 times a week with far-reaching consequences. Due to constant load dependent pain in the region of the right shoulder, standard diagnosis, X-ray, magnetic resonance imaging (MRI) and a computed tomography (CT) scan with 3-D reconstruction were done, showing a pseudoarthrosis of the first rib. Therefore, further treatment was conservative without pain relieve. At follow-up 5 years after onset of symptoms the patient did not play tennis, he did not complain pain, but control imaging still showed a pseudoarthrosis of the first rib. Our case shows that it is important, when treating shoulder pain in the overhead athlete, to think of the possibility of a stress fracture.

Effects of plasma expansion with albumin and paracentesis on haemodynamics and kidney function in critically ill cirrhotic patients with tense ascites and hepatorenal syndrome: a prospective uncontrolled trial

Introduction

Circulatory dysfunction in cirrhotic patients may cause a specific kind of functional renal failure termed hepato-renal syndrome (HRS). It contributes to the high incidence of renal failure in cirrhotic intensive care unit (ICU) patients. Fluid therapy may aggravate renal failure by increasing ascites and intra-abdominal pressure (IAP). This study investigates the short-term effects of paracentesis on haemodynamics and kidney function in volume resuscitated patients with HRS.

Methods

Nineteen consecutive cirrhotic patients with HRS were studied. Circulatory parameters and renal function were analysed before and after plasma expansion and paracentesis. Haemodynamic monitoring was performed by transpulmonary thermodilution.

Results

After infusion of 200 ml of 20% human albumin solution, mean arterial pressure (MAP) and central venous pressure remained unchanged. Global end-diastolic volume index (GEDVI) increased from 791 ml m^-2 (693 to 862) (median and 25th to 75th percentile) to 844 ml m^-2 (751 to 933). Cardiac index (CI) increased from 4.1 l min^-1 m^-2 (3.6 to 5.0) to 4.7 l min^-1 m^-2 (4.0 to 5.8), whereas systemic vascular resistance index (SVRI) decreased from 1,422 dyn s cm^-5 m^-2 (1,081 to 1,772) to 1,171 dyn s cm^-5 m^-2 (893 to 1,705). Creatinine clearance (CC) and fractional excretion of sodium (FeNa) were not affected. During paracentesis, IAP decreased from 22 mmHg (18 to 24) to 9 mmHg (8 to 12). MAP decreased from 81 mmHg (74 to 100) to 80 mmHg (71 to 89), and CI increased from 4.1 l min^-1 m^-2 (3.2 to 4.3) to 4.2 l min^-1 m^-2 (3.6 to 4.7), whereas SVRI decreased from 1,639 dyn s cm^-5 m^-2 (1,168 to 2,037) to 1,301 dyn s cm^-5 m^-2 (1,124 to 1,751). CC during the 12-hour interval after paracentesis was significantly higher than during the 12 hours before (33 ml min^-1 (16 to 50) compared with 23 ml min^-1 (12 to 49)). CC remained elevated for the rest of the observation period. FeNa increased after paracentesis but returned to baseline levels after 24 hours.

Conclusion

Paracentesis with parameter-guided fluid substitution and maintenance of central blood volume may improve renal function and is safe in the treatment of ICU patients with hepato-renal failure.

Model-based variance-stabilizing transformation for Illumina microarray data

Variance stabilization is a step in the preprocessing of microarray data that can greatly benefit the performance of subsequent statistical modeling and inference. Due to the often limited number of technical replicates for Affymetrix and cDNA arrays, achieving variance stabilization can be difficult. Although the Illumina microarray platform provides a larger number of technical replicates on each array (usually over 30 randomly distributed beads per probe), these replicates have not been leveraged in the current log2 data transformation process. We devised a variance-stabilizing transformation (VST) method that takes advantage of the technical replicates available on an Illumina microarray. We have compared VST with log2 and Variance-stabilizing normalization (VSN) by using the Kruglyak bead-level data (2006) and Barnes titration data (2005). The results of the Kruglyak data suggest that VST stabilizes variances of bead-replicates within an array. The results of the Barnes data show that VST can improve the detection of differentially expressed genes and reduce false-positive identifications. We conclude that although both VST and VSN are built upon the same model of measurement noise, VST stabilizes the variance better and more efficiently for the Illumina platform by leveraging the availability of a larger number of within-array replicates. The algorithms and Supplementary Data are included in the lumi package of Bioconductor, available at: www.bioconductor.org.

Delayed recovery and late development of complex regional pain syndrome in patients with an isolated fracture of the distal radius: prediction of a regional inflammatory response by early signs

We studied prospectively the regional inflammatory response to a unilateral distal radial fracture in 114 patients at eight to nine weeks after injury and again at one year. Our aim was to identify patients at risk for a delayed recovery and particularly those likely to develop complex regional pain syndrome. In order to quantify clinically the inflammatory response, a regional inflammatory score was developed. In addition, blood samples were collected from the antecubital veins of both arms for comparative biochemical and blood-gas analysis. The severity of the inflammatory response was related to the type of treatment (Kruskal-Wallis test, p = 0.002). A highly significantly-positive correlation was found between the regional inflammatory score and the length of time to full recovery (r(2) = 0.92, p = 0.01, linear regession). A regional inflammatory score of 5 points with a sensitivity of 100% but a specificity of only 16% also identified patients at risk of complex regional pain syndrome. None of the biochemical parameters studied correlated with regional inflammatory score or predicted the development of complex regional pain syndrome. Our study suggests that patients with a distal radial fracture and a regional inflammatory score of 5 points or more at eight to nine weeks after injury should be considered for specific anti-inflammatory treatment.

In situ analysis of cross-hybridisation on microarrays and the inference of expression correlation

BACKGROUND

Microarray co-expression signatures are an important tool for studying gene function and relations between genes. In addition to genuine biological co-expression, correlated signals can result from technical deficiencies like hybridization of reporters with off-target transcripts. An approach that is able to distinguish these factors permits the detection of more biologically relevant co-expression signatures.

RESULTS

We demonstrate a positive relation between off-target reporter alignment strength and expression correlation in data from oligonucleotide genechips. Furthermore, we describe a method that allows the identification, from their expression data, of individual probe sets affected by off-target hybridization.

CONCLUSION

The effects of off-target hybridization on expression correlation coefficients can be substantial, and can be alleviated by more accurate mapping between microarray reporters and the target transcriptome. We recommend attention to the mapping for any microarray analysis of gene expression patterns.

Estimating node degree in bait-prey graphs

MOTIVATION

Proteins work together to drive biological processes in cellular machines. Summarizing global and local properties of the set of protein interactions, the interactome, is necessary for describing cellular systems. We consider a relatively simple per-protein feature of the interactome: the number of interaction partners for a protein, which in graph terminology is the degree of the protein.

RESULTS

Using data subject to both stochastic and systematic sources of false positive and false negative observations, we develop an explicit probability model and resultant likelihood method to estimate node degree on portions of the interactome assayed by bait-prey technologies. This approach yields substantial improvement in degree estimation over the current practice that naively sums observed edges. Accurate modeling of observed data in relation to true but unknown parameters of interest gives a formal point of reference from which to draw conclusions about the system under study.

AVAILABILITY

All analyses discussed in this text can be performed using the ppiStats and ppiData packages available through the Bioconductor project (http://www.bioconductor.org).

Combinatorial effects of four histone modifications in transcription and differentiation

Nucleosomes are involved in DNA compaction and transcriptional regulation. Yet it is unclear whether histone modification marks are primary or secondary to transcription and whether they interact to form a histone code. We investigated the relationship between transcription and four histone modifications (H4ac, H3ac, H3K4me2/3) using ChIP-chip and expression microarray readouts from two murine cell lines, one in two differentiation stages. We found that their association with transcript levels strongly depends on the combination of histone modifications. H3K4me2 coincides with elevated expression levels only in combination with acetylation, while H3ac positive association is diminished by co-occurring modifications. During differentiation, upregulated transcripts frequently gain H4ac, while most modification conversions are uncorrelated with expression changes. Our results suggest histone modifications form a code, as their combinatorial composition is associated with distinct readouts. Histones may primarily function as signaling marks for specific effectors rather than being a sufficient driving force for or a consequence of transcription.

Rintact: enabling computational analysis of molecular interaction data from the IntAct repository

MOTIVATION

The IntAct repository is one of the largest and most widely used databases for the curation and storage of molecular interaction data. These datasets need to be analyzed by computational methods. Software packages in the statistical environment R provide powerful tools for conducting such analyses.

RESULTS

We introduce Rintact, a Bioconductor package that allows users to transform PSI-MI XML2.5 interaction data files from IntAct into R graph objects. On these, they can use methods from R and Bioconductor for a variety of tasks: determining cohesive subgraphs, computing summary statistics, fitting mathematical models to the data or rendering graphical layouts. Rintact provides a programmatic interface to the IntAct repository and allows the use of the analytic methods provided by R and Bioconductor.

AVAILABILITY

Rintact is freely available at http://bioconductor.org

Changes in intra-abdominal pressure, hemodynamics, and peak inspiratory pressure during gastroscopy in a porcine model

BACKGROUND AND STUDY AIMS

The aim of this experimental study was to assess the effect of gastric insufflation on intra-abdominal pressure (IAP) and associated hemodynamic and respiratory changes during upper gastrointestinal endoscopy.

METHODS

Measurements were taken from pigs under general anesthesia with controlled ventilation. Gastroscopy was carried out with continuous insufflation of air by a standard endoscopic light source/insufflator. The cardiac index and global end-diastolic volume index (GEDVI; reflecting preload) were measured by transpulmonary thermodilution. IAP, heart rate, mean arterial pressure (MAP), central venous pressure, systemic vascular resistance index (SVRI; reflecting afterload), peak inspiratory pressure (PIP), and oxygenation (SaO (2)) were also recorded.

RESULTS

A total of 266 paired measurements (at the time of transpulmonary thermodilution) were taken from 14 animals. During air insufflation, we observed a significant rise in IAP in all animals up to intermittent values of 22 mm Hg. IAP and PIP correlated well (r = 0.666, P < 0.001), with the latter reaching values as high as 45 mbar in one pig, leading to respiratory compromise. Only marginal changes in heart rate, and a continuous, almost significant rise in MAP (due to a significant increase in SVRI) were recorded. We observed a slight increase in GEDVI, predominantly during the initial phase of air insufflation. The cardiac index showed no substantial changes. There were no episodes of hemodynamic instability, nor a decline in SaO (2).

CONCLUSIONS

Air insufflation during gastroscopy resulted in a significant increase in IAP. The main clinically relevant finding was a steady increase in SVRI. Major increments in PIP suggest a role of intra-abdominal hypertension in otherwise unexplained respiratory compromise during upper gastrointestinal endoscopy.

Effect of pneumoperitoneum on hemodynamics and inspiratory pressures during natural orifice transluminal endoscopic surgery (NOTES): an experimental, controlled study in an acute porcine model

BACKGROUND AND STUDY AIM

Physiologic reactions during natural orifice transluminal endoscopic surgery (NOTES) may differ from those at laparoscopy. This experimental study assessed the effect of pneumoperitoneum induced by endoscope air pump on hemodynamics and inspiratory pressures during transgastric peritoneoscopy.

METHODS

Transgastric peritoneoscopy was performed in 11 female pigs (35 - 50 kg) under general anesthesia. Five pigs with controlled insufflation and no endoscopic intervention served as controls. Cardiac index and global end-diastolic volume index (GEDVI; reflecting preload) were measured every 3 minutes by transpulmonary thermodilution. We also recorded: intra-abdominal pressure (IAP), heart rate, mean arterial pressure (MAP), systemic vascular resistance index (SVRI; reflecting afterload), peak inspiratory pressure (PIP), and oxygenation.

RESULTS

One study group pig was excluded from analysis because of a major complication related to the gastric incision. In the remaining 15 animals we performed 264 paired measurements. On-demand insufflation in the study group produced wide variation in intra-abdominal pressures; the control group demonstrated minimal fluctuation around a predetermined value. In the study group, IAP and PIP correlated well ( R = 0.667, P = 0.000), with maximum PIP values of 40 mbar contrasting with the control group maximum of 26.5 mbar. Hemodynamically, there was a minor decrease of cardiac index in the study group (in contrast to the control group). Relative changes in cardiac index and IAP during transgastric peritoneoscopy correlated highly significantly ( R = - 0.416, P = 0.000). Neither group showed hemodynamic instability or decline in oxygen saturation.

CONCLUSIONS

On-demand insufflation with a standard endoscopic light source/insufflator resulted in a marked median increase and wide variation in IAP throughout transgastric peritoneoscopy. Hemodynamic changes were moderate. However, major increases in PIP suggest a need for stricter control of intra-abdominal hypertension during NOTES.

Graphs in molecular biology

Graph theoretical concepts are useful for the description and analysis of interactions and relationships in biological systems. We give a brief introduction into some of the concepts and their areas of application in molecular biology. We discuss software that is available through the Bioconductor project and present a simple example application to the integration of a protein-protein interaction and a co-expression network.