PDB file parser and structure class implemented in Python

The biopython project provides a set of bioinformatics tools implemented in Python. Recently, biopython was extended with a set of modules that deal with macromolecular structure. Biopython now contains a parser for PDB files that makes the atomic information available in an easy-to-use but powerful data structure. The parser and data structure deal with features that are often left out or handled inadequately by other packages, e.g. atom and residue disorder (if point mutants are present in the crystal), anisotropic B factors, multiple models and insertion codes. In addition, the parser performs some sanity checking to detect obvious errors. AVAILABILITY: The Biopython distribution (including source code and documentation) is freely available (under the Biopython license) from http://www.biopython.org     

A comparison of SCOP and CATH with respect to domain-domain interactions

The analysis and prediction of protein-protein interaction sites from structural data are restricted by the limited availability of structural complexes that represent the complete protein-protein interaction space. The domain classification schemes CATH and SCOP are normally used independently in the analysis and prediction of protein domain-domain interactions. In this article, the effect of different domain classification schemes on the number and type of domain-domain interactions observed in structural data is systematically evaluated for the SCOP and CATH hierarchies. Although there is a large overlap in domain assignments between SCOP and CATH, 23.6% of CATH interfaces had no SCOP equivalent and 37.3% of SCOP interfaces had no CATH equivalent in a nonredundant set. Therefore, combining both classifications gives an increase of between 23.6 and 37.3% in domain-domain interfaces. It is suggested that if possible, both domain classification schemes should be used together, but if only one is selected, SCOP provides better coverage than CATH. Employing both SCOP and CATH reduces the false negative rate of predictive methods, which employ homology matching to structural data to predict protein-protein interaction by an estimated 6.5%.     

Virtual microscope interface to high resolution histological images

The Hypertext Atlas of Dermatopathology, the Atlas of Fetal and Neonatal Pathology and Hypertext Atlas of Pathology (this one in Czech only) are available at http://www.muni.cz/atlases. These atlases offer many clinical, macroscopic and microscopic images, together with short introductory texts. Most of the images are annotated and arrows pointing to the important parts of the image can be activated.The Virtual Microscope interface is used for the access to the histological images obtained in high resolution using automated microscope and image stitching, possibly in more focusing planes. Parts of the image prepared in advance are downloaded on demand to save the memory of the user's computer. The virtual microscope is programmed in JavaScript only, works in Firefox/Mozilla and MSIE browsers without need to install any additional software.     

F2CS: FSSP to CATH and SCOP prediction server

The F2CS server provides access to the software, F2CS2.00, which implements an automated prediction method of SCOP and CATH classifications of proteins, based on their FSSP Z-scores. AVAILABILITY: Free at http://www.weizmann.ac.il/physics/complex/compphys/f2cs/ SUPPLEMENTARY INFORMATION: The site contains links to additional figures and tables.     

A Python library for FAIRer access and deposition to the Metabolomics Workbench Data Repository

Introduction

The Metabolomics Workbench Data Repository is a public repository of mass spectrometry and nuclear magnetic resonance data and metadata derived from a wide variety of metabolomics studies. The data and metadata for each study is deposited, stored, and accessed via files in the domain-specific ‘mwTab’ flat file format.

Objectives

In order to improve the accessibility, reusability, and interoperability of the data and metadata stored in ‘mwTab’ formatted files, we implemented a Python library and package. This Python package, named ‘mwtab’, is a parser for the domain-specific ‘mwTab’ flat file format, which provides facilities for reading, accessing, and writing ‘mwTab’ formatted files. Furthermore, the package provides facilities to validate both the format and required metadata elements of a given ‘mwTab’ formatted file.

Methods

In order to develop the ‘mwtab’ package we used the official ‘mwTab’ format specification. We used Git version control along with Python unit-testing framework as well as continuous integration service to run those tests on multiple versions of Python. Package documentation was developed using sphinx documentation generator.

Results

The ‘mwtab’ package provides both Python programmatic library interfaces and command-line interfaces for reading, writing, and validating ‘mwTab’ formatted files. Data and associated metadata are stored within Python dictionary- and list-based data structures, enabling straightforward, ‘pythonic’ access and manipulation of data and metadata. Also, the package provides facilities to convert ‘mwTab’ files into a JSON formatted equivalent, enabling easy reusability of the data by all modern programming languages that implement JSON parsers. The ‘mwtab’ package implements its metadata validation functionality based on a pre-defined JSON schema that can be easily specialized for specific types of metabolomics studies. The library also provides a command-line interface for interconversion between ‘mwTab’ and JSONized formats in raw text and a variety of compressed binary file formats.

Conclusions

The ‘mwtab’ package is an easy-to-use Python package that provides FAIRer utilization of the Metabolomics Workbench Data Repository. The source code is freely available on GitHub and via the Python Package Index. Documentation includes a ‘User Guide’, ‘Tutorial’, and ‘API Reference’. The GitHub repository also provides ‘mwtab’ package unit-tests via a continuous integration service.

     

A systematic comparison of protein structure classifications: SCOP, CATH and FSSP.

BACKGROUND: Several methods of structural classification have been developed to introduce some order to the large amount of data present in the Protein Data Bank. Such methods facilitate structural comparisons and provide a greater understanding of structure and function. The most widely used and comprehensive databases are SCOP, CATH and FSSP, which represent three unique methods of classifying protein structures: purely manual, a combination of manual and automated, and purely automated, respectively. In order to develop reliable template libraries and benchmarks for protein-fold recognition, a systematic comparison of these databases has been carried out to determine their overall agreement in classifying protein structures. RESULTS: Approximately two-thirds of the protein chains in each database are common to all three databases. Despite employing different methods, and basing their systems on different rules of protein structure and taxonomy, SCOP, CATH and FSSP agree on the majority of their classifications. Discrepancies and inconsistencies are accounted for by a small number of explanations. Other interesting features have been identified, and various differences between manual and automatic classification methods are presented. CONCLUSIONS: Using these databases requires an understanding of the rules upon which they are based; each method offers certain advantages depending on the biological requirements and knowledge of the user. The degree of discrepancy between the systems also has an impact on reliability of prediction methods that employ these schemes as benchmarks. To generate accurate fold templates for threading, we extract information from a consensus database, encompassing agreements between SCOP, CATH and FSSP.     

Evolutionarily consistent families in SCOP: sequence, structure and function

Background

HutZ is the sole heme storage protein identified in the pathogenic bacterium Vibrio cholerae and is required for optimal heme utilization. However, no heme oxygenase activity has been observed with this protein. Thus far, HutZ??s structure and heme-binding mechanism are unknown.

Results

We report the first crystal structure of HutZ in a homodimer determined at 2.0 ? resolution. The HutZ structure adopted a typical split-barrel fold. Through a docking study and site-directed mutagenesis, a heme-binding model for the HutZ dimer is proposed. Very interestingly, structural superimposition of HutZ and its homologous protein HugZ, a heme oxygenase from Helicobacter pylori, exhibited a structural mismatch of one amino acid residue in ??6 of HutZ, although residues involved in this region are highly conserved in both proteins. Derived homologous models of different single point variants with model evaluations suggested that Pro¹⁴⁰ of HutZ, corresponding to Phe²¹⁵ of HugZ, might have been the main contributor to the structural mismatch. This mismatch initiates more divergent structural characteristics towards their C-terminal regions, which are essential features for the heme-binding of HugZ as a heme oxygenase.

Conclusions

HutZ??s deficiency in heme oxygenase activity might derive from its residue shift relative to the heme oxygenase HugZ. This residue shift also emphasized a limitation of the traditional template selection criterion for homology modeling.     

A promoter directing high level expression in pistils of transgenic plants

The promoter of the potato (Solanum tuberosum L.) SK2 gene, encoding a pistil-specific basic endochitinase, was cloned. Various fragments of the SK2-promoter, from 1 kb down to 0.23 kb in length, were fused to the GUS reporter gene. Chimaeric SK2 promoter-GUS fusion constructs were transformed into potato by Agrobacterium tumefaciens-mediated transformation. The SK2-GUS transgenic potato plants exhibited a highly specific GUS activity in the pistil. Expression in the pistil was shown to be developmentally regulated. In addition to the GUS activity in pistils, transgenic plants also showed a much weaker ectopic expression in anthers. In other tissues no systematic expression was detectable. All SK2 promoter fragments analysed conferred pistil-specific expression without significant qualitative or quantitative differences, demonstrating that the regulatory elements mediating this expression pattern are located within a 230 bp SK2 promoter fragment. The SK2 promoter may be used to engineer high levels of expression in pistils of transgenic plants.     

A high molecular mass cranberry constituent reduces mutans streptococci level in saliva and inhibits in vitro adhesion to hydroxyapatite

Previous investigations showed that a high molecular mass, non-dialyzable material (NDM) from cranberries inhibits the adhesion of a number of bacterial species and prevents the co-aggregation of many oral bacterial pairs. In the present study we determined the effect of mouthwash supplemented with NDM on oral hygiene. Following 6 weeks of daily usage of cranberry-containing mouthwash by an experimental group (n = 29), we found that salivary mutans streptococci count as well as the total bacterial count were reduced significantly (ANOVA, P < 0.01) compared with those of the control (n = 30) using placebo mouthwash. No change in the plaque and gingival indices was observed. In vitro, the cranberry constituent inhibited the adhesion of Streptococcus sobrinus to saliva-coated hydroxyapatite. The data suggest that the ability to reduce mutans streptococci counts in vivo is due to the anti-adhesion activity of the cranberry constituent.     

A transgenic locus in soybean exhibits a high level of recombination

Summary We have examined transgene inheritance in over 300 progeny of a line of soybean (Glycine max) transformed by particle bombardment with a construct containing bovine β-casein under the control of the soybean lectin 5′ and 3′ regulatory elements. Four copies of the casein transgene, located at a single locus, exhibit a high frequency of recombination that resulted in novel patterns in approximately 16% of the progeny in both the T₁ and T₂ generations. Characterization of the transgene locus using restriction enzymes that do not cut the transformation plasmid showed that all four transgene copies are at a single locus no larger than approximately 40 kb in size. Therefore, the recombination events resulting in the loss of transgene DNA are taking place within a limited physical distance on the host chromosome. This is the first report extensively documenting transgene instability at the DNA level in a plant transformed via particle bombardment. As this report indicates, a seemingly simple phenotype (presence of the foreign protein) may conceal inherent genetic instability at the DNA level.     

Humoral regulation of heart rate during digestion in pythons (Python molurus and Python regius)

Pythons exhibit a doubling of heart rate when metabolism increases several times during digestion. Pythons, therefore, represent a promising model organism to study autonomic cardiovascular regulation during the postprandial state, and previous studies show that the postprandial tachycardia is governed by a release of vagal tone as well as a pronounced stimulation from nonadrenergic, noncholinergic (NANC) factors. Here we show that infusion of plasma from digesting donor pythons elicit a marked tachycardia in fasting snakes, demonstrating that the NANC factor resides in the blood. Injections of the gastrin and cholecystokinin receptor antagonist proglumide had no effect on double-blocked heart rate or blood pressure. Histamine has been recognized as a NANC factor in the early postprandial period in pythons, but the mechanism of its release has not been identified. Mast cells represent the largest repository of histamine in vertebrates, and it has been speculated that mast cells release histamine during digestion. Treatment with the mast cell stabilizer cromolyn significantly reduced postprandial heart rate in pythons compared with an untreated group but did not affect double-blocked heart rate. While this study indicates that histamine induces postprandial tachycardia in pythons, its release during digestion is not stimulated by gastrin or cholecystokinin nor is its release from mast cells a stimulant of postprandial tachycardia.     

Does high polyunsaturated free fatty acid level at the feto-maternal interface alter steroid hormone message during pregnancy?

Polyunsaturated fatty acids (PUFA) are important in pregnancy, fetal development and parturition. We measured free fatty acids (FFA), albumin and alpha-fetoprotein (AFP) in the maternal and fetal circulations of women undergoing elective Caesarean section at term. We also studied the impact of PUFAs on estrogen (ER) and progesterone receptors (PR) binding properties in vitro in the myometria of pregnant women and ex vivo in human myometrial cells in culture. FFA in intervillous blood (I) (feto-maternal interface) and maternal peripheral blood (M) were similar, while those in the umbilical vein (V) and arteries (A) were 2-4 fold lower (P<0.001). PUFA levels were low in M and 3 fold higher in I, A and V (P< 0.001); consequently C20:4 and C22:6 were most abundant in intervillous space. Albumin was uniformly distributed throughout the maternal-fetal unit, but there was a transplacental gradient in AFP. The AFP in the intervillous space had a special conformation (less immuno-reactive, more anionic), suggesting loading with PUFA. Physiological concentrations of C20:4 stimulated estradiol binding, but inhibited progestin binding. C20:4 inhibited progesterone binding by decreasing the number of binding sites, with no change in apparent affinity, in vitro in myometrial tissue and ex vivo in myometrial cells. Thus PUFA may modulate the steroid hormone message, so that the high C20:4 concentration at the maternal-fetal interface at term may help amplify the estrogen signal and inhibit the progesterone signal.     

Superoxide dismutase level in response to paraquat and high temperature in the cyanobacteriumGloeocapsa sp

Paraquat (methylviologen) at concentrations above 0.05 mM inhibited the growth of photoautotrophic cyanobacteriumGleeocapsa sp. in axenic cultures. The growth rate was not affected by concentrations of 0.01 mM or less. This concentration resulted after a lag period in a moderate increase in superoxide dismutase level. After removal of paraquat, the cyanobacterium continued to generate higher levels of superoxide dismutase. There was a lag period of one hour before resumption of normal enzyme activity. Addition of puromycin at concentration of 0.5 mg cm^?3 had no effect on cell survival, but greatly enhanced the sensitivity of the culture to the toxicity of paraquat. The data showed an increase of SOD activity by temperatures above the normal growth temperature level. However, this increase was suppressed by chloramphenicol which revealed that the induction of superoxide dismutase by high temperatures was associated withde novo protein synthesis.     

A high level of transferrin mRNA in the liver of analbuminemic rats

By means of immunological screening, a cDNA clone bearing the mRNA sequence for rat transferrin was isolated from a cDNA library of rat liver mRNA. The amounts of transferrin mRNA in livers of analbuminemic rats (NAR, Nagase analbuminemia rats) and normal rats were determined by RNA blot hybridization using a cloned transferrin cDNA probe. The level of transferrin mRNA in the NAR liver was about 1.7 times that in the normal rat liver. These findings suggest that the enhanced synthesis of transferrin in the NAR liver resulted from an increase in the transferrin mRNA level.     

Cardiovascular reactivity to emotional texts in subjects with low and high level of psychoticism

The article presents the results of comparative study of groups of subjects with low and high level of psychoticism. Heart rate, heart rate responses to inspiratory and expiratory Valsalva maneuvers, and blood pressure were measured before and after presentation of the texts with validated negative content in groups of subjects with low and high psychoticism scores. It was hypothesized that subjects with high level of psychoticism would be less engaged in the processing of negative contents of the texts and their physiological reactivity (physiological resources submitted for support of cognitive processing) would be less pronounced compared to subjects with low level of psychoticism. Significant main effect of psychoticism was obtained for changes in heart rate to expiratory Valsalva maneuver after presentations of the texts. Significant interaction effects of gender and psychoticism were obtained for systolic blood pressure. Other cardiovascular variables were not sensitive to the level of psychoticism. These effects of psychoticism were independent of other individual traits, such as neuroticism, extraversion, lie (social desirability), anger, trait anxiety and depression.     

A new distance for high level RNA secondary structure comparison

We describe an algorithm for comparing two RNA secondary structures coded in the form of trees that introduces two new operations, called node fusion and edge fusion, besides the tree edit operations of deletion, insertion, and relabeling classically used in the literature. This allows us to address some serious limitations of the more traditional tree edit operations when the trees represent RNAs and what is searched for is a common structural core of two RNAs. Although the algorithm complexity has an exponential term, this term depends only on the number of successive fusions that may be applied to a same node, not on the total number of fusions. The algorithm remains therefore efficient in practice and is used for illustrative purposes on ribosomal as well as on other types of RNAs.