Protein modeling of cathepsin C mutations found in Papillon–Lefèvre syndrome

Background

Papillon–Lefèvre syndrome (PLS) is a rare autosomal recessive disorder characterized by hyperkeratosis involving the palms, soles, elbows, and knees followed by periodontitis, destruction of alveolar bone, and loss of primary and permanent teeth. Mutations of the lysosomal protease cathepsin C gene (CTSC) have been shown to be the genetic cause of PLS. This study analyzed CTSC mutations in five Iranian families with PLS and modeled the protein for mutations found in two of them.

Methods

DNA analysis was performed by direct automated sequencing of genomic DNA amplified from exonic regions and associated splice intron site junctions of CTSC. RFLP analyses were performed to investigate the presence of previously unidentified mutation(s) in control groups. Protein homology modeling of the deduced novel mutations (P35 delL and R272P) was performed using the online Swiss-Prot server for automated modeling and analyzed and tested with special bioinformatics tools to better understand the structural effects caused by mutations in cathepsin C protein (CTSC).

Results

Six Iranian patients with PLS experienced premature tooth loss and palm plantar hyperkeratosis. Sequence analysis of CTSC revealed a novel mutation (P35delL) in exon 1 of Patient 1, and four previously reported mutations; R210X in Patient 2, R272P in Patient 3, Q312R in two siblings of family 4 (Patients 4 and 5), and CS043636 in Patient 6. RFLP analyses revealed different restriction fragment patterns between 50 healthy controls and patients for the P35delL mutation. Modeling of the mutations found in CTSC, P35delL in Patient 1 and R272P in Patient 3 revealed structural effects, which caused the functional abnormalities of the mutated proteins.

Conclusions

The presence of this mutation in these patients provides evidence for founder CTSC mutations in PLS. This newly identified P35delL mutation leads to the loss of a leucine residue in the protein. The result of this study indicates that the phenotypes observed in these two patients are likely due to CTSC mutations. Also, structural analyses of the altered proteins identified changes in energy and stereochemistry that likely alter protein function.     

Application of Maltodextrin as Chiral Selector in Capillary Electrophoresis for Quantification of Amlodipine Enantiomers in Commercial Tablets

Maltodextrin was investigated as a chiral selector in capillary electrophoresis (CE) analysis of amlodipine (AM) enantiomers. For development of a stereoselective CE method, various effective parameters on the enantioseparation were optimized. The best results were achieved on an uncoated fused silica capillary at 20 °C using phosphate buffer (100 mM, pH 4) containing 10% w/v maltodextrin (dextrose equivalent value 4–7). The UV detector was set at 214 nm and a constant voltage of 20 kV was applied. The range of quantitation was 2.5–250 µg/mL (R² > 0.999) for both enantiomers. Intra‐ (n = 5) and interday (n = 3) relative standard deviation (RSD) values were less than 7%. The limits of quantitation and detection were 1.7 µg/mL and 0.52 µg/mL, respectively. Recoveries of R(+) and S(?) enantiomers from tablet matrix were 97.2% and 97.8%, respectively. The method was applied for the quantification of AM enantiomers in commercial tablets. Also, the enantioseparation capability of heparin was evaluated and the results showed that heparin did not have any chiral selector activity in this study. Chirality 26:394–399, 2014. © 2014 Wiley Periodicals, Inc.     

Characterization of Turnip mosaic virus from the Asian‐BR Population in Iran

Brassicaceae crops in eight provinces of the North‐west Iran were surveyed for Turnip mosaic virus (TuMV) infection during 2011 and 2012. Many symptomatic plants (38%; 226 of 598) were found to be infected with TuMV. The highest frequency was in turnip (61%), followed by radish (55%), oilseed rape (38%), and brassica weeds including annual bastard cabbage (42%), small tumbleweed‐mustard (50%) and wild radish (45%), but not Brassica oleracea and Lepidium sativum. Using biological assays, Iranian TuMV isolates grouped in three [B], [B(R)] and [BR] host‐infecting types. Phylogenetic analysis using complete coat protein (CP) gene nucleotide sequences showed that the Iranian isolates belonged to the Basal‐B and Asian‐BR populations. No evidence of recombination was found in these isolates using different recombination‐detecting programmes. To our knowledge, our study shows for the first time the occurrence of TuMV Asian‐BR subpopulation in the mid Eurasian region of Iran. The data suggest that the Asian‐BR subtype population is found across southern Eurasia and might be a continuous population in East Asia (mostly Japan and China) and Minor Asia (Turkey), the places considered to be one of the origins of TuMV populations.     

Mechanisms of Phenytoin‐Induced Toxicity in Freshly Isolated Rat Hepatocytes and the Protective Effects of Taurine and/or Melatonin

Phenytoin is a widely used antiepileptic drug. However, hepatotoxicity is one of its adverse effects reported in some patients. The mechanism(s) by which phenytoin causes hepatotoxicity is not clear yet. This study was designed to evaluate the cytotoxic mechanism(s) of phenytoin toward rat hepatocytes (whose cytochrome P450 enzymes had been induced by Phenobarbital). Furthermore, the effect of taurine and/or melatonin on this toxicity was investigated. Cell death, reactive oxygen species (ROS) formation, lipid peroxidation (LPO), and mitochondrial depolarization were monitored as toxicity markers. Results showed that phenytoin caused an elevation in ROS formation, depletion of intracellular reduced glutathione, increase in cellular oxidized glutathione, enhancement of LPO, and mitochondrial damage. Taurine (1 mM) and/or melatonin (1 mM) administration decreased the intensity of cellular injury caused by phenytoin. This study suggests the protective role of taurine and/or melatonin against phenytoin‐induced cellular damage probably through their reactive radical scavenging properties and their effects on mitochondria.     

Deleterious effects of Bacillus thuringiensis on biological parameters of Habrobracon hebetor parasitizing Helicoverpa armigera

The bacterium Bacillus thuringiensis (Bt) Berliner and the braconid wasp Habrobracon hebetor Say are valuable biocontrol agents attacking larval stages of Helicoverpa armigera (Hübner). Little information is available regarding combination of these biocontrol agents during integrated management of H. armigera. To address this knowledge gap, we document sublethal effects of Bacillus thuringiensis var. kurstaki (Btk) on the H. hebetor attacking H. armigera larvae infected with Btk. The results revealed that the duration of different life stages and fecundity of H. hebetor was significantly affected by sublethal treatments with Btk. We also present data supporting that sublethal concentrations of Btk could adversely affect life table parameters of H. hebetor. Sublethal treatments reduced the net reproductive rate (R ₀) and there were also significant differences among the values of this parameter at all treatments tested. The intrinsic (r _m ) and finite (λ) rates of increase were also significantly lower in parasitoid wasps reared on the treated larvae of H. armigera compared to control. These findings will be useful to develop appropriate strategies for assessing the risks of Btk to the parasitoids and safe deployment of both organisms in integrated pest management programs for sustainable crop production.     

The mzTab Data Exchange Format: Communicating Mass-spectrometry-based Proteomics and Metabolomics Experimental Results to a Wider Audience

The HUPO Proteomics Standards Initiative has developed several standardized data formats to facilitate data sharing in mass spectrometry (MS)-based proteomics. These allow researchers to report their complete results in a unified way. However, at present, there is no format to describe the final qualitative and quantitative results for proteomics and metabolomics experiments in a simple tabular format. Many downstream analysis use cases are only concerned with the final results of an experiment and require an easily accessible format, compatible with tools such as Microsoft Excel or R.We developed the mzTab file format for MS-based proteomics and metabolomics results to meet this need. mzTab is intended as a lightweight supplement to the existing standard XML-based file formats (mzML, mzIdentML, mzQuantML), providing a comprehensive summary, similar in concept to the supplemental material of a scientific publication. mzTab files can contain protein, peptide, and small molecule identifications together with experimental metadata and basic quantitative information. The format is not intended to store the complete experimental evidence but provides mechanisms to report results at different levels of detail. These range from a simple summary of the final results to a representation of the results including the experimental design. This format is ideally suited to make MS-based proteomics and metabolomics results available to a wider biological community outside the field of MS. Several software tools for proteomics and metabolomics have already adapted the format as an output format. The comprehensive mzTab specification document and extensive additional documentation can be found online.Mass spectrometry (MS)¹ has become a major analysis tool in the life sciences (1). It is currently used in different modes for several “omics” approaches, proteomics and metabolomics being the most prominent. In both disciplines, one major burden in the exchange, communication, and large-scale (re-) analysis of MS-based data is the significant number of software pipelines and, consequently, heterogeneous file formats used to process, analyze, and store these experimental results, including both identification and quantification data. Publication guidelines from scientific journals and funding agencies'' requirements for public data availability have led to an increasing amount of MS-based proteomics and metabolomics data being submitted to public repositories, such as those of the ProteomeXchange consortium (2) or, in the case of metabolomics, the resources from the nascent COSMOS (Coordination of Standards in Metabolomics) initiative (3).In the past few years, the Human Proteome Organization Proteomics Standards Initiative (PSI) has developed several vendor-neutral standard data formats to overcome the representation heterogeneity. The Human Proteome Organization PSI promotes the usage of three XML file formats to fully report the data coming from MS-based proteomics experiments (including related metadata): mzML (4) to store the “primary” MS data (the spectra and chromatograms), mzIdentML (5) to report peptide identifications and inferred protein identifications, and mzQuantML (6) to store quantitative information associated with these results.Even though the existence of the PSI standard data formats represents a huge step forward, these formats cannot address all use cases related to proteomics and metabolomics data exchange and sharing equally well. During the development of mzML, mzIdentML, and mzQuantML, the main focus lay on providing an exact and comprehensive representation of the gathered results. All three formats can be used within analysis pipelines and as interchange formats between independent analysis tools. It is thus vital that these formats be capable of storing the full data and analysis that led to the results. Therefore, all three formats result in relatively complex schemas, a clear necessity for adequate representation of the complexity found in MS-based data.An inevitable drawback of this approach is that data consumers can find it difficult to quickly retrieve the required information. Several application programming interfaces (APIs) have been developed to simplify software development based on these formats (7–9), but profound proteomics and bioinformatics knowledge still is required in order to use them efficiently and take full advantage of the comprehensive information contained.The new file format presented here, mzTab, aims to describe the qualitative and quantitative results for MS-based proteomics and metabolomics experiments in a consistent, simpler tabular format, abstracting from the mass spectrometry details. The format contains identifications, basic quantitative information, and related metadata. With mzTab''s flexible design, it is possible to report results at different levels ranging from a simple summary or subset of the complete information (e.g. the final results) to fairly comprehensive representation of the results including the experimental design. Many downstream analysis use cases are only concerned with the final results of an experiment in an easily accessible format that is compatible with tools such as Microsoft Excel® or R (10) and can easily be adapted by existing bioinformatics tools. Therefore, mzTab is ideally suited to make MS proteomics and metabolomics results available to the wider biological community, beyond the field of MS.mzTab follows a similar philosophy as the other tab-delimited format recently developed by the PSI to represent molecular interaction data, MITAB (11). MITAB is a simpler tab-delimited format, whereas PSI-MI XML (12), the more detailed XML-based format, holds the complete evidence. The microarray community makes wide use of the format MAGE-TAB (13), another example of such a solution that can cover the main use cases and, for the sake of simplicity, is often preferred to the XML standard format MAGE-ML (14). Additionally, in MS-based proteomics, several software packages, such as Mascot (15), OMSSA (16), MaxQuant (17), OpenMS/TOPP (18, 19), and SpectraST (20), also support the export of their results in a tab-delimited format next to a more complete and complex default format. These simple formats do not contain the complete information but are nevertheless sufficient for the most frequent use cases.mzTab has been designed with the same purpose in mind. It can be used alone or in conjunction with mzML (or other related MS data formats such as mzXML (21) or text-based peak list formats such as MGF), mzIdentML, and/or mzQuantML. Several highly successful concepts taken from the development process of mzIdentML and mzQuantML were adapted to the text-based nature of mzTab.In addition, there is a trend to perform more integrated experimental workflows involving both proteomics and metabolomics data. Thus, we developed a standard format that can represent both types of information in a single file.