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PubMed2006

The application of sub-2-microm particle liquid chromatography-operated high mobile linear velocities coupled to orthogonal accelerated time-of-flight mass spectrometry for the analysis of ranitidine and its impurities.

Impurity profiling of pharmaceutical drug substances or dosage formulations require methods involving high sensitivity and resolution from LC and MS alike as well as an acceptable analysis time. While throughput can be increased, it is usually at the expense of chromatographic resolution. The application of sub-2-microm stationary phases and high mobile linear velocities has been combined with orthogonal acceleration (oa)-TOF MS for the impurity structural characterization analysis of small-molecule pharmaceutics. A pharmaceutical drug substance was forcefully degraded and used to test the proof of concept of developing an impurity profile method by ultra performance liquid chromatography (UPLC). Optimum conditions were identified by use of method development simulation software as well as traditional approaches of method scouting with columns and a varied range of pH. Further analysis illustrated the effectiveness of applying oa-TOF MS techniques to assist in achieving exact mass coupled with MS/MS to define the structural characterization of the related substances relative to the pharmaceutical active ingredient and identification of any unknown impurity substances. The barriers with trade-offs between resolution and speed are overcome by the application of UPLC, whereas the increased sensitivity provides for superior exact mass oa-TOF MS.

Chemistry Techniques, Analytical↗

PubMed2006

Visualisation and analysis of proteomic data from the procyclic form of Trypanosoma brucei.

We have undertaken a large scale study of the proteins expressed in the procyclic form of the parasite Trypanosoma brucei, which causes African sleeping sickness, using 2-DE and MS. The complete data set encompasses over 2000 identifications, of which 770 are distinct proteins. We have discovered that multiple protein isoforms appear to be common in T. brucei, as most proteins have been matched to more than one gel spot. We have developed visualisation software to investigate the differences between isoforms, based on the information from the results of database searches with MS data. We are able to highlight instances where PTMs are the most likely cause of variant forms. In other cases, spots that appear reproducibly across replicates contain fragments of proteins, arising either as experimental artefacts or as part of protein degradation. We are also able to classify clusters of gel spots into different groups based on the pattern of peptides that have been matched from MS data. The entire data set is stored within a relational database system that allows complex queries ( http://www.gla.ac.uk/functionalgenomics). Using specific proteins as examples, we demonstrate how the visualisation software and the database query facilities can be used.

Animals↗

PubMed2007

Complementarity of hydrophobic properties in ATP-protein binding: a new criterion to rank docking solutions.

ATP is an important substrate of numerous biochemical reactions in living cells. Molecular recognition of this ligand by proteins is very important for understanding enzymatic mechanisms. Considerable insight into the problem may be gained via molecular docking simulations. At the same time, standard docking protocols are often insufficient to predict correct conformations for protein-ATP complexes. Thus, in most cases the native-like solutions can be found among the docking poses, but current scoring functions have only limited ability to discriminate them from false positives. To improve the selection of correct docking solutions obtained with the GOLD software, we developed a new ranking criterion specific for ATP-protein binding. The method is based on detailed analysis of the intermolecular interactions in 40 high-resolution 3D structures of ATP-protein complexes (the training set). We found that the most important factors governing this recognition are hydrogen-bonding, stacking between adenine and aromatic protein residues, and hydrophobic contacts between adenine and protein residues. To address the latter, we applied the formalism of 3D molecular hydrophobicity potential. The results obtained were used to construct an ATP-oriented scoring criterion as a linear combination of the terms describing these intermolecular interactions. The criterion was then validated using the test set of 10 additional ATP-protein complexes. As compared with the standard scoring functions, the new ranking criterion significantly improved the selection of correct docking solutions in both sets and allowed considerable enrichment at the top of the list containing docking poses with correct solutions.

Adenine↗

PubMed2004

Mass spectrometry for the detection of differentially expressed proteins: a comparison of surface-enhanced laser desorption/ionization and capillary electrophoresis/mass spectrometry.

The discovery of biomarkers is currently attracting much interest as it harbors great potential for the diagnosis and monitoring of human diseases. Here we have used two advanced mass spectroscopy based technologies, surface enhanced laser desorption ionization (SELDI-MS) and capillary electrophoresis/mass spectrometry (CE/MS), to obtain proteomic patterns of urine samples from patients suffering from membranous glomerulonephritis (MGN) and healthy volunteers. The results indicate that CE/MS analysis is able to display a rich and complex pattern of polypeptides with high resolution and high mass accuracy. In order to analyze these patterns, the MosaiqueVisu software was developed for peak identification, deconvolution and the display of refined maps in a three-dimensional format. The polypeptide profiles obtained with SELDI-MS from the same samples are much sparser and show lower resolution and mass accuracy. The SELDI-MS profiles are further heavily dependent on analyte concentration. SELDI-MS analysis identified three differentially expressed polypeptides, which are potential biomarkers that can distinguish healthy donors from patients with MGN. In contrast, approximately 200 potential biomarkers could be identified by CE/MS. Thus, while SELDI-MS is easy to use and requires very little sample, CE/MS generates much richer data sets that enable an in-depth analysis.

Adult↗

PubMed2006

Examining the collision-induced decomposition spectra of ammoniated triglycerides as a function of fatty acid chain length and degree of unsaturation. II. The PXP/YPY series.

A series of positionally pure triglycerides (TAGs) of the form PXP and YPY, where P is the palmitate moiety and X and Y are large arrays of different fatty acid moieties, is synthesized and analyzed by reversed-phase high-performance liquid chromatography/tandem mass spectrometry. The intensities of the collision-induced decomposition (CID) products of ammoniated TAGs were examined as a function of chain length, degree of unsaturation, double-bond position, and cis/trans configuration of X and Y. The major CID products, the diglyceride (DAG) fragment ions and the MH(+) ions, are plotted as functions of chain length for the saturated and monounsaturated series of X and Y. Different trends for each of these series are observed. Trends in the intensities of these fragment ions are also characterized as a function of degree of unsaturation in the TAGs. In general, the fractional intensities of MH(+) increase with increasing degree of unsaturation in the TAGs. MH(+) is absent in the CID spectra of triglycerides containing three saturated fatty acid moieties, suggesting that the presence of double bonds fosters the formation of MH(+). Double bonds positioned close to the carbonyl carbon along the fatty acid chain promote the formation of the DAG fragment ion corresponding to the loss of the fatty acid. The collection of PXP/YPY data produced in this work is used to test the mechanisms of the formation and decomposition of ammoniated TAGs that were previously presented. The YPY data are used to predict the intensities of the fragment ions in the CID spectra of YPX-type TAGs. The limitations of the mathematical approach used in these predictions are discussed in context of a broader plan to develop a software platform for comprehensive analysis of complex TAG mixtures.

Chromatography, High Pressure Liquid↗

PubMed2006

Resolving stoichiometries and oligomeric states of glutamate synthase protein complexes with curve fitting and simulation of electrospray mass spectra.

A complicating factor in analyzing electrospray ionization mass spectra of intact macromolecular heterogeneous protein complexes is the potential overlap of ions from different species present in solution. Therefore, it is often not possible to assign all ion signals. With the aim of allowing the more efficient and comprehensive analysis of very complex mass spectra of intact heterogeneous protein complexes we developed a software program: SOMMS. The program uses simple user input parameters together with Gaussian curve fitting to simulate putative mass spectra of protein (sub)complexes within a specified charge state window. In addition, the program can simulate spectra for heterogeneous protein complexes using bi- and multinomial distributions and it can calculate zero-charge spectra and relatively quantify the abundance of each component in a mixture. As a proof of concept we analyzed the complex mass spectra of alpha-glutamate synthase and alphabeta-glutamate synthase from Azosprillum brasilense. Using our program we could determine that alpha-glutamate synthase is in equilibrium between its dimeric, tetrameric, hexameric and dodecameric conformation, whereas alphabeta-glutamate synthase forms up to 15 different heterooligomeric assemblies composed of alpha- and beta-subunits. Thus, SOMMS allows resolving stoichiometries and oligomeric states of protein complexes even from very complicated mass spectra. These complexes could not be assigned by using maximum entropy calculations. We compared our mass spectrometry data on glutamate synthases with available X-ray, small-angle X-ray scattering and size-exclusion chromatography data.

Azospirillum brasilense↗

PubMed2001

Automated molecular weight assignment of electrospray ionization mass spectra.

Process improvements in the synthesis of therapeutic agents and their intermediates are often facilitated by identification of reaction by-products. Analysis by liquid chromatography/mass spectrometry (LC/MS) with electrospray ionization is a powerful approach for obtaining molecular weight information for these compounds. Such analyses are well suited for 'open-access' mass spectrometry using generic chromatographic conditions, provided spectral interpretation for unknown compounds is facile. We have developed a software application (MassAssign) that facilitates automated data processing and molecular weight assignment for chromatographic peaks detected by any standard ultraviolet-visible wavelength detector. The program assigns [M + H](+) ions (and thus molecular weight) in the mass spectra using predetermined criteria. This evaluation process differentiates [M + H](+) ions from other signals in a complex mass spectrum such as those resulting from chromatographic coelution or the presence of multiple species (i.e., fragment ions, singly charged ions, doubly charged ions, adduct ions, proton-bound dimers, etc.). Once the program has evaluated all ions in a mass spectrum that exceed a preset abundance threshold, MassAssign reports either a numeric value-indicating the chromatographic peak consists of a single component having the displayed molecular weight, 'MC'-indicating the peak consisted of multiple components, or 'ND'-that a molecular weight could not be determined unequivocally. The performance of the program was evaluated by comparing mass assignments made by MassAssign against manual interpretation for 55 samples analyzed by positive electrospray ionization using a generic HPLC method. Correct molecular weight assignments were obtained in 90% of the cases.

Algorithms↗

PubMed2002

New early zygotic regulators expressed in endomesoderm of sea urchin embryos discovered by differential array hybridization.

Genes that are upregulated by LiCl treatment of sea urchin embryos and/or downregulated by injection into the egg of mRNA encoding an internal fragment of cadherin (Cad) were detected in a differential macroarray screen. The method was that recently described by J. P. Rast et al. (2000, Dev. Biol. 228, 270-296). Almost 10(5) clones from a 12-h cDNA library were screened. Measurements on internal standards showed that the screening procedure was sufficiently sensitive to afford detection of differentially expressed mRNAs of the most rare class, those present in only a few copies per average cell. The injection of Cad mRNA, which specifically blocks nuclearization of beta-catenin, resulted in many-fold decreases in the levels of transcripts of a suite of marker genes expressed zygotically during endomesoderm specification. These measurements substantiated the use of Cad mRNA as the basis for a differential screen for discovery of new endomesodermal genes. By use of the newly developed BioArray software for analysis of macroarray screens, 1106 clones representing differentially expressed genes and yielding useful sequence were recovered. The 367 clones that gave significant BLASTX matches to known cellular proteins fell into 264 nonredundant sequence classes. Those of particular interest for this work were clones encoding DNA-binding transcription factors, signal transduction pathway components, proteases, kinases, and phosphatases. Quantitative PCR analysis of 66 such selected clones revealed that the large majority of these clones had been selected because they are upregulated by LiCl treatment, which affects the expression of a much greater diversity and number of genes than are involved in endomesoderm specification. Seven transcript species were identified that responded sharply to injection of Cad mRNA, and that are not represented in maternal mRNA. Six of those encode transcription factors. We focused on three transcription factor genes of this set that were previously unknown in sea urchin embryos. By whole-mount in situ hybridization, these genes are expressed in specific domains of the endomesodermal territory. They are: (1) Speve, an evenskipped orthologue expressed very early in all vegetal blastomeres and then gradually shifting to veg(1) derivatives by the mesenchyme blastula stage; (2) Spgcm, an orthologue of the fruit fly gene glial cells missing, which is first expressed specifically and exclusively in part of the prospective secondary mesenchyme (mesodermal) domain at late-cleavage blastula stage; and (3) Spfoxc, which is first expressed in the early blastula only in the four small micromeres, and later only expressed in that coelomic pouch which gives rise to the mesoderm of the ventral surface of the adult rudiment.

Animals↗

PubMed1996

The EM Program Package: A Platform for Image Processing in Biological Electron Microscopy

EM is a software package developed for image processing in the field of biological electron microscopy. After a brief summary of its history, an outline of the package is given, by describing some characteristic features rather than by a complete report of all facilities. New developments, connected with the introduction of a UNIX version and the advent of automated electron microscopy, are described in more detail.

Journal Article↗

PubMedDate not supplied

Processing of electron diffraction patterns acquired on a slow-scan CCD camera.

We have developed two software packages for the processing of electron diffraction patterns acquired on a slow-scan CCD camera. Automated indexing and processing of these electron diffraction patterns is possible using a program called AUTO. To obtain a set of reliable reflections, AUTO applies a number of corrections, which are necessary due to the acquisition of the patterns with a slow-scan CCD camera. To index and process unknown lattices in electron diffraction patterns obtained from, for instance, a new protein or a new crystal form, an interactive program called EDP is available. It supports indexing in an interactive manner through a graphical user interface. Processing of the electron diffraction pattern is done using a script created by EDP. Both packages run on UNIX platforms, with EDP requiring the X Window System.

Automation↗

PubMed2003

Surgical navigation in the open MRI.

The introduction of MRI into neurosurgery has opened multiple avenues, but also introduced new challenges. The open-configuration intraoperative MRI installed at the Brigham and Women's Hospital in 1996 has been used for more than 500 open craniotomies and beyond 100 biopsies. Furthermore the versatile applicability, employing the same principles, is evident by its frequent use in other areas of the body. However, while intraoperative scanning in the SignaSP yielded unprecedented imaging during neurosurgical procedures their usage for navigation proved bulky and unhandy. To be fully integrated into the procedure, acquisition and display of intraoperative data have to be dynamic and primarily driven by the surgeon performing the procedure. To use the benefits of computer-assisted navigation systems together with immediate availability of intraoperative imaging we developed a software package. This "3D Slicer" has been used routinely for biopsies and open craniotomies. The system is stable and reliable. Pre- and intraoperative data can be visualized to plan and perform surgery, as well as to accommodate for intraoperative deformations, "brain shift", by providing online data acquisition.

Artifacts↗

PubMed1994

The nuclear position of pericentromeric DNA of chromosome 11 appears to be random in G0 and non-random in G1 human lymphocytes.

The nuclear topography of pericentromeric DNA of chromosome 11 was analyzed in G0 (nonstimulated) and G1 [phytohemagglutinin (PHA) stimulated] human lymphocytes by confocal microscopy. In addition to the nuclear center, the centrosome was used as a second point of reference in the three-dimensional (3D) analysis. Pericentromeric DNA of chromosome 11 and the centrosome were labeled using a combination of fluorescent in situ hybridization (FISH) and immunofluorescence. To preserve the 3D morphology of the cells, these techniques were performed on whole cells in suspension. Three-dimensional images of the cells were analyzed with a recently developed 3D software program (Interactive Measurement of Axes and Positioning in 3 Dimensions). The distribution of the chromosome 11 centromeres appeared to be random during the G0 stage but clearly non-random during the G1 stage, when the nuclear center was used as a reference point. Further statistical analysis of the G1 cells revealed that the centromeres were randomly distributed in a shell underlying the nuclear membrane. A topographical relationship between the centrosome and the centromeres appeared to be absent during the G0 and G1 stages of the cell cycle.

Cell Nucleus↗

PubMed1996

A microcomputer program for calculating cell population doubling time in vitro and in vivo.

Determination of the doubling time for a population of cells can involve tedious calculations. We have developed computer software for MS-DOS microcomputers to expedite the analysis of tumor cell growth in vitro and in vivo. This program, DOUBLE-TIME, assists in the collection of cell numbers into a database and calculates the doubling time for a population of cells from the plot of cell growth over time. For experiments where tumor mass is measured in vivo, the software collects measurements of tumor size, calculates tumor volume (mass), generates growth curves for tumor volume change over time, and determines the doubling time of the tumor and the mean for multiple tumors. DOUBLE-TIME plots both total and viable cell numbers over time, calculates standard error of the doubling time, and the doubling time for a selected portion of a growth curve. This software also automates the cell counting process with a software-generated cell counter that allows cell counts to be tallied directly into the computer via a mouse.

Animals↗

PubMed1991

A new teaching tool for dental and medical schools: multimedia CD-ROM on dental and skeletal development.

Multimedia teaching tools in Medicine are still very rare. Their presentation on a CD-ROM format is part of the emerging technologies in Medical Informatics. The Multimedia material presented here on Dental and Skeletal Development is mostly a Database and a Tutorial. The Database, which contains more than 2000 hand/wrist radiographs, is mostly intended for Pediatricians, Endocrinologists, Forensic Dentists and Physicians, as well as for Orthodontists and Pedodontists. The material is the result of 20-year of Longitudinal Growth study of children in Montreal. In this Multimedia CD-ROM, the research results are used for Medical teaching purposes.

Bone Development↗

PubMed1996

[Acoustic voice analysis. On documentation of voice rehabilitation after laser surgery laryngeal carcinoma resection].

Following curative minimal-invasive laser resection of T1-T3 laryngeal carcinomas, patients were subjected to an intensive voice rehabilitation. Therapy was effected twice a day for approximately 2 months, utilizing the concept of functional voice therapy. Before and after rehabilitation, acoustic analyses were made by using two different computer-supported measuring systems: (1) the "multidimensional voice program" (Kay Elementrics Corp.) and (2) a novel software program developed in Göttingen that includes a new voice quality parameter based on correlations between frequency bands. Acoustic analyses showed superiority of the glottal versus supraglottal compensatory phonation. Findings showed that not all acoustic parameters equally documented voice improvement after rehabilitation. The standard deviation of fundamental frequency was the only parameter showing a significant post-therapeutic improvement. A further suitable acoustic method proved to be the voice quality parameter that has been newly introduced by us. In contrast to analogous parameters of other methods, this approach is independent of the exact periodicity of the glottal excitation function, thus permitting reliable results to be obtained even with aphonic or heavily dysphonic voices.

Aged↗

PubMed2006

[A new parallel drill guide for navigating femoral neck screw placement. Development and evaluation].

BACKGROUND: Trauma navigation applications employ conventional mechanical surgical instruments for the simulation of drilling trajectories. Few complex mechanical targeting instruments, such as guides with fixed angles or with multiple parallel cannulas, have been adapted into trauma navigation systems. We have integrated a complex mechanical tool, the parallel drill guide (PDG) for the minimally invasive treatment of femoral neck fractures, into a trauma navigation module. The combined advantage of a complex yet commonly used mechanical tool with the benefits of fluoroscopic navigation was evaluated. MATERIAL AND METHODS: To adapt the conventional PDG to a fluoroscopic navigation system, the instrument was fitted with a non-detachable reflective marker array. Navigation engineers developed custom software to enable visualization of the navigated PDG. A comparison of conventional versus navigated PDG techniques was performed on plastic bone models and cadavers. No software or mechanical failures occurred with the navigated PDG procedures. RESULTS: While the total operative time was 30% more with navigation compared with conventional techniques, the total radiation time for the navigated group was reduced by more than 60%. This study demonstrates the successful integration of a cannulated parallel drill guide with a fluoroscopic navigation system. CONCLUSION: The continuous display of the complex PDG mechanical instrument, with multiple parallel virtual trajectories, enables safe and accurate parallel screw placement. The integration of complex mechanical instrumentation with navigation for the accurate placement of hardware represents an attractive direction in multiple trauma applications.

Bone Screws↗

PubMed1999

[Dental CT: examination method, radiation dosage and anatomy].

Traditionally oral surgeons and dentists have evaluated the jaws using intraoral films and panoramic radiographs. The involvement of radiologists has been limited. In the past few years dedicated CT-software-programs developed to evaluate dental implant patients have provided a new look at the jaws. The complex anatomy is described and identified on human skulls and on axial, panoramic, and cross-sectional images. With this anatomic description Dental-CT-scans are used to demonstrate the anatomy of maxilla and the mandible. An overview of the technique of Dental-CT is provided, furthermore the radiation dose of different organs is explained. Suggestions to reduce these doses by simple modifications of the recommended protocols are given.

Humans↗

PubMed2002

Influence of number and map distribution of AFLP markers on similarity estimates in carrot.

When genetic diversity among organisms was measured with molecular markers, the question of genome coverage was currently stressed out. In order to check if well-distributed, mapped AFLP markers were more efficient in assessing varietal identification of carrot accessions than randomly chosen markers, nine closely related genotypes were analysed. A software was developed to realise 1,000 random choices of 20 to 70 mapped or unmapped markers, offering numerous genome coverages. We statistically showed that taking into account marker position does not provide a better estimation of genetic distances. Moreover, in the case of carrot, we concluded that 60 AFLP markers offer the best compromise between the level of precision and minimal expense.

Chromosome Mapping↗