Studies on the synthesis of pentacyclic strychnos indole alkaloids. photocyclization of n-chloroacetyl-1,2,3,4,5,6-hexahydro-1,5-methanoazocino[4,3-b]indole derivatives

Photocyclization of 2-chloroacetyl-1,2,3,4,5,6-hexahydro-1, 5-methanoazocino[4,3-b]indole ($\text{5}$) takes place at the indole 4-position to give a 1 ,2 ,3 ,4 , 5 ,6-hexahydro-2 ,11-ethano-1 ,5-methanoazocino [4 , 3-6] indole system. Consequently, the method appears to be unsuitable for constructing the pyrrolidine ring of pentacyclic Strychnos indole alkaloids.     

TissueDistributionDBs: a repository of organism-specific tissue-distribution profiles

Tissue-distribution profiles are crucial for understanding the characteristics of cells and tissues in terms of their differential expression of genes. Most of the currently available resources for tissue-distribution profiles are either specialized for a few particular organisms, tissue types and disease stages or do not consider the “tissue ontology” levels for the calculation of the tissue-distribution profiles. Therefore, we have developed “TissueDistributionDBs”, a repository of tissue-distribution profiles based on the expressed sequence tags (ESTs) data extracted from the UniGene database by employing “Tissue Ontology” available at BRENDA. To overcome the occurrence of the natural language variations in the EST’s source tissue-type terms, we have generated a “tissue synonym library” and standardized these tissue-type terms by cross-referencing to the controlled vocabulary for tissue-type terms available at BRENDA “Tissue Ontology”. Furthermore, we have provided a quantitative expression for genes among the tissue types at various anatomical levels by constructing “tissue slims”. Concurrently, the expression among tissue types is used for tissue-distribution calculations. The resulting output profiles can be queried by the Sequence Retrieval System (SRS) and are currently available for 20 different model organisms. We benchmarked our database system against the Swissprot database using a set of 40 different tissue types. This database system is useful for the understanding of the tissue-specific expression patterns of genes, which have implications for the identification of possible new therapeutic drug targets, in gene discovery, and in the design and analysis of micro-arrays. TissueDistributionDBs can be accessed via the World Wide Web (www) at http://genius.embnet.dkfz-heidelberg.de/menu/tissue_db/.     

Inverse colloidal crystal membranes for hydrophobic interaction membrane chromatography

A collaborative study on the robustness and portability of a capillary electrophoresis‐mass spectrometry method for peptide mapping was performed by an international team, consisting of 13 independent laboratories from academia and industry. All participants used the same batch of samples, reagents and coated capillaries to run their assays, whereas they utilized the capillary electrophoresis‐mass spectrometry equipment available in their laboratories. The equipment used varied in model, type and instrument manufacturer. Furthermore, different types of sheath‐flow capillary electrophoresis–mass spectrometry interfaces were used. Migration time, peak height and peak area of ten representative target peptides of trypsin‐digested bovine serum albumin were determined by every laboratory on two consecutive days. The data were critically evaluated to identify outliers and final values for means, repeatability (precision within a laboratory) and reproducibility (precision between laboratories) were established. For relative migration time the repeatability was between 0.05 and 0.18% RSD and the reproducibility between 0.14 and 1.3% RSD. For relative peak area repeatability and reproducibility values obtained were 3–12 and 9–29% RSD, respectively. These results demonstrate that capillary electrophoresis‐mass spectrometry is robust enough to allow a method transfer across multiple laboratories and should promote a more widespread use of peptide mapping and other capillary electrophoresis‐mass spectrometry applications in biopharmaceutical analysis and related fields.     

Missing value imputation strategies for metabolomics data

The origin of missing values can be caused by different reasons and depending on these origins missing values should be considered differently and dealt with in different ways. In this research, four methods of imputation have been compared with respect to revealing their effects on the normality and variance of data, on statistical significance and on the approximation of a suitable threshold to accept missing data as truly missing. Additionally, the effects of different strategies for controlling familywise error rate or false discovery and how they work with the different strategies for missing value imputation have been evaluated. Missing values were found to affect normality and variance of data and k‐means nearest neighbour imputation was the best method tested for restoring this. Bonferroni correction was the best method for maximizing true positives and minimizing false positives and it was observed that as low as 40% missing data could be truly missing. The range between 40 and 70% missing values was defined as a “gray area” and therefore a strategy has been proposed that provides a balance between the optimal imputation strategy that was k‐means nearest neighbor and the best approximation of positioning real zeros.     

Study of the capillary electrophoresis profile of intact α-1-acid glycoprotein isoforms as a biomarker of atherothrombosis

α-1-Acid glycoprotein (AGP) is a serum glycoprotein that presents several isoforms. Changes in the isoforms of AGP have been related to different pathological states including cardiovascular diseases (CVDs) such as acute myocardial infarction. However, to our knowledge, the role of variations of AGP isoforms as a potential biomarker of atherothrombosis has not been addressed. In this work, a preliminary study about differences in the capillary zone electrophoresis (CZE) profile of intact (non-hydrolyzed) AGP isoforms between healthy individuals and patients with atherothrombosis, specifically abdominal aortic aneurysm (AAA) and carotid atherosclerosis (CTA), has been performed. Biological samples (plasmas and sera) were analyzed by CZE after immunoaffinity chromatography purification. Up to 13 peaks corresponding to groups of isoforms of intact AGP from plasma samples were detected by CZE-UV. Electrophoretic profiles were aligned, peaks assigned, and linear discriminant analysis (LDA) of percentage of the corrected areas of AGP peaks was employed to discriminate and classify the CZE profiles of AGP samples. LDA enabled to accomplish 92.9% of correct classification of the AGP samples when the three groups of samples were considered. Besides, the LDA model showed high predictive power in the groups healthy vs. sick, healthy vs. AAA, and healthy vs. CTA. The described method was a successful approach to study the potential of AGP isoforms profile as a biomarker of atherothrombosis. To the best of our knowledge this has been the first time that a possible role of the CZE profile of intact AGP isoforms as a biomarker of vascular diseases has been demonstrated.     

Batch Fermentation Model of Propionic Acid Production by Propionibacterium acidipropionici in Different Carbon Sources

Propionic acid (PA) is widely used as additive in animal feed and also in the manufacturing of cellulose-based plastics, herbicides, and perfumes. Salts of propionic acid are used as preservative in food. PA is mainly produced by chemical synthesis. Nowadays, PA production by fermentation of low-cost industrial wastes or renewable sources has been an interesting alternative. In the present investigation, PA production by Propionibacterium acidipropionici ATCC 4965 was studied using a basal medium with sugarcane molasses (BMSM), glycerol or lactate (BML) in small batch fermentation at 30 and 36 degrees C. Bacterial growth was carried out under low dissolved oxygen concentration and without pH control. Results indicated that P. acidipropionici produced more biomass in BMSM than in other media at 30 degrees C (7.55 g l(-1)) as well as at 36 degrees C (3.71 g l(-1)). PA and biomass production were higher at 30 degrees C than at 36 degrees C in all cases studied. The best productivity was obtained by using BML (0.113 g l(-1) h(-1)), although the yielding of this metabolite was higher when using glycerol as carbon source (0.724 g g(-1)) because there was no detection of acetic acid. By the way, when using the other two carbon sources, acetic acid emerged as an undesirable by-product for further PA purification.     

Characterization of proteins from Spirulina platensis microalga using capillary electrophoresis-ion trap-mass spectrometry and capillary electrophoresis-time of flight-mass spectrometry

In this work, a new capillary electrophoresis-mass spectrometry (CE-MS) procedure is developed to analyze proteins in Spirulina platensis microalgae. It is demonstrated that a fine optimization of several separation parameters is essential in order to achieve suitable CE-MS analysis of these proteins in natural extracts from microalgae. Namely, optimization of the composition of the separation buffer, electrospray conditions, and washing routine between runs are required in order to obtain reliable and reproducible CE-MS analyses of the main proteins found in this microalga (namely, allophycocyanin-alpha chain, allophycocyanin-beta, c-phycocyanin-alpha, and c-phycocyanin-beta). The relative molecular mass of these biopolymers is determined using two different MS instruments coupled to CE, i.e., CE-ion trap-MS and CE-time of flight-MS (CE-TOF-MS). A comparison between the results obtained with both instruments is carried out. The high resolution of the TOF-MS enables the distinction of small modifications in proteins and, thus, a more accurate mass determination. Interestingly, molecular mass values obtained by both CE-MS procedures agree very well while these experimental values are only in partial agreement with those theoretically expected (i.e., genetically derived masses). Some protein modifications due to amino acids exchange induced by nucleotide codon mutations are proposed to explain this difference.     

Detection and quantitation of a bioactive compound in Vicia narbonensis L. seeds by capillary electrophoresis-mass spectrometry: a comparative study with UV detection

Capillary zone electrophoresis with mass spectrometry (CE-MS) and UV detection (CE-UV) was applied to the quantitative determination of gamma-glutamyl-S-ethenyl-cysteine (GEC), a bioactive and unstable compound present in Vicia narbonensis L. seeds. This compound is responsible for, among other negative effects, palatability reduction and grain toxicity. In order to carry out the quantitative analysis of GEC, different conditions (such as composition, concentration and pH of the background electrolyte, and type and time of extraction) were studied. Also, adequate conditions for electrospray-mass spectrometry of this bioactive compound were investigated. The best extraction conditions of GEC from V. narbonensis L. seeds flour were obtained using ethanol-water (70:30 v/v) for 45 min. The use of a 20 m ammonium hydrogen carbonate at pH 7 provided adequate analytical conditions compatible with the unstable nature of GEC as well as with the requirements of CE-UV and CE-MS analysis. A comparative study was carried out between the different figures of merit of CE-UV and CE-MS for quantitative purposes. Both techniques provided similar limit of detection and can be applied with confidence within the same linear dynamic range. However, reproducibility and speed of analysis were better using CE-UV. The developed methods were readily applied to quantify GEC in seeds of 21 genotypes of V. narbonensis L. A good agreement between CE-MS and CE-UV results was observed corroborating the usefulness of both approaches for quantitative purposes.     

Microfluidic Device for the Manipulation of Microparticles for Flow Cytometry Application

This work produces a unique microfluidic device that acts as a “lab on a chip,” conducting separation, mixing, and concentration of microparticles similar to that required by cell sorting flow cytometry applications. The passive two-dimensional device shows to be successful at separating polystyrene (PS) beads between 5 and 20 µm in diameter, mixing them with an external media, and concentrating them by 250% continuously with minimal sample preparation, while still being inexpensive, and effective. By implementing the microfluidic device, the processing steps are done within seconds due to its high throughput of 2 mL min⁻¹, wherein different hydrodynamic phenomena such as Dean's forces, inertial lift forces, and enhanced diffusion are taken advantage of.