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At least 847 records · Page 47Linked to original sources
PubMed1989

Direct separation of albendazole sulfoxide enantiomers by liquid chromatography on a chiral column deriving from (S)-N-(3,5-dinitrobenzoyl) tyrosine: application to enantiomeric assays on plasma samples.

The direct enantiomeric resolution of albendazole sulfoxide (SOABZ), an anthelmintic drug belonging to the benzimidazole class, is reported on a chiral stationary phase (CSP) synthesized by covalent binding of (S)-N-(3,5-dinitrobenzoyl)tyrosine-O-(2-propen-1-yl) methyl ester on a gamma-mercaptopropyl-silanized silica gel. A comparison with the resolution achieved on commercially available Pirkle-type CSPs obtained from N-(3,5-dinitrobenzoyl) derivatives of (R)-phenyglycine or (S)-phenylalanine is described. Some structurally related chiral sulfoxides including oxfendazole (SOFBZ) are also studied. Optimization of the mobile phase nature and composition is investigated showing that a hexane-dioxane-ethanol ternary mixture affords an almost baseline resolution (Rs = 1.25); however, in this case, albendazole sulfone (SO2ABZ) is eluted between the two sulfoxide enantiomers; accordingly, a hexane-ethanol mobile phase would be preferred for biological samples containing both metabolites. The influence of temperature on the resolution is depicted with a hexane-ethanol mobile phase. Finally, application to the enantiomeric assays of SOABZ in plasmatic extracts of rat, sheep, bovin, and man after oral administration of albendazole (sulfoxidized to SOABZ and SO2ABZ) is reported. Some distortions in the enantiomeric ratios are evidenced depending on the species.

Albendazole↗
PubMed1989

Probe size and bound label conformation in colloidal gold-ligand labels and gold-immunolabels.

Colloidal gold can be produced in sizes ranging from 1.0nm to 150nm. All sizes of gold can be conjugated, principally by hydrophobic bonding, to a variety of molecules including ligands, enzymes and antibodies, as well as lectins and polysaccharides. The activity of most of these biological molecules is retained on conjugation with gold particles irregardless of size range, although the ratio of protein surface area to gold particle surface area varies widely depending on particle and protein size. We have employed low voltage high resolution scanning electron microscopy to compare, microscopically, the shapes of biological molecules unbound, bound to very small (3nm) gold particles, and bound to larger (18nm-30nm) gold particles. When very small gold particles are conjugated to large protein molecules, several particles bind along the length of each molecule, while smaller protein molecules often wrap around a single small gold particle. With larger gold particles, several biological molecules bind to a single gold particle. In addition, the shape of protein molecules bound to larger gold particles differs from that of molecules bound to small gold particles.

Animals↗
PubMed2004

Higher harmonic generation microscopy for developmental biology.

Optical higher harmonic generation, including second harmonic generation and third harmonic generation, leaves no energy deposition to its interacted matters due to an energy-conservation characteristic, providing the "noninvasiveness" nature desirable for biological studies. Combined with its nonlinearity, higher harmonic generation microscopy provides excellent three-dimensional (3D) sectioning capability, offering new insights into the studies of embryonic morphological changes and complex developmental processes. By choosing a laser working in the biological penetration window, here we present a noninvasive in vivo light microscopy with sub-micron 3D resolution and millimeter penetration, utilizing endogenous higher harmonic generation signals in live specimens. Noninvasive imaging was performed in live zebrafish (Danio rerio) embryos. The complex developmental processes within > 1-mm-thick zebrafish embryos can be observed in vivo without any treatment. No optical damage was found even with high illumination after long-term observations and the examined embryos all developed normally at least to the larval stage. The excellent 3D resolution of the demonstrated technology allows us to capture the subtle developmental information on the cellular or sub-cellular levels occurring deep inside the live embryos and larvae. This technique can not only provide in vivo observation of the cytoarchitecture dynamics during embryogenesis with submicron resolution and millimeter penetration depth, but would also make strong impact in developmental and structural biology studies.

Animals↗
PubMed2005

Space as the final frontier in stochastic simulations of biological systems.

Recent technological and theoretical advances are only now allowing the simulation of detailed kinetic models of biological systems that reflect the stochastic movement and reactivity of individual molecules within cellular compartments. The behavior of many systems could not be properly understood without this level of resolution, opening up new perspectives of using computer simulations to accelerate biological research. We review the modeling methodology applied to stochastic spatial models, also to the attention of non-expert potential users. Modeling choices, current limitations and perspectives of improvement of current general-purpose modeling/simulation platforms for biological systems are discussed.

Animals↗
PubMed2005

Embedding of large specimens in glycol methacrylate: prerequisites for multi-signal detection and high-resolution imaging.

Acrylic resin mixtures are commonly used to study microscopic sections of biological specimens, giving the advantage of good morphological preservation. Existing embedding protocols, however, are suitable for tissue blocks, not exceeding 1 mm in thickness. We have developed a protocol to embed larger specimens (up to 2 cm(3)) in Technovit 8100. This medium allowed us to perform classic histological (trichrome), silver, as well as immunohistochemical staining, needed for multi-signal detection at high-resolution imaging to reconstruct a three-dimensional interpretation of a serially sectioned muscle. The technique was applied to reconstruct the semitendinosus muscle of a fetal pig, 44 days post conception, featuring connective tissue, intramuscular nerves, blood vessels, and muscle fibre types. For the reconstruction, a technique was used that enabled us to insert high-resolution images of histological details into low-resolution images of the entire muscle.

Animals↗
PubMed1996

Collagen fibril surface: TMAFM, FEG-SEM and freeze-etching observations.

Native, unfixed collagen fibrils from rat tail tendon were dehydrated following different procedures and observed under a FEG-SEM and an AFM operated in Tapping Mode (TMAFM). Freeze-etched, untreated fibrils from the same tissue were also observed for comparison. The most notable features of the fibril surface, i.e., the gap/overlap alternation and three prominent intraperiod ridges, were simultaneously visible only in freeze-etched specimens, while under the SEM and the TMAFM their appearance was dependent on both the dehydration procedure and the visualization technique. The different susceptibility of the collagen fibril surface structures to various treatments clearly implies the existence of domains of different composition. Moreover, identical specimens were imaged differently by SEM and TMAFM, highlighting instrument-specific advantages and limitations. The onset of dehydration-dependent, procedure-specific artifacts should be considered in high-resolution studies of connective tissues. As for any biological specimen, the final aspect of collagen fibrils is determined no less by the preliminary treatments than by the visualization approach.

Animals↗
PubMed1980

Mass spectral fragmentation of phthalic acid esters.

Phthalic acid esters are among the most frequently encountered pollutants in biological extracts. They are very often detected in biological analysis using gas chromatography. Even using high resolution glass capillary columns, the identification of some of these esters remains difficult. In this paper the mass spectral fragmentation of a large number of phthalic acid esters is presented. Some criteria for the identification of the type of isomerism on the aromatic ring and the identification of the ester functions are also presented.

Esters↗
PubMed1998

Electrophoresis combined with novel mass spectrometry techniques: powerful tools for the analysis of proteins and proteomes.

Analytical and preparative electrophoresis separation techniques have been essential tools in protein biochemistry and the biological sciences in general. The combination of high resolution electrophoresis techniques with high performance analytical procedures has dramatically enhanced analytical protein biochemistry. In this report we describe the combination of electrophoretic separation techniques with electrospray ionization (ESI) tandem mass spectrometry (MS/MS). A series of different techniques, consisting of automated high performance liquid chromatography (HPLC)-MS/MS, capillary-HPLC-MS/MS, and solid phase extraction (SPE)-capillary zone electrophoresis (CZE)-MS/MS, are described in the context of the identification of high pmol to the low fmol amounts of proteins. Application of these powerful new tools for the analysis of proteins on a large proteome-wide scale is presented. Furthermore, the combination of orthogonal separation techniques, such as immobilized metal affinity chromatography (IMAC) with SPE-CZE-MS/MS, and IMAC followed by HPLC, and by SPE-CZE-MS/MS, are presented for the detailed investigation of post-translational modifications of specific proteins.

Amino Acid Sequence↗
PubMed2005

Whole genome SNP arrays using DNA derived from formalin-fixed, paraffin-embedded ovarian tumor tissue.

Array-based genotyping platforms, such as the Affymetrix mapping array, have been validated as reliable methods for obtaining high-resolution copy number and allele status information when using DNA derived from fresh tissue sources. However, the suitability of such systems for the examination of DNA derived from formalin-fixed, paraffin-embedded (FFPE) tissues has not been tested. Therefore, we analyzed DNA derived from five matching fresh frozen and FFPE ovarian tumors for gene copy number changes and loss of heterozygosity using the Affymetrix GeneChip Human Mapping 10 K Array Xba 131. The data was analyzed using Affymetrix proprietary software, GeneChip DNA Analysis Software, and Chromosome Copy Number Tool. The average SNP call rate (rate of successful genotype identification) of the fresh samples was 89.44% (range 78.72-96.22%, median 92.72%) and was only slightly lower for the matching FFPE samples at 83.48% (range 76.93-93.17%, median 82.60%). The average concordance (rate of agreement between successful genotype calls) between the fresh and matching FFPE samples was 97.06% (range 92.70-99.41%, median 97.52%). Loss of heterozygosity (LOH) profiles of the fresh and FFPE samples were essentially identical across all chromosomes. Copy number data was also comparable, although the quantification of copy number changes appears overstated in the FFPE samples. In conclusion, we have shown that it is possible to achieve high-performance outcomes using FFPE-derived DNA in the Affymetrix 10 K mapping array. This advance will open up vast archival tissue resources to high-resolution genetic analysis and unlock a wealth of biological information.

DNA↗
PubMedDate not supplied

Characterization of transcription factors by mass spectrometry and the role of SELDI-MS.

Over the last decade, much progress has been made in the field of biological mass spectrometry, with numerous advances in technology, resolution, and affinity capture. The field of genomics has also been transformed by the sequencing and characterization of entire genomes. Some of the next challenges lie in understanding the relationship between the genome and the proteome, the protein complement of the genome, and in characterizing the regulatory processes involved in progressing from gene to functional protein. In this new age of proteomics, development of mass spectrometry methods to characterize transcription factors promises to add greatly to our understanding of regulatory networks that govern expression. However, at this time, regulatory networks of transcription factors are mostly uncharted territory. In this review, we summarize the latest advances in characterization of transcription factors by mass spectrometry including affinity capture, identification of complexes of DNA-binding proteins, structural characterization, determination of protein-DNA and protein-protein interactions, assessment of modification sites and metal binding, studies of functional activity, and the latest chip technologies that use SELDI-MS that allow the rapid capture and identification of transcription factors.

Animals↗
PubMed2004

Structure of an anti-DNA fab complexed with a non-DNA ligand provides insights into cross-reactivity and molecular mimicry.

Antibodies that recognize DNA (anti-DNA) are part of the autoimmune response underlying systemic lupus erythematosus. To better understand molecular recognition by anti-DNA antibodies, crystallographic studies have been performed using an anti-ssDNA antigen-binding fragment (Fab) known as DNA-1. The previously determined structure of a DNA-1/dT5 complex revealed that thymine bases insert into a narrow groove, and that ligand recognition primarily involves the bases of DNA. We now report the 1.75-A resolution structure of DNA-1 complexed with the biological buffer HEPES (4-(2-Hydroxyethyl)piperazine-1-ethanesulfonic acid). All three light chain complementarity-determining regions (CDRs) and HCDR3 contribute to binding. The HEPES sulfonate hydrogen bonds to His L91, Asn L50, and to the backbone of Tyr H100 and Tyr H100A. The Tyr side-chains of L32, L92, H100, and H100A form nonpolar contacts with the HEPES ethylene and piperazine groups. Comparison to the DNA-1/dT5 structure reveals that the dual recognition of dT5 and HEPES requires a 13-A movement of HCDR3. This dramatic structural change converts the combining site from a narrow groove, appropriate for the edge-on insertion of thymine bases, to one sufficiently wide to accommodate the HEPES sulfonate and piperazine. Isothermal titration calorimetry verified the association of HEPES with DNA-1 under conditions similar those used for crystallization (2 M ammonium sulfate). Interestingly, the presence of 2 M ammonium sulfate increases the affinities of DNA-1 for both HEPES and dT5, suggesting that non-polar Fab-ligand interactions are important for molecular recognition in highly ionic solvent conditions. The structural and thermodynamic data suggest a molecular mimicry mechanism based on structural plasticity and hydrophobic interactions.

Antibodies, Antinuclear↗
PubMedDate not supplied

Patch-clamp capacitance measurements: new insights into the endocytic uptake of transferrin.

Since its introduction by Neher and Sakmann in 1976 the patch-clamp technique has been extensively used to study processes such as signalling and synaptic transmission, but also for monitoring endo- and exocytosis. Since biological membranes behave like electrical capacitors high-resolution measurements of membrane capacitance allow detection of small changes in membrane surface area that accompany exocytosis and endocytosis. We here describe our recent work on patch-clamp capacitance measurements in stably transfected HeLa cells expressing HFE, the hereditary hemochromatosis gene product, under the control of a tetracycline-sensitive promotor. By means of whole-cell and cell-attached techniques we were able to reveal transferrin-induced decreases in membrane capacitance reflecting increased endocytosis at the single cell level. Moreover, cell-attached recordings revealed significant alterations in the formation of single endocytic vesicles. Time-resolved measurements of cell membrane capacitance provide a new methodological approach to study the endocytic uptake of transferrin and its regulation by HFE, the hereditary hemochromatosis protein.

Cytoplasmic Vesicles↗
PubMedDate not supplied

Peptide analysis by rapid, orthogonal technologies with high separation selectivities and sensitivities.

This article examines the current status of peptide analysis by orthogonal micro-/nano-separation strategies, with emphasis on the complementary use of high performance capillary liquid chromatography (micro-HPLC), capillary zonal electrophoresis (HPCZE), open tubular capillary electrochromatography (ot -CEC) and packed capillary electrochromatography (p -CEC). The ability to interface these techniques with mass spectroscopic (MS) procedures has enabled substantial progress to be made in the analysis of very small quantities of peptides, as well as proteins and other bio-macromolecules. As a consequence, the staged application of these high resolution techniques as part of the standardisation of biological products via robust, sensitive protocols is rapidly becoming a reality. Recent conceptual and theoretical advances have also allowed improved levels of prediction and optimisation of these procedures. Since significant differences in selectivity can be achieved with micro-HPLC, HPCZE and HPCEC respectively, collectively these sophisticated techniques provide unprecedented opportunities for the rapid, orthogonal and sensitive separation of complex mixtures of peptides and proteins. Several advantages of using these technologies in tandem are highlighted.

Chromatography, High Pressure Liquid↗
PubMed1999

Identification of a locus on distal mouse chromosome 12 that controls resistance to tumor necrosis factor-induced lethal shock.

Administration of recombinant murine tumor necrosis factor (TNF) to mice results in lethal shock, characterized by hypotension, hypothermia, and dramatic induction of cytokines released in the circulation, such as interleukin-6 (IL-6). The sensitivity of mice to the effects of murine TNF varies from strain to strain. DBA/2 mice were found to be considerably more resistant to TNF than C57BL/6 mice. The resistance proved to be dominant since (C57BL/6 x DBA/2)F1 mice were also resistant. Using BXD recombinant inbred mice and a dose of TNF lethal for C57BL/6 but not for DBA/2 mice, we found that the resistance to TNF links to loci coding for corticosteroid-binding globulin (Cbg), alpha1-protease inhibitor (Spi1), contrapsin (Spi2) and the contrapsin-regulating gene Spi2r that form a gene cluster on chromosome 12. Quantitative trait-loci analysis of TNF-induced induction of IL-6 and of hypothermia also points to the importance of this locus (P < 0.0002 and P = 0.017, respectively), more particularly the Cbg and Spi2 loci, in the resistance to TNF. We propose to name the locus "TNF protection locus." The data suggest that endogenous protease inhibitors and/or glucocorticoids play a significant role in the attenuation of TNF-induced lethal shock. This study also demonstrates that loci affecting important biological responses can be identified with very high resolution using recombinant inbred mice.

Animals↗
PubMed1992

Polychlorinated biphenyls in the environment.

This review surveys the problems arising from the release of PCBs into the environment from the point of view of the analytical chemist. These problems are very complex and interdependent and so it is essential to recognize their mutual links rather than to separate one problem from another (sources of contamination, fate in the environment, toxic properties and particular capabilities, limitations and purposes of analytical methods). Prominent attention should be paid in the future to congener-specific analyses of "toxic" congeners using high-resolution gas chromatography and to toxicity-assessing biological methods.

Animals↗
PubMed1994

Rapid, high-resolution high-performance liquid chromatographic analysis of antibiotics.

A HPLC column devised for high separation speed combined with highly practical operating features has been found useful for separating antibiotics. Important characteristics involved compromises in packing particle size, column configuration and support-stationary phase combinations. We determined that these columns are useful for rapid, high-resolution separations with unmodified state-of-the-art HPLC equipment without the extra-column band-broadening effects typical of so-called "fast" HPLC columns. The proposed columns feature efficient sterically-protected monofunctional silane stationary phases that provide good separation reproducibility and high column stability. The combination of these unique bonded silanes and a highly purified, less-acidic silica support give superior peak shapes for antibiotic compounds. The proposed column configuration can halve separation times and double peak heights without loss in resolution, compared to widely used analytical columns. Increased mobile phase flow-rates permit even faster separations of antibiotics with only modest loss in resolution and peak heights for trace analyses in biological systems.

Animals↗
PubMed1995

Cloning and applications of the two/three-base restriction endonuclease R.CviJI from IL-3A virus-infected Chlorella.

The gene (cviJIR) encoding the two/three-base R.CviJI eukaryotic restriction endonuclease (ENase) from IL-3A virus-infected Chlorella was cloned into Escherichia coli. A high frequency of DNA cleavage by R.CviJI required overexpression of the gene encoding the M.CviJI methyltransferase prior to cloning the gene for the ENase. Both genes were sequenced and their organization was determined to be in head-to-tail order. The open reading frame coding for R.CviJI can potentially translate a 41.4-kDa protein; however, in the E. coli host, a truncated version of the enzyme is produced (32.5 kDa). The recombinant ENase does not exhibit ATP-induced 'star' activity (R.CviJI cleaves at RGCY, while R.CviJI* also cleaves at RGCR and YGCY, but not at YGCR), as is characteristic for native R.CviJI. The very high frequency of DNA cleavage by R.CviJI* was exploited in the development of a quasi-random shotgun library method. R.CviJI*-generated oligodeoxyribonucleotides were applied to improve certain molecular biology applications, i.e., DNA labeling, detection, high-resolution restriction mapping, amplification and epitope mapping.

Amino Acid Sequence↗
PubMed2004

Inkjet printing for high-throughput cell patterning.

The adaptation of inkjet printing technology to the complex fields of tissue engineering and biomaterial development presents the potential to increase progress in these emerging technologies through the implementation of this high-throughput capability via automated processes to enable precise control and repeatability. In this paper, a method of applying high-throughput inkjet printing to control cellular attachment and proliferation by precise, automated deposition of collagen is presented. The results indicate that commercial inkjet printing technology can be used to create viable cellular patterns with a resolution of 350 microm through the deposition of biologically active proteins. This method demonstrates a combination of off-the-shelf inkjet printing and biomaterials and has potential to be adapted to tissue engineering and colony patterning applications. Adapting this method into the three-dimensional construction of cellular structures for eventual high-throughput tissue engineering using a bottom-up approach is possible.

Animals↗