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At least 1,153 records · Page 64Linked to original sources

PubMed2000

Mohs surgery and processing: novel optimizations and enhancements.

OBJECTIVE: Simple yet effective modifications to Mohs surgery and processing may enhance procedural efficiency, ensure proper tissue orientation and tracking, while greatly reducing "recuts." Using the methods described, Mohs specimens no longer need to be incised or excised with any bevel, thus conserving tissue and facilitating closure. METHODS: A streamlined Mohs surgical tray is convertible to a closure tray within seconds. The excised tissue specimen is oriented on a sterile paper square on a reusable sterilized aluminum palette where partial thickness circumferential and radial scalpel cross-hatching allows epidermal edges complete freedom to later adhere to a flattening glass. The sterile paper can be labeled with patient name, stage number, and chuck number; then the specimen is inked. Rapid chuck freezing in a specially positioned liquid nitrogen immersion is followed by OCT (embedding compound) application. Uniquely numbered and modified cryostat chucks eliminate the possibility of OCT-chuck disunion. Rapid liquid nitrogen immersion of a glass surface allows the inked, cross-hatched specimen's epidermal edges and base to lay perfectly flat once forced against the supercooled glass surface using a special polymer glove. Inversion of the specimen-containing glass onto a frozen and gel state OCT interface of the chuck completes the embedding. RESULTS/CONCLUSION: These reproducible approaches to Mohs surgery described herein utilize multiple modifications that enhance the speed, efficiency, and reproducibility of Mohs specimen embedding, specimen preparation, while maintaining accuracy of interpretation.

Humans↗

PubMed2005

Crystal structure of the NAD biosynthetic enzyme quinolinate synthase.

A gene encoding a quinolinate synthase has been identified in the hyperthermophilic archaeon Pyrococcus horikoshii via genome sequencing. The gene was overexpressed in Escherichia coli, and the crystal structure of the produced enzyme was determined to 2.0 A resolution in the presence of malate, a substrate analogue. The overall structure exhibits a unique triangular architecture composed of a 3-fold repeat of three-layer (alphabetaalpha) sandwich folding. Although some aspects of the fold homologous to the each domain have been observed previously, the overall structure of quinolinate synthase shows no similarity to any known protein structure. The three analogous domains are related to a pseudo-3-fold symmetry. The active site is located at the interface of the three domains and is centered on the pseudo-3-fold axis. The malate molecule is tightly held near the bottom of the active site cavity. The model of the catalytic state during the first condensation step of the quinolinate synthase reaction indicates that the elimination of inorganic phosphate from dihydroxyacetone phosphate may precede the condensation reaction.

Archaeal Proteins↗

PubMed2025

Target and biomarker exploration portal for drug discovery.

MOTIVATION: The discovery of novel drug targets and precision biomarkers remains a major challenge in drug development, with traditional differential expression analysis often overlooking key regulatory proteins. Here, we present a novel, web-based bioinformatics tool, the Target and Biomarker Exploration Portal (TBEP), designed to accelerate the drug discovery process by integrating large-scale biomedical data with network analysis techniques. RESULTS: TBEP harnesses machine-learning approaches to mine and combine multimodal datasets, including human genetics, functional genomics, and protein-protein interaction networks, to decode causal disease mechanisms and uncover novel therapeutic targets and precision biomarkers for specific phenotypes. A unique feature of the tool is its ability to process large-scale data in real-time, facilitated by an efficient cloud-based architecture. Additionally, the tool incorporates an integrated large language model (LLM), which assists researchers in exploring and interpreting complex biological relationships within the generated networks and multi-omics data using natural language (English). By offering an intuitive, interactive interface, the LLM enhances the exploration of biological insights, making it easier for scientists to derive actionable conclusions. This powerful integration of network analysis, multi-omics data, and LLM provides a robust framework for accelerating the identification of novel drug targets. AVAILABILITY AND IMPLEMENTATION: The tool is publicly available at https://tbep.missouri.edu. The source code, documentation and installation instructions are available at GitHub repository: https://github.com/mizzoudbl/tbep.

Drug Discovery↗

PubMed1995

Transplanting a unique allosteric effect from crocodile into human haemoglobin.

Crocodiles are able to remain under water for more than one hour without surfacing to breathe and often kill their prey by drowning it. How do crocodiles stay under water for a long time? When they hold their breath, bicarbonate ions, the final product of respiration, accumulate and drastically reduce the oxygen affinity of haemoglobin, releasing a large fraction of haemoglobin-bound oxygen into the tissues. We have now located the bicarbonate-ion-binding site at the alpha 1 beta 2-subunit interface by making various human-crocodile chimaeric haemoglobins. Furthermore, we have been able to transplant the bicarbonate effect into human haemoglobin by replacing only a few residues, even though the amino-acid sequence identity between crocodile (Crocodylus niloticus) and human haemoglobins is only 68% for the alpha- and 51% for the beta-subunit. These results indicate that an entirely new function which enables species to adapt to a new environment could evolve in a protein by a relatively small number of amino-acid substitutions in key positions.

Alligators and Crocodiles↗

PubMed2003

Immediate loading of dental implants in the edentulous maxilla: case study of a unique protocol.

Although immediate loading of dental implants is increasingly gaining recognition as an important option for certain categories of implant patients, the maxillary arch has historically posed difficulties that have limited the number of immediate loading applications. To address the needs of patients who cannot tolerate maxillary removable complete dentures, an immediate loading protocol we call "Teeth in a Day" uses a conversion prosthesis that has been expanded to include complete-arch maxillary reconstruction. Use of a large number of implants to prevent micromotion at the bone-to-implant interface is a critical element in this protocol. A patient treatment is reported.

Clinical Protocols↗

PubMedDate not supplied

Matching pulmonary structure and perfusion via combined dynamic multislice CT and thin-slice high-resolution CT.

Taking advantage of two scan modes of an electron beam CT scanner (Imatron), we have developed a method utilizing x-ray CT for relating pulmonary perfusion to global and regional anatomy. A high temporal resolution mode, used to follow bolus contrast agent, is combined with a high spatial resolution mode to obtain the structure-function fusion. A software module has been developed for our image analysis package (VIDA) to automatically calculate physiologic parameters of flow and integrate these color coded functional measurements into a corresponding high spatial resolution data set. We present the scanning methodology details and give examples from our physiologic based research to demonstrate strengths of combining dynamic and high resolution CT to uniquely characterize pulmonary normal and pathophysiology.

Algorithms↗

PubMed2001

Virtual endoscopy.

Virtual endoscopy is a technique in which three-dimensional viewing of hollow structures is conducted through the utilization of high-resolution imaging and unique computer processing methods. The basic components of this technique and its applications for urology and other clinical disciplines are reviewed.

Bronchoscopy↗

PubMed1984

Characterization of the association of Electrophorus electricus acetylcholinesterase with sphingomyelin liposomes. Relevance to collagen-sphingomyelin interactions.

Electrophorus electricus acetylcholinesterase is a large polymorphic enzyme. Its native forms 18 S, 14 S and 8.5 S possess a tail having a collagen-like structure. It was suggested that this tail is involved in the anchorage of the enzyme at the terminal of the synapse. Watkins et al. [1] showed that all forms of the enzyme having a collagen segment also bind to sphingomyelin liposomes with almost no binding to phosphatidylcholine (PC) liposomes. In agreement with the above results, the binding of acetylcholinesterase reported here was independent of the following liposomal parameters (a) curvature, (b) the physical state of the bilayer, (c) the gel to liquid crystalline phase transition of sphingomyelin, (d) stereospecificity of the sphingomyelin, (e) acyl chain of the sphingomyelin. The binding was reduced with increasing PC content in sphingomyelin vesicles. The binding has no effect on the bilayer integrity. The enzymatic activity can be released from the vesicles by incubation with collagenase. The association of the enzyme with the liposomes had minimal effect on its kinetic parameters (Km, Vmax). The only detectable effect was increasing enzyme stability at low enzyme concentration. This suggested that the binding of the enzyme to sphingomyelin liposomes reduced its surface denaturation. Such association was not unique to acetylcholinesterase since collagen showed similar behavior. Collagen binding to sphingomyelin liposomes was 5-10-times larger than to PC liposomes. The exact details of the interaction of collagen and collagen-like peptides with sphingomyelin bilayers are yet unknown although it differs from the well documented hydrophobic or electrostatic interactions [7]. This work proposes hydrogen bonding as a third mechanism which involves the interface region of sphingolipids molecules and the collagen or collagen-like tail of acetylcholinesterase. This binding is also of interest due to its correlation to the accumulation of sphingomyelin and collagen during aging and the development of atherosclerosis in blood vessels of mammals.

Acetylcholinesterase↗

PubMed2000

NF-kappaB p65 (RelA) homodimer uses distinct mechanisms to recognize DNA targets.

BACKGROUND: The NF-kappaB family of dimeric transcription factors regulates the expression of several genes by binding to a variety of related DNA sequences. One of these dimers, p65(RelA), regulates a subclass of these targets. We have shown previously that p65 binds to the 5'-GGAA T TTTC-3' sequence asymmetrically. In that complex one subunit base specifically interacts with the preferred 5' half site and the other subunit binds non-specifically to the 3' half site. RESULTS: Here we describe the crystal structures of two new p65-DNA complexes. One complex contains a pseudosymmetric 5'-GGAA T TTCC-3' DNA sequence taken from the enhancer of the gene encoding interleukin 8 (IL-8) and the other contains the asymmetric 5'-GGAA T TCCC-3' target DNA taken from the enhancer of the gene encoding type VII collagen. As expected, the global positioning of the dimer on both DNA targets is roughly symmetric, however, the hydrogen-bonding patterns at the protein-DNA interfaces differ significantly. One of the p65 monomers in complex with the asymmetric DNA binds to an extra base pair located immediately upstream of the 5'-GGAA-3' half site. We also show that p65 binds to these targets with almost equal affinity and that different residues have variable roles in binding different kappaB targets. CONCLUSIONS: Taken together, these structures reveal that p65 exhibits the unique capability to specifically bind DNA targets of variable lengths from four to ten base pairs. Also, the small protein segment Arg41-Ser42-Ala43 is at least partially responsible for flexibility in DNA-binding modes.

Amino Acid Sequence↗

PubMed2005

Molecular dynamics simulation of swollen membrane of perfluorinated ionomer.

Molecular dynamics simulations of the swollen membrane of perfluorinated ionomer, which is composed of poly(tetrafluoroethylene) backbones and perfluosulfonic pendant side chains, have been undertaken to analyze the static and dynamic properties of the water and the side chain in the membrane. The calculations were carried out for four different water contents, 5, 10, 20 and 40 wt %, at 358.15 K and 0.1 MPa. The results are summarized as follows: (1) The sulfonic acid is the unique site to which water molecules can bind, and the other sites in the pendant side chain have no bound water even at high water concentration. (2) Sulfonic acids aggregate in the short range within 4.6-7.7 A despite the electrostatic repulsion between them. In such aggregates, a water molecule bridges two sulfonic acids. (3) Pendant side chains prefer to orient perpendicular to the hydrophilic/hydrophobic interface, and long-range correlation of side chain orientations is observed at 20 and 40 wt % water uptake membranes. (4) In a low water uptake membrane, the dynamics of water is substantially restricted due to strong attractive interactions with acidic sites. In contrast, at high water content, even the water locating near the sulfonic acid is relatively mobile. The short residence time of the bound water reveals that such water can frequently exchange position with relatively free water, which locates in the center of water cluster, in highly swollen membranes.

Journal Article↗

PubMed2004

The use of surface tension to predict the formation of 2D arrays of latex spheres formed via the Langmuir-Blodgett-like technique.

Highly ordered hexagonal arrays of latex spheres on highly ordered pyrolytic graphite (HOPG) have been prepared from a Langmuir-Blodgett-like (LB-like) technique using both polymers and surfactants as spreading agents. The role of spreading agent concentration in forming a well-ordered, stable monolayer at the air-liquid interface was studied by means of atomic force microscopy, scanning electron microscopy, optical microscopy, and surface tension measurements for three different systems: a nonionic surfactant, octylphenoxy poly(ethyleneoxy)ethanol (Igepal CO 630); an anionic surfactant, sodium dodecyl sulfate; and a low-molecular-weight, water-soluble polymer, polyacrylamide. For both the anionic surfactant and the water soluble polymer, a correlation was found between a unique feature in surface tension measurements of the latex-spreading agent mixture and the concentrations at which hexagonal arrays of latex spheres form on the surface of HOPG. For the nonionic surfactant, no ordered structures were found on HOPG for any surfactant concentration, consistent with no appearance of the unique feature in surface tension measurements. These results show that a tensiometer can be used to determine the conditions under which well-ordered latex films have the possibility of forming on a substrate using the LB-like technique; however, other factors, such as pulling speed and surface chemistry, play a role as well.

Acrylic Resins↗

PubMed1999

The structure of the human betaII-tryptase tetramer: fo(u)r better or worse.

Tryptases, the predominant serine proteinases of human mast cells, have recently been implicated as mediators in the pathogenesis of allergic and inflammatory conditions, most notably asthma. Their distinguishing features, their activity as a heparin-stabilized tetramer and resistance to most proteinaceous inhibitors, are perfectly explained by the 3-A crystal structure of human betaII-tryptase in complex with 4-amidinophenylpyruvic acid. The tetramer consists of four quasiequivalent monomers arranged in a flat frame-like structure. The active centers are directed toward a central pore whose narrow openings of approximately 40 A x 15 A govern the interaction with macromolecular substrates and inhibitors. The tryptase monomer exhibits the overall fold of trypsin-like serine proteinases but differs considerably in the conformation of six surface loops arranged around the active site. These loops border and shape the active site cleft to a large extent and form all contacts with neighboring monomers via two distinct interfaces. The smaller of these interfaces, which is exclusively hydrophobic, can be stabilized by the binding of heparin chains to elongated patches of positively charged residues on adjacent monomers or, alternatively, by high salt concentrations in vitro. On tetramer dissociation, the monomers are likely to undergo transformation into a zymogen-like conformation that is favored and stabilized by intramonomer interactions. The structure thus provides an improved understanding of the unique properties of the biologically active tryptase tetramer in solution and will be an incentive for the rational design of mono- and multifunctional tryptase inhibitors.

Amino Acid Sequence↗

PubMed2005

Structural mechanism governing the quaternary organization of monocot mannose-binding lectin revealed by the novel monomeric structure of an orchid lectin.

Two isoforms of an antifungal protein, gastrodianin, were isolated from two subspecies of the orchid Gastrodia elata, belonging to the protein superfamily of monocot mannose-specific lectins. In the context that all available structures in this superfamily are oligomers so far, the crystal structures of the orchid lectins, both at 2.0 A, revealed a novel monomeric structure. It resulted from the rearrangement of the C-terminal peptide inclusive of the 12th beta-strand, which changes from the "C-terminal exchange" into a "C-terminal self-assembly" mode. Thus, the overall tertiary scaffold is stabilized with an intramolecular beta-sheet instead of the hybrid observed on subunit/subunit interface in all known homologous dimeric or tetrameric lectins. In contrast to the constrained extended conformation with a cis peptide bond between residues 98 and 99 commonly occurring in oligomers, a beta-hairpin forms from position 97 to 101 with a normal trans peptide bond at the corresponding site in gastrodianin, which determines the topology of the C-terminal peptide and thereby its unique fold pattern. Sequence and structure comparison shows that residue replacement and insertion at the position where the beta-hairpin occurs in association with cis-trans inter-conversion of the specific peptide bond (97-98) are possibly responsible for such a radical structure switch between monomers and oligomers. Moreover, this seems to be a common melody controlling the quaternary states among bulb lectins through studies on sequence alignment. The observations revealed a structural mechanism by which the quaternary organization of monocot mannose binding lectins could be governed. The mutation experiment performed on maltose-binding protein-gastrodianin fusion protein followed by a few biochemical detections provides direct evidence to support this conclusion. Potential carbohydrate recognition sites and biological implications of the orchid lectin based on its monomeric state are also discussed in this paper.

Amino Acid Sequence↗

PubMed2004

ERGDB: Estrogen Responsive Genes Database.

ERGDB is an integrated knowledge database dedicated to genes responsive to estrogen. Genes included in ERGDB are those whose expression levels are experimentally proven to be either up-regulated or down-regulated by estrogen. Genes included are identified based on publications from the PubMed database and each record has been manually examined, evaluated and selected for inclusion by biologists. ERGDB aims to be a unified gateway to store, search, retrieve and update information about estrogen responsive genes. Each record contains links to relevant databases, such as GenBank, LocusLink, Refseq, PubMed and ATCC. The unique feature of ERGDB is that it contains information on the dependence of gene reactions on experimental conditions. In addition to basic information about the genes, information for each record includes gene functional description, experimental methods used, tissue or cell type, gene reaction, estrogen exposure time and the summary of putative estrogen response elements if the gene's promoter sequence was available. Through a web interface at http://sdmc.i2r.a-star.edu.sg/ergdb/ cgi-bin/explore.pl users can either browse or query ERGDB. Access is free for academic and non-profit users.

Animals↗

PubMed1998

[Structural, dynamic and interaction studies of proteins: the example of immunology].

The three-dimensional structure of a protein or of one of its functional domains cannot be predicted simply from the amino-acid sequence. It has to be determined either in the crystal, generally by X-ray diffraction, or in solution by high resolution NMR, or it can be modelled by comparison with a highly homologous protein. It cannot be represented simply by an average set of atomic coordinates. The dynamics of the molecule is part of its definition. The relative role of the structure and of the local and segmental mobility will be illustrated for recognition processes, mainly in immunological reactions. A unique conformational domain, member of the immunoglobulin superfamily, recognises differently its partners for an antigen-antibody reaction or for a cell adhesion process involving immunological determinants such as CD2 or CD4. Similar structural domains can be observed for completely different amino acid sequences, with the same type of dynamical properties, e.g. in neocarzinostatin. Restrained mobility of CDR loops and water molecules participation at the interface can explain the rapid binding of the ligands in AG/AB reactions, but cellular adhesion involves more hydrophobic and rigid interactions. This difference can be related to evolutionary aspects. Recognition mechanisms in cellular immunology, e.g. that of an intracellular foreign viral protein by a T lymphocyte cell, involve rather different biochemical processes in the so-called "peptidic self" model including proteolysis and cell surface presentation of the resulting peptides by MHC Class I proteins. These complexes are then recognised by the T cell receptors. The binding site of the TCR alpha and beta chains are structurally related to the antigen binding site of immunoglobulins. The peptide is anchored at both C- and N-terminals and should possess a restrained mobility. Recognition is thus a similar structural and dynamical process as in AG/AB reactions but is more secure due to the larger number of epitopes for a single protein.

Antigen-Antibody Reactions↗

PubMed2004

Three-dimensional structure of the intact Thermus thermophilus H+-ATPase/synthase by electron microscopy.

ATPases are unique rotary motors that are essential to all living organisms because of their role in energy interconversion. A three-dimensional reconstruction of the intact H+-ATPase/synthase from Thermus thermophilus has revealed the presence of two interconnected peripheral stalks, a well-defined central stalk, and a hexagonally shaped hydrophobic domain. The peripheral stalks are each attached to the water soluble sector at a noncatalytic subunit interface and extend down toward the membrane where they interact with a strong elongated tube of density that runs parallel to the membrane and connects the two stalks. The central stalk is well resolved, especially with respect to its interaction with a single catalytic subunit giving rise to an asymmetry comparable to that identified in F-ATPases. The hexagonal shape of the membrane domain might suggest the presence of 12 proteolipids arranged as dimers, analogous to the proposed arrangement in the related eukaryotic V-ATPases.

Animals↗

PubMed2002

Multiple developmental roles of Ahnak are suggested by localization to sites of placentation and neural plate fusion in the mouse conceptus.

Ahnak is a gigantic (700 kD) phosphoprotein with a unique structure whose expression and cellular localization are dynamically regulated during cell cycle progression. Here, we report that Ahnak is localized to sites of major morphogenesis during mouse placentation and neurulation. Ahnak was found in: (i) derivatives of trophectoderm, including chorionic ectoderm prior to and during union with the ectoplacental cone, presumptive syncytiotrophoblast cells in the chorionic labyrinth, and giant cells at the trophoblast-uterine interface; (ii) the allantois prior to, during, and after union with the chorion; and (iii) the tips of the neural plate during formation of the neural tube. On the basis of these observations, we suggest that Ahnak may play heretofore unrecognized roles in tissue union during normal mouse development.

Animals↗

PubMed2002

Multiple developmental roles of Ahnak are suggested by localization to sites of placentation and neural plate fusion in the mouse conceptus.

Allantois↗