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At least 1,207 records · Page 67Linked to original sources

PubMed2004

AANT: the Amino Acid-Nucleotide Interaction Database.

We have created an Amino Acid-Nucleotide Interaction Database (AANT; http://aant.icmb.utexas. edu/) that categorizes all amino acid-nucleotide interactions from experimentally determined protein-nucleic acid structures, and provides users with a graphic interface for visualizing these interactions in aggregate. AANT accomplishes this by extracting individual amino acid-nucleotide interactions from structures in the Protein Data Bank, combining and superimposing these interactions into multiple structure files (e.g. 20 amino acids x 5 nucleotides) and grouping structurally similar interactions into more readily identifiable clusters. Using the Chime web browser plug-in, users can view 3D representations of the superimpositions and clusters. The unique collection and representation of data on amino acid-nucleotide interactions facilitates understanding the specificity of protein-nucleic acid interactions at a more fundamental level, and allows comparison of otherwise extremely disparate sets of structures. Moreover, by modularly representing the fundamental interactions that govern binding specificity it may prove possible to better engineer nucleic acid binding proteins.

Amino Acids↗

PubMed2001

Functional metabolic characteristics of intact pig livers during prolonged extracorporeal perfusion: potential for a unique biological liver-assist device.

BACKGROUND: The clinical development of liver-support devices based on perfusion of either pig hepatocytes cartridges or whole pig livers has been hampered by the ability to use sufficient liver cell mass to provide adequate metabolic support, limited perfusion times, and the potential for patient exposure to pig zoonotic diseases. METHODS: We designed an original system in which an isolated intact pig liver was perfused extracorporeally under physiological conditions in a closed loop circuit with allogeneic pig blood and constant monitoring of major physiological and functional parameters. The perfusion circuit further included an interface membrane to provide for separation of patient and liver perfusion circulation. RESULTS: Prolonged (6-21 hr) liver perfusion did not produce significant liver damage as reflected by modest rises in the levels of the serum transaminases, stability of main biochemical parameters (including potassium), and the maintenance of normal cellular morphology. Optimal liver function was documented as measured by lactate consumption, control of glycemia, and the results of clotting studies and functional assays. The perfused liver cleared 82% and 79% of peak bilirubin and ammonia concentrations with clearing kinetics identical throughout perfusion. Indocyanine green clearance was identical to that observed in the living donor before explant surgery. CONCLUSIONS: In conclusion, the extracorporeal pig liver perfusion apparatus described here allows optimal pig liver function for prolonged periods of time. The microporous membrane to provide separation of donor organ and recipient and the high level of functional activity suggest that this form of liver metabolic support may have important clinical applications.

Ammonia↗

PubMed1999

Innovative ambulatory drug delivery system using an electrolytic hydrogel infusion pump.

This report describes an ambulatory infusion device developed to provide parenteral drug delivery at a precisely controlled rate. The device is based on the innovative and unique concept of utilizing electrohydrolysis of a negatively charged hydrogel. The system consists of two modules: a pump unit and an electronic control unit. The pump module, which can be a disposable unit, contains medication separated by a flexible membrane from a gas generating chamber; this latter is an electrolytic cell comprising a hydrogel block and two platinum electrodes. The microcontroller-based control module is constructed with a user interface which includes input keys and a liquid crystal display, as well as a control to alter driving current level, depending on the infusion rate required. A microprocessor instantaneously calculates the current level required; this is based on operator-selected infusion rate, ambient pressure, and temperature sensor output. The accuracy and precision of the device were verified for all flow rates and for different environmental conditions; in vitro test results showed acceptable accuracy with less than +/- 5% error over the whole operating range of 0.1-100 [ml/h]. The device is small, lightweight, simple and easy to manufacture, and is also designed to be comfortably and conveniently worn by patients. It can be used for a variety of regimens including, for example, chemotherapy, insulin delivery, and pain management, antibiotic and AIDS therapy.

Ambulatory Care↗

PubMed2005

Differential activation profiles of multiple transcription factors during dendritic cell maturation.

Immature dendritic cells (DC) at the environmental interfaces, such as the skin, constantly survey the tissue for the emergence of microbial products and pro-inflammatory mediators. Upon recognition of such "danger" signals, they undergo dynamic reprogramming of gene expression and functions, the process known as DC maturation, which plays critical roles in both innate and adaptive immune responses. Although DC have been shown to discriminate different maturation stimuli by expressing stimulus-specific signature genes and unique phenotypic and functional properties, underlying mechanisms for this extraordinary plasticity remain relatively unclear. We hypothesized that DC might activate unique sets of transcription factors (TF) upon sensing different stimuli. To test this hypothesis, we transduced a mouse epidermal-derived DC line XS106 to express the luciferase reporter gene under the control of each of 15 different cis-enhancer elements. The resulting DC panels were then exposed to 14 different microbial, endogenous, environmental, and pharmacological agents that produced unique maturational changes. This approach allowed systematic determination of TF activation profiles in DC. Our results revealed striking diversity, with different classes of stimuli triggering preferential activation of distinct sets of TF. We propose that differential TF usage represents a previously unrecognized mechanism regulating the direction of DC maturation.

Animals↗

PubMed1985

Histochemical studies on pseudocysts in adenoid cystic carcinoma of the human salivary gland.

Pseudocysts are unique structures found in adenoid cystic carcinomata of human salivary glands. They were studied in 13 such cases by histochemical and immunohistochemical means. The pseudocysts contained an abundance of mucoid materials which reacted strongly with both Alcian Blue and dialysed iron ferrocyanide. The mucoid material was digested with chondroitinase ABC and heparitinase, but was resistant to Streptomyces hyaluronidase. The inner surfaces of the pseudocysts were strongly reactive for laminin, whereas the interface between the tumour cell nests and the outer stromal area was intensely reactive for fibronectin. Numerous fibronectin-reactive fibrils and blood coagulation factor XIII (F-XIII)-positive cells were distributed extensively in the outer stromal area. The F-XIII-positive cells were also found within some pseudocysts. The results obtained in the present study have shown that the pseudocysts represent a peculiar structure consisting of basement membrane components; laminin, fibronectin, heparan sulphate and chondroitin sulphate.

Adolescent↗

PubMed2003

A novel mechanism of pore formation: membrane penetration by the N-terminal amphipathic region of equinatoxin.

Equinatoxin II is a representative of actinoporins, eukaryotic pore-forming toxins from sea anemones. It creates pores in natural and artificial lipid membranes by an association of three or four monomers. Cysteine-scanning mutagenesis was used to study the structure of the N terminus, which is proposed to be crucial in transmembrane pore formation. We provide data for two steps of pore formation: a lipid-bound monomeric intermediate state and a final oligomeric pore. Results show that residues 10-28 are organized as an alpha-helix in both steps. In the first step, the whole region is transferred to a lipid-water interface, laying flat on the membrane. In the pore-forming state, the hydrophilic side of the amphipathic helix lines the pore lumen. The pore has a restriction around Asp-10, according to the permeabilization ratio of ions flowing through pores formed by chemically modified mutants. A general model was introduced to derive the tilt angle of the helix from the ion current data. This study reveals that actinoporins use a unique single helix insertion mechanism for pore formation.

Amino Acid Sequence↗

PubMed1999

Crystal structure of human mitochondrial NAD(P)(+)-dependent malic enzyme: a new class of oxidative decarboxylases.

Background: Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate and CO(2) with the concomitant reduction of NAD(P)(+) to NAD(P)H. They are widely distributed in nature and have important biological functions. Human mitochondrial NAD(P)(+)-dependent malic enzyme (mNAD-ME) may have a crucial role in the metabolism of glutamine for energy production in rapidly dividing cells and tumors. Moreover, this isoform is unique among malic enzymes in that it is a cooperative enzyme, and its activity is controlled allosterically. Results: The crystal structure of human mNAD-ME has been determined at 2.5 Å resolution by the selenomethionyl multiwavelength anomalous diffraction method and refined to 2.1 Å resolution. The structure of the monomer can be divided into four domains; the active site of the enzyme is located in a deep cleft at the interface between three of the domains. Three acidic residues (Glu255, Asp256 and Asp279) were identified as ligands for the divalent cation that is required for catalysis by malic enzymes. Conclusions: The structure reveals that malic enzymes belong to a new class of oxidative decarboxylases. The tetramer of the enzyme appears to be a dimer of dimers. The active site of each monomer is located far from the tetramer interface. The structure also shows the binding of a second NAD(+) molecule in a pocket 35 Å away from the active site. The natural ligand for this second binding site may be ATP, an allosteric inhibitor of the enzyme.

Journal Article↗

PubMed1999

Crystal structure of human mitochondrial NAD(P)+-dependent malic enzyme: a new class of oxidative decarboxylases.

BACKGROUND: Malic enzymes catalyze the oxidative decarboxylation of malate to pyruvate and CO2 with the concomitant reduction of NAD(P)+ to NAD(P)H. They are widely distributed in nature and have important biological functions. Human mitochondrial NAD(P)+-dependent malic enzyme (mNAD-ME) may have a crucial role in the metabolism of glutamine for energy production in rapidly dividing cells and tumors. Moreover, this isoform is unique among malic enzymes in that it is a cooperative enzyme, and its activity is controlled allosterically. RESULTS: The crystal structure of human mNAD-ME has been determined at 2.5 A resolution by the selenomethionyl multiwavelength anomalous diffraction method and refined to 2.1 A resolution. The structure of the monomer can be divided into four domains; the active site of the enzyme is located in a deep cleft at the interface between three of the domains. Three acidic residues (Glu255, Asp256 and Asp279) were identified as ligands for the divalent cation that is required for catalysis by malic enzymes. CONCLUSIONS: The structure reveals that malic enzymes belong to a new class of oxidative decarboxylases. The tetramer of the enzyme appears to be a dimer of dimers. The active site of each monomer is located far from the tetramer interface. The structure also shows the binding of a second NAD+ molecule in a pocket 35 A away from the active site. The natural ligand for this second binding site may be ATP, an allosteric inhibitor of the enzyme.

Amino Acid Sequence↗

PubMed2004

ArrayPipe: a flexible processing pipeline for microarray data.

A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range from single slides to large data sets including replicates and dye-swaps. It handles output from most commonly used quantification software packages for dual-labelled arrays. Application features range from quality assessment of slides through various data visualizations to multi-step analyses including normalization, detection of differentially expressed genes, andcomparison and highlighting of gene lists. A highly customizable action set-up facilitates unrestricted arrangement of functions, which can be stored as action profiles. A unique combination of web-based and command-line functionality enables comfortable configuration of processes that can be repeatedly applied to large data sets in high throughput. The output consists of reports formatted as standard web pages and tab-delimited lists of calculated values that can be inserted into other analysis programs. Additional features, such as web-based spreadsheet functionality, auto-parallelization and password protection make this a powerful tool in microarray research for individuals and large groups alike.

Gene Expression Profiling↗

PubMed2003

Lipid interactions with transmembrane proteins.

Magnetic resonance results, principally from 2H-nuclear magnetic resonance, indicate that the mean lipid-chain ordering at the surface of transmembrane proteins is comparable to that in fluid lipid bilayers. Principally, it is the requirement for matching the hydrophobic lengths of lipid and protein that modulates the degree of chain ordering at the lipid-protein interface. The distribution of chain order parameters is, nonetheless, broader in the presence of integral proteins than in fluid lipid bi-layers. The chain configurations of the phospholipids that are resolved in crystals of integral membrane proteins display considerable conformational heterogeneity. Chain C-C dihedral angles are, however, not restricted to the energetically allowable trans and gauche rotamers.This indicates that the chains of a given lipid do not have a unique configuration in protein crystals.

Crystallization↗

PubMed2005

Intermolecular interactions of lysobisphosphatidic acid with phosphatidylcholine in mixed bilayers.

Lysobisphosphatidic acid (LBPA) can be regarded to represent a unique derivative of phosphatidylglycerol. This lipid is highly enriched in late endosomes where it can comprise up to 10-15 mol% of all lipids and in these membranes, LBPA appears to be segregated into microdomains. We studied the thermotropic behavior of pure dioleoyl-LBPA mono- and bilayers using Langmuir-lipid monolayers, electron microscopy, differential scanning calorimetry (DSC), and fluorescence spectroscopy. LBPA formed metastable, liquid-expanded monolayers at an air/buffer interface, and its compression isotherms lacked any indication for structural phase transitions. Neat LBPA formed multilamellar vesicles with no structural transitions or phase transitions between 10 and 80 degrees C at a pH range of 3.0-7.4. We then proceeded to study mixed LBPA/dipalmitoylphosphatidylcholine (DPPC) bilayers by DSC and fluorescence spectroscopy. Incorporating increasing amounts of LBPA (up to X(LBPA) (molar fraction)=0.10) decreased the co-operativity of the main transition for DPPC, and a decrease in the main phase transition as well as pretransition temperature of DPPC was observed yet with no effect on the enthalpy of this transition. In keeping with the DSC data for DPPC, 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC)/LBPA mixed bilayers were more fluid, and no evidence for lateral phase segregation was observed. These results were confirmed using fluorescence microscopy of Langmuir-lipid films composed of POPC and LBPA up to X(LBPA)=0.50 with no evidence for lateral phase separation. As late endosomes are eminently acidic, we examined the effect of lowering pH on lateral organization of mixed PC/LBPA bilayers by DSC and fluorescence spectroscopy. Even at pH 3.0, we find no evidence of LBPA-induced microdomain formation at LBPA contents found in cellular organelles.

Calorimetry, Differential Scanning↗

PubMed2003

Embryo-maternal signalling: how the embryo starts talking to its mother to accomplish implantation.

The process of implantation and trophoblast invasion is currently considered as the most limiting factor for the establishment of pregnancy. Molecular interactions at the embryo-maternal interface during the time of adhesion and subsequent invasion are crucial to the process of embryonic implantation. Both partners, the mother as well as the embryo, play equal roles in the embryo-maternal dialogue, the embryonic part being the main topic in this study. Investigations of the proteins in the extra-embryonic matrices (i.e. zona pellucida) indicate that the embryo participates intensively in this early embryo-maternal signalling. One unique feature during implantation process of primate embryos is the release of chorionic gonadotrophin, which seems to influence endometrial activity by two different mechanisms: (i) luteotrophic activity with increasing progesterone release and (ii) a direct action on the endometrium. Furthermore, embryonic interleukin-1beta may be involved in embryo-maternal signalling. Other significant signals in this interaction are most likely leukaemia inhibitory factor (LIF) and colony-stimulating factor (CSF), which stimulate matrix metalloproteinase (MMP)/insulin-like growth factor binding protein-1 (IGFBP-1) activity and the insulin-like growth factor (IGF) system, which is modulated by embryonic IGFBP-3. Similar significances are discussed for uteroglobin and haptoglobin. Finally, the phenomenon of maternal immunological tolerance, triggered by the presence of the early embryo, is fundamental to the understanding of implantation and trophoblast invasion. A tightly regulated balance between activated and inactivated T cells at the implantation site may control the beginning of adequate trophoblast invasion and also limit this invasion to a tolerable extent for the maternal system, consequently ensuring a biologically healthy haemo-chorial placenta.

Animals↗

PubMed2006

Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China.

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10(8) cells/g at the water-sediment interface to 10(7) cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.

Bacteroides↗

PubMed2006

Multilayer image grid reconstruction technology: four-dimensional interactive image reconstruction of microsurgical neuroanatomic dissections.

OBJECTIVE: Cadaveric dissection is the gold standard for training physicians in various surgical specialties. However, limitations in acquiring and storing sufficient cadaveric material, recent pressures in training opportunities, and progress in digital image technology have led to advances in virtual or artificial visual means to augment surgical training. For training neurosurgeons, the appearance of reality is still crucial for learning anatomic structures and procedures. We developed a four-dimensional (including time) multilayer digital image reconstruction technology (MIGRT) that allows users to manipulate a "volumetric" set of photographic image data from exquisite cadaveric intracranial dissections and to navigate through stages of neurosurgical procedures as the dissection progresses. METHODS: A robotic microscope with two digital cameras was used to capture dissection images, usually in stereoscopic mode. A grid space was created to define positions at which images are captured. Images were acquired from identical angles at the same grid coordinates but at different stages of various dissections. RESULTS: Image data are reconstructed according to the sequence of acquisition into a multilayer image grid system by the MIGRT software. The single interactive, four-dimensional montage is viewable a on common computer platform. CONCLUSION: MIGRT uniquely focuses on capturing anatomic content that preserves natural appearances, including procedure, texture, and color, which is far superior and preferable to images and a reconstructed image environment based on artificial or animated concepts. MIGRT shows time-dependent changes in procedures, provides depth perception by stereoscopy or unique sequential motion, and allows simultaneous interactivity at each step of the procedure.

Brain↗

PubMed1998

VR experience with neurological patients: basic cost/benefit issues.

The future of VR applications for mental health is currently regarded as depending on the rational development of ideas and systems. Criteria to guide this development have been suggested that are both clear and agreeable. Their application, however, may not be easy at this stage. While we may already be able to predict costs of specific VR applications, a period of more extensive clinical research is needed in order to assess adequately any benefit. In our still limited experience, the development of VR applications to increase the diagnostic sensitivity of traditional tests to strategy application disorders is worthwhile, but the uniqueness of VR assets may make the adherence to some of the proposed criteria somewhat problematic.

Brain Damage, Chronic↗

PubMed2002

Cycling at the interface between neurodevelopment and neurodegeneration.

The discovery of cell cycle regulators has directed cell research into uncharted territory. In dividing cells, cell cycle-associated protein kinases, which are referred to as cyclin-dependent-kinases (Cdks), regulate proliferation, differentiation, senescence and apoptosis. In contrast, all Cdks in post-mitotic neurons, with the notable exception of Cdk5, are silenced. Surprisingly, misregulation of Cdks occurs in neurons in a wide diversity of neurological disorders, including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Ectopic expression of these proteins in neurons potently induces cell death with hallmarks of apoptosis. Deregulation of the unique, cell cycle-unrelated Cdk5 by its truncated co-activator, p25 and p29, contributes to neurodegeneration by altering the phosphorylation state of non-membrane-associated proteins and possibly through the induction of cell cycle proteins. On the other hand, cycling Cdks such as Cdk2, Cdk4 and Cdk6, initiate death pathways by derepressing E2F-1/Rb-dependent transcription at the neuronal G1/S checkpoint. Thus, Cdk5 and cycling Cdks may have little in common in the healthy CNS, but they likely conspire in leading neurons to their demise.

Animals↗

PubMed1995

Water molecules participate in proteinase-inhibitor interactions: crystal structures of Leu18, Ala18, and Gly18 variants of turkey ovomucoid inhibitor third domain complexed with Streptomyces griseus proteinase B.

Crystal structures of the complexes of Streptomyces griseus proteinase B (SGPB) with three P1 variants of turkey ovomucoid inhibitor third domain (OMTKY3), Leu18, Ala18, and Gly18, have been determined and refined to high resolution. Comparisons among these structures and of each with native, uncomplexed SGPB reveal that each complex features a unique solvent structure in the S1 binding pocket. The number and relative positions of water molecules bound in the S1 binding pocket vary according to the size of the side chain of the P1 residue. Water molecules in the S1 binding pocket of SGPB are redistributed in response to the complex formation, probably to optimize hydrogen bonds between the enzyme and the inhibitor. There are extensive water-mediated hydrogen bonds in the interfaces of the complexes. In all complexes, Asn 36 of OMTKY3 participates in forming hydrogen bonds, via water molecules, with residues lining the S1 binding pocket of SGPB. For a homologous series of aliphatic straight side chains, Gly18, Ala18, Abu18, Ape18, and Ahp18 variants, the binding free energy is a linear function of the hydrophobic surface area buried in the interface of the corresponding complexes. The resulting constant of proportionality is 34.1 cal mol-1 A-2. These structures confirm that the binding of OMTKY3 to the preformed S1 pocket in SGPB involves no substantial structural disturbances that commonly occur in the site-directed mutagenesis studies of interior residues in other proteins, thus providing one of the most reliable assessments of the contribution of the hydrophobic effect to protein-complex stability.

Alanine↗

PubMed2006

Determination of the capacitance of solid-state potentiometric sensors: An electrochemical time-of-flight method.

A dual microelectrode electrochemical time-of-flight technique in which diffusion flux of Ag+, Cl-, or H+ ions electrochemically produced at a generator electrode is measured by recording potential-time transients with Ag, Ag/AgCl, or iridium oxide potentiometric microsensors, respectively, is developed. The generator and microsensor electrodes are typically spaced by 50-100 microm and are incorporated in the lithographically fabricated thin-layer-type devices. Under conditions of moderate rates of the ion electrogeneration, the potential-time (E-t) transients recorded with the three microsensors show excellent agreement with theory involving linear diffusion equations and the experimentally determined Nernstian slopes of the microsensors. However, when the generator current, or the initial concentration of the primary ion of interest is low, appreciable delays in the recorded E-t transients are observed due to the finite capacitance of the micropotentiometric sensors. The recorded delay in the E-t transients can be quantitatively accounted for by including the sensor capacitance (C) in the theoretical description of the transients. Direct comparison between the theoretical and the experimental E-t transients yields the sensor's capacitance. This capability of our new technique is unique in that it allows determination of the capacitance of a potentiometric sensor at open circuit. In the cases of silver electrodes, this method results in C = 31 +/- 2 microF/cm2, a value that is in agreement with those obtained by other methods. The results for silver chloride sensors yield a C in the range of 100-140 +/- 10 microF/cm2. The specific values depend on sensor preparation and the resulting roughness of the Ag/AgCl interface. Iridium oxide sensors show a capacitance that linearly depends on the thickness of the film. Specific capacitance of these microporous films was determined to be 59 +/- 6 F/cm3.

Electric Capacitance↗