SEARCH · PubMed Health

Results for “Unique interface”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,693 records · Page 94Linked to original sources

PubMed1996

Specificity of single LIM motifs in targeting and LIM/LIM interactions in situ.

The LIM motif defines a double zinc finger structure found in proteins involved in cell fate determination and growth control. LIM proteins, which include LIM homeo domain, LIM kinase, focal adhesion, and LIM-only proteins, usually contain two or more LIM motifs clustered at their amino- or carboxy-terminal end. At present, the mode of action of the LIM domain is not clear. In this study we have analyzed the binding properties of LIM motifs in the cellular environment. We show that MLP, CRP, and betaCRP define a subclass of LIM-only proteins with unique dual subcellular localization in the nucleus and along actin-based filaments in the cytosol. A double MLP construct that accumulated nearly exclusively along actin filaments promoted myogenic differentiation efficiently, arguing for a functional role of cytoskeleton-associated MLP. Binding of MLP to the actin cytoskeleton is specifically attributable to its second LIM motif. An additional LIM motif potentiates binding. Potentiating LIM motifs can be interchanged, resulting in differential targeting of interacting proteins. To analyze LIM-LIM interactions in situ, this property was exploited to develop a hybrid interaction approach based on the relocalization of LIM-containing constructs to the actin cytoskeleton. These experiments revealed the existence of marked selectivity in the interactions of single LIM motifs, and among LIM domains from different LIM-homeo domain and LIM-only proteins. Furthermore, the analysis suggested that the LIM motif has two interacting interfaces. On the basis of these findings, we propose that LIM motifs function as specific adapter elements to promote the assembly and targeting of multiprotein complexes.

3T3 Cells↗

PubMed2005

ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data.

ChIPOTle (Chromatin ImmunoPrecipitation On Tiled arrays) takes advantage of two unique properties of ChIP-chip data: the single-tailed nature of the data, caused by specific enrichment but not specific depletion of genomic fragments; and the predictable enrichment of DNA fragments adjacent to sites of direct protein-DNA interaction. Implemented as a Microsoft Excel macro written in Visual Basic, ChIPOTle uses a sliding window approach that yields improvements in the identification of bona fide sites of protein-DNA interaction.

Algorithms↗

PubMed1996

Nonclassical HLA-G molecules are classical peptide presenters.

BACKGROUND: The physiological functions of the classical HLA (human leukocyte antigen) molecules, HLA-A, HLA-B and HLA-C, are to present peptides to T cells and to inhibit the activity of natural killer cells. In contrast, the functions of nonclassical HLA-molecules, such as HLA-E, HLA-F and HLA-G, remain to be established. The expression of HLA-G is largely limited to the placental trophoblast, where it might mediate protection of the fetus from rejection by the mother. Achieving the aim of understanding the function of HLA-G should be facilitated by information on the biochemical properties of HLA-G molecules, especially on their potential ability to act as peptide receptors. RESULTS: To study peptide presentation by HLA-G, we used stably transfected LCL721.221 cells as a source of HLA-G molecules and analysed the spectrum of extracted peptides by individual and pool sequencing. Our results indicate that HLA-G molecules, like classical HLA molecules, are associated with a wide array of peptides derived from cellular proteins. Peptides presented by HLA-G usually consisted of 9 amino acids, and adhered to a specific sequence motif, with anchor residues at position 2 (isoleucine or leucine), position 3 (proline) and the carboxy-terminal position 9 (leucine). Thus, the HLA-G peptide ligand motif follows the principles of classical HLA motifs, although it displays its own unique features. Peptide-binding assays indicated that two of the three anchor residues were sufficient for binding, and that the three natural HLA-G ligands that we identified bound, not only to HLA-G, but also to HLA-A2. This was not surprising, because the binding pockets of HLA-A2 and HLA-G overlap in their ability to recognize anchor residues at positions 2 and 9. Likewise, some, but not all, HLA-A2 peptide ligands could also bind to HLA-G. CONCLUSIONS: Nonclassical HLA-G molecules present peptides essentially in the same way as classical HLA molecules do. We determined the peptide motif that is specifically recognized by HLA-G; its basic features are described by the sequence XI/LPXXXXXL: This information should help to elucidate the physiological role of HLA-G molecules at the fetal-maternal interface. Most likely, this role is to protect fetal cells from lysis by natural killer cells, and possibly to present foreign peptides to a class of T cells that has not yet been identified.

Amino Acid Sequence↗

PubMed2006

Helix triangle: unique peptide-based molecular architecture.

We here report a unique cyclic peptide structure, "helix triangle", as a unique example of peptide-based molecular architecture. The cyclic peptide is designed to have a triangular shape in which three 9mer helical peptide units make the sides and three pyrene derivatives make the apexes. The helical peptide units are ideally linear, and the pyrene units are ideal 60 degrees angular components. The yield of the cyclic peptide was relatively high despite its large cycle size. Absorption and fluorescence spectroscopy revealed that the three pyrene units do not interact with each other electronically, and circular dichroism spectroscopy indicated that the helical peptide units take 3(10)-helical conformation. Geometry optimization by the semi-empirical molecular orbital method gave a triangular structure with 3(10)-helices as the plausible molecular structure. To gain more information on the geometry and demonstrate one example of its self-assemblies, the monolayer of the cyclic peptide was prepared at the air/water interface, and its surface pressure-molecular area isotherm was studied. The isotherm indicated formation of a stable monolayer and suggested that the cyclic peptide actually takes the triangular structure predicted by the geometry optimization. The monolayer was then transferred onto a substrate and characterized by various methods. Ellipsometry and infrared reflection-absorption spectroscopy confirmed that the cyclic peptide has horizontal orientation to the surface in the monolayer. Furthermore, absorption and fluorescence spectroscopy showed that the isolated electronic properties of the pyrene units are intact even in a condensed state in the monolayer.

Air↗

PubMed2006

RankProd: a bioconductor package for detecting differentially expressed genes in meta-analysis.

UNLABELLED: While meta-analysis provides a powerful tool for analyzing microarray experiments by combining data from multiple studies, it presents unique computational challenges. The Bioconductor package RankProd provides a new and intuitive tool for this purpose in detecting differentially expressed genes under two experimental conditions. The package modifies and extends the rank product method proposed by Breitling et al., [(2004) FEBS Lett., 573, 83-92] to integrate multiple microarray studies from different laboratories and/or platforms. It offers several advantages over t-test based methods and accepts pre-processed expression datasets produced from a wide variety of platforms. The significance of the detection is assessed by a non-parametric permutation test, and the associated P-value and false discovery rate (FDR) are included in the output alongside the genes that are detected by user-defined criteria. A visualization plot is provided to view actual expression levels for each gene with estimated significance measurements. AVAILABILITY: RankProd is available at Bioconductor http://www.bioconductor.org. A web-based interface will soon be available at http://cactus.salk.edu/RankProd

Computational Biology↗

PubMed1992

Neuronal Ca2+/calmodulin-dependent protein kinases.

Widespread localization, responsiveness to numerous signal transduction systems, and broad substrate specificity enable the multifunctional CaM kinase to mediate regulation of many cellular functions. The abundance and diversity of CaM kinase substrates attest to its role as a multifunctional kinase. However, expanded identification of its in situ substrates as well as the consequences of their regulation by phosphorylation needs to be accomplished. Recently identified substrates have contributed to the list of potential functions for the CaM kinase. CREB is a hormonally stimulated transcriptional activator, and CaM kinase may lie on the pathway to its activation. This pathway could provide an interface between the potentiation of Ca2+ signals by CaM kinase and longer-term modifications of neuronal gene expression. The ryanodine receptor, as well as phospholamban, are involved in cardiac Ca2+ homeostasis, and their regulation by CaM kinase phosphorylation suggests the possibility of some feedback control of intracellular Ca2+ levels by CaM kinase. Regulation of neuronal plasticity by phosphorylation of synapsin I and of postsynaptic substrates necessary for long-term potentiation is another dynamic area of investigation. The study of substrates and their functions promises to continue providing exciting insights into the control of cellular signalling by Ca2+. Molecular cloning has enabled structural comparison of neuronal isoforms of the kinase, and has revealed the existence of closely related subunits. Subunits identified to data differ substantially only in two small variable domains, yet their expression in various tissues and during the course of development is precisely controlled. What unique properties do these small variable domains impart to the different isoforms? What directs high concentrations of kinase to a particular subcellular localization, and especially to the PSD? Further molecular cloning will undoubtedly determine whether other multifunctional CaM kinases with unique structures and properties exist. Finally, studies on the autoregulatory properties of CaM kinase have provided a fascinating picture of how this molecule can alone encode responses to Ca2+ signals, potentiating both the duration and magnitude of its activity. Autophosphorylation of the Thr286 autonomy site both traps calmodulin and permits Ca(2+)-independent activity after calmodulin dissociates. Further analysis of the role of the holoenzyme structure in these modulations will help clarify remaining mechanistic questions. Studies performed during the past few years have clearly established that this Ca(2+)-independent activity is generated in situ in response to a variety of cell stimuli.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed2005

A Taxonomic Search Engine: federating taxonomic databases using web services.

BACKGROUND: The taxonomic name of an organism is a key link between different databases that store information on that organism. However, in the absence of a single, comprehensive database of organism names, individual databases lack an easy means of checking the correctness of a name. Furthermore, the same organism may have more than one name, and the same name may apply to more than one organism. RESULTS: The Taxonomic Search Engine (TSE) is a web application written in PHP that queries multiple taxonomic databases (ITIS, Index Fungorum, IPNI, NCBI, and uBIO) and summarises the results in a consistent format. It supports "drill-down" queries to retrieve a specific record. The TSE can optionally suggest alternative spellings the user can try. It also acts as a Life Science Identifier (LSID) authority for the source taxonomic databases, providing globally unique identifiers (and associated metadata) for each name. CONCLUSION: The Taxonomic Search Engine is available at http://darwin.zoology.gla.ac.uk/~rpage/portal/ and provides a simple demonstration of the potential of the federated approach to providing access to taxonomic names.

Classification↗

PubMed1997

Engineering a tRNA and aminoacyl-tRNA synthetase for the site-specific incorporation of unnatural amino acids into proteins in vivo.

In an effort to expand the scope of protein mutagenesis, we have completed the first steps toward a general method to allow the site-specific incorporation of unnatural amino acids into proteins in vivo. Our approach involves the generation of an "orthogonal" suppressor tRNA that is uniquely acylated in Escherichia coli by an engineered aminoacyl-tRNA synthetase with the desired unnatural amino acid. To this end, eight mutations were introduced into tRNA2Gln based on an analysis of the x-ray crystal structure of the glutaminyl-tRNA aminoacyl synthetase (GlnRS)-tRNA2Gln complex and on previous biochemical data. The resulting tRNA satisfies the minimal requirements for the delivery of an unnatural amino acid: it is not acylated by any endogenous E. coli aminoacyl-tRNA synthetase including GlnRS, and it functions efficiently in protein translation. Repeated rounds of DNA shuffling and oligonucleotide-directed mutagenesis followed by genetic selection resulted in mutant GlnRS enzymes that efficiently acylate the engineered tRNA with glutamine in vitro. The mutant GlnRS and engineered tRNA also constitute a functional synthetase-tRNA pair in vivo. The nature of the GlnRS mutations, which occur both at the protein-tRNA interface and at sites further away, is discussed.

Cloning, Molecular↗

PubMed1998

The Middle/Upper Paleolithic interface and the relationship of Neanderthals and early modern humans in the Hrvatsko Zagorje, Croatia.

This paper presents the first detailed analysis of the artefacts from the Mousterian level G3 at Vindija Cave and a revision of the artefact analysis for the early Upper Paleolithic levels (j, i) at Velika Pećina, both in Croatia. Combined with an assessment of the artefacts from the crucial G1 level at Vindija, results of these analyses are used to argue that the combination of Middle and Upper Paleolithic elements in the upper G complex at Vindija is not necessarily the result of geological mixing but may well represent a natural cultural assemblage. Some Upper Paleolithic elements are possibly derived from the local Mousterian, while others result from extraneous cultural influences into this region. Interestingly, currently available radiocarbon dates indicate that Neanderthals (Vindija level G1) and early modern humans (Velika Pećina) were penecontemporaneous in this region at ca. 33 ka, or perhaps somewhat earlier if the radiocarbon dates are taken as minimum age estimates. Therefore some Upper Paleolithic tools associated with the Vindija G1 Neanderthals, such as bone points, may result from imitation of or trade with early modern people. While there is external influence on the development of the early Upper Paleolithic in this region, it exhibits a unique character which does not conform to that of classic Western or Central European Aurignacian.

Animals↗

PubMed1982

Skeletal metastasis: the effect on the immature skeleton.

The unique opportunity to study the entire appendicular skeleton of a child who died from metastatic angiosarcoma allowed detailed assessment of radiographically evident involvement. Virtually every portion of the appendicular skeleton had evidence of metastatic disease. However, the extent of involvement was extremely variable, especially when contralateral regions were assessed. The most likely region of metastasis, the metaphysis, is normally a fenestrated cortex of woven bone in the young child, rather than a well demarcated cortex formed by osteon (lamellar) bone, as it is in the adult. The pattern of destruction is such that less extensive areas may be involved before becoming radiographically evident, and trabecular bone involvement may be evident even without cortical damage. The metaphyseal metastatic spread supports the concept of arterial hematogenous dissemination, comparable to osteomyelitis in the child. Pathologic metaphyseal fractures involved both proximal humeri; the fracture also extended along a portion of the metaphyseal-physeal interface in one humerus. In one distal femur the physis readily separated from the metaphysis; this was a non-displaced type 1 growth mechanism injury.

Bone Neoplasms↗

PubMed2005

Lung surfactant gelation induced by epithelial cells exposed to air pollution or oxidative stress.

Lung surfactant lowers surface tension and adjusts interfacial rheology to facilitate breathing. A novel instrument, the interfacial stress rheometer (ISR), uses an oscillating magnetic needle to measure the shear viscosity and elasticity of a surfactant monolayer at the air-water interface. The ISR reveals that calf lung surfactant, Infasurf, exhibits remarkable fluidity, even when exposed to air pollution residual oil fly ash (ROFA), hydrogen peroxide (H2O2), or conditioned media from resting A549 alveolar epithelial cells (AEC). However, when Infasurf is exposed to a subphase of the soluble fraction of ROFA- or H2O2-treated AEC conditioned media, there is a prominent increase in surfactant elasticity and viscosity, representing two-dimensional gelation. Surfactant gelation is decreased when ROFA-AEC are pretreated with inhibitors of cellular reactive oxygen species (ROS), or with a mitochondrial anion channel inhibitor, as well as when A549-rho0 cells that lack mitochondrial DNA and functional electron transport are investigated. These results implicate both mitochondrial and nonmitochondrial ROS generation in ROFA-AEC-induced surfactant gelation. A549 cells treated with H2O2 demonstrate a dose-dependent increase in lung surfactant gelation. The ISR is a unique and sensitive instrument to characterize surfactant gelation induced by oxidatively stressed AEC.

Air Pollutants↗

PubMed2004

Informatics approaches to functional MRI odor mapping of the rodent olfactory bulb: OdorMapBuilder and OdorMapDB.

The present study applies informatics tools to aid and extend fMRI analysis of the coding mechanism of neural signals in the rodent olfactory system. Odor stimulation evokes unique spatial patterns of activity in the glomerular layer of the mammalian olfactory bulb (OB). An open-source software program, OdorMap-Builder, has been developed to process the high resolution anatomical and functional MRI images of the OB and to generate single two-dimensional flat maps, called odor maps, that describe the spatial activity patterns in the entire glomerular layer. Odor maps help identify the spatial activity patterns from the tremendous amount of fMRI data and they serve as ideal representation of space coding for the olfactory signals in the OB in response to a given odor stimulation. Based on the fMRI technology, OdorMapBuilder provides comparable odor maps on the intra-subject basis, a significant step towards the detailed analyses of the effects of odor types and/or concentrations. In addition, a new database, OdorMapDB, is developed to provide a repository for the generated odor maps. Web interfaces to the database are provided for the data entry, modification and retrieval. OdorMapDB is based on the EAV/CR (entity-attribute-value with classes and relationships) architecture and it is integrated with two other SenseLab olfactory databases: the olfactory receptor and odor databases. Both OdorMapBuilder and OdorMapDB should serve as useful tools and resources for the field and help facilitate experimental research in understanding the olfactory system and the mechanism for smell perception.

Animals↗

PubMed2003

The games psychologists play (and the data they provide).

Computer games and the technologies marketed to support them provide unique resources for psychological research. In contrast to the sterility, simplicity, and artificiality that characterizes many cognitive tests, game-like tasks can be complex, ecologically valid, and even fun. In the present paper,the history of psychological research with video games is reviewed, and several thematic benefits of this paradigm are identified. These benefits, as well as the possible pitfalls of research with computer game technology and game-like tasks, are illustrated with data from comparative and cognitive investigations.

Animals↗

PubMed2003

Differential modulation of subcortical target and cortex during deep brain stimulation.

The combination of electrical deep brain stimulation (DBS) with functional imaging offers a unique model for tracing brain circuitry and for testing the modulatory potential of electrical stimulation on a neuronal network in vivo. We therefore applied parametric positron emission tomography (PET) analyses that allow characterization of rCBF responses as linear and nonlinear functions of the experimentally modulated stimulus (variable stimulator setting). In patients with electrodes in the thalamic ventrointermediate nucleus (VIM) for the treatment of essential tremor (ET) here we show that variations in voltage and frequency of thalamic stimulation have differential effects in a thalamo-cortical circuitry. Increasing stimulation amplitude was associated with a linear raise in rCBF at the thalamic stimulation site, but with a nonlinear rCBF response in the primary sensorimotor cortex (M1/S1). The reverse pattern in rCBF changes was observed with increasing stimulation frequency. These results indicate close connectivity between the stimulated nucleus (VIM) and primary sensorimotor cortex. Likewise, stimulation parameter-specific modulation occurs at this simple interface between an electrical and a cerebral system and suggests that the scope of DBS extends beyond an ablation-like on-off effect: DBS could rather allow a gradual tuning of activity within a neuronal circuit.

Aged↗

PubMed2006

Structural determinants of selective alpha-conotoxin binding to a nicotinic acetylcholine receptor homolog AChBP.

The nicotinic acetylcholine receptor (nAChR) is the prototype member of the superfamily of pentameric ligand-gated ion channels. How the extracellular ligand-binding domain coordinates selective binding of ligand molecules to different subtypes of the receptor is unknown at the structural level. Here, we present the 2.2-A crystal structure of a homolog of the ligand-binding domain of the nAChR, Aplysia californica AChBP (Ac-AChBP), in complex with alpha-conotoxin ImI. This conotoxin is unique in its selectivity toward the neuronal alpha3beta2 and alpha7 nAChR, a feature that is reflected in its selective binding to Ac-AChBP compared with other AChBP homologs. We observe a network of interactions between the residues of the ligand-binding site and the toxin, in which ImI Arg-7 and Trp-10 play a key role. The toxin also forms interactions in the ligand-binding site that were not seen in the complex of Ac-AChBP with PnIA(A10L D14K), a conotoxin variant that lacks binding selectivity to AChBP homologs. In combination with electrophysiological recordings obtained by using the wild-type alpha7 nAChR and L247T mutant, we show that conotoxin ImI inhibits ion conduction by stabilizing the receptor in a desensitized conformation. Comparison of the Ac-AChBP-ImI crystal structure with existing AChBP structures offers structural insight into the extent of flexibility of the interface loops and how their movement may couple ligand binding to channel gating in the context of a nAChR.

Amino Acid Sequence↗

PubMed1998

Misadventures in the drug trade.

Dan Waldorf was a research sociologist who worked in the field of drug use and abuse for 27 years. Most of that time was either in San Francisco or New York City. He wrote two books, three monographs, and 38 articles on the subject--with this being his final article. Fate intervened because this article is autobiographical. Dan's work and his life were intertwined in ways that provided unique insights into drugs and addict lifestyles. The focus of much of his work was "to attack and demolish myths about drug users and heroin addicts" (his words). Dan's legacy is broad ranging, including historical accounts of morphine users and the federal response to close down morphine clinics in the first quarter of this century; he made snowball sampling methods respectable; he saw rationality in the actions of heroin addicts and demonstrated this drug was not all-consuming; and he performed a similar service for cocaine. He struggled to maintain his career as a drug researcher, often without the support of federal monies. As recently as two years before his death, he traveled around the country to document the history of underground needle exchange programs that were developing--using his retirement savings. This article documents his many scientific contributions to our understanding of drug use in general, and the interface of drug use and crime in particular. Dan led a simple yet ever so rich life because he never shied away from telling the truth, and the wisdom of his vision helped so many others of us to see. That is his greatest legacy--and his gift.

Behavior, Addictive↗

PubMed1994

Irreversible inhibition of nicotinic acetylcholine receptors by the bipinnatins. Toxin activation and kinetics of receptor inhibition.

Bipinnatin-A, -B, and -C belong to a family of naturally occurring marine neurotoxins known as the lophotoxins. The lophotoxins are unique in that they irreversibly inhibit nicotinic acetylcholine receptors by forming a covalent bond with a tyrosine residue at position 190 in the alpha-subunit of the receptor. In this study, we show that the inhibitory activity of the bipinnatins against the nicotinic receptor increased with preincubation of the toxins in aqueous buffer prior to incubation with the receptor. The parent species of the bipinnatins displayed little, if any, affinity for the nicotinic receptor. Preincubation of the toxins appeared to produce a single, relatively stable, active toxin species that irreversibly inhibited the two acetylcholine-binding sites on the nicotinic receptor with two distinguishable apparent pseudo first-order rates. The difference in the rates of irreversible inhibition of the two binding sites on the receptor was exploited to selectively inhibit one site for the pharmacological investigation of the other. The bipinnatins preferentially inhibited the binding site near the alpha/delta-subunit interface that displays low affinity for metocurine and high affinity for acetylcholine. The bimolecular reaction constants for the interaction of the bipinnatins with the nicotinic receptor decreased in the order bipinnatin-B > bipinnatin-A > bipinnatin-C for both acetylcholine-binding sites. The ratio of the bimolecular reaction constants for the two binding sites on the receptor was not the same for the three bipinnatins. This indicates that the reaction of the bipinnatins with the nicotinic receptor is sensitive to differences in the structure of the two acetylcholine-binding sites. The bipinnatins may be useful in the design of novel drugs for the nicotinic receptor that exclusively inhibit one of the two binding sites and for the investigation of structural differences between the two acetylcholine-binding sites of the receptor.

Animals↗

PubMed2006

Reward-related cortical inputs define a large striatal region in primates that interface with associative cortical connections, providing a substrate for incentive-based learning.

The anterior cingulate and orbital cortices and the ventral striatum process different aspects of reward evaluation, whereas the dorsolateral prefrontal cortex and the dorsal striatum are involved in cognitive function. Collectively, these areas are critical to decision making. We mapped the striatal area that receives information about reward evaluation. We also explored the extent to which terminals from reward-related cortical areas converge in the striatum with those from cognitive regions. Using three-dimensional-rendered reconstructions of corticostriatal projection fields along with two-dimensional chartings, we demonstrate the reward and cognitive territories in the primate striatum and show the convergence between these cortical inputs. The results show two labeling patterns: a focal projection field that consists of densely distributed terminal patches, and a diffuse projection consisting of clusters of fibers, extending throughout a wide area of the striatum. Together, these projection fields demonstrate a remarkably large, rostral, reward-related striatal territory that reaches into the dorsal striatum. Fibers from different reward-processing and cognitive cortical areas occupy both separate and converging territories. Furthermore, the diffuse projection may serve a separate integrative function by broadly disseminating general cortical activity. These findings show that the rostral striatum is in a unique position to mediate different aspects of incentive learning. Furthermore, areas of convergence may be particularly sensitive to dopamine modulation during decision making and habit formation.

Animals↗