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Results for “Integrative interaction”

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PubMed2001

Revealing and utilizing receptor recognition mechanisms in a high-throughput world.

Recent genomic mapping promises to identify essentially all of the proteins that underpin normal and aberrant biology in humans. What genomics leaves undone is to determine how these proteins interact and integrate into molecular pathways in health and disease. Specific molecular interactions provide the fundamental mechanism for selectivity in virtually every aspect of biological structure and function. The convergence of structural and mutational studies makes it possible to define what parts of a protein are important for recognition. Still, knowing what is important does not necessarily foretell how binding epitopes actually function. We have applied the approach of epitope randomization on phage to explore how structural elements in such receptor recruitment systems as interleukin-5 (IL-5) and HIV-1 function in receptor recognition. This work has led in the IL-5 case to differentiation of recognition and activation epitopes, and this in turn has potential to help in the design of non-activating mimetics that could stimulate development of therapeutic antagonists for allergic inflammations such as asthma. Whether it is possible to differentiate recognition and activation in designing inhibitors in cases such as HIV-1 cell attachment and infection remains a tantalizing, but unsolved goal at present. Overall, these studies portray advances as well as limitations in the effort to decipher protein recognition mechanisms and utilize the wisdom gained for mechanism-based antagonist design in an increasingly high throughput world stimulated by the advent of genomics and proteomics.

Binding Sites↗

PubMed1999

Structural details of an interaction between cardiolipin and an integral membrane protein.

Anionic lipids play a variety of key roles in biomembrane function, including providing the immediate environment for the integral membrane proteins that catalyze photosynthetic and respiratory energy transduction. Little is known about the molecular basis of these lipid-protein interactions. In this study, x-ray crystallography has been used to examine the structural details of an interaction between cardiolipin and the photoreaction center, a key light-driven electron transfer protein complex found in the cytoplasmic membrane of photosynthetic bacteria. X-ray diffraction data collected over the resolution range 30.0-2.1 A show that binding of the lipid to the protein involves a combination of ionic interactions between the protein and the lipid headgroup and van der Waals interactions between the lipid tails and the electroneutral intramembrane surface of the protein. In the headgroup region, ionic interactions involve polar groups of a number of residues, the protein backbone, and bound water molecules. The lipid tails sit along largely hydrophobic grooves in the irregular surface of the protein. In addition to providing new information on the immediate lipid environment of a key integral membrane protein, this study provides the first, to our knowledge, high-resolution x-ray crystal structure for cardiolipin. The possible significance of this interaction between an integral membrane protein and cardiolipin is considered.

Binding Sites↗

PubMed1999

Regulation of transcription factor C/ATF by the cAMP signal activation in hippocampal neurons, and molecular interaction of C/ATF with signal integrator CBP/p300.

The CCAAT/enhancer binding proteins related activating transcription factor, C/ATF, is a mouse leucine-zipper transcription factor which is structurally homologous to ApCREB2, a suppressor integral to long-term synaptic plasticity in Aplysia. To gain a clue to whether C/ATF is involved in long-term plasticities of brain, we examined if the expression levels of C/ATF are modulated by cAMP, an inducer crucial for memory formation in Aplysia, Drosophila and mice. Our in situ hybridization analysis revealed the expression of C/ATF mRNA in hippocampal neurons. C/ATF protein levels increased after the cAMP signal stimulation in hippocampal neurons, while C/ATF mRNA levels remained constant. The human activating transcription factor 4 (hATF4), another homolog of ApCREB2, interacts with multiple domains of the coactivator CREB-binding protein (CBP), resulting in the potentiation of its ability to activate transcription. As expected, C/ATF was found to interact with three domains of CBP including CREB binding domain or kinase-inducible interaction (KIX) domain, the third cysteine-histidine-rich region (CH3 domain) and the nuclear receptor coactivator p160/SRC-1-interacting domain. Interestingly, C/ATF was further found to interact strongly with CREB binding protein/p300 (CBP/p300) CH1 domain. Mammalian two hybrid assays indicated that the interaction between C/ATF and CBP/p300 can occur in mammalian cells, and that the p300 CH1 domain is critical for the interaction. Thus, C/ATF may be implicated in transcription-dependent phase of hippocampal long-term plasticities through the modulation of its protein level under cAMP signal and the interaction with signal integrator, CBP/p300.

Activating Transcription Factor 4↗

PubMed2004

A framework for the in vivo pathomechanics of osteoarthritis at the knee.

The in vivo pathomechanics of osteoarthritis (OA) at the knee is described in a framework that is based on an analysis of studies describing assays of biomarkers, cartilage morphology, and human function (gait analysis). The framework is divided into an Initiation Phase and a Progression Phase. The Initiation Phase is associated with kinematic changes that shift load bearing to infrequently loaded regions of the cartilage that cannot accommodate the loads. The Progression Phase is defined following cartilage breakdown. During the Progression Phase, the disease progresses more rapidly with increased load. While this framework was developed from an analysis of in vivo pathomechanics, it also explains how the convergence of biological, morphological, and neuromuscular changes to the musculoskeletal system during aging or during menopause lead to the increased rate of idiopathic OA with aging. Understanding the in vivo response of articular cartilage to its physical environment requires an integrated view of the problem that considers functional, anatomical, and biological interactions. The integrated in vivo framework presented here will be helpful for the interpretation of laboratory experiments as well as for the development of new methods for the evaluation of OA at the knee.

Aging↗

PubMed2005

Conserved patterns of protein interaction in multiple species.

To elucidate cellular machinery on a global scale, we performed a multiple comparison of the recently available protein-protein interaction networks of Caenorhabditis elegans, Drosophila melanogaster, and Saccharomyces cerevisiae. This comparison integrated protein interaction and sequence information to reveal 71 network regions that were conserved across all three species and many exclusive to the metazoans. We used this conservation, and found statistically significant support for 4,645 previously undescribed protein functions and 2,609 previously undescribed protein interactions. We tested 60 interaction predictions for yeast by two-hybrid analysis, confirming approximately half of these. Significantly, many of the predicted functions and interactions would not have been identified from sequence similarity alone, demonstrating that network comparisons provide essential biological information beyond what is gleaned from the genome.

Amino Acid Sequence↗

PubMed1975

The doctor-patient relationship in the practice of medicine.

The patient-doctor relationship is based on the principles of interaction, collecting data and integration of both interaction and data into an overall diagnosis/therapy. Patients with functional abdominal disorders are seen as representatives of today's general patients and a study of their management in present medical practice is reported, as revealed through literature. The literature reveals an almost complete neglect of intractional and intergrational principles. This holds true even for psychosomatically oriented literature, which offers some crude clinical guidelines at best. Thus the primary physician gets little support from psychosomatic medicine in understanding the full meaning of the doctor-patient relationship. The clinical implications of the relationship are demonstrated through a short case history and implications for future training are described which are based on the primary physician's actual working experiences.

Adaptation, Psychological↗

PubMedDate not supplied

Interactive data collection: benefits of integrating new media into pediatric research.

Despite the prevalence of children's computerized games for recreational and educational purposes, the use of interactive technology to obtain pediatric research data remains underexplored. This article describes the development of laptop interactive data collection (IDC) software for a children's health intervention study. The IDC integrates computer technology, children's developmental needs, and quantitative research methods that are engaging for school-age children as well as reliable and efficient for the pediatric health researcher. Using this methodology, researchers can address common problems such as maintaining a child's attention throughout an assessment session while potentially increasing their response rate and reducing missing data rates. The IDC also promises to produce more reliable data by eliminating the need for manual double entry of data and reducing much of the time and costs associated with data cleaning and management. Development and design considerations and recommendations for further use are discussed.

Child↗

PubMed1990

Effects of the training of integrity--promoting care on the interaction at a long-term ward. Analysis of video-recorded social activities.

A training programme in integrity-promoting care was given the staff of a long-term ward and practised during a three months intervention period. The effects were analysed in different parameters and compared with a control ward. This report describes analysis of video-recorded interactions (12 hs) during social activities between demented patients and caregivers and changes induced by the programme. The video-recorded episodes, containing mainly music and coffee sessions were interpreted from a model on interaction with demented patients suggested by Athlin & Norberg. The results indicate that the training programme and the guidance during the intervention resulted in increased understanding of demented patients' situation among the staff. They became more sensitive, adapted their cues and made the environment easier to interpret for the patients. This in turn led to the fact that the patients appeared more sensitive and clear in their cues. A positive circle developed.

Aged↗

PubMed2004

Towards integration of computer games in interactive health education environments: understanding gameplay challenge, narrative and spectacle.

CONTEXT: There is an alarming progress in the health status of the young in western countries, and new methods and tools for behavioural health interventions are urgently called for. OBJECTIVE: To explore how computer game designs can be integrated in the development of Interactive Health Education Environments. DESIGN: Qualitative analyses of adolescents' experiences of playing an action-adventure computer game, using data from in-depth interviews. RESULTS: A model is presented, where the gameplaying experience is connected to four components of computer games. Playing computer games was found to mainly be motivated by the challenges and competition represented in the gameplay scripts. CONCLUSIONS: Interactive health education environments can be improved by implementing challenging gameplay scripts, spectacular technical features and narratives.

Adolescent↗

PubMed2006

Analysis assistant for single-molecule force spectroscopy data on membrane proteins--MPTV.

UNLABELLED: Force-distance (F-D) curves of single membrane proteins reveal information on inter- and intramolecular interactions occurring within a protein and between proteins. However, the analysis of single-molecule force spectroscopy data is a time consuming and complex process requiring objective criteria. In most cases the user requires additional information to interpret F-D curves. Therefore we developed a software assistant representing the force or molecular interaction pattern and the topology or the 3D structure of the membrane protein. This representation establishes a basis for detailed interpretation of the protein structure and its underlying molecular interactions. Various integrated bioinformatic features further assist in the interpretation of measured and assigned molecular interactions that determine membrane protein folding, structure, stability and function. Web queries and programs about the topology are directly linked. Motifs, helix types, representation of Venn diagrams and the complete functionality of the program Jmol belong to it. AVAILABILITY: The program MPTV is freely available from the website at http://www.bioforscher.de/mptv.htm/.

Algorithms↗

PubMed2006

Procyanidins protect Caco-2 cells from bile acid- and oxidant-induced damage.

Procyanidins can exert cytoprotective, anti-inflammatory, and anticarcinogenic actions in the gastrointestinal tract. Previous evidence has shown that procyanidins can interact with synthetic membranes and protect them from oxidation and disruption. Thus, in this study we investigated the capacity of a hexameric procyanidin fraction (Hex) isolated from cocoa to protect Caco-2 cells from deoxycholic (DOC)-induced cytotoxicity, cell oxidant increase, and loss of monolayer integrity. Hex interacted with the cell membranes without affecting their integrity, as evidenced by a Hex-mediated increase in the transepithelial electrical resistance, and inhibition of DOC-induced cytotoxicity. DOC induced an increase in cell oxidants, alterations in the paracellular transport, and redistribution of the protein ZO-1 from cell-cell contacts into the cytoplasm. Hex partially inhibited all these events at concentrations ranging from 2.5 to 20 microM. Similarly, Hex (5-10 microM) inhibited the increase in cell oxidants, and the loss of integrity of polarized Caco-2 cell monolayers induced by a lipophilic oxidant (2,2'-azobis (2,4-dimethylvaleronitrile). Results show that the assayed procyanidin fraction can interact with cell membranes and protect Caco-2 cells from DOC-induced cytotoxicity, oxidant generation, and loss of monolayer integrity. At the gastrointestinal tract, large procyanidins may exert beneficial effects in pathologies such us inflammatory diseases, alterations in intestinal barrier permeability, and cancer.

Azo Compounds↗

PubMed2001

A Monte Carlo code for a direct estimation of radiation risk.

An example of pragmatic approach for predicting mixed field effects is presented. The method was initially applied adopting the following, commonly used, assumptions: a) radiation risk (typically cancer) is correlated with chromosome aberration induction; b) radiation-induced chromosome-exchange yield can be well described by a linear-quadratic dependence on particle fluences (mostly linear with high-LET radiation), with parameters depending on particle types and energies. Information on monochromatic field radiobiological effects was integrated in a condensed-history Monte Carlo transport code (FLUKA), able to simulate nuclear interactions. The integrated code provides the chromosome aberration yield (and thus an estimation of radiation risk) in each voxel of any irradiated volume, given any external mixed-field irradiation; in the present work, the method was tested for neutron irradiation of a water phantom. FLUKA was then coupled with a geometrical human phantom provided with different radiation shielding, in order to apply this approach to estimate radiation risk in manned space missions.

Chromosome Aberrations↗

PubMed2001

Competitive Hebbian learning and the hippocampal place cell system: modeling the interaction of visual and path integration cues.

The hippocampus has long been thought essential for implementing a cognitive map of the environment. However, almost 30 years since place cells were found in rodent hippocampal field CA1, it is still unclear how such an allocentric representation arises from an ego-centrically perceived world. By means of a competitive Hebbian learning rule responsible for coding visual and path integration cues, our model is able to explain the diversity of place cell responses observed in a large set of electrophysiological experiments with a single fixed set of parameters. Experiments included changes observed in place fields due to exploration of a new environment, darkness, retrosplenial cortex inactivation, and removal, rotation, and permutation of landmarks. To code for visual cues for each landmark, we defined two perceptual schemas representing landmark bearing and distance information over a linear array of cells. The information conveyed by the perceptual schemas is further processed through a network of adaptive layers which ultimately modulate the resulting activity of our simulated place cells. In path integration terms, our system is able to dynamically remap a bump of activity coding for the displacement of the animal in relation to an environmental anchor. We hypothesize that path integration information is computed in the rodent posterior parietal cortex and conveyed to the hippocampus where, together with visual information, it modulates place cell activity. The resulting network yields a more direct treatment of partial remapping of place fields than other models. In so doing, it makes new predictions regarding the nature of the interaction between visual and path integration cues during new learning and when the system is challenged with environmental changes.

Animals↗

PubMed2002

Discovering regulatory and signalling circuits in molecular interaction networks.

MOTIVATION: In model organisms such as yeast, large databases of protein-protein and protein-DNA interactions have become an extremely important resource for the study of protein function, evolution, and gene regulatory dynamics. In this paper we demonstrate that by integrating these interactions with widely-available mRNA expression data, it is possible to generate concrete hypotheses for the underlying mechanisms governing the observed changes in gene expression. To perform this integration systematically and at large scale, we introduce an approach for screening a molecular interaction network to identify active subnetworks, i.e., connected regions of the network that show significant changes in expression over particular subsets of conditions. The method we present here combines a rigorous statistical measure for scoring subnetworks with a search algorithm for identifying subnetworks with high score. RESULTS: We evaluated our procedure on a small network of 332 genes and 362 interactions and a large network of 4160 genes containing all 7462 protein-protein and protein-DNA interactions in the yeast public databases. In the case of the small network, we identified five significant subnetworks that covered 41 out of 77 (53%) of all significant changes in expression. Both network analyses returned several top-scoring subnetworks with good correspondence to known regulatory mechanisms in the literature. These results demonstrate how large-scale genomic approaches may be used to uncover signalling and regulatory pathways in a systematic, integrative fashion.

Algorithms↗

PubMed2006

Integrative proteomics: structure, function, and interaction report on the 3rd joint meeting of the British Society for Proteome Research and the European Bioinformatics Institute, July 2006.

This report summarizes the highlights of the recent British Society for Proteome Research (BSPR) meeting jointly organized with the European Bioinformatics Institute (EBI) which was held at the Wellcome Trust Genome Campus, Hinxton, Cambridge, UK in July 2006. This was the third annual scientific meeting organized by the BSPR and EBI and the theme of this years meeting was Integrative Proteomics: Structure, function and interaction. A wealth of local and overseas speakers were invited to discuss both their own work and specific challenges present in modern day proteomic based experiments.

Computational Biology↗

PubMed2005

Self-inactivating lentiviruses: versatile vectors for quantitative transduction of cerebellar granule neurons and their progenitors.

Cerebellar granule neurons (CGNs) undergo a well-defined, intrinsic differentiation program that is recapitulated in vitro. Thus, homogeneous cultures of CGNs provide an excellent opportunity to define the mechanisms underlying their development. The ability to alter endogenous gene expression in CGNs on a population-wide basis would greatly facilitate the elucidation of these events. In the present study, we show that self-inactivating lentiviruses efficiently infect both dividing progenitors and post-mitotic CGN cultures in a quantitative manner without altering their cellular properties. The time course for protein expression was biphasic for both types of cultures, with the first peak occurring during the initial infection period. Thus, lentiviruses can express proteins in CGNs both acutely and on a long-term basis to study developmental and other processes continuously over an extended time period. These vectors also infected CGNs in cerebellar slice preparations. In addition, lentiviruses harboring a transgene for the mouse GABA(A) receptor alpha6 subunit promoter recapitulated the differentiation-dependent expression of this gene in CGN cultures. Self-inactivating lentiviruses are extremely versatile vectors that offer important advantages for studies of protein function and gene regulation. The ability to alter protein function on a global scale in CGN cultures permits biochemical assessment of its impact on mRNA and protein populations, as well as on protein--protein and protein--DNA interactions. Further, integrated lentiviruses can be used to study chromatin-dependent promoter regulation and transcription factor interactions in CGNs over time in a facile manner.

Animals↗

PubMed1990

Regulation of gastric mucosal integrity by endogenous nitric oxide: interactions with prostanoids and sensory neuropeptides in the rat.

1. The interactions between nitric oxide (NO), prostacyclin and sensory neuropeptides in the maintenance of gastric mucosal integrity have been investigated in the anaesthetized rat. 2. Administration of either NG-monomethyl-L-arginine (L-NMMA) to inhibit endothelium-derived NO formation, indomethacin to inhibit prostanoid biosynthesis or chronic capsaicin pretreatment to deplete sensory neuropeptides, did not induce acute mucosal injury. 3. In capsaicin-pretreated rats, however, L-NMMA (12.5-100 mg kg-1 i.v.) dose-dependently induced acute mucosal damage, characterized as vasocongestion and haemorrhagic necrosis. The enatiomer D-NMMA (100 mg kg-1 i.v.) did not induce any detectable mucosal damage. 4. This mucosal injury induced by L-NMMA was inhibited by concurrent administration of L-arginine (300 mg kg-1 i.v.). 5. In indomethacin (5 mg kg-1 i.v.)-pretreated rats, L-NMMA also induced mucosal damage. Furthermore, following indomethacin administration in capsaicin-pretreated rats, L-NMMA induced widespread, severe haemorrhagic necrotic damage. 6. These findings suggest a role for endogenous NO formed from L-arginine, acting in concert with prostacyclin and sensory neuropeptides, in the modulation of gastric mucosal integrity.

Animals↗

PubMed1996

Integrating DXplain into a clinical information system using the World Wide Web.

The World Wide Web(WWW) offers a cross-platform environment and standard protocols that enable integration of various applications available on the Internet. The authors use the Web to facilitate interaction between their Web-based Clinical Information System and a decision-support system-DXplain, at the Massachusetts General Hospital-using local architecture and Common Gateway Interface programs. The current application translates patients laboratory test results into DXplain's terms to generate diagnostic hypotheses. Two different access methods are utilized for this model; Hypertext Transfer Protocol (HTTP) and TCP/IP function calls. While clinical aspects cannot be evaluated as yet, the model demonstrates the potential of Web-based applications for interaction and integration and how local architecture, with a controlled vocabulary server, can further facilitate such integration. This model serves to demonstrate some of the limitations of the current WWW technology and identifies issues such as control over Web resources and their utilization and liability issues as possible obstacles for further integration.

Computer Communication Networks↗